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A

AbstractAmdServant - Class in ome.services.blitz.impl
throttled implementation base class which can be used by _ServiceInterfaceOperations implementors and injected into a tie servant.
AbstractAmdServant(ServiceInterface, BlitzExecutor) - Constructor for class ome.services.blitz.impl.AbstractAmdServant
 
AbstractBuffer - Class in ome.io.nio
 
AbstractChecksumProvider - Class in ome.util.checksum
Abstract skeleton class implementing ChecksumProvider and providing implementations of the interface methods using a universal checksum class object.
AbstractChecksumProvider(HashFunction) - Constructor for class ome.util.checksum.AbstractChecksumProvider
Protected ctor.
AbstractClassIdsOptionsQuery - Class in ome.services.query
simple abstract class that provides a common Definitions containing: IdsQueryParameterDef, ome.services.query.OptionsQueryParameterDef, and ClassQueryParameterDef.
AbstractClassIdsOptionsQuery(Parameters) - Constructor for class ome.services.query.AbstractClassIdsOptionsQuery
 
AbstractCloseableAmdServant - Class in ome.services.blitz.impl
Base class for all servants that must guarantee proper clean-up of held resources on close.
AbstractCloseableAmdServant(ServiceInterface, BlitzExecutor) - Constructor for class ome.services.blitz.impl.AbstractCloseableAmdServant
 
AbstractExecFileTransfer - Class in ome.formats.importer.transfers
Local-only file transfer mechanism which makes use of soft-linking.
AbstractExecFileTransfer() - Constructor for class ome.formats.importer.transfers.AbstractExecFileTransfer
 
AbstractFileDeletions - Class in ome.services.delete.files
Base class for managing the removal of files from disk.
AbstractFileDeletions(AbstractFileSystemService, Set<Long>) - Constructor for class ome.services.delete.files.AbstractFileDeletions
 
AbstractFileExclusion - Class in ome.formats.importer.exclusions
Base FileExclusion implementation primarily providing a factory for FileExclusion implementations via AbstractFileExclusion.createExclusion(String).
AbstractFileExclusion() - Constructor for class ome.formats.importer.exclusions.AbstractFileExclusion
 
AbstractFileExclusion.Exclusion - Enum in ome.formats.importer.exclusions
Enum of well-known FileExclusion names.
AbstractFileSystemService - Class in ome.io.nio
 
AbstractFileSystemService(String) - Constructor for class ome.io.nio.AbstractFileSystemService
 
AbstractFileTransfer - Class in ome.formats.importer.transfers
AbstractFileTransfer() - Constructor for class ome.formats.importer.transfers.AbstractFileTransfer
 
AbstractFileTransfer.Transfers - Enum in ome.formats.importer.transfers
Enum of well-known FileTransfer names.
AbstractHierarchyGraphSpec - Class in ome.services.graphs
Deprecated.
will be removed in OMERO 5.2, so use the new graphs implementation
AbstractHierarchyGraphSpec(List<String>) - Constructor for class ome.services.graphs.AbstractHierarchyGraphSpec
Deprecated.
Creates a new instance.
AbstractLevel1Service - Class in ome.logic
service level 1
AbstractLevel1Service() - Constructor for class ome.logic.AbstractLevel1Service
 
AbstractLevel2Service - Class in ome.logic
service level 2
AbstractLevel2Service() - Constructor for class ome.logic.AbstractLevel2Service
 
AbstractPyramidServant - Class in ome.services.blitz.impl
Specialization of AbstractAmdServant to be used by any services which provide the PyramidService interface.
AbstractPyramidServant(ServiceInterface, BlitzExecutor) - Constructor for class ome.services.blitz.impl.AbstractPyramidServant
 
AbstractRedirector - Class in ome.services.blitz.redirect
AbstractRedirector(Executor) - Constructor for class ome.services.blitz.redirect.AbstractRedirector
 
AbstractRepositoryI - Class in ome.services.blitz.repo
Base repository class responsible for properly handling directory takeover and other lifecycle tasks.
AbstractRepositoryI(ObjectAdapter, Registry, Executor, Principal, String, PublicRepositoryI) - Constructor for class ome.services.blitz.repo.AbstractRepositoryI
 
AbstractRepositoryI(ObjectAdapter, Registry, Executor, Principal, FileMaker, PublicRepositoryI) - Constructor for class ome.services.blitz.repo.AbstractRepositoryI
 
AbstractSecurityFilter - Class in ome.security.basic
overrides FilterDefinitionFactoryBean in order to construct our security filter in code and not in XML.
AbstractSecurityFilter() - Constructor for class ome.security.basic.AbstractSecurityFilter
default constructor which calls all the necessary setters for this FactoryBean.
AbstractSecurityFilter(Roles) - Constructor for class ome.security.basic.AbstractSecurityFilter
 
AbstractSessionMessage - Class in ome.services.messages
InternalMessage implementations which carry relate to some Session bound event.
AbstractSessionMessage(Object, String) - Constructor for class ome.services.messages.AbstractSessionMessage
 
AbstractStatefulBean - Class in ome.services
Base bean implementation for stateful services.
AbstractStatefulBean() - Constructor for class ome.services.AbstractStatefulBean
 
AbstractStatsMessage - Class in ome.services.messages.stats
Published when some limit in user/group/session activity has been reached.
AbstractStatsMessage(Object) - Constructor for class ome.services.messages.stats.AbstractStatsMessage
 
AbstractStatsMessage(Object, boolean) - Constructor for class ome.services.messages.stats.AbstractStatsMessage
 
AbstractStepFactory - Class in ome.services.graphs
Deprecated.
will be removed in OMERO 5.2, so use the new graphs implementation
AbstractStepFactory() - Constructor for class ome.services.graphs.AbstractStepFactory
Deprecated.
 
AbstractThrottlingStrategy - Class in ome.services.throttling
Throttling implementation which uses the calling server Thread for execution.
AbstractThrottlingStrategy() - Constructor for class ome.services.throttling.AbstractThrottlingStrategy
 
accept(String, String) - Method in class ome.services.mail.MapAnnotationSubethaListener
Accepts all mails.
accept(Job) - Method in class ome.services.procs.ProcessorSkeleton
 
acceptFilter(Filter) - Method in class ome.model.acquisition.Arc
 
acceptFilter(Filter) - Method in class ome.model.acquisition.Detector
 
acceptFilter(Filter) - Method in class ome.model.acquisition.DetectorSettings
 
acceptFilter(Filter) - Method in class ome.model.acquisition.Dichroic
 
acceptFilter(Filter) - Method in class ome.model.acquisition.Filament
 
acceptFilter(Filter) - Method in class ome.model.acquisition.Filter
 
acceptFilter(Filter) - Method in class ome.model.acquisition.FilterSet
 
acceptFilter(Filter) - Method in class ome.model.acquisition.FilterSetEmissionFilterLink
 
acceptFilter(Filter) - Method in class ome.model.acquisition.FilterSetExcitationFilterLink
 
acceptFilter(Filter) - Method in class ome.model.acquisition.GenericExcitationSource
 
acceptFilter(Filter) - Method in class ome.model.acquisition.ImagingEnvironment
 
acceptFilter(Filter) - Method in class ome.model.acquisition.Instrument
 
acceptFilter(Filter) - Method in class ome.model.acquisition.Laser
 
acceptFilter(Filter) - Method in class ome.model.acquisition.LightEmittingDiode
 
acceptFilter(Filter) - Method in class ome.model.acquisition.LightPath
 
acceptFilter(Filter) - Method in class ome.model.acquisition.LightPathEmissionFilterLink
 
acceptFilter(Filter) - Method in class ome.model.acquisition.LightPathExcitationFilterLink
 
acceptFilter(Filter) - Method in class ome.model.acquisition.LightSettings
 
acceptFilter(Filter) - Method in class ome.model.acquisition.LightSource
 
acceptFilter(Filter) - Method in class ome.model.acquisition.Microscope
 
acceptFilter(Filter) - Method in class ome.model.acquisition.Objective
 
acceptFilter(Filter) - Method in class ome.model.acquisition.ObjectiveSettings
 
acceptFilter(Filter) - Method in class ome.model.acquisition.OTF
 
acceptFilter(Filter) - Method in class ome.model.acquisition.StageLabel
 
acceptFilter(Filter) - Method in class ome.model.acquisition.TransmittanceRange
 
acceptFilter(Filter) - Method in class ome.model.annotations.Annotation
 
acceptFilter(Filter) - Method in class ome.model.annotations.AnnotationAnnotationLink
 
acceptFilter(Filter) - Method in class ome.model.annotations.BasicAnnotation
 
acceptFilter(Filter) - Method in class ome.model.annotations.BooleanAnnotation
 
acceptFilter(Filter) - Method in class ome.model.annotations.ChannelAnnotationLink
 
acceptFilter(Filter) - Method in class ome.model.annotations.CommentAnnotation
 
acceptFilter(Filter) - Method in class ome.model.annotations.DatasetAnnotationLink
 
acceptFilter(Filter) - Method in class ome.model.annotations.DetectorAnnotationLink
 
acceptFilter(Filter) - Method in class ome.model.annotations.DichroicAnnotationLink
 
acceptFilter(Filter) - Method in class ome.model.annotations.DoubleAnnotation
 
acceptFilter(Filter) - Method in class ome.model.annotations.ExperimenterAnnotationLink
 
acceptFilter(Filter) - Method in class ome.model.annotations.ExperimenterGroupAnnotationLink
 
acceptFilter(Filter) - Method in class ome.model.annotations.FileAnnotation
 
acceptFilter(Filter) - Method in class ome.model.annotations.FilesetAnnotationLink
 
acceptFilter(Filter) - Method in class ome.model.annotations.FilterAnnotationLink
 
acceptFilter(Filter) - Method in class ome.model.annotations.ImageAnnotationLink
 
acceptFilter(Filter) - Method in class ome.model.annotations.InstrumentAnnotationLink
 
acceptFilter(Filter) - Method in class ome.model.annotations.LightPathAnnotationLink
 
acceptFilter(Filter) - Method in class ome.model.annotations.LightSourceAnnotationLink
 
acceptFilter(Filter) - Method in class ome.model.annotations.ListAnnotation
 
acceptFilter(Filter) - Method in class ome.model.annotations.LongAnnotation
 
acceptFilter(Filter) - Method in class ome.model.annotations.MapAnnotation
 
acceptFilter(Filter) - Method in class ome.model.annotations.NamespaceAnnotationLink
 
acceptFilter(Filter) - Method in class ome.model.annotations.NodeAnnotationLink
 
acceptFilter(Filter) - Method in class ome.model.annotations.NumericAnnotation
 
acceptFilter(Filter) - Method in class ome.model.annotations.ObjectiveAnnotationLink
 
acceptFilter(Filter) - Method in class ome.model.annotations.OriginalFileAnnotationLink
 
acceptFilter(Filter) - Method in class ome.model.annotations.PlaneInfoAnnotationLink
 
acceptFilter(Filter) - Method in class ome.model.annotations.PlateAcquisitionAnnotationLink
 
acceptFilter(Filter) - Method in class ome.model.annotations.PlateAnnotationLink
 
acceptFilter(Filter) - Method in class ome.model.annotations.ProjectAnnotationLink
 
acceptFilter(Filter) - Method in class ome.model.annotations.ReagentAnnotationLink
 
acceptFilter(Filter) - Method in class ome.model.annotations.RoiAnnotationLink
 
acceptFilter(Filter) - Method in class ome.model.annotations.ScreenAnnotationLink
 
acceptFilter(Filter) - Method in class ome.model.annotations.SessionAnnotationLink
 
acceptFilter(Filter) - Method in class ome.model.annotations.ShapeAnnotationLink
 
acceptFilter(Filter) - Method in class ome.model.annotations.TagAnnotation
 
acceptFilter(Filter) - Method in class ome.model.annotations.TermAnnotation
 
acceptFilter(Filter) - Method in class ome.model.annotations.TextAnnotation
 
acceptFilter(Filter) - Method in class ome.model.annotations.TimestampAnnotation
 
acceptFilter(Filter) - Method in class ome.model.annotations.TypeAnnotation
 
acceptFilter(Filter) - Method in class ome.model.annotations.WellAnnotationLink
 
acceptFilter(Filter) - Method in class ome.model.annotations.XmlAnnotation
 
acceptFilter(Filter) - Method in class ome.model.containers.Dataset
 
acceptFilter(Filter) - Method in class ome.model.containers.DatasetImageLink
 
acceptFilter(Filter) - Method in class ome.model.containers.Project
 
acceptFilter(Filter) - Method in class ome.model.containers.ProjectDatasetLink
 
acceptFilter(Filter) - Method in class ome.model.core.Channel
 
acceptFilter(Filter) - Method in class ome.model.core.Image
 
acceptFilter(Filter) - Method in class ome.model.core.LogicalChannel
 
acceptFilter(Filter) - Method in class ome.model.core.OriginalFile
 
acceptFilter(Filter) - Method in class ome.model.core.Pixels
 
acceptFilter(Filter) - Method in class ome.model.core.PixelsOriginalFileMap
 
acceptFilter(Filter) - Method in class ome.model.core.PlaneInfo
 
acceptFilter(Filter) - Method in class ome.model.display.ChannelBinding
 
acceptFilter(Filter) - Method in class ome.model.display.CodomainMapContext
 
acceptFilter(Filter) - Method in class ome.model.display.ContrastStretchingContext
 
acceptFilter(Filter) - Method in class ome.model.display.PlaneSlicingContext
 
acceptFilter(Filter) - Method in class ome.model.display.QuantumDef
 
acceptFilter(Filter) - Method in class ome.model.display.RenderingDef
 
acceptFilter(Filter) - Method in class ome.model.display.ReverseIntensityContext
 
acceptFilter(Filter) - Method in class ome.model.display.Thumbnail
 
acceptFilter(Filter) - Method in class ome.model.enums.AcquisitionMode
 
acceptFilter(Filter) - Method in class ome.model.enums.ArcType
 
acceptFilter(Filter) - Method in class ome.model.enums.Binning
 
acceptFilter(Filter) - Method in class ome.model.enums.ChecksumAlgorithm
 
acceptFilter(Filter) - Method in class ome.model.enums.ContrastMethod
 
acceptFilter(Filter) - Method in class ome.model.enums.Correction
 
acceptFilter(Filter) - Method in class ome.model.enums.DetectorType
 
acceptFilter(Filter) - Method in class ome.model.enums.DimensionOrder
 
acceptFilter(Filter) - Method in class ome.model.enums.EventType
 
acceptFilter(Filter) - Method in class ome.model.enums.ExperimentType
 
acceptFilter(Filter) - Method in class ome.model.enums.Family
 
acceptFilter(Filter) - Method in class ome.model.enums.FilamentType
 
acceptFilter(Filter) - Method in class ome.model.enums.FilterType
 
acceptFilter(Filter) - Method in class ome.model.enums.Format
 
acceptFilter(Filter) - Method in class ome.model.enums.Illumination
 
acceptFilter(Filter) - Method in class ome.model.enums.Immersion
 
acceptFilter(Filter) - Method in class ome.model.enums.LaserMedium
 
acceptFilter(Filter) - Method in class ome.model.enums.LaserType
 
acceptFilter(Filter) - Method in class ome.model.enums.Medium
 
acceptFilter(Filter) - Method in class ome.model.enums.MicrobeamManipulationType
 
acceptFilter(Filter) - Method in class ome.model.enums.MicroscopeType
 
acceptFilter(Filter) - Method in class ome.model.enums.PhotometricInterpretation
 
acceptFilter(Filter) - Method in class ome.model.enums.PixelsType
 
acceptFilter(Filter) - Method in class ome.model.enums.Pulse
 
acceptFilter(Filter) - Method in class ome.model.enums.RenderingModel
 
acceptFilter(Filter) - Method in class ome.model.experiment.Experiment
 
acceptFilter(Filter) - Method in class ome.model.experiment.MicrobeamManipulation
 
acceptFilter(Filter) - Method in class ome.model.fs.Fileset
 
acceptFilter(Filter) - Method in class ome.model.fs.FilesetEntry
 
acceptFilter(Filter) - Method in class ome.model.fs.FilesetJobLink
 
acceptFilter(Filter) - Method in class ome.model.internal.Details
 
acceptFilter(Filter) - Method in class ome.model.internal.Link
 
acceptFilter(Filter) - Method in class ome.model.jobs.ImportJob
 
acceptFilter(Filter) - Method in class ome.model.jobs.IndexingJob
 
acceptFilter(Filter) - Method in class ome.model.jobs.IntegrityCheckJob
 
acceptFilter(Filter) - Method in class ome.model.jobs.Job
 
acceptFilter(Filter) - Method in class ome.model.jobs.JobOriginalFileLink
 
acceptFilter(Filter) - Method in class ome.model.jobs.JobStatus
 
acceptFilter(Filter) - Method in class ome.model.jobs.MetadataImportJob
 
acceptFilter(Filter) - Method in class ome.model.jobs.ParseJob
 
acceptFilter(Filter) - Method in class ome.model.jobs.PixelDataJob
 
acceptFilter(Filter) - Method in class ome.model.jobs.ScriptJob
 
acceptFilter(Filter) - Method in class ome.model.jobs.ThumbnailGenerationJob
 
acceptFilter(Filter) - Method in class ome.model.jobs.UploadJob
 
acceptFilter(Filter) - Method in class ome.model.meta.DBPatch
 
acceptFilter(Filter) - Method in class ome.model.meta.Event
 
acceptFilter(Filter) - Method in class ome.model.meta.EventLog
 
acceptFilter(Filter) - Method in class ome.model.meta.Experimenter
 
acceptFilter(Filter) - Method in class ome.model.meta.ExperimenterGroup
 
acceptFilter(Filter) - Method in class ome.model.meta.ExternalInfo
 
acceptFilter(Filter) - Method in class ome.model.meta.GroupExperimenterMap
 
acceptFilter(Filter) - Method in class ome.model.meta.Namespace
 
acceptFilter(Filter) - Method in class ome.model.meta.Node
 
acceptFilter(Filter) - Method in class ome.model.meta.Session
 
acceptFilter(Filter) - Method in class ome.model.meta.Share
 
acceptFilter(Filter) - Method in class ome.model.meta.ShareMember
 
acceptFilter(Filter) - Method in class ome.model.roi.Ellipse
 
acceptFilter(Filter) - Method in class ome.model.roi.Label
 
acceptFilter(Filter) - Method in class ome.model.roi.Line
 
acceptFilter(Filter) - Method in class ome.model.roi.Mask
 
acceptFilter(Filter) - Method in class ome.model.roi.Path
 
acceptFilter(Filter) - Method in class ome.model.roi.Point
 
acceptFilter(Filter) - Method in class ome.model.roi.Polygon
 
acceptFilter(Filter) - Method in class ome.model.roi.Polyline
 
acceptFilter(Filter) - Method in class ome.model.roi.Rect
 
acceptFilter(Filter) - Method in class ome.model.roi.Roi
 
acceptFilter(Filter) - Method in class ome.model.roi.Shape
 
acceptFilter(Filter) - Method in class ome.model.screen.Plate
 
acceptFilter(Filter) - Method in class ome.model.screen.PlateAcquisition
 
acceptFilter(Filter) - Method in class ome.model.screen.Reagent
 
acceptFilter(Filter) - Method in class ome.model.screen.Screen
 
acceptFilter(Filter) - Method in class ome.model.screen.ScreenPlateLink
 
acceptFilter(Filter) - Method in class ome.model.screen.Well
 
acceptFilter(Filter) - Method in class ome.model.screen.WellReagentLink
 
acceptFilter(Filter) - Method in class ome.model.screen.WellSample
 
acceptFilter(Filter) - Method in class ome.model.stats.StatsInfo
 
acceptFilter(Filter) - Method in class ome.model.units.ElectricPotential
 
acceptFilter(Filter) - Method in class ome.model.units.Frequency
 
acceptFilter(Filter) - Method in class ome.model.units.Length
 
acceptFilter(Filter) - Method in class ome.model.units.Power
 
acceptFilter(Filter) - Method in class ome.model.units.Pressure
 
acceptFilter(Filter) - Method in class ome.model.units.Temperature
 
acceptFilter(Filter) - Method in class ome.model.units.Time
 
acceptFilter(Filter) - Method in interface ome.util.Filterable
 
access(File) - Method in class omero.util.TempFileManager
Returns true if the current user can write to the give directory.
acl - Variable in class ome.tools.hibernate.ProxyCleanupFilter
 
ACLCreateViolation - Exception in ome.conditions.acl
User does not have permissions to perform given action.
ACLCreateViolation(Class, Long, String) - Constructor for exception ome.conditions.acl.ACLCreateViolation
 
ACLDeleteViolation - Exception in ome.conditions.acl
User does not have permissions to perform given action.
ACLDeleteViolation(Class, Long, String) - Constructor for exception ome.conditions.acl.ACLDeleteViolation
 
ACLEventListener - Class in ome.security
responsible for intercepting all pre-INSERT, pre-UPDATE, pre-DELETE, and post-LOAD events to apply access control.
ACLEventListener(ACLVoter) - Constructor for class ome.security.ACLEventListener
main constructor. controls access to individual db rows..
ACLLoadViolation - Exception in ome.conditions.acl
User does not have permissions to perform given action.
ACLLoadViolation(Class, Long, String) - Constructor for exception ome.conditions.acl.ACLLoadViolation
 
ACLUpdateViolation - Exception in ome.conditions.acl
User does not have permissions to perform given action.
ACLUpdateViolation(Class, Long, String) - Constructor for exception ome.conditions.acl.ACLUpdateViolation
 
ACLViolation - Exception in ome.conditions.acl
User has attempted an action which is not permitted by the Permissions of a given instance.
ACLViolation(Class, Long, String) - Constructor for exception ome.conditions.acl.ACLViolation
 
aclVoter - Variable in class ome.logic.AdminImpl
 
ACLVoter - Interface in ome.security
helper security interface for all decisions on access control
acquireContext() - Method in class ome.services.util.BeanHelper
Lazy loads the application context, which means that if we're not in the application server, then the OmeroContext.MANAGED_CONTEXT should never get loaded.
acquireLock() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
 
acquireLock(String) - Method in class omero.util.ServantHolder
Acquires the given lock or if necessary creates a new one.
acquireProcessor(Job, int, Current) - Method in class ome.services.blitz.impl.SharedResourcesI
 
acquireProcessor(Job, int, Current) - Method in interface omero.grid.ParamsHelper.Acquirer
 
acquirer() - Method in class ome.services.blitz.impl.ScriptI
 
acquisitionData - Variable in class ome.parameters.Options
 
acquisitionData() - Method in class omero.sys.ParametersI
Sets the acquisition data parameter to true.
acquisitionDate - Variable in class ome.model.core.Image
 
ACQUISITIONDATE - Static variable in class ome.model.core.Image
 
AcquisitionMode - Class in ome.model.enums
 
AcquisitionMode() - Constructor for class ome.model.enums.AcquisitionMode
 
AcquisitionMode(Long) - Constructor for class ome.model.enums.AcquisitionMode
 
AcquisitionMode(Long, boolean) - Constructor for class ome.model.enums.AcquisitionMode
Main constructor.
AcquisitionMode(String) - Constructor for class ome.model.enums.AcquisitionMode
 
AcquisitionMode.Details - Class in ome.model.enums
 
AcquisitionMode.Details() - Constructor for class ome.model.enums.AcquisitionMode.Details
 
AcquisitionMode.Details(Object[]) - Constructor for class ome.model.enums.AcquisitionMode.Details
 
action - Variable in class ome.model.meta.EventLog
 
ACTION - Static variable in class ome.model.meta.EventLog
 
action(GraphStep.Callback, Session, SqlAction, GraphOpts) - Method in class ome.services.chgrp.ChgrpStep
Deprecated.
 
action(GraphStep.Callback, Session, SqlAction, GraphOpts) - Method in class ome.services.chown.ChownStep
Deprecated.
 
action(GraphStep.Callback, Session, SqlAction, GraphOpts) - Method in class ome.services.delete.DeleteStep
Deprecated.
 
action(GraphStep.Callback, Session, SqlAction, GraphOpts) - Method in class ome.services.export.ExporterStep
Deprecated.
 
action - Variable in class ome.services.graphs.GraphPolicy.Details
the current plan for the object, may be mutated by Policy#review(Map, Details, Map, Set)
action(GraphStep.Callback, Session, SqlAction, GraphOpts) - Method in class ome.services.graphs.GraphStep
Deprecated.
Primary action which should perform the main modifications required by the step.
action - Variable in class ome.services.messages.EventLogMessage
 
action - Variable in class ome.tools.hibernate.EventMethodInterceptor
 
activate(long) - Method in interface ome.api.IShare
Turns on the access control lists attached to the given share for the current session.
activate() - Method in interface ome.api.StatefulServiceInterface
Completely restore this service for active use from whatever passivation it has implemented.
activate() - Method in class ome.services.JobBean
Does almost nothing.
activate() - Method in class ome.services.RawFileBean
 
activate() - Method in class ome.services.RawPixelsBean
 
activate() - Method in class ome.services.RenderingBean
 
activate() - Method in class ome.services.SearchBean
 
activate(long) - Method in class ome.services.sharing.ShareBean
 
activate() - Method in class ome.services.ThumbnailBean
 
activate_async(AMD_StatefulServiceInterface_activate, Current) - Method in class ome.services.blitz.impl.AbstractAmdServant
 
activate_async(AMD_IShare_activate, long, Current) - Method in class ome.services.blitz.impl.ShareI
 
activate_async(AMD_StatefulServiceInterface_activate, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
activateAndWait(Current) - Method in class ome.services.blitz.impl.ProcessorCallbackI
Generates a UUID-based Identity with the category of PROCESSORCALLBACK.value and then calls {@link #activateAndWait(Current, Ice.Identity).
activateAndWait(Current, Identity) - Method in class ome.services.blitz.impl.ProcessorCallbackI
Primary method which adds this instance to IceStorm, waits for a response from any active processor services, and finally unregister itself before returning the first processor instance which responded.
active - Variable in class ome.model.display.ChannelBinding
 
ACTIVE - Static variable in class ome.model.display.ChannelBinding
 
active - Variable in class ome.model.meta.Share
 
ACTIVE - Static variable in class ome.model.meta.Share
 
activeQueries() - Method in interface ome.api.Search
Returns the number of active queries.
activeQueries() - Method in class ome.services.SearchBean
 
activeQueries_async(AMD_Search_activeQueries, Current) - Method in class ome.services.blitz.impl.SearchI
 
activeServices(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
activeSession(String) - Method in class ome.util.actions.PostgresSqlAction
 
activeSession(String) - Method in interface ome.util.SqlAction
Returns true if the given string is the UUID of a session that is currently active.
adapter - Variable in class ome.services.blitz.fire.SessionManagerI
 
Adapter - Class in ome.services.throttling
Simple adapter which takes a Executor.Work instance and executes it as a BlitzExecutor task.
Adapter(Object, Current, IceMapper, Executor, Principal, Executor.Work) - Constructor for class ome.services.throttling.Adapter
 
adapter - Variable in class omero.cmd.SessionI
 
Add(Conversion...) - Static method in class ome.model.units.Conversion
Static helper for creating Conversion.Add instances.
add(QueryParameter) - Method in class ome.parameters.Parameters
 
add(String) - Method in class ome.parameters.Period
 
add(EventLog) - Method in class ome.services.eventlogs.EventBacklog
Adds the given EventLog instance to the end of a queue for later popping if no equivalent EventLog is present.
add(GraphStep, long[]) - Method in class ome.services.export.ExporterIndex
Deprecated.
 
add(Document, String, String, LuceneOptions) - Method in class ome.services.fulltext.BridgeHelper
Helper method which takes the parameters from the #set(String, Object, Document, Store, org.apache.lucene.document.Field.Index, Float) method (possibly modified) as well as the parsed String value which should be added to the index, and adds two fields.
add() - Method in class ome.services.graphs.GraphState
Deprecated.
 
add() - Method in interface ome.services.graphs.GraphStep.Callback
Deprecated.
 
add(GraphEntry, long[][]) - Method in class ome.services.graphs.GraphTables
Deprecated.
 
add(CodomainMapContext) - Method in class omeis.providers.re.codomain.CodomainChain
Adds a map context to the chain.
add(String, RType) - Method in class omero.sys.ParametersI
 
add(Resources.Entry) - Method in class omero.util.Resources
 
addAction(SearchAction) - Method in class ome.services.SearchBean
 
addAlgorithm(String) - Method in class ome.parameters.Parameters
 
addAll(Parameters) - Method in class ome.parameters.Parameters
adds all the information from the passed in Parameters instance to this instance.
addAll(QueryParameter[]) - Method in class ome.parameters.Parameters
adds all the information from the passed in Parameters instance to this instance.
addAllDisabled(String...) - Method in class ome.security.basic.CurrentDetails
 
addAnnotationAnnotationLink(AnnotationAnnotationLink) - Method in class ome.model.annotations.Annotation
use instead of setAnnotationLinks .
addAnnotationAnnotationLink(AnnotationAnnotationLink, boolean) - Method in class ome.model.annotations.Annotation
Adds a ome.model.annotations.AnnotationAnnotationLink to annotationLinks, allowing for recursion -- whether or not addAnnotationAnnotationLink will be called on the addition if it is loaded
addAnnotationAnnotationLinkSet(Collection<AnnotationAnnotationLink>) - Method in class ome.model.annotations.Annotation
use like addAnnotationAnnotationLink.
addApplicationListener(ApplicationListener) - Method in class ome.services.messages.GlobalMulticaster
 
addApplicationListenerBean(String) - Method in class ome.services.messages.GlobalMulticaster
 
addArray(int[][], int, int, int) - Method in class pojos.util.UploadMask
Adds a Mask Shape to the appropriate ROIClass, creating one if necessary.
addBoolean(String, Boolean) - Method in class ome.parameters.Parameters
 
addCallback(String, SessionCallback) - Method in class ome.services.sessions.SessionManagerImpl
 
addCallback(CmdCallbackPrx, Current) - Method in class omero.cmd.HandleI
 
addChannel(Channel) - Method in class ome.model.core.LogicalChannel
use instead of setChannels .
addChannel(Channel) - Method in class ome.model.core.Pixels
use instead of setChannels .
addChannelAnnotationLink(ChannelAnnotationLink) - Method in class ome.model.core.Channel
use instead of setAnnotationLinks .
addChannelAnnotationLink(ChannelAnnotationLink, boolean) - Method in class ome.model.core.Channel
Adds a ome.model.annotations.ChannelAnnotationLink to annotationLinks, allowing for recursion -- whether or not addChannelAnnotationLink will be called on the addition if it is loaded
addChannelAnnotationLinkSet(Collection<ChannelAnnotationLink>) - Method in class ome.model.core.Channel
use like addChannelAnnotationLink.
addChannelBinding(ChannelBinding) - Method in class ome.model.display.RenderingDef
use instead of setWaveRendering .
addChannelBindingSet(Collection<ChannelBinding>) - Method in class ome.model.display.RenderingDef
use like addChannelBinding.
addChannelSet(Collection<Channel>) - Method in class ome.model.core.LogicalChannel
use like addChannel.
addChannelSet(Collection<Channel>) - Method in class ome.model.core.Pixels
use like addChannel.
addCircle(String, double, double, double) - Method in class ome.services.blitz.measurements.MeasurementStore
 
addCircle(String, double, double, double) - Method in interface ome.services.blitz.measurements.OmeroMeasurementStore
 
addClass(Class) - Method in class ome.parameters.Parameters
 
addClass(String, Class) - Method in class ome.parameters.Parameters
 
addCleanup(RegisterServiceCleanupMessage) - Method in class ome.security.basic.CurrentDetails
Add a RegisterServiceCleanupMessage to the current thread for cleanup by the ServiceHandler on exit.
addClientId(String) - Method in class omero.util.ServantHolder
 
addCodomainMap(CodomainMapContext) - Method in class ome.services.RenderingBean
Implemented as specified by the RenderingEngine interface.
addCodomainMap(CodomainMapContext) - Method in interface omeis.providers.re.RenderingEngine
Adds the context to the mapping chain.
addCodomainMap_async(AMD_RenderingEngine_addCodomainMap, CodomainMapContext, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
addCodomainMapContext(CodomainMapContext) - Method in class ome.model.display.RenderingDef
use instead of setSpatialDomainEnhancement .
addCodomainMapContextSet(Collection<CodomainMapContext>) - Method in class ome.model.display.RenderingDef
use like addCodomainMapContext.
addComment(long, String) - Method in interface ome.api.IShare
Creates comment for share.
addComment(long, String) - Method in class ome.services.sharing.ShareBean
 
addComment_async(AMD_IShare_addComment, long, String, Current) - Method in class ome.services.blitz.impl.ShareI
 
addContents(Document, String, OriginalFile, OriginalFilesService, Map<String, FileParser>, LuceneOptions) - Method in class ome.services.fulltext.BridgeHelper
Second helper method used when parsing files.
addDataset(String, String, Project) - Method in class ome.formats.OMEROMetadataStoreClient
 
addDatasetAnnotationLink(DatasetAnnotationLink) - Method in class ome.model.containers.Dataset
use instead of setAnnotationLinks .
addDatasetAnnotationLink(DatasetAnnotationLink, boolean) - Method in class ome.model.containers.Dataset
Adds a ome.model.annotations.DatasetAnnotationLink to annotationLinks, allowing for recursion -- whether or not addDatasetAnnotationLink will be called on the addition if it is loaded
addDatasetAnnotationLinkSet(Collection<DatasetAnnotationLink>) - Method in class ome.model.containers.Dataset
use like addDatasetAnnotationLink.
addDatasetImageLink(DatasetImageLink) - Method in class ome.model.containers.Dataset
use instead of setImageLinks .
addDatasetImageLink(DatasetImageLink, boolean) - Method in class ome.model.containers.Dataset
Adds a ome.model.containers.DatasetImageLink to imageLinks, allowing for recursion -- whether or not addDatasetImageLink will be called on the addition if it is loaded
addDatasetImageLink(DatasetImageLink) - Method in class ome.model.core.Image
use instead of setDatasetLinks .
addDatasetImageLink(DatasetImageLink, boolean) - Method in class ome.model.core.Image
Adds a ome.model.containers.DatasetImageLink to datasetLinks, allowing for recursion -- whether or not addDatasetImageLink will be called on the addition if it is loaded
addDatasetImageLinkSet(Collection<DatasetImageLink>) - Method in class ome.model.containers.Dataset
use like addDatasetImageLink.
addDatasetImageLinkSet(Collection<DatasetImageLink>) - Method in class ome.model.core.Image
use like addDatasetImageLink.
addDetector(Detector) - Method in class ome.model.acquisition.Instrument
use instead of setDetector .
addDetectorAnnotationLink(DetectorAnnotationLink) - Method in class ome.model.acquisition.Detector
use instead of setAnnotationLinks .
addDetectorAnnotationLink(DetectorAnnotationLink, boolean) - Method in class ome.model.acquisition.Detector
Adds a ome.model.annotations.DetectorAnnotationLink to annotationLinks, allowing for recursion -- whether or not addDetectorAnnotationLink will be called on the addition if it is loaded
addDetectorAnnotationLinkSet(Collection<DetectorAnnotationLink>) - Method in class ome.model.acquisition.Detector
use like addDetectorAnnotationLink.
addDetectorSet(Collection<Detector>) - Method in class ome.model.acquisition.Instrument
use like addDetector.
addDichroic(Dichroic) - Method in class ome.model.acquisition.Instrument
use instead of setDichroic .
addDichroicAnnotationLink(DichroicAnnotationLink) - Method in class ome.model.acquisition.Dichroic
use instead of setAnnotationLinks .
addDichroicAnnotationLink(DichroicAnnotationLink, boolean) - Method in class ome.model.acquisition.Dichroic
Adds a ome.model.annotations.DichroicAnnotationLink to annotationLinks, allowing for recursion -- whether or not addDichroicAnnotationLink will be called on the addition if it is loaded
addDichroicAnnotationLinkSet(Collection<DichroicAnnotationLink>) - Method in class ome.model.acquisition.Dichroic
use like addDichroicAnnotationLink.
addDichroicSet(Collection<Dichroic>) - Method in class ome.model.acquisition.Instrument
use like addDichroic.
addDisabled(String) - Method in class ome.security.basic.CurrentDetails
 
addError(Throwable, File, String[], String) - Method in class ome.formats.importer.util.ErrorHandler
Add detailed error to error container array
addEvent(Event) - Method in class ome.model.meta.Session
use instead of setEvents .
addEventLog(EventLog) - Method in class ome.model.meta.Event
use instead of setLogs .
addEventLog(Class<? extends IObject>, long) - Method in class ome.services.eventlogs.EventLogLoader
Adds an EventLog for the given Class and id to the backlog.
addEventLog(Class<? extends IObject>, long) - Method in class ome.services.eventlogs.EventLogQueue
Only schedule a new backlog event if there is no currently registered event of that type.
addEventLogSet(Collection<EventLog>) - Method in class ome.model.meta.Event
use like addEventLog.
addEventSet(Collection<Event>) - Method in class ome.model.meta.Session
use like addEvent.
addExperimenterAnnotationLink(ExperimenterAnnotationLink) - Method in class ome.model.meta.Experimenter
use instead of setAnnotationLinks .
addExperimenterAnnotationLink(ExperimenterAnnotationLink, boolean) - Method in class ome.model.meta.Experimenter
Adds a ome.model.annotations.ExperimenterAnnotationLink to annotationLinks, allowing for recursion -- whether or not addExperimenterAnnotationLink will be called on the addition if it is loaded
addExperimenterAnnotationLinkSet(Collection<ExperimenterAnnotationLink>) - Method in class ome.model.meta.Experimenter
use like addExperimenterAnnotationLink.
addExperimenterGroupAnnotationLink(ExperimenterGroupAnnotationLink) - Method in class ome.model.meta.ExperimenterGroup
use instead of setAnnotationLinks .
addExperimenterGroupAnnotationLink(ExperimenterGroupAnnotationLink, boolean) - Method in class ome.model.meta.ExperimenterGroup
Adds a ome.model.annotations.ExperimenterGroupAnnotationLink to annotationLinks, allowing for recursion -- whether or not addExperimenterGroupAnnotationLink will be called on the addition if it is loaded
addExperimenterGroupAnnotationLinkSet(Collection<ExperimenterGroupAnnotationLink>) - Method in class ome.model.meta.ExperimenterGroup
use like addExperimenterGroupAnnotationLink.
addExtendedRestrictions(Set<String>) - Method in class ome.model.internal.Permissions
 
addFile(String) - Method in class ome.formats.importer.util.ErrorContainer
 
addFilesetAnnotationLink(FilesetAnnotationLink) - Method in class ome.model.fs.Fileset
use instead of setAnnotationLinks .
addFilesetAnnotationLink(FilesetAnnotationLink, boolean) - Method in class ome.model.fs.Fileset
Adds a ome.model.annotations.FilesetAnnotationLink to annotationLinks, allowing for recursion -- whether or not addFilesetAnnotationLink will be called on the addition if it is loaded
addFilesetAnnotationLinkSet(Collection<FilesetAnnotationLink>) - Method in class ome.model.fs.Fileset
use like addFilesetAnnotationLink.
addFilesetEntry(FilesetEntry) - Method in class ome.model.core.OriginalFile
use instead of setFilesetEntries .
addFilesetEntry(FilesetEntry) - Method in class ome.model.fs.Fileset
use instead of setUsedFiles .
addFilesetEntrySet(Collection<FilesetEntry>) - Method in class ome.model.core.OriginalFile
use like addFilesetEntry.
addFilesetEntrySet(Collection<FilesetEntry>) - Method in class ome.model.fs.Fileset
use like addFilesetEntry.
addFilesetJobLink(FilesetJobLink) - Method in class ome.model.fs.Fileset
use instead of setJobLinks .
addFilesetJobLink(FilesetJobLink, boolean) - Method in class ome.model.fs.Fileset
Adds a ome.model.fs.FilesetJobLink to jobLinks, allowing for recursion -- whether or not addFilesetJobLink will be called on the addition if it is loaded
addFilesetJobLinkSet(Collection<FilesetJobLink>) - Method in class ome.model.fs.Fileset
use like addFilesetJobLink.
addFilter(Filter) - Method in class ome.model.acquisition.Instrument
use instead of setFilter .
addFilterAnnotationLink(FilterAnnotationLink) - Method in class ome.model.acquisition.Filter
use instead of setAnnotationLinks .
addFilterAnnotationLink(FilterAnnotationLink, boolean) - Method in class ome.model.acquisition.Filter
Adds a ome.model.annotations.FilterAnnotationLink to annotationLinks, allowing for recursion -- whether or not addFilterAnnotationLink will be called on the addition if it is loaded
addFilterAnnotationLinkSet(Collection<FilterAnnotationLink>) - Method in class ome.model.acquisition.Filter
use like addFilterAnnotationLink.
addFiltered(String) - Method in class ome.model.internal.Details
consider the collection named by collectionName to be a "filtered" representation of the DB.
addFiltered(Collection<String>) - Method in class ome.model.internal.Details
consider all the collections named by the elements of collection to be a "filtered" representation of the DB.
addFilterSet(Collection<Filter>) - Method in class ome.model.acquisition.Instrument
use like addFilter.
addFilterSet(FilterSet) - Method in class ome.model.acquisition.Instrument
use instead of setFilterSet .
addFilterSetEmissionFilterLink(FilterSetEmissionFilterLink) - Method in class ome.model.acquisition.Filter
use instead of setEmissionFilterLink .
addFilterSetEmissionFilterLink(FilterSetEmissionFilterLink, boolean) - Method in class ome.model.acquisition.Filter
Adds a ome.model.acquisition.FilterSetEmissionFilterLink to emissionFilterLink, allowing for recursion -- whether or not addFilterSetEmissionFilterLink will be called on the addition if it is loaded
addFilterSetEmissionFilterLink(FilterSetEmissionFilterLink) - Method in class ome.model.acquisition.FilterSet
use instead of setEmissionFilterLink .
addFilterSetEmissionFilterLink(FilterSetEmissionFilterLink, boolean) - Method in class ome.model.acquisition.FilterSet
Adds a ome.model.acquisition.FilterSetEmissionFilterLink to emissionFilterLink, allowing for recursion -- whether or not addFilterSetEmissionFilterLink will be called on the addition if it is loaded
addFilterSetEmissionFilterLinkSet(Collection<FilterSetEmissionFilterLink>) - Method in class ome.model.acquisition.Filter
use like addFilterSetEmissionFilterLink.
addFilterSetEmissionFilterLinkSet(Collection<FilterSetEmissionFilterLink>) - Method in class ome.model.acquisition.FilterSet
use like addFilterSetEmissionFilterLink.
addFilterSetExcitationFilterLink(FilterSetExcitationFilterLink) - Method in class ome.model.acquisition.Filter
use instead of setExcitationFilterLink .
addFilterSetExcitationFilterLink(FilterSetExcitationFilterLink, boolean) - Method in class ome.model.acquisition.Filter
Adds a ome.model.acquisition.FilterSetExcitationFilterLink to excitationFilterLink, allowing for recursion -- whether or not addFilterSetExcitationFilterLink will be called on the addition if it is loaded
addFilterSetExcitationFilterLink(FilterSetExcitationFilterLink) - Method in class ome.model.acquisition.FilterSet
use instead of setExcitationFilterLink .
addFilterSetExcitationFilterLink(FilterSetExcitationFilterLink, boolean) - Method in class ome.model.acquisition.FilterSet
Adds a ome.model.acquisition.FilterSetExcitationFilterLink to excitationFilterLink, allowing for recursion -- whether or not addFilterSetExcitationFilterLink will be called on the addition if it is loaded
addFilterSetExcitationFilterLinkSet(Collection<FilterSetExcitationFilterLink>) - Method in class ome.model.acquisition.Filter
use like addFilterSetExcitationFilterLink.
addFilterSetExcitationFilterLinkSet(Collection<FilterSetExcitationFilterLink>) - Method in class ome.model.acquisition.FilterSet
use like addFilterSetExcitationFilterLink.
addFilterSetSet(Collection<FilterSet>) - Method in class ome.model.acquisition.Instrument
use like addFilterSet.
addGraphIds(GraphStep) - Method in class ome.services.graphs.GraphState
Deprecated.
Add the actually processed ids to the current savepoint.
addGraphIds(GraphStep) - Method in interface ome.services.graphs.GraphStep.Callback
Deprecated.
 
addGroupExperimenterMap(GroupExperimenterMap) - Method in class ome.model.meta.Experimenter
use instead of setGroupExperimenterMap .
addGroupExperimenterMap(GroupExperimenterMap, boolean) - Method in class ome.model.meta.Experimenter
Adds a ome.model.meta.GroupExperimenterMap to groupExperimenterMap, allowing for recursion -- whether or not addGroupExperimenterMap will be called on the addition if it is loaded
addGroupExperimenterMap(GroupExperimenterMap) - Method in class ome.model.meta.ExperimenterGroup
use instead of setGroupExperimenterMap .
addGroupExperimenterMap(GroupExperimenterMap, boolean) - Method in class ome.model.meta.ExperimenterGroup
Adds a ome.model.meta.GroupExperimenterMap to groupExperimenterMap, allowing for recursion -- whether or not addGroupExperimenterMap will be called on the addition if it is loaded
addGroupExperimenterMapSet(Collection<GroupExperimenterMap>) - Method in class ome.model.meta.Experimenter
use like addGroupExperimenterMap.
addGroupExperimenterMapSet(Collection<GroupExperimenterMap>) - Method in class ome.model.meta.ExperimenterGroup
use like addGroupExperimenterMap.
addGroupOwners(ExperimenterGroup, Experimenter...) - Method in interface ome.api.IAdmin
adds the given users to the owner list for this group.
addGroupOwners(ExperimenterGroup, Experimenter...) - Method in class ome.logic.AdminImpl
 
addGroupOwners_async(AMD_IAdmin_addGroupOwners, ExperimenterGroup, List<Experimenter>, Current) - Method in class ome.services.blitz.impl.AdminI
 
addGroups(Experimenter, ExperimenterGroup...) - Method in interface ome.api.IAdmin
adds a user to the given groups.
addGroups(Experimenter, ExperimenterGroup...) - Method in class ome.logic.AdminImpl
 
addGroups(Experimenter, ExperimenterGroup...) - Method in interface ome.security.auth.RoleProvider
 
addGroups(Experimenter, ExperimenterGroup...) - Method in class ome.security.auth.SimpleRoleProvider
 
addGroups_async(AMD_IAdmin_addGroups, Experimenter, List<ExperimenterGroup>, Current) - Method in class ome.services.blitz.impl.AdminI
 
addGuest(long, String) - Method in interface ome.api.IShare
Add guest email address to the share.
addGuest(long, String) - Method in class ome.services.sharing.ShareBean
 
addGuest_async(AMD_IShare_addGuest, long, String, Current) - Method in class ome.services.blitz.impl.ShareI
 
addGuests(long, String...) - Method in interface ome.api.IShare
Adds guest email addresses to the share.
addGuests(long, String...) - Method in class ome.services.sharing.ShareBean
 
addGuests_async(AMD_IShare_addGuests, long, List<String>, Current) - Method in class ome.services.blitz.impl.ShareI
 
addId(Long) - Method in class ome.parameters.Parameters
 
addId(long) - Method in class omero.sys.ParametersI
 
addId(RLong) - Method in class omero.sys.ParametersI
 
addIds(Collection) - Method in class ome.parameters.Parameters
 
addIds(Collection<Long>) - Method in class omero.sys.ParametersI
 
addImage(Image) - Method in class ome.model.fs.Fileset
use instead of setImages .
addImage(Image) - Method in class ome.services.blitz.impl.OmeroMetadata
 
addImage(byte[], int, int, int) - Method in class pojos.util.UploadMask
Adds a Mask Shape to the appropriate ROIClass, creating one if necessary.
addImage_async(AMD_Exporter_addImage, long, Current) - Method in class ome.services.blitz.impl.ExporterI
 
addImageAnnotationLink(ImageAnnotationLink) - Method in class ome.model.core.Image
use instead of setAnnotationLinks .
addImageAnnotationLink(ImageAnnotationLink, boolean) - Method in class ome.model.core.Image
Adds a ome.model.annotations.ImageAnnotationLink to annotationLinks, allowing for recursion -- whether or not addImageAnnotationLink will be called on the addition if it is loaded
addImageAnnotationLinkSet(Collection<ImageAnnotationLink>) - Method in class ome.model.core.Image
use like addImageAnnotationLink.
addImageSet(Collection<Image>) - Method in class ome.model.fs.Fileset
use like addImage.
adding - Variable in class ome.services.eventlogs.EventBacklog
Switch between the adding and the removing states.
addInstrumentAnnotationLink(InstrumentAnnotationLink) - Method in class ome.model.acquisition.Instrument
use instead of setAnnotationLinks .
addInstrumentAnnotationLink(InstrumentAnnotationLink, boolean) - Method in class ome.model.acquisition.Instrument
Adds a ome.model.annotations.InstrumentAnnotationLink to annotationLinks, allowing for recursion -- whether or not addInstrumentAnnotationLink will be called on the addition if it is loaded
addInstrumentAnnotationLinkSet(Collection<InstrumentAnnotationLink>) - Method in class ome.model.acquisition.Instrument
use like addInstrumentAnnotationLink.
addInteger(String, Integer) - Method in class ome.parameters.Parameters
 
additions() - Method in class ome.security.basic.EventListenersFactoryBean
 
addJobOriginalFileLink(JobOriginalFileLink) - Method in class ome.model.jobs.Job
use instead of setOriginalFileLinks .
addJobOriginalFileLink(JobOriginalFileLink, boolean) - Method in class ome.model.jobs.Job
Adds a ome.model.jobs.JobOriginalFileLink to originalFileLinks, allowing for recursion -- whether or not addJobOriginalFileLink will be called on the addition if it is loaded
addJobOriginalFileLinkSet(Collection<JobOriginalFileLink>) - Method in class ome.model.jobs.Job
use like addJobOriginalFileLink.
addKeyword(String) - Method in class pojos.WorkflowData
Adds a new keyword to the workflow.
addLightPathAnnotationLink(LightPathAnnotationLink) - Method in class ome.model.acquisition.LightPath
use instead of setAnnotationLinks .
addLightPathAnnotationLink(LightPathAnnotationLink, boolean) - Method in class ome.model.acquisition.LightPath
Adds a ome.model.annotations.LightPathAnnotationLink to annotationLinks, allowing for recursion -- whether or not addLightPathAnnotationLink will be called on the addition if it is loaded
addLightPathAnnotationLinkSet(Collection<LightPathAnnotationLink>) - Method in class ome.model.acquisition.LightPath
use like addLightPathAnnotationLink.
addLightPathEmissionFilterLink(LightPathEmissionFilterLink) - Method in class ome.model.acquisition.LightPath
use instead of setEmissionFilterLink .
addLightPathEmissionFilterLink(LightPathEmissionFilterLink, boolean) - Method in class ome.model.acquisition.LightPath
Adds a ome.model.acquisition.LightPathEmissionFilterLink to emissionFilterLink, allowing for recursion -- whether or not addLightPathEmissionFilterLink will be called on the addition if it is loaded
addLightPathEmissionFilterLinkSet(Collection<LightPathEmissionFilterLink>) - Method in class ome.model.acquisition.LightPath
use like addLightPathEmissionFilterLink.
addLightPathExcitationFilterLink(LightPathExcitationFilterLink) - Method in class ome.model.acquisition.LightPath
use instead of setExcitationFilterLink .
addLightPathExcitationFilterLink(LightPathExcitationFilterLink, boolean) - Method in class ome.model.acquisition.LightPath
Adds a ome.model.acquisition.LightPathExcitationFilterLink to excitationFilterLink, allowing for recursion -- whether or not addLightPathExcitationFilterLink will be called on the addition if it is loaded
addLightPathExcitationFilterLinkSet(Collection<LightPathExcitationFilterLink>) - Method in class ome.model.acquisition.LightPath
use like addLightPathExcitationFilterLink.
addLightSettings(LightSettings) - Method in class ome.model.experiment.MicrobeamManipulation
use instead of setLightSourceSettings .
addLightSettingsSet(Collection<LightSettings>) - Method in class ome.model.experiment.MicrobeamManipulation
use like addLightSettings.
addLightSource(LightSource) - Method in class ome.model.acquisition.Instrument
use instead of setLightSource .
addLightSourceAnnotationLink(LightSourceAnnotationLink) - Method in class ome.model.acquisition.LightSource
use instead of setAnnotationLinks .
addLightSourceAnnotationLink(LightSourceAnnotationLink, boolean) - Method in class ome.model.acquisition.LightSource
Adds a ome.model.annotations.LightSourceAnnotationLink to annotationLinks, allowing for recursion -- whether or not addLightSourceAnnotationLink will be called on the addition if it is loaded
addLightSourceAnnotationLinkSet(Collection<LightSourceAnnotationLink>) - Method in class ome.model.acquisition.LightSource
use like addLightSourceAnnotationLink.
addLightSourceSet(Collection<LightSource>) - Method in class ome.model.acquisition.Instrument
use like addLightSource.
addList(String, List) - Method in class ome.parameters.Parameters
 
addLocalFile(File, long) - Method in class ome.services.delete.files.AbstractFileDeletions
Called during the creation of instances if a particular file should be handled by AbstractFileDeletions.deleteLocal().
addLog(String, Class, Long) - Method in class ome.security.basic.BasicSecuritySystem
 
addLog(String, Class, Long) - Method in class ome.security.basic.CurrentDetails
 
addLong(String, Long) - Method in class ome.parameters.Parameters
 
addLong(String, long) - Method in class omero.sys.ParametersI
 
addLong(String, RLong) - Method in class omero.sys.ParametersI
 
addLongs(String, Collection<Long>) - Method in class omero.sys.ParametersI
 
addMap(String, Map) - Method in class ome.parameters.Parameters
 
addMasks(Map<Integer, MaskData>) - Method in class pojos.util.ROIComponent
Adds the Masks in the maskSet to the component.
addMessageWithinDbPatchEnd(String, int, String) - Method in interface ome.util.SqlAction
Add a unique message to the DB patch table within the current patch.
addMessageWithinDbPatchEnd(String, int, String) - Method in class ome.util.SqlAction.Impl
 
addMessageWithinDbPatchStart(String, int, String) - Method in interface ome.util.SqlAction
Add a unique message to the DB patch table within the current patch.
addMessageWithinDbPatchStart(String, int, String) - Method in class ome.util.SqlAction.Impl
 
addMicrobeamManipulation(MicrobeamManipulation) - Method in class ome.model.experiment.Experiment
use instead of setMicrobeamManipulation .
addMicrobeamManipulationSet(Collection<MicrobeamManipulation>) - Method in class ome.model.experiment.Experiment
use like addMicrobeamManipulation.
addMimetypes(Collection<String>, Map<String, Object>) - Method in class ome.util.SqlAction.Impl
Returns the "and_mimetype" clause which must be appended to a given query.
addModelProcessor(ModelProcessor) - Method in class ome.formats.OMEROMetadataStoreClient
Adds a model processor to the end of the processing chain.
addNamespaceAnnotationLink(NamespaceAnnotationLink) - Method in class ome.model.meta.Namespace
use instead of setAnnotationLinks .
addNamespaceAnnotationLink(NamespaceAnnotationLink, boolean) - Method in class ome.model.meta.Namespace
Adds a ome.model.annotations.NamespaceAnnotationLink to annotationLinks, allowing for recursion -- whether or not addNamespaceAnnotationLink will be called on the addition if it is loaded
addNamespaceAnnotationLinkSet(Collection<NamespaceAnnotationLink>) - Method in class ome.model.meta.Namespace
use like addNamespaceAnnotationLink.
addNodeAnnotationLink(NodeAnnotationLink) - Method in class ome.model.meta.Node
use instead of setAnnotationLinks .
addNodeAnnotationLink(NodeAnnotationLink, boolean) - Method in class ome.model.meta.Node
Adds a ome.model.annotations.NodeAnnotationLink to annotationLinks, allowing for recursion -- whether or not addNodeAnnotationLink will be called on the addition if it is loaded
addNodeAnnotationLinkSet(Collection<NodeAnnotationLink>) - Method in class ome.model.meta.Node
use like addNodeAnnotationLink.
addObject(long, T) - Method in interface ome.api.IShare
Adds new item to share.
addObject(ObjectPrx) - Method in interface ome.services.blitz.fire.Registry
 
addObject(ObjectPrx) - Method in class ome.services.blitz.fire.Registry.Impl
 
addObject(String, IObject) - Method in class ome.services.blitz.measurements.MeasurementStore
 
addObject(String, IObject) - Method in interface ome.services.blitz.measurements.OmeroMeasurementStore
 
addObject(long, T) - Method in class ome.services.sharing.ShareBean
 
addObject_async(AMD_IShare_addObject, long, IObject, Current) - Method in class ome.services.blitz.impl.ShareI
 
addObjective(Objective) - Method in class ome.model.acquisition.Instrument
use instead of setObjective .
addObjectiveAnnotationLink(ObjectiveAnnotationLink) - Method in class ome.model.acquisition.Objective
use instead of setAnnotationLinks .
addObjectiveAnnotationLink(ObjectiveAnnotationLink, boolean) - Method in class ome.model.acquisition.Objective
Adds a ome.model.annotations.ObjectiveAnnotationLink to annotationLinks, allowing for recursion -- whether or not addObjectiveAnnotationLink will be called on the addition if it is loaded
addObjectiveAnnotationLinkSet(Collection<ObjectiveAnnotationLink>) - Method in class ome.model.acquisition.Objective
use like addObjectiveAnnotationLink.
addObjectiveSet(Collection<Objective>) - Method in class ome.model.acquisition.Instrument
use like addObjective.
addObjects(long, T...) - Method in interface ome.api.IShare
Adds new items to share.
addObjects(Map<String, IObject>) - Method in class ome.services.blitz.measurements.MeasurementStore
 
addObjects(Map<String, IObject>) - Method in interface ome.services.blitz.measurements.OmeroMeasurementStore
 
addObjects(long, T...) - Method in class ome.services.sharing.ShareBean
 
addObjects_async(AMD_IShare_addObjects, long, List<IObject>, Current) - Method in class ome.services.blitz.impl.ShareI
 
addObserver(IObserver) - Method in class ome.formats.importer.ImportLibrary
 
addObserver(IObserver) - Method in interface ome.formats.importer.IObservable
Add observer for notification
addObserver(IObserver) - Method in class ome.formats.importer.util.ClientKeepAlive
 
addObserver(IObserver) - Method in class ome.formats.importer.util.ErrorHandler
 
addObserver(IObserver) - Method in class ome.formats.importer.util.FileUploader
 
addOrderByAsc(String) - Method in interface ome.api.Search
A path from the target entity which will be added to the current stack of order statements applied to the query.
addOrderByAsc(String) - Method in class ome.services.SearchBean
 
addOrderByAsc_async(AMD_Search_addOrderByAsc, String, Current) - Method in class ome.services.blitz.impl.SearchI
 
addOrderByDesc(String) - Method in interface ome.api.Search
A path from the target entity which will be added to the current stack of order statements applied to the query.
addOrderByDesc(String) - Method in class ome.services.SearchBean
 
addOrderByDesc_async(AMD_Search_addOrderByDesc, String, Current) - Method in class ome.services.blitz.impl.SearchI
 
addOriginalFileAnnotationLink(OriginalFileAnnotationLink) - Method in class ome.model.core.OriginalFile
use instead of setAnnotationLinks .
addOriginalFileAnnotationLink(OriginalFileAnnotationLink, boolean) - Method in class ome.model.core.OriginalFile
Adds a ome.model.annotations.OriginalFileAnnotationLink to annotationLinks, allowing for recursion -- whether or not addOriginalFileAnnotationLink will be called on the addition if it is loaded
addOriginalFileAnnotationLinkSet(Collection<OriginalFileAnnotationLink>) - Method in class ome.model.core.OriginalFile
use like addOriginalFileAnnotationLink.
addOrReplace(RepoFile, Long) - Method in class ome.services.scripts.ScriptRepoHelper
 
addOrReplace(Session, SqlAction, ServiceFactory, RepoFile, Long) - Method in class ome.services.scripts.ScriptRepoHelper
 
addOTF(OTF) - Method in class ome.model.acquisition.Instrument
use instead of setOtf .
addOTFSet(Collection<OTF>) - Method in class ome.model.acquisition.Instrument
use like addOTF.
addParameters(Parameters) - Method in class ome.services.SearchBean
 
addPixels(Pixels) - Method in class ome.model.core.Image
use instead of setPixels .
addPixelsOriginalFileMap(PixelsOriginalFileMap) - Method in class ome.model.core.OriginalFile
use instead of setPixelsFileMaps .
addPixelsOriginalFileMap(PixelsOriginalFileMap, boolean) - Method in class ome.model.core.OriginalFile
Adds a ome.model.core.PixelsOriginalFileMap to pixelsFileMaps, allowing for recursion -- whether or not addPixelsOriginalFileMap will be called on the addition if it is loaded
addPixelsOriginalFileMap(PixelsOriginalFileMap) - Method in class ome.model.core.Pixels
use instead of setPixelsFileMaps .
addPixelsOriginalFileMap(PixelsOriginalFileMap, boolean) - Method in class ome.model.core.Pixels
Adds a ome.model.core.PixelsOriginalFileMap to pixelsFileMaps, allowing for recursion -- whether or not addPixelsOriginalFileMap will be called on the addition if it is loaded
addPixelsOriginalFileMapSet(Collection<PixelsOriginalFileMap>) - Method in class ome.model.core.OriginalFile
use like addPixelsOriginalFileMap.
addPixelsOriginalFileMapSet(Collection<PixelsOriginalFileMap>) - Method in class ome.model.core.Pixels
use like addPixelsOriginalFileMap.
addPixelsSet(Collection<Pixels>) - Method in class ome.model.core.Image
use like addPixels.
addPlaneInfo(PlaneInfo) - Method in class ome.model.core.Pixels
use instead of setPlaneInfo .
addPlaneInfoAnnotationLink(PlaneInfoAnnotationLink) - Method in class ome.model.core.PlaneInfo
use instead of setAnnotationLinks .
addPlaneInfoAnnotationLink(PlaneInfoAnnotationLink, boolean) - Method in class ome.model.core.PlaneInfo
Adds a ome.model.annotations.PlaneInfoAnnotationLink to annotationLinks, allowing for recursion -- whether or not addPlaneInfoAnnotationLink will be called on the addition if it is loaded
addPlaneInfoAnnotationLinkSet(Collection<PlaneInfoAnnotationLink>) - Method in class ome.model.core.PlaneInfo
use like addPlaneInfoAnnotationLink.
addPlaneInfoSet(Collection<PlaneInfo>) - Method in class ome.model.core.Pixels
use like addPlaneInfo.
addPlateAcquisition(PlateAcquisition) - Method in class ome.model.screen.Plate
use instead of setPlateAcquisitions .
addPlateAcquisitionAnnotationLink(PlateAcquisitionAnnotationLink) - Method in class ome.model.screen.PlateAcquisition
use instead of setAnnotationLinks .
addPlateAcquisitionAnnotationLink(PlateAcquisitionAnnotationLink, boolean) - Method in class ome.model.screen.PlateAcquisition
Adds a ome.model.annotations.PlateAcquisitionAnnotationLink to annotationLinks, allowing for recursion -- whether or not addPlateAcquisitionAnnotationLink will be called on the addition if it is loaded
addPlateAcquisitionAnnotationLinkSet(Collection<PlateAcquisitionAnnotationLink>) - Method in class ome.model.screen.PlateAcquisition
use like addPlateAcquisitionAnnotationLink.
addPlateAcquisitionSet(Collection<PlateAcquisition>) - Method in class ome.model.screen.Plate
use like addPlateAcquisition.
addPlateAnnotationLink(PlateAnnotationLink) - Method in class ome.model.screen.Plate
use instead of setAnnotationLinks .
addPlateAnnotationLink(PlateAnnotationLink, boolean) - Method in class ome.model.screen.Plate
Adds a ome.model.annotations.PlateAnnotationLink to annotationLinks, allowing for recursion -- whether or not addPlateAnnotationLink will be called on the addition if it is loaded
addPlateAnnotationLinkSet(Collection<PlateAnnotationLink>) - Method in class ome.model.screen.Plate
use like addPlateAnnotationLink.
addProcess(ProcessContainer.Process) - Method in class ome.services.blitz.repo.ProcessContainer
Called once the ManagedImportProcessI service is created.
addProcessor(ProcessorPrx, Current) - Method in class ome.services.blitz.impl.SharedResourcesI
 
addProject(String, String) - Method in class ome.formats.OMEROMetadataStoreClient
 
addProjectAnnotationLink(ProjectAnnotationLink) - Method in class ome.model.containers.Project
use instead of setAnnotationLinks .
addProjectAnnotationLink(ProjectAnnotationLink, boolean) - Method in class ome.model.containers.Project
Adds a ome.model.annotations.ProjectAnnotationLink to annotationLinks, allowing for recursion -- whether or not addProjectAnnotationLink will be called on the addition if it is loaded
addProjectAnnotationLinkSet(Collection<ProjectAnnotationLink>) - Method in class ome.model.containers.Project
use like addProjectAnnotationLink.
addProjectDatasetLink(ProjectDatasetLink) - Method in class ome.model.containers.Dataset
use instead of setProjectLinks .
addProjectDatasetLink(ProjectDatasetLink, boolean) - Method in class ome.model.containers.Dataset
Adds a ome.model.containers.ProjectDatasetLink to projectLinks, allowing for recursion -- whether or not addProjectDatasetLink will be called on the addition if it is loaded
addProjectDatasetLink(ProjectDatasetLink) - Method in class ome.model.containers.Project
use instead of setDatasetLinks .
addProjectDatasetLink(ProjectDatasetLink, boolean) - Method in class ome.model.containers.Project
Adds a ome.model.containers.ProjectDatasetLink to datasetLinks, allowing for recursion -- whether or not addProjectDatasetLink will be called on the addition if it is loaded
addProjectDatasetLinkSet(Collection<ProjectDatasetLink>) - Method in class ome.model.containers.Dataset
use like addProjectDatasetLink.
addProjectDatasetLinkSet(Collection<ProjectDatasetLink>) - Method in class ome.model.containers.Project
use like addProjectDatasetLink.
addReagent(Reagent) - Method in class ome.model.screen.Screen
use instead of setReagents .
addReagentAnnotationLink(ReagentAnnotationLink) - Method in class ome.model.screen.Reagent
use instead of setAnnotationLinks .
addReagentAnnotationLink(ReagentAnnotationLink, boolean) - Method in class ome.model.screen.Reagent
Adds a ome.model.annotations.ReagentAnnotationLink to annotationLinks, allowing for recursion -- whether or not addReagentAnnotationLink will be called on the addition if it is loaded
addReagentAnnotationLinkSet(Collection<ReagentAnnotationLink>) - Method in class ome.model.screen.Reagent
use like addReagentAnnotationLink.
addReagentSet(Collection<Reagent>) - Method in class ome.model.screen.Screen
use like addReagent.
addReference(LSID, LSID) - Method in interface ome.formats.model.IObjectContainerStore
Adds a reference to the reference cache.
addReference(LSID, LSID) - Method in class ome.formats.OMEROMetadataStoreClient
Adds a reference to the reference cache.
addRenderingDef(RenderingDef) - Method in class ome.model.core.Pixels
use instead of setSettings .
addRenderingDefSet(Collection<RenderingDef>) - Method in class ome.model.core.Pixels
use like addRenderingDef.
addReply(long, String, CommentAnnotation) - Method in interface ome.api.IShare
Creates comment which replies to an existing comment.
addReply(long, String, CommentAnnotation) - Method in class ome.services.sharing.ShareBean
 
addReply_async(AMD_IShare_addReply, long, String, TextAnnotation, Current) - Method in class ome.services.blitz.impl.ShareI
 
addResult(List<IObject>) - Method in class ome.services.SearchBean
 
addRoi(Roi) - Method in class ome.model.core.Image
use instead of setRois .
addRoiAnnotationLink(RoiAnnotationLink) - Method in class ome.model.roi.Roi
use instead of setAnnotationLinks .
addRoiAnnotationLink(RoiAnnotationLink, boolean) - Method in class ome.model.roi.Roi
Adds a ome.model.annotations.RoiAnnotationLink to annotationLinks, allowing for recursion -- whether or not addRoiAnnotationLink will be called on the addition if it is loaded
addRoiAnnotationLinkSet(Collection<RoiAnnotationLink>) - Method in class ome.model.roi.Roi
use like addRoiAnnotationLink.
addRoiSet(Collection<Roi>) - Method in class ome.model.core.Image
use like addRoi.
addRows(Object[][]) - Method in class ome.services.blitz.measurements.MeasurementStore
 
addRows(Object[][]) - Method in interface ome.services.blitz.measurements.OmeroMeasurementStore
Adds an array of rows (Object[]) to the store.
addScreen(String, String) - Method in class ome.formats.OMEROMetadataStoreClient
 
addScreenAnnotationLink(ScreenAnnotationLink) - Method in class ome.model.screen.Screen
use instead of setAnnotationLinks .
addScreenAnnotationLink(ScreenAnnotationLink, boolean) - Method in class ome.model.screen.Screen
Adds a ome.model.annotations.ScreenAnnotationLink to annotationLinks, allowing for recursion -- whether or not addScreenAnnotationLink will be called on the addition if it is loaded
addScreenAnnotationLinkSet(Collection<ScreenAnnotationLink>) - Method in class ome.model.screen.Screen
use like addScreenAnnotationLink.
addScreenPlateLink(ScreenPlateLink) - Method in class ome.model.screen.Plate
use instead of setScreenLinks .
addScreenPlateLink(ScreenPlateLink, boolean) - Method in class ome.model.screen.Plate
Adds a ome.model.screen.ScreenPlateLink to screenLinks, allowing for recursion -- whether or not addScreenPlateLink will be called on the addition if it is loaded
addScreenPlateLink(ScreenPlateLink) - Method in class ome.model.screen.Screen
use instead of setPlateLinks .
addScreenPlateLink(ScreenPlateLink, boolean) - Method in class ome.model.screen.Screen
Adds a ome.model.screen.ScreenPlateLink to plateLinks, allowing for recursion -- whether or not addScreenPlateLink will be called on the addition if it is loaded
addScreenPlateLinkSet(Collection<ScreenPlateLink>) - Method in class ome.model.screen.Plate
use like addScreenPlateLink.
addScreenPlateLinkSet(Collection<ScreenPlateLink>) - Method in class ome.model.screen.Screen
use like addScreenPlateLink.
addSeen(Object) - Method in class ome.util.ContextFilter
 
addSession(Session) - Method in class ome.model.meta.Node
use instead of setSessions .
addSessionAnnotationLink(SessionAnnotationLink) - Method in class ome.model.meta.Session
use instead of setAnnotationLinks .
addSessionAnnotationLink(SessionAnnotationLink, boolean) - Method in class ome.model.meta.Session
Adds a ome.model.annotations.SessionAnnotationLink to annotationLinks, allowing for recursion -- whether or not addSessionAnnotationLink will be called on the addition if it is loaded
addSessionAnnotationLinkSet(Collection<SessionAnnotationLink>) - Method in class ome.model.meta.Session
use like addSessionAnnotationLink.
addSessionCallback(String, SessionCallback) - Method in class ome.services.sessions.state.SessionCache
 
addSessionSet(Collection<Session>) - Method in class ome.model.meta.Node
use like addSession.
addSet(String, Set) - Method in class ome.parameters.Parameters
 
addShape(Shape) - Method in class ome.model.roi.Roi
use instead of setShapes .
addShapeAnnotationLink(ShapeAnnotationLink) - Method in class ome.model.roi.Shape
use instead of setAnnotationLinks .
addShapeAnnotationLink(ShapeAnnotationLink, boolean) - Method in class ome.model.roi.Shape
Adds a ome.model.annotations.ShapeAnnotationLink to annotationLinks, allowing for recursion -- whether or not addShapeAnnotationLink will be called on the addition if it is loaded
addShapeAnnotationLinkSet(Collection<ShapeAnnotationLink>) - Method in class ome.model.roi.Shape
use like addShapeAnnotationLink.
addShapeData(ShapeData) - Method in class pojos.ROIData
Adds ShapeData object to ROIData.
addShapeSet(Collection<Shape>) - Method in class ome.model.roi.Roi
use like addShape.
addString(String, String) - Method in class ome.parameters.Parameters
 
addThumbnail(Thumbnail) - Method in class ome.model.core.Pixels
use instead of setThumbnails .
addThumbnailSet(Collection<Thumbnail>) - Method in class ome.model.core.Pixels
use like addThumbnail.
addToTargets(String, long) - Method in class omero.cmd.graphs.ChgrpFacadeI
Deprecated.
Add the given model object to the chgrp request's target objects.
addToTargets(String, long) - Method in class omero.cmd.graphs.ChmodFacadeI
Deprecated.
Add the given model object to the chmod request's target objects.
addToTargets(String, long) - Method in class omero.cmd.graphs.ChownFacadeI
Deprecated.
Add the given model object to the chown request's target objects.
addToTargets(String, long) - Method in class omero.cmd.graphs.DeleteFacadeI
Deprecated.
Add the given model object to the delete request's target objects.
addUser(long, Experimenter) - Method in interface ome.api.IShare
addUser(Set<String>, Experimenter) - Method in class ome.services.mail.MailSender
 
addUser(Set<String>, Experimenter) - Method in class ome.services.mail.ObjectMailSender
 
addUser(long, Experimenter) - Method in class ome.services.sharing.ShareBean
 
addUser_async(AMD_IShare_addUser, long, Experimenter, Current) - Method in class ome.services.blitz.impl.ShareI
 
addUsers(long, Experimenter...) - Method in interface ome.api.IShare
addUsers(long, Experimenter...) - Method in class ome.services.sharing.ShareBean
 
addUsers_async(AMD_IShare_addUsers, long, List<Experimenter>, Current) - Method in class ome.services.blitz.impl.ShareI
 
addViolation(ACLViolation) - Method in exception ome.conditions.acl.CollectedACLViolations
 
addWell(Well) - Method in class ome.model.screen.Plate
use instead of setWells .
addWellAnnotationLink(WellAnnotationLink) - Method in class ome.model.screen.Well
use instead of setAnnotationLinks .
addWellAnnotationLink(WellAnnotationLink, boolean) - Method in class ome.model.screen.Well
Adds a ome.model.annotations.WellAnnotationLink to annotationLinks, allowing for recursion -- whether or not addWellAnnotationLink will be called on the addition if it is loaded
addWellAnnotationLinkSet(Collection<WellAnnotationLink>) - Method in class ome.model.screen.Well
use like addWellAnnotationLink.
addWellReagentLink(WellReagentLink) - Method in class ome.model.screen.Reagent
use instead of setWellLinks .
addWellReagentLink(WellReagentLink, boolean) - Method in class ome.model.screen.Reagent
Adds a ome.model.screen.WellReagentLink to wellLinks, allowing for recursion -- whether or not addWellReagentLink will be called on the addition if it is loaded
addWellReagentLink(WellReagentLink) - Method in class ome.model.screen.Well
use instead of setReagentLinks .
addWellReagentLink(WellReagentLink, boolean) - Method in class ome.model.screen.Well
Adds a ome.model.screen.WellReagentLink to reagentLinks, allowing for recursion -- whether or not addWellReagentLink will be called on the addition if it is loaded
addWellReagentLinkSet(Collection<WellReagentLink>) - Method in class ome.model.screen.Reagent
use like addWellReagentLink.
addWellReagentLinkSet(Collection<WellReagentLink>) - Method in class ome.model.screen.Well
use like addWellReagentLink.
addWellSample(WellSample) - Method in class ome.model.core.Image
use instead of setWellSamples .
addWellSample(WellSample) - Method in class ome.model.screen.PlateAcquisition
use instead of setWellSample .
addWellSample(WellSample) - Method in class ome.model.screen.Well
use instead of setWellSamples .
addWellSampleSet(Collection<WellSample>) - Method in class ome.model.core.Image
use like addWellSample.
addWellSampleSet(Collection<WellSample>) - Method in class ome.model.screen.PlateAcquisition
use like addWellSample.
addWellSampleSet(Collection<WellSample>) - Method in class ome.model.screen.Well
use like addWellSample.
addWellSet(Collection<Well>) - Method in class ome.model.screen.Plate
use like addWell.
adjustGraphPolicy(Function<GraphPolicy, GraphPolicy>) - Method in class omero.cmd.graphs.Chgrp2I
 
adjustGraphPolicy(Function<GraphPolicy, GraphPolicy>) - Method in class omero.cmd.graphs.Chmod2I
 
adjustGraphPolicy(Function<GraphPolicy, GraphPolicy>) - Method in class omero.cmd.graphs.Chown2I
 
adjustGraphPolicy(Function<GraphPolicy, GraphPolicy>) - Method in class omero.cmd.graphs.Delete2I
 
adjustGraphPolicy(Function<GraphPolicy, GraphPolicy>) - Method in interface omero.cmd.graphs.WrappableRequest
Transform the currently applicable graph policy for this request by the given function.
Adler32ChecksumProviderImpl - Class in ome.util.checksum
An implementation of the ChecksumProvider interface using Adler32 as the message digest algorithm.
Adler32ChecksumProviderImpl() - Constructor for class ome.util.checksum.Adler32ChecksumProviderImpl
 
admin - Variable in class ome.services.delete.DeleteBean
 
admin - Variable in class ome.services.sharing.ShareBean
 
AdminAction - Interface in ome.security
adminFlush() - Method in class ome.services.sharing.ShareBean
 
AdminI - Class in ome.services.blitz.impl
Implementation of the IAdmin service.
AdminI(IAdmin, BlitzExecutor) - Constructor for class ome.services.blitz.impl.AdminI
 
AdminImpl - Class in ome.logic
Provides methods for administering user accounts, passwords, as well as methods which require special privileges.
AdminImpl(SqlAction, SessionFactory, MailSender, SimpleMailMessage, ACLVoter, PasswordProvider, RoleProvider, LdapImpl, PasswordUtil, ChmodStrategy, ChecksumProviderFactory) - Constructor for class ome.logic.AdminImpl
 
advices - Variable in class ome.services.util.Executor.Impl
 
advUsage() - Static method in class ome.formats.importer.cli.CommandLineImporter
Prints advanced usage to STDERR and exits with return code 1.
afs - Variable in class ome.services.delete.Deletion.Builder
Deprecated.
 
afs - Variable in class ome.services.delete.files.AbstractFileDeletions
 
afterFilter(String, Object) - Method in class ome.util.ContextFilter
 
afterPropertiesSet() - Method in class ome.security.KeyAndTrustStoreConfiguration
 
afterPropertiesSet() - Method in class ome.system.metrics.DefaultMetrics
 
afterPropertiesSet() - Method in class ome.util.MapPut
 
afterTransactionBegin(Transaction) - Method in class ome.security.basic.OmeroInterceptor
 
afterTransactionCompletion(Transaction) - Method in class ome.security.basic.OmeroInterceptor
 
afterTransfer(int, List<String>) - Method in class ome.formats.importer.transfers.CopyFileTransfer
No cleanup action is taken.
afterTransfer(int, List<String>) - Method in class ome.formats.importer.transfers.CopyMoveFileTransfer
Deletes all copied files if there were no errors.
afterTransfer(int, List<String>) - Method in interface ome.formats.importer.transfers.FileTransfer
Callback which must be invoked after a related set of files has been processed.
afterTransfer(int, List<String>) - Method in class ome.formats.importer.transfers.HardlinkFileTransfer
No cleanup action is taken.
afterTransfer(int, List<String>) - Method in class ome.formats.importer.transfers.MoveFileTransfer
Deletes all hard-linked files if there were no errors.
afterTransfer(int, List<String>) - Method in class ome.formats.importer.transfers.SymlinkFileTransfer
No cleanup is needed for soft-linking.
afterTransfer(int, List<String>) - Method in class ome.formats.importer.transfers.UploadFileTransfer
Since the RawFileStorePrx instances are cleaned up after each transfer, there's no need to cleanup per File.
afterTransfer(int, List<String>) - Method in class ome.formats.importer.transfers.UploadRmFileTransfer
Deletes all uploaded files if there were no errors.
agent - Variable in class ome.formats.importer.ImportConfig
 
agent - Variable in class ome.services.sessions.SessionManager.CreationRequest
 
aggByQuery(String, String, String, Parameters) - Method in class ome.logic.QueryImpl
 
aggMapByQuery(String, String, String, String, Parameters) - Method in class ome.logic.QueryImpl
 
airPressure - Variable in class ome.model.acquisition.ImagingEnvironment
 
AIRPRESSURE - Static variable in class ome.model.acquisition.ImagingEnvironment
 
ALGORITHM - Static variable in class ome.parameters.Parameters
named parameter "algorithm".
all(String[]) - Static method in class prefs
Calls Preferences.childrenNames() and returns the array.
ALL_PROJECTIONS - Static variable in class ome.services.search.FullText
 
AllEntitiesPseudoLogLoader<T extends IObject> - Class in ome.services.eventlogs
EventLogLoader which iterates through each object model type (in no particular order) and returns each object from lowest to highest id.
AllEntitiesPseudoLogLoader() - Constructor for class ome.services.eventlogs.AllEntitiesPseudoLogLoader
 
allEnumerations(Class<T>) - Method in interface ome.api.ITypes
 
allEnumerations(Class<T>) - Method in class ome.logic.TypesImpl
 
allEnumerations_async(AMD_ITypes_allEnumerations, String, Current) - Method in class ome.services.blitz.impl.TypesI
 
AllEventsLogLoader - Class in ome.services.eventlogs
 
AllEventsLogLoader() - Constructor for class ome.services.eventlogs.AllEventsLogLoader
 
allExps() - Method in class ome.parameters.Parameters
 
allExps() - Method in class omero.sys.ParametersI
Removes the experimenter parameter from the map.
allgroups - Variable in class ome.security.SecurityFilterHolder
 
AllGroupsSecurityFilter - Class in ome.security.basic
overrides FilterDefinitionFactoryBean in order to construct our security filter in code and not in XML.
AllGroupsSecurityFilter(SqlAction) - Constructor for class ome.security.basic.AllGroupsSecurityFilter
default constructor which calls all the necessary setters for this FactoryBean.
AllGroupsSecurityFilter(SqlAction, Roles) - Constructor for class ome.security.basic.AllGroupsSecurityFilter
 
allGrps() - Method in class omero.sys.ParametersI
Removes the group parameter from the map.
allObjects(Collection<Set<GraphPolicy.Details>>, GraphPolicy.Details, Collection<Set<GraphPolicy.Details>>) - Static method in class ome.services.graphs.GraphPolicy
Utility method to return all the objects for review as a single set of objects.
allow(ObjectPrx) - Method in class omero.cmd.SessionI
 
ALLOW_LEADING_WILDCARD - Static variable in interface ome.api.Search
allowAdministration() - Method in class ome.services.blitz.Router
 
allowAnnotate(IObject, Details) - Method in interface ome.security.ACLVoter
test whether the given object should be annotatable given the trusted details.
allowAnnotate(IObject, Details) - Method in class ome.security.basic.BasicACLVoter
 
allowAnnotate(IObject, Details) - Method in class ome.security.CompositeACLVoter
 
allowAnnotate(IObject, Details) - Method in class ome.security.sharing.SharingACLVoter
 
allowChmod(IObject) - Method in interface ome.security.ACLVoter
test whether the given object can have its Permissions changed within the current security context.
allowChmod(IObject) - Method in class ome.security.basic.BasicACLVoter
 
allowChmod(IObject) - Method in class ome.security.CompositeACLVoter
 
allowChmod(IObject) - Method in class ome.security.sharing.SharingACLVoter
 
allowCreation(IObject) - Method in interface ome.security.ACLVoter
test whether the given object should be insertable into the DB.
allowCreation(IObject) - Method in class ome.security.basic.BasicACLVoter
 
allowCreation(IObject) - Method in class ome.security.CompositeACLVoter
 
allowCreation(IObject) - Method in class ome.security.sharing.SharingACLVoter
 
allowDelete(IObject, Details) - Method in interface ome.security.ACLVoter
test whether the given object should be deleteable given the trusted details.
allowDelete(IObject, Details) - Method in class ome.security.basic.BasicACLVoter
 
allowDelete(IObject, Details) - Method in class ome.security.CompositeACLVoter
 
allowDelete(IObject, Details) - Method in class ome.security.sharing.SharingACLVoter
 
allowLoad(Session, Class<? extends IObject>, Details, long) - Method in interface ome.security.ACLVoter
test whether the object of the given Class with the given Details should be loadable in the current security context.
allowLoad(Session, Class<? extends IObject>, Details, long) - Method in class ome.security.basic.BasicACLVoter
delegates to SecurityFilter because that is where the logic is defined for the read filter Ignores the id for the moment.
allowLoad(Session, Class<? extends IObject>, Details, long) - Method in class ome.security.CompositeACLVoter
 
allowLoad(Session, Class<? extends IObject>, Details, long) - Method in class ome.security.sharing.SharingACLVoter
 
allowUpdate(IObject, Details) - Method in interface ome.security.ACLVoter
test whether the given object should be updateable given the trusted details.
allowUpdate(IObject, Details) - Method in class ome.security.basic.BasicACLVoter
 
allowUpdate(IObject, Details) - Method in class ome.security.CompositeACLVoter
 
allowUpdate(IObject, Details) - Method in class ome.security.sharing.SharingACLVoter
 
allTimes() - Method in class omero.sys.ParametersI
Removes the time parameters from the map.
allTypes() - Method in interface ome.api.Search
Permits all types to be returned.
allTypes() - Method in class ome.services.SearchBean
 
allTypes_async(AMD_Search_allTypes, Current) - Method in class ome.services.blitz.impl.SearchI
 
alpha - Variable in class ome.model.core.Channel
 
ALPHA - Static variable in class ome.model.core.Channel
 
alpha - Variable in class ome.model.display.ChannelBinding
 
ALPHA - Static variable in class ome.model.display.ChannelBinding
 
alpha - Variable in class ome.model.screen.Well
 
ALPHA - Static variable in class ome.model.screen.Well
 
ALPHA_INDEX - Static variable in class ome.formats.model.ColorsFactory
Index of the red component of a color.
ALPHA_INDEX - Static variable in class omeis.providers.re.ColorsFactory
Index of the red component of a color.
ALPHA_TEXT - Static variable in class ome.formats.model.ChannelProcessor
Name of the blue component when it is a graphics image.
alphalessRendering - Variable in class omeis.providers.re.Optimizations
We can do alphaless rendering
alreadyRouted(Current) - Method in class ome.services.blitz.redirect.AbstractRedirector
 
alreadySeen(Object) - Method in class ome.tools.hibernate.UpdateFilter
 
alreadySucceeded(GraphStep) - Method in class ome.services.graphs.GraphSteps
Deprecated.
 
alreadyValidated(GraphStep) - Method in class ome.services.graphs.GraphSteps
Deprecated.
 
amplificationGain - Variable in class ome.model.acquisition.Detector
 
AMPLIFICATIONGAIN - Static variable in class ome.model.acquisition.Detector
 
analyzer - Variable in class ome.logic.QueryImpl
 
anchor - Variable in class ome.model.roi.Label
 
ANCHOR - Static variable in class ome.model.roi.Label
 
and() - Method in interface ome.api.Search
Applies the next by* method to the previous by* method, so that a call Search.hasNext(), Search.next(), or Search.results() sees only the intersection of the two calls.
and() - Method in class ome.services.SearchBean
 
and(String) - Method in class ome.tools.hibernate.QueryBuilder
Appends "and" plus your string unless this is the first where-spec in which case it is simply appended.
and_async(AMD_Search_and, Current) - Method in class ome.services.blitz.impl.SearchI
 
angle(PlanePoint) - Method in class ome.util.math.geom2D.PlanePoint
Calculates the angle between this vector and the specified argument, provided none of these vectors is the null vector.
annotatedBetween(AnnotationCriteria) - Method in class ome.services.search.SearchAction
 
annotatedBetween(QueryBuilder, String) - Method in class ome.services.search.SearchAction
 
annotatedBy(AnnotationCriteria) - Method in class ome.services.search.SearchAction
 
annotatedBy(QueryBuilder, String) - Method in class ome.services.search.SearchAction
 
annotatedBy - Variable in class ome.services.search.SearchValues
 
annotatedStart - Variable in class ome.services.search.SearchValues
 
annotatedStop - Variable in class ome.services.search.SearchValues
 
AnnotatedWith - Class in ome.services.search
Query for Search which uses an example Annotation instance as the basis for comparison.
AnnotatedWith(SearchValues, Annotation[], boolean, boolean) - Constructor for class ome.services.search.AnnotatedWith
 
ANNOTATERESTRICTION - Static variable in class ome.model.internal.Permissions
 
Annotation - Class in ome.model.annotations
These filter definitions are used by the security system to eliminate non-readable objects from queries.
Annotation() - Constructor for class ome.model.annotations.Annotation
 
Annotation(Long) - Constructor for class ome.model.annotations.Annotation
 
Annotation(Long, boolean) - Constructor for class ome.model.annotations.Annotation
Main constructor.
Annotation.Details - Class in ome.model.annotations
 
Annotation.Details() - Constructor for class ome.model.annotations.Annotation.Details
 
Annotation.Details(Object[]) - Constructor for class ome.model.annotations.Annotation.Details
 
AnnotationAnnotationLink - Class in ome.model.annotations
These filter definitions are used by the security system to eliminate non-readable objects from queries.
AnnotationAnnotationLink() - Constructor for class ome.model.annotations.AnnotationAnnotationLink
 
AnnotationAnnotationLink(Long) - Constructor for class ome.model.annotations.AnnotationAnnotationLink
 
AnnotationAnnotationLink(Long, boolean) - Constructor for class ome.model.annotations.AnnotationAnnotationLink
Main constructor.
AnnotationAnnotationLink(IObject, IObject) - Constructor for class ome.model.annotations.AnnotationAnnotationLink
 
AnnotationAnnotationLink.Details - Class in ome.model.annotations
 
AnnotationAnnotationLink.Details() - Constructor for class ome.model.annotations.AnnotationAnnotationLink.Details
 
AnnotationAnnotationLink.Details(Object[]) - Constructor for class ome.model.annotations.AnnotationAnnotationLink.Details
 
AnnotationData - Class in pojos
Holds a textual annotation of a given data object and a reference to the Experimenter that wrote it.
AnnotationData(Class<? extends Annotation>) - Constructor for class pojos.AnnotationData
Creates a new instance.
AnnotationData(A) - Constructor for class pojos.AnnotationData
Creates a new instance.
AnnotationGraphSpec - Class in ome.services.graphs
Deprecated.
will be removed in OMERO 5.2, so use the new graphs implementation
AnnotationGraphSpec(List<String>) - Constructor for class ome.services.graphs.AnnotationGraphSpec
Deprecated.
Creates a new instance.
AnnotationGraphSpec(Map<String, String>, List<String>) - Constructor for class ome.services.graphs.AnnotationGraphSpec
Deprecated.
Creates a new instance.
annotationLinks - Variable in class ome.model.acquisition.Detector
 
ANNOTATIONLINKS - Static variable in class ome.model.acquisition.Detector
 
annotationLinks - Variable in class ome.model.acquisition.Dichroic
 
ANNOTATIONLINKS - Static variable in class ome.model.acquisition.Dichroic
 
annotationLinks - Variable in class ome.model.acquisition.Filter
 
ANNOTATIONLINKS - Static variable in class ome.model.acquisition.Filter
 
annotationLinks - Variable in class ome.model.acquisition.Instrument
 
ANNOTATIONLINKS - Static variable in class ome.model.acquisition.Instrument
 
annotationLinks - Variable in class ome.model.acquisition.LightPath
 
ANNOTATIONLINKS - Static variable in class ome.model.acquisition.LightPath
 
annotationLinks - Variable in class ome.model.acquisition.LightSource
 
ANNOTATIONLINKS - Static variable in class ome.model.acquisition.LightSource
 
annotationLinks - Variable in class ome.model.acquisition.Objective
 
ANNOTATIONLINKS - Static variable in class ome.model.acquisition.Objective
 
annotationLinks - Variable in class ome.model.annotations.Annotation
 
ANNOTATIONLINKS - Static variable in class ome.model.annotations.Annotation
 
annotationLinks - Variable in class ome.model.containers.Dataset
 
ANNOTATIONLINKS - Static variable in class ome.model.containers.Dataset
 
annotationLinks - Variable in class ome.model.containers.Project
 
ANNOTATIONLINKS - Static variable in class ome.model.containers.Project
 
annotationLinks - Variable in class ome.model.core.Channel
 
ANNOTATIONLINKS - Static variable in class ome.model.core.Channel
 
annotationLinks - Variable in class ome.model.core.Image
 
ANNOTATIONLINKS - Static variable in class ome.model.core.Image
 
annotationLinks - Variable in class ome.model.core.OriginalFile
 
ANNOTATIONLINKS - Static variable in class ome.model.core.OriginalFile
 
annotationLinks - Variable in class ome.model.core.PlaneInfo
 
ANNOTATIONLINKS - Static variable in class ome.model.core.PlaneInfo
 
annotationLinks - Variable in class ome.model.fs.Fileset
 
ANNOTATIONLINKS - Static variable in class ome.model.fs.Fileset
 
annotationLinks - Variable in class ome.model.meta.Experimenter
 
ANNOTATIONLINKS - Static variable in class ome.model.meta.Experimenter
 
annotationLinks - Variable in class ome.model.meta.ExperimenterGroup
 
ANNOTATIONLINKS - Static variable in class ome.model.meta.ExperimenterGroup
 
annotationLinks - Variable in class ome.model.meta.Namespace
 
ANNOTATIONLINKS - Static variable in class ome.model.meta.Namespace
 
annotationLinks - Variable in class ome.model.meta.Node
 
ANNOTATIONLINKS - Static variable in class ome.model.meta.Node
 
annotationLinks - Variable in class ome.model.meta.Session
 
ANNOTATIONLINKS - Static variable in class ome.model.meta.Session
 
annotationLinks - Variable in class ome.model.roi.Roi
 
ANNOTATIONLINKS - Static variable in class ome.model.roi.Roi
 
annotationLinks - Variable in class ome.model.roi.Shape
 
ANNOTATIONLINKS - Static variable in class ome.model.roi.Shape
 
annotationLinks - Variable in class ome.model.screen.Plate
 
ANNOTATIONLINKS - Static variable in class ome.model.screen.Plate
 
annotationLinks - Variable in class ome.model.screen.PlateAcquisition
 
ANNOTATIONLINKS - Static variable in class ome.model.screen.PlateAcquisition
 
annotationLinks - Variable in class ome.model.screen.Reagent
 
ANNOTATIONLINKS - Static variable in class ome.model.screen.Reagent
 
annotationLinks - Variable in class ome.model.screen.Screen
 
ANNOTATIONLINKS - Static variable in class ome.model.screen.Screen
 
annotationLinks - Variable in class ome.model.screen.Well
 
ANNOTATIONLINKS - Static variable in class ome.model.screen.Well
 
ANNOTATIONLINKSCOUNTPEROWNER - Static variable in class ome.model.acquisition.Detector
 
ANNOTATIONLINKSCOUNTPEROWNER - Static variable in class ome.model.acquisition.Dichroic
 
ANNOTATIONLINKSCOUNTPEROWNER - Static variable in class ome.model.acquisition.Filter
 
ANNOTATIONLINKSCOUNTPEROWNER - Static variable in class ome.model.acquisition.Instrument
 
ANNOTATIONLINKSCOUNTPEROWNER - Static variable in class ome.model.acquisition.LightPath
 
ANNOTATIONLINKSCOUNTPEROWNER - Static variable in class ome.model.acquisition.LightSource
 
ANNOTATIONLINKSCOUNTPEROWNER - Static variable in class ome.model.acquisition.Objective
 
ANNOTATIONLINKSCOUNTPEROWNER - Static variable in class ome.model.annotations.Annotation
 
ANNOTATIONLINKSCOUNTPEROWNER - Static variable in class ome.model.containers.Dataset
 
ANNOTATIONLINKSCOUNTPEROWNER - Static variable in class ome.model.containers.Project
 
ANNOTATIONLINKSCOUNTPEROWNER - Static variable in class ome.model.core.Channel
 
ANNOTATIONLINKSCOUNTPEROWNER - Static variable in class ome.model.core.Image
 
ANNOTATIONLINKSCOUNTPEROWNER - Static variable in class ome.model.core.OriginalFile
 
ANNOTATIONLINKSCOUNTPEROWNER - Static variable in class ome.model.core.PlaneInfo
 
ANNOTATIONLINKSCOUNTPEROWNER - Static variable in class ome.model.fs.Fileset
 
ANNOTATIONLINKSCOUNTPEROWNER - Static variable in class ome.model.meta.Experimenter
 
ANNOTATIONLINKSCOUNTPEROWNER - Static variable in class ome.model.meta.ExperimenterGroup
 
ANNOTATIONLINKSCOUNTPEROWNER - Static variable in class ome.model.meta.Namespace
 
ANNOTATIONLINKSCOUNTPEROWNER - Static variable in class ome.model.meta.Node
 
ANNOTATIONLINKSCOUNTPEROWNER - Static variable in class ome.model.meta.Session
 
ANNOTATIONLINKSCOUNTPEROWNER - Static variable in class ome.model.roi.Roi
 
ANNOTATIONLINKSCOUNTPEROWNER - Static variable in class ome.model.roi.Shape
 
ANNOTATIONLINKSCOUNTPEROWNER - Static variable in class ome.model.screen.Plate
 
ANNOTATIONLINKSCOUNTPEROWNER - Static variable in class ome.model.screen.PlateAcquisition
 
ANNOTATIONLINKSCOUNTPEROWNER - Static variable in class ome.model.screen.Reagent
 
ANNOTATIONLINKSCOUNTPEROWNER - Static variable in class ome.model.screen.Screen
 
ANNOTATIONLINKSCOUNTPEROWNER - Static variable in class ome.model.screen.Well
 
annotations - Variable in class ome.formats.importer.ImportConfig
 
ANNOTATIONS - Static variable in class pojos.ChannelData
Identifies the Channel.ANNOTATIONLINKS field.
ANNOTATIONS - Static variable in class pojos.DatasetData
Identifies the Dataset#ANNOTATIONLINKS field.
ANNOTATIONS - Static variable in class pojos.ImageData
Identifies the Image#ANNOTATIONLINKS field.
ANNOTATIONS - Static variable in class pojos.PlateData
Identifies the Plate#ANNOTATIONLINKS field.
AnnotationUtils - Class in ome.annotations
Checks metadata constraints on API calls.
AnnotationUtils() - Constructor for class ome.annotations.AnnotationUtils
 
AopContextInitializer - Class in ome.services.blitz.fire
 
AopContextInitializer(ServiceFactory, Principal, AtomicBoolean) - Constructor for class ome.services.blitz.fire.AopContextInitializer
 
ApiConsistencyCheck - Class in ome.services.blitz.util
Checks all servant definitions (see: ome/services/blitz-servantDefinitions.xml) to guarantee that the RMI and the Blitz APIs match.
ApiConsistencyCheck() - Constructor for class ome.services.blitz.util.ApiConsistencyCheck
 
ApiConstraintChecker - Class in ome.annotations
Checks metadata constraints on API calls.
ApiConstraintChecker() - Constructor for class ome.annotations.ApiConstraintChecker
 
ApiUsageException - Exception in ome.conditions
Alerts a user to a misuse of an Omero method call.
ApiUsageException(String) - Constructor for exception ome.conditions.ApiUsageException
 
append(String, Object...) - Method in class ome.security.basic.EventListenersFactoryBean
appends the objects to the existing list identified by key.
append(String) - Method in class ome.tools.hibernate.QueryBuilder
Simple delegate method to allow appending arbitrary strings.
append(ILoggingEvent) - Method in class ome.util.logback.SiftingWhileRejectingDefaultAppender
 
appendDate(StringBuilder, Date) - Method in class ome.tools.hibernate.SqlArray
 
appendDbPoint(StringBuilder, Point) - Static method in class omero.model.SmartShape.Util
 
appendDbPoint(StringBuilder, double, double) - Static method in class omero.model.SmartShape.Util
 
appendSegement(StringBuilder, boolean, double, double) - Static method in class omero.model.SmartShape.Util
 
appendSpace() - Method in class ome.tools.hibernate.QueryBuilder
 
appendSvgPoint(StringBuilder, Point) - Static method in class omero.model.SmartShape.Util
 
appendSvgPoint(StringBuilder, double, double) - Static method in class omero.model.SmartShape.Util
 
apply(String) - Method in class ome.services.blitz.repo.path.MakePathComponentSafe
applyBeanPropertyValues(Object, String) - Method in class ome.system.OmeroContext
Uses the methods of this context's BeanFactory to autowire any Object based on the given beanName.
applyBeanPropertyValues(Object, Class<? extends ServiceInterface>) - Method in class ome.system.OmeroContext
Uses the methods of this context's BeanFactory to autowire any Object based on the service class.
applyContext(Details, boolean) - Method in class ome.security.basic.CurrentDetails
 
applyHardWiredInterceptors(List<HardWiredInterceptor>, AopContextInitializer) - Method in class ome.services.blitz.impl.AbstractAmdServant
Applies the hard-wired intercepting to this instance.
applyIfShareAccessible(QueryBuilder) - Method in class ome.services.sharing.ShareBean
If the current user is not an admin, then this methods adds a subclause to the HQL: AND ( share.owner.id = :userId or user.id = :userId ) QueryBuilder.where() should already have been called.
applySettingsToDataset(long, long) - Method in interface ome.api.IRenderingSettings
Applies rendering settings to all images in a given Dataset.
applySettingsToDataset(long, long) - Method in class ome.logic.RenderingSettingsImpl
Implemented as specified by the IRenderingSettings I/F.
applySettingsToDataset_async(AMD_IRenderingSettings_applySettingsToDataset, long, long, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
 
applySettingsToImage(long, long) - Method in interface ome.api.IRenderingSettings
Applies rendering settings to a given Image.
applySettingsToImage(long, long) - Method in class ome.logic.RenderingSettingsImpl
Implemented as specified by the IRenderingSettings I/F
applySettingsToImage_async(AMD_IRenderingSettings_applySettingsToImage, long, long, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
 
applySettingsToImages(long, List<Long>) - Method in interface ome.api.IRenderingSettings
Applies rendering settings to a given Image.
applySettingsToImages(long, List<Long>) - Method in class ome.logic.RenderingSettingsImpl
Implemented as specified by the IRenderingSettings I/F
applySettingsToImages_async(AMD_IRenderingSettings_applySettingsToImages, long, List<Long>, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
 
applySettingsToPixels(long, long) - Method in interface ome.api.IRenderingSettings
Applies rendering settings to a given Pixels.
applySettingsToPixels(long, long) - Method in class ome.logic.RenderingSettingsImpl
Implemented as specified by the IRenderingSettings I/F
applySettingsToPixels_async(AMD_IRenderingSettings_applySettingsToPixels, long, long, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
 
applySettingsToProject(long, long) - Method in interface ome.api.IRenderingSettings
Applies rendering settings to all images in all Datasets of a given Project.
applySettingsToProject(long, long) - Method in class ome.logic.RenderingSettingsImpl
Implemented as specified by the IRenderingSettings I/F.
applySettingsToProject_async(AMD_IRenderingSettings_applySettingsToProject, long, long, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
 
applySettingsToSet(long, Class<T>, Set<Long>) - Method in interface ome.api.IRenderingSettings
Applies rendering settings to one or many containers.
applySettingsToSet(long, Class<T>, Set<Long>) - Method in class ome.logic.RenderingSettingsImpl
Implemented as specified by the IRenderingSettings I/F.
applySettingsToSet_async(AMD_IRenderingSettings_applySettingsToSet, long, String, List<Long>, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
 
Arc - Class in ome.model.acquisition
 
Arc() - Constructor for class ome.model.acquisition.Arc
 
Arc(Long) - Constructor for class ome.model.acquisition.Arc
 
Arc(Long, boolean) - Constructor for class ome.model.acquisition.Arc
Main constructor.
Arc(ArcType) - Constructor for class ome.model.acquisition.Arc
 
ARC - Static variable in class pojos.LightSourceData
Indicates that the light source is a arc.
archived - Variable in class ome.model.core.Image
 
ARCHIVED - Static variable in class ome.model.core.Image
 
ArcType - Class in ome.model.enums
 
ArcType() - Constructor for class ome.model.enums.ArcType
 
ArcType(Long) - Constructor for class ome.model.enums.ArcType
 
ArcType(Long, boolean) - Constructor for class ome.model.enums.ArcType
Main constructor.
ArcType(String) - Constructor for class ome.model.enums.ArcType
 
ArcType.Details - Class in ome.model.enums
 
ArcType.Details() - Constructor for class ome.model.enums.ArcType.Details
 
ArcType.Details(Object[]) - Constructor for class ome.model.enums.ArcType.Details
 
areaPoints(SmartShape.PointCallback) - Method in class omero.model.SmartEllipseI
 
areaPoints(SmartShape.PointCallback) - Method in class omero.model.SmartLineI
 
areaPoints(SmartShape.PointCallback) - Method in class omero.model.SmartMaskI
 
areaPoints(SmartShape.PointCallback) - Method in class omero.model.SmartPathI
 
areaPoints(SmartShape.PointCallback) - Method in class omero.model.SmartPointI
 
areaPoints(SmartShape.PointCallback) - Method in class omero.model.SmartPolygonI
 
areaPoints(SmartShape.PointCallback) - Method in class omero.model.SmartPolylineI
 
areaPoints(SmartShape.PointCallback) - Method in class omero.model.SmartRectI
 
areaPoints(SmartShape.PointCallback) - Method in interface omero.model.SmartShape
Calls the SmartShape.PointCallback with all of the x/y coordinates which are within the shape.
areaPoints(SmartShape.PointCallback) - Method in class omero.model.SmartTextI
 
areTablesEnabled(Current) - Method in class ome.services.blitz.impl.SharedResourcesI
 
args() - Method in class ome.util.SqlAction.DeleteLog
 
args(String...) - Static method in class prefs
Converts varargs to a String-array.
asAnnotation() - Method in class pojos.DataObject
Returns the hosted IObject as an Annotation.
asAwtShape() - Method in class omero.model.SmartEllipseI
 
asAwtShape() - Method in class omero.model.SmartLineI
 
asAwtShape() - Method in class omero.model.SmartMaskI
 
asAwtShape() - Method in class omero.model.SmartPathI
 
asAwtShape() - Method in class omero.model.SmartPointI
 
asAwtShape() - Method in class omero.model.SmartPolygonI
 
asAwtShape() - Method in class omero.model.SmartPolylineI
 
asAwtShape() - Method in class omero.model.SmartRectI
 
asAwtShape() - Method in interface omero.model.SmartShape
Converst the current SmartShape to a Shape.
asAwtShape() - Method in class omero.model.SmartTextI
 
ASCENDING_LETTER - Static variable in class pojos.PlateData
Indicates that the column or row is a letter starting from A.
ASCENDING_NUMBER - Static variable in class pojos.PlateData
Indicates that the column or row is a number starting from 1.
asChannel() - Method in class pojos.DataObject
Returns the hosted IObject as a Well.
asClassOrNull(String) - Method in class ome.services.fulltext.FullTextIndexer
 
asDataset() - Method in class pojos.DataObject
Returns the hosted IObject as a Dataset.
asExperimenter() - Method in class pojos.DataObject
Returns the hosted IObject as an Experimenter.
asGroup() - Method in class pojos.DataObject
Returns the hosted IObject as an Experimenter Group.
asIAnnotated() - Method in class pojos.DataObject
not null; may through class-cast exception
asImage() - Method in class pojos.DataObject
Returns the hosted IObject as an Image.
asIObject() - Method in class pojos.DataObject
not null; no exceptions.
asOriginalFile(String) - Method in class ome.services.blitz.repo.CheckedPath
Creates an OriginalFile instance for the given CheckedPath even if it doesn't exist.
asPixels() - Method in class pojos.DataObject
Returns the hosted IObject as a Pixels.
asPlate() - Method in class pojos.DataObject
Returns the hosted IObject as a Plate.
asPoints() - Method in class omero.model.SmartEllipseI
 
asPoints() - Method in class omero.model.SmartLineI
 
asPoints() - Method in class omero.model.SmartMaskI
 
asPoints() - Method in class omero.model.SmartPathI
 
asPoints() - Method in class omero.model.SmartPointI
 
asPoints() - Method in class omero.model.SmartPolygonI
 
asPoints() - Method in class omero.model.SmartPolylineI
 
asPoints() - Method in class omero.model.SmartRectI
 
asPoints() - Method in interface omero.model.SmartShape
Provides some, possibly lossy, bounding polygon of this SmartShape via points.
asPoints() - Method in class omero.model.SmartTextI
 
asPojo(IObject) - Static method in class pojos.DataObject
Converts the passed IObject into its corresponding Pojo object.
asPojos(Collection) - Static method in class pojos.DataObject
Converts the collection of IObjects into the corresponding DataObjects
asPojos(Map) - Static method in class pojos.DataObject
Converts the map of IObjects into the corresponding DataObjects
asProject() - Method in class pojos.DataObject
Returns the hosted IObject as a Project.
asProperties() - Method in class ome.system.Login
produces a copy of the internal fields as a Properties instance.
asProperties() - Method in class ome.system.Server
produces a copy of the internal fields as a Properties instance.
asroot - Variable in class ome.services.sessions.SessionManagerImpl
A private session for use only by this instance for running methods via Executor.
asScreen() - Method in class pojos.DataObject
Returns the hosted IObject as a Screen.
assemble(Serializable, Object) - Method in class ome.model.units.GenericEnumType
 
assemble(Serializable, Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
 
assertManaged(IObject) - Method in class ome.logic.AdminImpl
 
assertMayProcess(String, long, Details) - Method in interface ome.services.graphs.GraphTraversal.Processor
Assert that an object with the given details may be processed.
assertMayProcess(String, long, Details) - Method in class omero.cmd.graphs.BaseGraphTraversalProcessor
 
assertNodes(Set<String>) - Method in class ome.services.blitz.fire.Ring
 
assertNoPolicyViolations() - Method in class ome.services.graphs.GraphTraversal
Check that there are no policy violations matched by p:error policy rules.
assertResponse(int) - Method in class omero.cmd.Helper
Checks the given steps against the number of times that this method has been called on this instance and then increments the call count.
assertStep(int, int) - Method in class omero.cmd.Helper
Throws an exception if the current step is not the expected value.
assertStep(int) - Method in class omero.cmd.Helper
Checks the given steps against the number of times that this method has been called on this instance and then increments the call count.
asWell() - Method in class pojos.DataObject
Returns the hosted IObject as a Well.
asWellSample() - Method in class pojos.DataObject
Returns the hosted IObject as a Well.
atime - Variable in class ome.model.core.OriginalFile
 
ATIME - Static variable in class ome.model.core.OriginalFile
 
attach(long) - Method in interface ome.api.JobHandle
 
attach(long) - Method in class ome.services.JobBean
 
attach_async(AMD_JobHandle_attach, long, Current) - Method in class ome.services.blitz.impl.JobHandleI
 
attenuation - Variable in class ome.model.acquisition.LightSettings
 
ATTENUATION - Static variable in class ome.model.acquisition.LightSettings
 
AttributeNewUserGroupBean - Class in ome.security.auth
Handles the "*_attribute" specifiers from etc/omero.properties.
AttributeNewUserGroupBean(String, boolean, boolean) - Constructor for class ome.security.auth.AttributeNewUserGroupBean
 
AttributeSet - Class in ome.security.auth
Specialized handling of all the attributes, multi or single valued.
AttributeSet(DirContextAdapter) - Constructor for class ome.security.auth.AttributeSet
 
AuthenticationException - Exception in ome.conditions
Invalid username and/or credential provided.
AuthenticationException(String) - Constructor for exception ome.conditions.AuthenticationException
 
autoClose - Variable in class ome.formats.importer.ImportConfig
 
available() - Method in class ome.services.pixeldata.PersistentEventLogLoader
 
AWTScaleService - Class in ome.logic
Provides methods for scaling buffered images.
AWTScaleService() - Constructor for class ome.logic.AWTScaleService
 

B

B_BAND - Static variable in class omeis.providers.re.RGBBuffer
Index of the blue band in the image's data buffer.
backOff - Variable in exception ome.conditions.ConcurrencyException
 
BackOff - Interface in ome.io.nio
Strategy interface which is used by PixelsService to calculate the appropriate backoff to report to users when pixel data is not available.
backOff - Variable in class ome.io.nio.PixelsService
BackOff implementation for calculating MissingPyramidExceptions
base - Variable in class ome.util.mem.ReadOnlyByteArray
The original array.
BASE_SCRIPT_FILTER - Static variable in class ome.services.scripts.ScriptRepoHelper
IOFileFilter instance used during ScriptRepoHelper.iterate() to find the matching scripts in the given directory.
BaseGraphPolicyAdjuster - Class in omero.cmd.graphs
The base class assists adjustment of an existing graph traversal policy.
BaseGraphPolicyAdjuster(GraphPolicy) - Constructor for class omero.cmd.graphs.BaseGraphPolicyAdjuster
Construct a new graph policy adjuster.
BaseGraphSpec - Class in ome.services.graphs
Deprecated.
will be removed in OMERO 5.2, so use the new graphs implementation
BaseGraphSpec(String, String...) - Constructor for class ome.services.graphs.BaseGraphSpec
Deprecated.
Simplified constructor, primarily used for testing.
BaseGraphSpec(List<String>) - Constructor for class ome.services.graphs.BaseGraphSpec
Deprecated.
 
BaseGraphSpec.SubSpecIterator - Class in ome.services.graphs
Deprecated.
Iterator which walks returns all GraphSpecs which are reachable from the given spec, depth first including the spec itself.
BaseGraphSpec.SubSpecIterator(GraphSpec) - Constructor for class ome.services.graphs.BaseGraphSpec.SubSpecIterator
Deprecated.
 
BaseGraphTraversalProcessor - Class in omero.cmd.graphs
Useful methods for GraphTraversal.Processor instances to share.
BaseGraphTraversalProcessor(Session) - Constructor for class omero.cmd.graphs.BaseGraphTraversalProcessor
 
baselineShift - Variable in class ome.model.roi.Label
 
BASELINESHIFT - Static variable in class ome.model.roi.Label
 
basename() - Method in class ome.services.scripts.RepoFile
 
BasePolicy - Class in ome.security.policy
Simple base class for Policy implementations which always returns true for BasePolicy.isRestricted(IObject) and always fails on BasePolicy.checkRestriction(IObject).
BasePolicy(Set<Class<IObject>>) - Constructor for class ome.security.policy.BasePolicy
 
basic - Variable in class ome.security.SecuritySystemHolder
 
BasicACLVoter - Class in ome.security.basic
 
BasicACLVoter(CurrentDetails, SystemTypes, TokenHolder, SecurityFilter, PolicyService) - Constructor for class ome.security.basic.BasicACLVoter
 
BasicACLVoter(CurrentDetails, SystemTypes, TokenHolder, SecurityFilter, PolicyService, Roles) - Constructor for class ome.security.basic.BasicACLVoter
 
BasicAnnotation - Class in ome.model.annotations
 
BasicAnnotation() - Constructor for class ome.model.annotations.BasicAnnotation
 
BasicAnnotation(Long) - Constructor for class ome.model.annotations.BasicAnnotation
 
BasicAnnotation(Long, boolean) - Constructor for class ome.model.annotations.BasicAnnotation
Main constructor.
BasicEventContext - Class in ome.security.basic
EventContext implementation for use within the security system.
BasicEventContext(Principal, SessionStats) - Constructor for class ome.security.basic.BasicEventContext
 
BasicEventContext(Principal, SessionStats, EventContext) - Constructor for class ome.security.basic.BasicEventContext
Copy-constructor to not have to allow the mutator SimpleEventContext.copy(EventContext) or BasicEventContext.copyContext(EventContext) out of the EventContext hierarchy.
BasicMethodSecurity - Class in ome.security.basic
Implementation of MethodSecurity which checks method security based on the RolesAllowed annotations of our implementation methods.
BasicMethodSecurity() - Constructor for class ome.security.basic.BasicMethodSecurity
 
BasicMethodSecurity(boolean) - Constructor for class ome.security.basic.BasicMethodSecurity
 
BasicSecuritySystem - Class in ome.security.basic
simplest implementation of SecuritySystem.
BasicSecuritySystem(OmeroInterceptor, SystemTypes, CurrentDetails, SessionManager, Roles, ServiceFactory, TokenHolder, SecurityFilter, PolicyService) - Constructor for class ome.security.basic.BasicSecuritySystem
Main public constructor for this SecuritySystem implementation.
BasicSecurityWiring - Class in ome.security.basic
Responsible for logging users in and out via the Principal before and after the actual invocation of OMERO methods.
BasicSecurityWiring() - Constructor for class ome.security.basic.BasicSecurityWiring
 
BasicSecurityWiring.CloseOnNoSessionContext - Class in ome.security.basic
 
BasicSecurityWiring.CloseOnNoSessionContext() - Constructor for class ome.security.basic.BasicSecurityWiring.CloseOnNoSessionContext
 
batch - Variable in class ome.services.fulltext.FullTextIndexer
 
batchSize - Variable in class ome.services.eventlogs.EventLogLoader
 
batchSize - Variable in class ome.services.search.SearchValues
 
batchTimer - Variable in class ome.services.fulltext.FullTextIndexer
 
be - Variable in class ome.services.blitz.impl.AbstractAmdServant
 
BeanHelper - Class in ome.services.util
Helper for all bean implementations.
BeanHelper(Class) - Constructor for class ome.services.util.BeanHelper
 
beforeFilter(String, Object) - Method in class ome.util.ContextFilter
 
beforeTransactionCompletion(Transaction) - Method in class ome.security.basic.OmeroInterceptor
 
BfPixelBuffer - Class in ome.io.bioformats
PixelBuffer implementation which uses Bio-Formats to read pixels data directly from original files.
BfPixelBuffer(String, IFormatReader) - Constructor for class ome.io.bioformats.BfPixelBuffer
We may want a constructor that takes the id of an imported file or that takes a File object?
BfPixelsStoreI - Class in ome.services.blitz.repo
 
BfPixelsStoreI(String, ImageReader) - Constructor for class ome.services.blitz.repo.BfPixelsStoreI
 
BfPixelsWrapper - Class in ome.io.bioformats
 
BfPixelsWrapper(String, IFormatReader) - Constructor for class ome.io.bioformats.BfPixelsWrapper
We may want a constructor that takes the id of an imported file or that takes a File object?
BfPyramidPixelBuffer - Class in ome.io.bioformats
PixelBuffer implementation which uses Bio-Formats to read pixels data directly from original files.
BfPyramidPixelBuffer(Pixels, String, boolean) - Constructor for class ome.io.bioformats.BfPyramidPixelBuffer
We may want a constructor that takes the id of an imported file or that takes a File object?
BfPyramidPixelBuffer(TileSizes, Pixels, String, boolean) - Constructor for class ome.io.bioformats.BfPyramidPixelBuffer
Full constructor taking a TileSizes implementation which defines how large the pyramid tiles will be.
BfPyramidPixelBuffer(TileSizes, Pixels, String, boolean, boolean) - Constructor for class ome.io.bioformats.BfPyramidPixelBuffer
 
bfReader - Variable in class ome.io.bioformats.BfPixelBuffer
 
bfSetId(ReaderWrapper) - Method in class ome.services.blitz.repo.CheckedPath
Perform BioFormats ReaderWrapper.setId(String) for this file.
BigResult - Exception in ome.model.units
Checked exception which is thrown from unit methods which can possibly overflow.
BigResult(BigDecimal, String) - Constructor for exception ome.model.units.BigResult
 
BinaryAccessPolicy - Class in ome.security.policy
Policy which should be checked anytime access to original binary files in OMERO is being attempted.
BinaryAccessPolicy(Set<Class<IObject>>, ACLVoter) - Constructor for class ome.security.policy.BinaryAccessPolicy
 
BinaryAccessPolicy(Set<Class<IObject>>, ACLVoter, String[]) - Constructor for class ome.security.policy.BinaryAccessPolicy
 
BinaryMaskQuantizer - Class in omeis.providers.re.quantum
Quantization process for binary masks.
BinaryMaskQuantizer(QuantumDef, Pixels) - Constructor for class omeis.providers.re.quantum.BinaryMaskQuantizer
Creates a new strategy.
binning - Variable in class ome.model.acquisition.DetectorSettings
 
BINNING - Static variable in class ome.model.acquisition.DetectorSettings
 
Binning - Class in ome.model.enums
 
Binning() - Constructor for class ome.model.enums.Binning
 
Binning(Long) - Constructor for class ome.model.enums.Binning
 
Binning(Long, boolean) - Constructor for class ome.model.enums.Binning
Main constructor.
Binning(String) - Constructor for class ome.model.enums.Binning
 
Binning.Details - Class in ome.model.enums
 
Binning.Details() - Constructor for class ome.model.enums.Binning.Details
 
Binning.Details(Object[]) - Constructor for class ome.model.enums.Binning.Details
 
bit(Permissions.Flag) - Static method in class ome.model.internal.Permissions
returns the order of the bit representing the given Permissions.Flag.
bit(Permissions.Role, Permissions.Right) - Static method in class ome.model.internal.Permissions
returns the order of the bit representing the given Permissions.Role and Permissions.Right.
BIT - Static variable in class ome.util.PixelData
Identifies the type used to store pixel values.
BIT - Static variable in class omeis.providers.re.data.PlaneFactory
Identifies the Bit data type used to store pixel values, as per OME spec.
BIT_EIGHT - Static variable in class omeis.providers.re.codomain.PlaneSlicingContext
Identifies the bit-plane 8 i.e.
BIT_FIVE - Static variable in class omeis.providers.re.codomain.PlaneSlicingContext
Identifies the bit-plane 5 i.e.
BIT_FOUR - Static variable in class omeis.providers.re.codomain.PlaneSlicingContext
Identifies the bit-plane 4 i.e.
BIT_ONE - Static variable in class omeis.providers.re.codomain.PlaneSlicingContext
Identifies the bit-plane 1 i.e.
BIT_SEVEN - Static variable in class omeis.providers.re.codomain.PlaneSlicingContext
Identifies the bit-plane 7 i.e.
BIT_SIX - Static variable in class omeis.providers.re.codomain.PlaneSlicingContext
Identifies the bit-plane 6 i.e.
BIT_THREE - Static variable in class omeis.providers.re.codomain.PlaneSlicingContext
Identifies the bit-plane 3 i.e.
BIT_TWO - Static variable in class omeis.providers.re.codomain.PlaneSlicingContext
Identifies the bit-plane 2 i.e.
BIT_ZERO - Static variable in class omeis.providers.re.codomain.PlaneSlicingContext
Identifies the bit-plane 0 i.e.
bitResolution - Variable in class ome.model.display.QuantumDef
 
BITRESOLUTION - Static variable in class ome.model.display.QuantumDef
 
bitSize - Variable in class ome.model.enums.PixelsType
 
BITSIZE - Static variable in class ome.model.enums.PixelsType
 
BlitzConfiguration - Class in ome.services.blitz.util
Factory bean which creates an instance as well as the proper ObjectAdapter and adds initial, well-known servants.
BlitzConfiguration(Ring, SessionManager, SecuritySystem, Executor, int) - Constructor for class ome.services.blitz.util.BlitzConfiguration
Single constructor which builds all Ice instances needed for the server runtime based on arguments provided.
BlitzConfiguration(InitializationData, Ring, SessionManager, SecuritySystem, Executor, int) - Constructor for class ome.services.blitz.util.BlitzConfiguration
Like #BlitzConfiguration(ome.services.sessions.SessionManager, SecuritySystem, Executor) but allows properties to be specified via an InitializationData instance.
BlitzExecutor - Interface in ome.services.blitz.util
Single-point of execution for all AMD blitz calls.
BlitzInstanceProvider - Class in ome.formats.model
An instance provider which uses reflection to fulfill the contract of an InstanceProvider.
BlitzInstanceProvider(EnumerationProvider) - Constructor for class ome.formats.model.BlitzInstanceProvider
Default constructor.
BlitzOnly - Interface in ome.services.blitz.util
Marker interface which specifies that an servant should not be checked for api consistency via ApiConsistencyCheck.
BlobShareStore - Class in ome.services.sharing
Implements ShareStore and provides functionality to work with binary Ice data from the share.
BlobShareStore() - Constructor for class ome.services.sharing.BlobShareStore
 
block(long) - Method in class omero.cmd.CmdCallbackI
Blocks for the given number of milliseconds unless CmdCallbackI.finished(Response, Status, Current) has been called in which case it returns immediately with true.
block(long) - Method in class omero.grid.ProcessCallbackI
Should only be used if the default logic of the process methods is kept in place.
blue - Variable in class ome.model.core.Channel
 
BLUE - Static variable in class ome.model.core.Channel
 
blue - Variable in class ome.model.display.ChannelBinding
 
BLUE - Static variable in class ome.model.display.ChannelBinding
 
blue - Variable in class ome.model.screen.Well
 
BLUE - Static variable in class ome.model.screen.Well
 
BLUE_INDEX - Static variable in class ome.formats.model.ColorsFactory
Index of the red component of a color.
BLUE_INDEX - Static variable in class omeis.providers.re.ColorsFactory
Index of the red component of a color.
BLUE_TEXT - Static variable in class ome.formats.model.ChannelProcessor
Name of the blue component when it is a graphics image.
BOOLEAN(Connection, List<Boolean>) - Method in interface ome.tools.hibernate.ListAsSQLArrayUserType.ArrayFactory
 
BooleanAnnotation - Class in ome.model.annotations
 
BooleanAnnotation() - Constructor for class ome.model.annotations.BooleanAnnotation
 
BooleanAnnotation(Long) - Constructor for class ome.model.annotations.BooleanAnnotation
 
BooleanAnnotation(Long, boolean) - Constructor for class ome.model.annotations.BooleanAnnotation
Main constructor.
BooleanAnnotationData - Class in pojos
Boolean annotation.
BooleanAnnotationData() - Constructor for class pojos.BooleanAnnotationData
Creates a new instance.
BooleanAnnotationData(boolean) - Constructor for class pojos.BooleanAnnotationData
Creates a new instance.
BooleanAnnotationData(BooleanAnnotation) - Constructor for class pojos.BooleanAnnotationData
Creates a new instance.
boolValue - Variable in class ome.model.annotations.BooleanAnnotation
 
BOOLVALUE - Static variable in class ome.model.annotations.BooleanAnnotation
 
breakSharing() - Method in class ome.util.mem.Handle
Subclasses must call this method before forwarding any call that modifies the Body's state.
bridge - Variable in class ome.services.fulltext.FullTextThread
 
BridgeHelper - Class in ome.services.fulltext
Base class for building custom FieldBridge implementations.
BridgeHelper() - Constructor for class ome.services.fulltext.BridgeHelper
 
buildLuceneQuery(List<String>, Date, Date, String, String) - Static method in class ome.util.search.LuceneQueryBuilder
Builds a query with the provided input terms over the given fields
buildLuceneQuery(List<String>, String) - Static method in class ome.util.search.LuceneQueryBuilder
Builds a query with the provided input terms over the given fields
buildOrObtainSession() - Method in class ome.tools.hibernate.CurrentSessionContext
 
buildParseJob(long) - Method in class omero.grid.ParamsHelper
Build a job for the script with id.
buildQuery(String[], GraphEntry, QueryBuilder, QueryBuilder, Session) - Method in class ome.services.graphs.BaseGraphSpec
Deprecated.
 
buildQuery(Session) - Method in class ome.services.query.CollectionCountQueryDefinition
 
buildQuery(Session) - Method in class ome.services.query.IObjectClassQuery
 
buildQuery(Session) - Method in class ome.services.query.PojosFindAnnotationsQueryDefinition
 
buildQuery(Session) - Method in class ome.services.query.PojosFindHierarchiesQueryDefinition
 
buildQuery(Session) - Method in class ome.services.query.PojosGetImagesByOptionsQueryDefinition
 
buildQuery(Session) - Method in class ome.services.query.PojosGetImagesQueryDefinition
 
buildQuery(Session) - Method in class ome.services.query.PojosGetUserImagesQueryDefinition
 
buildQuery(Session) - Method in class ome.services.query.PojosLoadHierarchyQueryDefinition
 
buildQuery(Session) - Method in class ome.services.query.Query
main point of entry for subclasses.
buildQuery(Session) - Method in class ome.services.query.StringQuery
 
buildQuery(QueryBuilder) - Method in class ome.services.scripts.ScriptRepoHelper
Adds a single clause of the form "AND (A OR B ...)" where each ScriptFileType A, B, etc. is given a chance to define its own clause.
buildResponse(int, Object) - Method in class ome.services.blitz.impl.commands.SaveI
 
buildResponse(int, Object) - Method in class ome.services.blitz.repo.ManagedImportRequestI
 
buildResponse(int, Object) - Method in class ome.services.blitz.repo.RawAccessRequestI
 
buildResponse(int, Object) - Method in class omero.cmd.admin.CurrentSessionsRequestI
 
buildResponse(int, Object) - Method in class omero.cmd.admin.ResetPasswordRequestI
 
buildResponse(int, Object) - Method in class omero.cmd.admin.UpdateSessionTimeoutRequestI
 
buildResponse(int, Object) - Method in class omero.cmd.basic.DoAllI
 
buildResponse(int, Object) - Method in class omero.cmd.basic.ListRequestsI
 
buildResponse(int, Object) - Method in class omero.cmd.basic.TimingI
 
buildResponse(int, Object) - Method in class omero.cmd.fs.ManageImageBinariesI
 
buildResponse(int, Object) - Method in class omero.cmd.fs.OriginalMetadataRequestI
 
buildResponse(int, Object) - Method in class omero.cmd.fs.UsedFilesRequestI
 
buildResponse(int, Object) - Method in class omero.cmd.graphs.Chgrp2I
 
buildResponse(int, Object) - Method in class omero.cmd.graphs.ChgrpFacadeI
Deprecated.
 
buildResponse(int, Object) - Method in class omero.cmd.graphs.ChgrpI
Deprecated.
 
buildResponse(int, Object) - Method in class omero.cmd.graphs.Chmod2I
 
buildResponse(int, Object) - Method in class omero.cmd.graphs.ChmodFacadeI
Deprecated.
 
buildResponse(int, Object) - Method in class omero.cmd.graphs.ChmodI
Deprecated.
 
buildResponse(int, Object) - Method in class omero.cmd.graphs.Chown2I
 
buildResponse(int, Object) - Method in class omero.cmd.graphs.ChownFacadeI
Deprecated.
 
buildResponse(int, Object) - Method in class omero.cmd.graphs.ChownI
Deprecated.
 
buildResponse(int, Object) - Method in class omero.cmd.graphs.Delete2I
 
buildResponse(int, Object) - Method in class omero.cmd.graphs.DeleteFacadeI
Deprecated.
 
buildResponse(int, Object) - Method in class omero.cmd.graphs.DeleteI
Deprecated.
 
buildResponse(int, Object) - Method in class omero.cmd.graphs.DiskUsageI
 
buildResponse(int, Object) - Method in class omero.cmd.graphs.GraphSpecListI
Deprecated.
 
buildResponse(int, Object) - Method in class omero.cmd.graphs.SkipHeadI
 
buildResponse(int, Object) - Method in interface omero.cmd.IRequest
Post-transaction chance to map from the return value of IRequest.step(int) to a Response object.
buildResponse(int, Object) - Method in class omero.cmd.mail.SendEmailRequestI
 
BULK_ANNOTATIONS_NS - Static variable in class pojos.FileAnnotationData
The name space used to indicate that the FileAnnotation is a Bulk Annotations file.
byAnnotatedWith(Annotation...) - Method in interface ome.api.Search
Finds entities annotated with an Annotation similar to the example.
byAnnotatedWith(Annotation...) - Method in class ome.services.SearchBean
 
byAnnotatedWith_async(AMD_Search_byAnnotatedWith, List<Annotation>, Current) - Method in class ome.services.blitz.impl.SearchI
 
byFullText(String) - Method in interface ome.api.Search
Passes the query as is to the Lucene backend.
byFullText(String) - Method in class ome.services.SearchBean
 
byFullText_async(AMD_Search_byFullText, String, Current) - Method in class ome.services.blitz.impl.SearchI
 
byGroupForTags(String) - Method in interface ome.api.Search
Returns transient (without ID) TagAnnotation instances which represent all the tags in the given group.
byGroupForTags(String) - Method in class ome.services.SearchBean
 
byGroupForTags_async(AMD_Search_byGroupForTags, String, Current) - Method in class ome.services.blitz.impl.SearchI
 
byHqlQuery(String, Parameters) - Method in interface ome.api.Search
Delegates to IQuery.findAllByQuery(String, Parameters) method to take advantage of the Search.and(), Search.or(), and Search.not() methods, or queue-semantics.
byHqlQuery(String, Parameters) - Method in class ome.services.SearchBean
 
byHqlQuery_async(AMD_Search_byHqlQuery, String, Parameters, Current) - Method in class ome.services.blitz.impl.SearchI
 
byLuceneQueryBuilder(String, String, String, String, String) - Method in interface ome.api.Search
Builds a Lucene query and passes it to the Lucene backend.
byLuceneQueryBuilder(String, String, String, String, String) - Method in class ome.services.SearchBean
 
byLuceneQueryBuilder_async(AMD_Search_byLuceneQueryBuilder, String, String, String, String, String, Current) - Method in class ome.services.blitz.impl.SearchI
 
byName - Static variable in enum omero.cmd.graphs.Preprocessor.TargetType
Deprecated.
lookup from initial-capital name to type, e.g.
bySimilarTerms(String...) - Method in interface ome.api.Search
Returns transient (without ID) TextAnnotation instances which represent terms which are similar to the give terms.
bySimilarTerms(String...) - Method in class ome.services.SearchBean
 
bySimilarTerms_async(AMD_Search_bySimilarTerms, List<String>, Current) - Method in class ome.services.blitz.impl.SearchI
 
bySomeMustNone(String[], String[], String[]) - Method in interface ome.api.Search
Builds a Lucene query and passes it to Search.byFullText(String).
bySomeMustNone(String[], String[], String[]) - Method in class ome.services.SearchBean
 
bySomeMustNone_async(AMD_Search_bySomeMustNone, List<String>, List<String>, List<String>, Current) - Method in class ome.services.blitz.impl.SearchI
 
bySymbol(String) - Static method in enum ome.model.enums.UnitsElectricPotential
 
bySymbol(String) - Static method in enum ome.model.enums.UnitsFrequency
 
bySymbol(String) - Static method in enum ome.model.enums.UnitsLength
 
bySymbol(String) - Static method in enum ome.model.enums.UnitsPower
 
bySymbol(String) - Static method in enum ome.model.enums.UnitsPressure
 
bySymbol(String) - Static method in enum ome.model.enums.UnitsTemperature
 
bySymbol(String) - Static method in enum ome.model.enums.UnitsTime
 
byTagForGroups(String) - Method in interface ome.api.Search
Creates a query which will return transient (without ID) TagAnnotation instances which represent all the tag groups which the given tag belongs to.
byTagForGroups(String) - Method in class ome.services.SearchBean
 
byTagForGroups_async(AMD_Search_byTagForGroups, String, Current) - Method in class ome.services.blitz.impl.SearchI
 
BYTE - Static variable in class ome.util.PixelData
Identifies the type used to store pixel values.
BYTE - Static variable in class omeis.providers.re.data.PlaneFactory
Identifies the type used to store pixel values.
ByteArray - Class in ome.util.mem
A read-write slice of a given array.
ByteArray(byte[], int, int) - Constructor for class ome.util.mem.ByteArray
Creates a read-write slice of base.
bytes - Variable in class ome.model.roi.Mask
 
BYTES - Static variable in class ome.model.roi.Mask
 
bytesPerPixel - Variable in class ome.util.PixelData
The number of bytes per pixel.
bytesPerPixel() - Method in class ome.util.PixelData
Returns the number of byte per pixel for the pixel data.
bytesPerPixel - Variable in class omeis.providers.re.data.Plane2D
How many bytes make up a pixel value.
byType - Static variable in enum omero.cmd.graphs.Preprocessor.TargetType
Deprecated.
lookup from type to initial-capital name, e.g.
byUUID(String[]) - Method in class ome.services.SearchBean
 

C

c2c() - Method in class ome.util.ModelMapper
TODO identity versus null mappings
c2c() - Method in class omero.util.IceMapper
 
cache - Variable in class ome.services.blitz.impl.ScriptI
 
cache - Variable in class ome.services.sessions.SessionManagerImpl
 
CacheFactory - Class in ome.services.sessions.state
 
CacheFactory() - Constructor for class ome.services.sessions.state.CacheFactory
 
CacheListener - Class in ome.services.sessions.state
Basic CacheEventListener which does nothing.
CacheListener() - Constructor for class ome.services.sessions.state.CacheListener
 
calculate(Pixels) - Method in class ome.io.nio.SimpleBackOff
 
calculate() - Method in class ome.io.nio.SimpleBackOff
 
calculateBackOff(int) - Method in class ome.services.db.SelfCorrectingDataSource
 
calculateMessageDigest() - Method in interface ome.api.RawPixelsStore
 
calculateMessageDigest() - Method in class ome.io.bioformats.BfPixelBuffer
 
calculateMessageDigest() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
 
calculateMessageDigest() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
 
calculateMessageDigest() - Method in interface ome.io.nio.PixelBuffer
Calculates a SHA-1 message digest for the entire pixel buffer.
calculateMessageDigest() - Method in class ome.io.nio.RomioPixelBuffer
Implemented as specified by PixelBuffer I/F.
calculateMessageDigest() - Method in class ome.services.RawPixelsBean
 
calculateMessageDigest_async(AMD_RawPixelsStore_calculateMessageDigest, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
calculateMessageDigest_async(AMD_RawPixelsStore_calculateMessageDigest, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
calculateXYWidths(Pixels, int) - Method in class ome.services.ThumbnailCtx
Calculates the ratio of the two sides of a Pixel set and returns the X and Y widths based on the longest side maintaining aspect ratio.
calibratedMagnification - Variable in class ome.model.acquisition.Objective
 
CALIBRATEDMAGNIFICATION - Static variable in class ome.model.acquisition.Objective
 
call(String, String, boolean) - Method in class ome.services.db.SelfCorrectingDataSource
 
call(MethodInvocation) - Method in class ome.tools.hibernate.EventMethodInterceptor.Action
 
call(MethodInvocation) - Method in class ome.tools.hibernate.EventMethodInterceptor.DisableAction
 
call(IObject) - Method in interface ome.util.CBlock
invoke this block.
call(IObject) - Method in class ome.util.IdBlock
 
call() - Method in interface omeis.providers.re.RenderingTask
Renders wavelength.
Callback - Class in ome.services.throttling
Manages AMD-based method dispatches from blitz.
Callback(Boolean, Boolean, ServiceInterface, IceMethodInvoker, Object, IceMapper, Current, Object...) - Constructor for class ome.services.throttling.Callback
 
Callback(ServiceInterface, IceMethodInvoker, IceMapper, Object, Current, Object...) - Constructor for class ome.services.throttling.Callback
 
callback - Variable in class omero.cmd.SessionI
 
Callback2<R> - Class in ome.services.throttling
Callable-based callback which guarantees that ice_response or ice_exception is called.
Callback2(Current, Object, boolean, Callable<R>) - Constructor for class ome.services.throttling.Callback2
 
CallContext - Class in omero.cmd
Interceptor which takes any context provided by the client and calls setContext on CurrentDetails.
CallContext(OmeroContext, String) - Constructor for class omero.cmd.CallContext
 
CallContext(CurrentDetails, String) - Constructor for class omero.cmd.CallContext
 
callContextWrapper(Object) - Method in class omero.cmd.SessionI
 
callInvokerOnMappedArgs(IceMapper, Object, Current, Object...) - Method in class ome.services.blitz.impl.AbstractAmdServant
 
callInvokerOnRawArgs(Object, Current, Object...) - Method in class ome.services.blitz.impl.AbstractAmdServant
 
callInvokerOnRawArgs(ServiceInterface, IceMethodInvoker, Object, Current, Object...) - Method in interface ome.services.blitz.util.BlitzExecutor
Uses the given IceMethodInvoker to make the method call.
callInvokerOnRawArgs(ServiceInterface, IceMethodInvoker, Object, Current, Object...) - Method in class ome.services.throttling.InThreadThrottlingStrategy
 
callInvokerOnRawArgs(ServiceInterface, IceMethodInvoker, Object, Current, Object...) - Method in class ome.services.throttling.SerialThrottlingStrategy
 
callInvokerWithMappedArgs(ServiceInterface, IceMethodInvoker, IceMapper, Object, Current, Object...) - Method in interface ome.services.blitz.util.BlitzExecutor
Passes the given arguments to IceMethodInvoker with the assumption that all conversion from omero.* to ome.* has taken place.
callInvokerWithMappedArgs(ServiceInterface, IceMethodInvoker, IceMapper, Object, Current, Object...) - Method in class ome.services.throttling.InThreadThrottlingStrategy
 
callInvokerWithMappedArgs(ServiceInterface, IceMethodInvoker, IceMapper, Object, Current, Object...) - Method in class ome.services.throttling.SerialThrottlingStrategy
 
callWithRetries(String, String, boolean) - Method in class ome.services.db.SelfCorrectingDataSource
 
canAnnotate(IObject) - Method in interface ome.api.local.LocalAdmin
Companion to IAdmin#canUpdate(IObject) but not yet remotely accessible.
canAnnotate(IObject) - Method in class ome.logic.AdminImpl
 
canAnnotate(Current) - Method in class omero.model.PermissionsI
 
canAnnotate() - Method in class pojos.DataObject
Returns true if the object can be annotated false otherwise, depending on permissions level.
cancel() - Method in class ome.formats.importer.ImportCandidates.SCANNING
Can be called to cancel the current action.
cancel(Current) - Method in class ome.services.blitz.impl.ScriptProcessI
 
cancel() - Method in interface ome.services.procs.Process
 
cancel() - Method in class ome.services.procs.ProcessSkeleton
 
cancel(String) - Method in class ome.services.sessions.events.ChangeSecurityContextEvent
 
cancel(Current) - Method in class omero.cmd.HandleI
 
cancel(ERR, Throwable, String, String...) - Method in class omero.cmd.Helper
Calls #cancel(ERR, Throwable, String, Map) with the output of Helper.params(String...).
cancel(ERR, Throwable, String, Map<String, String>) - Method in class omero.cmd.Helper
Like #fail(ERR, String, String...) throws a HandleI.Cancel exception.
cancelJob() - Method in interface ome.api.JobHandle
Marks a job for cancellation.
cancelJob() - Method in class ome.services.JobBean
 
cancelJob_async(AMD_JobHandle_cancelJob, Current) - Method in class ome.services.blitz.impl.JobHandleI
 
CANCELLED - Static variable in interface ome.api.JobHandle
 
cancelUploads - Variable in class ome.formats.importer.util.ErrorHandler
 
canDelete(Current) - Method in class omero.model.PermissionsI
 
canDelete() - Method in class pojos.DataObject
Returns true if the object can be deleted by the user currently logged in, false otherwise, depending on permissions level.
canEdit() - Method in class ome.services.blitz.repo.CheckedPath
 
canEdit(Current) - Method in class omero.model.PermissionsI
 
canEdit() - Method in class pojos.DataObject
Returns true if the object can be edited by the user currently logged in false otherwise, depending on permissions level.
canLink(Current) - Method in class omero.model.PermissionsI
 
canLink() - Method in class pojos.DataObject
Returns true if the object can be linked e.g. image add to dataset, by the user currently logged in, false otherwise, depending on permissions level.
canLogin() - Method in class ome.formats.importer.ImportConfig
Confirm all information for login is supplied
canMapReturnValue() - Method in class omero.util.IceMapper
True if this instance has a IceMapper.ReturnMapping
canRead() - Method in class ome.services.blitz.repo.CheckedPath
Check if this file is actually readable on the underlying filesystem.
canRead(EventContext, String) - Method in class ome.system.PreferenceContext
 
canRunScript_async(AMD_IScript_canRunScript, long, Current) - Method in class ome.services.blitz.impl.ScriptI
 
canUpdate(IObject) - Method in interface ome.api.IAdmin
Returns true if the currently logged in user can modify the given IObject.
canUpdate(IObject) - Method in class ome.logic.AdminImpl
 
canUpdate(IObject, Current) - Method in interface ome.services.blitz.repo.RepositoryDao
Delegates to IAdmin#canUpdate
canUpdate(IObject, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
 
canUpdate_async(AMD_IAdmin_canUpdate, IObject, Current) - Method in class ome.services.blitz.impl.AdminI
 
canWriteParentDirectory(ServiceFactory, SqlAction, String, CheckedPath) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
Throw a SecurityViolation if the current context cannot write to the parent directory.
caseSensitive - Variable in class ome.services.search.SearchValues
 
castChildOptions(Collection<ChildOption>) - Static method in class omero.cmd.graphs.ChildOptionI
Cast ChildOption[] to ChildOptionI[].
cb - Variable in class ome.services.throttling.Task
 
CBlock<E> - Interface in ome.util
Block template used to "C"ollect the results of some function called on each IObject in a collection.
cd - Variable in class ome.security.basic.BasicSecuritySystem
 
cd - Variable in class ome.security.basic.EventLogListener
 
cd - Variable in class ome.security.SecurityFilterHolder
 
cdEnd - Variable in class ome.model.display.QuantumDef
 
CDEND - Static variable in class ome.model.display.QuantumDef
 
cdStart - Variable in class ome.model.display.QuantumDef
 
CDSTART - Static variable in class ome.model.display.QuantumDef
 
ceId - Variable in class ome.system.SimpleEventContext
 
ceType - Variable in class ome.system.SimpleEventContext
 
cgId - Variable in class ome.system.SimpleEventContext
 
CGLIB_IDENTIFIER - Static variable in class ome.util.Utils
 
cgName - Variable in class ome.system.SimpleEventContext
 
chainedList - Variable in class ome.services.search.SearchAction
List of IObject instances which have currently been found.
chainedSearch(List<IObject>) - Method in class ome.services.search.SearchAction
Set the current list of found ids from previous searches, which should be chained in this search.
changeDistinguisedName(String, String) - Method in class ome.security.auth.PasswordProviders
 
changeExpiredCredentials(String, String, String) - Method in interface ome.api.IAdmin
Used after an ExpiredCredentialsException instance is thrown.
changeExpiredCredentials(String, String, String) - Method in class ome.logic.AdminImpl
 
changeExpiredCredentials_async(AMD_IAdmin_changeExpiredCredentials, String, String, String, Current) - Method in class ome.services.blitz.impl.AdminI
 
changeGroup(IObject, String) - Method in interface ome.api.IAdmin
call details.setGroup() on this instance.
changeGroup(IObject, String) - Method in class ome.logic.AdminImpl
 
changeGroup_async(AMD_IAdmin_changeGroup, IObject, String, Current) - Method in class ome.services.blitz.impl.AdminI
 
changeGroupPermissions(Long, Long) - Method in interface ome.util.SqlAction
 
changeGroupPermissions(Long, Long) - Method in class ome.util.SqlAction.Impl
 
changeOwner(IObject, String) - Method in interface ome.api.IAdmin
call details.setOwner() on this instance.
changeOwner(IObject, String) - Method in class ome.logic.AdminImpl
 
changeOwner_async(AMD_IAdmin_changeOwner, IObject, String, Current) - Method in class ome.services.blitz.impl.AdminI
 
changePassword(String) - Method in interface ome.api.IAdmin
change the password for the current user.
changePassword(String) - Method in class ome.logic.AdminImpl
 
changePassword(String, String) - Method in class ome.security.auth.ConfigurablePasswordProvider
Throws by default.
changePassword(String, String) - Method in class ome.security.auth.JdbcHashedPasswordProvider
 
changePassword(String, String) - Method in class ome.security.auth.JdbcPasswordProvider
 
changePassword(String, String, PasswordUtil.METHOD) - Method in class ome.security.auth.JdbcPasswordProvider
Actually perform the password change in the database and log the event against the user.
changePassword(String, String) - Method in interface ome.security.auth.PasswordProvider
Attempts to change the password for the given user.
changePassword(String, String) - Method in class ome.security.auth.PasswordProviders
 
changePassword_async(AMD_IAdmin_changePassword, RString, Current) - Method in class ome.services.blitz.impl.AdminI
 
changePasswordWithOldPassword(String, String) - Method in interface ome.api.IAdmin
change the password for the current user by passing the old password.
changePasswordWithOldPassword(String, String) - Method in class ome.logic.AdminImpl
 
changePasswordWithOldPassword_async(AMD_IAdmin_changePasswordWithOldPassword, RString, RString, Current) - Method in class ome.services.blitz.impl.AdminI
 
changePermissions(IObject, Permissions) - Method in interface ome.api.IAdmin
call defaults.setPermissions() on this instance.
changePermissions(IObject, Permissions) - Method in class ome.logic.AdminImpl
the implementation of this method is somewhat tricky in that Permissions changes must be allowed even when other updates are not.
changePermissions_async(AMD_IAdmin_changePermissions, IObject, Permissions, Current) - Method in class ome.services.blitz.impl.AdminI
 
ChangeSecurityContextEvent - Class in ome.services.sessions.events
InteralMessage published by the SessionManager when setSecurityContext() is called.
ChangeSecurityContextEvent(Object, String, IObject, IObject) - Constructor for class ome.services.sessions.events.ChangeSecurityContextEvent
 
changeTablePermissionsForGroup(String, Long, Long) - Method in interface ome.util.SqlAction
 
changeTablePermissionsForGroup(String, Long, Long) - Method in class ome.util.SqlAction.Impl
 
changeUserPassword(String, String) - Method in interface ome.api.IAdmin
change the password for the a given user.
changeUserPassword(String, String) - Method in class ome.logic.AdminImpl
 
changeUserPassword_async(AMD_IAdmin_changeUserPassword, String, RString, Current) - Method in class ome.services.blitz.impl.AdminI
 
changeUserPasswordById(Long, String) - Method in class ome.security.auth.PasswordUtil
Calls {@link #changeUserPasswordById(Long, String, boolean) with "false" as the value of the salt argument in order to provide backwards compatibility.
changeUserPasswordById(Long, String, PasswordUtil.METHOD) - Method in class ome.security.auth.PasswordUtil
Channel - Class in ome.model.core
These filter definitions are used by the security system to eliminate non-readable objects from queries.
Channel() - Constructor for class ome.model.core.Channel
 
Channel(Long) - Constructor for class ome.model.core.Channel
 
Channel(Long, boolean) - Constructor for class ome.model.core.Channel
Main constructor.
Channel(LogicalChannel, Pixels) - Constructor for class ome.model.core.Channel
 
Channel.Details - Class in ome.model.core
 
Channel.Details() - Constructor for class ome.model.core.Channel.Details
 
Channel.Details(Object[]) - Constructor for class ome.model.core.Channel.Details
 
Channel_EmissionWavelength - Static variable in class ome.formats.model.UnitsFactory
 
Channel_ExcitationWavelength - Static variable in class ome.formats.model.UnitsFactory
 
Channel_PinholeSize - Static variable in class ome.formats.model.UnitsFactory
 
ChannelAcquisitionData - Class in pojos
Object hosting the acquisition related to a logical channel.
ChannelAcquisitionData(LogicalChannel) - Constructor for class pojos.ChannelAcquisitionData
Creates a new instance.
ChannelAnnotationLink - Class in ome.model.annotations
These filter definitions are used by the security system to eliminate non-readable objects from queries.
ChannelAnnotationLink() - Constructor for class ome.model.annotations.ChannelAnnotationLink
 
ChannelAnnotationLink(Long) - Constructor for class ome.model.annotations.ChannelAnnotationLink
 
ChannelAnnotationLink(Long, boolean) - Constructor for class ome.model.annotations.ChannelAnnotationLink
Main constructor.
ChannelAnnotationLink(IObject, IObject) - Constructor for class ome.model.annotations.ChannelAnnotationLink
 
ChannelAnnotationLink.Details - Class in ome.model.annotations
 
ChannelAnnotationLink.Details() - Constructor for class ome.model.annotations.ChannelAnnotationLink.Details
 
ChannelAnnotationLink.Details(Object[]) - Constructor for class ome.model.annotations.ChannelAnnotationLink.Details
 
ChannelBinding - Class in ome.model.display
These filter definitions are used by the security system to eliminate non-readable objects from queries.
ChannelBinding() - Constructor for class ome.model.display.ChannelBinding
 
ChannelBinding(Long) - Constructor for class ome.model.display.ChannelBinding
 
ChannelBinding(Long, boolean) - Constructor for class ome.model.display.ChannelBinding
Main constructor.
ChannelBinding(RenderingDef, Family, Double, Double, Double, Boolean, Boolean, Integer, Integer, Integer, Integer) - Constructor for class ome.model.display.ChannelBinding
 
ChannelBinding.Details - Class in ome.model.display
 
ChannelBinding.Details() - Constructor for class ome.model.display.ChannelBinding.Details
 
ChannelBinding.Details(Object[]) - Constructor for class ome.model.display.ChannelBinding.Details
 
ChannelData - Class in ome.formats.model
Represents all the metadata required to make accurate decisions about channel colour and name.
ChannelData() - Constructor for class ome.formats.model.ChannelData
 
ChannelData - Class in pojos
The data that makes up an OME Channel along with links to its logical channel.
ChannelData(int) - Constructor for class pojos.ChannelData
Creates a new instance.
ChannelData(int, Channel) - Constructor for class pojos.ChannelData
Creates a new instance.
CHANNELID_QUERY - Static variable in class ome.services.delete.DeleteBean
 
ChannelProcessor - Class in ome.formats.model
Processes the pixels sets of an IObjectContainerStore and ensures that LogicalChannel containers are present in the container cache, and populating channel name and colour where appropriate.
ChannelProcessor() - Constructor for class ome.formats.model.ChannelProcessor
 
channels - Variable in class ome.model.core.LogicalChannel
 
CHANNELS - Static variable in class ome.model.core.LogicalChannel
 
channels - Variable in class ome.model.core.Pixels
 
CHANNELS - Static variable in class ome.model.core.Pixels
 
check(IObject, Object) - Method in class ome.security.basic.GroupChmodStrategy
Here we used the checks returned from ExtendedMetadata to iterate through every non-system table and check that it has no FKs which point to back to its rows and violate the read permissions which are being reduced.
check(IObject, Object) - Method in interface ome.security.ChmodStrategy
Performs one of the checks returned by ChmodStrategy.getChecks(IObject obj, String permissions).
check(String) - Method in class ome.services.query.Query
check that there is a definition for this Query with the provided argument as its name.
check() - Method in interface omero.util.Resources.Entry
Called during each cycle.
CheckAllJobs - Class in ome.services.blitz.util
 
CheckAllJobs(Executor, ObjectAdapter, TopicManager) - Constructor for class ome.services.blitz.util.CheckAllJobs
 
CheckAllJobs(Executor, ObjectAdapter, TopicManager, long) - Constructor for class ome.services.blitz.util.CheckAllJobs
 
checkAndCollapseGraph() - Method in class ome.formats.OMEROMetadataStore
Checks the entire object graph for sections that may be collapsed if the data is derived from a Plate.
checkAndRegister() - Method in class ome.services.JobBean
 
checkArgs(Object...) - Method in class ome.services.graphs.GraphEntry
Deprecated.
 
checkBounds(Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer
 
checkBounds(Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelsWrapper
 
checkBounds(Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
 
checkBounds(Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
 
checkBounds(Integer, Integer, Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer
Checks to ensure that no one particular axis has an offset out of bounds.
checkBounds(Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer
Implemented as specified by PixelBuffer I/F.
checkCluster() - Method in class ome.services.blitz.fire.Ring
Method called during initialization to get all the active uuids within the cluster, and remove any dead nodes.
checkDatabase(String) - Method in class ome.system.PreferenceContext
 
checkDelayedCallContext(BasicEventContext) - Method in class ome.security.basic.CurrentDetails
 
CheckedPath - Class in ome.services.blitz.repo
To prevent frequently re-calculating paths and re-creating File objects, CheckedPath objects store various interpretations of paths that are passed in by users.
CheckedPath(ServerFilePathTransformer, String, ChecksumProviderFactory, ChecksumAlgorithm) - Constructor for class ome.services.blitz.repo.CheckedPath
Construct a CheckedPath from a relative "/"-delimited path rooted at the repository.
checkedPaths - Variable in class ome.services.blitz.repo.ManagedImportLocationI
 
checkImageDelete(long, boolean) - Method in interface ome.api.IDelete
Returns all entities which would prevent the given Image id from being deleted.
checkImageDelete(long, boolean) - Method in class ome.services.delete.DeleteBean
 
checkIndex(int) - Method in class ome.util.mem.ReadOnlyByteArray
Makes sure that i is in [0, length).
checkLocation(File, RawFileStorePrx) - Method in class ome.formats.importer.transfers.AbstractExecFileTransfer
Check that the target location: 1) doesn't exist and 2) is properly written to by the server.
checkManagedDetails(IObject, Details) - Method in class ome.security.basic.BasicSecuritySystem
 
checkManagedDetails(IObject, Details) - Method in class ome.security.basic.OmeroInterceptor
 
checkManagedDetails(IObject, Details, Details) - Method in class ome.security.basic.OmeroInterceptor
Like OmeroInterceptor.checkManagedDetails(IObject, Details, Details) but allows passing in a specific Details instance.
checkManagedDetails(IObject, Details) - Method in interface ome.security.SecuritySystem
checks that a non-privileged user has not attempted to edit the entity's security details.
checkManagedDetails(IObject, Details) - Method in class ome.security.SecuritySystemHolder
 
checkManagedDetails(IObject, Details) - Method in class ome.security.sharing.SharingSecuritySystem
 
checkMethod(Object, Method, Principal, boolean) - Method in class ome.security.basic.BasicMethodSecurity
See MethodSecurity#checkMethod(Object, Method, Principal)
checkMethod(Object, Method, Principal, boolean) - Method in interface ome.security.MethodSecurity
Throws a SecurityViolation exception if the given Principal does not have the proper permissions to execute the given method.
checkNonNull(List<Point>) - Static method in class omero.model.SmartShape.Util
Used from assert statements of the form: assert Util.checkNonNull(points) : "Null points in " + this; in all the implementations of SmartShape.asPoints().
checkParameters() - Method in class ome.services.query.Query
check the Parameters instance against the Definitions instance for this Query.
checkPassword(String, String, boolean) - Method in interface ome.api.local.LocalAdmin
Checks password for given user.
checkPassword(String, String, boolean) - Method in class ome.logic.AdminImpl
If ldap plugin turned, creates Ldap accounts and authentication by LDAP available.
checkPassword(String, String, boolean) - Method in class ome.security.auth.ConfigurablePasswordProvider
If ConfigurablePasswordProvider.ignoreUnknown is true, returns null, since the base class knows no users.
checkPassword(String, String, boolean) - Method in class ome.security.auth.FilePasswordProvider
 
checkPassword(String, String, boolean) - Method in class ome.security.auth.JdbcPasswordProvider
Retrieves password from the database and calls ConfigurablePasswordProvider.comparePasswords(String, String).
checkPassword(String, String, boolean) - Method in class ome.security.auth.LdapPasswordProvider
 
checkPassword(String, String, boolean) - Method in interface ome.security.auth.PasswordProvider
Authenticates the give user given the password token.
checkPassword(String, String, boolean) - Method in class ome.security.auth.PasswordProviders
 
checkPassword(String, String, boolean) - Method in class ome.security.auth.providers.LdapPasswordProvider431
 
checkPassword(String) - Method in class ome.services.blitz.fire.Ring
Currently only returns false since if the regular password check performed by SessionManager cannot find the session, then the cluster has no extra information.
checkPath(String, ChecksumAlgorithm, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
Create a new CheckedPath object based on the given user input.
checkPermissions(String, String, StringHolder, Current) - Method in class ome.services.blitz.fire.PermissionsVerifierI
 
checkProperty(String, String) - Method in interface ome.api.local.LocalQuery
Checks if a property is defined on a mapped Hibernate type.
checkProperty(String, String) - Method in class ome.logic.PojosImpl
 
checkProperty(String, String) - Method in class ome.logic.QueryImpl
 
checkReady(String) - Method in class ome.security.basic.BasicSecuritySystem
checkRestriction(String, IObject) - Method in class ome.security.basic.BasicSecuritySystem
 
checkRestriction(IObject) - Method in class ome.security.policy.BasePolicy
 
checkRestriction(IObject) - Method in class ome.security.policy.BinaryAccessPolicy
 
checkRestriction(String, IObject) - Method in class ome.security.policy.DefaultPolicyService
 
checkRestriction(IObject) - Method in interface ome.security.policy.Policy
Like #isRestricted(Policy) but throws an appropriate SecurityViolation subclass if the restriction is active.
checkRestriction(String, IObject) - Method in interface ome.security.policy.PolicyService
Give each configured Policy instance the chance to throw a SecurityViolation from its Policy.checkRestriction(IObject) method.
checkRestriction(String, IObject) - Method in interface ome.security.SecuritySystem
Checks whether or not a ome.sercurity.Policy instance of matching name has been registered, considers itself active, and considers the passed context object to be restricted.
checkRestriction(String, IObject) - Method in class ome.security.SecuritySystemHolder
 
checkRestriction(String, IObject) - Method in class ome.security.sharing.SharingSecuritySystem
 
checkState() - Method in class ome.services.procs.ProcessSkeleton
 
checksum(String, ChecksumAlgorithm) - Method in class ome.formats.importer.exclusions.AbstractFileExclusion
 
CHECKSUM_ALGORITHM_NAMER - Static variable in class ome.services.blitz.util.ChecksumAlgorithmMapper
 
checksumAlgorithm - Variable in class ome.formats.importer.ImportConfig
 
ChecksumAlgorithm - Class in ome.model.enums
 
ChecksumAlgorithm() - Constructor for class ome.model.enums.ChecksumAlgorithm
 
ChecksumAlgorithm(Long) - Constructor for class ome.model.enums.ChecksumAlgorithm
 
ChecksumAlgorithm(Long, boolean) - Constructor for class ome.model.enums.ChecksumAlgorithm
Main constructor.
ChecksumAlgorithm(String) - Constructor for class ome.model.enums.ChecksumAlgorithm
 
ChecksumAlgorithm.Details - Class in ome.model.enums
 
ChecksumAlgorithm.Details() - Constructor for class ome.model.enums.ChecksumAlgorithm.Details
 
ChecksumAlgorithm.Details(Object[]) - Constructor for class ome.model.enums.ChecksumAlgorithm.Details
 
ChecksumAlgorithmMapper - Class in ome.services.blitz.util
Work with ChecksumAlgorithm enumeration instances, including mapping their values back to ChecksumTypes.
ChecksumAlgorithmMapper() - Constructor for class ome.services.blitz.util.ChecksumAlgorithmMapper
 
checksumAlgorithms - Variable in class ome.services.blitz.repo.PublicRepositoryI
 
checksumAsBytes() - Method in class ome.util.checksum.AbstractChecksumProvider
 
checksumAsBytes() - Method in interface ome.util.checksum.ChecksumProvider
Returns a byte array representation of the calculated checksum.
checksumAsBytes() - Method in class ome.util.checksum.FileSizeChecksumProviderImpl
 
checksumAsString() - Method in class ome.util.checksum.AbstractChecksumProvider
 
checksumAsString() - Method in interface ome.util.checksum.ChecksumProvider
Returns a String representing the checksum in hex form.
checksumAsString() - Method in class ome.util.checksum.FileSizeChecksumProviderImpl
 
ChecksumProvider - Interface in ome.util.checksum
An interface producing checksums or message digests (depending on the implementing class) of a given type of input.
checksumProviderFactory - Variable in class ome.services.blitz.repo.PublicRepositoryI
 
ChecksumProviderFactory - Interface in ome.util.checksum
A factory producing throw-away objects of the ChecksumProvider type.
ChecksumProviderFactoryImpl - Class in ome.util.checksum
An implementation of the ChecksumProviderFactory interface.
ChecksumProviderFactoryImpl() - Constructor for class ome.util.checksum.ChecksumProviderFactoryImpl
 
checksums - Variable in class ome.formats.importer.ImportEvent.FILESET_UPLOAD_END
 
ChecksumType - Enum in ome.util.checksum
Enumeration defining the possible algorithms used for calculating checksums.
checkTarget(File, TransferState) - Method in class ome.formats.importer.transfers.AbstractExecFileTransfer
Check that the server can properly read the copied file.
checkType(String) - Method in interface ome.api.local.LocalQuery
Checks if a type has been mapped in Hibernate.
checkType(String) - Method in class ome.logic.PojosImpl
 
checkType(String) - Method in class ome.logic.QueryImpl
 
checkUpgrade - Variable in class ome.formats.importer.ImportConfig
 
checkWriteOperationAllowed(Session) - Method in class ome.tools.spring.ManualFlushHibernateTemplate
 
Chgrp2I - Class in omero.cmd.graphs
Request to move model objects to a different experiment group, reimplementing ChgrpI.
Chgrp2I(ACLVoter, Roles, SystemTypes, GraphPathBean, Deletion, Set<Class<? extends IObject>>, GraphPolicy, SetMultimap<String, String>) - Constructor for class omero.cmd.graphs.Chgrp2I
Construct a new chgrp request; called from GraphRequestFactory.getRequest(Class).
ChgrpFacadeI - Class in omero.cmd.graphs
Deprecated.
will be removed in OMERO 5.3, so use the new graphs implementation
ChgrpFacadeI(GraphRequestFactory) - Constructor for class omero.cmd.graphs.ChgrpFacadeI
Deprecated.
Construct a new chgrp request; called from GraphRequestFactory.getRequest(Class).
ChgrpI - Class in omero.cmd.graphs
Deprecated.
will be removed in OMERO 5.2, so use the new graphs implementation
ChgrpI(Communicator, ChgrpStepFactory, ApplicationContext) - Constructor for class omero.cmd.graphs.ChgrpI
Deprecated.
 
chgrpQuery(EventContext, String, GraphOpts) - Method in class ome.services.graphs.BaseGraphSpec
Deprecated.
 
chgrpQuery(EventContext, String, GraphOpts) - Method in interface ome.services.graphs.GraphSpec
Deprecated.
Return a QueryBuilder which has been properly initialized to take the parameters "id" and "grp" and then have QueryBuilder.query(Session) called.
chgrpQuery(EventContext, String, GraphOpts) - Method in class ome.services.graphs.LightSourceGraphSpec
Deprecated.
 
ChgrpStep - Class in ome.services.chgrp
Deprecated.
will be removed in OMERO 5.2, so use the new graphs implementation
ChgrpStep(OmeroContext, ExtendedMetadata, Roles, int, List<GraphStep>, GraphSpec, GraphEntry, long[], long) - Constructor for class ome.services.chgrp.ChgrpStep
Deprecated.
 
ChgrpStepFactory - Class in ome.services.chgrp
Deprecated.
will be removed in OMERO 5.2, so use the new graphs implementation
ChgrpStepFactory(OmeroContext, ExtendedMetadata, Roles) - Constructor for class ome.services.chgrp.ChgrpStepFactory
Deprecated.
 
child - Variable in class ome.model.acquisition.FilterSetEmissionFilterLink
 
CHILD - Static variable in class ome.model.acquisition.FilterSetEmissionFilterLink
 
child() - Method in class ome.model.acquisition.FilterSetEmissionFilterLink
 
child - Variable in class ome.model.acquisition.FilterSetExcitationFilterLink
 
CHILD - Static variable in class ome.model.acquisition.FilterSetExcitationFilterLink
 
child() - Method in class ome.model.acquisition.FilterSetExcitationFilterLink
 
child - Variable in class ome.model.acquisition.LightPathEmissionFilterLink
 
CHILD - Static variable in class ome.model.acquisition.LightPathEmissionFilterLink
 
child() - Method in class ome.model.acquisition.LightPathEmissionFilterLink
 
child - Variable in class ome.model.acquisition.LightPathExcitationFilterLink
 
CHILD - Static variable in class ome.model.acquisition.LightPathExcitationFilterLink
 
child() - Method in class ome.model.acquisition.LightPathExcitationFilterLink
 
child - Variable in class ome.model.annotations.AnnotationAnnotationLink
 
CHILD - Static variable in class ome.model.annotations.AnnotationAnnotationLink
 
child() - Method in class ome.model.annotations.AnnotationAnnotationLink
 
child - Variable in class ome.model.annotations.ChannelAnnotationLink
 
CHILD - Static variable in class ome.model.annotations.ChannelAnnotationLink
 
child() - Method in class ome.model.annotations.ChannelAnnotationLink
 
child - Variable in class ome.model.annotations.DatasetAnnotationLink
 
CHILD - Static variable in class ome.model.annotations.DatasetAnnotationLink
 
child() - Method in class ome.model.annotations.DatasetAnnotationLink
 
child - Variable in class ome.model.annotations.DetectorAnnotationLink
 
CHILD - Static variable in class ome.model.annotations.DetectorAnnotationLink
 
child() - Method in class ome.model.annotations.DetectorAnnotationLink
 
child - Variable in class ome.model.annotations.DichroicAnnotationLink
 
CHILD - Static variable in class ome.model.annotations.DichroicAnnotationLink
 
child() - Method in class ome.model.annotations.DichroicAnnotationLink
 
child - Variable in class ome.model.annotations.ExperimenterAnnotationLink
 
CHILD - Static variable in class ome.model.annotations.ExperimenterAnnotationLink
 
child() - Method in class ome.model.annotations.ExperimenterAnnotationLink
 
child - Variable in class ome.model.annotations.ExperimenterGroupAnnotationLink
 
CHILD - Static variable in class ome.model.annotations.ExperimenterGroupAnnotationLink
 
child() - Method in class ome.model.annotations.ExperimenterGroupAnnotationLink
 
child - Variable in class ome.model.annotations.FilesetAnnotationLink
 
CHILD - Static variable in class ome.model.annotations.FilesetAnnotationLink
 
child() - Method in class ome.model.annotations.FilesetAnnotationLink
 
child - Variable in class ome.model.annotations.FilterAnnotationLink
 
CHILD - Static variable in class ome.model.annotations.FilterAnnotationLink
 
child() - Method in class ome.model.annotations.FilterAnnotationLink
 
child - Variable in class ome.model.annotations.ImageAnnotationLink
 
CHILD - Static variable in class ome.model.annotations.ImageAnnotationLink
 
child() - Method in class ome.model.annotations.ImageAnnotationLink
 
child - Variable in class ome.model.annotations.InstrumentAnnotationLink
 
CHILD - Static variable in class ome.model.annotations.InstrumentAnnotationLink
 
child() - Method in class ome.model.annotations.InstrumentAnnotationLink
 
child - Variable in class ome.model.annotations.LightPathAnnotationLink
 
CHILD - Static variable in class ome.model.annotations.LightPathAnnotationLink
 
child() - Method in class ome.model.annotations.LightPathAnnotationLink
 
child - Variable in class ome.model.annotations.LightSourceAnnotationLink
 
CHILD - Static variable in class ome.model.annotations.LightSourceAnnotationLink
 
child() - Method in class ome.model.annotations.LightSourceAnnotationLink
 
child - Variable in class ome.model.annotations.NamespaceAnnotationLink
 
CHILD - Static variable in class ome.model.annotations.NamespaceAnnotationLink
 
child() - Method in class ome.model.annotations.NamespaceAnnotationLink
 
child - Variable in class ome.model.annotations.NodeAnnotationLink
 
CHILD - Static variable in class ome.model.annotations.NodeAnnotationLink
 
child() - Method in class ome.model.annotations.NodeAnnotationLink
 
child - Variable in class ome.model.annotations.ObjectiveAnnotationLink
 
CHILD - Static variable in class ome.model.annotations.ObjectiveAnnotationLink
 
child() - Method in class ome.model.annotations.ObjectiveAnnotationLink
 
child - Variable in class ome.model.annotations.OriginalFileAnnotationLink
 
CHILD - Static variable in class ome.model.annotations.OriginalFileAnnotationLink
 
child() - Method in class ome.model.annotations.OriginalFileAnnotationLink
 
child - Variable in class ome.model.annotations.PlaneInfoAnnotationLink
 
CHILD - Static variable in class ome.model.annotations.PlaneInfoAnnotationLink
 
child() - Method in class ome.model.annotations.PlaneInfoAnnotationLink
 
child - Variable in class ome.model.annotations.PlateAcquisitionAnnotationLink
 
CHILD - Static variable in class ome.model.annotations.PlateAcquisitionAnnotationLink
 
child() - Method in class ome.model.annotations.PlateAcquisitionAnnotationLink
 
child - Variable in class ome.model.annotations.PlateAnnotationLink
 
CHILD - Static variable in class ome.model.annotations.PlateAnnotationLink
 
child() - Method in class ome.model.annotations.PlateAnnotationLink
 
child - Variable in class ome.model.annotations.ProjectAnnotationLink
 
CHILD - Static variable in class ome.model.annotations.ProjectAnnotationLink
 
child() - Method in class ome.model.annotations.ProjectAnnotationLink
 
child - Variable in class ome.model.annotations.ReagentAnnotationLink
 
CHILD - Static variable in class ome.model.annotations.ReagentAnnotationLink
 
child() - Method in class ome.model.annotations.ReagentAnnotationLink
 
child - Variable in class ome.model.annotations.RoiAnnotationLink
 
CHILD - Static variable in class ome.model.annotations.RoiAnnotationLink
 
child() - Method in class ome.model.annotations.RoiAnnotationLink
 
child - Variable in class ome.model.annotations.ScreenAnnotationLink
 
CHILD - Static variable in class ome.model.annotations.ScreenAnnotationLink
 
child() - Method in class ome.model.annotations.ScreenAnnotationLink
 
child - Variable in class ome.model.annotations.SessionAnnotationLink
 
CHILD - Static variable in class ome.model.annotations.SessionAnnotationLink
 
child() - Method in class ome.model.annotations.SessionAnnotationLink
 
child - Variable in class ome.model.annotations.ShapeAnnotationLink
 
CHILD - Static variable in class ome.model.annotations.ShapeAnnotationLink
 
child() - Method in class ome.model.annotations.ShapeAnnotationLink
 
child - Variable in class ome.model.annotations.WellAnnotationLink
 
CHILD - Static variable in class ome.model.annotations.WellAnnotationLink
 
child() - Method in class ome.model.annotations.WellAnnotationLink
 
child - Variable in class ome.model.containers.DatasetImageLink
 
CHILD - Static variable in class ome.model.containers.DatasetImageLink
 
child() - Method in class ome.model.containers.DatasetImageLink
 
child - Variable in class ome.model.containers.ProjectDatasetLink
 
CHILD - Static variable in class ome.model.containers.ProjectDatasetLink
 
child() - Method in class ome.model.containers.ProjectDatasetLink
 
child - Variable in class ome.model.core.PixelsOriginalFileMap
 
CHILD - Static variable in class ome.model.core.PixelsOriginalFileMap
 
child() - Method in class ome.model.core.PixelsOriginalFileMap
 
child - Variable in class ome.model.fs.FilesetJobLink
 
CHILD - Static variable in class ome.model.fs.FilesetJobLink
 
child() - Method in class ome.model.fs.FilesetJobLink
 
child - Variable in class ome.model.jobs.JobOriginalFileLink
 
CHILD - Static variable in class ome.model.jobs.JobOriginalFileLink
 
child() - Method in class ome.model.jobs.JobOriginalFileLink
 
child - Variable in class ome.model.meta.GroupExperimenterMap
 
CHILD - Static variable in class ome.model.meta.GroupExperimenterMap
 
child() - Method in class ome.model.meta.GroupExperimenterMap
 
child - Variable in class ome.model.meta.ShareMember
 
CHILD - Static variable in class ome.model.meta.ShareMember
 
child() - Method in class ome.model.meta.ShareMember
 
child - Variable in class ome.model.screen.ScreenPlateLink
 
CHILD - Static variable in class ome.model.screen.ScreenPlateLink
 
child() - Method in class ome.model.screen.ScreenPlateLink
 
child - Variable in class ome.model.screen.WellReagentLink
 
CHILD - Static variable in class ome.model.screen.WellReagentLink
 
child() - Method in class ome.model.screen.WellReagentLink
 
child(String) - Method in class ome.services.blitz.repo.CheckedPath
Returns a new CheckedPath that has the given path appended to the end of this instances path.
ChildOptionI - Class in omero.cmd.graphs
Child options adjust how child objects are treated according to their type and, if annotations, namespace, overriding the default graph traversal policy for orphans.
ChildOptionI(GraphPathBean, ImmutableSet<String>) - Constructor for class omero.cmd.graphs.ChildOptionI
Construct a new child option instance.
ChildOptionI(ChildOptionI) - Constructor for class omero.cmd.graphs.ChildOptionI
Construct a new child option instance identical to that given.
ChildOptionsPolicy - Class in omero.cmd.graphs
Adjust graph traversal policy for child objects according to their type and, if annotations, namespace.
ChildOptionsPolicy() - Constructor for class omero.cmd.graphs.ChildOptionsPolicy
 
chmod - Variable in class ome.logic.AdminImpl
 
chmod(IObject, String) - Method in class ome.security.basic.GroupChmodStrategy
 
chmod(IObject, String) - Method in interface ome.security.ChmodStrategy
Change the permissions for the given object.
Chmod2I - Class in omero.cmd.graphs
Request to change the permissions on model objects, reimplementing ChmodI.
Chmod2I(ACLVoter, Roles, SystemTypes, GraphPathBean, Deletion, Set<Class<? extends IObject>>, GraphPolicy, SetMultimap<String, String>) - Constructor for class omero.cmd.graphs.Chmod2I
Construct a new chmod request; called from GraphRequestFactory.getRequest(Class).
ChmodFacadeI - Class in omero.cmd.graphs
Deprecated.
will be removed in OMERO 5.3, so use the new graphs implementation
ChmodFacadeI(GraphRequestFactory) - Constructor for class omero.cmd.graphs.ChmodFacadeI
Deprecated.
Construct a new chmod request; called from GraphRequestFactory.getRequest(Class).
ChmodI - Class in omero.cmd.graphs
Deprecated.
will be removed in OMERO 5.2, so use the new graphs implementation
ChmodI(Communicator, ChmodStrategy) - Constructor for class omero.cmd.graphs.ChmodI
Deprecated.
 
chmodQuery(EventContext, String, GraphOpts) - Method in class ome.services.graphs.BaseGraphSpec
Deprecated.
 
chmodQuery(EventContext, String, GraphOpts) - Method in interface ome.services.graphs.GraphSpec
Deprecated.
 
ChmodStrategy - Interface in ome.security
Strategy for changing the permissions of objects in the database as well as verifying that the permissions for the modified objects are sensible after the change.
choose() - Method in class ome.security.CompositeACLVoter
 
choose() - Method in class ome.security.SecurityFilterHolder
 
choose() - Method in class ome.security.SecuritySystemHolder
 
chooseNextRedirect(Redirector.Context, Set<String>) - Method in class ome.services.blitz.redirect.ConfigRedirector
 
chooseNextRedirect(Redirector.Context, Set<String>) - Method in class ome.services.blitz.redirect.NullRedirector
Does nothing.
chooseNextRedirect(Redirector.Context, Set<String>) - Method in interface ome.services.blitz.redirect.Redirector
Gives the Redirector a chance to configure the next appropriate redirect based on the Set of current Node uuids.
chooseNextRedirect(Redirector.Context, Set<String>) - Method in class ome.services.blitz.redirect.ScaleRedirector
Chown2I - Class in omero.cmd.graphs
Request to give model objects to a different experimenter, reimplementing ChownI.
Chown2I(ACLVoter, Roles, SystemTypes, GraphPathBean, Deletion, Set<Class<? extends IObject>>, GraphPolicy, SetMultimap<String, String>) - Constructor for class omero.cmd.graphs.Chown2I
Construct a new chown request; called from GraphRequestFactory.getRequest(Class).
ChownFacadeI - Class in omero.cmd.graphs
Deprecated.
will be removed in OMERO 5.3, so use the new graphs implementation
ChownFacadeI(GraphRequestFactory) - Constructor for class omero.cmd.graphs.ChownFacadeI
Deprecated.
Construct a new chown request; called from GraphRequestFactory.getRequest(Class).
ChownI - Class in omero.cmd.graphs
Deprecated.
will be removed in OMERO 5.2, so use the new graphs implementation
ChownI(Communicator, ChownStepFactory, ApplicationContext) - Constructor for class omero.cmd.graphs.ChownI
Deprecated.
 
ChownStep - Class in ome.services.chown
Deprecated.
will be removed in OMERO 5.2, so use the new graphs implementation
ChownStep(OmeroContext, ExtendedMetadata, Roles, int, List<GraphStep>, GraphSpec, GraphEntry, long[], long) - Constructor for class ome.services.chown.ChownStep
Deprecated.
 
ChownStepFactory - Class in ome.services.chown
Deprecated.
will be removed in OMERO 5.2, so use the new graphs implementation
ChownStepFactory(OmeroContext, ExtendedMetadata, Roles) - Constructor for class ome.services.chown.ChownStepFactory
Deprecated.
 
CLASS - Static variable in class ome.parameters.Parameters
named parameter "class".
classes - Variable in class ome.services.fulltext.FullTextBridge
 
ClassQuerySource - Class in ome.services.query
creates a query based on the id string by interpreting it as a Class.
ClassQuerySource() - Constructor for class ome.services.query.ClassQuerySource
 
clean() - Method in class ome.services.RawFileBean
 
clean() - Method in class ome.services.RawPixelsBean
 
cleanServants(boolean) - Method in class omero.cmd.SessionI
cleanServants(boolean, String, ServantHolder, ObjectAdapter) - Static method in class omero.cmd.SessionI
Clean all servants that are in the current holder and remove them from the adapter.
cleanTempDir() - Method in class omero.util.TempFileManager
cleanThread() - Method in class ome.tools.hibernate.SessionHandler
 
cleanup() - Method in class ome.formats.importer.cli.CommandLineImporter
Cleans up after a successful or unsuccessful image import.
cleanup() - Method in class ome.services.util.ServiceHandler
 
cleanup() - Method in class omero.util.Resources
 
cleanup() - Method in interface omero.util.Resources.Entry
Gives an Resources.Entry a chance to cleanup resources before it is removed from checking.
cleanup() - Method in class omero.util.TempFileManager
CleanupFailure - Exception in ome.formats.importer.transfers
Exception thrown when cleaning up resources after transfer fails partially or completely.
CleanupFailure(List<File>) - Constructor for exception ome.formats.importer.transfers.CleanupFailure
 
cleanupSelf() - Method in class omero.cmd.SessionI
Called if this isn't a kill-everything event.
cleanupUpload(RawFileStorePrx, FileInputStream) - Method in class ome.formats.importer.transfers.AbstractFileTransfer
Utility method for closing resources.
cleanUserDir() - Method in class omero.util.TempFileManager
Attempts to delete all directories under self.userdir other than the one owned by this process.
clear() - Method in interface ome.api.local.LocalQuery
 
clear() - Method in class ome.formats.importer.ImportLibrary
 
clear() - Method in class ome.logic.QueryImpl
 
clear() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
reset all statistics
clearAnnotationLinks() - Method in class ome.model.acquisition.Detector
clears the set.
clearAnnotationLinks() - Method in class ome.model.acquisition.Dichroic
clears the set.
clearAnnotationLinks() - Method in class ome.model.acquisition.Filter
clears the set.
clearAnnotationLinks() - Method in class ome.model.acquisition.Instrument
clears the set.
clearAnnotationLinks() - Method in class ome.model.acquisition.LightPath
clears the set.
clearAnnotationLinks() - Method in class ome.model.acquisition.LightSource
clears the set.
clearAnnotationLinks() - Method in class ome.model.acquisition.Objective
clears the set.
clearAnnotationLinks() - Method in class ome.model.annotations.Annotation
clears the set.
clearAnnotationLinks() - Method in class ome.model.containers.Dataset
clears the set.
clearAnnotationLinks() - Method in class ome.model.containers.Project
clears the set.
clearAnnotationLinks() - Method in class ome.model.core.Channel
clears the set.
clearAnnotationLinks() - Method in class ome.model.core.Image
clears the set.
clearAnnotationLinks() - Method in class ome.model.core.OriginalFile
clears the set.
clearAnnotationLinks() - Method in class ome.model.core.PlaneInfo
clears the set.
clearAnnotationLinks() - Method in class ome.model.fs.Fileset
clears the set.
clearAnnotationLinks() - Method in interface ome.model.IAnnotated
 
clearAnnotationLinks() - Method in class ome.model.meta.Experimenter
clears the set.
clearAnnotationLinks() - Method in class ome.model.meta.ExperimenterGroup
clears the set.
clearAnnotationLinks() - Method in class ome.model.meta.Namespace
clears the set.
clearAnnotationLinks() - Method in class ome.model.meta.Node
clears the set.
clearAnnotationLinks() - Method in class ome.model.meta.Session
clears the set.
clearAnnotationLinks() - Method in class ome.model.roi.Roi
clears the set.
clearAnnotationLinks() - Method in class ome.model.roi.Shape
clears the set.
clearAnnotationLinks() - Method in class ome.model.screen.Plate
clears the set.
clearAnnotationLinks() - Method in class ome.model.screen.PlateAcquisition
clears the set.
clearAnnotationLinks() - Method in class ome.model.screen.Reagent
clears the set.
clearAnnotationLinks() - Method in class ome.model.screen.Screen
clears the set.
clearAnnotationLinks() - Method in class ome.model.screen.Well
clears the set.
clearChannels() - Method in class ome.model.core.LogicalChannel
clears the set.
clearChannels() - Method in class ome.model.core.Pixels
clears the set.
clearDatasetLinks() - Method in class ome.model.containers.Project
clears the set.
clearDatasetLinks() - Method in class ome.model.core.Image
clears the set.
clearDetector() - Method in class ome.model.acquisition.Instrument
clears the set.
clearDichroic() - Method in class ome.model.acquisition.Instrument
clears the set.
clearDisabled() - Method in class ome.security.basic.CurrentDetails
 
clearEmissionFilterLinks() - Method in class ome.model.acquisition.Filter
clears the set.
clearEmissionFilterLinks() - Method in class ome.model.acquisition.FilterSet
clears the set.
clearEmissionFilterLinks() - Method in class ome.model.acquisition.LightPath
clears the set.
clearErrors(int) - Method in class ome.formats.importer.util.ErrorHandler
 
clearEvents() - Method in class ome.model.meta.Session
clears the set.
clearExcitationFilterLinks() - Method in class ome.model.acquisition.Filter
clears the set.
clearExcitationFilterLinks() - Method in class ome.model.acquisition.FilterSet
clears the set.
clearExcitationFilterLinks() - Method in class ome.model.acquisition.LightPath
clears the set.
clearExperimenterGroupLinks() - Method in class ome.model.meta.Experimenter
clears the set.
clearExperimenterLinks() - Method in class ome.model.meta.ExperimenterGroup
clears the set.
clearFiles() - Method in class ome.formats.importer.util.ErrorContainer
Clear the list of files to upload.
clearFilesetEntries() - Method in class ome.model.core.OriginalFile
clears the set.
clearFilter() - Method in class ome.model.acquisition.Instrument
clears the set.
clearFiltered() - Method in class ome.model.internal.Details
all currently marked collections are released.
clearFilterSet() - Method in class ome.model.acquisition.Instrument
clears the set.
clearImageLinks() - Method in class ome.model.containers.Dataset
clears the set.
clearImages() - Method in class ome.model.fs.Fileset
clears the set.
clearJobLinks() - Method in class ome.model.fs.Fileset
clears the set.
clearLightSource() - Method in class ome.model.acquisition.Instrument
clears the set.
clearLightSourceSettings() - Method in class ome.model.experiment.MicrobeamManipulation
clears the set.
clearLogs() - Method in class ome.model.meta.Event
clears the set.
clearLogs() - Method in class ome.security.basic.BasicSecuritySystem
 
clearLogs() - Method in class ome.security.basic.CurrentDetails
 
clearMicrobeamManipulation() - Method in class ome.model.experiment.Experiment
clears the set.
clearObjective() - Method in class ome.model.acquisition.Instrument
clears the set.
clearOriginalFileLinks() - Method in class ome.model.core.Pixels
clears the set.
clearOriginalFileLinks() - Method in class ome.model.jobs.Job
clears the set.
clearOtf() - Method in class ome.model.acquisition.Instrument
clears the set.
clearPermissionsBit(String, long, int) - Method in interface ome.util.SqlAction
Sets the given permissions bit to 0.
clearPermissionsBit(String, long, int) - Method in class ome.util.SqlAction.Impl
 
clearPixels() - Method in class ome.model.core.Image
clears the set.
clearPixelsLinks() - Method in class ome.model.core.OriginalFile
clears the set.
clearPlaneInfo() - Method in class ome.model.core.Pixels
clears the set.
clearPlateAcquisitions() - Method in class ome.model.screen.Plate
clears the set.
clearPlateLinks() - Method in class ome.model.screen.Screen
clears the set.
clearProjectLinks() - Method in class ome.model.containers.Dataset
clears the set.
clearQueries() - Method in interface ome.api.Search
Removes all active queries (leaving settings alone), such that Search.activeQueries() will return 0.
clearQueries() - Method in class ome.services.SearchBean
 
clearQueries_async(AMD_Search_clearQueries, Current) - Method in class ome.services.blitz.impl.SearchI
 
clearReagentLinks() - Method in class ome.model.screen.Well
clears the set.
clearReagents() - Method in class ome.model.screen.Screen
clears the set.
clearRois() - Method in class ome.model.core.Image
clears the set.
clearScreenLinks() - Method in class ome.model.screen.Plate
clears the set.
clearSessions() - Method in class ome.model.meta.Node
clears the set.
clearSettings() - Method in class ome.model.core.Pixels
clears the set.
clearShapes() - Method in class ome.model.roi.Roi
clears the set.
clearSpatialDomainEnhancement() - Method in class ome.model.display.RenderingDef
clears the set.
clearThumbnails() - Method in class ome.model.core.Pixels
clears the set.
clearToken(GraphHolder) - Method in class ome.security.basic.TokenHolder
 
clearUsedFiles() - Method in class ome.model.fs.Fileset
clears the set.
clearWaveRendering() - Method in class ome.model.display.RenderingDef
clears the set.
clearWellLinks() - Method in class ome.model.screen.Reagent
clears the set.
clearWells() - Method in class ome.model.screen.Plate
clears the set.
clearWellSample() - Method in class ome.model.screen.PlateAcquisition
clears the set.
clearWellSamples() - Method in class ome.model.core.Image
clears the set.
clearWellSamples() - Method in class ome.model.screen.Well
clears the set.
client - Class in omero
Central client-side blitz entry point.
client() - Constructor for class omero.client
Calls client.client(Ice.InitializationData) with a new InitializationData
client(InitializationData) - Constructor for class omero.client
Creates an Communicator from a InitializationData instance.
client(String) - Constructor for class omero.client
Creates an Communicator pointing at the given server using the #DEFAULT_PORT.
client(String, int) - Constructor for class omero.client
Creates an Communicator pointing at the given server with the non-standard port.
client(String[]) - Constructor for class omero.client
Calls client.client(String[], Ice.InitializationData) with a new InitializationData
client(String[], InitializationData) - Constructor for class omero.client
Creates an Communicator from command-line arguments.
client(File...) - Constructor for class omero.client
Creates an Communicator from multiple files.
client(Map) - Constructor for class omero.client
Creates an Communicator from a Map instance.
client - Variable in class omero.model.DetailsI
 
CLIENT_CONTEXT - Static variable in class ome.system.OmeroContext
identifier for an OmeroContext configured in classpath*:beanRefContext.xml for use by remote (via JNDI/RMI) clients.
ClientError - Exception in omero
abstract superclass of all Omero exceptions.
ClientError(String) - Constructor for exception omero.ClientError
 
ClientFilePathTransformer - Class in ome.services.blitz.repo.path
Transform client-local File to repository FsFile path.
ClientFilePathTransformer(Function<String, String>) - Constructor for class ome.services.blitz.repo.path.ClientFilePathTransformer
Construct a new client-side file path transformer.
clientId - Variable in class omero.cmd.SessionI
 
clientId(Current) - Static method in class omero.cmd.SessionI
Helpers method to extract the CLIENTUUID out of the given Ice.Current.
clientIds - Variable in class omero.util.ServantHolder
An internal mapping to all client ids from SessionI for a given DB session since there is no method on ObjectAdapter to retrieve all servants.
ClientKeepAlive - Class in ome.formats.importer.util
A Runnable which keeps a Connector's server side resources from timing out.
ClientKeepAlive() - Constructor for class ome.formats.importer.util.ClientKeepAlive
 
clientPath - Variable in class ome.model.fs.FilesetEntry
 
CLIENTPATH - Static variable in class ome.model.fs.FilesetEntry
 
clone() - Method in class ome.services.sessions.state.CacheListener
 
close(boolean) - Method in class loci.ome.io.OmeroReader
 
close() - Method in interface ome.api.StatefulServiceInterface
signals the end of the service lifecycle.
close() - Method in class ome.formats.importer.OMEROWrapper
 
close() - Method in class ome.io.bioformats.BfPixelBuffer
 
close() - Method in class ome.io.bioformats.BfPixelsWrapper
 
close() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
 
close() - Method in class ome.io.bioformats.OmeroPixelsPyramidReader
 
close() - Method in class ome.io.bioformats.OmeroPixelsPyramidWriter
 
close() - Method in class ome.io.nio.FileBuffer
Closes the buffer, cleaning up file state.
close() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
 
close() - Method in interface ome.io.nio.PixelBuffer
Closes the buffer, cleaning up file state.
close() - Method in class ome.io.nio.RomioPixelBuffer
Closes the buffer, cleaning up file state.
close(Current) - Method in class ome.services.blitz.impl.AbstractCloseableAmdServant
 
close(boolean, Current) - Method in class ome.services.blitz.impl.ScriptProcessI
 
close(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
Deprecated.
close() - Method in class ome.services.blitz.repo.AbstractRepositoryI
 
close() - Method in class ome.services.blitz.repo.FileMaker
 
close() - Method in class ome.services.formats.OmeroReader
 
close(Signal, Integer) - Static method in class ome.services.fulltext.Main
 
close() - Method in class ome.services.JobBean
 
close() - Method in class ome.services.messages.ParserOpenFileMessage
Used to close the passed in resource.
close() - Method in class ome.services.messages.RegisterServiceCleanupMessage
Used to close the passed in resource.
close() - Method in class ome.services.RawFileBean
 
close() - Method in class ome.services.RawPixelsBean
 
close() - Method in class ome.services.RenderingBean
 
close() - Method in class ome.services.SearchBean
 
close() - Method in interface ome.services.sessions.SessionCallback
 
close(String) - Method in interface ome.services.sessions.SessionManager
If reference count for the session is less than 1, close the session.
close(String) - Method in class ome.services.sessions.SessionManagerImpl
 
close() - Method in class ome.services.sharing.ShareStore
 
close() - Method in class ome.services.ThumbnailBean
 
close() - Method in class omeis.providers.re.Renderer
Closes the buffer, cleaning up file state.
close(boolean) - Method in class omero.cmd.CmdCallbackI
First removes self from the adapter so as to no longer receive notifications, and the calls close on the remote handle if requested.
close(Current) - Method in class omero.cmd.HandleI
 
close(Current) - Method in class omero.grid.InteractiveProcessorI
 
close() - Method in class omero.grid.ProcessCallbackI
 
close(Current) - Method in interface omero.util.CloseableServant
 
close() - Method in class omero.util.RPSTileData
 
close() - Method in interface omero.util.TileData
 
close_async(AMD_StatefulServiceInterface_close, Current) - Method in class ome.services.blitz.impl.AbstractCloseableAmdServant
SessionHandler also specially catches close() calls, but cannot remove the servant from the ObjectAdapter and thereby prevent any further communication.
close_async(AMD_StatefulServiceInterface_close, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
CloseableServant - Interface in omero.util
Marker interface which distinguishes a servant which wants to have CloseableServant.close(Ice.Current) called on SessionI.doDestroy()
closeAll() - Method in interface ome.services.sessions.SessionManager
Close all sessions with checking for the necessary reference counts.
closeAll() - Method in class ome.services.sessions.SessionManagerImpl
 
closeAll() - Method in class ome.system.OmeroContext
closes all the nested OmeroContexts within this instance.
closeCalled(int) - Method in class ome.services.blitz.repo.ManagedImportProcessI
 
closeCompleted(ImportConfig) - Static method in class ome.formats.importer.cli.CommandLineImporter
Look for all ImportProcessPrx in the current session and close them if they return a non-null Response (i.e. they are done).
closed - Variable in class ome.model.meta.Session
 
CLOSED - Static variable in class ome.model.meta.Session
 
closeNode(String) - Method in interface ome.util.SqlAction
 
closeNode(String) - Method in class ome.util.SqlAction.Impl
 
closeNodeSessions(String) - Method in interface ome.util.SqlAction
 
closeNodeSessions(String) - Method in class ome.util.SqlAction.Impl
 
closeOnDestroy(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
closeParsedFiles() - Method in class ome.services.fulltext.ParserSession
 
closeQuietly(Closeable) - Static method in class ome.util.Utils
 
closeRaf() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
 
closeServices() - Method in class ome.formats.OMEROMetadataStoreClient
Closes all stateful services.
closeSession(Session) - Method in interface ome.api.ISession
Closes session and releases all resources.
closeSession(Session) - Method in class ome.services.sessions.SessionBean
 
closeSession() - Method in class ome.system.ServiceFactory
 
closeSession() - Method in class omero.client
Closes the session and nulls out the communicator.
closeSession() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
closeSession_async(AMD_ISession_closeSession, Session, Current) - Method in class ome.services.blitz.impl.SessionI
 
closeSessions(String) - Method in class ome.util.actions.PostgresSqlAction
 
closeSessions(String) - Method in interface ome.util.SqlAction
 
closeShare(long) - Method in interface ome.api.IShare
Closes share.
closeShare(long) - Method in class ome.services.sharing.ShareBean
 
closeShare_async(AMD_IShare_closeShare, long, Current) - Method in class ome.services.blitz.impl.ShareI
 
closeStatement() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
closeUploader() - Method in class ome.formats.importer.transfers.TransferState
Call StatefulServiceInterfacePrx.close() on the cached TransferState.prx instance if non-null and null the instance.
closeWriter() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
This method should never exit without releasing the lock.
CmdCallbackI - Class in omero.cmd
Callback servant used to wait until a HandlePrx would return non-null on getReponse.
CmdCallbackI(client, HandlePrx) - Constructor for class omero.cmd.CmdCallbackI
 
CmdCallbackI(ObjectAdapter, String, HandlePrx) - Constructor for class omero.cmd.CmdCallbackI
 
co2percent - Variable in class ome.model.acquisition.ImagingEnvironment
 
CO2PERCENT - Static variable in class ome.model.acquisition.ImagingEnvironment
 
CodomainChain - Class in omeis.providers.re.codomain
Queues the contexts that define the spatial domain transformations that have to be applied to the image.
CodomainChain(int, int) - Constructor for class omeis.providers.re.codomain.CodomainChain
Creates a new chain.
CodomainChain(int, int, List) - Constructor for class omeis.providers.re.codomain.CodomainChain
Creates a new chain.
CodomainMap - Interface in omeis.providers.re.codomain
Declares the interface common to all codomain maps.
CodomainMapContext - Class in ome.model.display
These filter definitions are used by the security system to eliminate non-readable objects from queries.
CodomainMapContext() - Constructor for class ome.model.display.CodomainMapContext
 
CodomainMapContext(Long) - Constructor for class ome.model.display.CodomainMapContext
 
CodomainMapContext(Long, boolean) - Constructor for class ome.model.display.CodomainMapContext
Main constructor.
CodomainMapContext(RenderingDef) - Constructor for class ome.model.display.CodomainMapContext
 
CodomainMapContext - Class in omeis.providers.re.codomain
Each concrete subclass defines transformation parameters for a CodomainMap implementation.
CodomainMapContext() - Constructor for class omeis.providers.re.codomain.CodomainMapContext
 
CodomainMapContext.Details - Class in ome.model.display
 
CodomainMapContext.Details() - Constructor for class ome.model.display.CodomainMapContext.Details
 
CodomainMapContext.Details(Object[]) - Constructor for class ome.model.display.CodomainMapContext.Details
 
coefficient - Variable in class ome.model.display.ChannelBinding
 
COEFFICIENT - Static variable in class ome.model.display.ChannelBinding
 
COLLAB_READLINK - Static variable in class ome.model.internal.Permissions
an immutable Permissions instance with read and write permissions for group members.
COLLAB_READONLY - Static variable in class ome.model.internal.Permissions
an immutable Permissions instance with permissions for group members to read other members' data.
collapse(boolean) - Method in class ome.services.graphs.GraphState
Deprecated.
 
collapse(boolean) - Method in interface ome.services.graphs.GraphStep.Callback
Deprecated.
 
collect(UnloadedCollector, Image) - Method in class ome.services.delete.DeleteBean
Walks the Image graph collecting unloaded instances of all entities for later delete.
collectAnnotationLinks(CBlock<E>) - Method in class ome.model.acquisition.Detector
takes a CBlock and calls the block once for each ome.model.annotations.DetectorAnnotationLink while collecting the results.
collectAnnotationLinks(CBlock<E>) - Method in class ome.model.acquisition.Dichroic
takes a CBlock and calls the block once for each ome.model.annotations.DichroicAnnotationLink while collecting the results.
collectAnnotationLinks(CBlock<E>) - Method in class ome.model.acquisition.Filter
takes a CBlock and calls the block once for each ome.model.annotations.FilterAnnotationLink while collecting the results.
collectAnnotationLinks(CBlock<E>) - Method in class ome.model.acquisition.Instrument
takes a CBlock and calls the block once for each ome.model.annotations.InstrumentAnnotationLink while collecting the results.
collectAnnotationLinks(CBlock<E>) - Method in class ome.model.acquisition.LightPath
takes a CBlock and calls the block once for each ome.model.annotations.LightPathAnnotationLink while collecting the results.
collectAnnotationLinks(CBlock<E>) - Method in class ome.model.acquisition.LightSource
takes a CBlock and calls the block once for each ome.model.annotations.LightSourceAnnotationLink while collecting the results.
collectAnnotationLinks(CBlock<E>) - Method in class ome.model.acquisition.Objective
takes a CBlock and calls the block once for each ome.model.annotations.ObjectiveAnnotationLink while collecting the results.
collectAnnotationLinks(CBlock<E>) - Method in class ome.model.annotations.Annotation
takes a CBlock and calls the block once for each ome.model.annotations.AnnotationAnnotationLink while collecting the results.
collectAnnotationLinks(CBlock<E>) - Method in class ome.model.containers.Dataset
takes a CBlock and calls the block once for each ome.model.annotations.DatasetAnnotationLink while collecting the results.
collectAnnotationLinks(CBlock<E>) - Method in class ome.model.containers.Project
takes a CBlock and calls the block once for each ome.model.annotations.ProjectAnnotationLink while collecting the results.
collectAnnotationLinks(CBlock<E>) - Method in class ome.model.core.Channel
takes a CBlock and calls the block once for each ome.model.annotations.ChannelAnnotationLink while collecting the results.
collectAnnotationLinks(CBlock<E>) - Method in class ome.model.core.Image
takes a CBlock and calls the block once for each ome.model.annotations.ImageAnnotationLink while collecting the results.
collectAnnotationLinks(CBlock<E>) - Method in class ome.model.core.OriginalFile
takes a CBlock and calls the block once for each ome.model.annotations.OriginalFileAnnotationLink while collecting the results.
collectAnnotationLinks(CBlock<E>) - Method in class ome.model.core.PlaneInfo
takes a CBlock and calls the block once for each ome.model.annotations.PlaneInfoAnnotationLink while collecting the results.
collectAnnotationLinks(CBlock<E>) - Method in class ome.model.fs.Fileset
takes a CBlock and calls the block once for each ome.model.annotations.FilesetAnnotationLink while collecting the results.
collectAnnotationLinks(CBlock<E>) - Method in interface ome.model.IAnnotated
 
collectAnnotationLinks(CBlock<E>) - Method in class ome.model.meta.Experimenter
takes a CBlock and calls the block once for each ome.model.annotations.ExperimenterAnnotationLink while collecting the results.
collectAnnotationLinks(CBlock<E>) - Method in class ome.model.meta.ExperimenterGroup
takes a CBlock and calls the block once for each ome.model.annotations.ExperimenterGroupAnnotationLink while collecting the results.
collectAnnotationLinks(CBlock<E>) - Method in class ome.model.meta.Namespace
takes a CBlock and calls the block once for each ome.model.annotations.NamespaceAnnotationLink while collecting the results.
collectAnnotationLinks(CBlock<E>) - Method in class ome.model.meta.Node
takes a CBlock and calls the block once for each ome.model.annotations.NodeAnnotationLink while collecting the results.
collectAnnotationLinks(CBlock<E>) - Method in class ome.model.meta.Session
takes a CBlock and calls the block once for each ome.model.annotations.SessionAnnotationLink while collecting the results.
collectAnnotationLinks(CBlock<E>) - Method in class ome.model.roi.Roi
takes a CBlock and calls the block once for each ome.model.annotations.RoiAnnotationLink while collecting the results.
collectAnnotationLinks(CBlock<E>) - Method in class ome.model.roi.Shape
takes a CBlock and calls the block once for each ome.model.annotations.ShapeAnnotationLink while collecting the results.
collectAnnotationLinks(CBlock<E>) - Method in class ome.model.screen.Plate
takes a CBlock and calls the block once for each ome.model.annotations.PlateAnnotationLink while collecting the results.
collectAnnotationLinks(CBlock<E>) - Method in class ome.model.screen.PlateAcquisition
takes a CBlock and calls the block once for each ome.model.annotations.PlateAcquisitionAnnotationLink while collecting the results.
collectAnnotationLinks(CBlock<E>) - Method in class ome.model.screen.Reagent
takes a CBlock and calls the block once for each ome.model.annotations.ReagentAnnotationLink while collecting the results.
collectAnnotationLinks(CBlock<E>) - Method in class ome.model.screen.Screen
takes a CBlock and calls the block once for each ome.model.annotations.ScreenAnnotationLink while collecting the results.
collectAnnotationLinks(CBlock<E>) - Method in class ome.model.screen.Well
takes a CBlock and calls the block once for each ome.model.annotations.WellAnnotationLink while collecting the results.
collectChannels(CBlock<E>) - Method in class ome.model.core.LogicalChannel
takes a CBlock and calls the block once for each ome.model.core.Channel while collecting the results.
collectChannels(CBlock<E>) - Method in class ome.model.core.Pixels
takes a CBlock and calls the block once for each ome.model.core.Channel while collecting the results.
collectDatasetLinks(CBlock<E>) - Method in class ome.model.containers.Project
takes a CBlock and calls the block once for each ome.model.containers.ProjectDatasetLink while collecting the results.
collectDatasetLinks(CBlock<E>) - Method in class ome.model.core.Image
takes a CBlock and calls the block once for each ome.model.containers.DatasetImageLink while collecting the results.
collectDetector(CBlock<E>) - Method in class ome.model.acquisition.Instrument
takes a CBlock and calls the block once for each ome.model.acquisition.Detector while collecting the results.
collectDichroic(CBlock<E>) - Method in class ome.model.acquisition.Instrument
takes a CBlock and calls the block once for each ome.model.acquisition.Dichroic while collecting the results.
CollectedACLViolations - Exception in ome.conditions.acl
User has attempted an action which is not permitted by the Permissions of a given instance.
CollectedACLViolations(String) - Constructor for exception ome.conditions.acl.CollectedACLViolations
 
collectEmissionFilterLink(CBlock<E>) - Method in class ome.model.acquisition.Filter
takes a CBlock and calls the block once for each ome.model.acquisition.FilterSetEmissionFilterLink while collecting the results.
collectEmissionFilterLink(CBlock<E>) - Method in class ome.model.acquisition.FilterSet
takes a CBlock and calls the block once for each ome.model.acquisition.FilterSetEmissionFilterLink while collecting the results.
collectEmissionFilterLink(CBlock<E>) - Method in class ome.model.acquisition.LightPath
takes a CBlock and calls the block once for each ome.model.acquisition.LightPathEmissionFilterLink while collecting the results.
collectEvents(CBlock<E>) - Method in class ome.model.meta.Session
takes a CBlock and calls the block once for each ome.model.meta.Event while collecting the results.
collectExcitationFilterLink(CBlock<E>) - Method in class ome.model.acquisition.Filter
takes a CBlock and calls the block once for each ome.model.acquisition.FilterSetExcitationFilterLink while collecting the results.
collectExcitationFilterLink(CBlock<E>) - Method in class ome.model.acquisition.FilterSet
takes a CBlock and calls the block once for each ome.model.acquisition.FilterSetExcitationFilterLink while collecting the results.
collectExcitationFilterLink(CBlock<E>) - Method in class ome.model.acquisition.LightPath
takes a CBlock and calls the block once for each ome.model.acquisition.LightPathExcitationFilterLink while collecting the results.
collectFilesetEntries(CBlock<E>) - Method in class ome.model.core.OriginalFile
takes a CBlock and calls the block once for each ome.model.fs.FilesetEntry while collecting the results.
collectFilter(CBlock<E>) - Method in class ome.model.acquisition.Instrument
takes a CBlock and calls the block once for each ome.model.acquisition.Filter while collecting the results.
collectFilterSet(CBlock<E>) - Method in class ome.model.acquisition.Instrument
takes a CBlock and calls the block once for each ome.model.acquisition.FilterSet while collecting the results.
collectGroupExperimenterMap(CBlock<E>) - Method in class ome.model.meta.Experimenter
takes a CBlock and calls the block once for each ome.model.meta.GroupExperimenterMap while collecting the results.
collectGroupExperimenterMap(CBlock<E>) - Method in class ome.model.meta.ExperimenterGroup
takes a CBlock and calls the block once for each ome.model.meta.GroupExperimenterMap while collecting the results.
collectImageLinks(CBlock<E>) - Method in class ome.model.containers.Dataset
takes a CBlock and calls the block once for each ome.model.containers.DatasetImageLink while collecting the results.
collectImages(CBlock<E>) - Method in class ome.model.fs.Fileset
takes a CBlock and calls the block once for each ome.model.core.Image while collecting the results.
CollectionCountQueryDefinition - Class in ome.services.query
counts the number of members in a collection.
CollectionCountQueryDefinition(Parameters) - Constructor for class ome.services.query.CollectionCountQueryDefinition
 
CollectionQueryParameterDef - Class in ome.services.query
extension of QueryParameterDef which restricts the type to a Collection, and specifies the element types of that Collection.
CollectionQueryParameterDef(String, boolean, Class) - Constructor for class ome.services.query.CollectionQueryParameterDef
 
collectJobLinks(CBlock<E>) - Method in class ome.model.fs.Fileset
takes a CBlock and calls the block once for each ome.model.fs.FilesetJobLink while collecting the results.
collectLightSource(CBlock<E>) - Method in class ome.model.acquisition.Instrument
takes a CBlock and calls the block once for each ome.model.acquisition.LightSource while collecting the results.
collectLightSourceSettings(CBlock<E>) - Method in class ome.model.experiment.MicrobeamManipulation
takes a CBlock and calls the block once for each ome.model.acquisition.LightSettings while collecting the results.
collectLogs(CBlock<E>) - Method in class ome.model.meta.Event
takes a CBlock and calls the block once for each ome.model.meta.EventLog while collecting the results.
collectMicrobeamManipulation(CBlock<E>) - Method in class ome.model.experiment.Experiment
takes a CBlock and calls the block once for each ome.model.experiment.MicrobeamManipulation while collecting the results.
collectObjective(CBlock<E>) - Method in class ome.model.acquisition.Instrument
takes a CBlock and calls the block once for each ome.model.acquisition.Objective while collecting the results.
collectOriginalFileLinks(CBlock<E>) - Method in class ome.model.jobs.Job
takes a CBlock and calls the block once for each ome.model.jobs.JobOriginalFileLink while collecting the results.
collectOtf(CBlock<E>) - Method in class ome.model.acquisition.Instrument
takes a CBlock and calls the block once for each ome.model.acquisition.OTF while collecting the results.
collectPixels(CBlock<E>) - Method in class ome.model.core.Image
takes a CBlock and calls the block once for each ome.model.core.Pixels while collecting the results.
collectPixelsFileMaps(CBlock<E>) - Method in class ome.model.core.OriginalFile
takes a CBlock and calls the block once for each ome.model.core.PixelsOriginalFileMap while collecting the results.
collectPixelsFileMaps(CBlock<E>) - Method in class ome.model.core.Pixels
takes a CBlock and calls the block once for each ome.model.core.PixelsOriginalFileMap while collecting the results.
collectPlaneInfo(CBlock<E>) - Method in class ome.model.core.Pixels
takes a CBlock and calls the block once for each ome.model.core.PlaneInfo while collecting the results.
collectPlateAcquisitions(CBlock<E>) - Method in class ome.model.screen.Plate
takes a CBlock and calls the block once for each ome.model.screen.PlateAcquisition while collecting the results.
collectPlateLinks(CBlock<E>) - Method in class ome.model.screen.Screen
takes a CBlock and calls the block once for each ome.model.screen.ScreenPlateLink while collecting the results.
collectProjectLinks(CBlock<E>) - Method in class ome.model.containers.Dataset
takes a CBlock and calls the block once for each ome.model.containers.ProjectDatasetLink while collecting the results.
collectReagentLinks(CBlock<E>) - Method in class ome.model.screen.Well
takes a CBlock and calls the block once for each ome.model.screen.WellReagentLink while collecting the results.
collectReagents(CBlock<E>) - Method in class ome.model.screen.Screen
takes a CBlock and calls the block once for each ome.model.screen.Reagent while collecting the results.
collectRois(CBlock<E>) - Method in class ome.model.core.Image
takes a CBlock and calls the block once for each ome.model.roi.Roi while collecting the results.
collectScreenLinks(CBlock<E>) - Method in class ome.model.screen.Plate
takes a CBlock and calls the block once for each ome.model.screen.ScreenPlateLink while collecting the results.
collectSessions(CBlock<E>) - Method in class ome.model.meta.Node
takes a CBlock and calls the block once for each ome.model.meta.Session while collecting the results.
collectSettings(CBlock<E>) - Method in class ome.model.core.Pixels
takes a CBlock and calls the block once for each ome.model.display.RenderingDef while collecting the results.
collectShapes(CBlock<E>) - Method in class ome.model.roi.Roi
takes a CBlock and calls the block once for each ome.model.roi.Shape while collecting the results.
collectSpatialDomainEnhancement(CBlock<E>) - Method in class ome.model.display.RenderingDef
takes a CBlock and calls the block once for each ome.model.display.CodomainMapContext while collecting the results.
collectThumbnails(CBlock<E>) - Method in class ome.model.core.Pixels
takes a CBlock and calls the block once for each ome.model.display.Thumbnail while collecting the results.
collectUsedFiles(CBlock<E>) - Method in class ome.model.fs.Fileset
takes a CBlock and calls the block once for each ome.model.fs.FilesetEntry while collecting the results.
collectWaveRendering(CBlock<E>) - Method in class ome.model.display.RenderingDef
takes a CBlock and calls the block once for each ome.model.display.ChannelBinding while collecting the results.
collectWellLinks(CBlock<E>) - Method in class ome.model.screen.Reagent
takes a CBlock and calls the block once for each ome.model.screen.WellReagentLink while collecting the results.
collectWells(CBlock<E>) - Method in class ome.model.screen.Plate
takes a CBlock and calls the block once for each ome.model.screen.Well while collecting the results.
collectWellSample(CBlock<E>) - Method in class ome.model.screen.PlateAcquisition
takes a CBlock and calls the block once for each ome.model.screen.WellSample while collecting the results.
collectWellSamples(CBlock<E>) - Method in class ome.model.core.Image
takes a CBlock and calls the block once for each ome.model.screen.WellSample while collecting the results.
collectWellSamples(CBlock<E>) - Method in class ome.model.screen.Well
takes a CBlock and calls the block once for each ome.model.screen.WellSample while collecting the results.
ColorsFactory - Class in ome.formats.model
Utility class to determine the color usually associated to a specified channel depending on its emission wavelength.
ColorsFactory() - Constructor for class ome.formats.model.ColorsFactory
 
ColorsFactory - Class in omeis.providers.re
Utility class to determine the color usually associated to a specified channel depending on its emission wavelength.
ColorsFactory() - Constructor for class omeis.providers.re.ColorsFactory
 
column - Variable in class ome.model.screen.Well
 
COLUMN - Static variable in class ome.model.screen.Well
 
columnNamingConvention - Variable in class ome.model.screen.Plate
 
COLUMNNAMINGCONVENTION - Static variable in class ome.model.screen.Plate
 
columns - Variable in class ome.model.screen.Plate
 
COLUMNS - Static variable in class ome.model.screen.Plate
 
columnSets(GraphEntry, long[]) - Method in class ome.services.graphs.GraphTables
Deprecated.
Returns all column sets where the first LENGTH - 1 members of "match" coincide with the values of the columns in the set.
COMBINED - Static variable in class ome.services.fulltext.BridgeHelper
Name of the Field which contains the union of all fields.
combineFacadeRequests(List<Request>) - Static method in class omero.cmd.graphs.GraphUtil
Deprecated.
because facade classes are deprecated
combineFilePathRestrictions(FilePathRestrictions...) - Static method in class ome.services.blitz.repo.path.FilePathRestrictions
Combine sets of rules to form a set that satisfies them all and that include transformations away from Unicode control characters.
CommandLineImporter - Class in ome.formats.importer.cli
The base entry point for the CLI version of the OMERO importer.
CommandLineImporter(ImportConfig, String[], boolean) - Constructor for class ome.formats.importer.cli.CommandLineImporter
Legacy constructor which uses a UploadFileTransfer.
CommandLineImporter(ImportConfig, String[], boolean, FileTransfer, int) - Constructor for class ome.formats.importer.cli.CommandLineImporter
Legacy constructor without any file exclusions.
CommandLineImporter(ImportConfig, String[], boolean, FileTransfer, List<FileExclusion>, int) - Constructor for class ome.formats.importer.cli.CommandLineImporter
Main entry class for the application.
CommentAnnotation - Class in ome.model.annotations
 
CommentAnnotation() - Constructor for class ome.model.annotations.CommentAnnotation
 
CommentAnnotation(Long) - Constructor for class ome.model.annotations.CommentAnnotation
 
CommentAnnotation(Long, boolean) - Constructor for class ome.model.annotations.CommentAnnotation
Main constructor.
commonRoot(List<FsFile>) - Method in class ome.services.blitz.repo.ManagedRepositoryI
From a list of paths, calculate the common root path that all share.
COMPANION_FILE_NS - Static variable in class pojos.FileAnnotationData
The name space used to indicate that the FileAnnotation is a companion file.
compare(LSID, LSID) - Method in class ome.formats.OMEXMLModelComparator
 
compare(Dataset, Dataset) - Method in class ome.formats.SortDatasetsByName
 
compare(Project, Project) - Method in class ome.formats.SortProjectsByName
 
compare(Object, Object) - Method in class pojos.ROICoordinate
Implemented as specified by the Comparator I/F.
comparePasswords(String, String) - Method in class ome.security.auth.ConfigurablePasswordProvider
Compares the password provided by the user (unhashed) against the given trusted password.
comparePasswords(Long, String, String) - Method in class ome.security.auth.ConfigurablePasswordProvider
Compares the password provided by the user (unhashed) against the given trusted password.
comparePasswords(Long, String, String, PasswordUtil) - Method in class ome.security.auth.ConfigurablePasswordProvider
 
comparePasswords(String, String) - Method in interface ome.security.auth.PasswordUtility
 
Complement - Class in ome.services.search
Complement SearchAction which combines two other search actions into one logical unit, e.g.
Complement(SearchValues, SearchAction, SearchAction) - Constructor for class ome.services.search.Complement
 
complete() - Method in class ome.formats.OverlayMetadataStore
Completes overlay population, flushing in memory ROI.
completeFast - Variable in class ome.services.fulltext.FullTextIndexer
 
completeSlow - Variable in class ome.services.fulltext.FullTextIndexer
 
COMPLEX_TYPE - Static variable in class pojos.PixelsData
Identifies the type used to store pixel values.
CompositeACLVoter - Class in ome.security
 
CompositeACLVoter(CurrentDetails, BasicACLVoter, SharingACLVoter) - Constructor for class ome.security.CompositeACLVoter
 
CompressImpl - Class in ome.logic
 
CompressImpl() - Constructor for class ome.logic.CompressImpl
 
compression - Variable in class ome.model.display.RenderingDef
 
COMPRESSION - Static variable in class ome.model.display.RenderingDef
 
compressToStream(BufferedImage, OutputStream) - Method in interface ome.api.local.LocalCompress
Compresses a buffered image to an output stream.
compressToStream(BufferedImage, OutputStream) - Method in class ome.logic.CompressImpl
 
computeLocationStats(Pixels, PixelBuffer, PlaneDef, int) - Method in class omeis.providers.re.metadata.StatsFactory
Helper object to determine the location of the pixels' values, the inputWindow i.e.
concatenate(FsFile...) - Static method in class ome.services.blitz.repo.path.FsFile
Concatenate paths.
ConcurrencyException - Exception in ome.conditions
Error due to simultaneous access of some resource.
ConcurrencyException(String, long) - Constructor for exception ome.conditions.ConcurrencyException
 
ConcurrentStatisticsImpl - Class in org.hibernate.stat
Implementation of Statistics, as well as StatisticsImplementor, based on the java.util.concurrent package introduced in Java 5.
ConcurrentStatisticsImpl() - Constructor for class org.hibernate.stat.ConcurrentStatisticsImpl
 
ConcurrentStatisticsImpl(SessionFactoryImplementor) - Constructor for class org.hibernate.stat.ConcurrentStatisticsImpl
 
config - Variable in class ome.formats.importer.cli.CommandLineImporter
Configuration used by all components
config - Variable in class ome.formats.importer.util.ErrorHandler
 
config - Variable in class ome.model.meta.ExperimenterGroup
 
CONFIG - Static variable in class ome.model.meta.ExperimenterGroup
 
CONFIG_KEY - Static variable in class ome.util.PixelData
 
configGroup(EventContext, List<Long>) - Method in class ome.security.basic.AllGroupsSecurityFilter
 
ConfigI - Class in ome.services.blitz.impl
Implementation of the IConfig service.
ConfigI(IConfig, BlitzExecutor) - Constructor for class ome.services.blitz.impl.ConfigI
 
ConfigImpl - Class in ome.logic
implementation of the IConfig service interface.
ConfigImpl() - Constructor for class ome.logic.ConfigImpl
 
ConfigRedirector - Class in ome.services.blitz.redirect
Redirector implementation which uses the REDIRECT config key via LocalConfig to know which Node is currently active.
ConfigRedirector(Executor) - Constructor for class ome.services.blitz.redirect.ConfigRedirector
 
ConfigurablePasswordProvider - Class in ome.security.auth
Base class for most PasswordProvider implementations, providing configuration for default behaviors.
ConfigurablePasswordProvider(PasswordUtil) - Constructor for class ome.security.auth.ConfigurablePasswordProvider
ConfigurablePasswordProvider(PasswordUtil, boolean) - Constructor for class ome.security.auth.ConfigurablePasswordProvider
ConfigurablePasswordProvider(PasswordUtil, boolean, boolean) - Constructor for class ome.security.auth.ConfigurablePasswordProvider
 
configure(List<HardWiredInterceptor>, OmeroContext) - Static method in class ome.logic.HardWiredInterceptor
 
configure(SelfConfigurableService) - Method in class ome.services.util.BeanHelper
 
configure(Type, Properties, Dialect) - Method in class ome.tools.hibernate.MySeqGenerator
If the parameters do not contain a SequenceGenerator.SEQUENCE name, we assign one based on the table name.
configure(Type, Properties, Dialect) - Method in class ome.util.TableIdGenerator
 
configureDebug(String) - Method in class ome.formats.importer.ImportConfig
Modifies the logging level of everything under the ome.formats, ome.services.blitz, ome.system and loci packages hierarchically.
ConfiguredTileSizes - Class in ome.io.nio
Implementation which has all values injected during configuration.
ConfiguredTileSizes() - Constructor for class ome.io.nio.ConfiguredTileSizes
 
ConfiguredTileSizes(int, int, int, int) - Constructor for class ome.io.nio.ConfiguredTileSizes
 
configureServant(Object) - Method in class omero.cmd.SessionI
Apply proper AOP and call setters for any known injection properties.
configValue(String) - Method in interface ome.util.SqlAction
 
configValue(String) - Method in class ome.util.SqlAction.Impl
 
conn - Variable in class ome.model.meta.Node
 
CONN - Static variable in class ome.model.meta.Node
 
connect() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
constant - Variable in class ome.model.display.PlaneSlicingContext
 
CONSTANT - Static variable in class ome.model.display.PlaneSlicingContext
 
containedExperimenters(long) - Method in interface ome.api.IAdmin
fetch all users contained in this group.
containedExperimenters(long) - Method in class ome.logic.AdminImpl
 
containedExperimenters_async(AMD_IAdmin_containedExperimenters, long, Current) - Method in class ome.services.blitz.impl.AdminI
 
containedGroups(long) - Method in interface ome.api.IAdmin
fetch all groups of which the given user is a member.
containedGroups(long) - Method in class ome.logic.AdminImpl
 
containedGroups_async(AMD_IAdmin_containedGroups, long, Current) - Method in class ome.services.blitz.impl.AdminI
 
container - Variable in class ome.formats.importer.ImportEvent.PROGRESS_EVENT
 
ContainerI - Class in ome.services.blitz.impl
Implementation of the IContainer service.
ContainerI(IContainer, BlitzExecutor) - Constructor for class ome.services.blitz.impl.ContainerI
 
containingEvent - Variable in class ome.model.meta.Event
 
CONTAININGEVENT - Static variable in class ome.model.meta.Event
 
contains(Object) - Method in interface ome.api.local.LocalQuery
Tests if an object is currently contained in the session.
contains(Object) - Method in class ome.logic.QueryImpl
 
contains(long, Class<T>, long) - Method in class ome.services.sharing.ShareStore
 
contains(double, double) - Method in class ome.util.math.geom2D.EllipseArea
Required by the Shape I/F.
contains(double, double, double, double) - Method in class ome.util.math.geom2D.EllipseArea
Required by the Shape I/F.
contains(Point2D) - Method in class ome.util.math.geom2D.EllipseArea
Required by the Shape I/F.
contains(Rectangle2D) - Method in class ome.util.math.geom2D.EllipseArea
Required by the Shape I/F.
contains(double, double) - Method in class ome.util.math.geom2D.RectangleArea
Required by the Shape I/F.
contains(double, double, double, double) - Method in class ome.util.math.geom2D.RectangleArea
Required by the Shape I/F.
contains(Point2D) - Method in class ome.util.math.geom2D.RectangleArea
Required by the Shape I/F.
contains(Rectangle2D) - Method in class ome.util.math.geom2D.RectangleArea
Required by the Shape I/F.
contains(String) - Method in class pojos.WorkflowData
Returns true if the keyword exist in the workflow, false otherwise.
containsKey(Object) - Method in class ome.services.query.Definitions
 
contentLength - Variable in class ome.formats.importer.ImportEvent.FILE_UPLOAD_EVENT
 
context - Variable in class ome.logic.AdminImpl
 
context - Variable in class ome.services.blitz.fire.SessionManagerI
 
context - Variable in class ome.services.blitz.repo.PublicRepositoryI
 
context - Variable in class ome.services.fulltext.FileParser
 
context - Variable in class ome.services.fulltext.FullTextIndexer
 
context - Variable in class ome.services.messages.ContextMessage
 
context - Variable in class ome.services.sessions.SessionManagerImpl
 
context - Variable in class ome.services.util.Executor.Impl
 
context - Variable in class omero.cmd.SessionI
 
contextAt(int) - Method in class ome.model.internal.Details
 
ContextFilter - Class in ome.util
modified (hierarchical) visitor pattern.
ContextFilter() - Constructor for class ome.util.ContextFilter
 
ContextMessage - Class in ome.services.messages
 
ContextMessage(Object, Map<String, String>) - Constructor for class ome.services.messages.ContextMessage
 
ContextMessage.Pop - Class in ome.services.messages
Published when an internal service is finished with the context previously signaled through publishing a ContextMessage.Push.
ContextMessage.Pop(Object, Map<String, String>) - Constructor for class ome.services.messages.ContextMessage.Pop
 
ContextMessage.Push - Class in ome.services.messages
Published when an internal service would like to modify the current EventContext.
ContextMessage.Push(Object, Map<String, String>) - Constructor for class ome.services.messages.ContextMessage.Push
 
contexts - Variable in class ome.model.internal.Details
 
contexts - Variable in class omero.cmd.admin.CurrentSessionsRequestI
 
contOnError - Variable in class ome.formats.importer.ImportConfig
 
contrastMethod - Variable in class ome.model.core.LogicalChannel
 
CONTRASTMETHOD - Static variable in class ome.model.core.LogicalChannel
 
ContrastMethod - Class in ome.model.enums
 
ContrastMethod() - Constructor for class ome.model.enums.ContrastMethod
 
ContrastMethod(Long) - Constructor for class ome.model.enums.ContrastMethod
 
ContrastMethod(Long, boolean) - Constructor for class ome.model.enums.ContrastMethod
Main constructor.
ContrastMethod(String) - Constructor for class ome.model.enums.ContrastMethod
 
ContrastMethod.Details - Class in ome.model.enums
 
ContrastMethod.Details() - Constructor for class ome.model.enums.ContrastMethod.Details
 
ContrastMethod.Details(Object[]) - Constructor for class ome.model.enums.ContrastMethod.Details
 
ContrastStretchingContext - Class in ome.model.display
 
ContrastStretchingContext() - Constructor for class ome.model.display.ContrastStretchingContext
 
ContrastStretchingContext(Long) - Constructor for class ome.model.display.ContrastStretchingContext
 
ContrastStretchingContext(Long, boolean) - Constructor for class ome.model.display.ContrastStretchingContext
Main constructor.
ContrastStretchingContext(Integer, Integer, Integer, Integer) - Constructor for class ome.model.display.ContrastStretchingContext
 
ContrastStretchingContext - Class in omeis.providers.re.codomain
Two points pStart and pEnd define the context of this transformation.
ContrastStretchingContext() - Constructor for class omeis.providers.re.codomain.ContrastStretchingContext
 
control - Variable in class omero.cmd.SessionI
 
Conversion - Class in ome.model.units
Base-functor like object which can be used for preparing complex equations for converting from one unit to another.
Conversion(Conversion...) - Constructor for class ome.model.units.Conversion
Primary constructor for a Conversion object.
Conversion.Add - Class in ome.model.units
Sums all Conversion instances via BigDecimal.add(BigDecimal).
Conversion.Add(Conversion[]) - Constructor for class ome.model.units.Conversion.Add
 
Conversion.Int - Class in ome.model.units
Simply is a representation of a possibly large integer.
Conversion.Int(long) - Constructor for class ome.model.units.Conversion.Int
 
Conversion.Int(String) - Constructor for class ome.model.units.Conversion.Int
 
Conversion.Mul - Class in ome.model.units
Multiplies all Conversion instances via BigDecimal.multiply(BigDecimal).
Conversion.Mul(Conversion[]) - Constructor for class ome.model.units.Conversion.Mul
 
Conversion.Pow - Class in ome.model.units
Exponentiates two Conversion instances via BigDecimal#pow(BigDecimal).
Conversion.Pow(long, int) - Constructor for class ome.model.units.Conversion.Pow
 
Conversion.Rat - Class in ome.model.units
Conversion.Rat(long, long) - Constructor for class ome.model.units.Conversion.Rat
 
Conversion.Rat(Conversion...) - Constructor for class ome.model.units.Conversion.Rat
 
Conversion.Sym - Class in ome.model.units
Simply represents the variable of the source unit so that Conversion.Sym.convert(double) just returns the value passed in.
Conversion.Sym(char) - Constructor for class ome.model.units.Conversion.Sym
 
Conversion.Sym(String) - Constructor for class ome.model.units.Conversion.Sym
 
conversions - Variable in class ome.model.units.Conversion
Conversions, if any, which are passed into the constructor of this instance.
convert(double) - Method in class ome.model.units.Conversion.Add
 
convert(double) - Method in class ome.model.units.Conversion
Primary operator for Conversion instances.
convert(double) - Method in class ome.model.units.Conversion.Int
Returns a BigDecimal representation of this int.
convert(double) - Method in class ome.model.units.Conversion.Mul
 
convert(double) - Method in class ome.model.units.Conversion.Pow
 
convert(double) - Method in class ome.model.units.Conversion.Rat
 
convert(double) - Method in class ome.model.units.Conversion.Sym
 
convert(ElectricPotential) - Static method in class omero.model.ElectricPotentialI
FIXME: this should likely take a default so that locations which don't want an exception can have log.warn("Using new PositiveFloat(1.0)!"
convert(Frequency) - Static method in class omero.model.FrequencyI
FIXME: this should likely take a default so that locations which don't want an exception can have log.warn("Using new PositiveFloat(1.0)!"
convert(Length) - Static method in class omero.model.LengthI
FIXME: this should likely take a default so that locations which don't want an exception can have log.warn("Using new PositiveFloat(1.0)!"
convert(Power) - Static method in class omero.model.PowerI
FIXME: this should likely take a default so that locations which don't want an exception can have log.warn("Using new PositiveFloat(1.0)!"
convert(Pressure) - Static method in class omero.model.PressureI
FIXME: this should likely take a default so that locations which don't want an exception can have log.warn("Using new PositiveFloat(1.0)!"
convert(Temperature) - Static method in class omero.model.TemperatureI
FIXME: this should likely take a default so that locations which don't want an exception can have log.warn("Using new PositiveFloat(1.0)!"
convert(Time) - Static method in class omero.model.TimeI
FIXME: this should likely take a default so that locations which don't want an exception can have log.warn("Using new PositiveFloat(1.0)!"
convert(IceMapper) - Method in interface omero.rtypes.Conversion
Convert the "val" field on the given RType instance to an ome.model.* representation.
convert(EventContext) - Static method in class omero.util.IceMapper
 
convert(RGBBuffer) - Static method in class omero.util.IceMapper
 
convert(PlaneDef) - Static method in class omero.util.IceMapper
Converts the passed Ice Object and returns the converted object.
convert(Principal) - Static method in class omero.util.IceMapper
 
convert(Roles) - Static method in class omero.util.IceMapper
 
convert(Date) - Static method in class omero.util.IceMapper
 
convert(RTime) - Static method in class omero.util.IceMapper
 
convert(Parameters) - Method in class omero.util.IceMapper
 
convert(String, Object) - Method in class omero.util.IceMapper
 
convert(Options) - Static method in class omero.util.IceMapper
 
convert(Filter) - Static method in class omero.util.IceMapper
 
convert(Permissions) - Static method in class omero.util.IceMapper
 
convert(Permissions) - Static method in class omero.util.IceMapper
 
convertElectricPotential(ElectricPotential) - Static method in class ome.formats.model.UnitsFactory
Convert a Bio-Formats ElectricPotential to an OMERO ElectricPotential.
convertElectricPotential(ElectricPotential) - Static method in class ome.formats.model.UnitsFactory
 
convertElectricPotential(ElectricPotential, Unit<ElectricPotential>) - Static method in class ome.formats.model.UnitsFactory
 
convertElectricPotential(ElectricPotential) - Static method in class ome.model.units.ElectricPotential
FIXME: this should likely take a default so that locations which don't want an exception can have log.warn("Using new PositiveFloat(1.0)!"
convertElectricPotential(ElectricPotential, Unit<ElectricPotential>) - Static method in class ome.model.units.ElectricPotential
 
convertElectricPotential(ElectricPotential, String) - Static method in class ome.model.units.ElectricPotential
 
convertElectricPotentialXML(ElectricPotential, String) - Static method in class ome.formats.model.UnitsFactory
 
convertFrequency(Frequency) - Static method in class ome.formats.model.UnitsFactory
Convert a Bio-Formats Frequency to an OMERO Frequency.
convertFrequency(Frequency) - Static method in class ome.formats.model.UnitsFactory
 
convertFrequency(Frequency, Unit<Frequency>) - Static method in class ome.formats.model.UnitsFactory
 
convertFrequency(Frequency) - Static method in class ome.model.units.Frequency
FIXME: this should likely take a default so that locations which don't want an exception can have log.warn("Using new PositiveFloat(1.0)!"
convertFrequency(Frequency, Unit<Frequency>) - Static method in class ome.model.units.Frequency
 
convertFrequency(Frequency, String) - Static method in class ome.model.units.Frequency
 
convertFrequencyXML(Frequency, String) - Static method in class ome.formats.model.UnitsFactory
 
convertLength(Length) - Static method in class ome.formats.model.UnitsFactory
Convert a Bio-Formats Length to an OMERO Length.
convertLength(Length) - Static method in class ome.formats.model.UnitsFactory
 
convertLength(Length, Unit<Length>) - Static method in class ome.formats.model.UnitsFactory
 
convertLength(Length) - Static method in class ome.model.units.Length
FIXME: this should likely take a default so that locations which don't want an exception can have log.warn("Using new PositiveFloat(1.0)!"
convertLength(Length, Unit<Length>) - Static method in class ome.model.units.Length
 
convertLength(Length, String) - Static method in class ome.model.units.Length
 
convertLengthXML(Length, String) - Static method in class ome.formats.model.UnitsFactory
 
convertMapPairs(List<MapPair>) - Static method in class omero.util.IceMapper
 
convertNamedValueList(List<NamedValue>) - Static method in class omero.util.IceMapper
 
convertPower(Power) - Static method in class ome.formats.model.UnitsFactory
Convert a Bio-Formats Power to an OMERO Power.
convertPower(Power) - Static method in class ome.formats.model.UnitsFactory
 
convertPower(Power, Unit<Power>) - Static method in class ome.formats.model.UnitsFactory
 
convertPower(Power) - Static method in class ome.model.units.Power
FIXME: this should likely take a default so that locations which don't want an exception can have log.warn("Using new PositiveFloat(1.0)!"
convertPower(Power, Unit<Power>) - Static method in class ome.model.units.Power
 
convertPower(Power, String) - Static method in class ome.model.units.Power
 
convertPowerXML(Power, String) - Static method in class ome.formats.model.UnitsFactory
 
convertPressure(Pressure) - Static method in class ome.formats.model.UnitsFactory
Convert a Bio-Formats Pressure to an OMERO Pressure.
convertPressure(Pressure) - Static method in class ome.formats.model.UnitsFactory
 
convertPressure(Pressure, Unit<Pressure>) - Static method in class ome.formats.model.UnitsFactory
 
convertPressure(Pressure) - Static method in class ome.model.units.Pressure
FIXME: this should likely take a default so that locations which don't want an exception can have log.warn("Using new PositiveFloat(1.0)!"
convertPressure(Pressure, Unit<Pressure>) - Static method in class ome.model.units.Pressure
 
convertPressure(Pressure, String) - Static method in class ome.model.units.Pressure
 
convertPressureXML(Pressure, String) - Static method in class ome.formats.model.UnitsFactory
 
convertStringStringMap(Map<String, String>) - Static method in class omero.util.IceMapper
Convert a String→String map's values to RStrings.
convertTemperature(Temperature) - Static method in class ome.formats.model.UnitsFactory
Convert a Bio-Formats Temperature to an OMERO Temperature.
convertTemperature(Temperature) - Static method in class ome.formats.model.UnitsFactory
 
convertTemperature(Temperature, Unit<Temperature>) - Static method in class ome.formats.model.UnitsFactory
 
convertTemperature(Temperature) - Static method in class ome.model.units.Temperature
FIXME: this should likely take a default so that locations which don't want an exception can have log.warn("Using new PositiveFloat(1.0)!"
convertTemperature(Temperature, Unit<Temperature>) - Static method in class ome.model.units.Temperature
 
convertTemperature(Temperature, String) - Static method in class ome.model.units.Temperature
 
convertTemperatureXML(Temperature, String) - Static method in class ome.formats.model.UnitsFactory
 
convertTime(Time) - Static method in class ome.formats.model.UnitsFactory
Convert a Bio-Formats Time to an OMERO Time.
convertTime(Time) - Static method in class ome.formats.model.UnitsFactory
 
convertTime(Time, Unit<Time>) - Static method in class ome.formats.model.UnitsFactory
 
convertTime(Time) - Static method in class ome.model.units.Time
FIXME: this should likely take a default so that locations which don't want an exception can have log.warn("Using new PositiveFloat(1.0)!"
convertTime(Time, Unit<Time>) - Static method in class ome.model.units.Time
 
convertTime(Time, String) - Static method in class ome.model.units.Time
 
convertTimeXML(Time, String) - Static method in class ome.formats.model.UnitsFactory
 
ConvertToBlitzExceptionMessage - Class in ome.services.blitz.util
Internal event which gives third party services a chance to map their exceptions to a blitz exception.
ConvertToBlitzExceptionMessage(Object, Throwable) - Constructor for class ome.services.blitz.util.ConvertToBlitzExceptionMessage
 
convertXml(MetadataRetrieve) - Method in class ome.services.blitz.impl.ExporterI
 
Copiable - Interface in ome.util.mem
Requires an implementing class to provide deep copies of its instances.
CopiableArray - Class in ome.util.mem
This abstract class provides an implementation of the Copiable interface.
CopiableArray(int) - Constructor for class ome.util.mem.CopiableArray
Creates a new instance.
copy() - Method in class ome.model.internal.Details
 
copy(Details) - Method in class ome.model.internal.Details
Method which takes all field values from the given Details instance and copies them into the current instance.
copy(SearchValues) - Method in class ome.services.search.SearchValues
 
copy(Parameters) - Method in class ome.services.search.SearchValues
Copies all known values from Parameters
copy(Session) - Method in class ome.services.sessions.SessionManagerImpl
 
copy(EventContext) - Method in class ome.system.SimpleEventContext
Copies all values directly from the given instance into this instance.
copy(Map) - Static method in class ome.tools.hibernate.HibernateUtils
 
copy(Collection) - Static method in class ome.tools.hibernate.HibernateUtils
 
copy() - Method in interface ome.util.mem.Copiable
Makes a copy of this object.
copy(int, int) - Method in class ome.util.mem.CopiableArray
Copies the Copiable from the specified position from into the specified position to.
copy() - Method in class ome.util.mem.CopiableArray
Implements the method as specified by Copiable.
copy() - Method in class ome.util.mem.Handle
Returns a deep copy of this object.
copy(T) - Method in class ome.util.ShallowCopy
 
copy() - Method in class omeis.providers.re.codomain.CodomainMapContext
Returns a deep copy of this object.
copy() - Method in class omeis.providers.re.codomain.ContrastStretchingContext
Implemented as specified by superclass.
copy() - Method in class omeis.providers.re.codomain.IdentityMapContext
Implemented as specified by superclass.
copy() - Method in class omeis.providers.re.codomain.PlaneSlicingContext
Implemented as specified by superclass.
copy() - Method in class omeis.providers.re.codomain.ReverseIntensityContext
Implemented as specified by superclass.
copy() - Method in class omero.cmd.graphs.ChgrpI
Deprecated.
 
copy() - Method in class omero.cmd.graphs.ChmodI
Deprecated.
copy() - Method in class omero.cmd.graphs.ChownI
Deprecated.
 
copy() - Method in class omero.cmd.graphs.DeleteI
Deprecated.
 
copy() - Method in interface omero.cmd.graphs.IGraphModifyRequest
Deprecated.
Produce a clone of this object.
copy(Current) - Method in class omero.model.ElectricPotentialI
 
copy(Current) - Method in class omero.model.FrequencyI
 
copy(Current) - Method in class omero.model.LengthI
 
copy(Current) - Method in class omero.model.PowerI
 
copy(Current) - Method in class omero.model.PressureI
 
copy(Current) - Method in class omero.model.TemperatureI
 
copy(Current) - Method in class omero.model.TimeI
 
copyAndResizeImage(long, Integer, Integer, Integer, Integer, List<Integer>, String, boolean) - Method in interface ome.api.IPixels
Copies the metadata, and only the metadata linked to a Image object into a new Image object of equal or differing size across one or many of its three physical dimensions or temporal dimension.
copyAndResizeImage(long, Integer, Integer, Integer, Integer, List<Integer>, String, boolean) - Method in class ome.logic.PixelsImpl
 
copyAndResizeImage_async(AMD_IPixels_copyAndResizeImage, long, RInt, RInt, RInt, RInt, List<Integer>, String, boolean, Current) - Method in class ome.services.blitz.impl.PixelsI
 
copyAndResizePixels(long, Integer, Integer, Integer, Integer, List<Integer>, String, boolean) - Method in interface ome.api.IPixels
Copies the metadata, and only the metadata linked to a Pixels object into a new Pixels object of equal or differing size across one or many of its three physical dimensions or temporal dimension.
copyAndResizePixels(long, Integer, Integer, Integer, Integer, List<Integer>, String, boolean) - Method in class ome.logic.PixelsImpl
 
copyAndResizePixels_async(AMD_IPixels_copyAndResizePixels, long, RInt, RInt, RInt, RInt, List<Integer>, String, boolean, Current) - Method in class ome.services.blitz.impl.PixelsI
 
copyClassListToArray(List<Class>) - Static method in class ome.services.search.SearchValues
 
copyDetails(Details) - Static method in class ome.services.search.SearchValues
 
copyExtendedRestrictions() - Method in class ome.model.internal.Permissions
Produce a copy of restrictions for use elsewhere.
copyFieldsTo(Chgrp2) - Method in class omero.cmd.graphs.Chgrp2I
 
copyFieldsTo(Chmod2) - Method in class omero.cmd.graphs.Chmod2I
 
copyFieldsTo(Chown2) - Method in class omero.cmd.graphs.Chown2I
 
copyFieldsTo(Delete2) - Method in class omero.cmd.graphs.Delete2I
 
copyFieldsTo(X) - Method in interface omero.cmd.graphs.WrappableRequest
Copy the fields of this request to that of the given request.
CopyFileTransfer - Class in ome.formats.importer.transfers
Local-only file transfer mechanism which makes use of the plaform copy command.
CopyFileTransfer() - Constructor for class ome.formats.importer.transfers.CopyFileTransfer
 
copyGroup(ExperimenterGroup) - Method in class ome.security.auth.SimpleRoleProvider
 
copyList(List<T>) - Static method in class ome.services.search.SearchValues
 
CopyMoveFileTransfer - Class in ome.formats.importer.transfers
Local-only file transfer mechanism which makes use of the local copy command followed by the deletion of the original source file.
CopyMoveFileTransfer() - Constructor for class ome.formats.importer.transfers.CopyMoveFileTransfer
 
copyObject(Filterable, ModelMapper) - Method in interface ome.model.ModelBased
 
copyObject(Filterable, ModelMapper) - Method in class omero.model.DetailsI
 
copyObject(Filterable, ModelMapper) - Method in class omero.model.ElectricPotentialI
 
copyObject(Filterable, ModelMapper) - Method in class omero.model.FrequencyI
 
copyObject(Filterable, ModelMapper) - Method in class omero.model.LengthI
 
copyObject(Filterable, ModelMapper) - Method in class omero.model.PermissionsI
 
copyObject(Filterable, ModelMapper) - Method in class omero.model.PowerI
 
copyObject(Filterable, ModelMapper) - Method in class omero.model.PressureI
 
copyObject(Filterable, ModelMapper) - Method in class omero.model.TemperatureI
 
copyObject(Filterable, ModelMapper) - Method in class omero.model.TimeI
 
copyOfValues() - Method in class ome.services.search.SearchAction
 
copyRestrictions() - Method in class ome.model.internal.Permissions
Produce a copy of restrictions for use elsewhere.
copyRestrictions(boolean[], String[]) - Method in class ome.model.internal.Permissions
Safely copy the source array.
copyRestrictions(int, Set<String>) - Method in class ome.model.internal.Permissions
Copy restrictions based on the integer returned by BasicACLVoter.
copyTimestamp(Timestamp) - Static method in class ome.services.search.SearchValues
 
copyToken(IObject, IObject) - Method in class ome.security.basic.BasicSecuritySystem
See {@link TokenHolder#copyToken(IObject, IObject)
copyToken(IObject, IObject) - Method in class ome.security.basic.TokenHolder
copy a token from one IObject to another.
copyUser(Experimenter) - Method in class ome.security.auth.SimpleRoleProvider
 
copyValues(EntityPersister, Object, Object, SessionImplementor, Map) - Method in class ome.security.basic.MergeEventListener
 
copyValues(EntityPersister, Object, Object, SessionImplementor, Map, ForeignKeyDirection) - Method in class ome.security.basic.MergeEventListener
 
copyWhereUnset(Details, Details) - Method in class ome.model.internal.Details
For any field of this which is null (and is NOT null on mask -- assuming mask is not null), copy the same value from copyFrom into this object.
correction - Variable in class ome.model.acquisition.Objective
 
CORRECTION - Static variable in class ome.model.acquisition.Objective
 
Correction - Class in ome.model.enums
 
Correction() - Constructor for class ome.model.enums.Correction
 
Correction(Long) - Constructor for class ome.model.enums.Correction
 
Correction(Long, boolean) - Constructor for class ome.model.enums.Correction
Main constructor.
Correction(String) - Constructor for class ome.model.enums.Correction
 
Correction.Details - Class in ome.model.enums
 
Correction.Details() - Constructor for class ome.model.enums.Correction.Details
 
Correction.Details(Object[]) - Constructor for class ome.model.enums.Correction.Details
 
correctionCollar - Variable in class ome.model.acquisition.ObjectiveSettings
 
CORRECTIONCOLLAR - Static variable in class ome.model.acquisition.ObjectiveSettings
 
count - Variable in class ome.io.nio.SimpleBackOff
 
count() - Method in class ome.services.messages.DeleteLogMessage
 
count() - Method in interface ome.services.sessions.SessionContext
Returns the SessionContext.Count instance held by this context.
count() - Method in class ome.services.sessions.SessionContextImpl
 
count - Variable in class ome.services.sessions.stats.LongCounter
 
countAnnotationsUsedNotOwned(Class, long) - Method in interface ome.api.IMetadata
Counts the number of annotation of a given type used by the specified user but not owned by the user.
countAnnotationsUsedNotOwned(Class, long) - Method in class ome.logic.MetadataImpl
Implemented as specified by the IMetadata I/F
countAnnotationsUsedNotOwned_async(AMD_IMetadata_countAnnotationsUsedNotOwned, String, long, Current) - Method in class ome.services.blitz.impl.MetadataI
 
countByPeriod_async(AMD_ITimeline_countByPeriod, List<String>, RTime, RTime, Parameters, Current) - Method in class ome.services.blitz.impl.TimelineI
 
countCachedContainers(Class<? extends IObject>, int...) - Method in interface ome.formats.model.IObjectContainerStore
Counts the number of containers the MetadataStore has of a given class and at a given index of the hierarchy if specified.
countCachedContainers(Class<? extends IObject>, int...) - Method in class ome.formats.OMEROMetadataStoreClient
 
countCachedReferences(Class<? extends IObject>, Class<? extends IObject>) - Method in interface ome.formats.model.IObjectContainerStore
Counts the number of references the MetadataStore has between objects of two classes.
countCachedReferences(Class<? extends IObject>, Class<? extends IObject>) - Method in class ome.formats.OMEROMetadataStoreClient
 
CountCollectionPersister - Class in ome.util
CollectionPersister which knows how to handle the count views generated by dsl/resources/ome/dsl/views.dm.
CountCollectionPersister(Collection, CollectionRegionAccessStrategy, Configuration, SessionFactoryImplementor) - Constructor for class ome.util.CountCollectionPersister
 
Counter - Interface in ome.system.metrics
Thin wrapper around Counter
counter(Object, String) - Method in class ome.system.metrics.DefaultMetrics
 
counter(Object, String) - Method in interface ome.system.metrics.Metrics
 
counter(Object, String) - Method in class ome.system.metrics.NullMetrics
 
CounterFactory - Class in ome.services.sessions.stats
Factory for creating counter objects.
CounterFactory() - Constructor for class ome.services.sessions.stats.CounterFactory
 
countFormat(String) - Method in class ome.util.actions.PostgresSqlAction
 
countFormat(String) - Method in interface ome.util.SqlAction
 
countInDb() - Method in class ome.services.scripts.ScriptRepoHelper
 
countInDb(SqlAction) - Method in class ome.services.scripts.ScriptRepoHelper
 
countLocks(Session, Long, String[][], String) - Method in interface ome.tools.hibernate.ExtendedMetadata
Takes the lock checks returned by ExtendedMetadata.getLockChecks(Class) and performs the actual check returning a map from class to total number of locks.
countLocks(Session, Long, String[][], String) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
 
countOnDisk() - Method in class ome.services.scripts.ScriptRepoHelper
Returns the number of files which match ScriptRepoHelper.scriptFilter in ScriptRepoHelper.dir.
countSpecifiedAnnotations(Class, Set<String>, Set<String>, Parameters) - Method in interface ome.api.IMetadata
Counts the number of annotation of a given type.
countSpecifiedAnnotations(Class, Set<String>, Set<String>, Parameters) - Method in class ome.logic.MetadataImpl
Implemented as specified by the IMetadata I/F
countSpecifiedAnnotations_async(AMD_IMetadata_countSpecifiedAnnotations, String, List<String>, List<String>, Parameters, Current) - Method in class ome.services.blitz.impl.MetadataI
 
countTiles(Pixels) - Method in class ome.io.nio.SimpleBackOff
 
cpf - Variable in class ome.logic.AdminImpl
 
cpf - Variable in class ome.services.blitz.impl.ScriptI
 
CRC32ChecksumProviderImpl - Class in ome.util.checksum
An implementation of the ChecksumProvider interface using CRC32 as the message digest algorithm.
CRC32ChecksumProviderImpl() - Constructor for class ome.util.checksum.CRC32ChecksumProviderImpl
 
create() - Static method in class ome.model.internal.Details
Call Details.create(Object[]) with null.
create(Object[]) - Static method in class ome.model.internal.Details
Factory method which returns a Details implementation for passing in API calls, but cannot be stored within an IObject instance.
create(String, SessionControlPrx, Current) - Method in class ome.services.blitz.fire.SessionManagerI
 
create(int, List<GraphStep>, GraphSpec, GraphEntry, long[]) - Method in class ome.services.chgrp.ChgrpStepFactory
Deprecated.
 
create(int, List<GraphStep>, GraphSpec, GraphEntry, long[]) - Method in class ome.services.chown.ChownStepFactory
Deprecated.
 
create(int, List<GraphStep>, GraphSpec, GraphEntry, long[]) - Method in class ome.services.delete.DeleteStepFactory
Deprecated.
 
create(int, List<GraphStep>, GraphSpec, GraphEntry, long[]) - Method in class ome.services.export.ExporterStepFactory
Deprecated.
 
create(int, List<GraphStep>, GraphSpec, GraphEntry, long[]) - Method in interface ome.services.graphs.GraphStepFactory
Deprecated.
 
create(String) - Method in class omero.util.ObjectFactoryRegistry.ObjectFactory
 
create(File) - Method in class omero.util.TempFileManager
If the given directory doesn't exist, creates it and returns true.
create_path() - Static method in class omero.util.TempFileManager
Calls TempFileManager.createPath(String, String, boolean) on TempFileManager.manager with defaults of "omero", ".tmp", and false.
create_path(String) - Static method in class omero.util.TempFileManager
create_path(String, String) - Static method in class omero.util.TempFileManager
create_path(String, String, boolean) - Static method in class omero.util.TempFileManager
createAdapter() - Method in class ome.services.blitz.util.BlitzConfiguration
Creates an adapter with the name "BlitzAdapter", which must be properly configured via --Ice.Config or ICE_CONFIG or similar.
createAndPrepareMissingRenderingSettings(Set<Long>) - Method in class ome.services.ThumbnailCtx
Resets a given set of Pixels rendering settings to the default effectively creating any which do not exist.
createAndRegisterManager(SessionManager, SecuritySystem, Executor) - Method in class ome.services.blitz.util.BlitzConfiguration
 
createAndRegisterVerifier(SessionManager, Executor) - Method in class ome.services.blitz.util.BlitzConfiguration
 
createBfPixelBuffer(String, int) - Method in class ome.io.nio.PixelsService
Helper method to properly log any exceptions raised by Bio-Formats.
createBfReader() - Method in class ome.io.nio.PixelsService
Create an IFormatReader with the appropriate ReaderWrapper instances and IFormatReader.setFlattenedResolutions(boolean) set to false.
createBufferedImage() - Method in class ome.services.SVGRasterizer
Returns the image that represents the SVG document.
createBufferedImage(int[], int, int) - Static method in class ome.util.ImageUtil
Creates a buffered image from a rendering engine RGB buffer without data copying.
createByName(String, Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
createCache(CacheEventListener...) - Method in class ome.services.sessions.state.CacheFactory
 
createCache(String, boolean, int) - Method in class ome.services.sessions.state.SessionCache
 
createCallback(ImportProcessPrx, HandlePrx, ImportContainer) - Method in class ome.formats.importer.ImportLibrary
 
createChildOption() - Method in class omero.cmd.graphs.GraphRequestFactory
 
createClient(boolean) - Method in class omero.client
Creates a possibly insecure client instance and calls client.joinSession(String) using the current session id.
createCommunicator() - Method in class ome.services.blitz.util.BlitzConfiguration
 
createCommunicator(String, String[]) - Method in class ome.services.blitz.util.BlitzConfiguration
 
createData() - Method in class omero.util.RPSTileLoop
 
createData() - Method in class omero.util.TileLoop
Subclasses must provide a fresh instance of TileData.
createDataObject(T, Parameters) - Method in interface ome.api.IContainer
Creates the specified data object.
createDataObject(IObject, Parameters) - Method in class ome.logic.PojosImpl
Implemented as specified by the IContainer I/F
createDataObject_async(AMD_IContainer_createDataObject, IObject, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI
 
createDataObjects(IObject[], Parameters) - Method in interface ome.api.IContainer
convenience method to save network calls.
createDataObjects(IObject[], Parameters) - Method in class ome.logic.PojosImpl
Implemented as specified by the IContainer I/F
createDataObjects_async(AMD_IContainer_createDataObjects, List<IObject>, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI
 
createDetails() - Method in class ome.security.basic.CurrentDetails
Creates a Details object for the current security context.
createDirectories() - Method in class ome.services.util.ServerDirectoryCheck
 
createdOrModified(Class, Criteria) - Method in class ome.services.search.SearchAction
 
createdOrModified(Class, QueryBuilder, String) - Method in class ome.services.search.SearchAction
 
createdStart - Variable in class ome.services.search.SearchValues
 
createdStop - Variable in class ome.services.search.SearchValues
 
createEnumeration(T) - Method in interface ome.api.ITypes
 
createEnumeration(T) - Method in class ome.logic.TypesImpl
 
createEnumeration_async(AMD_ITypes_createEnumeration, IObject, Current) - Method in class ome.services.blitz.impl.TypesI
 
createException(MethodInvocation) - Method in class ome.tools.hibernate.EventMethodInterceptor.DisableAction
 
createExclusion(String) - Static method in class ome.formats.importer.exclusions.AbstractFileExclusion
Factory method for instantiating FileTransfer objects from a string.
createExperimenter(Experimenter, ExperimenterGroup, ExperimenterGroup...) - Method in interface ome.api.IAdmin
create and return a new user in the given groups.
createExperimenter(Experimenter, ExperimenterGroup, ExperimenterGroup...) - Method in class ome.logic.AdminImpl
 
createExperimenter(Experimenter, ExperimenterGroup, ExperimenterGroup...) - Method in interface ome.security.auth.RoleProvider
 
createExperimenter(Experimenter, ExperimenterGroup, ExperimenterGroup...) - Method in class ome.security.auth.SimpleRoleProvider
 
createExperimenter_async(AMD_IAdmin_createExperimenter, Experimenter, ExperimenterGroup, List<ExperimenterGroup>, Current) - Method in class ome.services.blitz.impl.AdminI
 
createExperimenterWithPassword(Experimenter, String, ExperimenterGroup, ExperimenterGroup...) - Method in interface ome.api.IAdmin
create and return a new user in the given groups with password.
createExperimenterWithPassword(Experimenter, String, ExperimenterGroup, ExperimenterGroup...) - Method in class ome.logic.AdminImpl
 
createExperimenterWithPassword_async(AMD_IAdmin_createExperimenterWithPassword, Experimenter, RString, ExperimenterGroup, List<ExperimenterGroup>, Current) - Method in class ome.services.blitz.impl.AdminI
 
createExporter(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
createFactories(Communicator) - Method in class ome.services.blitz.impl.commands.RequestObjectFactoryRegistry
 
createFactories(Communicator) - Method in class ome.services.blitz.repo.RequestObjectFactoryRegistry
 
createFactories(Communicator) - Method in class ome.services.roi.RoiTypes.RoiTypesObjectFactoryRegistry
 
createFactories(Communicator) - Method in class omero.cmd.admin.CurrentSessionsRequestI.Factory
 
createFactories(Communicator) - Method in class omero.cmd.admin.UpdateSessionTimeoutRequestI.Factory
 
createFactories(Communicator) - Method in class omero.cmd.RequestObjectFactoryRegistry
 
createFactories(Communicator) - Method in class omero.rtypes.RTypeObjectFactoryRegistry
 
createFactories(Communicator) - Method in class omero.util.ObjectFactoryRegistry
 
createFromRequest(SessionManager.CreationRequest) - Method in interface ome.services.sessions.SessionManager
 
createFromRequest(SessionManager.CreationRequest) - Method in class ome.services.sessions.SessionManagerImpl
 
createFullTextThread(EventLogLoader) - Static method in class ome.services.fulltext.Main
 
createFullTextThread(EventLogLoader, boolean) - Static method in class ome.services.fulltext.Main
 
createGroup(ExperimenterGroup) - Method in interface ome.api.IAdmin
create and return a new group.
createGroup(ExperimenterGroup) - Method in class ome.logic.AdminImpl
 
createGroup(ExperimenterGroup) - Method in interface ome.security.auth.RoleProvider
 
createGroup(String, Permissions, boolean) - Method in interface ome.security.auth.RoleProvider
 
createGroup(String, Permissions, boolean, boolean) - Method in interface ome.security.auth.RoleProvider
 
createGroup(String, Permissions, boolean) - Method in class ome.security.auth.SimpleRoleProvider
 
createGroup(String, Permissions, boolean, boolean) - Method in class ome.security.auth.SimpleRoleProvider
 
createGroup(ExperimenterGroup) - Method in class ome.security.auth.SimpleRoleProvider
 
createGroup_async(AMD_IAdmin_createGroup, ExperimenterGroup, Current) - Method in class ome.services.blitz.impl.AdminI
 
createHandle(Request) - Method in class omero.cmd.HandleFactory
 
createIdsTempTable(Collection<Long>) - Method in interface ome.util.SqlAction
Creates a temporary table filled with the given ids and returns its name.
createIdsTempTable(Collection<Long>) - Method in class ome.util.SqlAction.Impl
 
createImage(int, int, int, int, List<Integer>, PixelsType, String, String) - Method in interface ome.api.IPixels
Creates the metadata, and only the metadata linked to an Image object.
createImage(int, int, int, int, List<Integer>, PixelsType, String, String) - Method in class ome.logic.PixelsImpl
 
createImage(int, int) - Method in class ome.services.SVGRasterizer.Rasterizer
 
createImage_async(AMD_IPixels_createImage, int, int, int, int, List<Integer>, PixelsType, String, String, Current) - Method in class ome.services.blitz.impl.PixelsI
 
createImport(ImportContainer) - Method in class ome.formats.importer.ImportLibrary
Provide initial configuration to the server in order to create the ImportProcessPrx which will manage state server-side.
createImportProcess(Fileset, ImportLocation, ImportSettings, Current) - Method in class ome.services.blitz.repo.ManagedRepositoryI
Creating the process will register itself in an appropriate container (i.e. a SessionI or similar) for the current user and therefore this instance no longer needs to worry about the maintenance of the object.
createInsertTrigger(String, String, String) - Method in interface ome.util.SqlAction
Creates an insert trigger of the given name, for the given table, with the given procedure.
createInsertTrigger(String, String, String) - Method in class ome.util.SqlAction.Impl
 
createInstance() - Method in class ome.security.basic.EventListenersFactoryBean
First, adds all default listeners.
createInstance() - Method in class ome.services.delete.Deletion.Builder
Deprecated.
 
createJob(ServiceFactory) - Method in class ome.services.scripts.ScriptFinder
Returns a fresh (unsaved) ScriptJob which can be passed to acquireProcessor for background processing.
createJobHandle(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
createJobHandle() - Method in class ome.system.ServiceFactory
create a new JobHandle proxy.
createJPEG(OutputStream) - Method in class ome.services.SVGRasterizer
Returns the image that represents the SVG document as a JPEG.
createMinMaxBfPixelBuffer(String, int, IMinMaxStore) - Method in class ome.io.nio.PixelsService
Helper method to properly log any exceptions raised by Bio-Formats and add a min/max calculator wrapper to the reader stack.
createNewRenderingDef(Pixels) - Method in interface ome.api.IRenderingSettings
Creates a new rendering definition object along with its sub-objects.
createNewRenderingDef(Pixels) - Method in class ome.logic.RenderingSettingsImpl
Implemented as specified by the IRenderingSettings I/F
createNewRenderingDef_async(AMD_IRenderingSettings_createNewRenderingDef, Pixels, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
 
createOrFixUserDir(String, List<CheckedPath>, Session, ServiceFactory, SqlAction) - Method in interface ome.services.blitz.repo.RepositoryDao
Checks that the given CheckedPath objects exist (via RepositoryDao.findRepoFile(String, CheckedPath, String, Ice.Current)) and are in the "user" group.
createOrFixUserDir(String, List<CheckedPath>, Session, ServiceFactory, SqlAction) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
 
createOriginalFile(ServiceFactory, SqlAction, String, List<CheckedPath>, ChecksumAlgorithm, String) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
Primary location for creating original files from a CheckedPath instance.
createPath(String, String, boolean) - Method in class omero.util.TempFileManager
Uses File.createTempFile(String, String, File) to create temporary files and folders under TempFileManager.dir.
createPixelBuffer(Pixels) - Method in class ome.io.nio.PixelsService
Creates a PixelBuffer for a given pixels set.
createPlane(PlaneDef, int, Pixels, PixelBuffer) - Static method in class omeis.providers.re.data.PlaneFactory
Factory method to fetch plane data and create an object to access it.
createPrincipal() - Method in class ome.system.SessionInitializer
 
createProcessBuilder(File, File) - Method in class ome.formats.importer.transfers.AbstractExecFileTransfer
Creates a ProcessBuilder instance ready to have ProcessBuilder.start() called on it.
createProcessBuilder(File, File) - Method in class ome.formats.importer.transfers.CopyFileTransfer
Executes "cp file location" (Unix) or "cp file location" (Windows) and fails on non-0 return codes.
createProcessBuilder(File, File) - Method in class ome.formats.importer.transfers.HardlinkFileTransfer
Executes "ln file location" (Unix) or "mklink /H location file" (Windows) and fails on non-0 return codes.
createProcessBuilder(File, File) - Method in class ome.formats.importer.transfers.SymlinkFileTransfer
Executes "ln -s file location" (Unix) or "mklink location file" (Windows) and fails on non-0 return codes.
createPyramidPixelBuffer(Pixels, String, boolean) - Method in class ome.io.nio.PixelsService
Helper method to properly log any exceptions raised by Bio-Formats.
createQueryBuilder(String[], GraphEntry) - Method in class ome.services.graphs.BaseGraphSpec
Deprecated.
 
createRawFileStore(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
createRawFileStore(OriginalFile, Current) - Method in class ome.services.blitz.repo.AbstractRepositoryI
 
createRawFileStore() - Method in class ome.system.ServiceFactory
create a new RawFileStore proxy.
createRawPixelsStore(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
createRawPixelsStore(OriginalFile, Current) - Method in class ome.services.blitz.repo.AbstractRepositoryI
 
createRawPixelsStore() - Method in class ome.system.ServiceFactory
create a new RawPixelsStore proxy.
createRenderingEngine(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
createRenderingEngine(OriginalFile, Current) - Method in class ome.services.blitz.repo.AbstractRepositoryI
 
createRenderingEngine() - Method in class ome.system.ServiceFactory
create a new RenderingEngine proxy.
createRepoRFS(CheckedPath, String, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
Create, initialize, and register an RepoRawFileStoreI with the proper setting (read or write).
createRomioPixelBuffer(String, Pixels, boolean) - Method in class ome.io.nio.PixelsService
Helper method to properlty create a RomioPixelBuffer.
createRoot() - Method in class ome.formats.OMEROMetadataStore
 
createRoot() - Method in class ome.formats.OMEROMetadataStoreClient
 
createRoot_async(AMD_MetadataStore_createRoot, Current) - Method in class ome.services.blitz.impl.MetadataStoreI
 
createSafeInputStream(Communicator, byte[]) - Static method in class ome.services.util.IceUtil
Creates an InputStream with the appropriate encoding.
createSafeOutputStream(Communicator) - Static method in class ome.services.util.IceUtil
Creates an OutputStream with the appropriate encoding.
createSavepoint(String) - Method in class ome.util.actions.PostgresSqlAction
 
createSavepoint(String) - Method in interface ome.util.SqlAction
 
createSearchService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
createSearchService() - Method in class ome.system.ServiceFactory
create a new Search proxy.
createServantDelegate(String) - Method in class omero.cmd.SessionI
Creates a proxy according to the ServantDefinition for the given name.
createSession(Principal, String) - Method in interface ome.api.ISession
Creates a new session and returns it to the user.
createSession(Principal, String) - Method in class ome.services.sessions.SessionBean
 
createSession() - Method in class omero.client
createSession(String, String) - Method in class omero.client
Performs the actual logic of logging in, which is done via the #getRouter().
createSession_async(AMD_ISession_createSession, Principal, String, Current) - Method in class ome.services.blitz.impl.SessionI
 
createSessionContext(List<?>, SessionContext) - Method in class ome.services.sessions.SessionManagerImpl
Takes a snapshot as from #executeSessionContextLookup(ServiceFactory, Principal) and turns it into a SessionContext instance.
CreateSessionMessage - Class in ome.services.messages
Published after a successful session creation.
CreateSessionMessage(Object, String) - Constructor for class ome.services.messages.CreateSessionMessage
 
createSessionWithTimeout(Principal, long) - Method in interface ome.api.ISession
Allows an admin to create a Session for the give Principal
createSessionWithTimeout(Principal, long) - Method in class ome.services.sessions.SessionBean
 
createSessionWithTimeout_async(AMD_ISession_createSessionWithTimeout, Principal, long, Current) - Method in class ome.services.blitz.impl.SessionI
 
createSessionWithTimeouts(Principal, long, long) - Method in interface ome.api.ISession
Allows an admin to create a Session for the give Principal
createSessionWithTimeouts(Principal, long, long) - Method in class ome.services.sessions.SessionBean
 
createSessionWithTimeouts_async(AMD_ISession_createSessionWithTimeouts, Principal, long, long, Current) - Method in class ome.services.blitz.impl.SessionI
 
createShare(String, Timestamp, List<T>, List<Experimenter>, List<String>, boolean) - Method in interface ome.api.IShare
Creates share with all related: items, members, and guests.
createShare(Principal, boolean, long, String, String, long) - Method in interface ome.services.sessions.SessionManager
 
createShare(Principal, boolean, long, String, String, long) - Method in class ome.services.sessions.SessionManagerImpl
 
createShare(String, Timestamp, List<T>, List<Experimenter>, List<String>, boolean) - Method in class ome.services.sharing.ShareBean
 
createShare_async(AMD_IShare_createShare, String, RTime, List<IObject>, List<Experimenter>, List<String>, boolean, Current) - Method in class ome.services.blitz.impl.ShareI
 
createStats() - Method in class ome.services.sessions.stats.CounterFactory
 
createStore() - Method in class ome.formats.importer.ImportConfig
Create and return a new OMEROMetadataStoreClient
createSubpath(String) - Method in class ome.io.nio.AbstractFileSystemService
Makes sure that for a given path, it's subpath exists.
createSystemUser(Experimenter) - Method in interface ome.api.IAdmin
create and return a new system user.
createSystemUser(Experimenter) - Method in class ome.logic.AdminImpl
 
createSystemUser_async(AMD_IAdmin_createSystemUser, Experimenter, Current) - Method in class ome.services.blitz.impl.AdminI
 
createTempFile(String, String) - Static method in class omero.util.TempFileManager
createTemplatePath(Object, Current) - Method in class ome.services.blitz.repo.ManagedRepositoryI
Expand the template path and create its directories with the correct ownership.
createThumbnail(Integer, Integer) - Method in interface ome.api.ThumbnailStore
Creates a thumbnail for a pixels set using a given set of rendering settings (RenderingDef) in the on-disk cache.
createThumbnail(Thumbnail, byte[]) - Method in class ome.io.nio.ThumbnailService
Creates thumbnail on disk using byte array
createThumbnail(Integer, Integer) - Method in class ome.services.ThumbnailBean
 
createThumbnail_async(AMD_ThumbnailStore_createThumbnail, RInt, RInt, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
 
createThumbnailMetadata(Pixels, Dimension) - Method in class ome.services.ThumbnailCtx
Creates metadata for a thumbnail of a given set of pixels set and X-Y dimensions.
createThumbnails() - Method in interface ome.api.ThumbnailStore
Creates thumbnails for a pixels set using a given set of rendering settings (RenderingDef) in the on-disk cache for every sizeX/sizeY combination already cached.
createThumbnails() - Method in class ome.services.ThumbnailBean
 
createThumbnails_async(AMD_ThumbnailStore_createThumbnails, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
 
createThumbnailsByLongestSideSet(Integer, Set<Long>) - Method in interface ome.api.ThumbnailStore
Creates thumbnails for a number of pixels sets using a given set of rendering settings (RenderingDef) in the on-disk cache.
createThumbnailsByLongestSideSet(Integer, Set<Long>) - Method in class ome.services.ThumbnailBean
 
createThumbnailsByLongestSideSet_async(AMD_ThumbnailStore_createThumbnailsByLongestSideSet, RInt, List<Long>, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
 
createThumbnailService() - Method in class ome.system.ServiceFactory
create a new ThumbnailStore proxy.
createThumbnailStore(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
createThumbnailStore(OriginalFile, Current) - Method in class ome.services.blitz.repo.AbstractRepositoryI
 
createTransfer(String) - Static method in class ome.formats.importer.transfers.AbstractFileTransfer
Factory method for instantiating FileTransfer objects from a string.
createUploadProcess(Fileset, ImportLocation, ImportSettings, Current, boolean) - Method in class ome.services.blitz.repo.ManagedRepositoryI
Creating the process will register itself in an appropriate container (i.e. a SessionI or similar) for the current user and therefore this instance no longer needs to worry about the maintenance of the object.
createUser(Experimenter, String) - Method in interface ome.api.IAdmin
create and return a new user.
createUser(String) - Method in interface ome.api.ILdap
Creates an Experimenter entry in the OMERO DB based on the supplied LDAP username.
createUser(Experimenter, String) - Method in class ome.logic.AdminImpl
 
createUser(String) - Method in class ome.logic.LdapImpl
Creates an Experimenter based on the supplied LDAP username.
createUser(String, String) - Method in class ome.logic.LdapImpl
Creates an Experimenter based on the supplied LDAP username.
createUser(String, String, boolean) - Method in class ome.logic.LdapImpl
Creates an Experimenter based on the supplied LDAP username.
createUser_async(AMD_IAdmin_createUser, Experimenter, String, Current) - Method in class ome.services.blitz.impl.AdminI
 
createUser_async(AMD_ILdap_createUser, String, Current) - Method in class ome.services.blitz.impl.LdapI
 
createUserFromLdap(String, String) - Method in class ome.logic.LdapImpl
Deprecated.
createUserSession(long, long, String) - Method in interface ome.api.ISession
Allows a user to open up another session for him/herself with the given defaults without needing to re-enter password.
createUserSession(long, long, String) - Method in class ome.services.sessions.SessionBean
 
createUserSession_async(AMD_ISession_createUserSession, long, long, String, Current) - Method in class ome.services.blitz.impl.SessionI
 
createWithAgent(Principal, String, String, String) - Method in interface ome.services.sessions.SessionManager
 
createWithAgent(Principal, String, String) - Method in interface ome.services.sessions.SessionManager
 
createWithAgent(Principal, String, String, String) - Method in class ome.services.sessions.SessionManagerImpl
 
createWithAgent(Principal, String, String) - Method in class ome.services.sessions.SessionManagerImpl
 
CREATIONEVENT - Static variable in class ome.model.internal.Details
 
credentials - Variable in class ome.services.sessions.SessionManager.CreationRequest
 
credentials - Variable in class ome.system.SessionInitializer
 
CRITICAL_USAGE - Static variable in class ome.logic.RepositoryInfoImpl
Percentage (100.0 - 0.0) of disk use which will cause an exception during RepositoryInfoImpl.sanityCheckRepository()
csId - Variable in class ome.system.SimpleEventContext
 
csName - Variable in class ome.system.SimpleEventContext
 
CSV - Static variable in class pojos.FileAnnotationData
Identifies the CSV file formats.
ctime - Variable in class ome.model.core.OriginalFile
 
CTIME - Static variable in class ome.model.core.OriginalFile
 
ctx - Variable in class ome.security.auth.ConfigurablePasswordProvider
 
ctx - Variable in class ome.security.basic.BasicSecuritySystem
 
ctx - Variable in class ome.services.blitz.impl.AbstractAmdServant
 
ctx - Variable in class ome.services.delete.Deletion.Builder
Deprecated.
 
ctx - Variable in class ome.services.sharing.BlobShareStore
 
ctx - Variable in class ome.services.throttling.AbstractThrottlingStrategy
 
ctx - Variable in class ome.system.ServiceFactory
the context instance which this ServiceFactory uses to look up all of its state.
cuId - Variable in class ome.system.SimpleEventContext
 
cuName - Variable in class ome.system.SimpleEventContext
 
curr - Variable in class ome.services.blitz.util.FindServiceFactoryMessage
 
current - Variable in class ome.security.SecurityFilterHolder
 
current - Variable in class ome.security.SecuritySystemHolder
 
current - Variable in class ome.services.throttling.Task
 
current - Variable in class ome.tools.hibernate.ProxyCleanupFilter
 
current - Variable in class omero.cmd.admin.CurrentSessionsRequestI
 
current - Variable in class omero.cmd.admin.UpdateSessionTimeoutRequestI
 
current_group - Static variable in class ome.security.basic.OneGroupSecurityFilter
 
current_user - Static variable in interface ome.security.SecurityFilter
 
currentContext(Principal) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
 
currentContext() - Method in class ome.util.ContextFilter
 
CurrentDetails - Class in ome.security.basic
Stores information related to the security context of the current thread.
CurrentDetails() - Constructor for class ome.security.basic.CurrentDetails
Default constructor.
CurrentDetails(SessionCache) - Constructor for class ome.security.basic.CurrentDetails
 
CurrentDetails(SessionCache, Roles) - Constructor for class ome.security.basic.CurrentDetails
 
currentMetadata() - Method in interface ome.api.Search
Provides access to the extra query information (for example Lucene score and boost values) for a single call to Search.next().
currentMetadata() - Method in class ome.services.SearchBean
 
currentMetadata_async(AMD_Search_currentMetadata, Current) - Method in class ome.services.blitz.impl.SearchI
 
currentMetadataList() - Method in interface ome.api.Search
Provides access to the extra query information (for example Lucene score and boost values) for a single call to Search.results().
currentMetadataList() - Method in class ome.services.SearchBean
 
currentMetadataList_async(AMD_Search_currentMetadataList, Current) - Method in class ome.services.blitz.impl.SearchI
 
currentPatch - Variable in class ome.model.meta.DBPatch
 
CURRENTPATCH - Static variable in class ome.model.meta.DBPatch
 
CurrentPlatform - Class in ome.services.blitz.util
Test under which platform OMERO is currently running.
CurrentPlatform() - Constructor for class ome.services.blitz.util.CurrentPlatform
 
CurrentSessionContext - Class in ome.tools.hibernate
Implementation of Hibernate's current_session_context_class extension point.
CurrentSessionContext(SessionFactoryImplementor) - Constructor for class ome.tools.hibernate.CurrentSessionContext
 
CurrentSessionsRequestI - Class in omero.cmd.admin
 
CurrentSessionsRequestI(CurrentDetails, SessionManager) - Constructor for class omero.cmd.admin.CurrentSessionsRequestI
 
CurrentSessionsRequestI.Factory - Class in omero.cmd.admin
 
CurrentSessionsRequestI.Factory(CurrentDetails, SessionManager) - Constructor for class omero.cmd.admin.CurrentSessionsRequestI.Factory
 
CurrentSessionStats - Class in ome.services.sessions.stats
Wrapper which delegates to a SessionStats instance acquired during construction.
CurrentSessionStats(CurrentDetails, SessionManager) - Constructor for class ome.services.sessions.stats.CurrentSessionStats
 
currentUser - Variable in class ome.security.basic.BasicACLVoter
 
currentUser(Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
 
currentUserNames() - Method in class ome.util.actions.PostgresSqlAction
 
currentUserNames() - Method in interface ome.util.SqlAction
 
currentVersion - Variable in class ome.model.meta.DBPatch
 
CURRENTVERSION - Static variable in class ome.model.meta.DBPatch
 
currValue(String) - Method in class ome.util.actions.PostgresSqlAction
 
currValue(String) - Method in interface ome.util.SqlAction
 
cutIn - Variable in class ome.model.acquisition.TransmittanceRange
 
CUTIN - Static variable in class ome.model.acquisition.TransmittanceRange
 
cutInTolerance - Variable in class ome.model.acquisition.TransmittanceRange
 
CUTINTOLERANCE - Static variable in class ome.model.acquisition.TransmittanceRange
 
cutOut - Variable in class ome.model.acquisition.TransmittanceRange
 
CUTOUT - Static variable in class ome.model.acquisition.TransmittanceRange
 
cutOutTolerance - Variable in class ome.model.acquisition.TransmittanceRange
 
CUTOUTTOLERANCE - Static variable in class ome.model.acquisition.TransmittanceRange
 
cx - Variable in class ome.model.roi.Ellipse
 
CX - Static variable in class ome.model.roi.Ellipse
 
cx - Variable in class ome.model.roi.Point
 
CX - Static variable in class ome.model.roi.Point
 
cy - Variable in class ome.model.roi.Ellipse
 
CY - Static variable in class ome.model.roi.Ellipse
 
cy - Variable in class ome.model.roi.Point
 
CY - Static variable in class ome.model.roi.Point
 

D

d - Variable in class ome.model.roi.Path
 
D - Static variable in class ome.model.roi.Path
 
data - Variable in class ome.model.meta.Share
 
DATA - Static variable in class ome.model.meta.Share
 
data - Variable in class ome.services.roi.GeomTool
 
data - Variable in class ome.services.roi.PixelData
 
data - Variable in class ome.util.PixelData
The pixels data backing buffer.
DatabaseBusyException - Exception in ome.conditions
No connections are currently available for the database.
DatabaseBusyException(String, long) - Constructor for exception ome.conditions.DatabaseBusyException
 
DatabaseIdentity - Class in ome.services.db
Represents the unique identity of this database, consisting of the omero.db.authority and omero.db.uuid properties.
DatabaseIdentity(String, SqlAction) - Constructor for class ome.services.db.DatabaseIdentity
 
DatabaseIdentity(String, String) - Constructor for class ome.services.db.DatabaseIdentity
 
DataObject - Class in pojos
Abstract superclass for objects that hold OMEDS data.
DataObject() - Constructor for class pojos.DataObject
 
dataPerUser - Variable in class ome.services.pixeldata.PersistentEventLogLoader
 
Dataset - Class in ome.model.containers
These filter definitions are used by the security system to eliminate non-readable objects from queries.
Dataset() - Constructor for class ome.model.containers.Dataset
 
Dataset(Long) - Constructor for class ome.model.containers.Dataset
 
Dataset(Long, boolean) - Constructor for class ome.model.containers.Dataset
Main constructor.
Dataset(String) - Constructor for class ome.model.containers.Dataset
 
Dataset.Details - Class in ome.model.containers
 
Dataset.Details() - Constructor for class ome.model.containers.Dataset.Details
 
Dataset.Details(Object[]) - Constructor for class ome.model.containers.Dataset.Details
 
DATASET_LINKS - Static variable in class pojos.ImageData
Identifies the Image#DATASETLINKS field.
DATASET_LINKS - Static variable in class pojos.ProjectData
Identifies the Project#DATASETLINKS field.
DatasetAnnotationLink - Class in ome.model.annotations
These filter definitions are used by the security system to eliminate non-readable objects from queries.
DatasetAnnotationLink() - Constructor for class ome.model.annotations.DatasetAnnotationLink
 
DatasetAnnotationLink(Long) - Constructor for class ome.model.annotations.DatasetAnnotationLink
 
DatasetAnnotationLink(Long, boolean) - Constructor for class ome.model.annotations.DatasetAnnotationLink
Main constructor.
DatasetAnnotationLink(IObject, IObject) - Constructor for class ome.model.annotations.DatasetAnnotationLink
 
DatasetAnnotationLink.Details - Class in ome.model.annotations
 
DatasetAnnotationLink.Details() - Constructor for class ome.model.annotations.DatasetAnnotationLink.Details
 
DatasetAnnotationLink.Details(Object[]) - Constructor for class ome.model.annotations.DatasetAnnotationLink.Details
 
DatasetData - Class in pojos
The data that makes up an OME Dataset along with links to its contained Images and enclosing Project as well as the Experimenter that owns this Dataset.
DatasetData() - Constructor for class pojos.DatasetData
Creates a new instance.
DatasetData(Dataset) - Constructor for class pojos.DatasetData
Creates a new instance.
DatasetImageLink - Class in ome.model.containers
These filter definitions are used by the security system to eliminate non-readable objects from queries.
DatasetImageLink() - Constructor for class ome.model.containers.DatasetImageLink
 
DatasetImageLink(Long) - Constructor for class ome.model.containers.DatasetImageLink
 
DatasetImageLink(Long, boolean) - Constructor for class ome.model.containers.DatasetImageLink
Main constructor.
DatasetImageLink(IObject, IObject) - Constructor for class ome.model.containers.DatasetImageLink
 
DatasetImageLink.Details - Class in ome.model.containers
 
DatasetImageLink.Details() - Constructor for class ome.model.containers.DatasetImageLink.Details
 
DatasetImageLink.Details(Object[]) - Constructor for class ome.model.containers.DatasetImageLink.Details
 
datasetLinks - Variable in class ome.model.containers.Project
 
DATASETLINKS - Static variable in class ome.model.containers.Project
 
datasetLinks - Variable in class ome.model.core.Image
 
DATASETLINKS - Static variable in class ome.model.core.Image
 
DATASETLINKSCOUNTPEROWNER - Static variable in class ome.model.containers.Project
 
DATASETLINKSCOUNTPEROWNER - Static variable in class ome.model.core.Image
 
DATE(Connection, List<Date>) - Method in interface ome.tools.hibernate.ListAsSQLArrayUserType.ArrayFactory
 
DATE_ACQUISITION - Static variable in class ome.util.search.LuceneQueryBuilder
 
DATE_IMPORT - Static variable in class ome.util.search.LuceneQueryBuilder
 
DATE_TYPE_ACQUISITION - Static variable in interface ome.api.Search
Treat date range as acquisition date
DATE_TYPE_IMPORT - Static variable in interface ome.api.Search
Treat date range as import date
DBEnumCheck - Class in ome.services.util
Hook run by the context to guarantee that various enumerations are up to date.
DBEnumCheck(Executor, PreferenceContext) - Constructor for class ome.services.util.DBEnumCheck
 
DBPatch - Class in ome.model.meta
 
DBPatch() - Constructor for class ome.model.meta.DBPatch
 
DBPatch(Long) - Constructor for class ome.model.meta.DBPatch
 
DBPatch(Long, boolean) - Constructor for class ome.model.meta.DBPatch
Main constructor.
DBPatch(String, Integer, String, Integer) - Constructor for class ome.model.meta.DBPatch
 
DBPatch.Details - Class in ome.model.meta
 
DBPatch.Details() - Constructor for class ome.model.meta.DBPatch.Details
 
DBPatch.Details(Object[]) - Constructor for class ome.model.meta.DBPatch.Details
 
DBPatchCheck - Class in ome.services.util
Hook run by the context.
DBPatchCheck(SqlAction, PreferenceContext) - Constructor for class ome.services.util.DBPatchCheck
 
dbPath(Shape) - Method in class ome.services.roi.GeomTool
 
DBUnicodeUnitsCheck - Class in ome.services.util
Checks that the database contains correctly encoded enumerations for units of measure.
DBUnicodeUnitsCheck(Executor, PreferenceContext) - Constructor for class ome.services.util.DBUnicodeUnitsCheck
 
DBUserCheck - Class in ome.services.util
Hook run by the context.
DBUserCheck(SqlAction, PreferenceContext) - Constructor for class ome.services.util.DBUserCheck
 
dbUuid() - Method in class ome.util.actions.PostgresSqlAction
 
dbUuid() - Method in interface ome.util.SqlAction
 
dbVersion - Static variable in class ome.formats.importer.Version
 
dbVersion() - Method in class ome.util.actions.PostgresSqlAction
 
dbVersion() - Method in interface ome.util.SqlAction
 
deactivate() - Method in interface ome.api.IShare
Turns off the access control lists with the current share.
deactivate() - Method in class ome.services.sharing.ShareBean
 
deactivate_async(AMD_IShare_deactivate, Current) - Method in class ome.services.blitz.impl.ShareI
 
debug - Variable in class ome.formats.importer.ImportConfig
 
debug(String, Object...) - Method in class omero.cmd.Helper
 
DEBUG - Static variable in class prefs
Activated by setting DBEUG=true in the environment.
debugAll - Variable in class ome.security.basic.EventListenersFactoryBean
 
dec() - Method in interface ome.system.metrics.Counter
 
dec() - Method in class ome.system.metrics.DefaultCounter
 
DECILE - Static variable in class omeis.providers.re.quantum.QuantumStrategy
Determines the number of sub-intervals of the [globalMin, globalMax] interval.
decoration - Variable in class ome.model.roi.Label
 
DECORATION - Static variable in class ome.model.roi.Label
 
decrement() - Method in class ome.services.sessions.SessionContext.Count
Decrement the current reference count and return the new value atomically.
deepCopy(Object) - Method in class ome.model.units.GenericEnumType
 
deepCopy(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
 
def(String[]) - Static method in class prefs
Returns the current default if no argument is given, or sets the default to the given string (or "" if null) otherwise returing "Default set to: ... ".
DEFAULT - Static variable in class ome.services.graphs.GraphEntry
Deprecated.
 
DEFAULT - Static variable in class pojos.GroupData
Identifies the default group.
DEFAULT - Static variable in class prefs
Key (and default value) of the property under prefs.ROOT which defines which "profile" (subnode} is in effect.
DEFAULT_BATCH_SIZE - Static variable in interface ome.api.Search
Default batch size
DEFAULT_BATCH_SIZE - Static variable in class ome.services.eventlogs.EventLogLoader
Currently 100.
DEFAULT_CASE_SENSITIVTY - Static variable in interface ome.api.Search
DEFAULT_COMPRESSION_QUALITY - Static variable in class ome.services.ThumbnailBean
The default compression quality in fractional percent.
DEFAULT_ENCODING - Static variable in class ome.security.auth.PasswordUtil
The default encoding for converting plain text passwords to byte arrays (UTF-8)
DEFAULT_FILL_COLOUR - Static variable in class pojos.ShapeSettingsData
The default fill color.
DEFAULT_FILL_COLOUR_ALPHA - Static variable in class pojos.ShapeSettingsData
The default fill color.
DEFAULT_FONT_FAMILY - Static variable in class pojos.ShapeSettingsData
The default font family.
DEFAULT_FONT_SIZE - Static variable in class pojos.ShapeSettingsData
The default font size in "pt".
DEFAULT_MAX - Static variable in class ome.services.eventlogs.EventLogQueue
Default maximum for the number of rows that will be loaded in a single call to SqlAction.getEventLogPartitions(java.util.Collection, java.util.Collection, long, long) .
DEFAULT_MERGED_BATCHES - Static variable in interface ome.api.Search
DEFAULT_MIME_TYPE - Static variable in class ome.services.ThumbnailBean
The default MIME type.
DEFAULT_MIME_TYPE - Static variable in class ome.services.ThumbnailCtx
Default thumbnail MIME type.
DEFAULT_PORT - Static variable in class loci.ome.io.OmeroReader
 
DEFAULT_PORT - Static variable in class ome.services.mail.SubethaSMTP
 
DEFAULT_PORT - Static variable in class ome.system.Server
 
DEFAULT_QABASEURL - Static variable in class ome.formats.importer.ImportConfig
 
DEFAULT_REPORTING_LOOPS - Static variable in class ome.services.fulltext.FullTextIndexer
Default number of loops to wait if no external value is set.
DEFAULT_RETURN_UNLOADED - Static variable in interface ome.api.Search
DEFAULT_STROKE_COLOUR - Static variable in class pojos.ShapeSettingsData
The default stroke color.
DEFAULT_STROKE_WIDTH - Static variable in class pojos.ShapeSettingsData
The default stroke width.
DEFAULT_TIMEOUT - Static variable in class ome.services.blitz.impl.SharedResourcesI
If no value is passed to this instance, this is the time (1 hour) which will be used for a script session.
DEFAULT_TIMEOUT - Static variable in class ome.system.UpgradeCheck
Default timeout is 10 seconds.
DEFAULT_USE_PROJECTIONS - Static variable in interface ome.api.Search
DEFAULT_WAIT - Static variable in class ome.formats.importer.cli.CommandLineImporter
 
DEFAULT_X_WIDTH - Static variable in class ome.services.ThumbnailBean
The default X-width for a thumbnail.
DEFAULT_Y_WIDTH - Static variable in class ome.services.ThumbnailBean
The default Y-width for a thumbnail.
DefaultCounter - Class in ome.system.metrics
Thin wrapper around Counter
DefaultCounter(Counter) - Constructor for class ome.system.metrics.DefaultCounter
 
defaultEventType - Variable in class ome.model.meta.Session
 
DEFAULTEVENTTYPE - Static variable in class ome.model.meta.Session
 
DefaultHistogram - Class in ome.system.metrics
Thin wrapper around Histogram
DefaultHistogram(Histogram) - Constructor for class ome.system.metrics.DefaultHistogram
 
DefaultMetrics - Class in ome.system.metrics
Spring bean for configuring metrics in this JVM.
DefaultMetrics() - Constructor for class ome.system.metrics.DefaultMetrics
 
DefaultPolicyService - Class in ome.security.policy
PolicyService which is configured with all Policy instances which are discovered in the Spring context and only focuses on a small subset of IObject types as specified by DefaultPolicyService.filterObject(IObject).
DefaultPolicyService() - Constructor for class ome.security.policy.DefaultPolicyService
 
defaultSample - Variable in class ome.model.screen.Plate
 
DEFAULTSAMPLE - Static variable in class ome.model.screen.Plate
 
DefaultSnapshot - Class in ome.system.metrics
Thin wrapper around Snapshot
DefaultSnapshot(Snapshot) - Constructor for class ome.system.metrics.DefaultSnapshot
 
defaultT - Variable in class ome.model.display.RenderingDef
 
DEFAULTT - Static variable in class ome.model.display.RenderingDef
 
DefaultTimer - Class in ome.system.metrics
Thin wrapper around Timer
DefaultTimer(Timer) - Constructor for class ome.system.metrics.DefaultTimer
 
DefaultTimer.Context - Class in ome.system.metrics
 
DefaultTimer.Context(Timer.Context) - Constructor for class ome.system.metrics.DefaultTimer.Context
 
defaultTimeToIdle - Variable in class ome.services.sessions.SessionManagerImpl
 
defaultTimeToLive - Variable in class ome.services.sessions.SessionManagerImpl
 
DEFAULTWORKFLOW - Static variable in class pojos.WorkflowData
The default workflow, i.e. nothing .
defaultZ - Variable in class ome.model.display.RenderingDef
 
DEFAULTZ - Static variable in class ome.model.display.RenderingDef
 
deferConstraints() - Method in class ome.util.actions.PostgresSqlAction
 
deferConstraints() - Method in interface ome.util.SqlAction
 
define(Session, String, String, long, SessionManager.CreationRequest) - Method in class ome.services.sessions.SessionManagerImpl
 
define(Session, String, String, long, long, long, String, String, String) - Method in class ome.services.sessions.SessionManagerImpl
 
Definitions - Class in ome.services.query
container for QueryParameterDef instances.
Definitions(QueryParameterDef...) - Constructor for class ome.services.query.Definitions
 
defs - Variable in class ome.services.query.Query
container of QueryParameterDef instances.
delConfigValue(String) - Method in interface ome.util.SqlAction
 
delConfigValue(String) - Method in class ome.util.SqlAction.Impl
 
delCurrentEventLog(String) - Method in class ome.util.actions.PostgresSqlAction
 
delCurrentEventLog(String) - Method in interface ome.util.SqlAction
 
delCurrentEventLog(String) - Method in class ome.util.SqlAction.Impl
 
DelegatingStats - Class in ome.services.sessions.stats
Delegates to a SessionStats which is acquired from DelegatingStats.stats().
DelegatingStats() - Constructor for class ome.services.sessions.stats.DelegatingStats
 
DelegatingStats(SessionStats[]) - Constructor for class ome.services.sessions.stats.DelegatingStats
 
delete(long) - Method in class ome.services.scripts.ScriptRepoHelper
 
delete(String) - Method in class ome.tools.hibernate.QueryBuilder
 
Delete2I - Class in omero.cmd.graphs
Request to delete model objects, reimplementing DeleteI.
Delete2I(ACLVoter, Roles, SystemTypes, GraphPathBean, Deletion, Set<Class<? extends IObject>>, GraphPolicy, SetMultimap<String, String>) - Constructor for class omero.cmd.graphs.Delete2I
Construct a new delete request; called from GraphRequestFactory.getRequest(Class).
deleteAnnotationLinks(AnnotationGraphSpec, Session, List<Long>) - Method in class ome.services.graphs.GraphStep
Deprecated.
 
DeleteBean - Class in ome.services.delete
Strict implementation of the IDelete service interface which will use the SecuritySystem via SecuritySystem.runAsAdmin(AdminAction) to forcibly delete instances.
DeleteBean(LocalAdmin, SessionFactory) - Constructor for class ome.services.delete.DeleteBean
 
deleteChannels(long) - Method in class ome.services.delete.DeleteBean
 
deleteComment(Annotation) - Method in interface ome.api.IShare
Deletes comment from the database.
deleteComment(Annotation) - Method in class ome.services.sharing.ShareBean
 
deleteComment_async(AMD_IShare_deleteComment, Annotation, Current) - Method in class ome.services.blitz.impl.ShareI
 
deleteCurrentId() - Method in class ome.services.eventlogs.PersistentEventLogLoader
 
deleteDataObject(IObject, Parameters) - Method in class ome.logic.PojosImpl
Implemented as specified by the IContainer I/F
deleteDataObjects(IObject[], Parameters) - Method in class ome.logic.PojosImpl
Implemented as specified by the IContainer I/F
deletedIds - Variable in class ome.services.delete.files.AbstractFileDeletions
 
deleteEntity(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
deleteEnumeration(T) - Method in interface ome.api.ITypes
deletes enumeration value specified by object
deleteEnumeration(T) - Method in class ome.logic.TypesImpl
 
deleteEnumeration_async(AMD_ITypes_deleteEnumeration, IObject, Current) - Method in class ome.services.blitz.impl.TypesI
 
DeleteException - Exception in ome.services.delete
Deprecated.
will be removed in OMERO 5.3
DeleteException(String) - Constructor for exception ome.services.delete.DeleteException
Deprecated.
 
deleteExperimenter(Experimenter) - Method in interface ome.api.IAdmin
removes a user by removing the password information for that user as well as all GroupExperimenterMap instances.
deleteExperimenter(Experimenter) - Method in class ome.logic.AdminImpl
 
deleteExperimenter_async(AMD_IAdmin_deleteExperimenter, Experimenter, Current) - Method in class ome.services.blitz.impl.AdminI
 
DeleteFacadeI - Class in omero.cmd.graphs
Deprecated.
will be removed in OMERO 5.3, so use the new graphs implementation
DeleteFacadeI(GraphRequestFactory) - Constructor for class omero.cmd.graphs.DeleteFacadeI
Deprecated.
Construct a new delete request; called from GraphRequestFactory.getRequest(Class).
deleteFiles() - Method in class ome.services.delete.Deletion
Deprecated.
For each Report use the map of tables to deleted ids to remove the files under Files, Pixels and Thumbnails if the ids no longer exist in the db.
deleteFiles(SetMultimap<String, Long>) - Method in class ome.services.delete.Deletion
Deprecated.
For each Report use the map of tables to deleted ids to remove the files under Files, Pixels and Thumbnails if the ids no longer exist in the db.
deleteFilesFromRepository(ImportContainer) - Method in class ome.formats.importer.ImportLibrary
Delete files from the managed repository.
deleteGroup(ExperimenterGroup) - Method in interface ome.api.IAdmin
removes a group by first removing all users in the group, and then deleting the actual ExperimenterGroup instance.
deleteGroup(ExperimenterGroup) - Method in class ome.logic.AdminImpl
 
deleteGroup_async(AMD_IAdmin_deleteGroup, ExperimenterGroup, Current) - Method in class ome.services.blitz.impl.AdminI
 
DeleteI - Class in omero.cmd.graphs
Deprecated.
will be removed in OMERO 5.2, so use the new graphs implementation
DeleteI(Communicator, Deletion) - Constructor for class omero.cmd.graphs.DeleteI
Deprecated.
 
deleteImage(long, boolean) - Method in interface ome.api.IDelete
Deletes an Image and all related (subordinate) metadata as defined below.
deleteImage(long, boolean) - Method in class ome.services.delete.DeleteBean
 
deleteImages(Set<Long>, boolean) - Method in interface ome.api.IDelete
Deletes several Image instances within a single transaction via the IDelete.deleteImage(long, boolean) method.
deleteImages(Set<Long>, boolean) - Method in class ome.services.delete.DeleteBean
 
deleteImagesByDataset(long, boolean) - Method in interface ome.api.IDelete
Deletes the user-visible Image instances of the given Dataset within a single transaction via the IDelete.deleteImage(long, boolean).
deleteImagesByDataset(long, boolean) - Method in class ome.services.delete.DeleteBean
 
deleteInstances(String, Collection<Long>) - Method in interface ome.services.graphs.GraphTraversal.Processor
Delete the given instances.
deleteInstances(String, Collection<Long>) - Method in class omero.cmd.graphs.BaseGraphTraversalProcessor
 
deleteLocal() - Method in class ome.services.delete.files.AbstractFileDeletions
Helper to delete and log.
DeleteLogMessage - Class in ome.services.messages
 
DeleteLogMessage(Object, long) - Constructor for class ome.services.messages.DeleteLogMessage
 
DeleteLogsMessage - Class in ome.services.messages
 
DeleteLogsMessage(Object, List<Long>) - Constructor for class ome.services.messages.DeleteLogsMessage
 
deleteObject(IObject) - Method in interface ome.api.IUpdate
Deletes a single entity.
deleteObject(IObject) - Method in class ome.logic.UpdateImpl
 
deleteObject_async(AMD_IUpdate_deleteObject, IObject, Current) - Method in class ome.services.blitz.impl.UpdateI
 
deleteObserver(IObserver) - Method in class ome.formats.importer.ImportLibrary
 
deleteObserver(IObserver) - Method in interface ome.formats.importer.IObservable
Delete observer
deleteObserver(IObserver) - Method in class ome.formats.importer.util.ClientKeepAlive
 
deleteObserver(IObserver) - Method in class ome.formats.importer.util.ErrorHandler
 
deleteObserver(IObserver) - Method in class ome.formats.importer.util.FileUploader
 
deletePaths(String[], boolean, boolean, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
Delete paths recursively as described in Repositories.ice.
deletePlate(long) - Method in interface ome.api.IDelete
Deletes all the images contained in a plate as if deleted by: deleteImage(id, true) so that all Dataset and Annotation links are broken, with WellSamples removed first.
deletePlate(long) - Method in class ome.services.delete.DeleteBean
 
deleteQuery(EventContext, String, GraphOpts) - Method in class ome.services.graphs.BaseGraphSpec
Deprecated.
 
deleteQuery(EventContext, String, GraphOpts) - Method in interface ome.services.graphs.GraphSpec
Deprecated.
 
deleteQuery(EventContext, String, GraphOpts) - Method in class ome.services.graphs.RenderingDefGraphSpec
Deprecated.
Uses direct SQL in order to workaround any security filters which may be in place since rdefs are considered outside of the security system.
deleteRepoDeleteLogs(SqlAction.DeleteLog, Current) - Method in interface ome.services.blitz.repo.RepositoryDao
Call SqlAction.deleteRepoDeleteLogs(DeleteLog) with the current context.
deleteRepoDeleteLogs(List<SqlAction.DeleteLog>, Current) - Method in interface ome.services.blitz.repo.RepositoryDao
Call SqlAction.deleteRepoDeleteLogs(DeleteLog) with the current context for a number of templates.
deleteRepoDeleteLogs(SqlAction.DeleteLog, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
 
deleteRepoDeleteLogs(List<SqlAction.DeleteLog>, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
 
deleteRepoDeleteLogs(SqlAction.DeleteLog) - Method in interface ome.util.SqlAction
Delete all SqlAction.DeleteLog entries which match all of the non-null fields provided in the template.
deleteRepoDeleteLogs(SqlAction.DeleteLog) - Method in class ome.util.SqlAction.Impl
 
DELETERESTRICTION - Static variable in class ome.model.internal.Permissions
 
deleteRows(PersistentCollection, Serializable, SessionImplementor) - Method in class ome.util.CountCollectionPersister
 
deleteScript_async(AMD_IScript_deleteScript, long, Current) - Method in class ome.services.blitz.impl.ScriptI
Delete the script with id from the server.
deleteSettings(long) - Method in interface ome.api.IDelete
Deletes all rendering settings for the given Pixel id.
deleteSettings(long) - Method in class ome.services.delete.DeleteBean
 
DeleteStep - Class in ome.services.delete
Deprecated.
will be removed in OMERO 5.2, so use the new graphs implementation
DeleteStep(ExtendedMetadata, OmeroContext, int, List<GraphStep>, GraphSpec, GraphEntry, long[]) - Constructor for class ome.services.delete.DeleteStep
Deprecated.
 
DeleteStepFactory - Class in ome.services.delete
Deprecated.
will be removed in OMERO 5.2, so use the new graphs implementation
DeleteStepFactory(OmeroContext, ExtendedMetadata) - Constructor for class ome.services.delete.DeleteStepFactory
Deprecated.
 
deleteTransferredFiles(int, List<String>) - Method in class ome.formats.importer.transfers.AbstractFileTransfer
Method used by subclasses during #afterTransfer(int, List) if they would like to remove all the files transferred in the set.
Deletion - Class in ome.services.delete
Deprecated.
all except setup and Deletion.deleteFiles(SetMultimap) will be removed in OMERO 5.2, so use the new graphs implementation
Deletion(ApplicationContext, DeleteStepFactory, AbstractFileSystemService, OmeroContext) - Constructor for class ome.services.delete.Deletion
Deprecated.
 
Deletion.Builder - Class in ome.services.delete
Deprecated.
Inner class which can be used to generate a Deletion.
Deletion.Builder(AbstractFileSystemService, ExtendedMetadata) - Constructor for class ome.services.delete.Deletion.Builder
Deprecated.
 
deliver(String, String, InputStream) - Method in class ome.services.mail.MapAnnotationSubethaListener
Stores each email as a map annotation with MapAnnotationSubethaListener.NAMESPACE set.
deltaT - Variable in class ome.model.core.PlaneInfo
 
DELTAT - Static variable in class ome.model.core.PlaneInfo
 
DEPTH - Static variable in class ome.formats.importer.ImportCandidates
 
depth - Variable in class ome.formats.importer.ImportCandidates.SCANNING
 
DEPTH_1BIT - Static variable in class omeis.providers.re.quantum.QuantumFactory
Flag to select a 1-bit depth (=2^1-1) output interval.
DEPTH_2BIT - Static variable in class omeis.providers.re.quantum.QuantumFactory
Flag to select a 2-bit depth (=2^2-1) output interval.
DEPTH_3BIT - Static variable in class omeis.providers.re.quantum.QuantumFactory
Flag to select a 3-bit depth (=2^3-1) output interval.
DEPTH_4BIT - Static variable in class omeis.providers.re.quantum.QuantumFactory
Flag to select a 4-bit depth (=2^4-1) output interval.
DEPTH_5BIT - Static variable in class omeis.providers.re.quantum.QuantumFactory
Flag to select a 5-bit depth (=2^5-1) output interval.
DEPTH_6BIT - Static variable in class omeis.providers.re.quantum.QuantumFactory
Flag to select a 6-bit depth (=2^6-1) output interval.
DEPTH_7BIT - Static variable in class omeis.providers.re.quantum.QuantumFactory
Flag to select a 7-bit depth (=2^7-1) output interval.
DEPTH_8BIT - Static variable in class omeis.providers.re.quantum.QuantumFactory
Flag to select a 8-bit depth (=2^8-1) output interval.
DESCENDING_LETTER - Static variable in class pojos.PlateData
Indicates that the column or row is a letter starting from Z or P.
DESCENDING_NUMBER - Static variable in class pojos.PlateData
Indicates that the column or row is a letter starting from 26 or 16.
description - Variable in class ome.model.annotations.Annotation
 
DESCRIPTION - Static variable in class ome.model.annotations.Annotation
 
description - Variable in class ome.model.containers.Dataset
 
DESCRIPTION - Static variable in class ome.model.containers.Dataset
 
description - Variable in class ome.model.containers.Project
 
DESCRIPTION - Static variable in class ome.model.containers.Project
 
description - Variable in class ome.model.core.Image
 
DESCRIPTION - Static variable in class ome.model.core.Image
 
description - Variable in class ome.model.experiment.Experiment
 
DESCRIPTION - Static variable in class ome.model.experiment.Experiment
 
description - Variable in class ome.model.experiment.MicrobeamManipulation
 
DESCRIPTION - Static variable in class ome.model.experiment.MicrobeamManipulation
 
description - Variable in class ome.model.jobs.ScriptJob
 
DESCRIPTION - Static variable in class ome.model.jobs.ScriptJob
 
description - Variable in class ome.model.meta.ExperimenterGroup
 
DESCRIPTION - Static variable in class ome.model.meta.ExperimenterGroup
 
description - Variable in class ome.model.meta.Namespace
 
DESCRIPTION - Static variable in class ome.model.meta.Namespace
 
description - Variable in class ome.model.roi.Roi
 
DESCRIPTION - Static variable in class ome.model.roi.Roi
 
description - Variable in class ome.model.screen.Plate
 
DESCRIPTION - Static variable in class ome.model.screen.Plate
 
description - Variable in class ome.model.screen.PlateAcquisition
 
DESCRIPTION - Static variable in class ome.model.screen.PlateAcquisition
 
description - Variable in class ome.model.screen.Reagent
 
DESCRIPTION - Static variable in class ome.model.screen.Reagent
 
description - Variable in class ome.model.screen.Screen
 
DESCRIPTION - Static variable in class ome.model.screen.Screen
 
description() - Method in class ome.services.procs.ProcessManager.Work
 
description() - Method in class ome.services.search.SearchAction
Returns the SearchAction subclass as the description.
description - Variable in class ome.services.util.Executor.Descriptive
 
description() - Method in class ome.services.util.Executor.Descriptive
 
description() - Method in interface ome.services.util.Executor.SqlWork
Return a description of what this work will be doing for logging purposes.
description() - Method in interface ome.services.util.Executor.Work
Returns a description of what this work will be doing for logging purposes.
DESCRIPTION - Static variable in class pojos.DatasetData
Identifies the Dataset#DESCRIPTION field.
DESCRIPTION - Static variable in class pojos.GroupData
Identifies the ExperimenterGroup#DESCRIPTION field.
DESCRIPTION - Static variable in class pojos.ImageData
Identifies the Image#DESCRIPTION field.
DESCRIPTION - Static variable in class pojos.PlateData
Identifies the Plate#DESCRIPTION field.
DESCRIPTION - Static variable in class pojos.ProjectData
Identifies the Project#DESCRIPTION field.
DESCRIPTION - Static variable in class pojos.ScreenData
Identifies the Screen#DESCRIPTION field.
destroy() - Method in class ome.services.blitz.fire.Ring
 
destroy() - Method in class ome.services.blitz.util.BlitzConfiguration
 
destroy() - Method in class ome.services.throttling.Queue
 
destroy() - Method in class ome.services.util.SleepTimer
This method is called by Spring during server shut-down.
destroy() - Method in class ome.tools.spring.ShutdownSafeEhcacheManagerFactoryBean
 
destroy(Current) - Method in class omero.cmd.SessionI
Destruction simply decrements the reference count for a session to allow reconnecting to it.
destroy() - Method in class omero.util.ObjectFactoryRegistry.ObjectFactory
 
DestroySessionMessage - Class in ome.services.messages
Published before a session destruction.
DestroySessionMessage(Object, String) - Constructor for class ome.services.messages.DestroySessionMessage
 
detach(String) - Method in interface ome.services.sessions.SessionManager
Allows decrementing the reference count for a session without calling the actual SessionManager.close(String) logic.
detach(String) - Method in class ome.services.sessions.SessionManagerImpl
 
detachOnDestroy(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
details - Variable in class ome.model.acquisition.Detector
 
DETAILS - Static variable in class ome.model.acquisition.Detector
 
details - Variable in class ome.model.acquisition.DetectorSettings
 
DETAILS - Static variable in class ome.model.acquisition.DetectorSettings
 
details - Variable in class ome.model.acquisition.Dichroic
 
DETAILS - Static variable in class ome.model.acquisition.Dichroic
 
details - Variable in class ome.model.acquisition.Filter
 
DETAILS - Static variable in class ome.model.acquisition.Filter
 
details - Variable in class ome.model.acquisition.FilterSet
 
DETAILS - Static variable in class ome.model.acquisition.FilterSet
 
details - Variable in class ome.model.acquisition.FilterSetEmissionFilterLink
 
DETAILS - Static variable in class ome.model.acquisition.FilterSetEmissionFilterLink
 
details - Variable in class ome.model.acquisition.FilterSetExcitationFilterLink
 
DETAILS - Static variable in class ome.model.acquisition.FilterSetExcitationFilterLink
 
details - Variable in class ome.model.acquisition.ImagingEnvironment
 
DETAILS - Static variable in class ome.model.acquisition.ImagingEnvironment
 
details - Variable in class ome.model.acquisition.Instrument
 
DETAILS - Static variable in class ome.model.acquisition.Instrument
 
details - Variable in class ome.model.acquisition.LightPath
 
DETAILS - Static variable in class ome.model.acquisition.LightPath
 
details - Variable in class ome.model.acquisition.LightPathEmissionFilterLink
 
DETAILS - Static variable in class ome.model.acquisition.LightPathEmissionFilterLink
 
details - Variable in class ome.model.acquisition.LightPathExcitationFilterLink
 
DETAILS - Static variable in class ome.model.acquisition.LightPathExcitationFilterLink
 
details - Variable in class ome.model.acquisition.LightSettings
 
DETAILS - Static variable in class ome.model.acquisition.LightSettings
 
details - Variable in class ome.model.acquisition.LightSource
 
DETAILS - Static variable in class ome.model.acquisition.LightSource
 
details - Variable in class ome.model.acquisition.Microscope
 
DETAILS - Static variable in class ome.model.acquisition.Microscope
 
details - Variable in class ome.model.acquisition.Objective
 
DETAILS - Static variable in class ome.model.acquisition.Objective
 
details - Variable in class ome.model.acquisition.ObjectiveSettings
 
DETAILS - Static variable in class ome.model.acquisition.ObjectiveSettings
 
details - Variable in class ome.model.acquisition.OTF
 
DETAILS - Static variable in class ome.model.acquisition.OTF
 
details - Variable in class ome.model.acquisition.StageLabel
 
DETAILS - Static variable in class ome.model.acquisition.StageLabel
 
details - Variable in class ome.model.acquisition.TransmittanceRange
 
DETAILS - Static variable in class ome.model.acquisition.TransmittanceRange
 
details - Variable in class ome.model.annotations.Annotation
 
DETAILS - Static variable in class ome.model.annotations.Annotation
 
details - Variable in class ome.model.annotations.AnnotationAnnotationLink
 
DETAILS - Static variable in class ome.model.annotations.AnnotationAnnotationLink
 
details - Variable in class ome.model.annotations.ChannelAnnotationLink
 
DETAILS - Static variable in class ome.model.annotations.ChannelAnnotationLink
 
details - Variable in class ome.model.annotations.DatasetAnnotationLink
 
DETAILS - Static variable in class ome.model.annotations.DatasetAnnotationLink
 
details - Variable in class ome.model.annotations.DetectorAnnotationLink
 
DETAILS - Static variable in class ome.model.annotations.DetectorAnnotationLink
 
details - Variable in class ome.model.annotations.DichroicAnnotationLink
 
DETAILS - Static variable in class ome.model.annotations.DichroicAnnotationLink
 
details - Variable in class ome.model.annotations.ExperimenterAnnotationLink
 
DETAILS - Static variable in class ome.model.annotations.ExperimenterAnnotationLink
 
details - Variable in class ome.model.annotations.ExperimenterGroupAnnotationLink
 
DETAILS - Static variable in class ome.model.annotations.ExperimenterGroupAnnotationLink
 
details - Variable in class ome.model.annotations.FilesetAnnotationLink
 
DETAILS - Static variable in class ome.model.annotations.FilesetAnnotationLink
 
details - Variable in class ome.model.annotations.FilterAnnotationLink
 
DETAILS - Static variable in class ome.model.annotations.FilterAnnotationLink
 
details - Variable in class ome.model.annotations.ImageAnnotationLink
 
DETAILS - Static variable in class ome.model.annotations.ImageAnnotationLink
 
details - Variable in class ome.model.annotations.InstrumentAnnotationLink
 
DETAILS - Static variable in class ome.model.annotations.InstrumentAnnotationLink
 
details - Variable in class ome.model.annotations.LightPathAnnotationLink
 
DETAILS - Static variable in class ome.model.annotations.LightPathAnnotationLink
 
details - Variable in class ome.model.annotations.LightSourceAnnotationLink
 
DETAILS - Static variable in class ome.model.annotations.LightSourceAnnotationLink
 
details - Variable in class ome.model.annotations.NamespaceAnnotationLink
 
DETAILS - Static variable in class ome.model.annotations.NamespaceAnnotationLink
 
details - Variable in class ome.model.annotations.NodeAnnotationLink
 
DETAILS - Static variable in class ome.model.annotations.NodeAnnotationLink
 
details - Variable in class ome.model.annotations.ObjectiveAnnotationLink
 
DETAILS - Static variable in class ome.model.annotations.ObjectiveAnnotationLink
 
details - Variable in class ome.model.annotations.OriginalFileAnnotationLink
 
DETAILS - Static variable in class ome.model.annotations.OriginalFileAnnotationLink
 
details - Variable in class ome.model.annotations.PlaneInfoAnnotationLink
 
DETAILS - Static variable in class ome.model.annotations.PlaneInfoAnnotationLink
 
details - Variable in class ome.model.annotations.PlateAcquisitionAnnotationLink
 
DETAILS - Static variable in class ome.model.annotations.PlateAcquisitionAnnotationLink
 
details - Variable in class ome.model.annotations.PlateAnnotationLink
 
DETAILS - Static variable in class ome.model.annotations.PlateAnnotationLink
 
details - Variable in class ome.model.annotations.ProjectAnnotationLink
 
DETAILS - Static variable in class ome.model.annotations.ProjectAnnotationLink
 
details - Variable in class ome.model.annotations.ReagentAnnotationLink
 
DETAILS - Static variable in class ome.model.annotations.ReagentAnnotationLink
 
details - Variable in class ome.model.annotations.RoiAnnotationLink
 
DETAILS - Static variable in class ome.model.annotations.RoiAnnotationLink
 
details - Variable in class ome.model.annotations.ScreenAnnotationLink
 
DETAILS - Static variable in class ome.model.annotations.ScreenAnnotationLink
 
details - Variable in class ome.model.annotations.SessionAnnotationLink
 
DETAILS - Static variable in class ome.model.annotations.SessionAnnotationLink
 
details - Variable in class ome.model.annotations.ShapeAnnotationLink
 
DETAILS - Static variable in class ome.model.annotations.ShapeAnnotationLink
 
details - Variable in class ome.model.annotations.WellAnnotationLink
 
DETAILS - Static variable in class ome.model.annotations.WellAnnotationLink
 
details - Variable in class ome.model.containers.Dataset
 
DETAILS - Static variable in class ome.model.containers.Dataset
 
details - Variable in class ome.model.containers.DatasetImageLink
 
DETAILS - Static variable in class ome.model.containers.DatasetImageLink
 
details - Variable in class ome.model.containers.Project
 
DETAILS - Static variable in class ome.model.containers.Project
 
details - Variable in class ome.model.containers.ProjectDatasetLink
 
DETAILS - Static variable in class ome.model.containers.ProjectDatasetLink
 
details - Variable in class ome.model.core.Channel
 
DETAILS - Static variable in class ome.model.core.Channel
 
details - Variable in class ome.model.core.Image
 
DETAILS - Static variable in class ome.model.core.Image
 
details - Variable in class ome.model.core.LogicalChannel
 
DETAILS - Static variable in class ome.model.core.LogicalChannel
 
details - Variable in class ome.model.core.OriginalFile
 
DETAILS - Static variable in class ome.model.core.OriginalFile
 
details - Variable in class ome.model.core.Pixels
 
DETAILS - Static variable in class ome.model.core.Pixels
 
details - Variable in class ome.model.core.PixelsOriginalFileMap
 
DETAILS - Static variable in class ome.model.core.PixelsOriginalFileMap
 
details - Variable in class ome.model.core.PlaneInfo
 
DETAILS - Static variable in class ome.model.core.PlaneInfo
 
details - Variable in class ome.model.display.ChannelBinding
 
DETAILS - Static variable in class ome.model.display.ChannelBinding
 
details - Variable in class ome.model.display.CodomainMapContext
 
DETAILS - Static variable in class ome.model.display.CodomainMapContext
 
details - Variable in class ome.model.display.QuantumDef
 
DETAILS - Static variable in class ome.model.display.QuantumDef
 
details - Variable in class ome.model.display.RenderingDef
 
DETAILS - Static variable in class ome.model.display.RenderingDef
 
details - Variable in class ome.model.display.Thumbnail
 
DETAILS - Static variable in class ome.model.display.Thumbnail
 
details - Variable in class ome.model.enums.AcquisitionMode
 
DETAILS - Static variable in class ome.model.enums.AcquisitionMode
 
details - Variable in class ome.model.enums.ArcType
 
DETAILS - Static variable in class ome.model.enums.ArcType
 
details - Variable in class ome.model.enums.Binning
 
DETAILS - Static variable in class ome.model.enums.Binning
 
details - Variable in class ome.model.enums.ChecksumAlgorithm
 
DETAILS - Static variable in class ome.model.enums.ChecksumAlgorithm
 
details - Variable in class ome.model.enums.ContrastMethod
 
DETAILS - Static variable in class ome.model.enums.ContrastMethod
 
details - Variable in class ome.model.enums.Correction
 
DETAILS - Static variable in class ome.model.enums.Correction
 
details - Variable in class ome.model.enums.DetectorType
 
DETAILS - Static variable in class ome.model.enums.DetectorType
 
details - Variable in class ome.model.enums.DimensionOrder
 
DETAILS - Static variable in class ome.model.enums.DimensionOrder
 
details - Variable in class ome.model.enums.EventType
 
DETAILS - Static variable in class ome.model.enums.EventType
 
details - Variable in class ome.model.enums.ExperimentType
 
DETAILS - Static variable in class ome.model.enums.ExperimentType
 
details - Variable in class ome.model.enums.Family
 
DETAILS - Static variable in class ome.model.enums.Family
 
details - Variable in class ome.model.enums.FilamentType
 
DETAILS - Static variable in class ome.model.enums.FilamentType
 
details - Variable in class ome.model.enums.FilterType
 
DETAILS - Static variable in class ome.model.enums.FilterType
 
details - Variable in class ome.model.enums.Format
 
DETAILS - Static variable in class ome.model.enums.Format
 
details - Variable in class ome.model.enums.Illumination
 
DETAILS - Static variable in class ome.model.enums.Illumination
 
details - Variable in class ome.model.enums.Immersion
 
DETAILS - Static variable in class ome.model.enums.Immersion
 
details - Variable in class ome.model.enums.LaserMedium
 
DETAILS - Static variable in class ome.model.enums.LaserMedium
 
details - Variable in class ome.model.enums.LaserType
 
DETAILS - Static variable in class ome.model.enums.LaserType
 
details - Variable in class ome.model.enums.Medium
 
DETAILS - Static variable in class ome.model.enums.Medium
 
details - Variable in class ome.model.enums.MicrobeamManipulationType
 
DETAILS - Static variable in class ome.model.enums.MicrobeamManipulationType
 
details - Variable in class ome.model.enums.MicroscopeType
 
DETAILS - Static variable in class ome.model.enums.MicroscopeType
 
details - Variable in class ome.model.enums.PhotometricInterpretation
 
DETAILS - Static variable in class ome.model.enums.PhotometricInterpretation
 
details - Variable in class ome.model.enums.PixelsType
 
DETAILS - Static variable in class ome.model.enums.PixelsType
 
details - Variable in class ome.model.enums.Pulse
 
DETAILS - Static variable in class ome.model.enums.Pulse
 
details - Variable in class ome.model.enums.RenderingModel
 
DETAILS - Static variable in class ome.model.enums.RenderingModel
 
details - Variable in class ome.model.experiment.Experiment
 
DETAILS - Static variable in class ome.model.experiment.Experiment
 
details - Variable in class ome.model.experiment.MicrobeamManipulation
 
DETAILS - Static variable in class ome.model.experiment.MicrobeamManipulation
 
details - Variable in class ome.model.fs.Fileset
 
DETAILS - Static variable in class ome.model.fs.Fileset
 
details - Variable in class ome.model.fs.FilesetEntry
 
DETAILS - Static variable in class ome.model.fs.FilesetEntry
 
details - Variable in class ome.model.fs.FilesetJobLink
 
DETAILS - Static variable in class ome.model.fs.FilesetJobLink
 
Details - Class in ome.model.internal
value type for low-level (row-level) details for all IObject objects.
Details() - Constructor for class ome.model.internal.Details
default constructor.
Details(Object[]) - Constructor for class ome.model.internal.Details
 
Details(Details) - Constructor for class ome.model.internal.Details
copy-constructor
details - Variable in class ome.model.internal.Link
 
DETAILS - Static variable in class ome.model.internal.Link
 
details - Variable in class ome.model.jobs.Job
 
DETAILS - Static variable in class ome.model.jobs.Job
 
details - Variable in class ome.model.jobs.JobOriginalFileLink
 
DETAILS - Static variable in class ome.model.jobs.JobOriginalFileLink
 
details - Variable in class ome.model.jobs.JobStatus
 
DETAILS - Static variable in class ome.model.jobs.JobStatus
 
details - Variable in class ome.model.meta.DBPatch
 
DETAILS - Static variable in class ome.model.meta.DBPatch
 
details - Variable in class ome.model.meta.Event
 
DETAILS - Static variable in class ome.model.meta.Event
 
details - Variable in class ome.model.meta.EventLog
 
DETAILS - Static variable in class ome.model.meta.EventLog
 
details - Variable in class ome.model.meta.Experimenter
 
DETAILS - Static variable in class ome.model.meta.Experimenter
 
details - Variable in class ome.model.meta.ExperimenterGroup
 
DETAILS - Static variable in class ome.model.meta.ExperimenterGroup
 
details - Variable in class ome.model.meta.ExternalInfo
 
DETAILS - Static variable in class ome.model.meta.ExternalInfo
 
details - Variable in class ome.model.meta.GroupExperimenterMap
 
DETAILS - Static variable in class ome.model.meta.GroupExperimenterMap
 
details - Variable in class ome.model.meta.Namespace
 
DETAILS - Static variable in class ome.model.meta.Namespace
 
details - Variable in class ome.model.meta.Node
 
DETAILS - Static variable in class ome.model.meta.Node
 
details - Variable in class ome.model.meta.Session
 
DETAILS - Static variable in class ome.model.meta.Session
 
details - Variable in class ome.model.meta.ShareMember
 
DETAILS - Static variable in class ome.model.meta.ShareMember
 
details - Variable in class ome.model.roi.Roi
 
DETAILS - Static variable in class ome.model.roi.Roi
 
details - Variable in class ome.model.roi.Shape
 
DETAILS - Static variable in class ome.model.roi.Shape
 
details - Variable in class ome.model.screen.Plate
 
DETAILS - Static variable in class ome.model.screen.Plate
 
details - Variable in class ome.model.screen.PlateAcquisition
 
DETAILS - Static variable in class ome.model.screen.PlateAcquisition
 
details - Variable in class ome.model.screen.Reagent
 
DETAILS - Static variable in class ome.model.screen.Reagent
 
details - Variable in class ome.model.screen.Screen
 
DETAILS - Static variable in class ome.model.screen.Screen
 
details - Variable in class ome.model.screen.ScreenPlateLink
 
DETAILS - Static variable in class ome.model.screen.ScreenPlateLink
 
details - Variable in class ome.model.screen.Well
 
DETAILS - Static variable in class ome.model.screen.Well
 
details - Variable in class ome.model.screen.WellReagentLink
 
DETAILS - Static variable in class ome.model.screen.WellReagentLink
 
details - Variable in class ome.model.screen.WellSample
 
DETAILS - Static variable in class ome.model.screen.WellSample
 
details - Variable in class ome.model.stats.StatsInfo
 
DETAILS - Static variable in class ome.model.stats.StatsInfo
 
DetailsFieldBridge - Class in ome.util
Delegating FieldBridge which passes the "fieldBridge" bean from the "ome.model" Spring ApplicationContext all arguments.
DetailsFieldBridge() - Constructor for class ome.util.DetailsFieldBridge
 
DetailsI - Class in omero.model
 
DetailsI() - Constructor for class omero.model.DetailsI
 
DetailsI(client) - Constructor for class omero.model.DetailsI
 
detailsIndex(String[]) - Static method in class ome.tools.hibernate.HibernateUtils
 
Detector - Class in ome.model.acquisition
These filter definitions are used by the security system to eliminate non-readable objects from queries.
Detector() - Constructor for class ome.model.acquisition.Detector
 
Detector(Long) - Constructor for class ome.model.acquisition.Detector
 
Detector(Long, boolean) - Constructor for class ome.model.acquisition.Detector
Main constructor.
Detector(DetectorType, Instrument) - Constructor for class ome.model.acquisition.Detector
 
detector - Variable in class ome.model.acquisition.DetectorSettings
 
DETECTOR - Static variable in class ome.model.acquisition.DetectorSettings
 
detector - Variable in class ome.model.acquisition.Instrument
 
DETECTOR - Static variable in class ome.model.acquisition.Instrument
 
Detector.Details - Class in ome.model.acquisition
 
Detector.Details() - Constructor for class ome.model.acquisition.Detector.Details
 
Detector.Details(Object[]) - Constructor for class ome.model.acquisition.Detector.Details
 
Detector_Voltage - Static variable in class ome.formats.model.UnitsFactory
 
DetectorAnnotationLink - Class in ome.model.annotations
These filter definitions are used by the security system to eliminate non-readable objects from queries.
DetectorAnnotationLink() - Constructor for class ome.model.annotations.DetectorAnnotationLink
 
DetectorAnnotationLink(Long) - Constructor for class ome.model.annotations.DetectorAnnotationLink
 
DetectorAnnotationLink(Long, boolean) - Constructor for class ome.model.annotations.DetectorAnnotationLink
Main constructor.
DetectorAnnotationLink(IObject, IObject) - Constructor for class ome.model.annotations.DetectorAnnotationLink
 
DetectorAnnotationLink.Details - Class in ome.model.annotations
 
DetectorAnnotationLink.Details() - Constructor for class ome.model.annotations.DetectorAnnotationLink.Details
 
DetectorAnnotationLink.Details(Object[]) - Constructor for class ome.model.annotations.DetectorAnnotationLink.Details
 
DetectorData - Class in pojos
Hosts a detector.
DetectorData(Detector) - Constructor for class pojos.DetectorData
Creates a new instance.
DetectorSettings - Class in ome.model.acquisition
These filter definitions are used by the security system to eliminate non-readable objects from queries.
DetectorSettings() - Constructor for class ome.model.acquisition.DetectorSettings
 
DetectorSettings(Long) - Constructor for class ome.model.acquisition.DetectorSettings
 
DetectorSettings(Long, boolean) - Constructor for class ome.model.acquisition.DetectorSettings
Main constructor.
DetectorSettings(Detector) - Constructor for class ome.model.acquisition.DetectorSettings
 
detectorSettings - Variable in class ome.model.core.LogicalChannel
 
DETECTORSETTINGS - Static variable in class ome.model.core.LogicalChannel
 
DetectorSettings.Details - Class in ome.model.acquisition
 
DetectorSettings.Details() - Constructor for class ome.model.acquisition.DetectorSettings.Details
 
DetectorSettings.Details(Object[]) - Constructor for class ome.model.acquisition.DetectorSettings.Details
 
DetectorSettings_ReadOutRate - Static variable in class ome.formats.model.UnitsFactory
 
DetectorSettings_Voltage - Static variable in class ome.formats.model.UnitsFactory
 
DetectorType - Class in ome.model.enums
 
DetectorType() - Constructor for class ome.model.enums.DetectorType
 
DetectorType(Long) - Constructor for class ome.model.enums.DetectorType
 
DetectorType(Long, boolean) - Constructor for class ome.model.enums.DetectorType
Main constructor.
DetectorType(String) - Constructor for class ome.model.enums.DetectorType
 
DetectorType.Details - Class in ome.model.enums
 
DetectorType.Details() - Constructor for class ome.model.enums.DetectorType.Details
 
DetectorType.Details(Object[]) - Constructor for class ome.model.enums.DetectorType.Details
 
determineColor(Length) - Static method in class ome.formats.model.ColorsFactory
Determines the color corresponding to the passed value.
Dichroic - Class in ome.model.acquisition
These filter definitions are used by the security system to eliminate non-readable objects from queries.
Dichroic() - Constructor for class ome.model.acquisition.Dichroic
 
Dichroic(Long) - Constructor for class ome.model.acquisition.Dichroic
 
Dichroic(Long, boolean) - Constructor for class ome.model.acquisition.Dichroic
Main constructor.
Dichroic(Instrument) - Constructor for class ome.model.acquisition.Dichroic
 
dichroic - Variable in class ome.model.acquisition.FilterSet
 
DICHROIC - Static variable in class ome.model.acquisition.FilterSet
 
dichroic - Variable in class ome.model.acquisition.Instrument
 
DICHROIC - Static variable in class ome.model.acquisition.Instrument
 
dichroic - Variable in class ome.model.acquisition.LightPath
 
DICHROIC - Static variable in class ome.model.acquisition.LightPath
 
Dichroic.Details - Class in ome.model.acquisition
 
Dichroic.Details() - Constructor for class ome.model.acquisition.Dichroic.Details
 
Dichroic.Details(Object[]) - Constructor for class ome.model.acquisition.Dichroic.Details
 
DichroicAnnotationLink - Class in ome.model.annotations
These filter definitions are used by the security system to eliminate non-readable objects from queries.
DichroicAnnotationLink() - Constructor for class ome.model.annotations.DichroicAnnotationLink
 
DichroicAnnotationLink(Long) - Constructor for class ome.model.annotations.DichroicAnnotationLink
 
DichroicAnnotationLink(Long, boolean) - Constructor for class ome.model.annotations.DichroicAnnotationLink
Main constructor.
DichroicAnnotationLink(IObject, IObject) - Constructor for class ome.model.annotations.DichroicAnnotationLink
 
DichroicAnnotationLink.Details - Class in ome.model.annotations
 
DichroicAnnotationLink.Details() - Constructor for class ome.model.annotations.DichroicAnnotationLink.Details
 
DichroicAnnotationLink.Details(Object[]) - Constructor for class ome.model.annotations.DichroicAnnotationLink.Details
 
DichroicData - Class in pojos
Hosts the dichroic.
DichroicData(Dichroic) - Constructor for class pojos.DichroicData
Creates a new instance.
diff(PlanePoint) - Method in class ome.util.math.geom2D.PlanePoint
Calculates the sum of this vector with the reciprocal of the specified argument.
dimensionOrder - Variable in class ome.model.core.Pixels
 
DIMENSIONORDER - Static variable in class ome.model.core.Pixels
 
DimensionOrder - Class in ome.model.enums
 
DimensionOrder() - Constructor for class ome.model.enums.DimensionOrder
 
DimensionOrder(Long) - Constructor for class ome.model.enums.DimensionOrder
 
DimensionOrder(Long, boolean) - Constructor for class ome.model.enums.DimensionOrder
Main constructor.
DimensionOrder(String) - Constructor for class ome.model.enums.DimensionOrder
 
DimensionOrder.Details - Class in ome.model.enums
 
DimensionOrder.Details() - Constructor for class ome.model.enums.DimensionOrder.Details
 
DimensionOrder.Details(Object[]) - Constructor for class ome.model.enums.DimensionOrder.Details
 
DimensionsOutOfBoundsException - Exception in ome.io.nio
 
DimensionsOutOfBoundsException(String) - Constructor for exception ome.io.nio.DimensionsOutOfBoundsException
 
dimOrder - Variable in class ome.formats.importer.ImportSize
 
direction - Variable in class ome.model.roi.Label
 
DIRECTION - Static variable in class ome.model.roi.Label
 
direction - Variable in class ome.util.math.geom2D.Line
The unit vector that, given the Line.origin point, identifies this line.
directionX1 - Variable in class ome.util.math.geom2D.Segment
The end point of the segment's first element.
directionX2 - Variable in class ome.util.math.geom2D.Segment
The end point of the segment's second element.
DIRECTORY_MIMETYPE - Static variable in class ome.services.blitz.repo.PublicRepositoryI
Mimetype used to connote a directory OriginalFile object.
dirname() - Method in class ome.services.scripts.RepoFile
 
dirtyMetadata(long) - Method in class ome.services.ThumbnailCtx
Whether or not the thumbnail metadata for a given Pixels ID is dirty (the RenderingDef has been updated since the Thumbnail was).
disable(Session) - Method in class ome.security.basic.AbstractSecurityFilter
 
disable(String...) - Method in class ome.security.basic.BasicSecuritySystem
 
disable(Session) - Method in interface ome.security.SecurityFilter
disable(Session) - Method in class ome.security.SecurityFilterHolder
 
disable(String...) - Method in interface ome.security.SecuritySystem
disables components of the backend for the current Thread.
disable(String...) - Method in class ome.security.SecuritySystemHolder
 
disable(String...) - Method in class ome.security.sharing.SharingSecuritySystem
 
disableBaseFilters(Session) - Method in class ome.security.basic.AbstractSecurityFilter
 
disabled(MethodInvocation) - Method in class ome.tools.hibernate.EventMethodInterceptor.DisableAction
 
disableFilters(Session) - Method in class ome.services.query.Query
turns the filters off that are listed in Query.newlyEnabledFilters
disableReadFilter(Object) - Method in class ome.security.basic.BasicSecuritySystem
disable this filer.
disassemble(Object) - Method in class ome.model.units.GenericEnumType
 
disassemble(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
 
discover() - Method in interface ome.api.ILdap
Discovers and lists Experimenters who are present in the remote LDAP server and in the local DB but have the ldap property set to false.
discover() - Method in class ome.logic.LdapImpl
 
discover_async(AMD_ILdap_discover, Current) - Method in class ome.services.blitz.impl.LdapI
 
discoverGroups() - Method in interface ome.api.ILdap
Discovers and lists ExperimenterGroups which are present in the remote LDAP server and in the local DB but have the ldap property set to false.
discoverGroups() - Method in class ome.logic.LdapImpl
 
discoverGroups_async(AMD_ILdap_discoverGroups, Current) - Method in class ome.services.blitz.impl.LdapI
 
discriminator(String) - Method in class ome.services.roi.GeomTool
Maps from multiple possible user-provided names of shapes (e.g.
DiskUsageI - Class in omero.cmd.graphs
Calculate the disk usage entailed by the given objects.
DiskUsageI(PixelsService, ThumbnailService, GraphPathBean) - Constructor for class omero.cmd.graphs.DiskUsageI
Construct a disk usage request.
dispatch(String[]) - Static method in class prefs
Uses the first string in the argument array to reflectively invoke another method with the same signature on prefs.
display - Variable in class ome.model.meta.Namespace
 
DISPLAY - Static variable in class ome.model.meta.Namespace
 
displayName - Variable in class ome.model.meta.Namespace
 
DISPLAYNAME - Static variable in class ome.model.meta.Namespace
 
dispose() - Method in class ome.services.sessions.state.CacheListener
 
dispose() - Method in class ome.util.PixelData
Attempt to free up any native memory resources associated with the data buffer.
distance(PlanePoint) - Method in class ome.util.math.geom2D.PlanePoint
Calculates the distance between this point and the specified argument.
doAction(SecureAction, T...) - Method in class ome.security.basic.BasicSecuritySystem
It would be better to catch the SecureAction#updateObject(IObject) method in a try/finally block, but since flush can be so poorly controlled that's not possible. instead, we use the one time token which is removed this Object is checked for privileges.
doAction(SecureAction, T...) - Method in interface ome.security.SecuritySystem
 
doAction(SecureAction, T...) - Method in class ome.security.SecuritySystemHolder
 
doAction(SecureAction, T...) - Method in class ome.security.sharing.SharingSecuritySystem
 
DoAllI - Class in omero.cmd.basic
Permits performing multiple operations
DoAllI(OmeroContext) - Constructor for class omero.cmd.basic.DoAllI
 
doCheck() - Method in class ome.services.util.DBEnumCheck
 
doCheck() - Method in class ome.services.util.DBUnicodeUnitsCheck
 
doCheckPassword(String, String, Properties, boolean) - Method in class ome.security.auth.FilePasswordProvider
 
doClose() - Method in class ome.services.sharing.BlobShareStore
 
doClose() - Method in class ome.services.sharing.ShareStore
 
doClose - Variable in class omero.cmd.SessionI
 
doContains(long, Class<T>, long) - Method in class ome.services.sharing.BlobShareStore
 
doContains(ShareData, Class<T>, long) - Method in class ome.services.sharing.BlobShareStore
 
doContains(long, Class<T>, long) - Method in class ome.services.sharing.ShareStore
 
doDestroy() - Method in class omero.cmd.SessionI
Performs the actual cleanup operation on all the resources shared between this and other ServiceFactoryI instances in the same Session.
doFilter(String, Object) - Method in class ome.tools.hibernate.ProxyCleanupFilter
 
doFilter(String, Filterable) - Method in class ome.tools.hibernate.ProxySafeFilter
 
doFilter(String, Collection) - Method in class ome.tools.hibernate.ProxySafeFilter
 
doFilter(String, Object) - Method in class ome.util.ContextFilter
 
doFilter(String, Filterable) - Method in class ome.util.ContextFilter
 
doFilter(String, Collection) - Method in class ome.util.ContextFilter
 
doImport() - Method in class ome.formats.importer.ImportFixture
runs import by looping through all files and then calling: ImportLibrary#open(String) ImportLibrary#calculateImageCount(String) ImportLibrary#importMetadata() ImportLibrary#importData(long, String)
doImport() - Method in class ome.formats.importer.util.TinyImportFixture
 
doImport() - Method in class ome.formats.OMEROImportFixture
runs import by looping through all files and then calling: ImportLibrary#open(String) ImportLibrary#calculateImageCount(String) ImportLibrary#importMetadata() ImportLibrary#importData(long, String, ome.formats.testclient.ImportLibrary.Step)
doIndexing(FullTextSession) - Method in class ome.services.fulltext.FullTextIndexer
 
doInHibernate(Session) - Method in class ome.services.query.Query
template method defined by HibernateTemplate.
doInit() - Method in class ome.services.sharing.BlobShareStore
 
doInit() - Method in class ome.services.sharing.ShareStore
 
doLogin(boolean, boolean) - Method in class ome.security.basic.EventHandler
 
doLookup(String, String, Long) - Method in class ome.services.query.HierarchyNavigator
Look up which objects of a given type relate to the given query object.
doLookup(T, E) - Method in class ome.services.query.HierarchyNavigatorWrap
Look up which objects of a given type relate to the given query object.
doMore(int) - Method in class ome.services.fulltext.FullTextIndexer
Default implementation suggests doing more if fewer than FullTextIndexer.reps runs have been made and if there are still more than EventLogLoader.batchSize x 100 backlog entries.
doParse(File) - Method in class ome.services.fulltext.FileParser
Template method to parse a File into manageable chunks.
doParse(File) - Method in class ome.services.fulltext.PdfParser
 
doRun() - Method in class ome.services.fulltext.FullTextThread
Passes the FullTextIndexer instance to Executor.Work#doWork(org.springframework.transaction.TransactionStatus, org.hibernate.Session, ome.system.ServiceFactory) between calls to DetailsFieldBridge.lock() and DetailsFieldBridge.unlock() in order to guarantee that no other FieldBridge can edit the property.
doRun() - Method in class ome.services.pixeldata.PixelDataThread
Loads event logs from the PixelDataHandler processing them all then in a background thread via a ExecutorCompletionService.
doRun() - Method in class ome.services.procs.ProcessManager
 
doRun() - Method in class ome.services.util.ExecutionThread
 
doSet(Share, ShareData, List<ShareItem>) - Method in class ome.services.sharing.BlobShareStore
 
doSet(Share, ShareData, List<ShareItem>) - Method in class ome.services.sharing.ShareStore
 
doStop() - Method in class omero.grid.InteractiveProcessorI
 
dot(PlanePoint) - Method in class ome.util.math.geom2D.PlanePoint
Calulates the dot product of this vector by the specified argument.
doThumbnails - Variable in class ome.formats.importer.ImportConfig
 
DOUBLE(Connection, List<Double>) - Method in interface ome.tools.hibernate.ListAsSQLArrayUserType.ArrayFactory
 
DOUBLE - Static variable in class ome.util.PixelData
Identifies the type used to store pixel values.
DOUBLE - Static variable in class omeis.providers.re.data.PlaneFactory
Identifies the type used to store pixel values.
DOUBLE_COMPLEX_TYPE - Static variable in class pojos.PixelsData
Identifies the type used to store pixel values.
DOUBLE_TYPE - Static variable in class omeis.providers.re.data.PlaneFactory
Identifies the DOUBLE data type used to store pixel values, as per OME spec.
DOUBLE_TYPE - Static variable in class pojos.PixelsData
Identifies the type used to store pixel values.
DoubleAnnotation - Class in ome.model.annotations
 
DoubleAnnotation() - Constructor for class ome.model.annotations.DoubleAnnotation
 
DoubleAnnotation(Long) - Constructor for class ome.model.annotations.DoubleAnnotation
 
DoubleAnnotation(Long, boolean) - Constructor for class ome.model.annotations.DoubleAnnotation
Main constructor.
DoubleAnnotationData - Class in pojos
Wraps a double annotation.
DoubleAnnotationData(double) - Constructor for class pojos.DoubleAnnotationData
Creates a new instance.
DoubleAnnotationData() - Constructor for class pojos.DoubleAnnotationData
Creates a new instance.
DoubleAnnotationData(DoubleAnnotation) - Constructor for class pojos.DoubleAnnotationData
Creates a new instance.
doubleValue - Variable in class ome.model.annotations.DoubleAnnotation
 
DOUBLEVALUE - Static variable in class ome.model.annotations.DoubleAnnotation
 
doUpdate() - Method in class ome.services.sessions.state.SessionCache
Will only ever be accessed by a single thread.
doUpdateRows(Serializable, PersistentCollection, SessionImplementor) - Method in class ome.util.CountCollectionPersister
 
down - Variable in class ome.model.meta.Node
 
DOWN - Static variable in class ome.model.meta.Node
 
down(String, Current) - Method in class ome.services.blitz.fire.Ring
Called when any node goes down.
download(long, File) - Method in class omero.client
 
download(long, File, int) - Method in class omero.client
 
doWork(Session, ServiceFactory) - Method in class ome.services.fulltext.FullTextIndexer
Runs FullTextIndexer.doIndexing(FullTextSession) within a Lucene transaction.
doWork(Session, ServiceFactory) - Method in class ome.services.pixeldata.PixelDataHandler
Loads #rep EventLog instances and returns them.
doWork(Session, ServiceFactory) - Method in class ome.services.procs.ProcessManager.Work
 
doWork(Session, ServiceFactory) - Method in class ome.services.search.AnnotatedWith
 
doWork(Session, ServiceFactory) - Method in class ome.services.search.Complement
 
doWork(Session, ServiceFactory) - Method in class ome.services.search.FullText
 
doWork(Session, ServiceFactory) - Method in class ome.services.search.HqlQuery
 
doWork(Session, ServiceFactory) - Method in class ome.services.search.Intersection
 
doWork(Session, ServiceFactory) - Method in class ome.services.search.SimilarTerms
 
doWork(Session, ServiceFactory) - Method in class ome.services.search.TagsAndGroups
 
doWork(Session, ServiceFactory) - Method in class ome.services.search.Union
 
doWork(SqlAction) - Method in interface ome.services.util.Executor.SqlWork
 
doWork(Session, ServiceFactory) - Method in interface ome.services.util.Executor.Work
Work method.
drop(String[]) - Static method in class prefs
Drops the entire profile (subnode) via Preferences.removeNode().
dryRun - Variable in class ome.services.fulltext.FullTextIndexer
 
dsAllQuery - Static variable in class ome.services.delete.QueryConstraints
 
dsNotOwnQuery - Static variable in class ome.services.delete.QueryConstraints
 
DUMMY - Static variable in class ome.model.internal.Permissions
Marker object which can be set on objects to show that the Permissions instance given contains no value.

E

eachLinkedAnnotation(CBlock<E>) - Method in class ome.model.acquisition.Detector
takes a CBlock and calls the block once for each ome.model.annotations.Annotation while collecting the results.
eachLinkedAnnotation(CBlock<E>) - Method in class ome.model.acquisition.Dichroic
takes a CBlock and calls the block once for each ome.model.annotations.Annotation while collecting the results.
eachLinkedAnnotation(CBlock<E>) - Method in class ome.model.acquisition.Filter
takes a CBlock and calls the block once for each ome.model.annotations.Annotation while collecting the results.
eachLinkedAnnotation(CBlock<E>) - Method in class ome.model.acquisition.Instrument
takes a CBlock and calls the block once for each ome.model.annotations.Annotation while collecting the results.
eachLinkedAnnotation(CBlock<E>) - Method in class ome.model.acquisition.LightPath
takes a CBlock and calls the block once for each ome.model.annotations.Annotation while collecting the results.
eachLinkedAnnotation(CBlock<E>) - Method in class ome.model.acquisition.LightSource
takes a CBlock and calls the block once for each ome.model.annotations.Annotation while collecting the results.
eachLinkedAnnotation(CBlock<E>) - Method in class ome.model.acquisition.Objective
takes a CBlock and calls the block once for each ome.model.annotations.Annotation while collecting the results.
eachLinkedAnnotation(CBlock<E>) - Method in class ome.model.annotations.Annotation
takes a CBlock and calls the block once for each ome.model.annotations.Annotation while collecting the results.
eachLinkedAnnotation(CBlock<E>) - Method in class ome.model.containers.Dataset
takes a CBlock and calls the block once for each ome.model.annotations.Annotation while collecting the results.
eachLinkedAnnotation(CBlock<E>) - Method in class ome.model.containers.Project
takes a CBlock and calls the block once for each ome.model.annotations.Annotation while collecting the results.
eachLinkedAnnotation(CBlock<E>) - Method in class ome.model.core.Channel
takes a CBlock and calls the block once for each ome.model.annotations.Annotation while collecting the results.
eachLinkedAnnotation(CBlock<E>) - Method in class ome.model.core.Image
takes a CBlock and calls the block once for each ome.model.annotations.Annotation while collecting the results.
eachLinkedAnnotation(CBlock<E>) - Method in class ome.model.core.OriginalFile
takes a CBlock and calls the block once for each ome.model.annotations.Annotation while collecting the results.
eachLinkedAnnotation(CBlock<E>) - Method in class ome.model.core.PlaneInfo
takes a CBlock and calls the block once for each ome.model.annotations.Annotation while collecting the results.
eachLinkedAnnotation(CBlock<E>) - Method in class ome.model.fs.Fileset
takes a CBlock and calls the block once for each ome.model.annotations.Annotation while collecting the results.
eachLinkedAnnotation(CBlock<E>) - Method in interface ome.model.IAnnotated
 
eachLinkedAnnotation(CBlock<E>) - Method in class ome.model.meta.Experimenter
takes a CBlock and calls the block once for each ome.model.annotations.Annotation while collecting the results.
eachLinkedAnnotation(CBlock<E>) - Method in class ome.model.meta.ExperimenterGroup
takes a CBlock and calls the block once for each ome.model.annotations.Annotation while collecting the results.
eachLinkedAnnotation(CBlock<E>) - Method in class ome.model.meta.Namespace
takes a CBlock and calls the block once for each ome.model.annotations.Annotation while collecting the results.
eachLinkedAnnotation(CBlock<E>) - Method in class ome.model.meta.Node
takes a CBlock and calls the block once for each ome.model.annotations.Annotation while collecting the results.
eachLinkedAnnotation(CBlock<E>) - Method in class ome.model.meta.Session
takes a CBlock and calls the block once for each ome.model.annotations.Annotation while collecting the results.
eachLinkedAnnotation(CBlock<E>) - Method in class ome.model.roi.Roi
takes a CBlock and calls the block once for each ome.model.annotations.Annotation while collecting the results.
eachLinkedAnnotation(CBlock<E>) - Method in class ome.model.roi.Shape
takes a CBlock and calls the block once for each ome.model.annotations.Annotation while collecting the results.
eachLinkedAnnotation(CBlock<E>) - Method in class ome.model.screen.Plate
takes a CBlock and calls the block once for each ome.model.annotations.Annotation while collecting the results.
eachLinkedAnnotation(CBlock<E>) - Method in class ome.model.screen.PlateAcquisition
takes a CBlock and calls the block once for each ome.model.annotations.Annotation while collecting the results.
eachLinkedAnnotation(CBlock<E>) - Method in class ome.model.screen.Reagent
takes a CBlock and calls the block once for each ome.model.annotations.Annotation while collecting the results.
eachLinkedAnnotation(CBlock<E>) - Method in class ome.model.screen.Screen
takes a CBlock and calls the block once for each ome.model.annotations.Annotation while collecting the results.
eachLinkedAnnotation(CBlock<E>) - Method in class ome.model.screen.Well
takes a CBlock and calls the block once for each ome.model.annotations.Annotation while collecting the results.
eachLinkedDataset(CBlock<E>) - Method in class ome.model.containers.Project
takes a CBlock and calls the block once for each ome.model.containers.Dataset while collecting the results.
eachLinkedDataset(CBlock<E>) - Method in class ome.model.core.Image
takes a CBlock and calls the block once for each ome.model.containers.Dataset while collecting the results.
eachLinkedEmissionFilter(CBlock<E>) - Method in class ome.model.acquisition.Filter
takes a CBlock and calls the block once for each ome.model.acquisition.FilterSet while collecting the results.
eachLinkedEmissionFilter(CBlock<E>) - Method in class ome.model.acquisition.FilterSet
takes a CBlock and calls the block once for each ome.model.acquisition.Filter while collecting the results.
eachLinkedEmissionFilter(CBlock<E>) - Method in class ome.model.acquisition.LightPath
takes a CBlock and calls the block once for each ome.model.acquisition.Filter while collecting the results.
eachLinkedExcitationFilter(CBlock<E>) - Method in class ome.model.acquisition.Filter
takes a CBlock and calls the block once for each ome.model.acquisition.FilterSet while collecting the results.
eachLinkedExcitationFilter(CBlock<E>) - Method in class ome.model.acquisition.FilterSet
takes a CBlock and calls the block once for each ome.model.acquisition.Filter while collecting the results.
eachLinkedExcitationFilter(CBlock<E>) - Method in class ome.model.acquisition.LightPath
takes a CBlock and calls the block once for each ome.model.acquisition.Filter while collecting the results.
eachLinkedExperimenter(CBlock<E>) - Method in class ome.model.meta.ExperimenterGroup
takes a CBlock and calls the block once for each ome.model.meta.Experimenter while collecting the results.
eachLinkedExperimenterGroup(CBlock<E>) - Method in class ome.model.meta.Experimenter
takes a CBlock and calls the block once for each ome.model.meta.ExperimenterGroup while collecting the results.
eachLinkedImage(CBlock<E>) - Method in class ome.model.containers.Dataset
takes a CBlock and calls the block once for each ome.model.core.Image while collecting the results.
eachLinkedJob(CBlock<E>) - Method in class ome.model.fs.Fileset
takes a CBlock and calls the block once for each ome.model.jobs.Job while collecting the results.
eachLinkedOriginalFile(CBlock<E>) - Method in class ome.model.core.Pixels
takes a CBlock and calls the block once for each ome.model.core.OriginalFile while collecting the results.
eachLinkedOriginalFile(CBlock<E>) - Method in class ome.model.jobs.Job
takes a CBlock and calls the block once for each ome.model.core.OriginalFile while collecting the results.
eachLinkedPixels(CBlock<E>) - Method in class ome.model.core.OriginalFile
takes a CBlock and calls the block once for each ome.model.core.Pixels while collecting the results.
eachLinkedPlate(CBlock<E>) - Method in class ome.model.screen.Screen
takes a CBlock and calls the block once for each ome.model.screen.Plate while collecting the results.
eachLinkedProject(CBlock<E>) - Method in class ome.model.containers.Dataset
takes a CBlock and calls the block once for each ome.model.containers.Project while collecting the results.
eachLinkedReagent(CBlock<E>) - Method in class ome.model.screen.Well
takes a CBlock and calls the block once for each ome.model.screen.Reagent while collecting the results.
eachLinkedScreen(CBlock<E>) - Method in class ome.model.screen.Plate
takes a CBlock and calls the block once for each ome.model.screen.Screen while collecting the results.
eachLinkedWell(CBlock<E>) - Method in class ome.model.screen.Reagent
takes a CBlock and calls the block once for each ome.model.screen.Well while collecting the results.
ec - Variable in class ome.services.graphs.GraphStep
Deprecated.
An event context which has been initialized for a particular group, i.e.
EDITRESTRICTION - Static variable in class ome.model.internal.Permissions
 
editScript_async(AMD_IScript_editScript, OriginalFile, String, Current) - Method in class ome.services.blitz.impl.ScriptI
 
ElectricPotential - Class in ome.model.units
class storing both a ElectricPotential and a unit for that ElectricPotential (e.g. m, in, ly, etc.) encapsulated in a UnitsElectricPotential instance.
ElectricPotential() - Constructor for class ome.model.units.ElectricPotential
Deprecated.
ElectricPotential(double, String) - Constructor for class ome.model.units.ElectricPotential
 
ElectricPotential(double, UnitsElectricPotential) - Constructor for class ome.model.units.ElectricPotential
 
ElectricPotential(double, Unit<ElectricPotential>) - Constructor for class ome.model.units.ElectricPotential
 
ElectricPotential(ElectricPotential) - Constructor for class ome.model.units.ElectricPotential
 
ElectricPotentialI - Class in omero.model
Blitz wrapper around the ElectricPotential class.
ElectricPotentialI() - Constructor for class omero.model.ElectricPotentialI
 
ElectricPotentialI(double, UnitsElectricPotential) - Constructor for class omero.model.ElectricPotentialI
 
ElectricPotentialI(double, Unit<ElectricPotential>) - Constructor for class omero.model.ElectricPotentialI
 
ElectricPotentialI(ElectricPotential, Unit<ElectricPotential>) - Constructor for class omero.model.ElectricPotentialI
Copy constructor that converts the given ElectricPotential based on the given ome-xml enum
ElectricPotentialI(double, UnitsElectricPotential) - Constructor for class omero.model.ElectricPotentialI
Copy constructor that converts the given ElectricPotential based on the given ome.model enum
ElectricPotentialI(ElectricPotential, String) - Constructor for class omero.model.ElectricPotentialI
Copy constructor that converts the given ElectricPotential based on the given enum string.
ElectricPotentialI(ElectricPotential, UnitsElectricPotential) - Constructor for class omero.model.ElectricPotentialI
Copy constructor that converts between units if possible.
ElectricPotentialI(ElectricPotential) - Constructor for class omero.model.ElectricPotentialI
Convert a Bio-Formats Length to an OMERO Length.
elementType - Variable in class ome.services.query.CollectionQueryParameterDef
 
Ellipse - Class in ome.model.roi
 
Ellipse() - Constructor for class ome.model.roi.Ellipse
 
Ellipse(Long) - Constructor for class ome.model.roi.Ellipse
 
Ellipse(Long, boolean) - Constructor for class ome.model.roi.Ellipse
Main constructor.
ellipse(double, double, double, double) - Method in class ome.services.roi.GeomTool
 
ellipse(double, double, double, double, int, int) - Method in class ome.services.roi.GeomTool
 
EllipseArea - Class in ome.util.math.geom2D
Represents an ellipse in the Euclidean space R2.
EllipseArea(float, float, float, float) - Constructor for class ome.util.math.geom2D.EllipseArea
Creates a new instance.
EllipseData - Class in pojos
Represents an ellipse in the Euclidean space R2.
EllipseData(Shape) - Constructor for class pojos.EllipseData
Creates a new instance of Ellipse data from an existing shape.
EllipseData() - Constructor for class pojos.EllipseData
Creates a new instance of EllipseData.
EllipseData(double, double, double, double) - Constructor for class pojos.EllipseData
Creates a new instance of the EllipseData.
em - Variable in class ome.services.delete.Deletion.Builder
Deprecated.
 
em - Variable in class ome.services.graphs.BaseGraphSpec
Deprecated.
 
em - Variable in class ome.services.graphs.GraphStep
Deprecated.
 
email - Variable in class ome.formats.importer.ImportConfig
 
email - Variable in class ome.model.meta.Experimenter
 
EMAIL - Static variable in class ome.model.meta.Experimenter
 
EMAIL - Static variable in class pojos.ExperimenterData
Identifies the Experimenter#EMAIL field.
emissionFilterLink - Variable in class ome.model.acquisition.Filter
 
EMISSIONFILTERLINK - Static variable in class ome.model.acquisition.Filter
 
emissionFilterLink - Variable in class ome.model.acquisition.FilterSet
 
EMISSIONFILTERLINK - Static variable in class ome.model.acquisition.FilterSet
 
emissionFilterLink - Variable in class ome.model.acquisition.LightPath
 
EMISSIONFILTERLINK - Static variable in class ome.model.acquisition.LightPath
 
EMISSIONFILTERLINKCOUNTPEROWNER - Static variable in class ome.model.acquisition.Filter
 
EMISSIONFILTERLINKCOUNTPEROWNER - Static variable in class ome.model.acquisition.FilterSet
 
EMISSIONFILTERLINKCOUNTPEROWNER - Static variable in class ome.model.acquisition.LightPath
 
emissionWave - Variable in class ome.model.core.LogicalChannel
 
EMISSIONWAVE - Static variable in class ome.model.core.LogicalChannel
 
empty() - Method in class ome.formats.importer.ImportConfig.StrValue
 
empty() - Method in class ome.formats.importer.ImportConfig.Value
 
EMPTY - Static variable in class ome.model.internal.Permissions
an immutable Permissions instance with all rights turned off.
EMPTY - Static variable in class ome.services.fulltext.FileParser
Iterable which returns an empty Iterator.
emptyCleanups() - Method in class ome.security.basic.CurrentDetails
Returns the current cleanups and resets the Set.
EmptyIterator<E> - Class in ome.util
utility iterator which does nothing as quickly as possible.
EmptyIterator() - Constructor for class ome.util.EmptyIterator
 
emptyPath - Static variable in class ome.services.blitz.repo.path.FsFile
the FsFile that has no path components
enable(Session, EventContext) - Method in class ome.security.basic.AllGroupsSecurityFilter
Since we assume that the group is "-1" for this method, we have to pass in lists of all groups as we did before group permissions (~4.2).
enable(String...) - Method in class ome.security.basic.BasicSecuritySystem
 
enable(Session, EventContext) - Method in class ome.security.basic.OneGroupSecurityFilter
 
enable(Session, EventContext) - Method in interface ome.security.SecurityFilter
Enables this filter with the settings from this filter.
enable(Session, EventContext) - Method in class ome.security.SecurityFilterHolder
 
enable(String...) - Method in interface ome.security.SecuritySystem
enables components of the backend for the current Thread.
enable(String...) - Method in class ome.security.SecuritySystemHolder
 
enable(String...) - Method in class ome.security.sharing.SharingSecuritySystem
 
enableBaseFilters(Session, int, Long) - Method in class ome.security.basic.AbstractSecurityFilter
 
enableFilters(Session) - Method in class ome.services.query.PojosFindHierarchiesQueryDefinition
 
enableFilters(Session) - Method in class ome.services.query.PojosGetImagesByOptionsQueryDefinition
 
enableFilters(Session) - Method in class ome.services.query.PojosGetImagesQueryDefinition
 
enableFilters(Session) - Method in class ome.services.query.PojosGetUserImagesQueryDefinition
 
enableFilters(Session) - Method in class ome.services.query.PojosLoadHierarchyQueryDefinition
 
enableFilters(Session) - Method in class ome.services.query.Query
does nothing by default, but can be overridden by subclasses to enable particular filters.
enableKeepAlive(int) - Method in class omero.client
Resets the "omero.keep_alive" property on the current Communicator which is used on initialization to determine the time-period between checks.
enableReadFilter(Object) - Method in class ome.security.basic.BasicSecuritySystem
enables the read filter such that graph queries will have non-visible entities silently removed from the return value.
encodePassword(String) - Method in class ome.security.auth.ConfigurablePasswordProvider
Encodes the password as it would be encoded for a check by ConfigurablePasswordProvider.comparePasswords(String, String)
encodePassword(Long, String, boolean, PasswordUtil) - Method in class ome.security.auth.ConfigurablePasswordProvider
 
encodePassword(String) - Method in interface ome.security.auth.PasswordUtility
 
encodeSaltedPassword(Long, String) - Method in class ome.security.auth.ConfigurablePasswordProvider
Encodes the password as it would be encoded for a check by ConfigurablePasswordProvider.comparePasswords(String, String) salting the password with the given userId if it's provided.
encryptedConnection - Variable in class ome.formats.importer.ImportConfig
 
endIO(int) - Method in class omeis.providers.re.RenderingStats
Notifies the end of pixels data retrieval for the specified wavelength (channel).
endMalloc() - Method in class omeis.providers.re.RenderingStats
Notifies the end of the allocation of an RGB memory buffers for the rendering process.
endRendering() - Method in class omeis.providers.re.RenderingStats
Notifies the end of the trasnformation of the raw pixels data.
endTime - Variable in class ome.model.screen.PlateAcquisition
 
ENDTIME - Static variable in class ome.model.screen.PlateAcquisition
 
endTime - Variable in class ome.parameters.Filter
 
endTime(Timestamp) - Method in class ome.parameters.Parameters
 
endTime(RTime) - Method in class omero.sys.ParametersI
Sets the value of the end time parameter.
endTransaction(boolean) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
enter(Object) - Method in class ome.util.ContextFilter
 
entityId - Variable in class ome.model.meta.EventLog
 
ENTITYID - Static variable in class ome.model.meta.EventLog
 
entityId - Variable in class ome.model.meta.ExternalInfo
 
ENTITYID - Static variable in class ome.model.meta.ExternalInfo
 
entityIds - Variable in class ome.services.messages.EventLogMessage
 
entityIsDetached(MergeEvent, Map) - Method in class ome.security.basic.MergeEventListener
 
entityIsTransient(MergeEvent, Map) - Method in class ome.security.basic.MergeEventListener
 
entityToStringLong(E) - Method in class ome.services.query.HierarchyNavigatorWrap
Convert a model object to the type string and database ID expected by HierarchyNavigator.
entityType - Variable in class ome.model.meta.EventLog
 
ENTITYTYPE - Static variable in class ome.model.meta.EventLog
 
entityType - Variable in class ome.model.meta.ExternalInfo
 
ENTITYTYPE - Static variable in class ome.model.meta.ExternalInfo
 
entityType - Variable in class ome.services.messages.EventLogMessage
 
entries - Variable in class ome.services.graphs.BaseGraphSpec
Deprecated.
The paths which make up this graph specification.
entries() - Method in class ome.services.graphs.BaseGraphSpec
Deprecated.
 
entries() - Method in interface ome.services.graphs.GraphSpec
Deprecated.
Returns a copy of the list of GraphEntry instances contained in this GraphSpec
Entry - Class in ome.services.blitz
OMERO.blitz startup code.
Entry(String) - Constructor for class ome.services.blitz.Entry
Stores name of the OmeroContext which is to be used by this instance.
entry - Variable in class ome.services.graphs.GraphStep
Deprecated.
GraphEntry instance which is active for this step.
entry(String, Object) - Method in class ome.util.RdfPrinter
 
entrySet() - Method in class ome.services.graphs.GraphState
Deprecated.
 
entrySet() - Method in interface ome.services.graphs.GraphStep.Callback
Deprecated.
 
EnumerationException - Exception in ome.formats.enums
 
EnumerationException(String, Class<? extends IObject>, String) - Constructor for exception ome.formats.enums.EnumerationException
 
EnumerationHandler - Interface in ome.formats.enums.handler
An enumeration handler whose purpose is to provide extra logic, such as regular expression matching, for the lookup of enumerations for a specific type.
EnumerationProvider - Interface in ome.formats.enums
An enumeration provider, whose job is to make OMERO enumerations available to a consumer based on a set of criteria.
EnumHandlerFactory - Class in ome.formats.enums.handler
Factory for all available enumeration handlers.
EnumHandlerFactory() - Constructor for class ome.formats.enums.handler.EnumHandlerFactory
 
env() - Method in class omero.client
Helper method to access session environment
ENV - Static variable in class prefs
Environment variable which can be set to override the current, active profile.
environment(String, String) - Method in class ome.services.sessions.SessionManagerImpl
 
EPSILON - Static variable in class ome.logic.RenderingSettingsImpl
The value used to compare double and float.
equals(Object) - Method in class ome.model.internal.NamedValue
 
equals(Object) - Method in class ome.model.units.ElectricPotential
 
equals(Object) - Method in class ome.model.units.Frequency
 
equals(Object, Object) - Method in class ome.model.units.GenericEnumType
 
equals(Object) - Method in class ome.model.units.Length
 
equals(Object) - Method in class ome.model.units.Power
 
equals(Object) - Method in class ome.model.units.Pressure
 
equals(Object) - Method in class ome.model.units.Temperature
 
equals(Object) - Method in class ome.model.units.Time
 
equals(Object) - Method in class ome.parameters.QueryParameter
 
equals(Object) - Method in class ome.services.blitz.repo.CheckedPath
Instances are equal if their string representations match.
equals(Object) - Method in class ome.services.blitz.repo.path.FsFile
Instances are equal if their string representations match.
equals(Object) - Method in class ome.tools.FileSystem
Public equals implementation based on name only (very loose equals)
equals(Object, Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
 
equals(Object) - Method in class ome.util.LSID
 
equals(Object) - Method in class ome.util.math.geom2D.Line
Overridden to reflect equality of abstract values (data object) as opposite to object identity.
equals(Object) - Method in class ome.util.math.geom2D.PlanePoint
Overridden to reflect equality of abstract values (data object) as opposite to object identity.
equals(double, double) - Method in class ome.util.math.geom2D.PlanePoint
Check to see if the point values are equal.
equals(double, double, double) - Method in class ome.util.math.geom2D.Segment
Performs an equality test based on a point on this line defined by k as in getPoint() and another given point.
equals(Object) - Method in class ome.util.math.geom2D.Segment
Overridden to reflect equality of abstract values (data object) as opposite to object identity.
equals(Object) - Method in class omeis.providers.re.codomain.CodomainMapContext
This method is overridden so that objects of the same class are considered the same.
equals(Object) - Method in class omeis.providers.re.data.PlaneDef
Overridden to reflect equality of abstract values (data object) as opposite to object identity.
equals(Object) - Method in class omero.cmd.graphs.Preprocessor.GraphModifyTarget
Deprecated.
 
equals(Object) - Method in class omero.model.ElectricPotentialI
 
equals(Object) - Method in class omero.model.FrequencyI
 
equals(Object) - Method in class omero.model.LengthI
 
equals(Object) - Method in class omero.model.PowerI
 
equals(Object) - Method in class omero.model.PressureI
 
equals(Object) - Method in class omero.model.TemperatureI
 
equals(Object) - Method in class omero.model.TimeI
 
equals(Object) - Method in class pojos.ROICoordinate
Overridden to control if the passed object equals the current one.
ERROR - Static variable in interface ome.api.JobHandle
 
error() - Method in class ome.services.delete.Deletion
Deprecated.
 
error(SqlAction.DeleteLog, Throwable) - Method in class ome.services.messages.DeleteLogMessage
 
error(String, Object...) - Method in class omero.cmd.Helper
 
error(Throwable, String, Object...) - Method in class omero.cmd.Helper
 
ErrorContainer - Class in ome.formats.importer.util
Container for errors
ErrorContainer() - Constructor for class ome.formats.importer.util.ErrorContainer
 
errorCount - Variable in class ome.formats.importer.ImportEvent.IMPORT_SUMMARY
 
errorCount() - Method in class ome.formats.importer.util.ErrorHandler
 
ErrorHandler - Class in ome.formats.importer.cli
IObserver based on the gui ErrorHandler code which collects all exceptions during ImportLibrary.importCandidates(ome.formats.importer.ImportConfig, ome.formats.importer.ImportCandidates) and after the import is finished offers to submit them via the feedback system.
ErrorHandler(ImportConfig) - Constructor for class ome.formats.importer.cli.ErrorHandler
 
ErrorHandler - Class in ome.formats.importer.util
Top of the error handling hierarchy.
ErrorHandler(ImportConfig) - Constructor for class ome.formats.importer.util.ErrorHandler
Initialize
ErrorHandler.EXCEPTION_EVENT - Class in ome.formats.importer.util
 
ErrorHandler.EXCEPTION_EVENT(Exception) - Constructor for class ome.formats.importer.util.ErrorHandler.EXCEPTION_EVENT
 
ErrorHandler.FILE_EXCEPTION - Class in ome.formats.importer.util
ErrorHandler.FILE_EXCEPTIONs are thrown any time in the context of a particular file and otherwise unspecified exception takes place.
ErrorHandler.FILE_EXCEPTION(String, Exception, String[], String) - Constructor for class ome.formats.importer.util.ErrorHandler.FILE_EXCEPTION
 
ErrorHandler.INTERNAL_EXCEPTION - Class in ome.formats.importer.util
 
ErrorHandler.INTERNAL_EXCEPTION(String, Exception, String[], String) - Constructor for class ome.formats.importer.util.ErrorHandler.INTERNAL_EXCEPTION
 
ErrorHandler.MISSING_LIBRARY - Class in ome.formats.importer.util
A ErrorHandler.FILE_EXCEPTION caused specifically by some library (native or otherwise) not being installed locally.
ErrorHandler.MISSING_LIBRARY(String, MissingLibraryException, String[], String) - Constructor for class ome.formats.importer.util.ErrorHandler.MISSING_LIBRARY
 
ErrorHandler.UNKNOWN_FORMAT - Class in ome.formats.importer.util
Unlike ErrorHandler.FILE_EXCEPTION, UNKNOWN_FORMAT does not have a reader since bio-formats is telling us that it does not know how to handle the given file.
ErrorHandler.UNKNOWN_FORMAT(String, Exception, Object) - Constructor for class ome.formats.importer.util.ErrorHandler.UNKNOWN_FORMAT
 
ErrorHandler.UNREADABLE_FILE - Class in ome.formats.importer.util
Similar to ErrorHandler.UNKNOWN_FORMAT UNREADABLE_FILE specifies that the file which is being accessed is unreadable (does not exist or canRead is false), so if the user is specifically saying that the file should be imported, there may be some underlying issue.
ErrorHandler.UNREADABLE_FILE(String, Exception, Object) - Constructor for class ome.formats.importer.util.ErrorHandler.UNREADABLE_FILE
 
errorIfInvalid(QueryParameter) - Method in class ome.services.query.CollectionQueryParameterDef
 
errorIfInvalid(QueryParameter) - Method in class ome.services.query.QueryParameterDef
validation method called by Query.checkParameters().
errorIfInvalidState() - Method in class ome.services.JobBean
 
errorIfInvalidState() - Method in class ome.services.RenderingBean
 
errorIfInvalidState() - Method in class ome.services.ThumbnailBean
 
errorIfNullPixels() - Method in class ome.services.RenderingBean
Throws an ApiUsageException if the pixels are not set.
errorIfNullPixels() - Method in class ome.services.ThumbnailBean
 
errorIfNullPixelsAndRenderingDef() - Method in class ome.services.ThumbnailBean
 
errorIfNullRenderer() - Method in class ome.services.RenderingBean
Reloads the rendering engine if null and has been made passive or throws an ApiUsageException if the rendering engine is not set.
errorIfNullRenderingDef() - Method in class ome.services.RenderingBean
Throws an ApiUsageException if the rendering settings are not set.
errorIfNullRenderingDef() - Method in class ome.services.ThumbnailBean
 
errorIfUnloaded() - Method in class ome.model.acquisition.Detector
 
errorIfUnloaded() - Method in class ome.model.acquisition.DetectorSettings
 
errorIfUnloaded() - Method in class ome.model.acquisition.Dichroic
 
errorIfUnloaded() - Method in class ome.model.acquisition.Filter
 
errorIfUnloaded() - Method in class ome.model.acquisition.FilterSet
 
errorIfUnloaded() - Method in class ome.model.acquisition.FilterSetEmissionFilterLink
 
errorIfUnloaded() - Method in class ome.model.acquisition.FilterSetExcitationFilterLink
 
errorIfUnloaded() - Method in class ome.model.acquisition.ImagingEnvironment
 
errorIfUnloaded() - Method in class ome.model.acquisition.Instrument
 
errorIfUnloaded() - Method in class ome.model.acquisition.LightPath
 
errorIfUnloaded() - Method in class ome.model.acquisition.LightPathEmissionFilterLink
 
errorIfUnloaded() - Method in class ome.model.acquisition.LightPathExcitationFilterLink
 
errorIfUnloaded() - Method in class ome.model.acquisition.LightSettings
 
errorIfUnloaded() - Method in class ome.model.acquisition.LightSource
 
errorIfUnloaded() - Method in class ome.model.acquisition.Microscope
 
errorIfUnloaded() - Method in class ome.model.acquisition.Objective
 
errorIfUnloaded() - Method in class ome.model.acquisition.ObjectiveSettings
 
errorIfUnloaded() - Method in class ome.model.acquisition.OTF
 
errorIfUnloaded() - Method in class ome.model.acquisition.StageLabel
 
errorIfUnloaded() - Method in class ome.model.acquisition.TransmittanceRange
 
errorIfUnloaded() - Method in class ome.model.annotations.Annotation
 
errorIfUnloaded() - Method in class ome.model.annotations.AnnotationAnnotationLink
 
errorIfUnloaded() - Method in class ome.model.annotations.ChannelAnnotationLink
 
errorIfUnloaded() - Method in class ome.model.annotations.DatasetAnnotationLink
 
errorIfUnloaded() - Method in class ome.model.annotations.DetectorAnnotationLink
 
errorIfUnloaded() - Method in class ome.model.annotations.DichroicAnnotationLink
 
errorIfUnloaded() - Method in class ome.model.annotations.ExperimenterAnnotationLink
 
errorIfUnloaded() - Method in class ome.model.annotations.ExperimenterGroupAnnotationLink
 
errorIfUnloaded() - Method in class ome.model.annotations.FilesetAnnotationLink
 
errorIfUnloaded() - Method in class ome.model.annotations.FilterAnnotationLink
 
errorIfUnloaded() - Method in class ome.model.annotations.ImageAnnotationLink
 
errorIfUnloaded() - Method in class ome.model.annotations.InstrumentAnnotationLink
 
errorIfUnloaded() - Method in class ome.model.annotations.LightPathAnnotationLink
 
errorIfUnloaded() - Method in class ome.model.annotations.LightSourceAnnotationLink
 
errorIfUnloaded() - Method in class ome.model.annotations.NamespaceAnnotationLink
 
errorIfUnloaded() - Method in class ome.model.annotations.NodeAnnotationLink
 
errorIfUnloaded() - Method in class ome.model.annotations.ObjectiveAnnotationLink
 
errorIfUnloaded() - Method in class ome.model.annotations.OriginalFileAnnotationLink
 
errorIfUnloaded() - Method in class ome.model.annotations.PlaneInfoAnnotationLink
 
errorIfUnloaded() - Method in class ome.model.annotations.PlateAcquisitionAnnotationLink
 
errorIfUnloaded() - Method in class ome.model.annotations.PlateAnnotationLink
 
errorIfUnloaded() - Method in class ome.model.annotations.ProjectAnnotationLink
 
errorIfUnloaded() - Method in class ome.model.annotations.ReagentAnnotationLink
 
errorIfUnloaded() - Method in class ome.model.annotations.RoiAnnotationLink
 
errorIfUnloaded() - Method in class ome.model.annotations.ScreenAnnotationLink
 
errorIfUnloaded() - Method in class ome.model.annotations.SessionAnnotationLink
 
errorIfUnloaded() - Method in class ome.model.annotations.ShapeAnnotationLink
 
errorIfUnloaded() - Method in class ome.model.annotations.WellAnnotationLink
 
errorIfUnloaded() - Method in class ome.model.containers.Dataset
 
errorIfUnloaded() - Method in class ome.model.containers.DatasetImageLink
 
errorIfUnloaded() - Method in class ome.model.containers.Project
 
errorIfUnloaded() - Method in class ome.model.containers.ProjectDatasetLink
 
errorIfUnloaded() - Method in class ome.model.core.Channel
 
errorIfUnloaded() - Method in class ome.model.core.Image
 
errorIfUnloaded() - Method in class ome.model.core.LogicalChannel
 
errorIfUnloaded() - Method in class ome.model.core.OriginalFile
 
errorIfUnloaded() - Method in class ome.model.core.Pixels
 
errorIfUnloaded() - Method in class ome.model.core.PixelsOriginalFileMap
 
errorIfUnloaded() - Method in class ome.model.core.PlaneInfo
 
errorIfUnloaded() - Method in class ome.model.display.ChannelBinding
 
errorIfUnloaded() - Method in class ome.model.display.CodomainMapContext
 
errorIfUnloaded() - Method in class ome.model.display.QuantumDef
 
errorIfUnloaded() - Method in class ome.model.display.RenderingDef
 
errorIfUnloaded() - Method in class ome.model.display.Thumbnail
 
errorIfUnloaded() - Method in class ome.model.enums.AcquisitionMode
 
errorIfUnloaded() - Method in class ome.model.enums.ArcType
 
errorIfUnloaded() - Method in class ome.model.enums.Binning
 
errorIfUnloaded() - Method in class ome.model.enums.ChecksumAlgorithm
 
errorIfUnloaded() - Method in class ome.model.enums.ContrastMethod
 
errorIfUnloaded() - Method in class ome.model.enums.Correction
 
errorIfUnloaded() - Method in class ome.model.enums.DetectorType
 
errorIfUnloaded() - Method in class ome.model.enums.DimensionOrder
 
errorIfUnloaded() - Method in class ome.model.enums.EventType
 
errorIfUnloaded() - Method in class ome.model.enums.ExperimentType
 
errorIfUnloaded() - Method in class ome.model.enums.Family
 
errorIfUnloaded() - Method in class ome.model.enums.FilamentType
 
errorIfUnloaded() - Method in class ome.model.enums.FilterType
 
errorIfUnloaded() - Method in class ome.model.enums.Format
 
errorIfUnloaded() - Method in class ome.model.enums.Illumination
 
errorIfUnloaded() - Method in class ome.model.enums.Immersion
 
errorIfUnloaded() - Method in class ome.model.enums.LaserMedium
 
errorIfUnloaded() - Method in class ome.model.enums.LaserType
 
errorIfUnloaded() - Method in class ome.model.enums.Medium
 
errorIfUnloaded() - Method in class ome.model.enums.MicrobeamManipulationType
 
errorIfUnloaded() - Method in class ome.model.enums.MicroscopeType
 
errorIfUnloaded() - Method in class ome.model.enums.PhotometricInterpretation
 
errorIfUnloaded() - Method in class ome.model.enums.PixelsType
 
errorIfUnloaded() - Method in class ome.model.enums.Pulse
 
errorIfUnloaded() - Method in class ome.model.enums.RenderingModel
 
errorIfUnloaded() - Method in class ome.model.experiment.Experiment
 
errorIfUnloaded() - Method in class ome.model.experiment.MicrobeamManipulation
 
errorIfUnloaded() - Method in class ome.model.fs.Fileset
 
errorIfUnloaded() - Method in class ome.model.fs.FilesetEntry
 
errorIfUnloaded() - Method in class ome.model.fs.FilesetJobLink
 
errorIfUnloaded() - Method in class ome.model.internal.Link
 
errorIfUnloaded() - Method in class ome.model.jobs.Job
 
errorIfUnloaded() - Method in class ome.model.jobs.JobOriginalFileLink
 
errorIfUnloaded() - Method in class ome.model.jobs.JobStatus
 
errorIfUnloaded() - Method in class ome.model.meta.DBPatch
 
errorIfUnloaded() - Method in class ome.model.meta.Event
 
errorIfUnloaded() - Method in class ome.model.meta.EventLog
 
errorIfUnloaded() - Method in class ome.model.meta.Experimenter
 
errorIfUnloaded() - Method in class ome.model.meta.ExperimenterGroup
 
errorIfUnloaded() - Method in class ome.model.meta.ExternalInfo
 
errorIfUnloaded() - Method in class ome.model.meta.GroupExperimenterMap
 
errorIfUnloaded() - Method in class ome.model.meta.Namespace
 
errorIfUnloaded() - Method in class ome.model.meta.Node
 
errorIfUnloaded() - Method in class ome.model.meta.Session
 
errorIfUnloaded() - Method in class ome.model.meta.ShareMember
 
errorIfUnloaded() - Method in class ome.model.roi.Roi
 
errorIfUnloaded() - Method in class ome.model.roi.Shape
 
errorIfUnloaded() - Method in class ome.model.screen.Plate
 
errorIfUnloaded() - Method in class ome.model.screen.PlateAcquisition
 
errorIfUnloaded() - Method in class ome.model.screen.Reagent
 
errorIfUnloaded() - Method in class ome.model.screen.Screen
 
errorIfUnloaded() - Method in class ome.model.screen.ScreenPlateLink
 
errorIfUnloaded() - Method in class ome.model.screen.Well
 
errorIfUnloaded() - Method in class ome.model.screen.WellReagentLink
 
errorIfUnloaded() - Method in class ome.model.screen.WellSample
 
errorIfUnloaded() - Method in class ome.model.stats.StatsInfo
 
errorOnViolation(Class, Method, Object[]) - Static method in class ome.annotations.ApiConstraintChecker
 
errors - Variable in class ome.formats.importer.util.ErrorHandler
 
evaluateLinkages(IObject) - Method in class ome.security.basic.OmeroInterceptor
Checks the details of the objects which the given object links to in order to guarantee that linkages are valid.
Event - Class in ome.model.meta
 
Event() - Constructor for class ome.model.meta.Event
 
Event(Long) - Constructor for class ome.model.meta.Event
 
Event(Long, boolean) - Constructor for class ome.model.meta.Event
Main constructor.
Event(Timestamp, Experimenter, ExperimenterGroup, EventType, Session) - Constructor for class ome.model.meta.Event
 
event - Variable in class ome.model.meta.EventLog
 
EVENT - Static variable in class ome.model.meta.EventLog
 
Event.Details - Class in ome.model.meta
 
Event.Details() - Constructor for class ome.model.meta.Event.Details
 
Event.Details(Object[]) - Constructor for class ome.model.meta.Event.Details
 
event2timestamp(Event) - Method in class ome.util.ModelMapper
 
EVENT_FILTER - Static variable in class ome.model.acquisition.Arc
 
EVENT_FILTER - Static variable in class ome.model.acquisition.Detector
 
EVENT_FILTER - Static variable in class ome.model.acquisition.DetectorSettings
 
EVENT_FILTER - Static variable in class ome.model.acquisition.Dichroic
 
EVENT_FILTER - Static variable in class ome.model.acquisition.Filament
 
EVENT_FILTER - Static variable in class ome.model.acquisition.Filter
 
EVENT_FILTER - Static variable in class ome.model.acquisition.FilterSet
 
EVENT_FILTER - Static variable in class ome.model.acquisition.FilterSetEmissionFilterLink
 
EVENT_FILTER - Static variable in class ome.model.acquisition.FilterSetExcitationFilterLink
 
EVENT_FILTER - Static variable in class ome.model.acquisition.GenericExcitationSource
 
EVENT_FILTER - Static variable in class ome.model.acquisition.ImagingEnvironment
 
EVENT_FILTER - Static variable in class ome.model.acquisition.Instrument
 
EVENT_FILTER - Static variable in class ome.model.acquisition.Laser
 
EVENT_FILTER - Static variable in class ome.model.acquisition.LightEmittingDiode
 
EVENT_FILTER - Static variable in class ome.model.acquisition.LightPath
 
EVENT_FILTER - Static variable in class ome.model.acquisition.LightPathEmissionFilterLink
 
EVENT_FILTER - Static variable in class ome.model.acquisition.LightPathExcitationFilterLink
 
EVENT_FILTER - Static variable in class ome.model.acquisition.LightSettings
 
EVENT_FILTER - Static variable in class ome.model.acquisition.LightSource
 
EVENT_FILTER - Static variable in class ome.model.acquisition.Microscope
 
EVENT_FILTER - Static variable in class ome.model.acquisition.Objective
 
EVENT_FILTER - Static variable in class ome.model.acquisition.ObjectiveSettings
 
EVENT_FILTER - Static variable in class ome.model.acquisition.OTF
 
EVENT_FILTER - Static variable in class ome.model.acquisition.StageLabel
 
EVENT_FILTER - Static variable in class ome.model.acquisition.TransmittanceRange
 
EVENT_FILTER - Static variable in class ome.model.annotations.Annotation
 
EVENT_FILTER - Static variable in class ome.model.annotations.AnnotationAnnotationLink
 
EVENT_FILTER - Static variable in class ome.model.annotations.BasicAnnotation
 
EVENT_FILTER - Static variable in class ome.model.annotations.BooleanAnnotation
 
EVENT_FILTER - Static variable in class ome.model.annotations.ChannelAnnotationLink
 
EVENT_FILTER - Static variable in class ome.model.annotations.CommentAnnotation
 
EVENT_FILTER - Static variable in class ome.model.annotations.DatasetAnnotationLink
 
EVENT_FILTER - Static variable in class ome.model.annotations.DetectorAnnotationLink
 
EVENT_FILTER - Static variable in class ome.model.annotations.DichroicAnnotationLink
 
EVENT_FILTER - Static variable in class ome.model.annotations.DoubleAnnotation
 
EVENT_FILTER - Static variable in class ome.model.annotations.ExperimenterAnnotationLink
 
EVENT_FILTER - Static variable in class ome.model.annotations.ExperimenterGroupAnnotationLink
 
EVENT_FILTER - Static variable in class ome.model.annotations.FileAnnotation
 
EVENT_FILTER - Static variable in class ome.model.annotations.FilesetAnnotationLink
 
EVENT_FILTER - Static variable in class ome.model.annotations.FilterAnnotationLink
 
EVENT_FILTER - Static variable in class ome.model.annotations.ImageAnnotationLink
 
EVENT_FILTER - Static variable in class ome.model.annotations.InstrumentAnnotationLink
 
EVENT_FILTER - Static variable in class ome.model.annotations.LightPathAnnotationLink
 
EVENT_FILTER - Static variable in class ome.model.annotations.LightSourceAnnotationLink
 
EVENT_FILTER - Static variable in class ome.model.annotations.ListAnnotation
 
EVENT_FILTER - Static variable in class ome.model.annotations.LongAnnotation
 
EVENT_FILTER - Static variable in class ome.model.annotations.MapAnnotation
 
EVENT_FILTER - Static variable in class ome.model.annotations.NamespaceAnnotationLink
 
EVENT_FILTER - Static variable in class ome.model.annotations.NodeAnnotationLink
 
EVENT_FILTER - Static variable in class ome.model.annotations.NumericAnnotation
 
EVENT_FILTER - Static variable in class ome.model.annotations.ObjectiveAnnotationLink
 
EVENT_FILTER - Static variable in class ome.model.annotations.OriginalFileAnnotationLink
 
EVENT_FILTER - Static variable in class ome.model.annotations.PlaneInfoAnnotationLink
 
EVENT_FILTER - Static variable in class ome.model.annotations.PlateAcquisitionAnnotationLink
 
EVENT_FILTER - Static variable in class ome.model.annotations.PlateAnnotationLink
 
EVENT_FILTER - Static variable in class ome.model.annotations.ProjectAnnotationLink
 
EVENT_FILTER - Static variable in class ome.model.annotations.ReagentAnnotationLink
 
EVENT_FILTER - Static variable in class ome.model.annotations.RoiAnnotationLink
 
EVENT_FILTER - Static variable in class ome.model.annotations.ScreenAnnotationLink
 
EVENT_FILTER - Static variable in class ome.model.annotations.SessionAnnotationLink
 
EVENT_FILTER - Static variable in class ome.model.annotations.ShapeAnnotationLink
 
EVENT_FILTER - Static variable in class ome.model.annotations.TagAnnotation
 
EVENT_FILTER - Static variable in class ome.model.annotations.TermAnnotation
 
EVENT_FILTER - Static variable in class ome.model.annotations.TextAnnotation
 
EVENT_FILTER - Static variable in class ome.model.annotations.TimestampAnnotation
 
EVENT_FILTER - Static variable in class ome.model.annotations.TypeAnnotation
 
EVENT_FILTER - Static variable in class ome.model.annotations.WellAnnotationLink
 
EVENT_FILTER - Static variable in class ome.model.annotations.XmlAnnotation
 
EVENT_FILTER - Static variable in class ome.model.containers.Dataset
 
EVENT_FILTER - Static variable in class ome.model.containers.DatasetImageLink
 
EVENT_FILTER - Static variable in class ome.model.containers.Project
 
EVENT_FILTER - Static variable in class ome.model.containers.ProjectDatasetLink
 
EVENT_FILTER - Static variable in class ome.model.core.Channel
 
EVENT_FILTER - Static variable in class ome.model.core.Image
 
EVENT_FILTER - Static variable in class ome.model.core.LogicalChannel
 
EVENT_FILTER - Static variable in class ome.model.core.OriginalFile
 
EVENT_FILTER - Static variable in class ome.model.core.Pixels
 
EVENT_FILTER - Static variable in class ome.model.core.PixelsOriginalFileMap
 
EVENT_FILTER - Static variable in class ome.model.core.PlaneInfo
 
EVENT_FILTER - Static variable in class ome.model.display.ChannelBinding
 
EVENT_FILTER - Static variable in class ome.model.display.CodomainMapContext
 
EVENT_FILTER - Static variable in class ome.model.display.ContrastStretchingContext
 
EVENT_FILTER - Static variable in class ome.model.display.PlaneSlicingContext
 
EVENT_FILTER - Static variable in class ome.model.display.QuantumDef
 
EVENT_FILTER - Static variable in class ome.model.display.RenderingDef
 
EVENT_FILTER - Static variable in class ome.model.display.ReverseIntensityContext
 
EVENT_FILTER - Static variable in class ome.model.display.Thumbnail
 
EVENT_FILTER - Static variable in class ome.model.experiment.Experiment
 
EVENT_FILTER - Static variable in class ome.model.experiment.MicrobeamManipulation
 
EVENT_FILTER - Static variable in class ome.model.fs.Fileset
 
EVENT_FILTER - Static variable in class ome.model.fs.FilesetEntry
 
EVENT_FILTER - Static variable in class ome.model.fs.FilesetJobLink
 
EVENT_FILTER - Static variable in class ome.model.internal.Link
 
EVENT_FILTER - Static variable in class ome.model.jobs.ImportJob
 
EVENT_FILTER - Static variable in class ome.model.jobs.IndexingJob
 
EVENT_FILTER - Static variable in class ome.model.jobs.IntegrityCheckJob
 
EVENT_FILTER - Static variable in class ome.model.jobs.Job
 
EVENT_FILTER - Static variable in class ome.model.jobs.JobOriginalFileLink
 
EVENT_FILTER - Static variable in class ome.model.jobs.MetadataImportJob
 
EVENT_FILTER - Static variable in class ome.model.jobs.ParseJob
 
EVENT_FILTER - Static variable in class ome.model.jobs.PixelDataJob
 
EVENT_FILTER - Static variable in class ome.model.jobs.ScriptJob
 
EVENT_FILTER - Static variable in class ome.model.jobs.ThumbnailGenerationJob
 
EVENT_FILTER - Static variable in class ome.model.jobs.UploadJob
 
EVENT_FILTER - Static variable in class ome.model.meta.ExternalInfo
 
EVENT_FILTER - Static variable in class ome.model.roi.Ellipse
 
EVENT_FILTER - Static variable in class ome.model.roi.Label
 
EVENT_FILTER - Static variable in class ome.model.roi.Line
 
EVENT_FILTER - Static variable in class ome.model.roi.Mask
 
EVENT_FILTER - Static variable in class ome.model.roi.Path
 
EVENT_FILTER - Static variable in class ome.model.roi.Point
 
EVENT_FILTER - Static variable in class ome.model.roi.Polygon
 
EVENT_FILTER - Static variable in class ome.model.roi.Polyline
 
EVENT_FILTER - Static variable in class ome.model.roi.Rect
 
EVENT_FILTER - Static variable in class ome.model.roi.Roi
 
EVENT_FILTER - Static variable in class ome.model.roi.Shape
 
EVENT_FILTER - Static variable in class ome.model.screen.Plate
 
EVENT_FILTER - Static variable in class ome.model.screen.PlateAcquisition
 
EVENT_FILTER - Static variable in class ome.model.screen.Reagent
 
EVENT_FILTER - Static variable in class ome.model.screen.Screen
 
EVENT_FILTER - Static variable in class ome.model.screen.ScreenPlateLink
 
EVENT_FILTER - Static variable in class ome.model.screen.Well
 
EVENT_FILTER - Static variable in class ome.model.screen.WellReagentLink
 
EVENT_FILTER - Static variable in class ome.model.screen.WellSample
 
EVENT_FILTER - Static variable in class ome.model.stats.StatsInfo
 
EVENT_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.acquisition.Detector
 
EVENT_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.acquisition.Dichroic
 
EVENT_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.acquisition.Filter
 
EVENT_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.acquisition.Instrument
 
EVENT_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.acquisition.LightPath
 
EVENT_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.acquisition.LightSource
 
EVENT_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.acquisition.Objective
 
EVENT_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.annotations.Annotation
 
EVENT_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.containers.Dataset
 
EVENT_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.containers.Project
 
EVENT_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.core.Channel
 
EVENT_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.core.Image
 
EVENT_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.core.OriginalFile
 
EVENT_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.core.PlaneInfo
 
EVENT_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.fs.Fileset
 
EVENT_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.meta.Experimenter
 
EVENT_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.meta.ExperimenterGroup
 
EVENT_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.meta.Namespace
 
EVENT_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.meta.Node
 
EVENT_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.meta.Session
 
EVENT_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.roi.Roi
 
EVENT_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.roi.Shape
 
EVENT_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.screen.Plate
 
EVENT_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.screen.PlateAcquisition
 
EVENT_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.screen.Reagent
 
EVENT_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.screen.Screen
 
EVENT_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.screen.Well
 
EVENT_FILTER_CHANNELS - Static variable in class ome.model.core.LogicalChannel
 
EVENT_FILTER_CHANNELS - Static variable in class ome.model.core.Pixels
 
EVENT_FILTER_DATASETLINKS - Static variable in class ome.model.containers.Project
 
EVENT_FILTER_DATASETLINKS - Static variable in class ome.model.core.Image
 
EVENT_FILTER_DETECTOR - Static variable in class ome.model.acquisition.Instrument
 
EVENT_FILTER_DICHROIC - Static variable in class ome.model.acquisition.Instrument
 
EVENT_FILTER_EMISSIONFILTERLINK - Static variable in class ome.model.acquisition.Filter
 
EVENT_FILTER_EMISSIONFILTERLINK - Static variable in class ome.model.acquisition.FilterSet
 
EVENT_FILTER_EMISSIONFILTERLINK - Static variable in class ome.model.acquisition.LightPath
 
EVENT_FILTER_EXCITATIONFILTERLINK - Static variable in class ome.model.acquisition.Filter
 
EVENT_FILTER_EXCITATIONFILTERLINK - Static variable in class ome.model.acquisition.FilterSet
 
EVENT_FILTER_EXCITATIONFILTERLINK - Static variable in class ome.model.acquisition.LightPath
 
EVENT_FILTER_FILESETENTRIES - Static variable in class ome.model.core.OriginalFile
 
EVENT_FILTER_FILTER - Static variable in class ome.model.acquisition.Instrument
 
EVENT_FILTER_FILTERSET - Static variable in class ome.model.acquisition.Instrument
 
EVENT_FILTER_IMAGELINKS - Static variable in class ome.model.containers.Dataset
 
EVENT_FILTER_IMAGES - Static variable in class ome.model.fs.Fileset
 
EVENT_FILTER_JOBLINKS - Static variable in class ome.model.fs.Fileset
 
EVENT_FILTER_LIGHTSOURCE - Static variable in class ome.model.acquisition.Instrument
 
EVENT_FILTER_LIGHTSOURCESETTINGS - Static variable in class ome.model.experiment.MicrobeamManipulation
 
EVENT_FILTER_MICROBEAMMANIPULATION - Static variable in class ome.model.experiment.Experiment
 
EVENT_FILTER_OBJECTIVE - Static variable in class ome.model.acquisition.Instrument
 
EVENT_FILTER_ORIGINALFILELINKS - Static variable in class ome.model.jobs.Job
 
EVENT_FILTER_OTF - Static variable in class ome.model.acquisition.Instrument
 
EVENT_FILTER_PIXELS - Static variable in class ome.model.core.Image
 
EVENT_FILTER_PIXELSFILEMAPS - Static variable in class ome.model.core.OriginalFile
 
EVENT_FILTER_PIXELSFILEMAPS - Static variable in class ome.model.core.Pixels
 
EVENT_FILTER_PLANEINFO - Static variable in class ome.model.core.Pixels
 
EVENT_FILTER_PLATEACQUISITIONS - Static variable in class ome.model.screen.Plate
 
EVENT_FILTER_PLATELINKS - Static variable in class ome.model.screen.Screen
 
EVENT_FILTER_PROJECTLINKS - Static variable in class ome.model.containers.Dataset
 
EVENT_FILTER_REAGENTLINKS - Static variable in class ome.model.screen.Well
 
EVENT_FILTER_REAGENTS - Static variable in class ome.model.screen.Screen
 
EVENT_FILTER_ROIS - Static variable in class ome.model.core.Image
 
EVENT_FILTER_SCREENLINKS - Static variable in class ome.model.screen.Plate
 
EVENT_FILTER_SETTINGS - Static variable in class ome.model.core.Pixels
 
EVENT_FILTER_SHAPES - Static variable in class ome.model.roi.Roi
 
EVENT_FILTER_SPATIALDOMAINENHANCEMENT - Static variable in class ome.model.display.RenderingDef
 
EVENT_FILTER_THUMBNAILS - Static variable in class ome.model.core.Pixels
 
EVENT_FILTER_USEDFILES - Static variable in class ome.model.fs.Fileset
 
EVENT_FILTER_WAVERENDERING - Static variable in class ome.model.display.RenderingDef
 
EVENT_FILTER_WELLLINKS - Static variable in class ome.model.screen.Reagent
 
EVENT_FILTER_WELLS - Static variable in class ome.model.screen.Plate
 
EVENT_FILTER_WELLSAMPLE - Static variable in class ome.model.screen.PlateAcquisition
 
EVENT_FILTER_WELLSAMPLES - Static variable in class ome.model.core.Image
 
EVENT_FILTER_WELLSAMPLES - Static variable in class ome.model.screen.Well
 
EventBacklog - Class in ome.services.eventlogs
Thread-safe java.util-like Container for storing EventLog instances for later parsing.
EventBacklog() - Constructor for class ome.services.eventlogs.EventBacklog
 
EventContext - Interface in ome.system
manages authenticated principals and other context for a given event.
EventHandler - Class in ome.security.basic
method interceptor responsible for login and creation of Events.
EventHandler(SqlAction, BasicSecuritySystem, SessionFactory, TransactionAttributeSource) - Constructor for class ome.security.basic.EventHandler
only public constructor, used for dependency injection.
EventHandler(SqlAction, BasicSecuritySystem, SessionFactory, TransactionAttributeSource, boolean) - Constructor for class ome.security.basic.EventHandler
 
eventId - Variable in class ome.util.SqlAction.DeleteLog
 
EventListenersFactoryBean - Class in ome.security.basic
configuring all the possible event listeners within XML can be cumbersome.
EventListenersFactoryBean(CurrentDetails, TokenHolder, ACLVoter, OmeroInterceptor) - Constructor for class ome.security.basic.EventListenersFactoryBean
 
EventLog - Class in ome.model.meta
 
EventLog() - Constructor for class ome.model.meta.EventLog
 
EventLog(Long) - Constructor for class ome.model.meta.EventLog
 
EventLog(Long, boolean) - Constructor for class ome.model.meta.EventLog
Main constructor.
EventLog(Long, String, String, Event) - Constructor for class ome.model.meta.EventLog
 
EventLog.Details - Class in ome.model.meta
 
EventLog.Details() - Constructor for class ome.model.meta.EventLog.Details
 
EventLog.Details(Object[]) - Constructor for class ome.model.meta.EventLog.Details
 
EventLogFailure - Class in ome.services.eventlogs
Signifies that the processing of a EventLog has failed.
EventLogFailure(EventLogLoader, EventLog, Throwable) - Constructor for class ome.services.eventlogs.EventLogFailure
 
EventLogListener - Class in ome.security.basic
responsible for responding to all Hibernate Events.
EventLogListener(CurrentDetails) - Constructor for class ome.security.basic.EventLogListener
main constructor.
EventLogLoader - Class in ome.services.eventlogs
Data access object for the FullTextIndexer which provides an Iterator interface for EventLog instances to be properly indexed.
EventLogLoader() - Constructor for class ome.services.eventlogs.EventLogLoader
 
EventLogMessage - Class in ome.services.messages
Published only when an event log should be saved at the end of a transaction.
EventLogMessage(Object, String, Class<? extends IObject>, List<Long>) - Constructor for class ome.services.messages.EventLogMessage
 
EventLogQueue - Class in ome.services.eventlogs
PersistentEventLogLoader implementation which loads many rows at the same time, culling out duplicates in order to speed up indexing.
EventLogQueue() - Constructor for class ome.services.eventlogs.EventLogQueue
 
EventLogQueue(Metrics, int, String[], String[]) - Constructor for class ome.services.eventlogs.EventLogQueue
 
EventLogsMessage - Class in ome.services.messages
Published with the final collection of EventLog instances which will be saved.
EventLogsMessage(Object, Multimap<String, EventLog>) - Constructor for class ome.services.messages.EventLogsMessage
 
EventMethodInterceptor - Class in ome.tools.hibernate
filter which can be added to any event type in order to catch execution.
EventMethodInterceptor() - Constructor for class ome.tools.hibernate.EventMethodInterceptor
 
EventMethodInterceptor(EventMethodInterceptor.Action) - Constructor for class ome.tools.hibernate.EventMethodInterceptor
 
EventMethodInterceptor.Action - Class in ome.tools.hibernate
 
EventMethodInterceptor.Action() - Constructor for class ome.tools.hibernate.EventMethodInterceptor.Action
 
EventMethodInterceptor.DisableAction - Class in ome.tools.hibernate
 
EventMethodInterceptor.DisableAction() - Constructor for class ome.tools.hibernate.EventMethodInterceptor.DisableAction
 
events - Variable in class ome.model.meta.Session
 
EVENTS - Static variable in class ome.model.meta.Session
 
EventType - Class in ome.model.enums
 
EventType() - Constructor for class ome.model.enums.EventType
 
EventType(Long) - Constructor for class ome.model.enums.EventType
 
EventType(Long, boolean) - Constructor for class ome.model.enums.EventType
Main constructor.
EventType(String) - Constructor for class ome.model.enums.EventType
 
EventType.Details - Class in ome.model.enums
 
EventType.Details() - Constructor for class ome.model.enums.EventType.Details
 
EventType.Details(Object[]) - Constructor for class ome.model.enums.EventType.Details
 
evict(Object) - Method in interface ome.api.local.LocalQuery
Removes an object graph from the session.
evict(Object) - Method in class ome.logic.QueryImpl
 
ex - Variable in class ome.services.roi.GeomTool
 
exception - Variable in class ome.formats.importer.ImportEvent.FILE_UPLOAD_EVENT
 
exception - Variable in class ome.formats.importer.util.ErrorHandler.EXCEPTION_EVENT
 
exception - Variable in class ome.services.throttling.Task
 
exception(Throwable, OmeroContext) - Method in class ome.services.throttling.Task
 
excitationFilterLink - Variable in class ome.model.acquisition.Filter
 
EXCITATIONFILTERLINK - Static variable in class ome.model.acquisition.Filter
 
excitationFilterLink - Variable in class ome.model.acquisition.FilterSet
 
EXCITATIONFILTERLINK - Static variable in class ome.model.acquisition.FilterSet
 
excitationFilterLink - Variable in class ome.model.acquisition.LightPath
 
EXCITATIONFILTERLINK - Static variable in class ome.model.acquisition.LightPath
 
EXCITATIONFILTERLINKCOUNTPEROWNER - Static variable in class ome.model.acquisition.Filter
 
EXCITATIONFILTERLINKCOUNTPEROWNER - Static variable in class ome.model.acquisition.FilterSet
 
EXCITATIONFILTERLINKCOUNTPEROWNER - Static variable in class ome.model.acquisition.LightPath
 
excitationWave - Variable in class ome.model.core.LogicalChannel
 
EXCITATIONWAVE - Static variable in class ome.model.core.LogicalChannel
 
excludes - Variable in class ome.services.eventlogs.EventLogLoader
Array of class types which will get excluded from indexing.
exclusions - Variable in class ome.formats.importer.cli.CommandLineImporter
FileExclusion mechanisms for skipping candidates
exec(File, File) - Method in class ome.formats.importer.transfers.AbstractExecFileTransfer
Executes a local command and fails on non-0 return codes.
execute(HibernateCallback) - Method in interface ome.api.local.LocalQuery
Executes a HibernateCallback
execute(Query<T>) - Method in interface ome.api.local.LocalQuery
Executes a locally defined Query.
execute(String[]) - Method in class ome.formats.importer.ImportCandidates
Method called during ImportCandidates.ImportCandidates(OMEROWrapper, String[], IObserver) to operate on all the given paths.
execute(HibernateCallback) - Method in class ome.logic.QueryImpl
 
execute(Query<T>) - Method in class ome.logic.QueryImpl
 
execute(int) - Method in class ome.services.delete.Deletion
Deprecated.
 
execute(int) - Method in class ome.services.graphs.GraphState
Deprecated.
 
execute() - Method in interface ome.services.graphs.GraphTraversal.PlanExecutor
Perform the planned action.
execute(Principal, Executor.Work) - Method in interface ome.services.util.Executor
Call #execute(Map, Principal, Work) with a null call context.
execute(Map<String, String>, Principal, Executor.Work) - Method in interface ome.services.util.Executor
Executes a Executor.Work instance wrapped in two layers of AOP.
execute(Principal, Executor.Work) - Method in class ome.services.util.Executor.Impl
Call #execute(Map, Principal, Work) with a null call context.
execute(Map<String, String>, Principal, Executor.Work) - Method in class ome.services.util.Executor.Impl
Executes a Executor.Work instance wrapped in two layers of AOP.
execute(RMap, Current) - Method in class omero.grid.InteractiveProcessorI
 
executePasswordCheck(String, String) - Method in interface ome.services.sessions.SessionManager
Executes a password check using the Executor framework.
executePasswordCheck(String, String) - Method in class ome.services.sessions.SessionManagerImpl
 
executePost(String, Map<String, String>) - Method in class ome.formats.importer.util.ErrorHandler
Execute a post with the given post list.
executePost() - Method in class ome.formats.importer.util.HtmlMessenger
Execute a post action and retrieve server reply This method executes the post created when this class is instantiated
executeSql(Executor.SqlWork) - Method in interface ome.services.util.Executor
Executes a Executor.SqlWork wrapped with a transaction.
executeSql(Executor.SqlWork) - Method in class ome.services.util.Executor.Impl
Executes a SqkWork in transaction.
ExecutionThread - Class in ome.services.util
Thread which can be started and will appropriately acquire a session, then use the Executor to complete its work.
ExecutionThread(SessionManager, Executor, Executor.Work, Principal) - Constructor for class ome.services.util.ExecutionThread
Main constructor.
executor - Variable in class ome.logic.UpdateImpl
 
executor - Variable in class ome.services.blitz.fire.SessionManagerI
 
executor - Variable in class ome.services.blitz.redirect.AbstractRedirector
 
executor - Variable in class ome.services.blitz.repo.RepositoryDaoImpl
 
executor - Variable in class ome.services.sessions.SessionManagerImpl
 
executor - Variable in class ome.services.sharing.ShareBean
 
executor - Variable in class ome.services.util.ExecutionThread
 
Executor - Interface in ome.services.util
Simple execution/work interface which can be used for internal tasks which need to have a full working implementation.
executor - Variable in class omero.cmd.SessionI
Executor to be used by servant implementations which do not delegate to the server package where all instances are wrapped with AOP for dealing with Hibernate.
Executor.Descriptive - Class in ome.services.util
 
Executor.Descriptive(Object, String, Object...) - Constructor for class ome.services.util.Executor.Descriptive
 
Executor.Descriptive(String, String, Object...) - Constructor for class ome.services.util.Executor.Descriptive
 
Executor.Impl - Class in ome.services.util
 
Executor.Impl(CurrentDetails, SessionFactory, SqlAction, String[]) - Constructor for class ome.services.util.Executor.Impl
 
Executor.Impl(CurrentDetails, SessionFactory, SqlAction, String[], ExecutorService) - Constructor for class ome.services.util.Executor.Impl
 
Executor.Priority - Enum in ome.services.util
 
Executor.SimpleSqlWork - Class in ome.services.util
Simple adapter which takes a String for Executor.Descriptive.description
Executor.SimpleSqlWork(Object, String, Object...) - Constructor for class ome.services.util.Executor.SimpleSqlWork
 
Executor.SimpleWork - Class in ome.services.util
Simple adapter which takes a String for Executor.Descriptive.description
Executor.SimpleWork(Object, String, Object...) - Constructor for class ome.services.util.Executor.SimpleWork
 
Executor.SqlWork - Interface in ome.services.util
Work SPI to perform actions related to stateless sessions.
Executor.StatefulWork - Interface in ome.services.util
In the case of a stateful work order, the bean itself needs to be associated with the sessionHandler and thread rather than the word instance itself.
Executor.Work<X> - Interface in ome.services.util
Work SPI to perform actions within the server as if they were fully wrapped in our service logic.
executorWorkCall(Executor.Work) - Method in class ome.services.blitz.impl.AbstractAmdServant
 
exists() - Method in interface ome.api.RawFileStore
Checks to see if a raw file exists with the file ID that the service was initialized with.
exists(OriginalFile) - Method in class ome.io.nio.OriginalFilesService
Returns whether or not an OriginalFile exists on disk.
exists() - Method in class ome.services.blitz.repo.CheckedPath
Check if this file actually exists on the underlying filesystem.
exists() - Method in class ome.services.RawFileBean
 
exists_async(AMD_RawFileStore_exists, Current) - Method in class ome.services.blitz.impl.RawFileStoreI
 
exit(Object) - Method in class ome.util.ContextFilter
 
exit(String[]) - Static method in class prefs
Uses the length of the argument array as the exit code.
exp(long) - Method in class ome.parameters.Parameters
 
exp(RLong) - Method in class omero.sys.ParametersI
Sets the value of the experimenter parameter.
expandTemplateRootOwnedPath(EventContext, ServiceFactory) - Method in class ome.services.blitz.repo.ManagedRepositoryI
Expand the root-owned segment of the template path.
experiment - Variable in class ome.model.core.Image
 
EXPERIMENT - Static variable in class ome.model.core.Image
 
Experiment - Class in ome.model.experiment
These filter definitions are used by the security system to eliminate non-readable objects from queries.
Experiment() - Constructor for class ome.model.experiment.Experiment
 
Experiment(Long) - Constructor for class ome.model.experiment.Experiment
 
Experiment(Long, boolean) - Constructor for class ome.model.experiment.Experiment
Main constructor.
Experiment(ExperimentType) - Constructor for class ome.model.experiment.Experiment
 
experiment - Variable in class ome.model.experiment.MicrobeamManipulation
 
EXPERIMENT - Static variable in class ome.model.experiment.MicrobeamManipulation
 
Experiment.Details - Class in ome.model.experiment
 
Experiment.Details() - Constructor for class ome.model.experiment.Experiment.Details
 
Experiment.Details(Object[]) - Constructor for class ome.model.experiment.Experiment.Details
 
experimenter - Variable in class ome.model.meta.Event
 
EXPERIMENTER - Static variable in class ome.model.meta.Event
 
Experimenter - Class in ome.model.meta
 
Experimenter() - Constructor for class ome.model.meta.Experimenter
 
Experimenter(Long) - Constructor for class ome.model.meta.Experimenter
 
Experimenter(Long, boolean) - Constructor for class ome.model.meta.Experimenter
Main constructor.
Experimenter(String, String, String, Boolean) - Constructor for class ome.model.meta.Experimenter
 
Experimenter.Details - Class in ome.model.meta
 
Experimenter.Details() - Constructor for class ome.model.meta.Experimenter.Details
 
Experimenter.Details(Object[]) - Constructor for class ome.model.meta.Experimenter.Details
 
EXPERIMENTER_PHOTO_NS - Static variable in class pojos.FileAnnotationData
The name space used to identify the experimenter photo.
ExperimenterAnnotationLink - Class in ome.model.annotations
These filter definitions are used by the security system to eliminate non-readable objects from queries.
ExperimenterAnnotationLink() - Constructor for class ome.model.annotations.ExperimenterAnnotationLink
 
ExperimenterAnnotationLink(Long) - Constructor for class ome.model.annotations.ExperimenterAnnotationLink
 
ExperimenterAnnotationLink(Long, boolean) - Constructor for class ome.model.annotations.ExperimenterAnnotationLink
Main constructor.
ExperimenterAnnotationLink(IObject, IObject) - Constructor for class ome.model.annotations.ExperimenterAnnotationLink
 
ExperimenterAnnotationLink.Details - Class in ome.model.annotations
 
ExperimenterAnnotationLink.Details() - Constructor for class ome.model.annotations.ExperimenterAnnotationLink.Details
 
ExperimenterAnnotationLink.Details(Object[]) - Constructor for class ome.model.annotations.ExperimenterAnnotationLink.Details
 
ExperimenterData - Class in pojos
The data that makes up an OME Experimenter along with information about the Group the Experimenter belongs in.
ExperimenterData() - Constructor for class pojos.ExperimenterData
Creates a new instance.
ExperimenterData(Experimenter) - Constructor for class pojos.ExperimenterData
Creates a new instance.
experimenterGroup - Variable in class ome.model.meta.Event
 
EXPERIMENTERGROUP - Static variable in class ome.model.meta.Event
 
ExperimenterGroup - Class in ome.model.meta
 
ExperimenterGroup() - Constructor for class ome.model.meta.ExperimenterGroup
 
ExperimenterGroup(Long) - Constructor for class ome.model.meta.ExperimenterGroup
 
ExperimenterGroup(Long, boolean) - Constructor for class ome.model.meta.ExperimenterGroup
Main constructor.
ExperimenterGroup(String, Boolean) - Constructor for class ome.model.meta.ExperimenterGroup
 
ExperimenterGroup.Details - Class in ome.model.meta
 
ExperimenterGroup.Details() - Constructor for class ome.model.meta.ExperimenterGroup.Details
 
ExperimenterGroup.Details(Object[]) - Constructor for class ome.model.meta.ExperimenterGroup.Details
 
ExperimenterGroupAnnotationLink - Class in ome.model.annotations
These filter definitions are used by the security system to eliminate non-readable objects from queries.
ExperimenterGroupAnnotationLink() - Constructor for class ome.model.annotations.ExperimenterGroupAnnotationLink
 
ExperimenterGroupAnnotationLink(Long) - Constructor for class ome.model.annotations.ExperimenterGroupAnnotationLink
 
ExperimenterGroupAnnotationLink(Long, boolean) - Constructor for class ome.model.annotations.ExperimenterGroupAnnotationLink
Main constructor.
ExperimenterGroupAnnotationLink(IObject, IObject) - Constructor for class ome.model.annotations.ExperimenterGroupAnnotationLink
 
ExperimenterGroupAnnotationLink.Details - Class in ome.model.annotations
 
ExperimenterGroupAnnotationLink.Details() - Constructor for class ome.model.annotations.ExperimenterGroupAnnotationLink.Details
 
ExperimenterGroupAnnotationLink.Details(Object[]) - Constructor for class ome.model.annotations.ExperimenterGroupAnnotationLink.Details
 
ExperimentType - Class in ome.model.enums
 
ExperimentType() - Constructor for class ome.model.enums.ExperimentType
 
ExperimentType(Long) - Constructor for class ome.model.enums.ExperimentType
 
ExperimentType(Long, boolean) - Constructor for class ome.model.enums.ExperimentType
Main constructor.
ExperimentType(String) - Constructor for class ome.model.enums.ExperimentType
 
ExperimentType.Details - Class in ome.model.enums
 
ExperimentType.Details() - Constructor for class ome.model.enums.ExperimentType.Details
 
ExperimentType.Details(Object[]) - Constructor for class ome.model.enums.ExperimentType.Details
 
expirationAsLong(long, Timestamp) - Static method in class ome.services.sharing.ShareBean
Convert a expiration into a long which can be set on Session.setTimeToLive(Long).
ExpiredCredentialException - Exception in ome.conditions
Correct username and credentials provided, but credentials expired.
ExpiredCredentialException(String) - Constructor for exception ome.conditions.ExpiredCredentialException
 
ExpiredServantMessage - Class in ome.services.blitz.util
ApplicationEvent which gets raised on CacheEventListener.notifyElementExpired(net.sf.ehcache.Ehcache, net.sf.ehcache.Element)
ExpiredServantMessage(Object, String) - Constructor for class ome.services.blitz.util.ExpiredServantMessage
 
expires(Current) - Method in class omero.grid.InteractiveProcessorI
 
EXPONENTIAL - Static variable in class omeis.providers.re.quantum.QuantumFactory
Flag to select a exponential map for the quantization process.
ExponentialMap - Class in omeis.providers.re.quantum
This class implements the QuantumMap interface.
ExponentialMap() - Constructor for class omeis.providers.re.quantum.ExponentialMap
 
export(String[]) - Static method in class prefs
Exports all properties in the current profile to System.out, or if a single argument is given, that is take to be the name of a target ouput file.
ExporterI - Class in ome.services.blitz.impl
Implementation of the Exporter service.
ExporterI(BlitzExecutor, DatabaseIdentity, PixelsService) - Constructor for class ome.services.blitz.impl.ExporterI
 
ExporterIndex - Class in ome.services.export
Deprecated.
will be removed in OMERO 5.2, so use the new graphs implementation
ExporterIndex(int) - Constructor for class ome.services.export.ExporterIndex
Deprecated.
 
ExporterStep - Class in ome.services.export
Deprecated.
will be removed in OMERO 5.2, so use the new graphs implementation
ExporterStep(ExtendedMetadata, int, List<GraphStep>, GraphSpec, GraphEntry, long[]) - Constructor for class ome.services.export.ExporterStep
Deprecated.
 
ExporterStepFactory - Class in ome.services.export
Deprecated.
will be removed in OMERO 5.2, so use the new graphs implementation
ExporterStepFactory(Executor, Principal, ExtendedMetadata) - Constructor for class ome.services.export.ExporterStepFactory
Deprecated.
 
exposureTime - Variable in class ome.model.core.PlaneInfo
 
EXPOSURETIME - Static variable in class ome.model.core.PlaneInfo
 
ExtendedMetadata - Interface in ome.tools.hibernate
extension of the model metadata provided by SessionFactory.
ExtendedMetadata.Immutables - Class in ome.tools.hibernate
 
ExtendedMetadata.Impl - Class in ome.tools.hibernate
Sole implementation of ExtendedMetadata.
ExtendedMetadata.Impl() - Constructor for class ome.tools.hibernate.ExtendedMetadata.Impl
 
ExtendedMetadata.Locks - Class in ome.tools.hibernate
inner class which wraps the information (index number, path, etc) related to what fields a particular object can lock.
ExtendedMetadata.Relationship - Class in ome.tools.hibernate
externalDescription - Variable in class ome.model.screen.Well
 
EXTERNALDESCRIPTION - Static variable in class ome.model.screen.Well
 
externalIdentifier - Variable in class ome.model.screen.Plate
 
EXTERNALIDENTIFIER - Static variable in class ome.model.screen.Plate
 
externalIdentifier - Variable in class ome.model.screen.Well
 
EXTERNALIDENTIFIER - Static variable in class ome.model.screen.Well
 
EXTERNALINFO - Static variable in class ome.model.internal.Details
 
ExternalInfo - Class in ome.model.meta
These filter definitions are used by the security system to eliminate non-readable objects from queries.
ExternalInfo() - Constructor for class ome.model.meta.ExternalInfo
 
ExternalInfo(Long) - Constructor for class ome.model.meta.ExternalInfo
 
ExternalInfo(Long, boolean) - Constructor for class ome.model.meta.ExternalInfo
Main constructor.
ExternalInfo(Long, String) - Constructor for class ome.model.meta.ExternalInfo
 
ExternalInfo.Details - Class in ome.model.meta
 
ExternalInfo.Details() - Constructor for class ome.model.meta.ExternalInfo.Details
 
ExternalInfo.Details(Object[]) - Constructor for class ome.model.meta.ExternalInfo.Details
 

F

factory - Variable in class ome.security.basic.EventHandler
 
factory - Variable in class ome.services.blitz.impl.RoiI
 
factory - Variable in class ome.services.blitz.impl.ScriptI
 
factory - Variable in class ome.services.blitz.impl.TimelineI
 
factory - Variable in class ome.services.roi.GeomTool
 
factory - Variable in class ome.services.sessions.SessionManagerImpl
 
factory - Variable in class ome.services.util.Executor.Impl
 
factory - Variable in class ome.tools.hibernate.ListAsSQLArrayUserType
 
FACTORY - Static variable in class ome.tools.hibernate.SqlArray
 
Factory - Static variable in class omero.model.DetailsI
 
Factory - Static variable in class omero.model.ElectricPotentialI
 
Factory - Static variable in class omero.model.FrequencyI
 
Factory - Static variable in class omero.model.LengthI
 
Factory - Static variable in class omero.model.PermissionsI
 
Factory - Static variable in class omero.model.PowerI
 
Factory - Static variable in class omero.model.PressureI
 
Factory - Static variable in class omero.model.TemperatureI
 
Factory - Static variable in class omero.model.TimeI
 
fail(File, Long, Long) - Method in class ome.services.delete.files.AbstractFileDeletions
 
fail(ERR, Throwable, String, String...) - Method in class omero.cmd.Helper
Calls #fail(ERR, String, Map) with the output of Helper.params(String...).
fail(ERR, Throwable, String, Map<String, String>) - Method in class omero.cmd.Helper
Sets the status.flags and the ERR properties appropriately and also stores the message and stacktrace of the throwable in the parameters.
FailedLoginMailSender - Class in ome.services.mail
On an LoginAttemptMessage potentially send an email to administrators or the user herself to alert of possible security issues.
FailedLoginMailSender() - Constructor for class ome.services.mail.FailedLoginMailSender
 
failingChecksums - Variable in class ome.formats.importer.ImportEvent.FILESET_UPLOAD_END
 
failLocationCheck(File, String) - Method in class ome.formats.importer.transfers.AbstractExecFileTransfer
 
family - Variable in class ome.model.display.ChannelBinding
 
FAMILY - Static variable in class ome.model.display.ChannelBinding
 
Family - Class in ome.model.enums
 
Family() - Constructor for class ome.model.enums.Family
 
Family(Long) - Constructor for class ome.model.enums.Family
 
Family(Long, boolean) - Constructor for class ome.model.enums.Family
Main constructor.
Family(String) - Constructor for class ome.model.enums.Family
 
Family.Details - Class in ome.model.enums
 
Family.Details() - Constructor for class ome.model.enums.Family.Details
 
Family.Details(Object[]) - Constructor for class ome.model.enums.Family.Details
 
FETCH - Static variable in class ome.services.query.Query
imported constant for ease of use
fetchAlso(String...) - Method in interface ome.api.Search
Adds a fetch clause for loading non-annotation fields of returned entities.
fetchAlso(Map<T, String>) - Method in class ome.services.SearchBean
 
fetchAlso(String...) - Method in class ome.services.SearchBean
 
fetchAlso_async(AMD_Search_fetchAlso, List<String>, Current) - Method in class ome.services.blitz.impl.SearchI
 
fetchAnnotations(Class...) - Method in interface ome.api.Search
Queries the database for all annotations of the given types for all returned instances.
fetchAnnotations - Variable in class ome.services.search.SearchValues
 
fetchAnnotations(Class...) - Method in class ome.services.SearchBean
 
fetchAnnotations_async(AMD_Search_fetchAnnotations, List<String>, Current) - Method in class ome.services.blitz.impl.SearchI
 
fetchChildren(Criteria, Class, int) - Static method in class ome.services.query.Hierarchy
 
fetchCollection(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
fetchEntity(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
fetches - Variable in class ome.services.search.SearchValues
 
fetchParents(Criteria, Class, int) - Static method in class ome.services.query.Hierarchy
 
FIELDS - Static variable in class ome.model.acquisition.Arc
 
fields() - Method in class ome.model.acquisition.Arc
 
FIELDS - Static variable in class ome.model.acquisition.Detector
 
fields() - Method in class ome.model.acquisition.Detector
 
FIELDS - Static variable in class ome.model.acquisition.DetectorSettings
 
fields() - Method in class ome.model.acquisition.DetectorSettings
 
FIELDS - Static variable in class ome.model.acquisition.Dichroic
 
fields() - Method in class ome.model.acquisition.Dichroic
 
FIELDS - Static variable in class ome.model.acquisition.Filament
 
fields() - Method in class ome.model.acquisition.Filament
 
FIELDS - Static variable in class ome.model.acquisition.Filter
 
fields() - Method in class ome.model.acquisition.Filter
 
FIELDS - Static variable in class ome.model.acquisition.FilterSet
 
fields() - Method in class ome.model.acquisition.FilterSet
 
FIELDS - Static variable in class ome.model.acquisition.FilterSetEmissionFilterLink
 
fields() - Method in class ome.model.acquisition.FilterSetEmissionFilterLink
 
FIELDS - Static variable in class ome.model.acquisition.FilterSetExcitationFilterLink
 
fields() - Method in class ome.model.acquisition.FilterSetExcitationFilterLink
 
FIELDS - Static variable in class ome.model.acquisition.GenericExcitationSource
 
fields() - Method in class ome.model.acquisition.GenericExcitationSource
 
FIELDS - Static variable in class ome.model.acquisition.ImagingEnvironment
 
fields() - Method in class ome.model.acquisition.ImagingEnvironment
 
FIELDS - Static variable in class ome.model.acquisition.Instrument
 
fields() - Method in class ome.model.acquisition.Instrument
 
FIELDS - Static variable in class ome.model.acquisition.Laser
 
fields() - Method in class ome.model.acquisition.Laser
 
FIELDS - Static variable in class ome.model.acquisition.LightEmittingDiode
 
fields() - Method in class ome.model.acquisition.LightEmittingDiode
 
FIELDS - Static variable in class ome.model.acquisition.LightPath
 
fields() - Method in class ome.model.acquisition.LightPath
 
FIELDS - Static variable in class ome.model.acquisition.LightPathEmissionFilterLink
 
fields() - Method in class ome.model.acquisition.LightPathEmissionFilterLink
 
FIELDS - Static variable in class ome.model.acquisition.LightPathExcitationFilterLink
 
fields() - Method in class ome.model.acquisition.LightPathExcitationFilterLink
 
FIELDS - Static variable in class ome.model.acquisition.LightSettings
 
fields() - Method in class ome.model.acquisition.LightSettings
 
FIELDS - Static variable in class ome.model.acquisition.LightSource
 
fields() - Method in class ome.model.acquisition.LightSource
 
FIELDS - Static variable in class ome.model.acquisition.Microscope
 
fields() - Method in class ome.model.acquisition.Microscope
 
FIELDS - Static variable in class ome.model.acquisition.Objective
 
fields() - Method in class ome.model.acquisition.Objective
 
FIELDS - Static variable in class ome.model.acquisition.ObjectiveSettings
 
fields() - Method in class ome.model.acquisition.ObjectiveSettings
 
FIELDS - Static variable in class ome.model.acquisition.OTF
 
fields() - Method in class ome.model.acquisition.OTF
 
FIELDS - Static variable in class ome.model.acquisition.StageLabel
 
fields() - Method in class ome.model.acquisition.StageLabel
 
FIELDS - Static variable in class ome.model.acquisition.TransmittanceRange
 
fields() - Method in class ome.model.acquisition.TransmittanceRange
 
FIELDS - Static variable in class ome.model.annotations.Annotation
 
fields() - Method in class ome.model.annotations.Annotation
 
FIELDS - Static variable in class ome.model.annotations.AnnotationAnnotationLink
 
fields() - Method in class ome.model.annotations.AnnotationAnnotationLink
 
FIELDS - Static variable in class ome.model.annotations.BasicAnnotation
 
fields() - Method in class ome.model.annotations.BasicAnnotation
 
FIELDS - Static variable in class ome.model.annotations.BooleanAnnotation
 
fields() - Method in class ome.model.annotations.BooleanAnnotation
 
FIELDS - Static variable in class ome.model.annotations.ChannelAnnotationLink
 
fields() - Method in class ome.model.annotations.ChannelAnnotationLink
 
FIELDS - Static variable in class ome.model.annotations.CommentAnnotation
 
fields() - Method in class ome.model.annotations.CommentAnnotation
 
FIELDS - Static variable in class ome.model.annotations.DatasetAnnotationLink
 
fields() - Method in class ome.model.annotations.DatasetAnnotationLink
 
FIELDS - Static variable in class ome.model.annotations.DetectorAnnotationLink
 
fields() - Method in class ome.model.annotations.DetectorAnnotationLink
 
FIELDS - Static variable in class ome.model.annotations.DichroicAnnotationLink
 
fields() - Method in class ome.model.annotations.DichroicAnnotationLink
 
FIELDS - Static variable in class ome.model.annotations.DoubleAnnotation
 
fields() - Method in class ome.model.annotations.DoubleAnnotation
 
FIELDS - Static variable in class ome.model.annotations.ExperimenterAnnotationLink
 
fields() - Method in class ome.model.annotations.ExperimenterAnnotationLink
 
FIELDS - Static variable in class ome.model.annotations.ExperimenterGroupAnnotationLink
 
fields() - Method in class ome.model.annotations.ExperimenterGroupAnnotationLink
 
FIELDS - Static variable in class ome.model.annotations.FileAnnotation
 
fields() - Method in class ome.model.annotations.FileAnnotation
 
FIELDS - Static variable in class ome.model.annotations.FilesetAnnotationLink
 
fields() - Method in class ome.model.annotations.FilesetAnnotationLink
 
FIELDS - Static variable in class ome.model.annotations.FilterAnnotationLink
 
fields() - Method in class ome.model.annotations.FilterAnnotationLink
 
FIELDS - Static variable in class ome.model.annotations.ImageAnnotationLink
 
fields() - Method in class ome.model.annotations.ImageAnnotationLink
 
FIELDS - Static variable in class ome.model.annotations.InstrumentAnnotationLink
 
fields() - Method in class ome.model.annotations.InstrumentAnnotationLink
 
FIELDS - Static variable in class ome.model.annotations.LightPathAnnotationLink
 
fields() - Method in class ome.model.annotations.LightPathAnnotationLink
 
FIELDS - Static variable in class ome.model.annotations.LightSourceAnnotationLink
 
fields() - Method in class ome.model.annotations.LightSourceAnnotationLink
 
FIELDS - Static variable in class ome.model.annotations.ListAnnotation
 
fields() - Method in class ome.model.annotations.ListAnnotation
 
FIELDS - Static variable in class ome.model.annotations.LongAnnotation
 
fields() - Method in class ome.model.annotations.LongAnnotation
 
FIELDS - Static variable in class ome.model.annotations.MapAnnotation
 
fields() - Method in class ome.model.annotations.MapAnnotation
 
FIELDS - Static variable in class ome.model.annotations.NamespaceAnnotationLink
 
fields() - Method in class ome.model.annotations.NamespaceAnnotationLink
 
FIELDS - Static variable in class ome.model.annotations.NodeAnnotationLink
 
fields() - Method in class ome.model.annotations.NodeAnnotationLink
 
FIELDS - Static variable in class ome.model.annotations.NumericAnnotation
 
fields() - Method in class ome.model.annotations.NumericAnnotation
 
FIELDS - Static variable in class ome.model.annotations.ObjectiveAnnotationLink
 
fields() - Method in class ome.model.annotations.ObjectiveAnnotationLink
 
FIELDS - Static variable in class ome.model.annotations.OriginalFileAnnotationLink
 
fields() - Method in class ome.model.annotations.OriginalFileAnnotationLink
 
FIELDS - Static variable in class ome.model.annotations.PlaneInfoAnnotationLink
 
fields() - Method in class ome.model.annotations.PlaneInfoAnnotationLink
 
FIELDS - Static variable in class ome.model.annotations.PlateAcquisitionAnnotationLink
 
fields() - Method in class ome.model.annotations.PlateAcquisitionAnnotationLink
 
FIELDS - Static variable in class ome.model.annotations.PlateAnnotationLink
 
fields() - Method in class ome.model.annotations.PlateAnnotationLink
 
FIELDS - Static variable in class ome.model.annotations.ProjectAnnotationLink
 
fields() - Method in class ome.model.annotations.ProjectAnnotationLink
 
FIELDS - Static variable in class ome.model.annotations.ReagentAnnotationLink
 
fields() - Method in class ome.model.annotations.ReagentAnnotationLink
 
FIELDS - Static variable in class ome.model.annotations.RoiAnnotationLink
 
fields() - Method in class ome.model.annotations.RoiAnnotationLink
 
FIELDS - Static variable in class ome.model.annotations.ScreenAnnotationLink
 
fields() - Method in class ome.model.annotations.ScreenAnnotationLink
 
FIELDS - Static variable in class ome.model.annotations.SessionAnnotationLink
 
fields() - Method in class ome.model.annotations.SessionAnnotationLink
 
FIELDS - Static variable in class ome.model.annotations.ShapeAnnotationLink
 
fields() - Method in class ome.model.annotations.ShapeAnnotationLink
 
FIELDS - Static variable in class ome.model.annotations.TagAnnotation
 
fields() - Method in class ome.model.annotations.TagAnnotation
 
FIELDS - Static variable in class ome.model.annotations.TermAnnotation
 
fields() - Method in class ome.model.annotations.TermAnnotation
 
FIELDS - Static variable in class ome.model.annotations.TextAnnotation
 
fields() - Method in class ome.model.annotations.TextAnnotation
 
FIELDS - Static variable in class ome.model.annotations.TimestampAnnotation
 
fields() - Method in class ome.model.annotations.TimestampAnnotation
 
FIELDS - Static variable in class ome.model.annotations.TypeAnnotation
 
fields() - Method in class ome.model.annotations.TypeAnnotation
 
FIELDS - Static variable in class ome.model.annotations.WellAnnotationLink
 
fields() - Method in class ome.model.annotations.WellAnnotationLink
 
FIELDS - Static variable in class ome.model.annotations.XmlAnnotation
 
fields() - Method in class ome.model.annotations.XmlAnnotation
 
FIELDS - Static variable in class ome.model.containers.Dataset
 
fields() - Method in class ome.model.containers.Dataset
 
FIELDS - Static variable in class ome.model.containers.DatasetImageLink
 
fields() - Method in class ome.model.containers.DatasetImageLink
 
FIELDS - Static variable in class ome.model.containers.Project
 
fields() - Method in class ome.model.containers.Project
 
FIELDS - Static variable in class ome.model.containers.ProjectDatasetLink
 
fields() - Method in class ome.model.containers.ProjectDatasetLink
 
FIELDS - Static variable in class ome.model.core.Channel
 
fields() - Method in class ome.model.core.Channel
 
FIELDS - Static variable in class ome.model.core.Image
 
fields() - Method in class ome.model.core.Image
 
FIELDS - Static variable in class ome.model.core.LogicalChannel
 
fields() - Method in class ome.model.core.LogicalChannel
 
FIELDS - Static variable in class ome.model.core.OriginalFile
 
fields() - Method in class ome.model.core.OriginalFile
 
FIELDS - Static variable in class ome.model.core.Pixels
 
fields() - Method in class ome.model.core.Pixels
 
FIELDS - Static variable in class ome.model.core.PixelsOriginalFileMap
 
fields() - Method in class ome.model.core.PixelsOriginalFileMap
 
FIELDS - Static variable in class ome.model.core.PlaneInfo
 
fields() - Method in class ome.model.core.PlaneInfo
 
FIELDS - Static variable in class ome.model.display.ChannelBinding
 
fields() - Method in class ome.model.display.ChannelBinding
 
FIELDS - Static variable in class ome.model.display.CodomainMapContext
 
fields() - Method in class ome.model.display.CodomainMapContext
 
FIELDS - Static variable in class ome.model.display.ContrastStretchingContext
 
fields() - Method in class ome.model.display.ContrastStretchingContext
 
FIELDS - Static variable in class ome.model.display.PlaneSlicingContext
 
fields() - Method in class ome.model.display.PlaneSlicingContext
 
FIELDS - Static variable in class ome.model.display.QuantumDef
 
fields() - Method in class ome.model.display.QuantumDef
 
FIELDS - Static variable in class ome.model.display.RenderingDef
 
fields() - Method in class ome.model.display.RenderingDef
 
FIELDS - Static variable in class ome.model.display.ReverseIntensityContext
 
fields() - Method in class ome.model.display.ReverseIntensityContext
 
FIELDS - Static variable in class ome.model.display.Thumbnail
 
fields() - Method in class ome.model.display.Thumbnail
 
FIELDS - Static variable in class ome.model.enums.AcquisitionMode
 
fields() - Method in class ome.model.enums.AcquisitionMode
 
FIELDS - Static variable in class ome.model.enums.ArcType
 
fields() - Method in class ome.model.enums.ArcType
 
FIELDS - Static variable in class ome.model.enums.Binning
 
fields() - Method in class ome.model.enums.Binning
 
FIELDS - Static variable in class ome.model.enums.ChecksumAlgorithm
 
fields() - Method in class ome.model.enums.ChecksumAlgorithm
 
FIELDS - Static variable in class ome.model.enums.ContrastMethod
 
fields() - Method in class ome.model.enums.ContrastMethod
 
FIELDS - Static variable in class ome.model.enums.Correction
 
fields() - Method in class ome.model.enums.Correction
 
FIELDS - Static variable in class ome.model.enums.DetectorType
 
fields() - Method in class ome.model.enums.DetectorType
 
FIELDS - Static variable in class ome.model.enums.DimensionOrder
 
fields() - Method in class ome.model.enums.DimensionOrder
 
FIELDS - Static variable in class ome.model.enums.EventType
 
fields() - Method in class ome.model.enums.EventType
 
FIELDS - Static variable in class ome.model.enums.ExperimentType
 
fields() - Method in class ome.model.enums.ExperimentType
 
FIELDS - Static variable in class ome.model.enums.Family
 
fields() - Method in class ome.model.enums.Family
 
FIELDS - Static variable in class ome.model.enums.FilamentType
 
fields() - Method in class ome.model.enums.FilamentType
 
FIELDS - Static variable in class ome.model.enums.FilterType
 
fields() - Method in class ome.model.enums.FilterType
 
FIELDS - Static variable in class ome.model.enums.Format
 
fields() - Method in class ome.model.enums.Format
 
FIELDS - Static variable in class ome.model.enums.Illumination
 
fields() - Method in class ome.model.enums.Illumination
 
FIELDS - Static variable in class ome.model.enums.Immersion
 
fields() - Method in class ome.model.enums.Immersion
 
FIELDS - Static variable in class ome.model.enums.LaserMedium
 
fields() - Method in class ome.model.enums.LaserMedium
 
FIELDS - Static variable in class ome.model.enums.LaserType
 
fields() - Method in class ome.model.enums.LaserType
 
FIELDS - Static variable in class ome.model.enums.Medium
 
fields() - Method in class ome.model.enums.Medium
 
FIELDS - Static variable in class ome.model.enums.MicrobeamManipulationType
 
fields() - Method in class ome.model.enums.MicrobeamManipulationType
 
FIELDS - Static variable in class ome.model.enums.MicroscopeType
 
fields() - Method in class ome.model.enums.MicroscopeType
 
FIELDS - Static variable in class ome.model.enums.PhotometricInterpretation
 
fields() - Method in class ome.model.enums.PhotometricInterpretation
 
FIELDS - Static variable in class ome.model.enums.PixelsType
 
fields() - Method in class ome.model.enums.PixelsType
 
FIELDS - Static variable in class ome.model.enums.Pulse
 
fields() - Method in class ome.model.enums.Pulse
 
FIELDS - Static variable in class ome.model.enums.RenderingModel
 
fields() - Method in class ome.model.enums.RenderingModel
 
FIELDS - Static variable in class ome.model.experiment.Experiment
 
fields() - Method in class ome.model.experiment.Experiment
 
FIELDS - Static variable in class ome.model.experiment.MicrobeamManipulation
 
fields() - Method in class ome.model.experiment.MicrobeamManipulation
 
FIELDS - Static variable in class ome.model.fs.Fileset
 
fields() - Method in class ome.model.fs.Fileset
 
FIELDS - Static variable in class ome.model.fs.FilesetEntry
 
fields() - Method in class ome.model.fs.FilesetEntry
 
FIELDS - Static variable in class ome.model.fs.FilesetJobLink
 
fields() - Method in class ome.model.fs.FilesetJobLink
 
FIELDS - Static variable in class ome.model.internal.Link
 
fields() - Method in class ome.model.internal.Link
 
fields() - Method in interface ome.model.IObject
returns a Set of field names that belong to this class
FIELDS - Static variable in class ome.model.jobs.ImportJob
 
fields() - Method in class ome.model.jobs.ImportJob
 
FIELDS - Static variable in class ome.model.jobs.IndexingJob
 
fields() - Method in class ome.model.jobs.IndexingJob
 
FIELDS - Static variable in class ome.model.jobs.IntegrityCheckJob
 
fields() - Method in class ome.model.jobs.IntegrityCheckJob
 
FIELDS - Static variable in class ome.model.jobs.Job
 
fields() - Method in class ome.model.jobs.Job
 
FIELDS - Static variable in class ome.model.jobs.JobOriginalFileLink
 
fields() - Method in class ome.model.jobs.JobOriginalFileLink
 
FIELDS - Static variable in class ome.model.jobs.JobStatus
 
fields() - Method in class ome.model.jobs.JobStatus
 
FIELDS - Static variable in class ome.model.jobs.MetadataImportJob
 
fields() - Method in class ome.model.jobs.MetadataImportJob
 
FIELDS - Static variable in class ome.model.jobs.ParseJob
 
fields() - Method in class ome.model.jobs.ParseJob
 
FIELDS - Static variable in class ome.model.jobs.PixelDataJob
 
fields() - Method in class ome.model.jobs.PixelDataJob
 
FIELDS - Static variable in class ome.model.jobs.ScriptJob
 
fields() - Method in class ome.model.jobs.ScriptJob
 
FIELDS - Static variable in class ome.model.jobs.ThumbnailGenerationJob
 
fields() - Method in class ome.model.jobs.ThumbnailGenerationJob
 
FIELDS - Static variable in class ome.model.jobs.UploadJob
 
fields() - Method in class ome.model.jobs.UploadJob
 
FIELDS - Static variable in class ome.model.meta.DBPatch
 
fields() - Method in class ome.model.meta.DBPatch
 
FIELDS - Static variable in class ome.model.meta.Event
 
fields() - Method in class ome.model.meta.Event
 
FIELDS - Static variable in class ome.model.meta.EventLog
 
fields() - Method in class ome.model.meta.EventLog
 
FIELDS - Static variable in class ome.model.meta.Experimenter
 
fields() - Method in class ome.model.meta.Experimenter
 
FIELDS - Static variable in class ome.model.meta.ExperimenterGroup
 
fields() - Method in class ome.model.meta.ExperimenterGroup
 
FIELDS - Static variable in class ome.model.meta.ExternalInfo
 
fields() - Method in class ome.model.meta.ExternalInfo
 
FIELDS - Static variable in class ome.model.meta.GroupExperimenterMap
 
fields() - Method in class ome.model.meta.GroupExperimenterMap
 
FIELDS - Static variable in class ome.model.meta.Namespace
 
fields() - Method in class ome.model.meta.Namespace
 
FIELDS - Static variable in class ome.model.meta.Node
 
fields() - Method in class ome.model.meta.Node
 
FIELDS - Static variable in class ome.model.meta.Session
 
fields() - Method in class ome.model.meta.Session
 
FIELDS - Static variable in class ome.model.meta.Share
 
fields() - Method in class ome.model.meta.Share
 
FIELDS - Static variable in class ome.model.meta.ShareMember
 
fields() - Method in class ome.model.meta.ShareMember
 
FIELDS - Static variable in class ome.model.roi.Ellipse
 
fields() - Method in class ome.model.roi.Ellipse
 
FIELDS - Static variable in class ome.model.roi.Label
 
fields() - Method in class ome.model.roi.Label
 
FIELDS - Static variable in class ome.model.roi.Line
 
fields() - Method in class ome.model.roi.Line
 
FIELDS - Static variable in class ome.model.roi.Mask
 
fields() - Method in class ome.model.roi.Mask
 
FIELDS - Static variable in class ome.model.roi.Path
 
fields() - Method in class ome.model.roi.Path
 
FIELDS - Static variable in class ome.model.roi.Point
 
fields() - Method in class ome.model.roi.Point
 
FIELDS - Static variable in class ome.model.roi.Polygon
 
fields() - Method in class ome.model.roi.Polygon
 
FIELDS - Static variable in class ome.model.roi.Polyline
 
fields() - Method in class ome.model.roi.Polyline
 
FIELDS - Static variable in class ome.model.roi.Rect
 
fields() - Method in class ome.model.roi.Rect
 
FIELDS - Static variable in class ome.model.roi.Roi
 
fields() - Method in class ome.model.roi.Roi
 
FIELDS - Static variable in class ome.model.roi.Shape
 
fields() - Method in class ome.model.roi.Shape
 
FIELDS - Static variable in class ome.model.screen.Plate
 
fields() - Method in class ome.model.screen.Plate
 
FIELDS - Static variable in class ome.model.screen.PlateAcquisition
 
fields() - Method in class ome.model.screen.PlateAcquisition
 
FIELDS - Static variable in class ome.model.screen.Reagent
 
fields() - Method in class ome.model.screen.Reagent
 
FIELDS - Static variable in class ome.model.screen.Screen
 
fields() - Method in class ome.model.screen.Screen
 
FIELDS - Static variable in class ome.model.screen.ScreenPlateLink
 
fields() - Method in class ome.model.screen.ScreenPlateLink
 
FIELDS - Static variable in class ome.model.screen.Well
 
fields() - Method in class ome.model.screen.Well
 
FIELDS - Static variable in class ome.model.screen.WellReagentLink
 
fields() - Method in class ome.model.screen.WellReagentLink
 
FIELDS - Static variable in class ome.model.screen.WellSample
 
fields() - Method in class ome.model.screen.WellSample
 
FIELDS - Static variable in class ome.model.stats.StatsInfo
 
fields() - Method in class ome.model.stats.StatsInfo
 
Filament - Class in ome.model.acquisition
 
Filament() - Constructor for class ome.model.acquisition.Filament
 
Filament(Long) - Constructor for class ome.model.acquisition.Filament
 
Filament(Long, boolean) - Constructor for class ome.model.acquisition.Filament
Main constructor.
Filament(FilamentType) - Constructor for class ome.model.acquisition.Filament
 
FILAMENT - Static variable in class pojos.LightSourceData
Indicates that the light source is a filament.
FilamentType - Class in ome.model.enums
 
FilamentType() - Constructor for class ome.model.enums.FilamentType
 
FilamentType(Long) - Constructor for class ome.model.enums.FilamentType
 
FilamentType(Long, boolean) - Constructor for class ome.model.enums.FilamentType
Main constructor.
FilamentType(String) - Constructor for class ome.model.enums.FilamentType
 
FilamentType.Details - Class in ome.model.enums
 
FilamentType.Details() - Constructor for class ome.model.enums.FilamentType.Details
 
FilamentType.Details(Object[]) - Constructor for class ome.model.enums.FilamentType.Details
 
file - Variable in class ome.formats.importer.ImportCandidates.SCANNING
 
file - Variable in class ome.model.annotations.FileAnnotation
 
FILE - Static variable in class ome.model.annotations.FileAnnotation
 
file - Variable in class ome.security.auth.FilePasswordProvider
Flat file read on each invocation with name, value pairs in Java Properties notation.
file(String, String, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
 
file() - Method in class ome.services.scripts.RepoFile
 
FILE_TRANSFER_NS - Static variable in class pojos.AnnotationData
The name space used to identify the file transfer type.
FileAnnotation - Class in ome.model.annotations
 
FileAnnotation() - Constructor for class ome.model.annotations.FileAnnotation
 
FileAnnotation(Long) - Constructor for class ome.model.annotations.FileAnnotation
 
FileAnnotation(Long, boolean) - Constructor for class ome.model.annotations.FileAnnotation
Main constructor.
FileAnnotationData - Class in pojos
Annotation to upload files to the server.
FileAnnotationData(File) - Constructor for class pojos.FileAnnotationData
Creates a new instance.
FileAnnotationData(FileAnnotation) - Constructor for class pojos.FileAnnotationData
Creates a new instance.
FileBuffer - Class in ome.io.nio
Raw file buffer which provides I/O operations within the OMERO file repository.
FileBuffer(String, String) - Constructor for class ome.io.nio.FileBuffer
Default constructor allowing to pass in a non-"rw" file mode.
fileById(long, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
 
fileContext(long, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
Create a String-String map which can be used as the context for a call to Executor.execute based on the group of the file object.
FileData - Class in pojos
DataObject used to handle the file visible via FS.
FileData(OriginalFile) - Constructor for class pojos.FileData
Creates a new instance.
FileData(OriginalFile, boolean) - Constructor for class pojos.FileData
Creates a new instance.
FileData(OriginalFile, boolean, boolean) - Constructor for class pojos.FileData
Creates a new instance.
FileDeleter - Class in ome.services.delete.files
Helper class which sorts through a number of file-based deletions before processing them.
FileDeleter(OmeroContext, AbstractFileSystemService, SetMultimap<String, Long>) - Constructor for class ome.services.delete.files.FileDeleter
 
FileDeleterGraphState - Class in ome.services.delete.files
Deprecated.
will be removed in OMERO 5.2, so use the new graphs implementation
FileDeleterGraphState(OmeroContext, AbstractFileSystemService, GraphState, String, long) - Constructor for class ome.services.delete.files.FileDeleterGraphState
Deprecated.
 
FileExclusion - Interface in ome.formats.importer.exclusions
Voter given the opportunity by the ImportLibrary to cancel the importing of a given file.
fileExists(String, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
 
fileId - Variable in class ome.util.SqlAction.DeleteLog
 
fileIdsInDb(String, Set<String>) - Method in interface ome.util.SqlAction
Return all IDs matching the given mimetypes, or all IDs if mimetypes is null.
fileIdsInDb(String, Set<String>) - Method in class ome.util.SqlAction.Impl
 
fileIndex - Variable in class ome.formats.importer.ImportEvent.FILE_UPLOAD_EVENT
 
FileMaker - Class in ome.services.blitz.repo
Utility class for creating and cleaning up a repository lock file.
FileMaker(String) - Constructor for class ome.services.blitz.repo.FileMaker
 
filename - Variable in class ome.formats.importer.ImportEvent.FILE_UPLOAD_EVENT
 
fileName - Variable in class ome.formats.importer.ImportSize
 
filename - Variable in class ome.formats.importer.util.ErrorHandler.FILE_EXCEPTION
 
filename - Variable in class ome.formats.importer.util.ErrorHandler.INTERNAL_EXCEPTION
 
filename - Variable in class ome.formats.importer.util.ErrorHandler.UNKNOWN_FORMAT
 
filename - Variable in class ome.formats.importer.util.ErrorHandler.UNREADABLE_FILE
 
FILENAME - Static variable in class ome.formats.importer.util.TinyImportFixture
Hard-coded filename of the image to be imported
FilenameExclusion - Class in ome.formats.importer.exclusions
Voter which checks the filename (not full path) of a given File along with the checksum to detect duplicates.
FilenameExclusion() - Constructor for class ome.formats.importer.exclusions.FilenameExclusion
 
FileParser - Class in ome.services.fulltext
Object which attempts to parse any file given to it.
FileParser() - Constructor for class ome.services.fulltext.FileParser
 
FilePasswordProvider - Class in ome.security.auth
Example password provider which uses the given file as password lookup.
FilePasswordProvider(PasswordUtil, File) - Constructor for class ome.security.auth.FilePasswordProvider
 
FilePasswordProvider(PasswordUtil, File, boolean) - Constructor for class ome.security.auth.FilePasswordProvider
 
filePath - Variable in class ome.io.bioformats.BfPixelBuffer
 
FilePathNamingValidator - Class in ome.services.blitz.repo.path
 
FilePathNamingValidator(FilePathRestrictions...) - Constructor for class ome.services.blitz.repo.path.FilePathNamingValidator
 
FilePathResolver - Interface in ome.io.nio
Resolver for file paths and related metadata.
FilePathRestrictionInstance - Enum in ome.services.blitz.repo.path
 
FilePathRestrictions - Class in ome.services.blitz.repo.path
Capture a set of rules by which local files may not be named on the file-system.
FilePathRestrictions(SetMultimap<Integer, Integer>, Set<String>, Set<String>, Set<String>, Set<Character>) - Constructor for class ome.services.blitz.repo.path.FilePathRestrictions
Construct a set of rules by which local files may not be named on the file-system.
filePathRestrictions - Variable in class ome.services.blitz.repo.PublicRepositoryI
 
fileRepo(long) - Method in interface ome.util.SqlAction
 
fileRepo(long) - Method in class ome.util.SqlAction.Impl
 
files - Variable in class ome.services.fulltext.FullTextBridge
 
FILES_PATH - Static variable in class ome.io.nio.AbstractFileSystemService
 
fileset - Variable in class ome.formats.importer.ImportEvent.IMPORT_DONE
 
fileset - Variable in class ome.model.core.Image
 
FILESET - Static variable in class ome.model.core.Image
 
Fileset - Class in ome.model.fs
These filter definitions are used by the security system to eliminate non-readable objects from queries.
Fileset() - Constructor for class ome.model.fs.Fileset
 
Fileset(Long) - Constructor for class ome.model.fs.Fileset
 
Fileset(Long, boolean) - Constructor for class ome.model.fs.Fileset
Main constructor.
Fileset(String) - Constructor for class ome.model.fs.Fileset
 
fileset - Variable in class ome.model.fs.FilesetEntry
 
FILESET - Static variable in class ome.model.fs.FilesetEntry
 
Fileset.Details - Class in ome.model.fs
 
Fileset.Details() - Constructor for class ome.model.fs.Fileset.Details
 
Fileset.Details(Object[]) - Constructor for class ome.model.fs.Fileset.Details
 
FilesetAnnotationLink - Class in ome.model.annotations
These filter definitions are used by the security system to eliminate non-readable objects from queries.
FilesetAnnotationLink() - Constructor for class ome.model.annotations.FilesetAnnotationLink
 
FilesetAnnotationLink(Long) - Constructor for class ome.model.annotations.FilesetAnnotationLink
 
FilesetAnnotationLink(Long, boolean) - Constructor for class ome.model.annotations.FilesetAnnotationLink
Main constructor.
FilesetAnnotationLink(IObject, IObject) - Constructor for class ome.model.annotations.FilesetAnnotationLink
 
FilesetAnnotationLink.Details - Class in ome.model.annotations
 
FilesetAnnotationLink.Details() - Constructor for class ome.model.annotations.FilesetAnnotationLink.Details
 
FilesetAnnotationLink.Details(Object[]) - Constructor for class ome.model.annotations.FilesetAnnotationLink.Details
 
FilesetData - Class in pojos
Wraps a file set object.
FilesetData(Fileset) - Constructor for class pojos.FilesetData
Creates a new instance.
filesetEntries - Variable in class ome.model.core.OriginalFile
 
FILESETENTRIES - Static variable in class ome.model.core.OriginalFile
 
FilesetEntry - Class in ome.model.fs
These filter definitions are used by the security system to eliminate non-readable objects from queries.
FilesetEntry() - Constructor for class ome.model.fs.FilesetEntry
 
FilesetEntry(Long) - Constructor for class ome.model.fs.FilesetEntry
 
FilesetEntry(Long, boolean) - Constructor for class ome.model.fs.FilesetEntry
Main constructor.
FilesetEntry(Fileset, OriginalFile, String) - Constructor for class ome.model.fs.FilesetEntry
 
FilesetEntry.Details - Class in ome.model.fs
 
FilesetEntry.Details() - Constructor for class ome.model.fs.FilesetEntry.Details
 
FilesetEntry.Details(Object[]) - Constructor for class ome.model.fs.FilesetEntry.Details
 
FilesetJobLink - Class in ome.model.fs
These filter definitions are used by the security system to eliminate non-readable objects from queries.
FilesetJobLink() - Constructor for class ome.model.fs.FilesetJobLink
 
FilesetJobLink(Long) - Constructor for class ome.model.fs.FilesetJobLink
 
FilesetJobLink(Long, boolean) - Constructor for class ome.model.fs.FilesetJobLink
Main constructor.
FilesetJobLink(IObject, IObject) - Constructor for class ome.model.fs.FilesetJobLink
 
FilesetJobLink.Details - Class in ome.model.fs
 
FilesetJobLink.Details() - Constructor for class ome.model.fs.FilesetJobLink.Details
 
FilesetJobLink.Details(Object[]) - Constructor for class ome.model.fs.FilesetJobLink.Details
 
FileSizeChecksumProviderImpl - Class in ome.util.checksum
Trivial checksum provider whose hash is simply the number of bytes that were put into the calculation.
FileSizeChecksumProviderImpl() - Constructor for class ome.util.checksum.FileSizeChecksumProviderImpl
 
filesService - Variable in class ome.services.blitz.impl.MetadataStoreI
 
filesToString(File...) - Static method in class omero.client
 
FileSystem - Class in ome.tools
Extends Sun Microsystems java.io.File for J2SE 5 only.
FileSystem(String) - Constructor for class ome.tools.FileSystem
pass-thru constructor
FileSystem(URI) - Constructor for class ome.tools.FileSystem
pass-thru constructor
FileSystem(String, String) - Constructor for class ome.tools.FileSystem
pass-thru constructor
FileSystem(File, String) - Constructor for class ome.tools.FileSystem
pass-thru constructor
fileTotal - Variable in class ome.formats.importer.ImportEvent.FILE_UPLOAD_EVENT
 
FileTransfer - Interface in ome.formats.importer.transfers
Abstracted concept of "getting the file to the server".
FileUploader - Class in ome.formats.importer.util
 
FileUploader(CloseableHttpClient) - Constructor for class ome.formats.importer.util.FileUploader
Initialize upload with httpClient
fileUploadErrors - Variable in class ome.formats.importer.util.ErrorHandler
 
fillColor - Variable in class ome.model.roi.Shape
 
FILLCOLOR - Static variable in class ome.model.roi.Shape
 
fillData(ImportSettings, Fileset, ClientFilePathTransformer) - Method in class ome.formats.importer.ImportContainer
 
fillData(ImportSettings, Fileset, ClientFilePathTransformer, FileTransfer) - Method in class ome.formats.importer.ImportContainer
 
fillData(ImportConfig, ImportSettings, Fileset, ClientFilePathTransformer) - Method in class ome.formats.importer.ImportContainer
 
fillData(ImportConfig, ImportSettings, Fileset, ClientFilePathTransformer, FileTransfer) - Method in class ome.formats.importer.ImportContainer
 
fillObject(ReverseModelMapper) - Method in interface ome.model.ModelBased
 
fillObject(ReverseModelMapper) - Method in class omero.model.DetailsI
 
fillObject(ReverseModelMapper) - Method in class omero.model.ElectricPotentialI
 
fillObject(ReverseModelMapper) - Method in class omero.model.FrequencyI
 
fillObject(ReverseModelMapper) - Method in class omero.model.LengthI
 
fillObject(ReverseModelMapper) - Method in class omero.model.PermissionsI
 
fillObject(ReverseModelMapper) - Method in class omero.model.PowerI
 
fillObject(ReverseModelMapper) - Method in class omero.model.PressureI
 
fillObject(ReverseModelMapper) - Method in class omero.model.TemperatureI
 
fillObject(ReverseModelMapper) - Method in class omero.model.TimeI
 
fillRelationships(SessionFactoryImplementor, Map<String, ExtendedMetadata.Relationship>) - Method in class ome.tools.hibernate.ExtendedMetadata.Locks
For each of the fields contained in this ExtendedMetadata.Locks object, parse out the type and the field name and store those as the key and value in the "value" argument.
fillReplacement(MergeEvent) - Method in class ome.security.basic.MergeEventListener
 
fillRule - Variable in class ome.model.roi.Shape
 
FILLRULE - Static variable in class ome.model.roi.Shape
 
fillServerError(ServerError, Throwable) - Static method in class omero.util.IceMapper
 
fillVersionInfo(List<NamedValue>) - Method in class ome.formats.importer.ImportConfig
Note useful version information that can be extracted from this system, as provenance that is useful for debugging.
Filter - Class in ome.model.acquisition
These filter definitions are used by the security system to eliminate non-readable objects from queries.
Filter() - Constructor for class ome.model.acquisition.Filter
 
Filter(Long) - Constructor for class ome.model.acquisition.Filter
 
Filter(Long, boolean) - Constructor for class ome.model.acquisition.Filter
Main constructor.
Filter(Instrument) - Constructor for class ome.model.acquisition.Filter
 
filter - Variable in class ome.model.acquisition.Instrument
 
FILTER - Static variable in class ome.model.acquisition.Instrument
 
Filter - Class in ome.parameters
parameter to generally reduce the size of a query result set.
Filter() - Constructor for class ome.parameters.Filter
 
filter - Variable in class ome.security.basic.BasicSecuritySystem
 
filter(String, Filterable) - Method in class ome.tools.hibernate.ProxyCleanupFilter
 
filter(String, Collection) - Method in class ome.tools.hibernate.ProxyCleanupFilter
 
filter(String, Map) - Method in class ome.tools.hibernate.ProxyCleanupFilter
 
filter(String, Filter) - Method in class ome.tools.hibernate.QueryBuilder
 
filter(String, Filterable) - Method in class ome.tools.hibernate.ReloadFilter
 
filter(String, Object) - Method in class ome.tools.hibernate.UpdateFilter
overrides ContextFilter.filter(String, Object) to allow only certain types to enter the Hibernate system
filter(String, Filterable) - Method in class ome.tools.hibernate.UpdateFilter
overrides ContextFilter.filter(String, Filterable) to return previously merged or previously checked items.
filter(String, Collection) - Method in class ome.tools.hibernate.UpdateFilter
overrides ContextFilter.filter(String, Collection) to return previously checked collections.
filter(String, Map) - Method in class ome.tools.hibernate.UpdateFilter
Prevents CountPerOwner from being loaded unnecessarily.
filter(String, Filterable) - Method in class ome.util.ContextFilter
 
filter(String, Collection) - Method in class ome.util.ContextFilter
iterates over the contents of the collection and filters each.
filter(String, Map) - Method in class ome.util.ContextFilter
filters both the key and value sets of the map.
filter(String, Object) - Method in class ome.util.ContextFilter
used when type is unknown. this is possibly omittable with generics
filter(String, ContextFilter.Entry) - Method in class ome.util.ContextFilter
doesn't return a new entry. only changes key and value
Filter - Interface in ome.util
marks objects which can be filtered using {see FIXME }.
filter(String, Filterable) - Method in interface ome.util.Filter
 
filter(String, Collection) - Method in interface ome.util.Filter
 
filter(String, Map) - Method in interface ome.util.Filter
 
filter(String, Object) - Method in interface ome.util.Filter
 
filter(String, Filterable) - Method in class ome.util.ModelMapper
 
filter(String, Collection) - Method in class ome.util.ModelMapper
 
filter(String, Map) - Method in class ome.util.ModelMapper
 
filter(String, Object) - Method in class ome.util.RdfPrinter
 
filter(String, Filterable) - Method in class ome.util.RdfPrinter
 
filter(String, Collection) - Method in class ome.util.RdfPrinter
 
filter(String, Filterable) - Method in class omero.util.IceMapper
 
Filter.Details - Class in ome.model.acquisition
 
Filter.Details() - Constructor for class ome.model.acquisition.Filter.Details
 
Filter.Details(Object[]) - Constructor for class ome.model.acquisition.Filter.Details
 
Filterable - Interface in ome.util
marks objects which can be filtered using {see FIXME }.
FILTERABLE - Static variable in class omero.util.IceMapper
 
FILTERABLE_ARRAY - Static variable in class omero.util.IceMapper
 
FILTERABLE_COLLECTION - Static variable in class omero.util.IceMapper
 
FILTERABLE_PRIMITIVE_MAP - Static variable in class omero.util.IceMapper
 
FilterAnnotationLink - Class in ome.model.annotations
These filter definitions are used by the security system to eliminate non-readable objects from queries.
FilterAnnotationLink() - Constructor for class ome.model.annotations.FilterAnnotationLink
 
FilterAnnotationLink(Long) - Constructor for class ome.model.annotations.FilterAnnotationLink
 
FilterAnnotationLink(Long, boolean) - Constructor for class ome.model.annotations.FilterAnnotationLink
Main constructor.
FilterAnnotationLink(IObject, IObject) - Constructor for class ome.model.annotations.FilterAnnotationLink
 
FilterAnnotationLink.Details - Class in ome.model.annotations
 
FilterAnnotationLink.Details() - Constructor for class ome.model.annotations.FilterAnnotationLink.Details
 
FilterAnnotationLink.Details(Object[]) - Constructor for class ome.model.annotations.FilterAnnotationLink.Details
 
filterByType(Collection<Preprocessor.GraphModifyTarget>, Preprocessor.TargetType) - Static method in class omero.cmd.graphs.Preprocessor.GraphModifyTarget
Deprecated.
Return only the targets of the given type.
FilterData - Class in pojos
Object hosting a filter.
FilterData(Filter) - Constructor for class pojos.FilterData
Creates a new instance.
filteredSet() - Method in class ome.model.internal.Details
copy of the current collection of filtered names.
filteredSize() - Method in class ome.model.internal.Details
the count of collections which were filtered.
filterFileIdsByRepo(String, List<Long>) - Method in interface ome.util.SqlAction
Find the original file IDs among those given that are in the given repository.
filterFileIdsByRepo(String, List<Long>) - Method in class ome.util.SqlAction.Impl
 
filterFilesByRepository(String, List<Long>, Current) - Method in interface ome.services.blitz.repo.RepositoryDao
Find the original file IDs among those given that are in the given repository.
filterFilesByRepository(String, List<Long>, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
 
filterName - Static variable in class ome.security.basic.AllGroupsSecurityFilter
 
filterNow() - Method in class ome.tools.hibernate.QueryBuilder
In order to support the order() method in addition to a filter, we allow applying the filter and nulling the instance eagerly before the user calls order.
filterObject(IObject) - Method in class ome.security.policy.DefaultPolicyService
Limit the objects to which Policy instances are applied.
FilterSet - Class in ome.model.acquisition
These filter definitions are used by the security system to eliminate non-readable objects from queries.
FilterSet() - Constructor for class ome.model.acquisition.FilterSet
 
FilterSet(Long) - Constructor for class ome.model.acquisition.FilterSet
 
FilterSet(Long, boolean) - Constructor for class ome.model.acquisition.FilterSet
Main constructor.
FilterSet(Instrument) - Constructor for class ome.model.acquisition.FilterSet
 
filterSet - Variable in class ome.model.acquisition.Instrument
 
FILTERSET - Static variable in class ome.model.acquisition.Instrument
 
filterSet - Variable in class ome.model.acquisition.OTF
 
FILTERSET - Static variable in class ome.model.acquisition.OTF
 
filterSet - Variable in class ome.model.core.LogicalChannel
 
FILTERSET - Static variable in class ome.model.core.LogicalChannel
 
FilterSet.Details - Class in ome.model.acquisition
 
FilterSet.Details() - Constructor for class ome.model.acquisition.FilterSet.Details
 
FilterSet.Details(Object[]) - Constructor for class ome.model.acquisition.FilterSet.Details
 
FilterSetData - Class in pojos
Object hosting a filterSet.
FilterSetData(FilterSet) - Constructor for class pojos.FilterSetData
Creates a new instance.
FilterSetEmissionFilterLink - Class in ome.model.acquisition
These filter definitions are used by the security system to eliminate non-readable objects from queries.
FilterSetEmissionFilterLink() - Constructor for class ome.model.acquisition.FilterSetEmissionFilterLink
 
FilterSetEmissionFilterLink(Long) - Constructor for class ome.model.acquisition.FilterSetEmissionFilterLink
 
FilterSetEmissionFilterLink(Long, boolean) - Constructor for class ome.model.acquisition.FilterSetEmissionFilterLink
Main constructor.
FilterSetEmissionFilterLink(IObject, IObject) - Constructor for class ome.model.acquisition.FilterSetEmissionFilterLink
 
FilterSetEmissionFilterLink.Details - Class in ome.model.acquisition
 
FilterSetEmissionFilterLink.Details() - Constructor for class ome.model.acquisition.FilterSetEmissionFilterLink.Details
 
FilterSetEmissionFilterLink.Details(Object[]) - Constructor for class ome.model.acquisition.FilterSetEmissionFilterLink.Details
 
FilterSetExcitationFilterLink - Class in ome.model.acquisition
These filter definitions are used by the security system to eliminate non-readable objects from queries.
FilterSetExcitationFilterLink() - Constructor for class ome.model.acquisition.FilterSetExcitationFilterLink
 
FilterSetExcitationFilterLink(Long) - Constructor for class ome.model.acquisition.FilterSetExcitationFilterLink
 
FilterSetExcitationFilterLink(Long, boolean) - Constructor for class ome.model.acquisition.FilterSetExcitationFilterLink
Main constructor.
FilterSetExcitationFilterLink(IObject, IObject) - Constructor for class ome.model.acquisition.FilterSetExcitationFilterLink
 
FilterSetExcitationFilterLink.Details - Class in ome.model.acquisition
 
FilterSetExcitationFilterLink.Details() - Constructor for class ome.model.acquisition.FilterSetExcitationFilterLink.Details
 
FilterSetExcitationFilterLink.Details(Object[]) - Constructor for class ome.model.acquisition.FilterSetExcitationFilterLink.Details
 
FilterType - Class in ome.model.enums
 
FilterType() - Constructor for class ome.model.enums.FilterType
 
FilterType(Long) - Constructor for class ome.model.enums.FilterType
 
FilterType(Long, boolean) - Constructor for class ome.model.enums.FilterType
Main constructor.
FilterType(String) - Constructor for class ome.model.enums.FilterType
 
FilterType.Details - Class in ome.model.enums
 
FilterType.Details() - Constructor for class ome.model.enums.FilterType.Details
 
FilterType.Details(Object[]) - Constructor for class ome.model.enums.FilterType.Details
 
filterWheel - Variable in class ome.model.acquisition.Filter
 
FILTERWHEEL - Static variable in class ome.model.acquisition.Filter
 
finalize() - Method in class omero.cmd.fs.UsedFilesRequestI
 
finalizePixelStore() - Method in class ome.formats.OMEROMetadataStoreClient
Closes the active raw pixels store.
find(Class<T>, long) - Method in interface ome.api.IQuery
lookup an entity by class and id.
find(Class, long) - Method in class ome.logic.QueryImpl
 
find(String) - Method in interface ome.services.sessions.SessionManager
 
find(String) - Method in class ome.services.sessions.SessionManagerImpl
 
find_async(AMD_IQuery_find, String, long, Current) - Method in class ome.services.blitz.impl.QueryI
 
findAll(Class<T>, Filter) - Method in interface ome.api.IQuery
lookup all entities that belong to this class and match filter.
findAll(Class<T>, Filter) - Method in class ome.logic.QueryImpl
 
findAll_async(AMD_IQuery_findAll, String, Filter, Current) - Method in class ome.services.blitz.impl.QueryI
 
findAllByExample(T, Filter) - Method in interface ome.api.IQuery
search based on provided example entity.
findAllByExample(T, Filter) - Method in class ome.logic.QueryImpl
 
findAllByExample_async(AMD_IQuery_findAllByExample, IObject, Filter, Current) - Method in class ome.services.blitz.impl.QueryI
 
findAllByFullText(Class<T>, String, Parameters) - Method in interface ome.api.IQuery
executes a full text search based on Lucene.
findAllByFullText(Class<T>, String, Parameters) - Method in class ome.logic.QueryImpl
 
findAllByFullText_async(AMD_IQuery_findAllByFullText, String, String, Parameters, Current) - Method in class ome.services.blitz.impl.QueryI
 
findAllByQuery(String, Parameters) - Method in interface ome.api.IQuery
executes the stored query with the given name.
findAllByQuery(String, Parameters) - Method in class ome.logic.QueryImpl
 
findAllByQuery_async(AMD_IQuery_findAllByQuery, String, Parameters, Current) - Method in class ome.services.blitz.impl.QueryI
 
findAllByString(Class<T>, String, String, boolean, Filter) - Method in interface ome.api.IQuery
search a given field matching against a String.
findAllByString(Class<T>, String, String, boolean, Filter) - Method in class ome.logic.QueryImpl
 
findAllByString_async(AMD_IQuery_findAllByString, String, String, String, boolean, Filter, Current) - Method in class ome.services.blitz.impl.QueryI
 
findAnnotationAnnotationLink(Annotation) - Method in class ome.model.annotations.Annotation
find all ome.model.annotations.AnnotationAnnotationLink which have the argument as their child.
findByExample(T) - Method in interface ome.api.IQuery
search based on provided example entity.
findByExample(T) - Method in class ome.logic.QueryImpl
 
findByExample_async(AMD_IQuery_findByExample, IObject, Current) - Method in class ome.services.blitz.impl.QueryI
 
findByImage_async(AMD_IRoi_findByImage, long, RoiOptions, Current) - Method in class ome.services.blitz.impl.RoiI
 
findByMimetype(String) - Method in class ome.services.scripts.ScriptRepoHelper
Search through all ScriptFileType instances and find one with a matching mimetype string.
findByPlane_async(AMD_IRoi_findByPlane, long, int, int, RoiOptions, Current) - Method in class ome.services.blitz.impl.RoiI
 
findByQuery(String, Parameters) - Method in interface ome.api.IQuery
executes the stored query with the given name.
findByQuery(String, Parameters) - Method in class ome.logic.QueryImpl
 
findByQuery_async(AMD_IQuery_findByQuery, String, Parameters, Current) - Method in class ome.services.blitz.impl.QueryI
 
findByRoi_async(AMD_IRoi_findByRoi, long, RoiOptions, Current) - Method in class ome.services.blitz.impl.RoiI
 
findByString(Class<T>, String, String) - Method in interface ome.api.IQuery
search a given field matching against a String.
findByString(Class<T>, String, String) - Method in class ome.logic.QueryImpl
 
findByString_async(AMD_IQuery_findByString, String, String, String, Current) - Method in class ome.services.blitz.impl.QueryI
 
findByUser(String) - Method in interface ome.services.sessions.SessionManager
 
findByUser(String) - Method in class ome.services.sessions.SessionManagerImpl
 
findByUserAndAgent(String, String...) - Method in interface ome.services.sessions.SessionManager
Returns a non-null, possibly empty list of session instances belonging to the given user and with one of the given agents.
findByUserAndAgent(String, String...) - Method in class ome.services.sessions.SessionManagerImpl
 
findChannelAnnotationLink(Annotation) - Method in class ome.model.core.Channel
find all ome.model.annotations.ChannelAnnotationLink which have the argument as their child.
findClass(Class) - Method in class ome.util.ModelMapper
 
findCollection(Collection) - Method in class ome.util.ModelMapper
 
findCollection(Collection) - Method in class omero.util.IceMapper
Overrides the findCollection logic of ModelMapper, since all Collections should be Lists in Ice.
findCollectionTarget(Object) - Method in class ome.util.ModelMapper
extension point which subclasses can override to better map the values of collections and maps.
findCollectionTarget(Object) - Method in class omero.util.RTypeMapper
 
findContainerHierarchies(Class<T>, Set<Long>, Parameters) - Method in interface ome.api.IContainer
Retrieves hierarchy trees in various hierarchies that contain the specified Images.
findContainerHierarchies(Class, Set, Parameters) - Method in class ome.logic.PojosImpl
Implemented as specified by the IContainer I/F
findContainerHierarchies_async(AMD_IContainer_findContainerHierarchies, String, List<Long>, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI
 
findDatasetAnnotationLink(Annotation) - Method in class ome.model.containers.Dataset
find all ome.model.annotations.DatasetAnnotationLink which have the argument as their child.
findDatasetImageLink(Image) - Method in class ome.model.containers.Dataset
find all ome.model.containers.DatasetImageLink which have the argument as their child.
findDatasetImageLink(Dataset) - Method in class ome.model.core.Image
find all ome.model.containers.DatasetImageLink which have the argument as their parent.
findDetectorAnnotationLink(Annotation) - Method in class ome.model.acquisition.Detector
find all ome.model.annotations.DetectorAnnotationLink which have the argument as their child.
findDichroicAnnotationLink(Annotation) - Method in class ome.model.acquisition.Dichroic
find all ome.model.annotations.DichroicAnnotationLink which have the argument as their child.
findDirty(Object, Serializable, Object[], Object[], String[], Type[]) - Method in class ome.security.basic.OmeroInterceptor
default logic
findDN(String) - Method in interface ome.api.ILdap
Searches unique Distinguished Name - String in LDAP for Common Name equals username.
findDN(String) - Method in class ome.logic.LdapImpl
 
findDN_async(AMD_ILdap_findDN, String, Current) - Method in class ome.services.blitz.impl.LdapI
 
findEnumeration(HashMap<String, IObject>, String) - Method in interface ome.formats.enums.handler.EnumerationHandler
Attempt to find an enumeration from an existing set of enumeration values.
findExperimenter(String) - Method in interface ome.api.ILdap
Searches Experimenter by unique Distinguished Name - String in LDAP for Common Name equals username.
findExperimenter(String) - Method in class ome.logic.LdapImpl
 
findExperimenter_async(AMD_ILdap_findExperimenter, String, Current) - Method in class ome.services.blitz.impl.LdapI
 
findExperimenterAnnotationLink(Annotation) - Method in class ome.model.meta.Experimenter
find all ome.model.annotations.ExperimenterAnnotationLink which have the argument as their child.
findExperimenterGroupAnnotationLink(Annotation) - Method in class ome.model.meta.ExperimenterGroup
find all ome.model.annotations.ExperimenterGroupAnnotationLink which have the argument as their child.
findFilesetAnnotationLink(Annotation) - Method in class ome.model.fs.Fileset
find all ome.model.annotations.FilesetAnnotationLink which have the argument as their child.
findFilesetJobLink(Job) - Method in class ome.model.fs.Fileset
find all ome.model.fs.FilesetJobLink which have the argument as their child.
findFilterAnnotationLink(Annotation) - Method in class ome.model.acquisition.Filter
find all ome.model.annotations.FilterAnnotationLink which have the argument as their child.
findFilterSetEmissionFilterLink(FilterSet) - Method in class ome.model.acquisition.Filter
find all ome.model.acquisition.FilterSetEmissionFilterLink which have the argument as their parent.
findFilterSetEmissionFilterLink(Filter) - Method in class ome.model.acquisition.FilterSet
find all ome.model.acquisition.FilterSetEmissionFilterLink which have the argument as their child.
findFilterSetExcitationFilterLink(FilterSet) - Method in class ome.model.acquisition.Filter
find all ome.model.acquisition.FilterSetExcitationFilterLink which have the argument as their parent.
findFilterSetExcitationFilterLink(Filter) - Method in class ome.model.acquisition.FilterSet
find all ome.model.acquisition.FilterSetExcitationFilterLink which have the argument as their child.
findGroup(String) - Method in interface ome.api.ILdap
Looks up a specific ExperimenterGroup in LDAP using the provided group name.
findGroup(String) - Method in class ome.logic.LdapImpl
 
findGroup_async(AMD_ILdap_findGroup, String, Current) - Method in class ome.services.blitz.impl.LdapI
 
findGroupDN(String) - Method in interface ome.api.ILdap
Looks up the DN for a group.
findGroupDN(String) - Method in class ome.logic.LdapImpl
 
findGroupDN_async(AMD_ILdap_findGroupDN, String, Current) - Method in class ome.services.blitz.impl.LdapI
 
findGroupExperimenterMap(ExperimenterGroup) - Method in class ome.model.meta.Experimenter
find all ome.model.meta.GroupExperimenterMap which have the argument as their parent.
findGroupExperimenterMap(Experimenter) - Method in class ome.model.meta.ExperimenterGroup
find all ome.model.meta.GroupExperimenterMap which have the argument as their child.
findImageAnnotationLink(Annotation) - Method in class ome.model.core.Image
find all ome.model.annotations.ImageAnnotationLink which have the argument as their child.
findImproperIncomingLinks(Session, String[]) - Method in class ome.services.chgrp.ChgrpStep
Deprecated.
 
findImproperIncomingLinks(Session, String[]) - Method in class ome.services.chown.ChownStep
Deprecated.
 
findImproperIncomingLinks(Session, String[]) - Method in class ome.services.delete.DeleteStep
Deprecated.
 
findImproperIncomingLinks(Session, String[]) - Method in class ome.services.graphs.GraphStep
Deprecated.
 
findInDb(CheckedPath, String, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
Find the given path in the DB or create.
findInDb(String, boolean) - Method in class ome.services.scripts.ScriptRepoHelper
 
findInDb(RepoFile, boolean) - Method in class ome.services.scripts.ScriptRepoHelper
 
findInDb(SqlAction, RepoFile, boolean) - Method in class ome.services.scripts.ScriptRepoHelper
Looks to see if a path is contained in the repository.
findInstrumentAnnotationLink(Annotation) - Method in class ome.model.acquisition.Instrument
find all ome.model.annotations.InstrumentAnnotationLink which have the argument as their child.
findJobOriginalFileLink(OriginalFile) - Method in class ome.model.jobs.Job
find all ome.model.jobs.JobOriginalFileLink which have the argument as their child.
findKeyTarget(Object) - Method in class ome.util.ModelMapper
extension point which subclasses can override to better map the keys of maps.
findKeyTarget(Object) - Method in class omero.util.RTypeMapper
 
findLightPathAnnotationLink(Annotation) - Method in class ome.model.acquisition.LightPath
find all ome.model.annotations.LightPathAnnotationLink which have the argument as their child.
findLightPathEmissionFilterLink(Filter) - Method in class ome.model.acquisition.LightPath
find all ome.model.acquisition.LightPathEmissionFilterLink which have the argument as their child.
findLightPathExcitationFilterLink(Filter) - Method in class ome.model.acquisition.LightPath
find all ome.model.acquisition.LightPathExcitationFilterLink which have the argument as their child.
findLightSourceAnnotationLink(Annotation) - Method in class ome.model.acquisition.LightSource
find all ome.model.annotations.LightSourceAnnotationLink which have the argument as their child.
findMap(Map) - Method in class ome.util.ModelMapper
 
findMethodAnnotations(Class, Method) - Static method in class ome.annotations.AnnotationUtils
finds all parameter annotations for the given class including on all implemented interfaces.
findNamespaceAnnotationLink(Annotation) - Method in class ome.model.meta.Namespace
find all ome.model.annotations.NamespaceAnnotationLink which have the argument as their child.
findNodeAnnotationLink(Annotation) - Method in class ome.model.meta.Node
find all ome.model.annotations.NodeAnnotationLink which have the argument as their child.
findObjectiveAnnotationLink(Annotation) - Method in class ome.model.acquisition.Objective
find all ome.model.annotations.ObjectiveAnnotationLink which have the argument as their child.
findOrCreateInDb(CheckedPath, String, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
 
findOrCreateInDb(CheckedPath, String, String, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
 
findOriginalFileAnnotationLink(Annotation) - Method in class ome.model.core.OriginalFile
find all ome.model.annotations.OriginalFileAnnotationLink which have the argument as their child.
findParameterAnnotations(Class, Method) - Static method in class ome.annotations.AnnotationUtils
finds all parameter annotations for the given class including on all implemented interfaces.
findPixelsOriginalFileMap(Pixels) - Method in class ome.model.core.OriginalFile
find all ome.model.core.PixelsOriginalFileMap which have the argument as their child.
findPixelsOriginalFileMap(OriginalFile) - Method in class ome.model.core.Pixels
find all ome.model.core.PixelsOriginalFileMap which have the argument as their parent.
findPlaneInfoAnnotationLink(Annotation) - Method in class ome.model.core.PlaneInfo
find all ome.model.annotations.PlaneInfoAnnotationLink which have the argument as their child.
findPlateAcquisitionAnnotationLink(Annotation) - Method in class ome.model.screen.PlateAcquisition
find all ome.model.annotations.PlateAcquisitionAnnotationLink which have the argument as their child.
findPlateAnnotationLink(Annotation) - Method in class ome.model.screen.Plate
find all ome.model.annotations.PlateAnnotationLink which have the argument as their child.
findProjectAnnotationLink(Annotation) - Method in class ome.model.containers.Project
find all ome.model.annotations.ProjectAnnotationLink which have the argument as their child.
findProjectDatasetLink(Project) - Method in class ome.model.containers.Dataset
find all ome.model.containers.ProjectDatasetLink which have the argument as their parent.
findProjectDatasetLink(Dataset) - Method in class ome.model.containers.Project
find all ome.model.containers.ProjectDatasetLink which have the argument as their child.
findProxy(Redirector.Context, String) - Method in class ome.services.blitz.redirect.AbstractRedirector
 
findReagentAnnotationLink(Annotation) - Method in class ome.model.screen.Reagent
find all ome.model.annotations.ReagentAnnotationLink which have the argument as their child.
findRepoDeleteLogs(SqlAction.DeleteLog, Current) - Method in interface ome.services.blitz.repo.RepositoryDao
Call SqlAction.findRepoDeleteLogs(DeleteLog) with the current context.
findRepoDeleteLogs(List<SqlAction.DeleteLog>, Current) - Method in interface ome.services.blitz.repo.RepositoryDao
As #findRepoDeleteLogs(DeleteLog, Current) but for a collection of templates.
findRepoDeleteLogs(SqlAction.DeleteLog, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
 
findRepoDeleteLogs(List<SqlAction.DeleteLog>, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
 
findRepoDeleteLogs(SqlAction.DeleteLog) - Method in interface ome.util.SqlAction
Find all SqlAction.DeleteLog entries which match all of the non-null fields provided in the template.
findRepoDeleteLogs(SqlAction.DeleteLog) - Method in class ome.util.SqlAction.Impl
 
findRepoFile(String, CheckedPath, String, Current) - Method in interface ome.services.blitz.repo.RepositoryDao
Delegate to SqlAction.findRepoFile(String, String, String, String) for looking up the id of the file, and then load it normally via IQuery.
findRepoFile(ServiceFactory, SqlAction, String, CheckedPath, String) - Method in interface ome.services.blitz.repo.RepositoryDao
As RepositoryDao.findRepoFile(String, CheckedPath, String, Current) but can be called from within a transaction.
findRepoFile(String, CheckedPath, String, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
 
findRepoFile(ServiceFactory, SqlAction, String, CheckedPath, String) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
 
findRepoFile(String, String, String) - Method in interface ome.util.SqlAction
Calls #findRepoFile(String, String, String, Set) passing null.
findRepoFile(String, String, String, String) - Method in interface ome.util.SqlAction
Calls #findRepoFile(String, String, String, Set)
findRepoFile(String, String, String, Set<String>) - Method in interface ome.util.SqlAction
Lookup the id of an OriginalFile in a given repository or return null if none is found.
findRepoFile(String, String, String) - Method in class ome.util.SqlAction.Impl
 
findRepoFile(String, String, String, String) - Method in class ome.util.SqlAction.Impl
 
findRepoFile(String, String, String, Set<String>) - Method in class ome.util.SqlAction.Impl
 
findRepoFilePath(String, long) - Method in interface ome.util.SqlAction
 
findRepoFilePath(String, long) - Method in class ome.util.SqlAction.Impl
 
findRepoFiles(String, String, List<String>, Set<String>) - Method in interface ome.util.SqlAction
Like SqlAction.findRepoFile(String, String, String, Set), but queries in bulk and returns a map for the found IDs.
findRepoFiles(String, String) - Method in interface ome.util.SqlAction
Return a list of original file ids that all have a path value matching the passed dirname in the given repository.
findRepoFiles(String, String, List<String>, Set<String>) - Method in class ome.util.SqlAction.Impl
 
findRepoFiles(String, String) - Method in class ome.util.SqlAction.Impl
 
findRepoImageFromPixels(long) - Method in class ome.util.actions.PostgresSqlAction
 
findRepoImageFromPixels(long) - Method in interface ome.util.SqlAction
 
findRepoPixels(String, String, String) - Method in class ome.util.actions.PostgresSqlAction
 
findRepoPixels(String, String, String) - Method in interface ome.util.SqlAction
 
findRepoRootPath(String) - Method in interface ome.util.SqlAction
Find the path of the repository root.
findRepoRootPath(String) - Method in class ome.util.SqlAction.Impl
 
findRoiAnnotationLink(Annotation) - Method in class ome.model.roi.Roi
find all ome.model.annotations.RoiAnnotationLink which have the argument as their child.
findScreenAnnotationLink(Annotation) - Method in class ome.model.screen.Screen
find all ome.model.annotations.ScreenAnnotationLink which have the argument as their child.
findScreenPlateLink(Screen) - Method in class ome.model.screen.Plate
find all ome.model.screen.ScreenPlateLink which have the argument as their parent.
findScreenPlateLink(Plate) - Method in class ome.model.screen.Screen
find all ome.model.screen.ScreenPlateLink which have the argument as their child.
FindServiceFactoryMessage - Class in ome.services.blitz.util
InternalMessage raised when a servant needs to find the ServiceFactoryI instance that the current user is working with.
FindServiceFactoryMessage(Object, Identity) - Constructor for class ome.services.blitz.util.FindServiceFactoryMessage
 
FindServiceFactoryMessage(Object, Current) - Constructor for class ome.services.blitz.util.FindServiceFactoryMessage
 
findSessionAnnotationLink(Annotation) - Method in class ome.model.meta.Session
find all ome.model.annotations.SessionAnnotationLink which have the argument as their child.
findShapeAnnotationLink(Annotation) - Method in class ome.model.roi.Shape
find all ome.model.annotations.ShapeAnnotationLink which have the argument as their child.
findTarget(Object) - Method in class ome.util.ModelMapper
known immutables are return unchanged.
findWellAnnotationLink(Annotation) - Method in class ome.model.screen.Well
find all ome.model.annotations.WellAnnotationLink which have the argument as their child.
findWellReagentLink(Well) - Method in class ome.model.screen.Reagent
find all ome.model.screen.WellReagentLink which have the argument as their parent.
findWellReagentLink(Reagent) - Method in class ome.model.screen.Well
find all ome.model.screen.WellReagentLink which have the argument as their child.
finish(TransferState, long) - Method in class ome.formats.importer.transfers.AbstractFileTransfer
Save the current state to disk and finish all timing and logging.
finish() - Method in class ome.services.blitz.impl.commands.SaveI
 
finish() - Method in class ome.services.blitz.repo.ManagedImportRequestI
 
finish() - Method in class ome.services.blitz.repo.RawAccessRequestI
 
finish() - Method in class ome.services.delete.Deletion
Deprecated.
Should be called within the transaction boundaries but as the last processing step.
finish() - Method in interface ome.services.procs.Process
 
finish() - Method in class ome.services.procs.ProcessSkeleton
 
finish() - Method in class omero.cmd.admin.CurrentSessionsRequestI
 
finish() - Method in class omero.cmd.admin.ResetPasswordRequestI
 
finish() - Method in class omero.cmd.admin.UpdateSessionTimeoutRequestI
 
finish() - Method in class omero.cmd.basic.DoAllI
 
finish() - Method in class omero.cmd.basic.ListRequestsI
 
finish() - Method in class omero.cmd.basic.TimingI
 
finish() - Method in class omero.cmd.fs.ManageImageBinariesI
 
finish() - Method in class omero.cmd.fs.OriginalMetadataRequestI
 
finish() - Method in class omero.cmd.fs.UsedFilesRequestI
 
finish() - Method in class omero.cmd.graphs.Chgrp2I
 
finish() - Method in class omero.cmd.graphs.ChgrpFacadeI
Deprecated.
 
finish() - Method in class omero.cmd.graphs.ChgrpI
Deprecated.
 
finish() - Method in class omero.cmd.graphs.Chmod2I
 
finish() - Method in class omero.cmd.graphs.ChmodFacadeI
Deprecated.
 
finish() - Method in class omero.cmd.graphs.ChmodI
Deprecated.
finish() - Method in class omero.cmd.graphs.Chown2I
 
finish() - Method in class omero.cmd.graphs.ChownFacadeI
Deprecated.
 
finish() - Method in class omero.cmd.graphs.ChownI
Deprecated.
 
finish() - Method in class omero.cmd.graphs.Delete2I
 
finish() - Method in class omero.cmd.graphs.DeleteFacadeI
Deprecated.
 
finish() - Method in class omero.cmd.graphs.DeleteI
Deprecated.
 
finish() - Method in class omero.cmd.graphs.DiskUsageI
 
finish() - Method in class omero.cmd.graphs.GraphSpecListI
Deprecated.
 
finish() - Method in class omero.cmd.graphs.SkipHeadI
 
finish() - Method in interface omero.cmd.IRequest
Method within the transaction boundaries after all processing has occurred.
finish() - Method in class omero.cmd.mail.SendEmailRequestI
 
finishCancelled() - Method in class ome.formats.importer.util.ErrorHandler
Action to take when finish cancelled
finishComplete() - Method in class ome.formats.importer.util.ErrorHandler
Action to take when finish completed
FINISHED - Static variable in interface ome.api.JobHandle
 
finished - Variable in class ome.model.jobs.Job
 
FINISHED - Static variable in class ome.model.jobs.Job
 
finished - Variable in class ome.model.meta.DBPatch
 
FINISHED - Static variable in class ome.model.meta.DBPatch
 
finished(Response, Status, Current) - Method in class omero.cmd.CmdCallbackI
Called when the command has completed.
finishWithErroredFiles() - Method in class ome.formats.importer.util.ErrorHandler
Action to take when finish completed but with some errors (For example, missing files)
firstIdOrNull(String) - Method in class omero.cmd.fs.OriginalMetadataRequestI
Use IQuery.projection(String, Parameters) to load the first long which matches the given query.
firstName - Variable in class ome.model.meta.Experimenter
 
FIRSTNAME - Static variable in class ome.model.meta.Experimenter
 
FIRSTNAME - Static variable in class pojos.ExperimenterData
Identifies the Experimenter#FIRSTNAME field.
firstPlane() - Method in class pojos.ROIData
Return the first plane that the ROI starts on.
fixNulledOrFilteredCollections(IObject, IObject, EntityPersister, SessionImplementor) - Static method in class ome.tools.hibernate.HibernateUtils
loads collections which have been filtered or nulled by the user
FLIM - Static variable in class ome.services.util.NamespaceCheck
 
FLIM_NS - Static variable in class pojos.FileAnnotationData
Identifies the FLIM namespace.
flipState() - Method in class ome.services.eventlogs.EventBacklog
Flips the EventBacklog to the "adding" state if it is empty, otherwise to the "removing" state.
FLOAT(Connection, List<Float>) - Method in interface ome.tools.hibernate.ListAsSQLArrayUserType.ArrayFactory
 
FLOAT - Static variable in class ome.util.PixelData
Identifies the type used to store pixel values.
FLOAT - Static variable in class omeis.providers.re.data.PlaneFactory
Identifies the type used to store pixel values.
FLOAT_TYPE - Static variable in class omeis.providers.re.data.PlaneFactory
Identifies the FLOAT data type used to store pixel values, as per OME spec.
FLOAT_TYPE - Static variable in class pojos.PixelsData
Identifies the type used to store pixel values.
fluor - Variable in class ome.model.core.LogicalChannel
 
FLUOR - Static variable in class ome.model.core.LogicalChannel
 
flush() - Method in interface ome.api.local.LocalUpdate
 
flush(boolean) - Method in class ome.io.nio.FileBuffer
Flush the buffer, writing any pending content to the underlying storage device, optionally also the file's metadata.
flush() - Method in class ome.logic.UpdateImpl
 
flush() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
flushPreferences() - Method in class ome.formats.importer.util.IniFileLoader
Flush preferences to disk
FONT_BOLD - Static variable in class pojos.ShapeSettingsData
Set if font bold.
FONT_BOLD_ITALIC - Static variable in class pojos.ShapeSettingsData
Set if font bold.
FONT_ITALIC - Static variable in class pojos.ShapeSettingsData
Set if font italic.
FONT_REGULAR - Static variable in class pojos.ShapeSettingsData
Set if font bold.
fontFamily - Variable in class ome.model.roi.Shape
 
FONTFAMILY - Static variable in class ome.model.roi.Shape
 
fontSize - Variable in class ome.model.roi.Shape
 
FONTSIZE - Static variable in class ome.model.roi.Shape
 
fontStretch - Variable in class ome.model.roi.Shape
 
FONTSTRETCH - Static variable in class ome.model.roi.Shape
 
fontStyle - Variable in class ome.model.roi.Shape
 
FONTSTYLE - Static variable in class ome.model.roi.Shape
 
fontVariant - Variable in class ome.model.roi.Shape
 
FONTVARIANT - Static variable in class ome.model.roi.Shape
 
fontWeight - Variable in class ome.model.roi.Shape
 
FONTWEIGHT - Static variable in class ome.model.roi.Shape
 
ForceTransactionAttributeSource - Class in ome.tools.spring
Requires that all method calls have some other form of attribute source by throwing an exception if accessed;
ForceTransactionAttributeSource() - Constructor for class ome.tools.spring.ForceTransactionAttributeSource
 
forEachTile(TileLoopIteration, PixelBuffer, int, int) - Static method in class ome.io.nio.Utils
Iterates over every tile in a given pixel buffer based on the over arching dimensions and a requested maximum tile width and height.
forEachTile(TileLoopIteration, int, int, int, int, int, int, int) - Static method in class ome.io.nio.Utils
Iterates over every tile in a given pixel buffer based on the over arching dimensions and a requested maximum tile width and height.
forEachTile(int, int, TileLoopIteration) - Method in class omero.util.RPSTileLoop
Iterates over every tile in a given pixel based on the over arching dimensions and a requested maximum tile width and height.
forEachTile(int, int, int, int, int, int, int, TileLoopIteration) - Method in class omero.util.TileLoop
Iterates over every tile in a given pixel based on the over arching dimensions and a requested maximum tile width and height.
foreground(boolean, String[]) - Static method in class ome.services.fulltext.Main
Uses a PersistentEventLogLoader and cycles through all the remaining logs.
format - Variable in class ome.model.core.Image
 
FORMAT - Static variable in class ome.model.core.Image
 
Format - Class in ome.model.enums
 
Format() - Constructor for class ome.model.enums.Format
 
Format(Long) - Constructor for class ome.model.enums.Format
 
Format(Long, boolean) - Constructor for class ome.model.enums.Format
Main constructor.
Format(String) - Constructor for class ome.model.enums.Format
 
Format.Details - Class in ome.model.enums
 
Format.Details() - Constructor for class ome.model.enums.Format.Details
 
Format.Details(Object[]) - Constructor for class ome.model.enums.Format.Details
 
free(String) - Method in class ome.tools.FileSystem
This method will return the free space in kilobytes TODO - resolve the slash mount
free() - Method in class ome.tools.hibernate.SqlArray
 
Frequency - Class in ome.model.units
class storing both a Frequency and a unit for that Frequency (e.g. m, in, ly, etc.) encapsulated in a UnitsFrequency instance.
Frequency() - Constructor for class ome.model.units.Frequency
Deprecated.
Frequency(double, String) - Constructor for class ome.model.units.Frequency
 
Frequency(double, UnitsFrequency) - Constructor for class ome.model.units.Frequency
 
Frequency(double, Unit<Frequency>) - Constructor for class ome.model.units.Frequency
 
Frequency(Frequency) - Constructor for class ome.model.units.Frequency
 
FrequencyI - Class in omero.model
Blitz wrapper around the Frequency class.
FrequencyI() - Constructor for class omero.model.FrequencyI
 
FrequencyI(double, UnitsFrequency) - Constructor for class omero.model.FrequencyI
 
FrequencyI(double, Unit<Frequency>) - Constructor for class omero.model.FrequencyI
 
FrequencyI(Frequency, Unit<Frequency>) - Constructor for class omero.model.FrequencyI
Copy constructor that converts the given Frequency based on the given ome-xml enum
FrequencyI(double, UnitsFrequency) - Constructor for class omero.model.FrequencyI
Copy constructor that converts the given Frequency based on the given ome.model enum
FrequencyI(Frequency, String) - Constructor for class omero.model.FrequencyI
Copy constructor that converts the given Frequency based on the given enum string.
FrequencyI(Frequency, UnitsFrequency) - Constructor for class omero.model.FrequencyI
Copy constructor that converts between units if possible.
FrequencyI(Frequency) - Constructor for class omero.model.FrequencyI
Convert a Bio-Formats Length to an OMERO Length.
frequencyMultiplication - Variable in class ome.model.acquisition.Laser
 
FREQUENCYMULTIPLICATION - Static variable in class ome.model.acquisition.Laser
 
from - Variable in class ome.services.blitz.util.ConvertToBlitzExceptionMessage
 
FROM - Static variable in class ome.services.mail.MapAnnotationSubethaListener
 
from(String, String) - Method in class ome.tools.hibernate.QueryBuilder
 
fromClass(Class) - Static method in class ome.services.blitz.measurements.Helper
Factory method to generate Helper instances from the Class of a given column.
fromdbvalue(String) - Method in enum ome.model.units.UNITS
Perform the reverse lookup from UNITS.todbvalue(Object) converting the DB's enums which contain invalid characters to the upper-cased CODE-based enums used elsewhere.
fromLsid(String) - Static method in class ome.services.blitz.measurements.Helper
Factory method to generate Helper instances from the LSID of a given column.
fromObjectContainerStore(IObjectContainerStore, int, int) - Static method in class ome.formats.model.ChannelData
Retrieves channel data from an object container store.
fromPoints(String) - Method in class pojos.ShapeData
Parses out the type from the points string.
fromRType(RType) - Method in class omero.util.IceMapper
Uses the omero.rtypes hierarchy to properly convert any RType to its internal representation.
fromString(String) - Method in class ome.formats.importer.ImportConfig.AnnotationListValue
 
fromString(String) - Method in class ome.formats.importer.ImportConfig.BoolValue
 
fromString(String) - Method in class ome.formats.importer.ImportConfig.DoubleArrayValue
 
fromString(String) - Method in class ome.formats.importer.ImportConfig.FileValue
 
fromString(String) - Method in class ome.formats.importer.ImportConfig.IntValue
 
fromString(String) - Method in class ome.formats.importer.ImportConfig.LongValue
 
fromString(String) - Method in class ome.formats.importer.ImportConfig.StrValue
 
fromString(String) - Method in class ome.formats.importer.ImportConfig.Value
 
fsFile - Variable in class ome.services.blitz.repo.CheckedPath
 
FsFile - Class in ome.services.blitz.repo.path
An analog of File representing an FS repository file-path.
FsFile(Collection<String>) - Constructor for class ome.services.blitz.repo.path.FsFile
Construct an instance.
FsFile(String...) - Constructor for class ome.services.blitz.repo.path.FsFile
Construct an instance.
FsFile(FsFile, int) - Constructor for class ome.services.blitz.repo.path.FsFile
Construct an instance by trimming parent directories from an existing instance such that the depth does not exceed the given maximum.
FsFile(File) - Constructor for class ome.services.blitz.repo.path.FsFile
Construct an instance.
FsFile(String) - Constructor for class ome.services.blitz.repo.path.FsFile
Construct an instance.
fullImport(File, String) - Method in class ome.formats.OMEROImportFixture
Provides one complete import cycle.
fullname() - Method in class ome.services.scripts.RepoFile
 
FullText - Class in ome.services.search
Search based on Lucene's Query class.
FullText(SearchValues, String, String, String, String, String, Class<? extends Analyzer>) - Constructor for class ome.services.search.FullText
Constructs a new instance; Builds a Lucence query with the provided arguments and passes it on the Lucene parser
FullText(SearchValues, String, Class<? extends Analyzer>) - Constructor for class ome.services.search.FullText
Creates a new instance; Passes the query directly on to the Lucene parser.
FullTextAnalyzer - Class in ome.services.fulltext
Analyzer implementation based largely on SimpleAnalyzer, but with extensions for handling scientific and OS-type strings.
FullTextAnalyzer() - Constructor for class ome.services.fulltext.FullTextAnalyzer
 
fullTextBridge - Variable in class ome.logic.UpdateImpl
 
FullTextBridge - Class in ome.services.fulltext
Primary definition of what will be indexed via Hibernate Search.
FullTextBridge() - Constructor for class ome.services.fulltext.FullTextBridge
Since this constructor provides the instance with no way of parsing OriginalFile binaries, all files will be assumed to have blank content.
FullTextBridge(OriginalFilesService, Map<String, FileParser>) - Constructor for class ome.services.fulltext.FullTextBridge
Constructor which provides an empty set of custom bridges.
FullTextBridge(OriginalFilesService, Map<String, FileParser>, Class<FieldBridge>[]) - Constructor for class ome.services.fulltext.FullTextBridge
Main constructor.
FullTextIndexer - Class in ome.services.fulltext
Simple action which can be done in an asynchronous thread in order to index Hibernate entities.
FullTextIndexer(EventLogLoader) - Constructor for class ome.services.fulltext.FullTextIndexer
 
FullTextIndexer(EventLogLoader, Metrics) - Constructor for class ome.services.fulltext.FullTextIndexer
 
FullTextThread - Class in ome.services.fulltext
Library entry-point for indexing.
FullTextThread(SessionManager, Executor, FullTextIndexer, FullTextBridge) - Constructor for class ome.services.fulltext.FullTextThread
Uses default Principal for indexing
FullTextThread(SessionManager, Executor, FullTextIndexer, FullTextBridge, boolean) - Constructor for class ome.services.fulltext.FullTextThread
Uses default Principal for indexing
FullTextThread(SessionManager, Executor, FullTextIndexer, FullTextBridge, Principal) - Constructor for class ome.services.fulltext.FullTextThread
Main constructor.
FullTextThread(SessionManager, Executor, FullTextIndexer, FullTextBridge, Principal, boolean) - Constructor for class ome.services.fulltext.FullTextThread
Main constructor.

G

g - Variable in class ome.model.roi.Shape
 
G - Static variable in class ome.model.roi.Shape
 
G_BAND - Static variable in class omeis.providers.re.RGBBuffer
Index of the green band in the image's data buffer.
gain - Variable in class ome.model.acquisition.Detector
 
GAIN - Static variable in class ome.model.acquisition.Detector
 
gain - Variable in class ome.model.acquisition.DetectorSettings
 
GAIN - Static variable in class ome.model.acquisition.DetectorSettings
 
generate(SessionImplementor, Object) - Method in class ome.util.TableIdGenerator
 
generateRandomPasswd() - Method in class ome.security.auth.PasswordUtil
 
generateRepoUuid() - Method in class ome.services.blitz.repo.AbstractRepositoryI
Called when this repository is creating a new OriginalFile repository object.
generateRepoUuid() - Method in class ome.services.blitz.repo.ScriptRepositoryI
 
generateScriptParams(long, boolean, Current) - Method in class omero.grid.ParamsHelper
Acquires an InteractiveProcessorPrx and runs a ParseJob.
generateThumbnails(ThumbnailGenerationJob) - Method in class ome.services.blitz.repo.ManagedImportRequestI
 
generateTiff_async(AMD_Exporter_generateTiff, Current) - Method in class ome.services.blitz.impl.ExporterI
 
generateXml(MetadataRetrieve) - Method in class ome.services.blitz.impl.ExporterI
 
generateXml_async(AMD_Exporter_generateXml, Current) - Method in class ome.services.blitz.impl.ExporterI
Generate XML and return the length
GenericEnumType<E extends Enum<E>> - Class in ome.model.units
http://octagen.at/2014/10/postgresql-custom-data-types-enum-in-hibernate/
GenericEnumType() - Constructor for class ome.model.units.GenericEnumType
 
GenericExcitationSource - Class in ome.model.acquisition
 
GenericExcitationSource() - Constructor for class ome.model.acquisition.GenericExcitationSource
 
GenericExcitationSource(Long) - Constructor for class ome.model.acquisition.GenericExcitationSource
 
GenericExcitationSource(Long, boolean) - Constructor for class ome.model.acquisition.GenericExcitationSource
Main constructor.
geomTool - Variable in class ome.services.blitz.impl.RoiI
 
GeomTool - Class in ome.services.roi
Strategy for handling the conversion between shapes and database-specific geometries.
GeomTool(PixelData, SqlAction, SessionFactory) - Constructor for class ome.services.roi.GeomTool
 
GeomTool(PixelData, SqlAction, SessionFactory, Executor, String) - Constructor for class ome.services.roi.GeomTool
 
get(Class<T>, long) - Method in interface ome.api.IQuery
lookup an entity by class and id.
get() - Method in class ome.formats.importer.ImportConfig.FileValue
 
get() - Method in class ome.formats.importer.ImportConfig.Value
Returns the generic type contained by this holder.
get(Class, long) - Method in class ome.logic.QueryImpl
 
get(String) - Method in class ome.parameters.Parameters
lookup a QueryParameter by name.
get(String, DirContextAdapter) - Method in class ome.security.auth.GroupContextMapper
 
get(String, DirContextAdapter) - Method in class ome.security.auth.PersonContextMapper
 
get() - Method in class ome.services.blitz.util.ResultHolder
 
get(Session, Class, long) - Method in class ome.services.fulltext.FullTextIndexer
 
get(int) - Method in class ome.services.graphs.GraphSteps
Deprecated.
 
get(Object) - Method in class ome.services.query.Definitions
 
get(String) - Method in class ome.services.query.Query
get the QueryParameter for this name argument.
get(PixelBuffer, int, int, int, int, int) - Method in class ome.services.roi.PixelData
 
get() - Method in class ome.services.sessions.SessionContext.Count
Return the current number of references which this session is aware of.
get(long) - Method in class ome.services.sharing.BlobShareStore
 
get(long) - Method in class ome.services.sharing.ShareStore
 
get(Future<T>) - Method in interface ome.services.util.Executor
Helper method to perform Future.get() and properly unwrap the exceptions.
get(Future<T>) - Method in class ome.services.util.Executor.Impl
 
get(int) - Method in class ome.util.mem.CopiableArray
Return the Copiable at the specified position.
get(int) - Method in class ome.util.mem.ReadOnlyByteArray
Reads the element at the index position within this slice.
get(Identity) - Method in class omero.util.ServantHolder
 
get(String[]) - Static method in class prefs
Returns either the given key=value pairs (or all if no argument is given).
get75thPercentile() - Method in class ome.system.metrics.DefaultSnapshot
 
get75thPercentile() - Method in interface ome.system.metrics.Snapshot
 
get95thPercentile() - Method in class ome.system.metrics.DefaultSnapshot
 
get95thPercentile() - Method in interface ome.system.metrics.Snapshot
 
get98thPercentile() - Method in class ome.system.metrics.DefaultSnapshot
 
get98thPercentile() - Method in interface ome.system.metrics.Snapshot
 
get999thPercentile() - Method in class ome.system.metrics.DefaultSnapshot
 
get999thPercentile() - Method in interface ome.system.metrics.Snapshot
 
get99thPercentile() - Method in class ome.system.metrics.DefaultSnapshot
 
get99thPercentile() - Method in interface ome.system.metrics.Snapshot
 
get_async(AMD_IQuery_get, String, long, Current) - Method in class ome.services.blitz.impl.QueryI
 
getA0() - Method in class omeis.providers.re.codomain.ContrastStretchingContext
Returns the slope of the first line.
getA1() - Method in class omeis.providers.re.codomain.ContrastStretchingContext
Returns the slope of the second line.
getA2() - Method in class omeis.providers.re.codomain.ContrastStretchingContext
Returns the slope of the third line.
getAbsolutePath() - Method in class ome.formats.importer.util.ErrorContainer
get path for file
getAbsolutePath() - Method in class pojos.FileData
Returns the absolute path.
getAbsolutePaths() - Method in class pojos.FilesetData
Returns the collections of absolute paths.
getAcquisitionData() - Method in class omero.sys.ParametersI
 
getAcquisitionDate() - Method in class ome.model.core.Image
Simple field ome.model.core.Image.acquisitionDate (java.sql.Timestamp)
getAcquisitionDate() - Method in class pojos.ImageData
Returns the acquisition date.
getAction() - Method in class ome.model.meta.EventLog
Simple field ome.model.meta.EventLog.action (java.lang.String)
getAction() - Method in class ome.services.mail.ObjectMailSender
 
getActionForStarting() - Method in class omero.cmd.graphs.Chgrp2I
 
getActionForStarting() - Method in class omero.cmd.graphs.Chmod2I
 
getActionForStarting() - Method in class omero.cmd.graphs.Chown2I
 
getActionForStarting() - Method in class omero.cmd.graphs.Delete2I
 
getActionForStarting() - Method in interface omero.cmd.graphs.WrappableRequest
 
getActive() - Method in class ome.model.display.ChannelBinding
Simple field ome.model.display.ChannelBinding.active (java.lang.Boolean)
getActive() - Method in class ome.model.meta.Share
Simple field ome.model.meta.Share.active (java.lang.Boolean)
getActiveConnections(long) - Method in interface ome.api.IShare
Gets actual active connections to share.
getActiveConnections(long) - Method in class ome.services.sharing.ShareBean
 
getActiveConnections_async(AMD_IShare_getActiveConnections, long, Current) - Method in class ome.services.blitz.impl.ShareI
 
getActualDeletes() - Method in class ome.services.delete.Deletion
Deprecated.
 
getAdapter() - Method in class omero.client
 
getAdapter() - Method in class omero.cmd.SessionI
 
getAdminService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
getAdminService() - Method in class ome.system.ServiceFactory
 
getAdminSession() - Method in interface ome.services.blitz.fire.Registry
Create a new AdminSessionPrx with the RegistryPrx.
getAdminSession() - Method in class ome.services.blitz.fire.Registry.Impl
 
getAgent(Current) - Method in class ome.services.blitz.fire.SessionManagerI
 
getAirPressure() - Method in class ome.model.acquisition.ImagingEnvironment
Enum-mapped unit-based field ome.model.acquisition.ImagingEnvironment.airPressure (ome.model.units.Pressure)
getAirPressure(UnitsPressure) - Method in class pojos.ImageAcquisitionData
Returns the air pressure in bar
getAirPressure() - Method in class pojos.ImageAcquisitionData
getAll(String) - Method in class ome.security.auth.AttributeSet
 
getAllChecksumAlgorithms() - Static method in class ome.services.blitz.util.ChecksumAlgorithmMapper
 
getAllDatasets() - Method in interface ome.api.IAnalysis
 
getAllEnumerations(Class<T>) - Method in interface ome.api.IPixels
Retrieves the exhaustive list of enumerations for a given enumeration class.
getAllEnumerations(Class<T>) - Method in class ome.logic.PixelsImpl
 
getAllEnumerations_async(AMD_IPixels_getAllEnumerations, String, Current) - Method in class ome.services.blitz.impl.PixelsI
 
getAllForImage(long) - Method in interface ome.api.IAnalysis
 
getAllGuests(long) - Method in interface ome.api.IShare
Get the email addresses for all share guests.
getAllGuests(long) - Method in class ome.services.sharing.ShareBean
 
getAllGuests_async(AMD_IShare_getAllGuests, long, Current) - Method in class ome.services.blitz.impl.ShareI
 
getAllMembers(long) - Method in interface ome.api.IShare
Get all users who are a member of the share.
getAllMembers(long) - Method in class ome.services.sharing.ShareBean
 
getAllMembers_async(AMD_IShare_getAllMembers, long, Current) - Method in class ome.services.blitz.impl.ShareI
 
getAllPixels() - Method in class pojos.ImageData
Returns all the sets of pixels related to this image.
getAllSystemUsers(boolean) - Method in class ome.services.mail.MailSender
 
getAllUsers(long) - Method in interface ome.api.IShare
Get a single set containing the login names of the Experimenters as well email addresses for guests.
getAllUsers(long) - Method in class ome.services.sharing.ShareBean
 
getAllUsers_async(AMD_IShare_getAllUsers, long, Current) - Method in class ome.services.blitz.impl.ShareI
 
getAlpha() - Method in class ome.model.core.Channel
Simple field ome.model.core.Channel.alpha (java.lang.Integer)
getAlpha() - Method in class ome.model.display.ChannelBinding
Simple field ome.model.display.ChannelBinding.alpha (java.lang.Integer)
getAlpha() - Method in class ome.model.screen.Well
Simple field ome.model.screen.Well.alpha (java.lang.Integer)
getAlpha() - Method in class pojos.WellData
Returns the alpha component of the color associated to the well, or -1.
getAmplificationGain() - Method in class ome.model.acquisition.Detector
Simple field ome.model.acquisition.Detector.amplificationGain (java.lang.Double)
getAmplificationGain() - Method in class pojos.DetectorData
Returns the amplification gain of the detector.
getAnalysisService() - Method in class ome.system.ServiceFactory
 
getAnchor() - Method in class ome.model.roi.Label
Simple field ome.model.roi.Label.anchor (java.lang.String)
getAndLogException(Throwable) - Method in class ome.services.util.ServiceHandler
 
getAnnotatableTypes() - Method in interface ome.tools.hibernate.ExtendedMetadata
Returns all the classes which implement IAnnotated
getAnnotatableTypes() - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
 
getAnnotationLinks() - Method in class ome.model.acquisition.Detector
returns annotationLinks .
getAnnotationLinks() - Method in class ome.model.acquisition.Dichroic
returns annotationLinks .
getAnnotationLinks() - Method in class ome.model.acquisition.Filter
returns annotationLinks .
getAnnotationLinks() - Method in class ome.model.acquisition.Instrument
returns annotationLinks .
getAnnotationLinks() - Method in class ome.model.acquisition.LightPath
returns annotationLinks .
getAnnotationLinks() - Method in class ome.model.acquisition.LightSource
returns annotationLinks .
getAnnotationLinks() - Method in class ome.model.acquisition.Objective
returns annotationLinks .
getAnnotationLinks() - Method in class ome.model.annotations.Annotation
returns annotationLinks .
getAnnotationLinks() - Method in class ome.model.containers.Dataset
returns annotationLinks .
getAnnotationLinks() - Method in class ome.model.containers.Project
returns annotationLinks .
getAnnotationLinks() - Method in class ome.model.core.Channel
returns annotationLinks .
getAnnotationLinks() - Method in class ome.model.core.Image
returns annotationLinks .
getAnnotationLinks() - Method in class ome.model.core.OriginalFile
returns annotationLinks .
getAnnotationLinks() - Method in class ome.model.core.PlaneInfo
returns annotationLinks .
getAnnotationLinks() - Method in class ome.model.fs.Fileset
returns annotationLinks .
getAnnotationLinks() - Method in class ome.model.meta.Experimenter
returns annotationLinks .
getAnnotationLinks() - Method in class ome.model.meta.ExperimenterGroup
returns annotationLinks .
getAnnotationLinks() - Method in class ome.model.meta.Namespace
returns annotationLinks .
getAnnotationLinks() - Method in class ome.model.meta.Node
returns annotationLinks .
getAnnotationLinks() - Method in class ome.model.meta.Session
returns annotationLinks .
getAnnotationLinks() - Method in class ome.model.roi.Roi
returns annotationLinks .
getAnnotationLinks() - Method in class ome.model.roi.Shape
returns annotationLinks .
getAnnotationLinks() - Method in class ome.model.screen.Plate
returns annotationLinks .
getAnnotationLinks() - Method in class ome.model.screen.PlateAcquisition
returns annotationLinks .
getAnnotationLinks() - Method in class ome.model.screen.Reagent
returns annotationLinks .
getAnnotationLinks() - Method in class ome.model.screen.Screen
returns annotationLinks .
getAnnotationLinks() - Method in class ome.model.screen.Well
returns annotationLinks .
getAnnotationLinksCountPerOwner() - Method in class ome.model.acquisition.Detector
If fetched, returns the count(*) of ome.model.annotations.DetectorAnnotationLink that a user has.
getAnnotationLinksCountPerOwner() - Method in class ome.model.acquisition.Dichroic
If fetched, returns the count(*) of ome.model.annotations.DichroicAnnotationLink that a user has.
getAnnotationLinksCountPerOwner() - Method in class ome.model.acquisition.Filter
If fetched, returns the count(*) of ome.model.annotations.FilterAnnotationLink that a user has.
getAnnotationLinksCountPerOwner() - Method in class ome.model.acquisition.Instrument
If fetched, returns the count(*) of ome.model.annotations.InstrumentAnnotationLink that a user has.
getAnnotationLinksCountPerOwner() - Method in class ome.model.acquisition.LightPath
If fetched, returns the count(*) of ome.model.annotations.LightPathAnnotationLink that a user has.
getAnnotationLinksCountPerOwner() - Method in class ome.model.acquisition.LightSource
If fetched, returns the count(*) of ome.model.annotations.LightSourceAnnotationLink that a user has.
getAnnotationLinksCountPerOwner() - Method in class ome.model.acquisition.Objective
If fetched, returns the count(*) of ome.model.annotations.ObjectiveAnnotationLink that a user has.
getAnnotationLinksCountPerOwner() - Method in class ome.model.annotations.Annotation
If fetched, returns the count(*) of ome.model.annotations.AnnotationAnnotationLink that a user has.
getAnnotationLinksCountPerOwner() - Method in class ome.model.containers.Dataset
If fetched, returns the count(*) of ome.model.annotations.DatasetAnnotationLink that a user has.
getAnnotationLinksCountPerOwner() - Method in class ome.model.containers.Project
If fetched, returns the count(*) of ome.model.annotations.ProjectAnnotationLink that a user has.
getAnnotationLinksCountPerOwner() - Method in class ome.model.core.Channel
If fetched, returns the count(*) of ome.model.annotations.ChannelAnnotationLink that a user has.
getAnnotationLinksCountPerOwner() - Method in class ome.model.core.Image
If fetched, returns the count(*) of ome.model.annotations.ImageAnnotationLink that a user has.
getAnnotationLinksCountPerOwner() - Method in class ome.model.core.OriginalFile
If fetched, returns the count(*) of ome.model.annotations.OriginalFileAnnotationLink that a user has.
getAnnotationLinksCountPerOwner() - Method in class ome.model.core.PlaneInfo
If fetched, returns the count(*) of ome.model.annotations.PlaneInfoAnnotationLink that a user has.
getAnnotationLinksCountPerOwner() - Method in class ome.model.fs.Fileset
If fetched, returns the count(*) of ome.model.annotations.FilesetAnnotationLink that a user has.
getAnnotationLinksCountPerOwner() - Method in class ome.model.meta.Experimenter
If fetched, returns the count(*) of ome.model.annotations.ExperimenterAnnotationLink that a user has.
getAnnotationLinksCountPerOwner() - Method in class ome.model.meta.ExperimenterGroup
If fetched, returns the count(*) of ome.model.annotations.ExperimenterGroupAnnotationLink that a user has.
getAnnotationLinksCountPerOwner() - Method in class ome.model.meta.Namespace
If fetched, returns the count(*) of ome.model.annotations.NamespaceAnnotationLink that a user has.
getAnnotationLinksCountPerOwner() - Method in class ome.model.meta.Node
If fetched, returns the count(*) of ome.model.annotations.NodeAnnotationLink that a user has.
getAnnotationLinksCountPerOwner() - Method in class ome.model.meta.Session
If fetched, returns the count(*) of ome.model.annotations.SessionAnnotationLink that a user has.
getAnnotationLinksCountPerOwner() - Method in class ome.model.roi.Roi
If fetched, returns the count(*) of ome.model.annotations.RoiAnnotationLink that a user has.
getAnnotationLinksCountPerOwner() - Method in class ome.model.roi.Shape
If fetched, returns the count(*) of ome.model.annotations.ShapeAnnotationLink that a user has.
getAnnotationLinksCountPerOwner() - Method in class ome.model.screen.Plate
If fetched, returns the count(*) of ome.model.annotations.PlateAnnotationLink that a user has.
getAnnotationLinksCountPerOwner() - Method in class ome.model.screen.PlateAcquisition
If fetched, returns the count(*) of ome.model.annotations.PlateAcquisitionAnnotationLink that a user has.
getAnnotationLinksCountPerOwner() - Method in class ome.model.screen.Reagent
If fetched, returns the count(*) of ome.model.annotations.ReagentAnnotationLink that a user has.
getAnnotationLinksCountPerOwner() - Method in class ome.model.screen.Screen
If fetched, returns the count(*) of ome.model.annotations.ScreenAnnotationLink that a user has.
getAnnotationLinksCountPerOwner() - Method in class ome.model.screen.Well
If fetched, returns the count(*) of ome.model.annotations.WellAnnotationLink that a user has.
getAnnotations() - Method in class pojos.DatasetData
Returns the annotations related to this dataset.
getAnnotations() - Method in class pojos.ImageData
Returns the annotations
getAnnotationsCounts() - Method in class pojos.DatasetData
Returns the number of annotations linked to the object, key: id of the user, value: number of annotation.
getAnnotationsCounts() - Method in class pojos.ImageData
Returns the number of annotations linked to the object, key: id of the user, value: number of annotation.
getAnnotationsCounts() - Method in class pojos.PlateAcquisitionData
Returns the number of annotations linked to the object, key: id of the user, value: number of annotation.
getAnnotationsCounts() - Method in class pojos.PlateData
Returns the number of annotations linked to the object, key: id of the user, value: number of annotation.
getAnnotationsCounts() - Method in class pojos.ProjectData
Returns the number of annotations linked to the object, key: id of the user, value: number of annotation.
getAnnotationsCounts() - Method in class pojos.ScreenData
Returns the number of annotations linked to the object, key: id of the user, value: number of annotation.
getAnnotationsCounts() - Method in class pojos.WellData
Returns the number of annotations linked to the object, key: id of the user, value: number of annotation.
getAnnotationTypes() - Method in interface ome.api.ITypes
Returns a list of classes which implement IAnnotated.
getAnnotationTypes() - Method in class ome.logic.TypesImpl
 
getAnnotationTypes() - Method in interface ome.tools.hibernate.ExtendedMetadata
Returns all the classes which subclass Annotation
getAnnotationTypes() - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
 
getAnnotationTypes_async(AMD_ITypes_getAnnotationTypes, Current) - Method in class ome.services.blitz.impl.TypesI
 
getAppTitle() - Method in class ome.formats.importer.ImportConfig
 
getAppTitle() - Method in class ome.formats.importer.util.IniFileLoader
 
getAppVersion() - Method in class ome.formats.importer.util.ErrorContainer
 
getArchived() - Method in class ome.model.core.Image
Simple field ome.model.core.Image.archived (java.lang.Boolean)
getArray() - Method in class ome.tools.hibernate.SqlArray
 
getArray(long, int) - Method in class ome.tools.hibernate.SqlArray
 
getArray(Map<String, Class<?>>) - Method in class ome.tools.hibernate.SqlArray
 
getArray(long, int, Map<String, Class<?>>) - Method in class ome.tools.hibernate.SqlArray
 
getAtime() - Method in class ome.model.core.OriginalFile
Simple field ome.model.core.OriginalFile.atime (java.sql.Timestamp)
getAttachedFile() - Method in class pojos.FileAnnotationData
Returns the file to upload to the server.
getAttenuation() - Method in class ome.model.acquisition.LightSettings
Simple field ome.model.acquisition.LightSettings.attenuation (java.lang.Double)
getAttribute(T) - Method in class ome.security.auth.OmeroModelContextMapper
 
getAttributeSet(T) - Method in class ome.security.auth.OmeroModelContextMapper
 
getAuthoritativeContainerCache() - Method in interface ome.formats.model.IObjectContainerStore
Returns the current authoritative LSID container cache.
getAuthoritativeContainerCache() - Method in class ome.formats.OMEROMetadataStoreClient
 
getAuthority() - Method in class ome.services.db.DatabaseIdentity
 
getAvailableFamilies() - Method in class ome.services.RenderingBean
Implemented as specified by the RenderingEngine interface.
getAvailableFamilies() - Method in interface omeis.providers.re.RenderingEngine
Returns the list of mapping families supported by the Rendering engine.
getAvailableFamilies_async(AMD_RenderingEngine_getAvailableFamilies, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
getAvailableModels() - Method in class ome.services.RenderingBean
Implemented as specified by the RenderingEngine interface.
getAvailableModels() - Method in interface omeis.providers.re.RenderingEngine
Returns the list of color models supported by the Rendering engine.
getAvailableModels_async(AMD_RenderingEngine_getAvailableModels, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
getAvailableTypes() - Method in interface ome.util.checksum.ChecksumProviderFactory
 
getAvailableTypes() - Method in class ome.util.checksum.ChecksumProviderFactoryImpl
 
getB0() - Method in class omeis.providers.re.codomain.ContrastStretchingContext
Returns the y-intercept of the first line.
getB1() - Method in class omeis.providers.re.codomain.ContrastStretchingContext
Returns the y-intercept of the second line.
getB2() - Method in class omeis.providers.re.codomain.ContrastStretchingContext
Returns the y-intercept of the third line.
getBaselineShift() - Method in class ome.model.roi.Label
Simple field ome.model.roi.Label.baselineShift (java.lang.String)
getBaseType() - Method in class ome.tools.hibernate.SqlArray
 
getBaseTypeName() - Method in class ome.tools.hibernate.SqlArray
 
getBatchSize() - Method in interface ome.api.Search
Returns the current batch size.
getBatchSize() - Method in class ome.services.eventlogs.EventLogLoader
 
getBatchSize() - Method in class ome.services.SearchBean
 
getBatchSize_async(AMD_Search_getBatchSize, Current) - Method in class ome.services.blitz.impl.SearchI
 
getBeanHelper() - Method in class ome.logic.AbstractLevel1Service
 
getBeanHelper() - Method in class ome.logic.AbstractLevel2Service
 
getBeanHelper() - Method in class ome.services.AbstractStatefulBean
 
getBfReader(Pixels) - Method in class ome.io.nio.PixelsService
Short-cut in the FS case where we know that we are dealing with a FS-lite file, and want to retrieve the actual file as opposed to a pyramid or anything else.
getBinning() - Method in class ome.model.acquisition.DetectorSettings
Many-to-one field ome.model.acquisition.DetectorSettings.binning (ome.model.enums.Binning)
getBioFormatsVersion() - Method in class ome.formats.importer.ImportConfig
 
getBit(byte[], int) - Method in class pojos.MaskData
Sets the bit value in a byte array at position bit to be the value value.
getBitDepth(PixelsType) - Method in interface ome.api.IPixels
Bit depth for a given pixel type.
getBitDepth(PixelsType) - Method in class ome.logic.PixelsImpl
 
getBitDepth(String) - Static method in class ome.util.PixelData
Retrieves the bit width of a particular PixelsType.
getBitDepth_async(AMD_IPixels_getBitDepth, PixelsType, Current) - Method in class ome.services.blitz.impl.PixelsI
 
getBitResolution() - Method in class ome.model.display.QuantumDef
Simple field ome.model.display.QuantumDef.bitResolution (java.lang.Integer)
getBitSize() - Method in class ome.model.enums.PixelsType
Simple field ome.model.enums.PixelsType.bitSize (java.lang.Integer)
getBlitzAdapter() - Method in class ome.services.blitz.util.BlitzConfiguration
 
getBlitzManager() - Method in class ome.services.blitz.util.BlitzConfiguration
 
getBlitzVerifier() - Method in class ome.services.blitz.util.BlitzConfiguration
 
getBlue() - Method in class ome.model.core.Channel
Simple field ome.model.core.Channel.blue (java.lang.Integer)
getBlue() - Method in class ome.model.display.ChannelBinding
Simple field ome.model.display.ChannelBinding.blue (java.lang.Integer)
getBlue() - Method in class ome.model.screen.Well
Simple field ome.model.screen.Well.blue (java.lang.Integer)
getBlue() - Method in class pojos.WellData
Returns the blue component of the color associated to the well, or -1.
getBlueBand() - Method in class omeis.providers.re.RGBBuffer
Returns the data buffer for the blue band.
getBlueValue(int) - Method in class omeis.providers.re.RGBAIntBuffer
Retrieves the Blue value for a particular pixel index.
getBlueValue(int) - Method in class omeis.providers.re.RGBBuffer
Retrieves the Blue value for a particular pixel index.
getBlueValue(int) - Method in class omeis.providers.re.RGBIntBuffer
Retrieves the Blue value for a particular pixel index.
getBody() - Method in class ome.util.mem.Handle
Returns a reference to the Body object that is currently paired up with this handle.
getBooleanAnnotationCount() - Method in class ome.services.blitz.impl.OmeroMetadata
 
getBooleanAnnotationDescription(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getBooleanAnnotationID(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getBooleanAnnotationNamespace(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getBooleanAnnotationValue(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getBoolValue() - Method in class ome.model.annotations.BooleanAnnotation
Simple field ome.model.annotations.BooleanAnnotation.boolValue (java.lang.Boolean)
getBoost() - Method in class ome.services.fulltext.SimpleLuceneOptions
 
getBounds() - Method in class ome.util.math.geom2D.EllipseArea
Required by the Shape I/F.
getBounds() - Method in class ome.util.math.geom2D.RectangleArea
Required by the Shape I/F.
getBounds2D() - Method in class ome.util.math.geom2D.EllipseArea
Required by the Shape I/F.
getBounds2D() - Method in class ome.util.math.geom2D.RectangleArea
Required by the Shape I/F.
getBuffer() - Method in class ome.formats.importer.transfers.TransferState
(Not thread safe) Get a moderately large buffer for use in reading/writing data.
getBuffer(long) - Method in class ome.services.roi.PixelData
 
getByName(String, Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
getByPeriod_async(AMD_ITimeline_getByPeriod, List<String>, RTime, RTime, Parameters, boolean, Current) - Method in class ome.services.blitz.impl.TimelineI
 
getByteOrder() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
Returns the current pixel byte order.
getBytes() - Method in class ome.model.roi.Mask
Simple field ome.model.roi.Mask.bytes (byte[])
getBytesFailed() - Method in class ome.services.delete.files.AbstractFileDeletions
 
getByteWidth() - Method in interface ome.api.RawPixelsStore
 
getByteWidth() - Method in class ome.io.bioformats.BfPixelBuffer
 
getByteWidth() - Method in class ome.io.bioformats.BfPixelsWrapper
 
getByteWidth() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
 
getByteWidth() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
 
getByteWidth() - Method in interface ome.io.nio.PixelBuffer
Returns the byte width for the pixel buffer.
getByteWidth() - Method in class ome.io.nio.RomioPixelBuffer
Implemented as specified by PixelBuffer I/F.
getByteWidth() - Method in class ome.services.RawPixelsBean
 
getByteWidth_async(AMD_RawPixelsStore_getByteWidth, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
getByteWidth_async(AMD_RawPixelsStore_getByteWidth, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
getC() - Method in class pojos.ShapeData
Returns the channel.
getCalibratedMagnification() - Method in class ome.model.acquisition.Objective
Simple field ome.model.acquisition.Objective.calibratedMagnification (java.lang.Double)
getCalibratedMagnification() - Method in class pojos.ObjectiveData
Returns the objective's calibrated magnification factor.
getCallbackObject(String, String) - Method in class ome.services.sessions.SessionManagerImpl
 
getCallContext() - Method in class ome.security.basic.BasicEventContext
 
getCallContext() - Method in class ome.services.blitz.impl.commands.SaveI
 
getCallContext() - Method in class ome.services.blitz.repo.ManagedImportRequestI
 
getCallContext() - Method in class ome.services.blitz.repo.RawAccessRequestI
 
getCallContext() - Method in class omero.cmd.admin.CurrentSessionsRequestI
 
getCallContext() - Method in class omero.cmd.admin.ResetPasswordRequestI
 
getCallContext() - Method in class omero.cmd.admin.UpdateSessionTimeoutRequestI
 
getCallContext() - Method in class omero.cmd.basic.DoAllI
 
getCallContext() - Method in class omero.cmd.basic.ListRequestsI
 
getCallContext() - Method in class omero.cmd.basic.TimingI
 
getCallContext() - Method in class omero.cmd.fs.ManageImageBinariesI
 
getCallContext() - Method in class omero.cmd.fs.OriginalMetadataRequestI
 
getCallContext() - Method in class omero.cmd.fs.UsedFilesRequestI
 
getCallContext() - Method in class omero.cmd.graphs.Chgrp2I
 
getCallContext() - Method in class omero.cmd.graphs.ChgrpFacadeI
Deprecated.
 
getCallContext() - Method in class omero.cmd.graphs.ChgrpI
Deprecated.
 
getCallContext() - Method in class omero.cmd.graphs.Chmod2I
 
getCallContext() - Method in class omero.cmd.graphs.ChmodFacadeI
Deprecated.
 
getCallContext() - Method in class omero.cmd.graphs.ChmodI
Deprecated.
 
getCallContext() - Method in class omero.cmd.graphs.Chown2I
 
getCallContext() - Method in class omero.cmd.graphs.ChownFacadeI
Deprecated.
 
getCallContext() - Method in class omero.cmd.graphs.ChownI
Deprecated.
 
getCallContext() - Method in class omero.cmd.graphs.Delete2I
 
getCallContext() - Method in class omero.cmd.graphs.DeleteFacadeI
Deprecated.
 
getCallContext() - Method in class omero.cmd.graphs.DeleteI
Deprecated.
 
getCallContext() - Method in class omero.cmd.graphs.DiskUsageI
 
getCallContext() - Method in class omero.cmd.graphs.GraphSpecListI
Deprecated.
 
getCallContext() - Method in class omero.cmd.graphs.SkipHeadI
 
getCallContext() - Method in interface omero.cmd.IRequest
Returns the desired call context for this request.
getCallContext() - Method in class omero.cmd.mail.SendEmailRequestI
 
getCallContext() - Method in class omero.model.DetailsI
 
getCategory() - Method in class omero.client
Returns the category which should be used for all callbacks passed to the server.
getCdEnd() - Method in class ome.model.display.QuantumDef
Simple field ome.model.display.QuantumDef.cdEnd (java.lang.Integer)
getCdStart() - Method in class ome.model.display.QuantumDef
Simple field ome.model.display.QuantumDef.cdStart (java.lang.Integer)
getChannel() - Method in class ome.formats.model.ChannelData
Returns the channel this channel data is for.
getChannel(int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
getChannel(int) - Method in class ome.model.core.Pixels
Gets the ome.model.core.Channel at the given index.
getChannelAcquisitionMode(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getChannelBinding(int) - Method in class ome.model.display.RenderingDef
Gets the ome.model.display.ChannelBinding at the given index.
getChannelBindings() - Method in class omeis.providers.re.Renderer
Returns an array containing the channel bindings.
getChannelBindingsAsList() - Method in class omeis.providers.re.Renderer
Returns a list containing the channel bindings.
getChannelColor(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getChannelContrastMethod(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getChannelCount(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getChannelCurveCoefficient(int) - Method in class ome.services.RenderingBean
Implemented as specified by the RenderingEngine interface.
getChannelCurveCoefficient(int) - Method in interface omeis.providers.re.RenderingEngine
Returns the coefficient identifying a map in the family.
getChannelCurveCoefficient_async(AMD_RenderingEngine_getChannelCurveCoefficient, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
getChannelEmissionWavelength(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getChannelExcitationWavelength(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getChannelFamily(int) - Method in class ome.services.RenderingBean
Implemented as specified by the RenderingEngine interface.
getChannelFamily(int) - Method in interface omeis.providers.re.RenderingEngine
Returns the family associated to the specified channel.
getChannelFamily_async(AMD_RenderingEngine_getChannelFamily, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
getChannelFluor(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getChannelID(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getChannelIlluminationType(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getChannelIndex() - Method in class ome.formats.model.ChannelData
Returns the index of the channel this channel data is for.
getChannelLabeling() - Method in class pojos.ChannelData
Returns the label of the channel.
getChannelLookupTable(int) - Method in class ome.services.RenderingBean
 
getChannelLookupTable(int) - Method in interface omeis.providers.re.RenderingEngine
 
getChannelLookupTable_async(AMD_RenderingEngine_getChannelLookupTable, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
getChannelName(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getChannelNDFilter(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getChannelNoiseReduction(int) - Method in class ome.services.RenderingBean
Implemented as specified by the RenderingEngine interface.
getChannelNoiseReduction(int) - Method in interface omeis.providers.re.RenderingEngine
Returns true if the noise reduction algorithm used to map the pixels intensity values is turned on, false if the algorithm is turned off.
getChannelNoiseReduction_async(AMD_RenderingEngine_getChannelNoiseReduction, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
getChannelPinholeSize(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getChannelPockelCellSetting(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getChannels() - Method in class ome.model.core.LogicalChannel
returns channels .
getChannels() - Method in class ome.model.core.Pixels
returns channels .
getChannelSamplesPerPixel(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getChannelStats(int) - Method in class ome.services.RenderingBean
Implemented as specified by the RenderingEngine interface.
getChannelStats(int) - Method in interface omeis.providers.re.RenderingEngine
 
getChannelStats_async(AMD_RenderingEngine_getChannelStats, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
getChannelWindowEnd(int) - Method in class ome.services.RenderingBean
Implemented as specified by the RenderingEngine interface.
getChannelWindowEnd(int) - Method in interface omeis.providers.re.RenderingEngine
Returns the upper bound of the pixels intensity interval.
getChannelWindowEnd_async(AMD_RenderingEngine_getChannelWindowEnd, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
getChannelWindowStart(int) - Method in class ome.services.RenderingBean
Implemented as specified by the RenderingEngine interface.
getChannelWindowStart(int) - Method in interface omeis.providers.re.RenderingEngine
Returns the lower bound of the pixels intensity interval.
getChannelWindowStart_async(AMD_RenderingEngine_getChannelWindowStart, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
getCheckDone() - Method in class ome.services.util.DBEnumCheck
 
getChecks(IObject, String) - Method in class ome.security.basic.GroupChmodStrategy
 
getChecks(IObject, String) - Method in interface ome.security.ChmodStrategy
Return all the checks necessary to validate the given object if it were to have its permissions.
getChecksum() - Method in class ome.formats.importer.transfers.TransferState
Get the digest string for the local file.
getChecksumAlgorithm() - Method in class ome.formats.importer.ImportContainer
 
getChecksumAlgorithm(String, Current) - Method in interface ome.services.blitz.repo.RepositoryDao
Retrieve the checksum algorithm of the given name.
getChecksumAlgorithm(String, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
 
getChecksumAlgorithm(String) - Static method in class ome.services.blitz.util.ChecksumAlgorithmMapper
 
getChecksumProvider() - Method in class ome.formats.importer.transfers.TransferState
Get the ChecksumProvider passed to the constructor.
getChecksumType(ChecksumAlgorithm) - Static method in class ome.services.blitz.util.ChecksumAlgorithmMapper
 
getChecksumType(ChecksumAlgorithm) - Static method in class ome.services.blitz.util.ChecksumAlgorithmMapper
 
getChild() - Method in class ome.model.acquisition.FilterSetEmissionFilterLink
Many-to-one field ome.model.acquisition.FilterSetEmissionFilterLink.child (ome.model.acquisition.Filter)
getChild() - Method in class ome.model.acquisition.FilterSetExcitationFilterLink
Many-to-one field ome.model.acquisition.FilterSetExcitationFilterLink.child (ome.model.acquisition.Filter)
getChild() - Method in class ome.model.acquisition.LightPathEmissionFilterLink
Many-to-one field ome.model.acquisition.LightPathEmissionFilterLink.child (ome.model.acquisition.Filter)
getChild() - Method in class ome.model.acquisition.LightPathExcitationFilterLink
Many-to-one field ome.model.acquisition.LightPathExcitationFilterLink.child (ome.model.acquisition.Filter)
getChild() - Method in class ome.model.annotations.AnnotationAnnotationLink
Many-to-one field ome.model.annotations.AnnotationAnnotationLink.child (ome.model.annotations.Annotation)
getChild() - Method in class ome.model.annotations.ChannelAnnotationLink
Many-to-one field ome.model.annotations.ChannelAnnotationLink.child (ome.model.annotations.Annotation)
getChild() - Method in class ome.model.annotations.DatasetAnnotationLink
Many-to-one field ome.model.annotations.DatasetAnnotationLink.child (ome.model.annotations.Annotation)
getChild() - Method in class ome.model.annotations.DetectorAnnotationLink
Many-to-one field ome.model.annotations.DetectorAnnotationLink.child (ome.model.annotations.Annotation)
getChild() - Method in class ome.model.annotations.DichroicAnnotationLink
Many-to-one field ome.model.annotations.DichroicAnnotationLink.child (ome.model.annotations.Annotation)
getChild() - Method in class ome.model.annotations.ExperimenterAnnotationLink
Many-to-one field ome.model.annotations.ExperimenterAnnotationLink.child (ome.model.annotations.Annotation)
getChild() - Method in class ome.model.annotations.ExperimenterGroupAnnotationLink
Many-to-one field ome.model.annotations.ExperimenterGroupAnnotationLink.child (ome.model.annotations.Annotation)
getChild() - Method in class ome.model.annotations.FilesetAnnotationLink
Many-to-one field ome.model.annotations.FilesetAnnotationLink.child (ome.model.annotations.Annotation)
getChild() - Method in class ome.model.annotations.FilterAnnotationLink
Many-to-one field ome.model.annotations.FilterAnnotationLink.child (ome.model.annotations.Annotation)
getChild() - Method in class ome.model.annotations.ImageAnnotationLink
Many-to-one field ome.model.annotations.ImageAnnotationLink.child (ome.model.annotations.Annotation)
getChild() - Method in class ome.model.annotations.InstrumentAnnotationLink
Many-to-one field ome.model.annotations.InstrumentAnnotationLink.child (ome.model.annotations.Annotation)
getChild() - Method in class ome.model.annotations.LightPathAnnotationLink
Many-to-one field ome.model.annotations.LightPathAnnotationLink.child (ome.model.annotations.Annotation)
getChild() - Method in class ome.model.annotations.LightSourceAnnotationLink
Many-to-one field ome.model.annotations.LightSourceAnnotationLink.child (ome.model.annotations.Annotation)
getChild() - Method in class ome.model.annotations.NamespaceAnnotationLink
Many-to-one field ome.model.annotations.NamespaceAnnotationLink.child (ome.model.annotations.Annotation)
getChild() - Method in class ome.model.annotations.NodeAnnotationLink
Many-to-one field ome.model.annotations.NodeAnnotationLink.child (ome.model.annotations.Annotation)
getChild() - Method in class ome.model.annotations.ObjectiveAnnotationLink
Many-to-one field ome.model.annotations.ObjectiveAnnotationLink.child (ome.model.annotations.Annotation)
getChild() - Method in class ome.model.annotations.OriginalFileAnnotationLink
Many-to-one field ome.model.annotations.OriginalFileAnnotationLink.child (ome.model.annotations.Annotation)
getChild() - Method in class ome.model.annotations.PlaneInfoAnnotationLink
Many-to-one field ome.model.annotations.PlaneInfoAnnotationLink.child (ome.model.annotations.Annotation)
getChild() - Method in class ome.model.annotations.PlateAcquisitionAnnotationLink
Many-to-one field ome.model.annotations.PlateAcquisitionAnnotationLink.child (ome.model.annotations.Annotation)
getChild() - Method in class ome.model.annotations.PlateAnnotationLink
Many-to-one field ome.model.annotations.PlateAnnotationLink.child (ome.model.annotations.Annotation)
getChild() - Method in class ome.model.annotations.ProjectAnnotationLink
Many-to-one field ome.model.annotations.ProjectAnnotationLink.child (ome.model.annotations.Annotation)
getChild() - Method in class ome.model.annotations.ReagentAnnotationLink
Many-to-one field ome.model.annotations.ReagentAnnotationLink.child (ome.model.annotations.Annotation)
getChild() - Method in class ome.model.annotations.RoiAnnotationLink
Many-to-one field ome.model.annotations.RoiAnnotationLink.child (ome.model.annotations.Annotation)
getChild() - Method in class ome.model.annotations.ScreenAnnotationLink
Many-to-one field ome.model.annotations.ScreenAnnotationLink.child (ome.model.annotations.Annotation)
getChild() - Method in class ome.model.annotations.SessionAnnotationLink
Many-to-one field ome.model.annotations.SessionAnnotationLink.child (ome.model.annotations.Annotation)
getChild() - Method in class ome.model.annotations.ShapeAnnotationLink
Many-to-one field ome.model.annotations.ShapeAnnotationLink.child (ome.model.annotations.Annotation)
getChild() - Method in class ome.model.annotations.WellAnnotationLink
Many-to-one field ome.model.annotations.WellAnnotationLink.child (ome.model.annotations.Annotation)
getChild() - Method in class ome.model.containers.DatasetImageLink
Many-to-one field ome.model.containers.DatasetImageLink.child (ome.model.core.Image)
getChild() - Method in class ome.model.containers.ProjectDatasetLink
Many-to-one field ome.model.containers.ProjectDatasetLink.child (ome.model.containers.Dataset)
getChild() - Method in class ome.model.core.PixelsOriginalFileMap
Many-to-one field ome.model.core.PixelsOriginalFileMap.child (ome.model.core.Pixels)
getChild() - Method in class ome.model.fs.FilesetJobLink
Many-to-one field ome.model.fs.FilesetJobLink.child (ome.model.jobs.Job)
getChild() - Method in interface ome.model.ILink
 
getChild() - Method in class ome.model.jobs.JobOriginalFileLink
Many-to-one field ome.model.jobs.JobOriginalFileLink.child (ome.model.core.OriginalFile)
getChild() - Method in class ome.model.meta.GroupExperimenterMap
Many-to-one field ome.model.meta.GroupExperimenterMap.child (ome.model.meta.Experimenter)
getChild() - Method in class ome.model.meta.ShareMember
Many-to-one field ome.model.meta.ShareMember.child (ome.model.meta.Experimenter)
getChild() - Method in class ome.model.screen.ScreenPlateLink
Many-to-one field ome.model.screen.ScreenPlateLink.child (ome.model.screen.Plate)
getChild() - Method in class ome.model.screen.WellReagentLink
Many-to-one field ome.model.screen.WellReagentLink.child (ome.model.screen.Reagent)
getChildOptionsPolicy(GraphPolicy, Collection<ChildOptionI>, Set<GraphPolicy.Ability>) - Static method in class omero.cmd.graphs.ChildOptionsPolicy
Adjust an existing graph traversal policy so that child objects may be included or excluded regardless of if they are truly orphans.
getChildTransformer(Class) - Static method in class ome.services.query.Hierarchy
 
getClass(String) - Method in class ome.services.graphs.GraphState
Deprecated.
 
getClass(String) - Method in interface ome.services.graphs.GraphStep.Callback
Deprecated.
 
getClasses() - Method in interface ome.tools.hibernate.ExtendedMetadata
 
getClasses() - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
 
getClassForSimpleName(String) - Method in class ome.services.graphs.GraphPathBean
 
getCleanInstance() - Method in class ome.services.graphs.GraphPolicy
Create a clone of this graph policy that has fresh state.
getCleanInstance() - Method in class omero.cmd.graphs.BaseGraphPolicyAdjuster
 
getClient() - Method in class ome.formats.importer.util.ClientKeepAlive
 
getClient() - Method in class omero.model.DetailsI
 
getClientConfigDefaults() - Method in interface ome.api.IConfig
reads the etc/omero.properties file and returns all the key/value pairs that are found there which match the prefix "omero.client".
getClientConfigDefaults() - Method in class ome.logic.ConfigImpl
 
getClientConfigDefaults_async(AMD_IConfig_getClientConfigDefaults, Current) - Method in class ome.services.blitz.impl.ConfigI
 
getClientConfigValues() - Method in interface ome.api.IConfig
retrieves configuration values like IConfig.getConfigValues(String) but only those with the prefix "omero.client".
getClientConfigValues() - Method in class ome.logic.ConfigImpl
 
getClientConfigValues_async(AMD_IConfig_getClientConfigValues, Current) - Method in class ome.services.blitz.impl.ConfigI
 
getClientContext() - Static method in class ome.system.OmeroContext
create (if necessary) and return the single default client OmeroContext.
getClientContext(Properties) - Static method in class ome.system.OmeroContext
initialize a new client OmeroContext (named OmeroContext.CLIENT_CONTEXT), using the OmeroContext.getContext(Properties, String) method.
getClientIds() - Method in class omero.util.ServantHolder
 
getClientPath() - Method in class ome.model.fs.FilesetEntry
Simple field ome.model.fs.FilesetEntry.clientPath (java.lang.String)
getClosed() - Method in class ome.model.meta.Session
Simple field ome.model.meta.Session.closed (java.sql.Timestamp)
getCloseStatementCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
getCo2percent() - Method in class ome.model.acquisition.ImagingEnvironment
Simple field ome.model.acquisition.ImagingEnvironment.co2percent (java.lang.Double)
getCo2Percent() - Method in class pojos.ImageAcquisitionData
Returns the Co2 level, this is a percent value in the interval [0, 1].
getCodomainChain() - Method in class omeis.providers.re.Renderer
Returns the object that defines the sequence of spatial transformations to be applied to quantized data.
getCodomainMapContext(int) - Method in class ome.model.display.RenderingDef
Gets the ome.model.display.CodomainMapContext at the given index.
getCoefficient() - Method in class ome.model.display.ChannelBinding
Simple field ome.model.display.ChannelBinding.coefficient (java.lang.Double)
getCol(int, int, int, int) - Method in interface ome.api.RawPixelsStore
 
getCol(Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer
 
getCol(Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPixelsWrapper
 
getCol(Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
 
getCol(Integer, Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
 
getCol(Integer, Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer
Retrieves a particular column from this pixel buffer.
getCol(Integer, Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer
Implemented as specified by PixelBuffer I/F.
getCol(int, int, int, int) - Method in class ome.services.RawPixelsBean
 
getCol_async(AMD_RawPixelsStore_getCol, int, int, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
getCol_async(AMD_RawPixelsStore_getCol, int, int, int, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
getColDirect(Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPixelBuffer
 
getColDirect(Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
 
getColDirect(Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
 
getColDirect(Integer, Integer, Integer, Integer, byte[]) - Method in interface ome.io.nio.PixelBuffer
Retrieves a particular column from this pixel buffer.
getColDirect(Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.nio.RomioPixelBuffer
Implemented as specified by PixelBuffer I/F.
getCollectionCount(String, String, Set<Long>, Parameters) - Method in interface ome.api.IContainer
Counts the number of members in a collection for a given object.
getCollectionCount(String, String, Set, Parameters) - Method in class ome.logic.PojosImpl
Implemented as specified by the IContainer I/F
getCollectionCount_async(AMD_IContainer_getCollectionCount, String, String, List<Long>, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI
 
getCollectionFetchCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
getCollectionLoadCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
getCollectionRecreateCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
getCollectionRemoveCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
getCollectionRoleNames() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
Get the names of all collection roles
getCollectionStatistics(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
Get collection statistics per role
getCollectionUpdateCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
getColor(ChannelData) - Static method in class ome.formats.model.ColorsFactory
Determines the color usually associated to the specified wavelength or explicitly defined for a particular channel.
getColor(int, Channel) - Static method in class omeis.providers.re.ColorsFactory
Determines the color usually associated to the specified wavelength.
getColor(int, Channel, LogicalChannel) - Static method in class omeis.providers.re.ColorsFactory
Determines the color usually associated to the specified wavelength.
getColorArray(ChannelBinding) - Static method in class omeis.providers.re.Renderer
Returns an array whose ascending indices represent the color components Red, Green and Blue.
getColSize() - Method in class ome.io.bioformats.BfPixelBuffer
 
getColSize() - Method in class ome.io.bioformats.BfPixelsWrapper
 
getColSize() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
 
getColSize() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
 
getColSize() - Method in interface ome.io.nio.PixelBuffer
Retrieves the in memory size of a column of pixels in this pixel buffer.
getColSize() - Method in class ome.io.nio.RomioPixelBuffer
Implemented as specified by PixelBuffer I/F.
getColumn() - Method in class ome.model.screen.Well
Simple field ome.model.screen.Well.column (java.lang.Integer)
getColumn() - Method in class pojos.WellData
Returns the column used to indicate the location of the well on the grid.
getColumnNamingConvention() - Method in class ome.model.screen.Plate
Simple field ome.model.screen.Plate.columnNamingConvention (java.lang.String)
getColumns() - Method in class ome.model.screen.Plate
Simple field ome.model.screen.Plate.columns (java.lang.Integer)
getColumnSequenceIndex() - Method in class pojos.PlateData
Returns the index indicating how to label a column.
getComment() - Method in class ome.formats.importer.util.ErrorContainer
 
getCommentAnnotationCount() - Method in class ome.services.blitz.impl.OmeroMetadata
 
getCommentAnnotationDescription(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getCommentAnnotationID(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getCommentAnnotationNamespace(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getCommentAnnotationValue(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getCommentCount(Set<Long>) - Method in interface ome.api.IShare
Returns a map from share id to comment count.
getCommentCount(Set<Long>) - Method in class ome.services.sharing.ShareBean
 
getCommentCount_async(AMD_IShare_getCommentCount, List<Long>, Current) - Method in class ome.services.blitz.impl.ShareI
 
getComments(long) - Method in interface ome.api.IShare
Looks up all comments which belong to the share.
getComments(long) - Method in class ome.services.sharing.ShareBean
 
getComments_async(AMD_IShare_getComments, long, Current) - Method in class ome.services.blitz.impl.ShareI
 
getCommentType() - Method in class ome.formats.importer.util.ErrorContainer
 
getCommunicationLink(String) - Method in class ome.formats.importer.util.HtmlMessenger
Creates a client to communicate.
getCommunicator() - Method in class ome.services.blitz.fire.Ring
 
getCommunicator() - Method in interface ome.services.blitz.redirect.Redirector.Context
Active communicator for use by the Redirector instance.
getCommunicator() - Method in class ome.services.blitz.repo.AbstractRepositoryI
 
getCommunicator() - Method in class ome.services.blitz.repo.InternalRepositoryConfig
 
getCommunicator() - Method in class ome.services.blitz.util.BlitzConfiguration
 
getCommunicator() - Method in class omero.client
Returns the Communicator for this instance or throws an exception if null.
getComponents() - Method in class ome.services.blitz.repo.path.FsFile
Get the path components of this instance.
getComponents() - Method in class pojos.MultiImageData
Returns the collection of images composing the file.
getCompression() - Method in class ome.model.display.RenderingDef
Simple field ome.model.display.RenderingDef.compression (java.lang.Double)
getCompressionLevel() - Method in interface ome.api.local.LocalCompress
Returns the current compression level for the service.
getCompressionLevel() - Method in class ome.logic.CompressImpl
 
getCompressionLevel() - Method in class ome.services.RenderingBean
Implemented as specified by the RenderingEngine interface.
getCompressionLevel() - Method in interface omeis.providers.re.RenderingEngine
Returns the current compression level for the service.
getCompressionLevel_async(AMD_RenderingEngine_getCompressionLevel, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
getConfig() - Method in class ome.formats.importer.OMEROWrapper
 
getConfig() - Method in class ome.model.meta.ExperimenterGroup
 
getConfigDefaults() - Method in interface ome.api.IConfig
reads the etc/omero.properties file and returns all the key/value pairs that are found there.
getConfigDefaults() - Method in class ome.logic.ConfigImpl
 
getConfigDefaults_async(AMD_IConfig_getConfigDefaults, Current) - Method in class ome.services.blitz.impl.ConfigI
 
getConfigService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
getConfigService() - Method in class ome.system.ServiceFactory
 
getConfigValue(String) - Method in interface ome.api.IConfig
retrieve a configuration value from the backend store.
getConfigValue(String) - Method in class ome.formats.OMEROMetadataStoreClient
Retrieves a configuration value from the IConfig service.
getConfigValue(String) - Method in class ome.logic.ConfigImpl
getConfigValue_async(AMD_IConfig_getConfigValue, String, Current) - Method in class ome.services.blitz.impl.ConfigI
 
getConfigValues(String) - Method in interface ome.api.IConfig
retrieves configuration values from the backend store which match the given regex.
getConfigValues(String) - Method in class ome.logic.ConfigImpl
 
getConfigValues_async(AMD_IConfig_getConfigValues, String, Current) - Method in class ome.services.blitz.impl.ConfigI
 
getConn() - Method in class ome.model.meta.Node
Simple field ome.model.meta.Node.conn (java.lang.String)
getConnectCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
getConnection() - Method in class ome.services.db.SelfCorrectingDataSource
 
getConnection(String, String) - Method in class ome.services.db.SelfCorrectingDataSource
 
getConstant() - Method in class ome.model.display.PlaneSlicingContext
Simple field ome.model.display.PlaneSlicingContext.constant (java.lang.Boolean)
getConstraints() - Method in exception ome.services.graphs.GraphConstraintException
Deprecated.
 
getContainerCache() - Method in interface ome.formats.model.IObjectContainerStore
Returns the current container cache.
getContainerCache() - Method in class ome.formats.OMEROMetadataStoreClient
 
getContainers() - Method in class ome.formats.importer.ImportCandidates
 
getContainerService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
getContainerService() - Method in class ome.system.ServiceFactory
 
getContainerTypes() - Method in class ome.logic.TypesImpl
 
getContainingEvent() - Method in class ome.model.meta.Event
Many-to-one field ome.model.meta.Event.containingEvent (ome.model.meta.Event)
getContent() - Method in class pojos.AnnotationData
Returns the content of the annotation.
getContent() - Method in class pojos.BooleanAnnotationData
Returns the textual content of the annotation.
getContent() - Method in class pojos.DoubleAnnotationData
Returns the value.
getContent() - Method in class pojos.FileAnnotationData
Returns the original file.
getContent() - Method in class pojos.LongAnnotationData
Returns the rating value.
getContent() - Method in class pojos.MapAnnotationData
 
getContent() - Method in class pojos.RatingAnnotationData
Returns the rating value.
getContent() - Method in class pojos.TagAnnotationData
Returns the textual content of the annotation.
getContent() - Method in class pojos.TermAnnotationData
Returns the textual content of the annotation.
getContent() - Method in class pojos.TextualAnnotationData
Returns the textual content of the annotation.
getContent() - Method in class pojos.TimeAnnotationData
Returns the timestamp of the annotation.
getContent() - Method in class pojos.XMLAnnotationData
Returns the content of the annotation.
getContentAsString() - Method in class pojos.AnnotationData
Returns the content of the annotation as a String, which is parsed on a Class-by-Class basis.
getContentAsString() - Method in class pojos.BooleanAnnotationData
Returns the textual content of the annotation.
getContentAsString() - Method in class pojos.DoubleAnnotationData
Returns the value as a string.
getContentAsString() - Method in class pojos.FileAnnotationData
Returns the absolute path to the file
getContentAsString() - Method in class pojos.LongAnnotationData
Returns the value as a string.
getContentAsString() - Method in class pojos.MapAnnotationData
 
getContentAsString() - Method in class pojos.RatingAnnotationData
Returns the rating value as a string.
getContentAsString() - Method in class pojos.TagAnnotationData
Returns the textual content of the annotation.
getContentAsString() - Method in class pojos.TermAnnotationData
Returns the textual content of the annotation.
getContentAsString() - Method in class pojos.TextualAnnotationData
Returns the textual content of the annotation.
getContentAsString() - Method in class pojos.TimeAnnotationData
Returns the time as a string.
getContentAsString() - Method in class pojos.XMLAnnotationData
Returns the textual content of the annotation.
getContentMap(long) - Method in interface ome.api.IShare
Returns the contents of the share keyed by type.
getContentMap(long) - Method in class ome.services.sharing.ShareBean
 
getContentMap_async(AMD_IShare_getContentMap, long, Current) - Method in class ome.services.blitz.impl.ShareI
 
getContents(long) - Method in interface ome.api.IShare
Looks up all items belong to the share.
getContents(long) - Method in class ome.services.sharing.ShareBean
 
getContents_async(AMD_IShare_getContents, long, Current) - Method in class ome.services.blitz.impl.ShareI
 
getContentSize(long) - Method in interface ome.api.IShare
Returns the number of items in the share.
getContentSize(long) - Method in class ome.services.sharing.ShareBean
 
getContentSize_async(AMD_IShare_getContentSize, long, Current) - Method in class ome.services.blitz.impl.ShareI
 
getContentSubList(long, int, int) - Method in interface ome.api.IShare
Returns a range of items from the share.
getContentSubList(long, int, int) - Method in class ome.services.sharing.ShareBean
 
getContentSubList_async(AMD_IShare_getContentSubList, long, int, int, Current) - Method in class ome.services.blitz.impl.ShareI
 
getContext() - Method in class ome.model.internal.Details
reference to the entity which this Details is contained in.
getContext() - Method in class ome.security.basic.CurrentDetails
 
getContext() - Method in interface ome.services.util.Executor
Provides access to the context for Work-API consumers who need to publish events, etc.
getContext() - Method in class ome.services.util.Executor.Impl
 
getContext(Properties, String) - Static method in class ome.system.OmeroContext
initialize a new client OmeroContext using the Properties provided as values for property (e.g.
getContext() - Method in class ome.system.ServiceFactory
Deprecated. 
getContrastMethod() - Method in class ome.model.core.LogicalChannel
Many-to-one field ome.model.core.LogicalChannel.contrastMethod (ome.model.enums.ContrastMethod)
getContrastMethod() - Method in class pojos.ChannelAcquisitionData
Returns the contrast method.
getContrastMethod() - Method in class pojos.ChannelData
Returns the contrast method.
getContrastMethodAsEnum() - Method in class pojos.ChannelData
Returns the contrast method enumeration value.
getControls() - Method in class ome.security.auth.GroupContextMapper
 
getControls() - Method in class ome.security.auth.PersonContextMapper
 
getCorrection() - Method in class ome.model.acquisition.Objective
Many-to-one field ome.model.acquisition.Objective.correction (ome.model.enums.Correction)
getCorrection() - Method in class pojos.ObjectiveData
Returns the correction value of the objective.
getCorrectionCollar() - Method in class ome.model.acquisition.ObjectiveSettings
Simple field ome.model.acquisition.ObjectiveSettings.correctionCollar (java.lang.Double)
getCorrectionCollar() - Method in class pojos.ImageAcquisitionData
Returns the correction collar of the objective.
getCount() - Method in class ome.io.nio.SimpleBackOff
 
getCount(String) - Method in class ome.services.export.ExporterStepFactory
Deprecated.
 
getCount() - Method in interface ome.system.metrics.Counter
 
getCount() - Method in class ome.system.metrics.DefaultCounter
 
getCount() - Method in class ome.system.metrics.DefaultTimer
 
getCount() - Method in interface ome.system.metrics.Timer
 
getCountQuery(String) - Method in interface ome.tools.hibernate.ExtendedMetadata
Returns the query for obtaining the number of collection items to a particular instance.
getCountQuery(String) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
Returns the query for obtaining the number of collection items to a particular instance.
getCreated() - Method in class pojos.DataObject
Returns the creation time of the object.
getCreationEvent() - Method in class ome.model.acquisition.Detector.Details
 
getCreationEvent() - Method in class ome.model.acquisition.DetectorSettings.Details
 
getCreationEvent() - Method in class ome.model.acquisition.Dichroic.Details
 
getCreationEvent() - Method in class ome.model.acquisition.Filter.Details
 
getCreationEvent() - Method in class ome.model.acquisition.FilterSet.Details
 
getCreationEvent() - Method in class ome.model.acquisition.FilterSetEmissionFilterLink.Details
 
getCreationEvent() - Method in class ome.model.acquisition.FilterSetExcitationFilterLink.Details
 
getCreationEvent() - Method in class ome.model.acquisition.ImagingEnvironment.Details
 
getCreationEvent() - Method in class ome.model.acquisition.Instrument.Details
 
getCreationEvent() - Method in class ome.model.acquisition.LightPath.Details
 
getCreationEvent() - Method in class ome.model.acquisition.LightPathEmissionFilterLink.Details
 
getCreationEvent() - Method in class ome.model.acquisition.LightPathExcitationFilterLink.Details
 
getCreationEvent() - Method in class ome.model.acquisition.LightSettings.Details
 
getCreationEvent() - Method in class ome.model.acquisition.LightSource.Details
 
getCreationEvent() - Method in class ome.model.acquisition.Microscope.Details
 
getCreationEvent() - Method in class ome.model.acquisition.Objective.Details
 
getCreationEvent() - Method in class ome.model.acquisition.ObjectiveSettings.Details
 
getCreationEvent() - Method in class ome.model.acquisition.OTF.Details
 
getCreationEvent() - Method in class ome.model.acquisition.StageLabel.Details
 
getCreationEvent() - Method in class ome.model.acquisition.TransmittanceRange.Details
 
getCreationEvent() - Method in class ome.model.annotations.Annotation.Details
 
getCreationEvent() - Method in class ome.model.annotations.AnnotationAnnotationLink.Details
 
getCreationEvent() - Method in class ome.model.annotations.ChannelAnnotationLink.Details
 
getCreationEvent() - Method in class ome.model.annotations.DatasetAnnotationLink.Details
 
getCreationEvent() - Method in class ome.model.annotations.DetectorAnnotationLink.Details
 
getCreationEvent() - Method in class ome.model.annotations.DichroicAnnotationLink.Details
 
getCreationEvent() - Method in class ome.model.annotations.ExperimenterAnnotationLink.Details
 
getCreationEvent() - Method in class ome.model.annotations.ExperimenterGroupAnnotationLink.Details
 
getCreationEvent() - Method in class ome.model.annotations.FilesetAnnotationLink.Details
 
getCreationEvent() - Method in class ome.model.annotations.FilterAnnotationLink.Details
 
getCreationEvent() - Method in class ome.model.annotations.ImageAnnotationLink.Details
 
getCreationEvent() - Method in class ome.model.annotations.InstrumentAnnotationLink.Details
 
getCreationEvent() - Method in class ome.model.annotations.LightPathAnnotationLink.Details
 
getCreationEvent() - Method in class ome.model.annotations.LightSourceAnnotationLink.Details
 
getCreationEvent() - Method in class ome.model.annotations.NamespaceAnnotationLink.Details
 
getCreationEvent() - Method in class ome.model.annotations.NodeAnnotationLink.Details
 
getCreationEvent() - Method in class ome.model.annotations.ObjectiveAnnotationLink.Details
 
getCreationEvent() - Method in class ome.model.annotations.OriginalFileAnnotationLink.Details
 
getCreationEvent() - Method in class ome.model.annotations.PlaneInfoAnnotationLink.Details
 
getCreationEvent() - Method in class ome.model.annotations.PlateAcquisitionAnnotationLink.Details
 
getCreationEvent() - Method in class ome.model.annotations.PlateAnnotationLink.Details
 
getCreationEvent() - Method in class ome.model.annotations.ProjectAnnotationLink.Details
 
getCreationEvent() - Method in class ome.model.annotations.ReagentAnnotationLink.Details
 
getCreationEvent() - Method in class ome.model.annotations.RoiAnnotationLink.Details
 
getCreationEvent() - Method in class ome.model.annotations.ScreenAnnotationLink.Details
 
getCreationEvent() - Method in class ome.model.annotations.SessionAnnotationLink.Details
 
getCreationEvent() - Method in class ome.model.annotations.ShapeAnnotationLink.Details
 
getCreationEvent() - Method in class ome.model.annotations.WellAnnotationLink.Details
 
getCreationEvent() - Method in class ome.model.containers.Dataset.Details
 
getCreationEvent() - Method in class ome.model.containers.DatasetImageLink.Details
 
getCreationEvent() - Method in class ome.model.containers.Project.Details
 
getCreationEvent() - Method in class ome.model.containers.ProjectDatasetLink.Details
 
getCreationEvent() - Method in class ome.model.core.Channel.Details
 
getCreationEvent() - Method in class ome.model.core.Image.Details
 
getCreationEvent() - Method in class ome.model.core.LogicalChannel.Details
 
getCreationEvent() - Method in class ome.model.core.OriginalFile.Details
 
getCreationEvent() - Method in class ome.model.core.Pixels.Details
 
getCreationEvent() - Method in class ome.model.core.PixelsOriginalFileMap.Details
 
getCreationEvent() - Method in class ome.model.core.PlaneInfo.Details
 
getCreationEvent() - Method in class ome.model.display.ChannelBinding.Details
 
getCreationEvent() - Method in class ome.model.display.CodomainMapContext.Details
 
getCreationEvent() - Method in class ome.model.display.QuantumDef.Details
 
getCreationEvent() - Method in class ome.model.display.RenderingDef.Details
 
getCreationEvent() - Method in class ome.model.display.Thumbnail.Details
 
getCreationEvent() - Method in class ome.model.experiment.Experiment.Details
 
getCreationEvent() - Method in class ome.model.experiment.MicrobeamManipulation.Details
 
getCreationEvent() - Method in class ome.model.fs.Fileset.Details
 
getCreationEvent() - Method in class ome.model.fs.FilesetEntry.Details
 
getCreationEvent() - Method in class ome.model.fs.FilesetJobLink.Details
 
getCreationEvent() - Method in interface ome.model.IDetails
 
getCreationEvent() - Method in class ome.model.internal.Details
 
getCreationEvent() - Method in class ome.model.internal.Link.Details
 
getCreationEvent() - Method in class ome.model.jobs.Job.Details
 
getCreationEvent() - Method in class ome.model.jobs.JobOriginalFileLink.Details
 
getCreationEvent() - Method in class ome.model.meta.ExternalInfo.Details
 
getCreationEvent() - Method in class ome.model.roi.Roi.Details
 
getCreationEvent() - Method in class ome.model.roi.Shape.Details
 
getCreationEvent() - Method in class ome.model.screen.Plate.Details
 
getCreationEvent() - Method in class ome.model.screen.PlateAcquisition.Details
 
getCreationEvent() - Method in class ome.model.screen.Reagent.Details
 
getCreationEvent() - Method in class ome.model.screen.Screen.Details
 
getCreationEvent() - Method in class ome.model.screen.ScreenPlateLink.Details
 
getCreationEvent() - Method in class ome.model.screen.Well.Details
 
getCreationEvent() - Method in class ome.model.screen.WellReagentLink.Details
 
getCreationEvent() - Method in class ome.model.screen.WellSample.Details
 
getCreationEvent() - Method in class ome.model.stats.StatsInfo.Details
 
getCreationEvent(Current) - Method in class omero.model.DetailsI
 
getCtime() - Method in class ome.model.core.OriginalFile
Simple field ome.model.core.OriginalFile.ctime (java.sql.Timestamp)
getCurrent() - Method in class ome.services.blitz.util.FindServiceFactoryMessage
 
getCurrent() - Method in class ome.services.blitz.util.UnregisterServantMessage
 
getCurrentEventContext() - Method in interface ome.api.StatefulServiceInterface
Returns the current EventContext for this instance.
getCurrentEventContext() - Method in class ome.security.basic.CurrentDetails
Public view on the data contained here.
getCurrentEventContext() - Method in class ome.services.AbstractStatefulBean
 
getCurrentEventContext() - Method in class ome.services.RenderingBean
Implemented as specified by the RenderingEngine interface.
getCurrentEventContext() - Method in class ome.services.ThumbnailBean
 
getCurrentEventContext_async(AMD_StatefulServiceInterface_getCurrentEventContext, Current) - Method in class ome.services.blitz.impl.AbstractAmdServant
 
getCurrentEventContext_async(AMD_StatefulServiceInterface_getCurrentEventContext, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
getCurrentEventId() - Method in class ome.services.sessions.SessionContextImpl
 
getCurrentEventId() - Method in interface ome.system.EventContext
 
getCurrentEventId() - Method in class ome.system.SimpleEventContext
 
getCurrentEventType() - Method in class ome.services.sessions.SessionContextImpl
 
getCurrentEventType() - Method in interface ome.system.EventContext
 
getCurrentEventType() - Method in class ome.system.SimpleEventContext
 
getCurrentGroupId() - Method in class ome.services.sessions.SessionContextImpl
 
getCurrentGroupId() - Method in interface ome.system.EventContext
 
getCurrentGroupId() - Method in class ome.system.SimpleEventContext
 
getCurrentGroupName() - Method in class ome.services.sessions.SessionContextImpl
 
getCurrentGroupName() - Method in interface ome.system.EventContext
 
getCurrentGroupName() - Method in class ome.system.SimpleEventContext
 
getCurrentGroupPermissions() - Method in class ome.services.sessions.SessionContextImpl
 
getCurrentGroupPermissions() - Method in interface ome.system.EventContext
 
getCurrentGroupPermissions() - Method in class ome.system.SimpleEventContext
 
getCurrentId() - Method in class ome.services.eventlogs.PersistentEventLogLoader
Get current EventLog id.
getCurrentPatch() - Method in class ome.model.meta.DBPatch
Simple field ome.model.meta.DBPatch.currentPatch (java.lang.Integer)
getCurrentSessionId() - Method in class ome.services.sessions.SessionContextImpl
 
getCurrentSessionId() - Method in interface ome.system.EventContext
 
getCurrentSessionId() - Method in class ome.system.SimpleEventContext
 
getCurrentSessionUuid() - Method in class ome.services.sessions.SessionContextImpl
 
getCurrentSessionUuid() - Method in interface ome.system.EventContext
 
getCurrentSessionUuid() - Method in class ome.system.SimpleEventContext
 
getCurrentShareId() - Method in class ome.services.sessions.SessionContextImpl
 
getCurrentShareId() - Method in interface ome.system.EventContext
 
getCurrentShareId() - Method in class ome.system.SimpleEventContext
 
getCurrentUmask() - Method in class ome.services.sessions.SessionContextImpl
 
getCurrentUmask() - Method in class ome.system.SimpleEventContext
 
getCurrentUserId() - Method in class ome.services.sessions.SessionContextImpl
 
getCurrentUserId() - Method in interface ome.system.EventContext
 
getCurrentUserId() - Method in class ome.system.SimpleEventContext
 
getCurrentUserName() - Method in class ome.services.sessions.SessionContextImpl
 
getCurrentUserName() - Method in interface ome.system.EventContext
 
getCurrentUserName() - Method in class ome.system.SimpleEventContext
 
getCurrentVersion() - Method in class ome.model.meta.DBPatch
Simple field ome.model.meta.DBPatch.currentVersion (java.lang.String)
getCurveCoefficient() - Method in class omeis.providers.re.quantum.QuantumStrategy
Returns the coefficient identifying a curve within a given family.
getCustomAnnotationList() - Method in class ome.formats.importer.ImportContainer
The list of custom, user specified, annotations to link to all images represented by this container.
getCustomImageNaming() - Method in class ome.formats.importer.ImportConfig
 
getCustomImageNaming() - Method in class ome.formats.importer.util.IniFileLoader
 
getCutIn() - Method in class ome.model.acquisition.TransmittanceRange
Enum-mapped unit-based field ome.model.acquisition.TransmittanceRange.cutIn (ome.model.units.Length)
getCutIn(UnitsLength) - Method in class pojos.FilterData
Returns the cut in value or null.
getCutIn() - Method in class pojos.FilterData
Deprecated.
getCutInTolerance() - Method in class ome.model.acquisition.TransmittanceRange
Enum-mapped unit-based field ome.model.acquisition.TransmittanceRange.cutInTolerance (ome.model.units.Length)
getCutInTolerance(UnitsLength) - Method in class pojos.FilterData
Returns the cut in tolerance value or null.
getCutInTolerance() - Method in class pojos.FilterData
getCutOut() - Method in class ome.model.acquisition.TransmittanceRange
Enum-mapped unit-based field ome.model.acquisition.TransmittanceRange.cutOut (ome.model.units.Length)
getCutOut(UnitsLength) - Method in class pojos.FilterData
Returns the cut out value or null.
getCutOut() - Method in class pojos.FilterData
Deprecated.
getCutOutTolerance() - Method in class ome.model.acquisition.TransmittanceRange
Enum-mapped unit-based field ome.model.acquisition.TransmittanceRange.cutOutTolerance (ome.model.units.Length)
getCutOutTolerance(UnitsLength) - Method in class pojos.FilterData
Returns the cut out tolerance value or null.
getCutOutTolerance() - Method in class pojos.FilterData
getCx() - Method in class ome.model.roi.Ellipse
Simple field ome.model.roi.Ellipse.cx (java.lang.Double)
getCx() - Method in class ome.model.roi.Point
Simple field ome.model.roi.Point.cx (java.lang.Double)
getCy() - Method in class ome.model.roi.Ellipse
Simple field ome.model.roi.Ellipse.cy (java.lang.Double)
getCy() - Method in class ome.model.roi.Point
Simple field ome.model.roi.Point.cy (java.lang.Double)
getD() - Method in class ome.model.roi.Path
Simple field ome.model.roi.Path.d (java.lang.String)
getData() - Method in class ome.io.nio.ReorderedPixelData
Returns the backing buffer for the pixel data.
getData() - Method in class ome.model.meta.Share
Simple field ome.model.meta.Share.data (byte[])
getData() - Method in class ome.util.PixelData
Returns the backing buffer for the pixel data.
getData() - Method in class omeis.providers.re.data.Plane2D
Returns the pixel data that is used to back this Plane.
getDataAsArray(Connection, Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.BOOLEAN
 
getDataAsArray(Connection, Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.DATE
 
getDataAsArray(Connection, Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.DOUBLE
 
getDataAsArray(Connection, Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.ENUM
 
getDataAsArray(Connection, Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.FLOAT
 
getDataAsArray(Connection, Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
 
getDataAsArray(Connection, Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.INTEGER
 
getDataAsArray(Connection, Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.STRING
 
getDataAsArray(Connection, Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.STRING2
 
getDatabaseTime() - Method in interface ome.api.IConfig
checks the database for it's time using a SELECT statement.
getDatabaseTime() - Method in class ome.logic.ConfigImpl
getDatabaseTime_async(AMD_IConfig_getDatabaseTime, Current) - Method in class ome.services.blitz.impl.ConfigI
 
getDatabaseUuid() - Method in interface ome.api.IConfig
Provides the UUID for this OMERO (database) instance.
getDatabaseUuid() - Method in class ome.logic.ConfigImpl
 
getDatabaseUuid_async(AMD_IConfig_getDatabaseUuid, Current) - Method in class ome.services.blitz.impl.ConfigI
 
getDatabaseVersion() - Method in interface ome.api.local.LocalConfig
Retrieves the newest database patch.
getDatabaseVersion() - Method in class ome.logic.ConfigImpl
 
getDataBuffer() - Method in class omeis.providers.re.RGBAIntBuffer
Retrieves the data buffer that contains the pixel values.
getDataBuffer() - Method in class omeis.providers.re.RGBIntBuffer
Retrieves the data buffer that contains the pixel values.
getDataFromArray(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.BOOLEAN
 
getDataFromArray(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.DATE
 
getDataFromArray(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.DOUBLE
 
getDataFromArray(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.ENUM
 
getDataFromArray(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.FLOAT
 
getDataFromArray(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
 
getDataFromArray(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.INTEGER
 
getDataFromArray(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.STRING
 
getDataFromArray(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.STRING2
 
getDataObjects() - Method in class pojos.TagAnnotationData
Returns the collection of data objects related to this tag.
getDataset() - Method in class ome.formats.importer.util.TinyImportFixture
provides access to the created Dataset instance.
getDatasetLinks() - Method in class ome.model.containers.Project
returns datasetLinks .
getDatasetLinks() - Method in class ome.model.core.Image
returns datasetLinks .
getDatasetLinksCountPerOwner() - Method in class ome.model.containers.Project
If fetched, returns the count(*) of ome.model.containers.ProjectDatasetLink that a user has.
getDatasetLinksCountPerOwner() - Method in class ome.model.core.Image
If fetched, returns the count(*) of ome.model.containers.DatasetImageLink that a user has.
getDatasets(Project) - Method in class ome.formats.OMEROMetadataStoreClient
 
getDatasets() - Method in class pojos.ImageData
Returns the datasets containing this image.
getDatasets() - Method in class pojos.ProjectData
Returns the datasets contained in this project.
getDatasetsForProject(long) - Method in interface ome.api.IAnalysis
 
getDatasetsWithoutProjects() - Method in class ome.formats.OMEROMetadataStoreClient
 
getDataValue() - Method in class pojos.DoubleAnnotationData
Returns the value.
getDataValue() - Method in class pojos.LongAnnotationData
Returns the value.
getDate(Class) - Static method in class ome.system.Version
Parses the given class for its RevisionDate annotation.
getDebugLevel() - Method in class ome.formats.importer.ImportConfig
 
getDebugLevel() - Method in class ome.formats.importer.util.IniFileLoader
Returns the level of debugging which should be set on ImportConfig Any value lower than null will not call configureDebug.
getDecoration() - Method in class ome.model.roi.Label
Simple field ome.model.roi.Label.decoration (java.lang.String)
getDefaultBatchSize() - Method in class ome.formats.OMEROMetadataStoreClient
 
getDefaultBlockSize() - Method in class ome.formats.OMEROMetadataStoreClient
 
getDefaultBlockSize() - Method in class omero.client
Returns the user configured setting for "omero.block_size" or DEFAULTBLOCKSIZE if none is set.
getDefaultBody() - Method in class ome.services.mail.MailSender
 
getDefaultCondition() - Method in class ome.security.basic.AllGroupsSecurityFilter
 
getDefaultCondition() - Method in class ome.security.basic.OneGroupSecurityFilter
 
getDefaultCondition() - Method in interface ome.security.SecurityFilter
Return the string to be used as the condition.
getDefaultCondition() - Method in class ome.security.SecurityFilterHolder
 
getDefaultContext() - Method in class ome.system.ServiceFactory
used when no context name is provided to the constructor.
getDefaultContext() - Method in class ome.tools.spring.InternalServiceFactory
returns null to prevent the lookup of any context, but rather wait on injection as a ApplicationContextAware
getDefaultContext() - Method in class ome.tools.spring.ManagedServiceFactory
returns null to prevent the lookup of any context, but rather wait on injection as a ApplicationContextAware
getDefaultEventType() - Method in class ome.model.meta.Session
Simple field ome.model.meta.Session.defaultEventType (java.lang.String)
getDefaultGroup(long) - Method in interface ome.api.IAdmin
retrieve the default group for the given user id.
getDefaultGroup(long) - Method in class ome.logic.AdminImpl
 
getDefaultGroup() - Method in class pojos.ExperimenterData
Returns the default Group for this Experimenter
getDefaultGroup_async(AMD_IAdmin_getDefaultGroup, long, Current) - Method in class ome.services.blitz.impl.AdminI
 
getDefaultGroupLevel() - Method in class ome.formats.OMEROMetadataStoreClient
Deprecated.
getDefaultGroupName() - Method in class ome.formats.OMEROMetadataStoreClient
Retrieve the default group's name
getDefaultPixels() - Method in class pojos.ImageData
Returns the default set of pixels.
getDefaultSample() - Method in class ome.model.screen.Plate
Simple field ome.model.screen.Plate.defaultSample (java.lang.Integer)
getDefaultSample() - Method in class pojos.PlateData
Returns the currently selected field or 0.
getDefaultScriptDir() - Static method in class ome.services.scripts.ScriptRepoHelper
Directory which will be used as the root of this repository if no directory is passed to a constructor.
getDefaultT() - Method in class ome.model.display.RenderingDef
Simple field ome.model.display.RenderingDef.defaultT (java.lang.Integer)
getDefaultT() - Method in class ome.services.RenderingBean
Implemented as specified by the RenderingEngine interface.
getDefaultT() - Method in interface omeis.providers.re.RenderingEngine
Returns the default timepoint index.
getDefaultT_async(AMD_RenderingEngine_getDefaultT, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
getDefaultZ() - Method in class ome.model.display.RenderingDef
Simple field ome.model.display.RenderingDef.defaultZ (java.lang.Integer)
getDefaultZ() - Method in class ome.services.RenderingBean
Implemented as specified by the RenderingEngine interface.
getDefaultZ() - Method in interface omeis.providers.re.RenderingEngine
Returns the index of the default focal section.
getDefaultZ_async(AMD_RenderingEngine_getDefaultZ, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
getDeletedIds(String) - Method in class ome.util.actions.PostgresSqlAction
 
getDeletedIds(String) - Method in interface ome.util.SqlAction
 
getDeleteService() - Method in class ome.system.ServiceFactory
 
getDeletion() - Method in class omero.cmd.graphs.DeleteI
Deprecated.
 
getDeltaT() - Method in class ome.model.core.PlaneInfo
Enum-mapped unit-based field ome.model.core.PlaneInfo.deltaT (ome.model.units.Time)
getDescription() - Method in class ome.model.annotations.Annotation
Simple field ome.model.annotations.Annotation.description (java.lang.String)
getDescription() - Method in class ome.model.containers.Dataset
Simple field ome.model.containers.Dataset.description (java.lang.String)
getDescription() - Method in class ome.model.containers.Project
Simple field ome.model.containers.Project.description (java.lang.String)
getDescription() - Method in class ome.model.core.Image
Simple field ome.model.core.Image.description (java.lang.String)
getDescription() - Method in class ome.model.experiment.Experiment
Simple field ome.model.experiment.Experiment.description (java.lang.String)
getDescription() - Method in class ome.model.experiment.MicrobeamManipulation
Simple field ome.model.experiment.MicrobeamManipulation.description (java.lang.String)
getDescription() - Method in class ome.model.jobs.ScriptJob
Simple field ome.model.jobs.ScriptJob.description (java.lang.String)
getDescription() - Method in class ome.model.meta.ExperimenterGroup
Simple field ome.model.meta.ExperimenterGroup.description (java.lang.String)
getDescription() - Method in class ome.model.meta.Namespace
Simple field ome.model.meta.Namespace.description (java.lang.String)
getDescription() - Method in class ome.model.roi.Roi
Simple field ome.model.roi.Roi.description (java.lang.String)
getDescription() - Method in class ome.model.screen.Plate
Simple field ome.model.screen.Plate.description (java.lang.String)
getDescription() - Method in class ome.model.screen.PlateAcquisition
Simple field ome.model.screen.PlateAcquisition.description (java.lang.String)
getDescription() - Method in class ome.model.screen.Reagent
Simple field ome.model.screen.Reagent.description (java.lang.String)
getDescription() - Method in class ome.model.screen.Screen
Simple field ome.model.screen.Screen.description (java.lang.String)
getDescription(Current) - Method in class ome.services.blitz.repo.AbstractRepositoryI
 
getDescription(long) - Method in class ome.services.blitz.repo.AbstractRepositoryI
 
getDescription() - Method in class pojos.AnnotationData
Retrieves the description of the underlying Annotation instance.
getDescription() - Method in class pojos.DatasetData
Returns the description of the dataset.
getDescription() - Method in class pojos.FileAnnotationData
Returns the description of the annotation.
getDescription() - Method in class pojos.FileData
Returns the description of the file.
getDescription() - Method in class pojos.GroupData
Returns the description of the group.
getDescription() - Method in class pojos.ImageData
Returns the description of the image.
getDescription() - Method in class pojos.PlateAcquisitionData
Returns the description of the plate acquisition.
getDescription() - Method in class pojos.PlateData
Returns the description of the plate.
getDescription() - Method in class pojos.ProjectData
Returns the description of the project.
getDescription() - Method in class pojos.ScreenData
Returns the description of the screen.
getDescription() - Method in class pojos.XMLAnnotationData
Returns the description of the annotation.
getDetails() - Method in class ome.model.acquisition.Detector
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.acquisition.DetectorSettings
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.acquisition.Dichroic
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.acquisition.Filter
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.acquisition.FilterSet
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.acquisition.FilterSetEmissionFilterLink
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.acquisition.FilterSetExcitationFilterLink
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.acquisition.ImagingEnvironment
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.acquisition.Instrument
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.acquisition.LightPath
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.acquisition.LightPathEmissionFilterLink
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.acquisition.LightPathExcitationFilterLink
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.acquisition.LightSettings
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.acquisition.LightSource
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.acquisition.Microscope
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.acquisition.Objective
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.acquisition.ObjectiveSettings
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.acquisition.OTF
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.acquisition.StageLabel
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.acquisition.TransmittanceRange
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.annotations.Annotation
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.annotations.AnnotationAnnotationLink
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.annotations.ChannelAnnotationLink
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.annotations.DatasetAnnotationLink
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.annotations.DetectorAnnotationLink
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.annotations.DichroicAnnotationLink
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.annotations.ExperimenterAnnotationLink
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.annotations.ExperimenterGroupAnnotationLink
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.annotations.FilesetAnnotationLink
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.annotations.FilterAnnotationLink
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.annotations.ImageAnnotationLink
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.annotations.InstrumentAnnotationLink
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.annotations.LightPathAnnotationLink
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.annotations.LightSourceAnnotationLink
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.annotations.NamespaceAnnotationLink
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.annotations.NodeAnnotationLink
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.annotations.ObjectiveAnnotationLink
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.annotations.OriginalFileAnnotationLink
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.annotations.PlaneInfoAnnotationLink
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.annotations.PlateAcquisitionAnnotationLink
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.annotations.PlateAnnotationLink
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.annotations.ProjectAnnotationLink
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.annotations.ReagentAnnotationLink
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.annotations.RoiAnnotationLink
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.annotations.ScreenAnnotationLink
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.annotations.SessionAnnotationLink
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.annotations.ShapeAnnotationLink
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.annotations.WellAnnotationLink
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.containers.Dataset
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.containers.DatasetImageLink
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.containers.Project
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.containers.ProjectDatasetLink
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.core.Channel
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.core.Image
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.core.LogicalChannel
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.core.OriginalFile
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.core.Pixels
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.core.PixelsOriginalFileMap
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.core.PlaneInfo
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.display.ChannelBinding
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.display.CodomainMapContext
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.display.QuantumDef
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.display.RenderingDef
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.display.Thumbnail
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.enums.AcquisitionMode
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.enums.ArcType
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.enums.Binning
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.enums.ChecksumAlgorithm
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.enums.ContrastMethod
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.enums.Correction
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.enums.DetectorType
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.enums.DimensionOrder
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.enums.EventType
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.enums.ExperimentType
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.enums.Family
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.enums.FilamentType
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.enums.FilterType
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.enums.Format
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.enums.Illumination
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.enums.Immersion
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.enums.LaserMedium
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.enums.LaserType
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.enums.Medium
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.enums.MicrobeamManipulationType
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.enums.MicroscopeType
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.enums.PhotometricInterpretation
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.enums.PixelsType
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.enums.Pulse
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.enums.RenderingModel
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.experiment.Experiment
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.experiment.MicrobeamManipulation
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.fs.Fileset
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.fs.FilesetEntry
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.fs.FilesetJobLink
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.internal.Link
The details of this object correspond to low-level system information.
getDetails() - Method in interface ome.model.IObject
Value (i.e. not entity) which is available on all rows in the database.
getDetails() - Method in class ome.model.jobs.Job
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.jobs.JobOriginalFileLink
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.jobs.JobStatus
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.meta.DBPatch
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.meta.Event
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.meta.EventLog
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.meta.Experimenter
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.meta.ExperimenterGroup
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.meta.ExternalInfo
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.meta.GroupExperimenterMap
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.meta.Namespace
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.meta.Node
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.meta.Session
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.meta.ShareMember
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.roi.Roi
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.roi.Shape
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.screen.Plate
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.screen.PlateAcquisition
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.screen.Reagent
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.screen.Screen
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.screen.ScreenPlateLink
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.screen.Well
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.screen.WellReagentLink
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.screen.WellSample
The details of this object correspond to low-level system information.
getDetails() - Method in class ome.model.stats.StatsInfo
The details of this object correspond to low-level system information.
getDetails(Object[], String[]) - Static method in class ome.tools.hibernate.HibernateUtils
 
getDetails() - Method in class pojos.DataObject
Returns the details of the object.
getDetector(int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
getDetector() - Method in class ome.model.acquisition.DetectorSettings
Many-to-one field ome.model.acquisition.DetectorSettings.detector (ome.model.acquisition.Detector)
getDetector() - Method in class ome.model.acquisition.Instrument
returns detector .
getDetector() - Method in class pojos.ChannelAcquisitionData
Returns the detector used for that channel.
getDetectorBinningAsEnum() - Method in class pojos.ChannelAcquisitionData
Returns the binning enumeration value.
getDetectors() - Method in class pojos.InstrumentData
Returns the collection of detectors.
getDetectorSettings() - Method in class ome.model.core.LogicalChannel
Many-to-one field ome.model.core.LogicalChannel.detectorSettings (ome.model.acquisition.DetectorSettings)
getDetectorSettingsBinning() - Method in class pojos.ChannelAcquisitionData
Returns the Binning factor.
getDetectorSettingsGain() - Method in class pojos.ChannelAcquisitionData
Returns the gain set on the detector.
getDetectorSettingsOffset() - Method in class pojos.ChannelAcquisitionData
Returns the offset set on the detector.
getDetectorSettingsReadOutRate(UnitsFrequency) - Method in class pojos.ChannelAcquisitionData
Returns the Read out rate set on the detector.
getDetectorSettingsReadOutRate() - Method in class pojos.ChannelAcquisitionData
getDetectorSettingsVoltage(UnitsElectricPotential) - Method in class pojos.ChannelAcquisitionData
Returns the voltage set on the detector.
getDetectorSettingsVoltage() - Method in class pojos.ChannelAcquisitionData
getDichroic() - Method in class ome.model.acquisition.FilterSet
Many-to-one field ome.model.acquisition.FilterSet.dichroic (ome.model.acquisition.Dichroic)
getDichroic() - Method in class ome.model.acquisition.Instrument
returns dichroic .
getDichroic() - Method in class ome.model.acquisition.LightPath
Many-to-one field ome.model.acquisition.LightPath.dichroic (ome.model.acquisition.Dichroic)
getDichroic() - Method in class pojos.FilterSetData
Returns the dichroic if any.
getDichroic() - Method in class pojos.LightPathData
Returns the dichroic if any.
getDichroics() - Method in class pojos.InstrumentData
Returns the collection of dichroics.
getDimensionOrder() - Method in class ome.model.core.Pixels
Many-to-one field ome.model.core.Pixels.dimensionOrder (ome.model.enums.DimensionOrder)
getDir() - Method in class ome.services.blitz.repo.FileMaker
 
getDirection() - Method in class ome.model.roi.Label
Simple field ome.model.roi.Label.direction (java.lang.String)
getDirectProxy() - Method in class ome.services.blitz.fire.Ring
Returns the proxy information for the local SessionManager.
getDirectProxy() - Method in interface ome.services.blitz.redirect.Redirector.Context
String representation of the proxy to the local node which may be contacted to create new sessions.
getDirectProxy() - Method in class ome.services.blitz.util.BlitzConfiguration
Return a direct proxy to the session manager in this object adapter.
getDirname() - Method in class ome.services.blitz.repo.CheckedPath
Assuming this is a directory, return relative path plus name with a final slash.
getDisabledSubsystems() - Method in class ome.security.basic.BasicEventContext
 
getDisplay() - Method in class ome.model.meta.Namespace
Simple field ome.model.meta.Namespace.display (java.lang.Boolean)
getDisplayName() - Method in class ome.model.meta.Namespace
Simple field ome.model.meta.Namespace.displayName (java.lang.String)
getDn(T) - Method in class ome.security.auth.OmeroModelContextMapper
 
getDnById(Long) - Method in class ome.security.auth.PasswordUtil
 
getDoThumbnails() - Method in class ome.formats.importer.ImportContainer
Retrieves whether or not we are performing thumbnail creation upon import completion.
getDoubleAnnotationCount() - Method in class ome.services.blitz.impl.OmeroMetadata
 
getDoubleAnnotationDescription(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getDoubleAnnotationID(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getDoubleAnnotationNamespace(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getDoubleAnnotationValue(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getDoubleValue() - Method in class ome.model.annotations.DoubleAnnotation
Simple field ome.model.annotations.DoubleAnnotation.doubleValue (java.lang.Double)
getDown() - Method in class ome.model.meta.Node
Simple field ome.model.meta.Node.down (java.sql.Timestamp)
getEffectiveUID() - Method in class ome.security.basic.BasicSecuritySystem
Returns the Id of the currently logged in user.
getEffectiveUID() - Method in interface ome.security.SecuritySystem
Returns UID based on whether a share is active, etc.
getEffectiveUID() - Method in class ome.security.SecuritySystemHolder
 
getEffectiveUID() - Method in class ome.security.sharing.SharingSecuritySystem
 
getEmail() - Method in class ome.formats.importer.util.ErrorContainer
 
getEmail() - Method in class ome.model.meta.Experimenter
Simple field ome.model.meta.Experimenter.email (java.lang.String)
getEmail() - Method in class pojos.ExperimenterData
Returns the e-mail of the experimenter.
getEmissionFilterLink() - Method in class ome.model.acquisition.Filter
returns emissionFilterLink .
getEmissionFilterLink() - Method in class ome.model.acquisition.FilterSet
returns emissionFilterLink .
getEmissionFilterLink() - Method in class ome.model.acquisition.LightPath
returns emissionFilterLink .
getEmissionFilterLinkCountPerOwner() - Method in class ome.model.acquisition.Filter
If fetched, returns the count(*) of ome.model.acquisition.FilterSetEmissionFilterLink that a user has.
getEmissionFilterLinkCountPerOwner() - Method in class ome.model.acquisition.FilterSet
If fetched, returns the count(*) of ome.model.acquisition.FilterSetEmissionFilterLink that a user has.
getEmissionFilterLinkCountPerOwner() - Method in class ome.model.acquisition.LightPath
If fetched, returns the count(*) of ome.model.acquisition.LightPathEmissionFilterLink that a user has.
getEmissionFilters() - Method in class pojos.FilterSetData
Returns the collections of emission filters if any.
getEmissionFilters() - Method in class pojos.LightPathData
Returns the collections of emission filters if any.
getEmissionWave() - Method in class ome.model.core.LogicalChannel
Enum-mapped unit-based field ome.model.core.LogicalChannel.emissionWave (ome.model.units.Length)
getEmissionWavelength(UnitsLength) - Method in class pojos.ChannelData
Returns the emission wavelength of the channel.
getEmissionWavelength() - Method in class pojos.ChannelData
getEndTime() - Method in class ome.model.screen.PlateAcquisition
Simple field ome.model.screen.PlateAcquisition.endTime (java.sql.Timestamp)
getEndTime() - Method in class ome.parameters.Parameters
 
getEndTime() - Method in class omero.sys.ParametersI
Returns the value of the end time parameter.
getEndTime() - Method in class pojos.PlateAcquisitionData
Returns the time when the last image was collected.
getEntity(String, Serializable) - Method in class ome.security.basic.OmeroInterceptor
 
getEntityDeleteCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
getEntityFetchCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
getEntityId() - Method in class ome.model.meta.EventLog
Simple field ome.model.meta.EventLog.entityId (java.lang.Long)
getEntityId() - Method in class ome.model.meta.ExternalInfo
Simple field ome.model.meta.ExternalInfo.entityId (java.lang.Long)
getEntityInsertCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
getEntityLoadCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
getEntityName(Object) - Method in class ome.security.basic.OmeroInterceptor
 
getEntityNames() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
Get the names of all entities
getEntityStatistics(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
find entity statistics per name
getEntityType() - Method in class ome.model.meta.EventLog
Simple field ome.model.meta.EventLog.entityType (java.lang.String)
getEntityType() - Method in class ome.model.meta.ExternalInfo
Simple field ome.model.meta.ExternalInfo.entityType (java.lang.String)
getEntityUpdateCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
getEnumeration(Class<T>, String) - Method in interface ome.api.IPixels
Retrieves a particular enumeration for a given enumeration class.
getEnumeration(Class<T>, String) - Method in interface ome.api.ITypes
lookup an enumeration value.
getEnumeration(Class<T>, String, boolean) - Method in interface ome.formats.enums.EnumerationProvider
Retrieves an enumeration.
getEnumeration(Class<T>, String, boolean) - Method in class ome.formats.enums.IQueryEnumProvider
 
getEnumeration(Class<T>, String) - Method in class ome.logic.PixelsImpl
 
getEnumeration(Class<T>, String) - Method in class ome.logic.TypesImpl
 
getEnumeration_async(AMD_IPixels_getEnumeration, String, String, Current) - Method in class ome.services.blitz.impl.PixelsI
 
getEnumeration_async(AMD_ITypes_getEnumeration, String, String, Current) - Method in class ome.services.blitz.impl.TypesI
 
getEnumerationProvider() - Method in class ome.formats.OMEROMetadataStoreClient
Retrieves the active enumeration provider.
getEnumerations(Class<T>) - Method in interface ome.formats.enums.EnumerationProvider
Retrieves all enumerations of a specific type.
getEnumerations(Class<T>) - Method in class ome.formats.enums.IQueryEnumProvider
 
getEnumerationsWithEntries() - Method in interface ome.api.ITypes
Gets all metadata classes which are IEnum type with contained objects.
getEnumerationsWithEntries() - Method in class ome.logic.TypesImpl
 
getEnumerationsWithEntries_async(AMD_ITypes_getEnumerationsWithEntries, Current) - Method in class ome.services.blitz.impl.TypesI
 
getEnumerationTypes() - Method in interface ome.api.ITypes
Gets all metadata classes which are IEnum type.
getEnumerationTypes() - Method in class ome.logic.TypesImpl
 
getEnumerationTypes_async(AMD_ITypes_getEnumerationTypes, Current) - Method in class ome.services.blitz.impl.TypesI
 
getError() - Method in class ome.formats.importer.util.ErrorContainer
 
getError() - Method in class ome.services.delete.Deletion
Deprecated.
 
getEvent() - Method in class ome.model.meta.EventLog
Many-to-one field ome.model.meta.EventLog.event (ome.model.meta.Event)
getEvent() - Method in class ome.security.basic.BasicEventContext
 
getEvent() - Method in class ome.security.basic.CurrentDetails
 
getEvent(Current) - Method in class ome.services.blitz.fire.SessionManagerI
 
getEvent() - Method in class ome.system.Login
simple getter for the event type passed into the constructor
getEventContext() - Method in interface ome.api.IAdmin
returns an implementation of EventContext loaded with the security for the current user and thread.
getEventContext() - Method in class ome.logic.AdminImpl
 
getEventContext(boolean) - Method in class ome.security.basic.BasicSecuritySystem
 
getEventContext() - Method in class ome.security.basic.BasicSecuritySystem
 
getEventContext() - Method in interface ome.security.SecuritySystem
Calls SecuritySystem.getEventContext(boolean) with a false as "refresh".
getEventContext(boolean) - Method in interface ome.security.SecuritySystem
If refresh is false, returns the current EventContext stored in the session.
getEventContext() - Method in class ome.security.SecuritySystemHolder
 
getEventContext(boolean) - Method in class ome.security.SecuritySystemHolder
 
getEventContext() - Method in class ome.security.sharing.SharingSecuritySystem
 
getEventContext(boolean) - Method in class ome.security.sharing.SharingSecuritySystem
 
getEventContext() - Method in class ome.services.blitz.impl.ServiceFactoryI
Doesn't take current into account
getEventContext(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
Takes current into account
getEventContext(Current) - Method in interface ome.services.blitz.repo.RepositoryDao
Look up information for the current session as specified in the ctx field of the current.
getEventContext(Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
 
getEventContext(Principal) - Method in interface ome.services.sessions.SessionManager
Provides a partial EventContext for the current Session.
getEventContext(Principal) - Method in class ome.services.sessions.SessionManagerImpl
 
getEventContext() - Method in class omero.cmd.Helper
Provides an EventContext instance without reloading the session, via LocalAdmin.getEventContextQuiet().
getEventContext() - Method in class omero.model.DetailsI
 
getEventContext_async(AMD_IAdmin_getEventContext, Current) - Method in class ome.services.blitz.impl.AdminI
 
getEventContextQuiet() - Method in interface ome.api.local.LocalAdmin
Like IAdmin.getEventContext() but will not reload the context.
getEventContextQuiet() - Method in class ome.logic.AdminImpl
 
getEventLogPartitions(Collection<String>, Collection<String>, long, long) - Method in interface ome.util.SqlAction
Loads up to "limit" event logs using partioning so that only the last event log of a particular (type, id) pair is returned.
getEventLogPartitions(Collection<String>, Collection<String>, long, long) - Method in class ome.util.SqlAction.Impl
 
getEventLogPercent(String) - Method in interface ome.util.SqlAction
Returns the percent (e.g. 0-100%) as calculated by the number of rows represented as completed by the configuration table row of this key divided by the total number of rows in the event log.
getEventLogPercent(String) - Method in class ome.util.SqlAction.Impl
 
getEventLogsByPeriod_async(AMD_ITimeline_getEventLogsByPeriod, RTime, RTime, Parameters, Current) - Method in class ome.services.blitz.impl.TimelineI
 
getEvents(long, Experimenter, Timestamp, Timestamp) - Method in interface ome.api.IShare
Gets events for share per experimenter for period of time.
getEvents() - Method in class ome.model.meta.Session
returns events .
getEvents(long, Experimenter, Timestamp, Timestamp) - Method in class ome.services.sharing.ShareBean
 
getEvents_async(AMD_IShare_getEvents, long, Experimenter, RTime, RTime, Current) - Method in class ome.services.blitz.impl.ShareI
 
getEventType() - Method in class ome.system.Principal
 
getException() - Method in exception ome.util.messages.MessageException
Get the exception which this instance wraps.
getExceptionThrown() - Method in class ome.system.UpgradeCheck
 
getExcitationFilterLink() - Method in class ome.model.acquisition.Filter
returns excitationFilterLink .
getExcitationFilterLink() - Method in class ome.model.acquisition.FilterSet
returns excitationFilterLink .
getExcitationFilterLink() - Method in class ome.model.acquisition.LightPath
returns excitationFilterLink .
getExcitationFilterLinkCountPerOwner() - Method in class ome.model.acquisition.Filter
If fetched, returns the count(*) of ome.model.acquisition.FilterSetExcitationFilterLink that a user has.
getExcitationFilterLinkCountPerOwner() - Method in class ome.model.acquisition.FilterSet
If fetched, returns the count(*) of ome.model.acquisition.FilterSetExcitationFilterLink that a user has.
getExcitationFilterLinkCountPerOwner() - Method in class ome.model.acquisition.LightPath
If fetched, returns the count(*) of ome.model.acquisition.LightPathExcitationFilterLink that a user has.
getExcitationFilters() - Method in class pojos.FilterSetData
Returns the collections of excitation filters if any.
getExcitationFilters() - Method in class pojos.LightPathData
Returns the collections of excitation filters if any.
getExcitationWave() - Method in class ome.model.core.LogicalChannel
Enum-mapped unit-based field ome.model.core.LogicalChannel.excitationWave (ome.model.units.Length)
getExcitationWavelength(UnitsLength) - Method in class pojos.ChannelData
Returns the excitation wavelength of the channel.
getExcitationWavelength() - Method in class pojos.ChannelData
getExclude(int) - Method in class ome.services.graphs.AnnotationGraphSpec
Deprecated.
Returns the value from "...
getExecutor() - Method in class ome.services.mail.MailSender
 
getExecutor() - Method in class ome.services.scheduler.ThreadPool
 
getExecutor() - Method in class omero.cmd.SessionI
 
getExperiment() - Method in class ome.model.core.Image
Many-to-one field ome.model.core.Image.experiment (ome.model.experiment.Experiment)
getExperiment() - Method in class ome.model.experiment.MicrobeamManipulation
Many-to-one field ome.model.experiment.MicrobeamManipulation.experiment (ome.model.experiment.Experiment)
getExperimenter(long) - Method in interface ome.api.IAdmin
fetch an Experimenter and all related groups.
getExperimenter(long) - Method in class ome.logic.AdminImpl
 
getExperimenter() - Method in class ome.model.meta.Event
Many-to-one field ome.model.meta.Event.experimenter (ome.model.meta.Experimenter)
getExperimenter() - Method in class ome.parameters.Parameters
Fulfills the old PojoOptions requirement for returning null if no owner set.
getExperimenter() - Method in class omero.sys.ParametersI
Returns the value of the experimenter parameter.
getExperimenter_async(AMD_IAdmin_getExperimenter, long, Current) - Method in class ome.services.blitz.impl.AdminI
 
getExperimenterGroup() - Method in class ome.model.meta.Event
Many-to-one field ome.model.meta.Event.experimenterGroup (ome.model.meta.ExperimenterGroup)
getExperimenterID() - Method in class ome.formats.OMEROMetadataStoreClient
 
getExperimenters() - Method in class pojos.GroupData
Returns the experimenters contained in this group.
getExposureTime() - Method in class ome.model.core.PlaneInfo
Enum-mapped unit-based field ome.model.core.PlaneInfo.exposureTime (ome.model.units.Time)
getExtendedMetadata() - Method in class ome.logic.AbstractLevel2Service
 
getExternalDescription() - Method in class ome.model.screen.Well
Simple field ome.model.screen.Well.externalDescription (java.lang.String)
getExternalDescription() - Method in class pojos.WellData
Returns the external description of the well.
getExternalIdentifier() - Method in class ome.model.screen.Plate
Simple field ome.model.screen.Plate.externalIdentifier (java.lang.String)
getExternalIdentifier() - Method in class ome.model.screen.Well
Simple field ome.model.screen.Well.externalIdentifier (java.lang.String)
getExternalIdentifier() - Method in class pojos.PlateData
Returns the external identifier of the plate.
getExternalInfo() - Method in class ome.model.acquisition.Detector.Details
 
getExternalInfo() - Method in class ome.model.acquisition.DetectorSettings.Details
 
getExternalInfo() - Method in class ome.model.acquisition.Dichroic.Details
 
getExternalInfo() - Method in class ome.model.acquisition.Filter.Details
 
getExternalInfo() - Method in class ome.model.acquisition.FilterSet.Details
 
getExternalInfo() - Method in class ome.model.acquisition.FilterSetEmissionFilterLink.Details
 
getExternalInfo() - Method in class ome.model.acquisition.FilterSetExcitationFilterLink.Details
 
getExternalInfo() - Method in class ome.model.acquisition.ImagingEnvironment.Details
 
getExternalInfo() - Method in class ome.model.acquisition.Instrument.Details
 
getExternalInfo() - Method in class ome.model.acquisition.LightPath.Details
 
getExternalInfo() - Method in class ome.model.acquisition.LightPathEmissionFilterLink.Details
 
getExternalInfo() - Method in class ome.model.acquisition.LightPathExcitationFilterLink.Details
 
getExternalInfo() - Method in class ome.model.acquisition.LightSettings.Details
 
getExternalInfo() - Method in class ome.model.acquisition.LightSource.Details
 
getExternalInfo() - Method in class ome.model.acquisition.Microscope.Details
 
getExternalInfo() - Method in class ome.model.acquisition.Objective.Details
 
getExternalInfo() - Method in class ome.model.acquisition.ObjectiveSettings.Details
 
getExternalInfo() - Method in class ome.model.acquisition.OTF.Details
 
getExternalInfo() - Method in class ome.model.acquisition.StageLabel.Details
 
getExternalInfo() - Method in class ome.model.acquisition.TransmittanceRange.Details
 
getExternalInfo() - Method in class ome.model.annotations.Annotation.Details
 
getExternalInfo() - Method in class ome.model.annotations.AnnotationAnnotationLink.Details
 
getExternalInfo() - Method in class ome.model.annotations.ChannelAnnotationLink.Details
 
getExternalInfo() - Method in class ome.model.annotations.DatasetAnnotationLink.Details
 
getExternalInfo() - Method in class ome.model.annotations.DetectorAnnotationLink.Details
 
getExternalInfo() - Method in class ome.model.annotations.DichroicAnnotationLink.Details
 
getExternalInfo() - Method in class ome.model.annotations.ExperimenterAnnotationLink.Details
 
getExternalInfo() - Method in class ome.model.annotations.ExperimenterGroupAnnotationLink.Details
 
getExternalInfo() - Method in class ome.model.annotations.FilesetAnnotationLink.Details
 
getExternalInfo() - Method in class ome.model.annotations.FilterAnnotationLink.Details
 
getExternalInfo() - Method in class ome.model.annotations.ImageAnnotationLink.Details
 
getExternalInfo() - Method in class ome.model.annotations.InstrumentAnnotationLink.Details
 
getExternalInfo() - Method in class ome.model.annotations.LightPathAnnotationLink.Details
 
getExternalInfo() - Method in class ome.model.annotations.LightSourceAnnotationLink.Details
 
getExternalInfo() - Method in class ome.model.annotations.NamespaceAnnotationLink.Details
 
getExternalInfo() - Method in class ome.model.annotations.NodeAnnotationLink.Details
 
getExternalInfo() - Method in class ome.model.annotations.ObjectiveAnnotationLink.Details
 
getExternalInfo() - Method in class ome.model.annotations.OriginalFileAnnotationLink.Details
 
getExternalInfo() - Method in class ome.model.annotations.PlaneInfoAnnotationLink.Details
 
getExternalInfo() - Method in class ome.model.annotations.PlateAcquisitionAnnotationLink.Details
 
getExternalInfo() - Method in class ome.model.annotations.PlateAnnotationLink.Details
 
getExternalInfo() - Method in class ome.model.annotations.ProjectAnnotationLink.Details
 
getExternalInfo() - Method in class ome.model.annotations.ReagentAnnotationLink.Details
 
getExternalInfo() - Method in class ome.model.annotations.RoiAnnotationLink.Details
 
getExternalInfo() - Method in class ome.model.annotations.ScreenAnnotationLink.Details
 
getExternalInfo() - Method in class ome.model.annotations.SessionAnnotationLink.Details
 
getExternalInfo() - Method in class ome.model.annotations.ShapeAnnotationLink.Details
 
getExternalInfo() - Method in class ome.model.annotations.WellAnnotationLink.Details
 
getExternalInfo() - Method in class ome.model.containers.Dataset.Details
 
getExternalInfo() - Method in class ome.model.containers.DatasetImageLink.Details
 
getExternalInfo() - Method in class ome.model.containers.Project.Details
 
getExternalInfo() - Method in class ome.model.containers.ProjectDatasetLink.Details
 
getExternalInfo() - Method in class ome.model.core.Channel.Details
 
getExternalInfo() - Method in class ome.model.core.Image.Details
 
getExternalInfo() - Method in class ome.model.core.LogicalChannel.Details
 
getExternalInfo() - Method in class ome.model.core.OriginalFile.Details
 
getExternalInfo() - Method in class ome.model.core.Pixels.Details
 
getExternalInfo() - Method in class ome.model.core.PixelsOriginalFileMap.Details
 
getExternalInfo() - Method in class ome.model.core.PlaneInfo.Details
 
getExternalInfo() - Method in class ome.model.display.ChannelBinding.Details
 
getExternalInfo() - Method in class ome.model.display.CodomainMapContext.Details
 
getExternalInfo() - Method in class ome.model.display.QuantumDef.Details
 
getExternalInfo() - Method in class ome.model.display.RenderingDef.Details
 
getExternalInfo() - Method in class ome.model.display.Thumbnail.Details
 
getExternalInfo() - Method in class ome.model.enums.AcquisitionMode.Details
 
getExternalInfo() - Method in class ome.model.enums.ArcType.Details
 
getExternalInfo() - Method in class ome.model.enums.Binning.Details
 
getExternalInfo() - Method in class ome.model.enums.ChecksumAlgorithm.Details
 
getExternalInfo() - Method in class ome.model.enums.ContrastMethod.Details
 
getExternalInfo() - Method in class ome.model.enums.Correction.Details
 
getExternalInfo() - Method in class ome.model.enums.DetectorType.Details
 
getExternalInfo() - Method in class ome.model.enums.DimensionOrder.Details
 
getExternalInfo() - Method in class ome.model.enums.EventType.Details
 
getExternalInfo() - Method in class ome.model.enums.ExperimentType.Details
 
getExternalInfo() - Method in class ome.model.enums.Family.Details
 
getExternalInfo() - Method in class ome.model.enums.FilamentType.Details
 
getExternalInfo() - Method in class ome.model.enums.FilterType.Details
 
getExternalInfo() - Method in class ome.model.enums.Format.Details
 
getExternalInfo() - Method in class ome.model.enums.Illumination.Details
 
getExternalInfo() - Method in class ome.model.enums.Immersion.Details
 
getExternalInfo() - Method in class ome.model.enums.LaserMedium.Details
 
getExternalInfo() - Method in class ome.model.enums.LaserType.Details
 
getExternalInfo() - Method in class ome.model.enums.Medium.Details
 
getExternalInfo() - Method in class ome.model.enums.MicrobeamManipulationType.Details
 
getExternalInfo() - Method in class ome.model.enums.MicroscopeType.Details
 
getExternalInfo() - Method in class ome.model.enums.PhotometricInterpretation.Details
 
getExternalInfo() - Method in class ome.model.enums.PixelsType.Details
 
getExternalInfo() - Method in class ome.model.enums.Pulse.Details
 
getExternalInfo() - Method in class ome.model.enums.RenderingModel.Details
 
getExternalInfo() - Method in class ome.model.experiment.Experiment.Details
 
getExternalInfo() - Method in class ome.model.experiment.MicrobeamManipulation.Details
 
getExternalInfo() - Method in class ome.model.fs.Fileset.Details
 
getExternalInfo() - Method in class ome.model.fs.FilesetEntry.Details
 
getExternalInfo() - Method in class ome.model.fs.FilesetJobLink.Details
 
getExternalInfo() - Method in class ome.model.internal.Details
 
getExternalInfo() - Method in class ome.model.internal.Link.Details
 
getExternalInfo() - Method in class ome.model.jobs.Job.Details
 
getExternalInfo() - Method in class ome.model.jobs.JobOriginalFileLink.Details
 
getExternalInfo() - Method in class ome.model.jobs.JobStatus.Details
 
getExternalInfo() - Method in class ome.model.meta.DBPatch.Details
 
getExternalInfo() - Method in class ome.model.meta.Event.Details
 
getExternalInfo() - Method in class ome.model.meta.EventLog.Details
 
getExternalInfo() - Method in class ome.model.meta.Experimenter.Details
 
getExternalInfo() - Method in class ome.model.meta.ExperimenterGroup.Details
 
getExternalInfo() - Method in class ome.model.meta.ExternalInfo.Details
 
getExternalInfo() - Method in class ome.model.meta.GroupExperimenterMap.Details
 
getExternalInfo() - Method in class ome.model.meta.Namespace.Details
 
getExternalInfo() - Method in class ome.model.meta.Node.Details
 
getExternalInfo() - Method in class ome.model.meta.Session.Details
 
getExternalInfo() - Method in class ome.model.meta.ShareMember.Details
 
getExternalInfo() - Method in class ome.model.roi.Roi.Details
 
getExternalInfo() - Method in class ome.model.roi.Shape.Details
 
getExternalInfo() - Method in class ome.model.screen.Plate.Details
 
getExternalInfo() - Method in class ome.model.screen.PlateAcquisition.Details
 
getExternalInfo() - Method in class ome.model.screen.Reagent.Details
 
getExternalInfo() - Method in class ome.model.screen.Screen.Details
 
getExternalInfo() - Method in class ome.model.screen.ScreenPlateLink.Details
 
getExternalInfo() - Method in class ome.model.screen.Well.Details
 
getExternalInfo() - Method in class ome.model.screen.WellReagentLink.Details
 
getExternalInfo() - Method in class ome.model.screen.WellSample.Details
 
getExternalInfo() - Method in class ome.model.stats.StatsInfo.Details
 
getExternalInfo(Current) - Method in class omero.model.DetailsI
 
getExtra() - Method in class ome.formats.importer.util.ErrorContainer
 
getFactory(String, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
 
getFailedFiles() - Method in exception ome.formats.importer.transfers.CleanupFailure
 
getFailedFilesCount() - Method in class ome.services.delete.files.FileDeleter
 
getFailureClass() - Method in exception ome.formats.enums.EnumerationException
 
getFailureClass() - Method in exception ome.formats.model.ModelException
Returns the class that was used during a failed instantiation.
getFamily() - Method in class ome.model.display.ChannelBinding
Many-to-one field ome.model.display.ChannelBinding.family (ome.model.enums.Family)
getFamily(String) - Method in class omeis.providers.re.quantum.QuantumFactory
Helper method to retrieve a Family enumeration from the database.
getFamily() - Method in class omeis.providers.re.quantum.QuantumStrategy
Returns the mapping family.
getFeedbackUrl() - Method in class ome.formats.importer.ImportConfig
 
getFilament(int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
getFile() - Method in class ome.formats.importer.ImportContainer
 
getFile() - Method in class ome.formats.importer.transfers.TransferState
Return the target file passed to the constructor.
getFile() - Method in class ome.model.annotations.FileAnnotation
Many-to-one field ome.model.annotations.FileAnnotation.file (ome.model.core.OriginalFile)
getFile(long, Current, String) - Method in interface ome.services.blitz.repo.RepositoryDao
Get an FsFile object based on its ID.
getFile(long, Current, String) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
 
getFile(ServiceFactory) - Method in class ome.services.scripts.ScriptFinder
 
getFileBuffer(OriginalFile, String) - Method in class ome.io.nio.OriginalFilesService
Returns FileBuffer based on OriginalFile path
getFileBuffer(String) - Method in class ome.services.blitz.repo.CheckedPath
Get a FileBuffer corresponding to this instance.
getFileFilter() - Method in class ome.services.scripts.ScriptFileType
A file-pattern (most likely of the form "*.EXT") which will be used to determine if a file is of this type.
getFileFormat() - Method in class ome.formats.importer.util.ErrorContainer
get the file format for import
getFileFormat() - Method in class pojos.FileAnnotationData
Returns the format of the uploaded file.
getFileId() - Method in interface ome.api.RawFileStore
Returns the current file id or null if none has been set.
getFileId() - Method in class ome.services.messages.DeleteLogMessage
 
getFileId() - Method in class ome.services.RawFileBean
 
getFileID() - Method in class pojos.FileAnnotationData
Returns the id of the file.
getFileId_async(AMD_RawFileStore_getFileId, Current) - Method in class ome.services.blitz.impl.RawFileStoreI
 
getFileIds() - Method in class ome.tools.RepositoryTask
This public method is used to return a list of file ids that require deletion from the disk repository.
getFileKind() - Method in class pojos.FileAnnotationData
Returns a user readable description of the file.
getFileName() - Method in class pojos.FileAnnotationData
Returns the name of the file.
getFilePath(OriginalFile, Current) - Method in class ome.services.blitz.repo.AbstractRepositoryI
 
getFilePath(OriginalFile, Current) - Method in class ome.services.blitz.repo.InternalRepositoryI
 
getFilePath(OriginalFile, Current) - Method in class ome.services.blitz.repo.LegacyRepositoryI
 
getFilePath(OriginalFile, Current) - Method in class ome.services.blitz.repo.ScriptRepositoryI
 
getFilePath(OriginalFile, Current) - Method in class ome.services.blitz.repo.TemporaryRepositoryI
 
getFilePath() - Method in class pojos.FileAnnotationData
Returns the absolute path to the file.
getFilePathRestrictions(String...) - Static method in enum ome.services.blitz.repo.path.FilePathRestrictionInstance
Get a set of rules by which local files may not be named on the file-system, formed by combining the rules of the given names with rules against control characters.
getFilePathRestrictions(FilePathRestrictionInstance...) - Static method in enum ome.services.blitz.repo.path.FilePathRestrictionInstance
Get a set of rules by which local files may not be named on the file-system, formed by combining the given rules identifiers with rules against control characters.
getFileRepo(OriginalFile) - Method in class ome.services.blitz.repo.AbstractRepositoryI
 
getFiles() - Method in class ome.formats.importer.util.ErrorContainer
 
getFileset() - Method in class ome.model.core.Image
Many-to-one field ome.model.core.Image.fileset (ome.model.fs.Fileset)
getFileset() - Method in class ome.model.fs.FilesetEntry
Many-to-one field ome.model.fs.FilesetEntry.fileset (ome.model.fs.Fileset)
getFileset() - Method in class ome.services.blitz.repo.ManagedImportProcessI
 
getFileset() - Method in interface ome.services.blitz.repo.ProcessContainer.Process
 
getFilesetEntries() - Method in class ome.model.core.OriginalFile
returns filesetEntries .
getFilesetEntry(int) - Method in class ome.model.fs.Fileset
Gets the ome.model.fs.FilesetEntry at the given index.
getFilesetId() - Method in class ome.services.delete.DeleteStep
Deprecated.
 
getFilesetId() - Method in class pojos.ImageData
Returns the ID of the fileset to which this image belongs.
getFilesetJobLink(int) - Method in class ome.model.fs.Fileset
Gets the ome.model.fs.FilesetJobLink at the given index.
getFileSize() - Method in class pojos.FileAnnotationData
Returns the size of the file.
getFilesPath(Long) - Method in class ome.io.nio.AbstractFileSystemService
Returns a numbered path relative to the root of this service, but is ignorant of FS and similar constructs.
getFileType() - Method in class ome.formats.importer.util.ErrorContainer
 
getFill() - Method in class pojos.ShapeSettingsData
Returns the fill color.
getFillColor() - Method in class ome.model.roi.Shape
Simple field ome.model.roi.Shape.fillColor (java.lang.Integer)
getFillRule() - Method in class ome.model.roi.Shape
Simple field ome.model.roi.Shape.fillRule (java.lang.String)
getFillRule() - Method in class pojos.ShapeSettingsData
Returns the fill rule.
getFilter() - Method in class ome.model.acquisition.Instrument
returns filter .
getFilters() - Method in class pojos.InstrumentData
Returns the collection of filters.
getFilterSet() - Method in class ome.formats.model.ChannelData
Returns the filter set for the logical channel of this channel data.
getFilterSet(int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
getFilterSet() - Method in class ome.model.acquisition.Instrument
returns filterSet .
getFilterSet() - Method in class ome.model.acquisition.OTF
Many-to-one field ome.model.acquisition.OTF.filterSet (ome.model.acquisition.FilterSet)
getFilterSet() - Method in class ome.model.core.LogicalChannel
Many-to-one field ome.model.core.LogicalChannel.filterSet (ome.model.acquisition.FilterSet)
getFilterSet() - Method in class pojos.ChannelAcquisitionData
Returns the filter set or null.
getFilterSet() - Method in class pojos.OTFData
Returns the associated filter set.
getFilterSetEmissionFilter() - Method in class ome.formats.model.ChannelData
Returns the filter set's emission filter for the logical channel of this channel data.
getFilterSetExcitationFilter() - Method in class ome.formats.model.ChannelData
Returns the filter set's excitation filter for the logical channel of this channel data.
getFilterSets() - Method in class pojos.InstrumentData
Returns the collection of filter sets.
getFilterWheel() - Method in class ome.model.acquisition.Filter
Simple field ome.model.acquisition.Filter.filterWheel (java.lang.String)
getFilterWheel() - Method in class pojos.FilterData
Returns the wheel.
getFinished() - Method in class ome.model.jobs.Job
Simple field ome.model.jobs.Job.finished (java.sql.Timestamp)
getFinished() - Method in class ome.model.meta.DBPatch
Simple field ome.model.meta.DBPatch.finished (java.sql.Timestamp)
getFirst(String) - Method in class ome.security.auth.AttributeSet
 
getFirstName() - Method in class ome.model.meta.Experimenter
Simple field ome.model.meta.Experimenter.firstName (java.lang.String)
getFirstName() - Method in class pojos.ExperimenterData
Returns the first name of the experimenter.
getFluor() - Method in class ome.model.core.LogicalChannel
Simple field ome.model.core.LogicalChannel.fluor (java.lang.String)
getFluor() - Method in class pojos.ChannelData
Returns the Fluorophore used.
getFlushCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
getFont() - Method in class pojos.ShapeSettingsData
Get the style of the font for Shape.
getFontFamily() - Method in class ome.model.roi.Shape
Simple field ome.model.roi.Shape.fontFamily (java.lang.String)
getFontFamily() - Method in class pojos.ShapeSettingsData
Returns the stroke.
getFontSize() - Method in class ome.model.roi.Shape
Enum-mapped unit-based field ome.model.roi.Shape.fontSize (ome.model.units.Length)
getFontSize() - Method in class pojos.ShapeSettingsData
getFontSize(UnitsLength) - Method in class pojos.ShapeSettingsData
Returns the stroke.
getFontStretch() - Method in class ome.model.roi.Shape
Simple field ome.model.roi.Shape.fontStretch (java.lang.String)
getFontStyle() - Method in class ome.model.roi.Shape
Simple field ome.model.roi.Shape.fontStyle (java.lang.String)
getFontStyle() - Method in class pojos.ShapeSettingsData
Returns the font style.
getFontVariant() - Method in class ome.model.roi.Shape
Simple field ome.model.roi.Shape.fontVariant (java.lang.String)
getFontWeight() - Method in class ome.model.roi.Shape
Simple field ome.model.roi.Shape.fontWeight (java.lang.String)
getForceFileArchiveOn() - Method in class ome.formats.importer.ImportConfig
 
getForceFileArchiveOn() - Method in class ome.formats.importer.util.IniFileLoader
 
getFormat() - Method in class ome.model.core.Image
Many-to-one field ome.model.core.Image.format (ome.model.enums.Format)
getFormat() - Method in class pojos.ImageData
Returns the format of the image.
getForumUrl() - Method in class ome.formats.importer.ImportConfig
 
getForumUrl() - Method in class ome.formats.importer.util.IniFileLoader
 
getFreeSpaceInKilobytes() - Method in interface ome.api.IRepositoryInfo
This method returns the free or available space on this file system including nested subdirectories.
getFreeSpaceInKilobytes() - Method in class ome.logic.RepositoryInfoImpl
 
getFreeSpaceInKilobytes_async(AMD_IRepositoryInfo_getFreeSpaceInKilobytes, Current) - Method in class ome.services.blitz.impl.RepositoryInfoI
 
getFrequencyMultiplication() - Method in class ome.model.acquisition.Laser
Simple field ome.model.acquisition.Laser.frequencyMultiplication (java.lang.Integer)
getFsFileFromClientFile(File, int) - Method in class ome.services.blitz.repo.path.ClientFilePathTransformer
Given a client-local File, and a path component depth, returns the corresponding repository path.
getFsFileFromServerFile(File) - Method in class ome.services.blitz.repo.path.ServerFilePathTransformer
Given a server-local File, returns the corresponding repository path.
getFullFsPath() - Method in class ome.services.blitz.repo.CheckedPath
The full path of the entity to which this path corresponds.
getG() - Method in class ome.model.roi.Shape
Simple field ome.model.roi.Shape.g (java.lang.String)
getGain() - Method in class ome.model.acquisition.Detector
Simple field ome.model.acquisition.Detector.gain (java.lang.Double)
getGain() - Method in class ome.model.acquisition.DetectorSettings
Simple field ome.model.acquisition.DetectorSettings.gain (java.lang.Double)
getGain() - Method in class pojos.DetectorData
Returns the gain of the detector.
getGlobalMax() - Method in class ome.model.stats.StatsInfo
Simple field ome.model.stats.StatsInfo.globalMax (java.lang.Double)
getGlobalMax() - Method in class omeis.providers.re.quantum.QuantumStrategy
Returns the maximum of all maxima.
getGlobalMax() - Method in class pojos.ChannelData
Returns the global maximum of the channel i.e. the maximum of all maxima.
getGlobalMin() - Method in class ome.model.stats.StatsInfo
Simple field ome.model.stats.StatsInfo.globalMin (java.lang.Double)
getGlobalMin() - Method in class omeis.providers.re.quantum.QuantumStrategy
Returns the minimum of all minima.
getGlobalMin() - Method in class pojos.ChannelData
Returns the global minimum of the channel i.e. the minimum of all minima.
getGlyphOrientationVertical() - Method in class ome.model.roi.Label
Simple field ome.model.roi.Label.glyphOrientationVertical (java.lang.Integer)
getGraphHolder() - Method in class ome.model.acquisition.Detector
 
getGraphHolder() - Method in class ome.model.acquisition.DetectorSettings
 
getGraphHolder() - Method in class ome.model.acquisition.Dichroic
 
getGraphHolder() - Method in class ome.model.acquisition.Filter
 
getGraphHolder() - Method in class ome.model.acquisition.FilterSet
 
getGraphHolder() - Method in class ome.model.acquisition.FilterSetEmissionFilterLink
 
getGraphHolder() - Method in class ome.model.acquisition.FilterSetExcitationFilterLink
 
getGraphHolder() - Method in class ome.model.acquisition.ImagingEnvironment
 
getGraphHolder() - Method in class ome.model.acquisition.Instrument
 
getGraphHolder() - Method in class ome.model.acquisition.LightPath
 
getGraphHolder() - Method in class ome.model.acquisition.LightPathEmissionFilterLink
 
getGraphHolder() - Method in class ome.model.acquisition.LightPathExcitationFilterLink
 
getGraphHolder() - Method in class ome.model.acquisition.LightSettings
 
getGraphHolder() - Method in class ome.model.acquisition.LightSource
 
getGraphHolder() - Method in class ome.model.acquisition.Microscope
 
getGraphHolder() - Method in class ome.model.acquisition.Objective
 
getGraphHolder() - Method in class ome.model.acquisition.ObjectiveSettings
 
getGraphHolder() - Method in class ome.model.acquisition.OTF
 
getGraphHolder() - Method in class ome.model.acquisition.StageLabel
 
getGraphHolder() - Method in class ome.model.acquisition.TransmittanceRange
 
getGraphHolder() - Method in class ome.model.annotations.Annotation
 
getGraphHolder() - Method in class ome.model.annotations.AnnotationAnnotationLink
 
getGraphHolder() - Method in class ome.model.annotations.ChannelAnnotationLink
 
getGraphHolder() - Method in class ome.model.annotations.DatasetAnnotationLink
 
getGraphHolder() - Method in class ome.model.annotations.DetectorAnnotationLink
 
getGraphHolder() - Method in class ome.model.annotations.DichroicAnnotationLink
 
getGraphHolder() - Method in class ome.model.annotations.ExperimenterAnnotationLink
 
getGraphHolder() - Method in class ome.model.annotations.ExperimenterGroupAnnotationLink
 
getGraphHolder() - Method in class ome.model.annotations.FilesetAnnotationLink
 
getGraphHolder() - Method in class ome.model.annotations.FilterAnnotationLink
 
getGraphHolder() - Method in class ome.model.annotations.ImageAnnotationLink
 
getGraphHolder() - Method in class ome.model.annotations.InstrumentAnnotationLink
 
getGraphHolder() - Method in class ome.model.annotations.LightPathAnnotationLink
 
getGraphHolder() - Method in class ome.model.annotations.LightSourceAnnotationLink
 
getGraphHolder() - Method in class ome.model.annotations.NamespaceAnnotationLink
 
getGraphHolder() - Method in class ome.model.annotations.NodeAnnotationLink
 
getGraphHolder() - Method in class ome.model.annotations.ObjectiveAnnotationLink
 
getGraphHolder() - Method in class ome.model.annotations.OriginalFileAnnotationLink
 
getGraphHolder() - Method in class ome.model.annotations.PlaneInfoAnnotationLink
 
getGraphHolder() - Method in class ome.model.annotations.PlateAcquisitionAnnotationLink
 
getGraphHolder() - Method in class ome.model.annotations.PlateAnnotationLink
 
getGraphHolder() - Method in class ome.model.annotations.ProjectAnnotationLink
 
getGraphHolder() - Method in class ome.model.annotations.ReagentAnnotationLink
 
getGraphHolder() - Method in class ome.model.annotations.RoiAnnotationLink
 
getGraphHolder() - Method in class ome.model.annotations.ScreenAnnotationLink
 
getGraphHolder() - Method in class ome.model.annotations.SessionAnnotationLink
 
getGraphHolder() - Method in class ome.model.annotations.ShapeAnnotationLink
 
getGraphHolder() - Method in class ome.model.annotations.WellAnnotationLink
 
getGraphHolder() - Method in class ome.model.containers.Dataset
 
getGraphHolder() - Method in class ome.model.containers.DatasetImageLink
 
getGraphHolder() - Method in class ome.model.containers.Project
 
getGraphHolder() - Method in class ome.model.containers.ProjectDatasetLink
 
getGraphHolder() - Method in class ome.model.core.Channel
 
getGraphHolder() - Method in class ome.model.core.Image
 
getGraphHolder() - Method in class ome.model.core.LogicalChannel
 
getGraphHolder() - Method in class ome.model.core.OriginalFile
 
getGraphHolder() - Method in class ome.model.core.Pixels
 
getGraphHolder() - Method in class ome.model.core.PixelsOriginalFileMap
 
getGraphHolder() - Method in class ome.model.core.PlaneInfo
 
getGraphHolder() - Method in class ome.model.display.ChannelBinding
 
getGraphHolder() - Method in class ome.model.display.CodomainMapContext
 
getGraphHolder() - Method in class ome.model.display.QuantumDef
 
getGraphHolder() - Method in class ome.model.display.RenderingDef
 
getGraphHolder() - Method in class ome.model.display.Thumbnail
 
getGraphHolder() - Method in class ome.model.enums.AcquisitionMode
 
getGraphHolder() - Method in class ome.model.enums.ArcType
 
getGraphHolder() - Method in class ome.model.enums.Binning
 
getGraphHolder() - Method in class ome.model.enums.ChecksumAlgorithm
 
getGraphHolder() - Method in class ome.model.enums.ContrastMethod
 
getGraphHolder() - Method in class ome.model.enums.Correction
 
getGraphHolder() - Method in class ome.model.enums.DetectorType
 
getGraphHolder() - Method in class ome.model.enums.DimensionOrder
 
getGraphHolder() - Method in class ome.model.enums.EventType
 
getGraphHolder() - Method in class ome.model.enums.ExperimentType
 
getGraphHolder() - Method in class ome.model.enums.Family
 
getGraphHolder() - Method in class ome.model.enums.FilamentType
 
getGraphHolder() - Method in class ome.model.enums.FilterType
 
getGraphHolder() - Method in class ome.model.enums.Format
 
getGraphHolder() - Method in class ome.model.enums.Illumination
 
getGraphHolder() - Method in class ome.model.enums.Immersion
 
getGraphHolder() - Method in class ome.model.enums.LaserMedium
 
getGraphHolder() - Method in class ome.model.enums.LaserType
 
getGraphHolder() - Method in class ome.model.enums.Medium
 
getGraphHolder() - Method in class ome.model.enums.MicrobeamManipulationType
 
getGraphHolder() - Method in class ome.model.enums.MicroscopeType
 
getGraphHolder() - Method in class ome.model.enums.PhotometricInterpretation
 
getGraphHolder() - Method in class ome.model.enums.PixelsType
 
getGraphHolder() - Method in class ome.model.enums.Pulse
 
getGraphHolder() - Method in class ome.model.enums.RenderingModel
 
getGraphHolder() - Method in class ome.model.experiment.Experiment
 
getGraphHolder() - Method in class ome.model.experiment.MicrobeamManipulation
 
getGraphHolder() - Method in class ome.model.fs.Fileset
 
getGraphHolder() - Method in class ome.model.fs.FilesetEntry
 
getGraphHolder() - Method in class ome.model.fs.FilesetJobLink
 
getGraphHolder() - Method in class ome.model.internal.Link
 
getGraphHolder() - Method in interface ome.model.IObject
retrieves the GraphHolder for this entity.
getGraphHolder() - Method in class ome.model.jobs.Job
 
getGraphHolder() - Method in class ome.model.jobs.JobOriginalFileLink
 
getGraphHolder() - Method in class ome.model.jobs.JobStatus
 
getGraphHolder() - Method in class ome.model.meta.DBPatch
 
getGraphHolder() - Method in class ome.model.meta.Event
 
getGraphHolder() - Method in class ome.model.meta.EventLog
 
getGraphHolder() - Method in class ome.model.meta.Experimenter
 
getGraphHolder() - Method in class ome.model.meta.ExperimenterGroup
 
getGraphHolder() - Method in class ome.model.meta.ExternalInfo
 
getGraphHolder() - Method in class ome.model.meta.GroupExperimenterMap
 
getGraphHolder() - Method in class ome.model.meta.Namespace
 
getGraphHolder() - Method in class ome.model.meta.Node
 
getGraphHolder() - Method in class ome.model.meta.Session
 
getGraphHolder() - Method in class ome.model.meta.ShareMember
 
getGraphHolder() - Method in class ome.model.roi.Roi
 
getGraphHolder() - Method in class ome.model.roi.Shape
 
getGraphHolder() - Method in class ome.model.screen.Plate
 
getGraphHolder() - Method in class ome.model.screen.PlateAcquisition
 
getGraphHolder() - Method in class ome.model.screen.Reagent
 
getGraphHolder() - Method in class ome.model.screen.Screen
 
getGraphHolder() - Method in class ome.model.screen.ScreenPlateLink
 
getGraphHolder() - Method in class ome.model.screen.Well
 
getGraphHolder() - Method in class ome.model.screen.WellReagentLink
 
getGraphHolder() - Method in class ome.model.screen.WellSample
 
getGraphHolder() - Method in class ome.model.stats.StatsInfo
 
getGraphPathBean() - Method in class omero.cmd.graphs.GraphRequestFactory
 
getGreen() - Method in class ome.model.core.Channel
Simple field ome.model.core.Channel.green (java.lang.Integer)
getGreen() - Method in class ome.model.display.ChannelBinding
Simple field ome.model.display.ChannelBinding.green (java.lang.Integer)
getGreen() - Method in class ome.model.screen.Well
Simple field ome.model.screen.Well.green (java.lang.Integer)
getGreen() - Method in class pojos.WellData
Returns the green component of the color associated to the well, or -1.
getGreenBand() - Method in class omeis.providers.re.RGBBuffer
Returns the data buffer for the green band.
getGreenValue(int) - Method in class omeis.providers.re.RGBAIntBuffer
Retrieves the Green value for a particular pixel index.
getGreenValue(int) - Method in class omeis.providers.re.RGBBuffer
Retrieves the Green value for a particular pixel index.
getGreenValue(int) - Method in class omeis.providers.re.RGBIntBuffer
Retrieves the Green value for a particular pixel index.
getGridQuery() - Method in interface ome.services.blitz.fire.Registry
Returns an active QueryPrx or null if none is available.
getGridQuery() - Method in class ome.services.blitz.fire.Registry.Impl
 
getGroup(long) - Method in interface ome.api.IAdmin
fetch an ExperimenterGroup and all contained users.
getGroup(long) - Method in class ome.logic.AdminImpl
 
getGroup() - Method in class ome.model.acquisition.Detector.Details
 
getGroup() - Method in class ome.model.acquisition.DetectorSettings.Details
 
getGroup() - Method in class ome.model.acquisition.Dichroic.Details
 
getGroup() - Method in class ome.model.acquisition.Filter.Details
 
getGroup() - Method in class ome.model.acquisition.FilterSet.Details
 
getGroup() - Method in class ome.model.acquisition.FilterSetEmissionFilterLink.Details
 
getGroup() - Method in class ome.model.acquisition.FilterSetExcitationFilterLink.Details
 
getGroup() - Method in class ome.model.acquisition.ImagingEnvironment.Details
 
getGroup() - Method in class ome.model.acquisition.Instrument.Details
 
getGroup() - Method in class ome.model.acquisition.LightPath.Details
 
getGroup() - Method in class ome.model.acquisition.LightPathEmissionFilterLink.Details
 
getGroup() - Method in class ome.model.acquisition.LightPathExcitationFilterLink.Details
 
getGroup() - Method in class ome.model.acquisition.LightSettings.Details
 
getGroup() - Method in class ome.model.acquisition.LightSource.Details
 
getGroup() - Method in class ome.model.acquisition.Microscope.Details
 
getGroup() - Method in class ome.model.acquisition.Objective.Details
 
getGroup() - Method in class ome.model.acquisition.ObjectiveSettings.Details
 
getGroup() - Method in class ome.model.acquisition.OTF.Details
 
getGroup() - Method in class ome.model.acquisition.StageLabel.Details
 
getGroup() - Method in class ome.model.acquisition.TransmittanceRange.Details
 
getGroup() - Method in class ome.model.annotations.Annotation.Details
 
getGroup() - Method in class ome.model.annotations.AnnotationAnnotationLink.Details
 
getGroup() - Method in class ome.model.annotations.ChannelAnnotationLink.Details
 
getGroup() - Method in class ome.model.annotations.DatasetAnnotationLink.Details
 
getGroup() - Method in class ome.model.annotations.DetectorAnnotationLink.Details
 
getGroup() - Method in class ome.model.annotations.DichroicAnnotationLink.Details
 
getGroup() - Method in class ome.model.annotations.ExperimenterAnnotationLink.Details
 
getGroup() - Method in class ome.model.annotations.ExperimenterGroupAnnotationLink.Details
 
getGroup() - Method in class ome.model.annotations.FilesetAnnotationLink.Details
 
getGroup() - Method in class ome.model.annotations.FilterAnnotationLink.Details
 
getGroup() - Method in class ome.model.annotations.ImageAnnotationLink.Details
 
getGroup() - Method in class ome.model.annotations.InstrumentAnnotationLink.Details
 
getGroup() - Method in class ome.model.annotations.LightPathAnnotationLink.Details
 
getGroup() - Method in class ome.model.annotations.LightSourceAnnotationLink.Details
 
getGroup() - Method in class ome.model.annotations.NamespaceAnnotationLink.Details
 
getGroup() - Method in class ome.model.annotations.NodeAnnotationLink.Details
 
getGroup() - Method in class ome.model.annotations.ObjectiveAnnotationLink.Details
 
getGroup() - Method in class ome.model.annotations.OriginalFileAnnotationLink.Details
 
getGroup() - Method in class ome.model.annotations.PlaneInfoAnnotationLink.Details
 
getGroup() - Method in class ome.model.annotations.PlateAcquisitionAnnotationLink.Details
 
getGroup() - Method in class ome.model.annotations.PlateAnnotationLink.Details
 
getGroup() - Method in class ome.model.annotations.ProjectAnnotationLink.Details
 
getGroup() - Method in class ome.model.annotations.ReagentAnnotationLink.Details
 
getGroup() - Method in class ome.model.annotations.RoiAnnotationLink.Details
 
getGroup() - Method in class ome.model.annotations.ScreenAnnotationLink.Details
 
getGroup() - Method in class ome.model.annotations.SessionAnnotationLink.Details
 
getGroup() - Method in class ome.model.annotations.ShapeAnnotationLink.Details
 
getGroup() - Method in class ome.model.annotations.WellAnnotationLink.Details
 
getGroup() - Method in class ome.model.containers.Dataset.Details
 
getGroup() - Method in class ome.model.containers.DatasetImageLink.Details
 
getGroup() - Method in class ome.model.containers.Project.Details
 
getGroup() - Method in class ome.model.containers.ProjectDatasetLink.Details
 
getGroup() - Method in class ome.model.core.Channel.Details
 
getGroup() - Method in class ome.model.core.Image.Details
 
getGroup() - Method in class ome.model.core.LogicalChannel.Details
 
getGroup() - Method in class ome.model.core.OriginalFile.Details
 
getGroup() - Method in class ome.model.core.Pixels.Details
 
getGroup() - Method in class ome.model.core.PixelsOriginalFileMap.Details
 
getGroup() - Method in class ome.model.core.PlaneInfo.Details
 
getGroup() - Method in class ome.model.display.ChannelBinding.Details
 
getGroup() - Method in class ome.model.display.CodomainMapContext.Details
 
getGroup() - Method in class ome.model.display.QuantumDef.Details
 
getGroup() - Method in class ome.model.display.RenderingDef.Details
 
getGroup() - Method in class ome.model.display.Thumbnail.Details
 
getGroup() - Method in class ome.model.experiment.Experiment.Details
 
getGroup() - Method in class ome.model.experiment.MicrobeamManipulation.Details
 
getGroup() - Method in class ome.model.fs.Fileset.Details
 
getGroup() - Method in class ome.model.fs.FilesetEntry.Details
 
getGroup() - Method in class ome.model.fs.FilesetJobLink.Details
 
getGroup() - Method in class ome.model.internal.Details
 
getGroup() - Method in class ome.model.internal.Link.Details
 
getGroup() - Method in class ome.model.jobs.Job.Details
 
getGroup() - Method in class ome.model.jobs.JobOriginalFileLink.Details
 
getGroup() - Method in class ome.model.meta.ExternalInfo.Details
 
getGroup() - Method in class ome.model.meta.Share
Many-to-one field ome.model.meta.Share.group (ome.model.meta.ExperimenterGroup)
getGroup() - Method in class ome.model.roi.Roi.Details
 
getGroup() - Method in class ome.model.roi.Shape.Details
 
getGroup() - Method in class ome.model.screen.Plate.Details
 
getGroup() - Method in class ome.model.screen.PlateAcquisition.Details
 
getGroup() - Method in class ome.model.screen.Reagent.Details
 
getGroup() - Method in class ome.model.screen.Screen.Details
 
getGroup() - Method in class ome.model.screen.ScreenPlateLink.Details
 
getGroup() - Method in class ome.model.screen.Well.Details
 
getGroup() - Method in class ome.model.screen.WellReagentLink.Details
 
getGroup() - Method in class ome.model.screen.WellSample.Details
 
getGroup() - Method in class ome.model.stats.StatsInfo.Details
 
getGroup() - Method in class ome.parameters.Parameters
Fulfills the old PojoOptions requirement for returning null if no owner set.
getGroup() - Method in class ome.security.basic.BasicEventContext
 
getGroup() - Method in class ome.security.basic.CurrentDetails
 
getGroup(Current) - Method in class ome.services.blitz.fire.SessionManagerI
 
getGroup() - Method in class ome.services.blitz.repo.ManagedImportProcessI
 
getGroup() - Method in interface ome.services.blitz.repo.ProcessContainer.Process
 
getGroup() - Method in class ome.system.Login
simple getter for the group name passed into the constructor
getGroup() - Method in class ome.system.Principal
 
getGroup(Current) - Method in class omero.model.DetailsI
 
getGroup() - Method in class omero.sys.ParametersI
Returns the value of the group parameter.
getGroup_async(AMD_IAdmin_getGroup, long, Current) - Method in class ome.services.blitz.impl.AdminI
 
getGroupAttribute(String) - Method in class ome.security.auth.LdapConfig
 
getGroupExperimenterMap() - Method in class ome.model.meta.Experimenter
returns groupExperimenterMap .
getGroupExperimenterMap(int) - Method in class ome.model.meta.Experimenter
Gets the ome.model.meta.GroupExperimenterMap at the given index.
getGroupExperimenterMap() - Method in class ome.model.meta.ExperimenterGroup
returns groupExperimenterMap .
getGroupFilter() - Method in class ome.security.auth.LdapConfig
 
getGroupId() - Method in class pojos.DataObject
Returns the id of the group.
getGroupId() - Method in class pojos.ExperimenterData
Overridden to return the id of the default group.
getGroupId() - Method in class pojos.GroupData
Overridden to return the id of the object.
getGroupIds(Collection<String>) - Method in interface ome.util.SqlAction
 
getGroupIds(Collection<String>) - Method in class ome.util.SqlAction.Impl
 
getGroupname() - Method in class ome.model.jobs.Job
Simple field ome.model.jobs.Job.groupname (java.lang.String)
getGroupPermissions(long) - Method in interface ome.util.SqlAction
Returns the permissions for the given group id.
getGroupPermissions(long) - Method in class ome.util.SqlAction.Impl
 
getGroups() - Method in class pojos.ExperimenterData
Returns the groups the experimenter is a member of.
getGuestGroupId() - Method in class ome.system.Roles
 
getGuestGroupName() - Method in class ome.system.Roles
 
getGuestId() - Method in class ome.system.Roles
 
getGuestName() - Method in class ome.system.Roles
 
getHandle(Current) - Method in class ome.services.blitz.repo.ManagedImportProcessI
 
getHandler(Class<? extends IObject>) - Method in class ome.formats.enums.handler.EnumHandlerFactory
Returns an enumeration handler for a specific enumeration type.
getHandler(Class<? extends IObject>) - Method in class ome.formats.model.handler.ModelObjectHandlerFactory
Returns an enumeration handler for a specific enumeration type.
getHash() - Method in class ome.model.core.OriginalFile
Simple field ome.model.core.OriginalFile.hash (java.lang.String)
getHasher() - Method in class ome.model.core.OriginalFile
Many-to-one field ome.model.core.OriginalFile.hasher (ome.model.enums.ChecksumAlgorithm)
getHeight() - Method in class ome.model.roi.Mask
Simple field ome.model.roi.Mask.height (java.lang.Double)
getHeight() - Method in class ome.model.roi.Rect
Simple field ome.model.roi.Rect.height (java.lang.Double)
getHeight() - Method in class omeis.providers.re.data.RegionDef
Returns the height of the region.
getHeight() - Method in class pojos.MaskData
Returns the height of the mask.
getHeight() - Method in class pojos.RectangleData
Returns the height untransformed rectangle.
getHibernateClass(String) - Method in class ome.services.graphs.BaseGraphSpec
Deprecated.
 
getHibernateClass(String) - Method in interface ome.services.graphs.GraphSpec
Deprecated.
Return the Hibernate type (ome.model.*) for the given table.
getHibernateClass(String) - Method in interface ome.tools.hibernate.ExtendedMetadata
Given the name of a database table or alternatively the simple class name (non-fully qualified) of an IObject, this method returns the class which Hibernate will map that table to.
getHibernateClass(String) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
 
getHolder() - Method in class ome.services.blitz.util.UnregisterServantMessage
 
getHomeUrl() - Method in class ome.formats.importer.ImportConfig
 
getHomeUrl() - Method in class ome.formats.importer.util.IniFileLoader
 
getHost() - Method in class ome.system.Server
simple getter for the server host passed into the constructor
getHumidity() - Method in class ome.model.acquisition.ImagingEnvironment
Simple field ome.model.acquisition.ImagingEnvironment.humidity (java.lang.Double)
getHumidity() - Method in class pojos.ImageAcquisitionData
Returns the humidity level, this is a value in the interval [0, 1]
getHypercube(List<Integer>, List<Integer>, List<Integer>) - Method in interface ome.api.RawPixelsStore
 
getHypercube(List<Integer>, List<Integer>, List<Integer>) - Method in class ome.io.bioformats.BfPixelBuffer
 
getHypercube(List<Integer>, List<Integer>, List<Integer>, byte[]) - Method in class ome.io.bioformats.BfPixelsWrapper
 
getHypercube(List<Integer>, List<Integer>, List<Integer>) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
 
getHypercube(List<Integer>, List<Integer>, List<Integer>) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
 
getHypercube(List<Integer>, List<Integer>, List<Integer>) - Method in interface ome.io.nio.PixelBuffer
Retrieves a hypercube from this pixel buffer.
getHypercube(List<Integer>, List<Integer>, List<Integer>) - Method in class ome.io.nio.RomioPixelBuffer
Implemented as specified by PixelBuffer I/F.
getHypercube(List<Integer>, List<Integer>, List<Integer>) - Method in class ome.services.RawPixelsBean
 
getHypercube_async(AMD_RawPixelsStore_getHypercube, List<Integer>, List<Integer>, List<Integer>, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
getHypercube_async(AMD_RawPixelsStore_getHypercube, List<Integer>, List<Integer>, List<Integer>, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
getHypercubeDirect(List<Integer>, List<Integer>, List<Integer>, byte[]) - Method in class ome.io.bioformats.BfPixelBuffer
 
getHypercubeDirect(List<Integer>, List<Integer>, List<Integer>, byte[]) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
 
getHypercubeDirect(List<Integer>, List<Integer>, List<Integer>, byte[]) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
 
getHypercubeDirect(List<Integer>, List<Integer>, List<Integer>, byte[]) - Method in interface ome.io.nio.PixelBuffer
Retrieves a hypercube from the given pixels directly.
getHypercubeDirect(List<Integer>, List<Integer>, List<Integer>, byte[]) - Method in class ome.io.nio.RomioPixelBuffer
Implemented as specified by PixelBuffer I/F.
getHypercubeSize(List<Integer>, List<Integer>, List<Integer>) - Method in class ome.io.bioformats.BfPixelBuffer
 
getHypercubeSize(List<Integer>, List<Integer>, List<Integer>) - Method in class ome.io.bioformats.BfPixelsWrapper
 
getHypercubeSize(List<Integer>, List<Integer>, List<Integer>) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
 
getHypercubeSize(List<Integer>, List<Integer>, List<Integer>) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
 
getHypercubeSize(List<Integer>, List<Integer>, List<Integer>) - Method in interface ome.io.nio.PixelBuffer
Retrieves a the size of a hypercube from this pixel buffer.
getHypercubeSize(List<Integer>, List<Integer>, List<Integer>) - Method in class ome.io.nio.RomioPixelBuffer
 
getId() - Method in class ome.io.bioformats.BfPixelBuffer
 
getId() - Method in class ome.io.bioformats.BfPixelsWrapper
 
getId() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
 
getId() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
 
getId() - Method in interface ome.io.nio.PixelBuffer
Delegates to Pixels.getId().
getId() - Method in class ome.io.nio.RomioPixelBuffer
Implemented as specified by PixelBuffer I/F.
getId() - Method in class ome.model.acquisition.Detector
The DB unique identifier for this object.
getId() - Method in class ome.model.acquisition.DetectorSettings
The DB unique identifier for this object.
getId() - Method in class ome.model.acquisition.Dichroic
The DB unique identifier for this object.
getId() - Method in class ome.model.acquisition.Filter
The DB unique identifier for this object.
getId() - Method in class ome.model.acquisition.FilterSet
The DB unique identifier for this object.
getId() - Method in class ome.model.acquisition.FilterSetEmissionFilterLink
The DB unique identifier for this object.
getId() - Method in class ome.model.acquisition.FilterSetExcitationFilterLink
The DB unique identifier for this object.
getId() - Method in class ome.model.acquisition.ImagingEnvironment
The DB unique identifier for this object.
getId() - Method in class ome.model.acquisition.Instrument
The DB unique identifier for this object.
getId() - Method in class ome.model.acquisition.LightPath
The DB unique identifier for this object.
getId() - Method in class ome.model.acquisition.LightPathEmissionFilterLink
The DB unique identifier for this object.
getId() - Method in class ome.model.acquisition.LightPathExcitationFilterLink
The DB unique identifier for this object.
getId() - Method in class ome.model.acquisition.LightSettings
The DB unique identifier for this object.
getId() - Method in class ome.model.acquisition.LightSource
The DB unique identifier for this object.
getId() - Method in class ome.model.acquisition.Microscope
The DB unique identifier for this object.
getId() - Method in class ome.model.acquisition.Objective
The DB unique identifier for this object.
getId() - Method in class ome.model.acquisition.ObjectiveSettings
The DB unique identifier for this object.
getId() - Method in class ome.model.acquisition.OTF
The DB unique identifier for this object.
getId() - Method in class ome.model.acquisition.StageLabel
The DB unique identifier for this object.
getId() - Method in class ome.model.acquisition.TransmittanceRange
The DB unique identifier for this object.
getId() - Method in class ome.model.annotations.Annotation
The DB unique identifier for this object.
getId() - Method in class ome.model.annotations.AnnotationAnnotationLink
The DB unique identifier for this object.
getId() - Method in class ome.model.annotations.ChannelAnnotationLink
The DB unique identifier for this object.
getId() - Method in class ome.model.annotations.DatasetAnnotationLink
The DB unique identifier for this object.
getId() - Method in class ome.model.annotations.DetectorAnnotationLink
The DB unique identifier for this object.
getId() - Method in class ome.model.annotations.DichroicAnnotationLink
The DB unique identifier for this object.
getId() - Method in class ome.model.annotations.ExperimenterAnnotationLink
The DB unique identifier for this object.
getId() - Method in class ome.model.annotations.ExperimenterGroupAnnotationLink
The DB unique identifier for this object.
getId() - Method in class ome.model.annotations.FilesetAnnotationLink
The DB unique identifier for this object.
getId() - Method in class ome.model.annotations.FilterAnnotationLink
The DB unique identifier for this object.
getId() - Method in class ome.model.annotations.ImageAnnotationLink
The DB unique identifier for this object.
getId() - Method in class ome.model.annotations.InstrumentAnnotationLink
The DB unique identifier for this object.
getId() - Method in class ome.model.annotations.LightPathAnnotationLink
The DB unique identifier for this object.
getId() - Method in class ome.model.annotations.LightSourceAnnotationLink
The DB unique identifier for this object.
getId() - Method in class ome.model.annotations.NamespaceAnnotationLink
The DB unique identifier for this object.
getId() - Method in class ome.model.annotations.NodeAnnotationLink
The DB unique identifier for this object.
getId() - Method in class ome.model.annotations.ObjectiveAnnotationLink
The DB unique identifier for this object.
getId() - Method in class ome.model.annotations.OriginalFileAnnotationLink
The DB unique identifier for this object.
getId() - Method in class ome.model.annotations.PlaneInfoAnnotationLink
The DB unique identifier for this object.
getId() - Method in class ome.model.annotations.PlateAcquisitionAnnotationLink
The DB unique identifier for this object.
getId() - Method in class ome.model.annotations.PlateAnnotationLink
The DB unique identifier for this object.
getId() - Method in class ome.model.annotations.ProjectAnnotationLink
The DB unique identifier for this object.
getId() - Method in class ome.model.annotations.ReagentAnnotationLink
The DB unique identifier for this object.
getId() - Method in class ome.model.annotations.RoiAnnotationLink
The DB unique identifier for this object.
getId() - Method in class ome.model.annotations.ScreenAnnotationLink
The DB unique identifier for this object.
getId() - Method in class ome.model.annotations.SessionAnnotationLink
The DB unique identifier for this object.
getId() - Method in class ome.model.annotations.ShapeAnnotationLink
The DB unique identifier for this object.
getId() - Method in class ome.model.annotations.WellAnnotationLink
The DB unique identifier for this object.
getId() - Method in class ome.model.containers.Dataset
The DB unique identifier for this object.
getId() - Method in class ome.model.containers.DatasetImageLink
The DB unique identifier for this object.
getId() - Method in class ome.model.containers.Project
The DB unique identifier for this object.
getId() - Method in class ome.model.containers.ProjectDatasetLink
The DB unique identifier for this object.
getId() - Method in class ome.model.core.Channel
The DB unique identifier for this object.
getId() - Method in class ome.model.core.Image
The DB unique identifier for this object.
getId() - Method in class ome.model.core.LogicalChannel
The DB unique identifier for this object.
getId() - Method in class ome.model.core.OriginalFile
The DB unique identifier for this object.
getId() - Method in class ome.model.core.Pixels
The DB unique identifier for this object.
getId() - Method in class ome.model.core.PixelsOriginalFileMap
The DB unique identifier for this object.
getId() - Method in class ome.model.core.PlaneInfo
The DB unique identifier for this object.
getId() - Method in class ome.model.display.ChannelBinding
The DB unique identifier for this object.
getId() - Method in class ome.model.display.CodomainMapContext
The DB unique identifier for this object.
getId() - Method in class ome.model.display.QuantumDef
The DB unique identifier for this object.
getId() - Method in class ome.model.display.RenderingDef
The DB unique identifier for this object.
getId() - Method in class ome.model.display.Thumbnail
The DB unique identifier for this object.
getId() - Method in class ome.model.enums.AcquisitionMode
The DB unique identifier for this object.
getId() - Method in class ome.model.enums.ArcType
The DB unique identifier for this object.
getId() - Method in class ome.model.enums.Binning
The DB unique identifier for this object.
getId() - Method in class ome.model.enums.ChecksumAlgorithm
The DB unique identifier for this object.
getId() - Method in class ome.model.enums.ContrastMethod
The DB unique identifier for this object.
getId() - Method in class ome.model.enums.Correction
The DB unique identifier for this object.
getId() - Method in class ome.model.enums.DetectorType
The DB unique identifier for this object.
getId() - Method in class ome.model.enums.DimensionOrder
The DB unique identifier for this object.
getId() - Method in class ome.model.enums.EventType
The DB unique identifier for this object.
getId() - Method in class ome.model.enums.ExperimentType
The DB unique identifier for this object.
getId() - Method in class ome.model.enums.Family
The DB unique identifier for this object.
getId() - Method in class ome.model.enums.FilamentType
The DB unique identifier for this object.
getId() - Method in class ome.model.enums.FilterType
The DB unique identifier for this object.
getId() - Method in class ome.model.enums.Format
The DB unique identifier for this object.
getId() - Method in class ome.model.enums.Illumination
The DB unique identifier for this object.
getId() - Method in class ome.model.enums.Immersion
The DB unique identifier for this object.
getId() - Method in class ome.model.enums.LaserMedium
The DB unique identifier for this object.
getId() - Method in class ome.model.enums.LaserType
The DB unique identifier for this object.
getId() - Method in class ome.model.enums.Medium
The DB unique identifier for this object.
getId() - Method in class ome.model.enums.MicrobeamManipulationType
The DB unique identifier for this object.
getId() - Method in class ome.model.enums.MicroscopeType
The DB unique identifier for this object.
getId() - Method in class ome.model.enums.PhotometricInterpretation
The DB unique identifier for this object.
getId() - Method in class ome.model.enums.PixelsType
The DB unique identifier for this object.
getId() - Method in class ome.model.enums.Pulse
The DB unique identifier for this object.
getId() - Method in class ome.model.enums.RenderingModel
The DB unique identifier for this object.
getId() - Method in class ome.model.experiment.Experiment
The DB unique identifier for this object.
getId() - Method in class ome.model.experiment.MicrobeamManipulation
The DB unique identifier for this object.
getId() - Method in class ome.model.fs.Fileset
The DB unique identifier for this object.
getId() - Method in class ome.model.fs.FilesetEntry
The DB unique identifier for this object.
getId() - Method in class ome.model.fs.FilesetJobLink
The DB unique identifier for this object.
getId() - Method in class ome.model.internal.Link
The DB unique identifier for this object.
getId() - Method in interface ome.model.IObject
primary key of this object.
getId() - Method in class ome.model.jobs.Job
The DB unique identifier for this object.
getId() - Method in class ome.model.jobs.JobOriginalFileLink
The DB unique identifier for this object.
getId() - Method in class ome.model.jobs.JobStatus
The DB unique identifier for this object.
getId() - Method in class ome.model.meta.DBPatch
The DB unique identifier for this object.
getId() - Method in class ome.model.meta.Event
The DB unique identifier for this object.
getId() - Method in class ome.model.meta.EventLog
The DB unique identifier for this object.
getId() - Method in class ome.model.meta.Experimenter
The DB unique identifier for this object.
getId() - Method in class ome.model.meta.ExperimenterGroup
The DB unique identifier for this object.
getId() - Method in class ome.model.meta.ExternalInfo
The DB unique identifier for this object.
getId() - Method in class ome.model.meta.GroupExperimenterMap
The DB unique identifier for this object.
getId() - Method in class ome.model.meta.Namespace
The DB unique identifier for this object.
getId() - Method in class ome.model.meta.Node
The DB unique identifier for this object.
getId() - Method in class ome.model.meta.Session
The DB unique identifier for this object.
getId() - Method in class ome.model.meta.ShareMember
The DB unique identifier for this object.
getId() - Method in class ome.model.roi.Roi
The DB unique identifier for this object.
getId() - Method in class ome.model.roi.Shape
The DB unique identifier for this object.
getId() - Method in class ome.model.screen.Plate
The DB unique identifier for this object.
getId() - Method in class ome.model.screen.PlateAcquisition
The DB unique identifier for this object.
getId() - Method in class ome.model.screen.Reagent
The DB unique identifier for this object.
getId() - Method in class ome.model.screen.Screen
The DB unique identifier for this object.
getId() - Method in class ome.model.screen.ScreenPlateLink
The DB unique identifier for this object.
getId() - Method in class ome.model.screen.Well
The DB unique identifier for this object.
getId() - Method in class ome.model.screen.WellReagentLink
The DB unique identifier for this object.
getId() - Method in class ome.model.screen.WellSample
The DB unique identifier for this object.
getId() - Method in class ome.model.stats.StatsInfo
The DB unique identifier for this object.
getId() - Method in class ome.services.blitz.repo.CheckedPath
 
getId() - Method in class ome.services.graphs.GraphEntry
Deprecated.
 
getId() - Method in class pojos.DataObject
Returns the database id of the IObject or -1 if null
getIdByOrder(int) - Method in class ome.services.export.ExporterIndex
Deprecated.
Returns the id of an object based on the order in which it was added.
getIdentifierProperty(String) - Method in class ome.services.graphs.GraphPathBean
Get the identifier property for the given class.
getIdentity() - Method in class ome.services.blitz.util.FindServiceFactoryMessage
 
getIdentity(String) - Method in class omero.cmd.SessionI
 
getIdentity(String) - Method in class omero.util.ServantHolder
Constructs an Identity from the current session and from the given String which for stateless services are defined by the instance fields #adminKey, #configKey, etc. and for stateful services are UUIDs.
getIds() - Method in class ome.services.graphs.GraphStep
Deprecated.
Currently returns the ID array without copying therefore values should not be leaked to code outside of the ome.services.graphs hierarchy.
getIds() - Method in class ome.services.sessions.state.SessionCache
Since all methods which use SessionCache.getIds() will subsequently check for the existing session, we do not block here.
getIllumination() - Method in class ome.model.core.LogicalChannel
Many-to-one field ome.model.core.LogicalChannel.illumination (ome.model.enums.Illumination)
getIllumination() - Method in class pojos.ChannelAcquisitionData
Returns the illumination.
getIllumination() - Method in class pojos.ChannelData
Returns the illumination.
getIlluminationAsEnum() - Method in class pojos.ChannelData
Returns the illumination enumeration value.
getImage() - Method in class ome.model.core.Pixels
Many-to-one field ome.model.core.Pixels.image (ome.model.core.Image)
getImage() - Method in class ome.model.roi.Roi
Many-to-one field ome.model.roi.Roi.image (ome.model.core.Image)
getImage() - Method in class ome.model.screen.WellSample
Many-to-one field ome.model.screen.WellSample.image (ome.model.core.Image)
getImage(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getImage() - Method in class pojos.PixelsData
Returns the image linked to this pixels' set.
getImage() - Method in class pojos.ROIData
Returns the image for the ROI.
getImage() - Method in class pojos.WellSampleData
Returns the image related to that sample if any.
getImageAcquisitionDate(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getImageAndCount(Image[], long, UnloadedCollector) - Method in class ome.services.delete.DeleteBean
Uses the locally defined query to load an Image and calls DeleteBean.collect(UnloadedCollector, Image) in order to define a list of what will be deleted.
getImageAnnotationRef(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getImageAnnotationRefCount(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getImageCount() - Method in class ome.services.blitz.impl.OmeroMetadata
 
getImageDescription() - Method in class ome.model.jobs.ImportJob
Simple field ome.model.jobs.ImportJob.imageDescription (java.lang.String)
getImageDescription(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getImageID(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getImageIds() - Method in class pojos.FilesetData
Returns the collection of images related to the file set.
getImageLinks() - Method in class ome.model.containers.Dataset
returns imageLinks .
getImageLinksCountPerOwner() - Method in class ome.model.containers.Dataset
If fetched, returns the count(*) of ome.model.containers.DatasetImageLink that a user has.
getImageName() - Method in class ome.model.jobs.ImportJob
Simple field ome.model.jobs.ImportJob.imageName (java.lang.String)
getImageName(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getImageNames() - Method in class ome.formats.ImageNameMetadataStore
Retrieves the current map of Image names held.
getImageReader() - Method in class ome.formats.importer.OMEROWrapper
Return the base image reader
getImages(Class<T>, Set<Long>, Parameters) - Method in interface ome.api.IContainer
Retrieve a user's (or all users') images within any given container.
getImages(Class, Set, Parameters) - Method in class ome.logic.PojosImpl
Implemented as specified by the IContainer I/F
getImages() - Method in class ome.model.fs.Fileset
returns images .
getImages() - Method in class pojos.DatasetData
Returns a set of images contained in the dataset.
getImages_async(AMD_IContainer_getImages, String, List<Long>, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI
 
getImagesByOptions(Parameters) - Method in interface ome.api.IContainer
Retrieve images by options.
getImagesByOptions(Parameters) - Method in class ome.logic.PojosImpl
Implemented as specified by the IContainer I/F
getImagesByOptions_async(AMD_IContainer_getImagesByOptions, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI
 
getImagesBySplitFilesets(Map<Class<? extends IObject>, List<Long>>, Parameters) - Method in interface ome.api.IContainer
Given a list of IDs of certain entity types, calculates which filesets are split such that a non-empty proper subset of their images are referenced, directly or indirectly, as being included.
getImagesBySplitFilesets(Map<Class<? extends IObject>, List<Long>>, Parameters) - Method in class ome.logic.PojosImpl
Implemented as specified by the IContainer I/F
getImagesBySplitFilesets_async(AMD_IContainer_getImagesBySplitFilesets, Map<String, List<Long>>, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI
 
getImagesForDataset(long) - Method in interface ome.api.IAnalysis
 
getImageSize(PlaneDef) - Method in class omeis.providers.re.Renderer
Returns the size, in bytes, of the RGBBuffer that would be rendered from the plane selected by pd.
getImagingEnvironment(int) - Method in class ome.formats.OMEROMetadataStoreClient
 
getImagingEnvironment() - Method in class ome.model.core.Image
Many-to-one field ome.model.core.Image.imagingEnvironment (ome.model.acquisition.ImagingEnvironment)
getImagingEnvironmentId() - Method in class pojos.ImageAcquisitionData
Returns the id of the StageLabel or -1 if not already linked to the image.
getImmersion() - Method in class ome.model.acquisition.Objective
Many-to-one field ome.model.acquisition.Objective.immersion (ome.model.enums.Immersion)
getImmersion() - Method in class pojos.ObjectiveData
Returns the immersion value of the objective.
getImmutableFields() - Method in class ome.tools.hibernate.ExtendedMetadata.Immutables
 
getImmutableFields(Class<? extends IObject>) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
 
getImplicitContext() - Method in class omero.client
Returns the ImplicitContext which defines what properties will be sent on every method invocation.
getImportResponse() - Method in class ome.formats.importer.ImportLibrary.ImportCallback
Assumes that users have already waited on proper completion, i.e. that ImportLibrary.ImportCallback.onFinished(Response, Status, Current) has been called.
getImportSettings(Current) - Method in class ome.services.blitz.repo.ManagedImportProcessI
 
getImportTypes() - Method in class ome.logic.TypesImpl
 
getIndex() - Method in class ome.formats.importer.util.ErrorContainer
get the index for this error container
getIndex() - Method in class ome.services.fulltext.SimpleLuceneOptions
 
getIndex() - Method in class pojos.ChannelData
Returns the channel's index.
getIndex() - Method in class pojos.ImageData
Returns the index of the image within the multi-images file.
getIndexes() - Method in class ome.util.LSID
Returns the indexes for this LSID within the OME-XML data model.
getIniVersionNumber() - Method in class ome.formats.importer.ImportConfig
 
getInput(String, String) - Method in interface ome.api.ISession
Retrieves an entry from the given session's input environment.
getInput(String, String) - Method in class ome.services.sessions.SessionBean
 
getInput(String, String) - Method in interface ome.services.sessions.SessionManager
Returns the input environment Object stored under the given key or null if none present.
getInput(String, String) - Method in class ome.services.sessions.SessionManagerImpl
 
getInput(String) - Method in class omero.client
Retrieves an item from the "input" shared (session) memory.
getInput_async(AMD_ISession_getInput, String, String, Current) - Method in class ome.services.blitz.impl.SessionI
 
getInputEnd() - Method in class ome.model.display.ChannelBinding
Simple field ome.model.display.ChannelBinding.inputEnd (java.lang.Double)
getInputEnd() - Method in class omeis.providers.re.metadata.StatsFactory
Returns the input end.
getInputKeys(String) - Method in interface ome.api.ISession
Retrieves all keys in the sesson's input environment.
getInputKeys(String) - Method in class ome.services.sessions.SessionBean
 
getInputKeys() - Method in class omero.client
Returns a list of keys for all items in the "input" shared (session) memory
getInputKeys_async(AMD_ISession_getInputKeys, String, Current) - Method in class ome.services.blitz.impl.SessionI
 
getInputs(String) - Method in interface ome.api.ISession
Retrieves all inputs from the given session's input environment.
getInputs(String) - Method in class ome.services.sessions.SessionBean
 
getInputs_async(AMD_ISession_getInputs, String, Current) - Method in class ome.services.blitz.impl.SessionI
 
getInputStart() - Method in class ome.model.display.ChannelBinding
Simple field ome.model.display.ChannelBinding.inputStart (java.lang.Double)
getInputStart() - Method in class omeis.providers.re.metadata.StatsFactory
Returns the input start.
getInserted() - Method in class pojos.ImageData
Returns the insertion time of the image.
getInstance(Class<T>) - Method in class ome.formats.model.BlitzInstanceProvider
 
getInstance(Class<T>) - Method in interface ome.formats.model.InstanceProvider
Retrieves an instance.
getInstance(String) - Static method in class ome.system.OmeroContext
create (if necessary) and return the single default OmeroContext named by the beanFactoryName parameter.
getInstanceProvider() - Method in class ome.formats.OMEROMetadataStoreClient
Retrieves the active enumeration provider.
getInstitution() - Method in class ome.model.meta.Experimenter
Simple field ome.model.meta.Experimenter.institution (java.lang.String)
getInstitution() - Method in class pojos.ExperimenterData
Returns the institution where the experimenter works.
getInstrument() - Method in class ome.model.acquisition.Detector
Many-to-one field ome.model.acquisition.Detector.instrument (ome.model.acquisition.Instrument)
getInstrument() - Method in class ome.model.acquisition.Dichroic
Many-to-one field ome.model.acquisition.Dichroic.instrument (ome.model.acquisition.Instrument)
getInstrument() - Method in class ome.model.acquisition.Filter
Many-to-one field ome.model.acquisition.Filter.instrument (ome.model.acquisition.Instrument)
getInstrument() - Method in class ome.model.acquisition.FilterSet
Many-to-one field ome.model.acquisition.FilterSet.instrument (ome.model.acquisition.Instrument)
getInstrument() - Method in class ome.model.acquisition.LightSource
Many-to-one field ome.model.acquisition.LightSource.instrument (ome.model.acquisition.Instrument)
getInstrument() - Method in class ome.model.acquisition.Objective
Many-to-one field ome.model.acquisition.Objective.instrument (ome.model.acquisition.Instrument)
getInstrument() - Method in class ome.model.acquisition.OTF
Many-to-one field ome.model.acquisition.OTF.instrument (ome.model.acquisition.Instrument)
getInstrument() - Method in class ome.model.core.Image
Many-to-one field ome.model.core.Image.instrument (ome.model.acquisition.Instrument)
getInstrumentId() - Method in class pojos.ImageData
Returns the id of the instrument if any.
getIntegration() - Method in class ome.model.acquisition.DetectorSettings
Simple field ome.model.acquisition.DetectorSettings.integration (java.lang.Integer)
getInternalServiceFactory(String, String, int, int, String) - Method in interface ome.services.blitz.fire.Registry
Try to return a ServiceFactory from the grid.
getInternalServiceFactory(String, String, int, int, String) - Method in class ome.services.blitz.fire.Registry.Impl
 
getInternalValue(String) - Method in interface ome.api.local.LocalConfig
Provides a configuration value, ignoring the visibility of the given value.
getInternalValue(String) - Method in class ome.logic.ConfigImpl
 
getIntervalEnd() - Method in class omeis.providers.re.codomain.CodomainChain
Returns the upper bound of the codomain interval.
getIntervalStart() - Method in class omeis.providers.re.codomain.CodomainChain
Returns the lower bound of the codomain interval.
getIObjectContainer(Class<? extends IObject>, LinkedHashMap<Index, Integer>) - Method in interface ome.formats.model.IObjectContainerStore
Retrieves an IObject container for a given class and location within the OME-XML data model.
getIObjectContainer(Class<? extends IObject>, LinkedHashMap<Index, Integer>) - Method in class ome.formats.OMEROMetadataStoreClient
 
getIObjectContainers(Class<? extends IObject>) - Method in interface ome.formats.model.IObjectContainerStore
Retrieves all IObject containers of a given class.
getIObjectContainers(Class<? extends IObject>) - Method in class ome.formats.OMEROMetadataStoreClient
 
getIP(Current) - Method in class ome.services.blitz.fire.SessionManagerI
 
getIQuery() - Method in class ome.formats.OMEROMetadataStoreClient
 
getIris() - Method in class ome.model.acquisition.Objective
Simple field ome.model.acquisition.Objective.iris (java.lang.Boolean)
getIsSPW() - Method in class ome.formats.importer.ImportContainer
Return true if this import container contains a Screen/Plate/Well image group.
getItemCount() - Method in class ome.model.meta.Share
Simple field ome.model.meta.Share.itemCount (java.lang.Long)
getIterator() - Method in class pojos.ROIData
Returns the iterator of the collection of the map.
getJavaClass() - Method in class ome.util.LSID
Returns the Java class which qualifies the type of object this LSID represents.
getJavaClasspath() - Method in class ome.formats.importer.util.ErrorContainer
 
getJavaVersion() - Method in class ome.formats.importer.util.ErrorContainer
 
getJob() - Method in interface ome.api.JobHandle
 
getJob(Current) - Method in class ome.services.blitz.impl.ScriptProcessI
 
getJob() - Method in class ome.services.JobBean
 
getJob(Current) - Method in class omero.grid.InteractiveProcessorI
 
getJob_async(AMD_JobHandle_getJob, Current) - Method in class ome.services.blitz.impl.JobHandleI
 
getJobLinks() - Method in class ome.model.fs.Fileset
returns jobLinks .
getJobLinksCountPerOwner() - Method in class ome.model.fs.Fileset
If fetched, returns the count(*) of ome.model.fs.FilesetJobLink that a user has.
getKeepAlive() - Method in class ome.formats.OMEROMetadataStoreClient
Returns clientKeepAlive created in store
getKey() - Method in class ome.services.eventlogs.PersistentEventLogLoader
 
getKeySet() - Method in class ome.system.PreferenceContext
 
getKeywords() - Method in class ome.model.meta.Namespace
Simple field ome.model.meta.Namespace.keywords (java.util.List)
getKeywords() - Method in class ome.model.roi.Roi
Simple field ome.model.roi.Roi.keywords (java.util.List)
getKeywords() - Method in class pojos.WorkflowData
Returns the keywords of this workflow.
getKeywordsAsList() - Method in class pojos.WorkflowData
Returns the keywords of this workflow as a list.
getKind() - Method in class pojos.LightSourceData
Returns the kind of light source.
getLabel() - Method in class pojos.PlateAcquisitionData
Returns the label associated to the plate acquisition.
getLabelName() - Method in class pojos.ImageAcquisitionData
Returns the name of the stage label.
getLaser(int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
getLaserFrequencyMultiplication() - Method in class pojos.LightSourceData
Returns the frequency multiplication of the laser.
getLaserMedium() - Method in class ome.model.acquisition.Laser
Many-to-one field ome.model.acquisition.Laser.laserMedium (ome.model.enums.LaserMedium)
getLaserMedium() - Method in class pojos.LightSourceData
Returns the laser's medium.
getLaserPockelCell() - Method in class pojos.LightSourceData
Returns the pockel cell flag of the laser.
getLaserPulse() - Method in class pojos.LightSourceData
Returns the pulse of the laser.
getLaserPump() - Method in class pojos.LightSourceData
Returns the pump.
getLaserRepetitionRate(UnitsFrequency) - Method in class pojos.LightSourceData
Returns the repetition rate (Hz) if the laser is repetitive.
getLaserRepetitionRate() - Method in class pojos.LightSourceData
getLaserTuneable() - Method in class pojos.LightSourceData
Returns the value of the tuneable field or null if no value set.
getLaserWavelength(UnitsLength) - Method in class pojos.LightSourceData
Returns the laser's wavelength.
getLaserWavelength() - Method in class pojos.LightSourceData
getLast() - Method in class ome.security.basic.CurrentDetails
 
getLast() - Method in interface ome.security.basic.PrincipalHolder
Get the last, i.e. currently active, principal.
getLastModified() - Method in class pojos.AnnotationData
Returns the time when the annotation was last modified.
getLastName() - Method in class ome.model.meta.Experimenter
Simple field ome.model.meta.Experimenter.lastName (java.lang.String)
getLastName() - Method in class pojos.ExperimenterData
Returns the last name of the experimenter.
getLastUpdated() - Method in class ome.services.sessions.state.SessionCache
 
getLauncher() - Method in class ome.services.scripts.ScriptFileType
Return the name of the launcher (".
getLauncher(String) - Method in class ome.services.scripts.ScriptRepoHelper
Find an "omero.launcher..." property string for the given mimetype or return "" if none is found.
getLdap() - Method in class ome.model.meta.Experimenter
Simple field ome.model.meta.Experimenter.ldap (java.lang.Boolean)
getLdap() - Method in class ome.model.meta.ExperimenterGroup
Simple field ome.model.meta.ExperimenterGroup.ldap (java.lang.Boolean)
getLdapExperimenters() - Method in interface ome.util.SqlAction
Gets the experimenters who have the ldap attribute enabled.
getLdapExperimenters() - Method in class ome.util.SqlAction.Impl
 
getLdapService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
getLdapService() - Method in class ome.system.ServiceFactory
 
getLeaderOfGroupIds(Experimenter) - Method in interface ome.api.IAdmin
Finds the ids for all groups for which the given Experimenter is owner/leader.
getLeaderOfGroupIds(Experimenter) - Method in class ome.logic.AdminImpl
 
getLeaderOfGroupIds_async(AMD_IAdmin_getLeaderOfGroupIds, Experimenter, Current) - Method in class ome.services.blitz.impl.AdminI
 
getLeaderOfGroupsList() - Method in class ome.security.basic.BasicEventContext
 
getLeaderOfGroupsList() - Method in class ome.services.sessions.SessionContextImpl
 
getLeaderOfGroupsList() - Method in interface ome.system.EventContext
 
getLeaderOfGroupsList() - Method in class ome.system.SimpleEventContext
 
getLeaders() - Method in class pojos.GroupData
Returns the experimenters contained in this group.
getLeaves() - Method in class omero.sys.ParametersI
 
getLength() - Method in class ome.formats.importer.transfers.TransferState
Return the length of the target file.
getLensNA() - Method in class ome.model.acquisition.Objective
Simple field ome.model.acquisition.Objective.lensNA (java.lang.Double)
getLensNA() - Method in class pojos.ObjectiveData
Returns the objective's LensNA.
getLightEmittingDiode(int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
getLightPath() - Method in class ome.model.core.LogicalChannel
Many-to-one field ome.model.core.LogicalChannel.lightPath (ome.model.acquisition.LightPath)
getLightPath() - Method in class pojos.ChannelAcquisitionData
Returns the light path or null.
getLightPathEmissionFilters() - Method in class ome.formats.model.ChannelData
Returns the collection of emission filters in the light path.
getLightPathExcitationFilterLink(int) - Method in class ome.model.acquisition.LightPath
Gets the ome.model.acquisition.LightPathExcitationFilterLink at the given index.
getLightPathExcitationFilters() - Method in class ome.formats.model.ChannelData
Returns the collection of excitation filters in the light path.
getLightSettingsAttenuation() - Method in class pojos.ChannelAcquisitionData
Returns the attenuation of the light source, percent value between 0 and 1.
getLightSettingsWavelength(UnitsLength) - Method in class pojos.ChannelAcquisitionData
Returns the wavelength of the light source.
getLightSettingsWavelength() - Method in class pojos.ChannelAcquisitionData
getLightSource() - Method in class ome.formats.model.ChannelData
Returns the light source for the light source settings of this channel data.
getLightSource() - Method in class ome.model.acquisition.Instrument
returns lightSource .
getLightSource() - Method in class ome.model.acquisition.LightSettings
Many-to-one field ome.model.acquisition.LightSettings.lightSource (ome.model.acquisition.LightSource)
getLightSource() - Method in class pojos.ChannelAcquisitionData
Returns the source of light.
getLightSourceModel() - Method in class pojos.LightSourceData
Returns the model of the light source.
getLightSources() - Method in class pojos.InstrumentData
Returns the collection of light sources.
getLightSourceSettings() - Method in class ome.formats.model.ChannelData
Returns the light source settings for the logical channel of this channel data.
getLightSourceSettings() - Method in class ome.model.core.LogicalChannel
Many-to-one field ome.model.core.LogicalChannel.lightSourceSettings (ome.model.acquisition.LightSettings)
getLightSourceSettings() - Method in class ome.model.experiment.MicrobeamManipulation
returns lightSourceSettings .
getLimit() - Method in class ome.parameters.Parameters
 
getLimit() - Method in class omero.sys.ParametersI
Returns the value of the limit parameter.
getLine(int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
getLine() - Method in class ome.services.blitz.repo.FileMaker
 
getLineCap() - Method in class pojos.ShapeSettingsData
Returns the shape of the end of the line..
getLinkedBy(String) - Method in class ome.services.graphs.GraphPathBean
Get the classes and properties that link to the given class.
getLinkedTo(String) - Method in class ome.services.graphs.GraphPathBean
Get the classes and properties to which the given class links.
getListAnnotation(int) - Method in class ome.formats.OMEROMetadataStoreClient
 
getLocalLocation(OriginalFile, OriginalFile) - Method in class ome.formats.importer.transfers.AbstractExecFileTransfer
Build a path of the form "root.path/root.name/file.path/file.name".
getLocationStats() - Method in class omeis.providers.re.metadata.StatsFactory
Returns the statistics.
getLockCandidateChecks(Class<? extends IObject>, boolean) - Method in interface ome.tools.hibernate.ExtendedMetadata
Rather than iterating over an IObject like ExtendedMetadata.getLockCandidates(IObject) this method returns type/field name pairs (like ExtendedMetadata.getLockChecks(Class)) to allow performing the queries manually.
getLockCandidateChecks(Class<? extends IObject>, boolean) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
 
getLockCandidateChecks(boolean) - Method in class ome.tools.hibernate.ExtendedMetadata.Locks
 
getLockCandidates() - Method in class ome.security.basic.BasicEventContext
 
getLockCandidates(IObject) - Method in interface ome.tools.hibernate.ExtendedMetadata
walks the IObject argument non-recursively and gathers all IObject instances which will be linked to by the creation or updating of the argument.
getLockCandidates(IObject) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
walks the IObject argument non-recursively and gathers all IObject instances which will be linkd to by the creation or updating of the argument.
getLockCandidates(IObject) - Method in class ome.tools.hibernate.ExtendedMetadata.Locks
 
getLockChecks(Class<? extends IObject>) - Method in interface ome.tools.hibernate.ExtendedMetadata
returns all class/field name pairs which may possibly link to an object of type klass.
getLockChecks(Class<? extends IObject>) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
returns all class/field name pairs which may possibly link to an object of type klass.
getLocked() - Method in class ome.model.roi.Shape
Simple field ome.model.roi.Shape.locked (java.lang.Boolean)
getLockingIds(Class<IObject>, long, Long) - Method in interface ome.api.local.LocalAdmin
Returns a map from Class (as string) to a count for all entities which point to the given IObject.
getLockingIds(IObject) - Method in class ome.logic.AdminImpl
 
getLockingIds(Class<IObject>, long, Long) - Method in class ome.logic.AdminImpl
 
getLogFile() - Method in class ome.formats.importer.ImportConfig
 
getLogFile() - Method in class ome.formats.importer.util.IniFileLoader
 
getLogFile() - Method in class ome.services.blitz.repo.ManagedImportLocationI
Return the server-side CheckedPath instance which can be used for writing a log file for a fileset.
getLogger() - Method in class ome.services.util.BeanHelper
 
getLogicalChannel() - Method in class ome.formats.model.ChannelData
Returns the logical channel for this channel data.
getLogicalChannel() - Method in class ome.model.core.Channel
Many-to-one field ome.model.core.Channel.logicalChannel (ome.model.core.LogicalChannel)
getLogs() - Method in class ome.model.meta.Event
returns logs .
getLogs() - Method in class ome.security.basic.BasicEventContext
 
getLogs() - Method in class ome.security.basic.BasicSecuritySystem
 
getLogs() - Method in class ome.security.basic.CurrentDetails
 
getLogString(SelfConfigurableService) - Method in class ome.services.util.BeanHelper
 
getLongAnnotation(int) - Method in class ome.formats.OMEROMetadataStoreClient
 
getLongAnnotationCount() - Method in class ome.services.blitz.impl.OmeroMetadata
 
getLongAnnotationDescription(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getLongAnnotationID(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getLongAnnotationNamespace(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getLongAnnotationValue(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getLongValue() - Method in class ome.model.annotations.LongAnnotation
Simple field ome.model.annotations.LongAnnotation.longValue (java.lang.Long)
getLookupTable() - Method in class ome.model.core.Channel
Simple field ome.model.core.Channel.lookupTable (java.lang.String)
getLookupTable() - Method in class ome.model.display.ChannelBinding
Simple field ome.model.display.ChannelBinding.lookupTable (java.lang.String)
getLotNumber() - Method in class ome.model.acquisition.Detector
Simple field ome.model.acquisition.Detector.lotNumber (java.lang.String)
getLotNumber() - Method in class ome.model.acquisition.Dichroic
Simple field ome.model.acquisition.Dichroic.lotNumber (java.lang.String)
getLotNumber() - Method in class ome.model.acquisition.Filter
Simple field ome.model.acquisition.Filter.lotNumber (java.lang.String)
getLotNumber() - Method in class ome.model.acquisition.FilterSet
Simple field ome.model.acquisition.FilterSet.lotNumber (java.lang.String)
getLotNumber() - Method in class ome.model.acquisition.LightSource
Simple field ome.model.acquisition.LightSource.lotNumber (java.lang.String)
getLotNumber() - Method in class ome.model.acquisition.Microscope
Simple field ome.model.acquisition.Microscope.lotNumber (java.lang.String)
getLotNumber() - Method in class ome.model.acquisition.Objective
Simple field ome.model.acquisition.Objective.lotNumber (java.lang.String)
getLotNumber() - Method in class pojos.DetectorData
Returns the lot number of the detector.
getLotNumber() - Method in class pojos.DichroicData
Returns the lot number.
getLotNumber() - Method in class pojos.FilterData
Returns the lot number.
getLotNumber() - Method in class pojos.FilterSetData
Returns the lot number.
getLotNumber() - Method in class pojos.LightSourceData
Returns the lot of number the light source.
getLotNumber() - Method in class pojos.ObjectiveData
Returns the lot number of the detector.
getLowerLimit() - Method in class ome.model.display.PlaneSlicingContext
Simple field ome.model.display.PlaneSlicingContext.lowerLimit (java.lang.Integer)
getLowerLimit() - Method in class omeis.providers.re.codomain.PlaneSlicingContext
Returns the constant level for bit-planes < planeSelected w.r.t the higher-order bits.
getLsid() - Method in class ome.model.meta.ExternalInfo
Simple field ome.model.meta.ExternalInfo.lsid (java.lang.String)
getMailUtil() - Method in class ome.services.mail.MailSender
 
getManagedServerContext() - Static method in class ome.system.OmeroContext
create (if necessary) and return the single default managed OmeroContext.
getManagerList(boolean) - Method in class ome.services.blitz.fire.Ring
 
getManagerList(boolean) - Method in interface ome.services.blitz.redirect.Redirector.Context
Return all known managers in the current cluster context, possibly filtering out the inactive ones.
getManufacturer() - Method in class ome.model.acquisition.Detector
Simple field ome.model.acquisition.Detector.manufacturer (java.lang.String)
getManufacturer() - Method in class ome.model.acquisition.Dichroic
Simple field ome.model.acquisition.Dichroic.manufacturer (java.lang.String)
getManufacturer() - Method in class ome.model.acquisition.Filter
Simple field ome.model.acquisition.Filter.manufacturer (java.lang.String)
getManufacturer() - Method in class ome.model.acquisition.FilterSet
Simple field ome.model.acquisition.FilterSet.manufacturer (java.lang.String)
getManufacturer() - Method in class ome.model.acquisition.LightSource
Simple field ome.model.acquisition.LightSource.manufacturer (java.lang.String)
getManufacturer() - Method in class ome.model.acquisition.Microscope
Simple field ome.model.acquisition.Microscope.manufacturer (java.lang.String)
getManufacturer() - Method in class ome.model.acquisition.Objective
Simple field ome.model.acquisition.Objective.manufacturer (java.lang.String)
getManufacturer() - Method in class pojos.DetectorData
Returns the manufacturer of the detector.
getManufacturer() - Method in class pojos.DichroicData
Returns the manufacturer.
getManufacturer() - Method in class pojos.FilterData
Returns the manufacturer.
getManufacturer() - Method in class pojos.FilterSetData
Returns the manufacturer.
getManufacturer() - Method in class pojos.LightSourceData
Returns the manufacturer of the light source.
getManufacturer() - Method in class pojos.ObjectiveData
Returns the manufacturer of the detector.
getMap() - Method in class ome.model.acquisition.GenericExcitationSource
 
getMap() - Method in class ome.model.acquisition.ImagingEnvironment
 
getMapProperties(String) - Method in interface ome.tools.hibernate.ExtendedMetadata
Get the names of any String→RString map properties this class has, otherwise an empty set if none.
getMapProperties(String) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
 
getMapValue() - Method in class ome.model.annotations.MapAnnotation
 
getMarkerEnd() - Method in class pojos.ShapeSettingsData
Returns the marker end.
getMarkerStart() - Method in class pojos.ShapeSettingsData
Returns the marker start.
getMask(int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
getMask() - Method in class pojos.MaskData
Returns the mask as a byte array.
getMaskAsBinaryArray() - Method in class pojos.MaskData
Returns the mask image.
getMaskAsBufferedImage() - Method in class pojos.MaskData
Returns the mask image.
getMaskPoints() - Method in class pojos.PolygonData
Returns the points in the polygon.
getMaskPoints() - Method in class pojos.PolylineData
Returns the points in the Polyline.
getMatcher(String) - Method in class ome.services.graphs.GraphEntry
Deprecated.
 
getMax() - Method in class ome.system.metrics.DefaultSnapshot
 
getMax() - Method in interface ome.system.metrics.Snapshot
 
getMaximum() - Method in class ome.util.PixelData
Returns the minimum pixel value this pixel data supports.
getMaximumFieldCount() - Method in class ome.model.screen.PlateAcquisition
Simple field ome.model.screen.PlateAcquisition.maximumFieldCount (java.lang.Integer)
getMaximumFieldCount() - Method in class pojos.PlateAcquisitionData
Returns the maximum number of fields in any well.
getMaxPlaneHeight() - Method in class ome.io.nio.ConfiguredTileSizes
 
getMaxPlaneHeight() - Method in interface ome.io.nio.TileSizes
 
getMaxPlaneWidth() - Method in class ome.io.nio.ConfiguredTileSizes
 
getMaxPlaneWidth() - Method in interface ome.io.nio.TileSizes
 
getMean() - Method in class ome.system.metrics.DefaultSnapshot
 
getMean() - Method in interface ome.system.metrics.Snapshot
 
getMeasuredRois_async(AMD_IRoi_getMeasuredRois, long, long, RoiOptions, Current) - Method in class ome.services.blitz.impl.RoiI
 
getMeasuredRoisMap_async(AMD_IRoi_getMeasuredRoisMap, long, List<Long>, RoiOptions, Current) - Method in class ome.services.blitz.impl.RoiI
 
getMedian() - Method in class ome.system.metrics.DefaultSnapshot
 
getMedian() - Method in interface ome.system.metrics.Snapshot
 
getMedium() - Method in class ome.model.acquisition.ObjectiveSettings
Many-to-one field ome.model.acquisition.ObjectiveSettings.medium (ome.model.enums.Medium)
getMedium() - Method in class pojos.ImageAcquisitionData
Returns the medium of the objective.
getMediumAsEnum() - Method in class pojos.ImageAcquisitionData
Returns the medium enumeration value.
getMemberCount(Set<Long>) - Method in interface ome.api.IShare
Returns a map from share id to the count of total members (including the owner).
getMemberCount(Set<Long>) - Method in class ome.services.sharing.ShareBean
 
getMemberCount_async(AMD_IShare_getMemberCount, List<Long>, Current) - Method in class ome.services.blitz.impl.ShareI
 
getMemberOfGroupIds(Experimenter) - Method in interface ome.api.IAdmin
Finds the ids for all groups for which the given Experimenter is a member.
getMemberOfGroupIds(Experimenter) - Method in class ome.logic.AdminImpl
 
getMemberOfGroupIds_async(AMD_IAdmin_getMemberOfGroupIds, Experimenter, Current) - Method in class ome.services.blitz.impl.AdminI
 
getMemberOfGroupsList() - Method in class ome.security.basic.BasicEventContext
 
getMemberOfGroupsList() - Method in class ome.services.sessions.SessionContextImpl
 
getMemberOfGroupsList() - Method in interface ome.system.EventContext
 
getMemberOfGroupsList() - Method in class ome.system.SimpleEventContext
 
getMemberShares(boolean) - Method in interface ome.api.IShare
Gets all shares where current Experimenter is a member.
getMemberShares(boolean) - Method in class ome.services.sharing.ShareBean
 
getMemberShares_async(AMD_IShare_getMemberShares, boolean, Current) - Method in class ome.services.blitz.impl.ShareI
 
getMemberSharesFor(Experimenter, boolean) - Method in interface ome.api.IShare
Gets all shares where given Experimenter is a member.
getMemberSharesFor(Experimenter, boolean) - Method in class ome.services.sharing.ShareBean
 
getMemberSharesFor_async(AMD_IShare_getMemberSharesFor, Experimenter, boolean, Current) - Method in class ome.services.blitz.impl.ShareI
 
getMembersOnly() - Method in class pojos.GroupData
Returns the list of experimenters that are not owners of the group.
getMemoizerDirectory() - Method in class ome.io.nio.PixelsService
 
getMemoizerWait() - Method in class ome.io.nio.PixelsService
 
getMessage() - Method in exception ome.conditions.acl.ACLViolation
 
getMessage() - Method in exception ome.conditions.acl.CollectedACLViolations
 
getMessage() - Method in exception ome.io.nio.PixelBufferException
 
getMessage() - Method in class ome.model.jobs.Job
Simple field ome.model.jobs.Job.message (java.lang.String)
getMessage() - Method in class ome.model.meta.DBPatch
Simple field ome.model.meta.DBPatch.message (java.lang.String)
getMessage() - Method in class ome.model.meta.Session
Simple field ome.model.meta.Session.message (java.lang.String)
getMessageDigest() - Method in class ome.io.bioformats.BfPixelsWrapper
 
getMessages() - Method in class ome.services.messages.DeleteLogsMessage
 
getMetadata(long) - Method in class ome.services.ThumbnailCtx
Retrieves the Thumbnail object for a given Pixels ID.
getMetadata() - Method in class omeis.providers.re.Renderer
Returns the Pixels set the rendering engine is for.
getMetadataOptions() - Method in class ome.formats.importer.OMEROWrapper
 
getMetadataService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
getMetadataService() - Method in class ome.system.ServiceFactory
 
getMethod(String) - Method in class ome.services.blitz.util.IceMethodInvoker
For testing the cached method.
getMethodCount() - Method in class ome.services.messages.stats.MethodStatsMessage
 
getMethodology() - Method in class ome.model.core.Pixels
Simple field ome.model.core.Pixels.methodology (java.lang.String)
getMicrobeamManipulation(int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
getMicrobeamManipulation() - Method in class ome.model.acquisition.LightSettings
Many-to-one field ome.model.acquisition.LightSettings.microbeamManipulation (ome.model.experiment.MicrobeamManipulation)
getMicrobeamManipulation() - Method in class ome.model.experiment.Experiment
returns microbeamManipulation .
getMicrobeamManipulationLightSourceSettings(int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
getMicroscope() - Method in class ome.model.acquisition.Instrument
Many-to-one field ome.model.acquisition.Instrument.microscope (ome.model.acquisition.Microscope)
getMicroscopeLotNumber() - Method in class pojos.InstrumentData
Returns the lot number of the microscope.
getMicroscopeManufacturer() - Method in class pojos.InstrumentData
Returns the model of the microscope.
getMicroscopeModel() - Method in class pojos.InstrumentData
Returns the model of the microscope.
getMicroscopeSerialNumber() - Method in class pojos.InstrumentData
Returns the serial number of the microscope.
getMicroscopeType() - Method in class pojos.InstrumentData
Returns the type of microscope.
getMiddleName() - Method in class ome.model.meta.Experimenter
Simple field ome.model.meta.Experimenter.middleName (java.lang.String)
getMiddleName() - Method in class pojos.ExperimenterData
Returns the middle name of the experimenter.
getMiddleRange(double) - Method in class omeis.providers.re.quantum.QuantumStrategy
Returns the range the values belongs to.
getMimetype() - Method in class ome.model.core.OriginalFile
Simple field ome.model.core.OriginalFile.mimetype (java.lang.String)
getMimeType() - Method in class ome.model.display.Thumbnail
Simple field ome.model.display.Thumbnail.mimeType (java.lang.String)
getMimetype() - Method in class ome.services.blitz.repo.CheckedPath
Get the mimetype for a file.
getMimetype() - Method in class ome.services.scripts.ScriptFileType
Returns the mimetype that must be set on an original file instance in order to be considered of this type.
getMin() - Method in class ome.system.metrics.DefaultSnapshot
 
getMin() - Method in interface ome.system.metrics.Snapshot
 
getMinimum() - Method in class ome.util.PixelData
Returns the minimum pixel value this pixel data supports.
getMinimumDepth(Collection<File>) - Method in class ome.services.blitz.repo.path.ClientFilePathTransformer
Get the smallest path component depth that allows the given set of Files to be disambiguated.
getMode() - Method in class ome.model.core.LogicalChannel
Many-to-one field ome.model.core.LogicalChannel.mode (ome.model.enums.AcquisitionMode)
getMode() - Method in class pojos.ChannelAcquisitionData
Returns the mode.
getMode() - Method in class pojos.ChannelData
Returns the mode.
getModeAsEnum() - Method in class pojos.ChannelData
Returns the acquisition enumeration value.
getModel() - Method in class ome.model.acquisition.Detector
Simple field ome.model.acquisition.Detector.model (java.lang.String)
getModel() - Method in class ome.model.acquisition.Dichroic
Simple field ome.model.acquisition.Dichroic.model (java.lang.String)
getModel() - Method in class ome.model.acquisition.Filter
Simple field ome.model.acquisition.Filter.model (java.lang.String)
getModel() - Method in class ome.model.acquisition.FilterSet
Simple field ome.model.acquisition.FilterSet.model (java.lang.String)
getModel() - Method in class ome.model.acquisition.LightSource
Simple field ome.model.acquisition.LightSource.model (java.lang.String)
getModel() - Method in class ome.model.acquisition.Microscope
Simple field ome.model.acquisition.Microscope.model (java.lang.String)
getModel() - Method in class ome.model.acquisition.Objective
Simple field ome.model.acquisition.Objective.model (java.lang.String)
getModel() - Method in class ome.model.display.RenderingDef
Many-to-one field ome.model.display.RenderingDef.model (ome.model.enums.RenderingModel)
getModel() - Method in class ome.services.RenderingBean
Implemented as specified by the RenderingEngine interface.
getModel() - Method in interface omeis.providers.re.RenderingEngine
Returns the model that dictates how transformed raw data has to be mapped onto a color space.
getModel() - Method in class pojos.DetectorData
Returns the manufacturer of the detector.
getModel() - Method in class pojos.DichroicData
Returns the model.
getModel() - Method in class pojos.FilterData
Returns the model.
getModel() - Method in class pojos.FilterSetData
Returns the model.
getModel() - Method in class pojos.ObjectiveData
Returns the model of the objective.
getModel_async(AMD_RenderingEngine_getModel, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
getModelProcessors() - Method in class ome.formats.OMEROMetadataStoreClient
Retrieves the current list of model processors the metadata store is using.
getMostRecentAnnotationLinks_async(AMD_ITimeline_getMostRecentAnnotationLinks, List<String>, List<String>, List<String>, Parameters, Current) - Method in class ome.services.blitz.impl.TimelineI
 
getMostRecentObjects_async(AMD_ITimeline_getMostRecentObjects, List<String>, Parameters, boolean, Current) - Method in class ome.services.blitz.impl.TimelineI
 
getMostRecentShareCommentLinks_async(AMD_ITimeline_getMostRecentShareCommentLinks, Parameters, Current) - Method in class ome.services.blitz.impl.TimelineI
 
getMtime() - Method in class ome.model.core.OriginalFile
Simple field ome.model.core.OriginalFile.mtime (java.sql.Timestamp)
getMultivalued() - Method in class ome.model.meta.Namespace
Simple field ome.model.meta.Namespace.multivalued (java.lang.Boolean)
getMyOpenAgentSessions(String) - Method in interface ome.api.ISession
Like ISession.getMyOpenSessions() but returns only those sessions with the given agent string.
getMyOpenAgentSessions(String) - Method in class ome.services.sessions.SessionBean
 
getMyOpenAgentSessions_async(AMD_ISession_getMyOpenAgentSessions, String, Current) - Method in class ome.services.blitz.impl.SessionI
 
getMyOpenClientSessions() - Method in interface ome.api.ISession
Like ISession.getMyOpenSessions() but returns only those sessions started by official OMERO clients.
getMyOpenClientSessions() - Method in class ome.services.sessions.SessionBean
 
getMyOpenClientSessions_async(AMD_ISession_getMyOpenClientSessions, Current) - Method in class ome.services.blitz.impl.SessionI
 
getMyOpenSessions() - Method in interface ome.api.ISession
Returns a list of open sessions for the current user.
getMyOpenSessions() - Method in class ome.services.sessions.SessionBean
 
getMyOpenSessions_async(AMD_ISession_getMyOpenSessions, Current) - Method in class ome.services.blitz.impl.SessionI
 
getMyUserPhotos() - Method in interface ome.api.IAdmin
Retrieve the OriginalFile objectd attached to this user as specified by {@link #uploadMyUserPhoto(String, String, byte[]).
getMyUserPhotos() - Method in class ome.logic.AdminImpl
 
getMyUserPhotos_async(AMD_IAdmin_getMyUserPhotos, Current) - Method in class ome.services.blitz.impl.AdminI
 
getName() - Method in class ome.logic.HardWiredInterceptor
Can be implemented by all subclasses, so that they can configure themselves in HardWiredInterceptor.selfConfigure(OmeroContext).
getName() - Method in class ome.model.acquisition.StageLabel
Simple field ome.model.acquisition.StageLabel.name (java.lang.String)
getName() - Method in class ome.model.annotations.Annotation
Simple field ome.model.annotations.Annotation.name (java.lang.String)
getName() - Method in class ome.model.containers.Dataset
Simple field ome.model.containers.Dataset.name (java.lang.String)
getName() - Method in class ome.model.containers.Project
Simple field ome.model.containers.Project.name (java.lang.String)
getName() - Method in class ome.model.core.Image
Simple field ome.model.core.Image.name (java.lang.String)
getName() - Method in class ome.model.core.LogicalChannel
Simple field ome.model.core.LogicalChannel.name (java.lang.String)
getName() - Method in class ome.model.core.OriginalFile
Simple field ome.model.core.OriginalFile.name (java.lang.String)
getName() - Method in class ome.model.display.RenderingDef
Simple field ome.model.display.RenderingDef.name (java.lang.String)
getName() - Method in class ome.model.internal.NamedValue
 
getName() - Method in class ome.model.meta.ExperimenterGroup
Simple field ome.model.meta.ExperimenterGroup.name (java.lang.String)
getName() - Method in class ome.model.meta.Namespace
Simple field ome.model.meta.Namespace.name (java.lang.String)
getName() - Method in class ome.model.roi.Roi
Simple field ome.model.roi.Roi.name (java.lang.String)
getName() - Method in class ome.model.screen.Plate
Simple field ome.model.screen.Plate.name (java.lang.String)
getName() - Method in class ome.model.screen.PlateAcquisition
Simple field ome.model.screen.PlateAcquisition.name (java.lang.String)
getName() - Method in class ome.model.screen.Reagent
Simple field ome.model.screen.Reagent.name (java.lang.String)
getName() - Method in class ome.model.screen.Screen
Simple field ome.model.screen.Screen.name (java.lang.String)
getName() - Method in class ome.security.basic.AbstractSecurityFilter
 
getName() - Method in class ome.security.basic.BasicSecurityWiring
Lookup name.
getName() - Method in class ome.security.policy.BasePolicy
 
getName() - Method in class ome.security.policy.BinaryAccessPolicy
 
getName() - Method in interface ome.security.policy.Policy
Unique name for a class of restrictions that this Policy will enforce.
getName() - Method in interface ome.security.SecurityFilter
Name of this security filter.
getName() - Method in class ome.security.SecurityFilterHolder
 
getName() - Method in class ome.services.blitz.repo.CheckedPath
Get the last component of this path, the entity to which the path corresponds.
getName() - Method in class ome.services.graphs.BaseGraphSpec
Deprecated.
 
getName() - Method in class ome.services.graphs.GraphEntry
Deprecated.
 
getName(Matcher) - Method in class ome.services.graphs.GraphEntry
Deprecated.
 
getName() - Method in interface ome.services.graphs.GraphPolicyRulePredicate
 
getName() - Method in interface ome.services.graphs.GraphSpec
Deprecated.
The name of this specification.
getName() - Method in class ome.services.graphs.GroupPredicate
 
getName() - Method in class ome.services.graphs.PermissionsPredicate
 
getName() - Method in class ome.services.roi.PopulateRoiJob
 
getName() - Method in class ome.services.scripts.ScriptFinder
Subclasses should override to return the name of the file under scripts/ which should be uploaded.
getName() - Method in interface ome.services.sessions.SessionCallback
 
getName() - Method in class ome.services.sessions.SessionCallback.SimpleCloseCallback
 
getName() - Method in class ome.system.Login
simple getter for the user name passed into the constructor
getName() - Method in class ome.system.Preference
 
getName() - Method in class ome.system.Principal
 
getName() - Method in class pojos.ChannelData
Returns the name of the channel.
getName() - Method in class pojos.DatasetData
Returns the name of the dataset.
getName() - Method in class pojos.FileData
Returns the name of the file.
getName() - Method in class pojos.GroupData
Returns the name of the group.
getName() - Method in class pojos.ImageData
Returns the name of the image.
getName() - Method in class pojos.PlateAcquisitionData
Returns the name of the plate acquisition.
getName() - Method in class pojos.PlateData
Returns the name of the plate.
getName() - Method in class pojos.ProjectData
Returns the name of the project.
getName() - Method in class pojos.ScreenData
Returns the name of the screen.
getNameSpace() - Method in class pojos.AnnotationData
Retrieves the nameSpace of the underlying Annotation instance.
getNameSpace() - Method in class pojos.WorkflowData
Returns the namespace of this workflow.
getNamespaceKeywords(String) - Method in class pojos.ROIData
Returns the keywords of the namespace on the ROI.
getNamespaceKeywords() - Method in class pojos.ROIData
Returns the keywords of the ROI.
getNamespaces() - Method in class ome.model.roi.Roi
Simple field ome.model.roi.Roi.namespaces (java.util.List)
getNamespaces() - Method in class pojos.ROIData
Returns the namespace of the ROI.
getNdFilter() - Method in class ome.model.core.LogicalChannel
Simple field ome.model.core.LogicalChannel.ndFilter (java.lang.Double)
getNDFilter() - Method in class pojos.ChannelData
Returns the ND filter wavelength of the channel.
getNewUserGroup() - Method in class ome.security.auth.LdapConfig
 
getNewUserGroupOwner() - Method in class ome.security.auth.LdapConfig
 
getNode() - Method in class ome.model.meta.Session
Many-to-one field ome.model.meta.Session.node (ome.model.meta.Node)
getNodeUuid(Current) - Method in class ome.services.blitz.fire.Ring
 
getNoiseReduction() - Method in class ome.model.display.ChannelBinding
Simple field ome.model.display.ChannelBinding.noiseReduction (java.lang.Boolean)
getNoiseReduction() - Method in class omeis.providers.re.quantum.QuantumStrategy
Returns true if the noise reduction algorithm is turned on, false if turned off.
getNominalMagnification() - Method in class ome.model.acquisition.Objective
Simple field ome.model.acquisition.Objective.nominalMagnification (java.lang.Double)
getNominalMagnification() - Method in class pojos.ObjectiveData
Returns the objective's nominal magnification factor.
getNoStatsInfo() - Method in class ome.formats.importer.ImportContainer
Retrieves whether or not we disabling StatsInfo population.
getNs() - Method in class ome.model.annotations.Annotation
Simple field ome.model.annotations.Annotation.ns (java.lang.String)
getNumOfDirectories() - Method in class ome.formats.importer.ImportConfig
 
getNumOfDirectories() - Method in class ome.formats.importer.util.IniFileLoader
 
getObject(String, int) - Method in class ome.services.export.ExporterStepFactory
Deprecated.
 
getObject() - Method in interface ome.services.sessions.SessionCallback
 
getObject() - Method in class ome.services.sessions.SessionCallback.SimpleCloseCallback
 
getObject() - Method in class ome.services.sessions.state.CacheFactory
 
getObjectAdapter() - Method in class ome.services.blitz.repo.AbstractRepositoryI
 
getObjectAdapter() - Method in class ome.services.blitz.repo.InternalRepositoryConfig
 
getObjectByLSID(LSID) - Method in class ome.formats.OMEROMetadataStore
Retrieves an object from the internal object graph by LSID.
getObjectClass() - Method in class ome.services.mail.ObjectMailSender
 
getObjective(int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
getObjective() - Method in class ome.model.acquisition.Instrument
returns objective .
getObjective() - Method in class ome.model.acquisition.ObjectiveSettings
Many-to-one field ome.model.acquisition.ObjectiveSettings.objective (ome.model.acquisition.Objective)
getObjective() - Method in class ome.model.acquisition.OTF
Many-to-one field ome.model.acquisition.OTF.objective (ome.model.acquisition.Objective)
getObjective() - Method in class pojos.ImageAcquisitionData
Returns the objective used to capture the image.
getObjective() - Method in class pojos.OTFData
Returns the associated objective.
getObjectives() - Method in class pojos.InstrumentData
Returns the collection of objectives.
getObjectiveSettings(int) - Method in class ome.formats.OMEROMetadataStoreClient
 
getObjectiveSettings() - Method in class ome.model.core.Image
Many-to-one field ome.model.core.Image.objectiveSettings (ome.model.acquisition.ObjectiveSettings)
getObjectiveSettingsId() - Method in class pojos.ImageAcquisitionData
Returns the id of the Objective settings or -1 if not already linked to the image.
getObjectsRead() - Method in class ome.services.messages.stats.ObjectsReadStatsMessage
 
getObjectsWritten() - Method in class ome.services.messages.stats.ObjectsWrittenStatsMessage
 
getObjectType() - Method in class ome.security.basic.EventListenersFactoryBean
this FactoryBean produces a Map instance for use in LocalSessionFactoryBean.setEventListeners(Map)
getObjectType() - Method in class ome.services.delete.Deletion.Builder
Deprecated.
 
getObjectVoidMethods(Class<T>) - Static method in class ome.util.Utils
primarily used in Grinder to discover what methods to call
getOffset() - Method in class ome.parameters.Parameters
 
getOffset() - Method in class omero.sys.ParametersI
Returns the value of the offset parameter.
getOffset() - Method in class pojos.DetectorData
Returns the offset of the detector.
getOffsetValue() - Method in class ome.model.acquisition.Detector
Simple field ome.model.acquisition.Detector.offsetValue (java.lang.Double)
getOffsetValue() - Method in class ome.model.acquisition.DetectorSettings
Simple field ome.model.acquisition.DetectorSettings.offsetValue (java.lang.Double)
getOmeName() - Method in class ome.model.meta.Experimenter
Simple field ome.model.meta.Experimenter.omeName (java.lang.String)
getOmeroVersion() - Method in class ome.formats.importer.ImportConfig
 
getOp(Matcher) - Method in class ome.services.graphs.GraphEntry
Deprecated.
 
getOpString() - Method in class ome.services.graphs.GraphEntry
Deprecated.
Primarily used for passing back a string representation of the default operation to users for setting options.
getOpticalAxisAveraged() - Method in class ome.model.acquisition.OTF
Simple field ome.model.acquisition.OTF.opticalAxisAveraged (java.lang.Boolean)
getOptimisticFailureCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
getOptimizations() - Method in class omeis.providers.re.Renderer
Returns the optimizations that the renderer currently has enabled.
getOpts() - Method in class ome.services.graphs.GraphState
Deprecated.
 
getOrCreateParams(long, Current) - Method in class omero.grid.ParamsHelper
Get the script params for the file.
getOrder() - Method in class ome.io.nio.ReorderedPixelData
Returns the byte order of the backing buffer.
getOrder() - Method in class ome.util.PixelData
Returns the byte order of the backing buffer.
getOriginalEnumerations() - Method in interface ome.api.ITypes
Gets all original values.
getOriginalEnumerations() - Method in class ome.logic.TypesImpl
 
getOriginalEnumerations_async(AMD_ITypes_getOriginalEnumerations, Current) - Method in class ome.services.blitz.impl.TypesI
 
getOriginalFile() - Method in class ome.formats.importer.transfers.TransferState
Find original file as defined by the ID in the RawFileStorePrx regardless of group.
getOriginalFile() - Method in class ome.model.fs.FilesetEntry
Many-to-one field ome.model.fs.FilesetEntry.originalFile (ome.model.core.OriginalFile)
getOriginalFile(long, Current) - Method in interface ome.services.blitz.repo.RepositoryDao
Gets the original file instance for a given file ID.
getOriginalFile(long, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
 
getOriginalFileLinks() - Method in class ome.model.jobs.Job
returns originalFileLinks .
getOriginalFileLinksCountPerOwner() - Method in class ome.model.jobs.Job
If fetched, returns the count(*) of ome.model.jobs.JobOriginalFileLink that a user has.
getOriginalFilePath(AbstractFileSystemService, Pixels) - Method in interface ome.io.nio.FilePathResolver
Retrieves the original file path for a given set of pixels.
getOriginalFilePath(Pixels) - Method in class ome.io.nio.PixelsService
Retrieves the original file path for a given set of pixels.
getOriginalFilePath(AbstractFileSystemService, Pixels) - Method in class ome.services.OmeroFilePathResolver
 
getOriginalFiles(String, CheckedPath, Current) - Method in interface ome.services.blitz.repo.RepositoryDao
Return a non-null, possibly empty list of OriginalFile elements which are accessible to the given user at the given path.
getOriginalFiles(String, CheckedPath, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
 
getOriginalFiles(ServiceFactory, SqlAction, String, CheckedPath) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
 
getOriginalFileWithHasher(long, Current) - Method in interface ome.services.blitz.repo.RepositoryDao
Retrieve the original file of the given ID.
getOriginalFileWithHasher(long, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
 
getOriginalGlobalMax() - Method in class omeis.providers.re.quantum.QuantumStrategy
Returns the original maximum of all minima.
getOriginalGlobalMin() - Method in class omeis.providers.re.quantum.QuantumStrategy
Returns the original minimum of all minima.
getOriginalMimetype() - Method in class pojos.FileAnnotationData
Returns the format of the original file.
getOrphan() - Method in class omero.sys.ParametersI
 
getOSArch() - Method in class ome.formats.importer.util.ErrorContainer
 
getOSName() - Method in class ome.formats.importer.util.ErrorContainer
 
getOSVersion() - Method in class ome.formats.importer.util.ErrorContainer
 
getOtf() - Method in class ome.model.acquisition.Instrument
returns otf .
getOtf() - Method in class ome.model.core.LogicalChannel
Many-to-one field ome.model.core.LogicalChannel.otf (ome.model.acquisition.OTF)
getOTF() - Method in class pojos.ChannelAcquisitionData
Returns the OTF used for that channel.
getOTF() - Method in class pojos.InstrumentData
Returns the collection of OTFs.
getOutput(String, String) - Method in interface ome.api.ISession
Retrieves an entry from the session's output environment.
getOutput(String, String) - Method in class ome.services.sessions.SessionBean
 
getOutput(String, String) - Method in interface ome.services.sessions.SessionManager
Returns the output environment Object stored under the given key or null if none present.
getOutput(String, String) - Method in class ome.services.sessions.SessionManagerImpl
 
getOutput(String) - Method in class omero.client
Retrieves an item from the "output" shared (session) memory.
getOutput_async(AMD_ISession_getOutput, String, String, Current) - Method in class ome.services.blitz.impl.SessionI
 
getOutputKeys(String) - Method in interface ome.api.ISession
Retrieves all keys in the sesson's output environment.
getOutputKeys(String) - Method in class ome.services.sessions.SessionBean
 
getOutputKeys() - Method in class omero.client
Returns a list of keys for all items in the "output" shared (session) memory
getOutputKeys_async(AMD_ISession_getOutputKeys, String, Current) - Method in class ome.services.blitz.impl.SessionI
 
getOutputs(String) - Method in interface ome.api.ISession
Retrieves all outputs from the given session's input environment.
getOutputs(String) - Method in class ome.services.sessions.SessionBean
 
getOutputs_async(AMD_ISession_getOutputs, String, Current) - Method in class ome.services.blitz.impl.SessionI
 
getOverlays() - Method in class omeis.providers.re.Renderer
Returns the current set of overlays to be rendered.
getOwnedGroups() - Method in class ome.logic.LdapImpl.GroupLoader
Return the found owned groups for the given username.
getOwner() - Method in class ome.model.acquisition.Detector.Details
 
getOwner() - Method in class ome.model.acquisition.DetectorSettings.Details
 
getOwner() - Method in class ome.model.acquisition.Dichroic.Details
 
getOwner() - Method in class ome.model.acquisition.Filter.Details
 
getOwner() - Method in class ome.model.acquisition.FilterSet.Details
 
getOwner() - Method in class ome.model.acquisition.FilterSetEmissionFilterLink.Details
 
getOwner() - Method in class ome.model.acquisition.FilterSetExcitationFilterLink.Details
 
getOwner() - Method in class ome.model.acquisition.ImagingEnvironment.Details
 
getOwner() - Method in class ome.model.acquisition.Instrument.Details
 
getOwner() - Method in class ome.model.acquisition.LightPath.Details
 
getOwner() - Method in class ome.model.acquisition.LightPathEmissionFilterLink.Details
 
getOwner() - Method in class ome.model.acquisition.LightPathExcitationFilterLink.Details
 
getOwner() - Method in class ome.model.acquisition.LightSettings.Details
 
getOwner() - Method in class ome.model.acquisition.LightSource.Details
 
getOwner() - Method in class ome.model.acquisition.Microscope.Details
 
getOwner() - Method in class ome.model.acquisition.Objective.Details
 
getOwner() - Method in class ome.model.acquisition.ObjectiveSettings.Details
 
getOwner() - Method in class ome.model.acquisition.OTF.Details
 
getOwner() - Method in class ome.model.acquisition.StageLabel.Details
 
getOwner() - Method in class ome.model.acquisition.TransmittanceRange.Details
 
getOwner() - Method in class ome.model.annotations.Annotation.Details
 
getOwner() - Method in class ome.model.annotations.AnnotationAnnotationLink.Details
 
getOwner() - Method in class ome.model.annotations.ChannelAnnotationLink.Details
 
getOwner() - Method in class ome.model.annotations.DatasetAnnotationLink.Details
 
getOwner() - Method in class ome.model.annotations.DetectorAnnotationLink.Details
 
getOwner() - Method in class ome.model.annotations.DichroicAnnotationLink.Details
 
getOwner() - Method in class ome.model.annotations.ExperimenterAnnotationLink.Details
 
getOwner() - Method in class ome.model.annotations.ExperimenterGroupAnnotationLink.Details
 
getOwner() - Method in class ome.model.annotations.FilesetAnnotationLink.Details
 
getOwner() - Method in class ome.model.annotations.FilterAnnotationLink.Details
 
getOwner() - Method in class ome.model.annotations.ImageAnnotationLink.Details
 
getOwner() - Method in class ome.model.annotations.InstrumentAnnotationLink.Details
 
getOwner() - Method in class ome.model.annotations.LightPathAnnotationLink.Details
 
getOwner() - Method in class ome.model.annotations.LightSourceAnnotationLink.Details
 
getOwner() - Method in class ome.model.annotations.NamespaceAnnotationLink.Details
 
getOwner() - Method in class ome.model.annotations.NodeAnnotationLink.Details
 
getOwner() - Method in class ome.model.annotations.ObjectiveAnnotationLink.Details
 
getOwner() - Method in class ome.model.annotations.OriginalFileAnnotationLink.Details
 
getOwner() - Method in class ome.model.annotations.PlaneInfoAnnotationLink.Details
 
getOwner() - Method in class ome.model.annotations.PlateAcquisitionAnnotationLink.Details
 
getOwner() - Method in class ome.model.annotations.PlateAnnotationLink.Details
 
getOwner() - Method in class ome.model.annotations.ProjectAnnotationLink.Details
 
getOwner() - Method in class ome.model.annotations.ReagentAnnotationLink.Details
 
getOwner() - Method in class ome.model.annotations.RoiAnnotationLink.Details
 
getOwner() - Method in class ome.model.annotations.ScreenAnnotationLink.Details
 
getOwner() - Method in class ome.model.annotations.SessionAnnotationLink.Details
 
getOwner() - Method in class ome.model.annotations.ShapeAnnotationLink.Details
 
getOwner() - Method in class ome.model.annotations.WellAnnotationLink.Details
 
getOwner() - Method in class ome.model.containers.Dataset.Details
 
getOwner() - Method in class ome.model.containers.DatasetImageLink.Details
 
getOwner() - Method in class ome.model.containers.Project.Details
 
getOwner() - Method in class ome.model.containers.ProjectDatasetLink.Details
 
getOwner() - Method in class ome.model.core.Channel.Details
 
getOwner() - Method in class ome.model.core.Image.Details
 
getOwner() - Method in class ome.model.core.LogicalChannel.Details
 
getOwner() - Method in class ome.model.core.OriginalFile.Details
 
getOwner() - Method in class ome.model.core.Pixels.Details
 
getOwner() - Method in class ome.model.core.PixelsOriginalFileMap.Details
 
getOwner() - Method in class ome.model.core.PlaneInfo.Details
 
getOwner() - Method in class ome.model.display.ChannelBinding.Details
 
getOwner() - Method in class ome.model.display.CodomainMapContext.Details
 
getOwner() - Method in class ome.model.display.QuantumDef.Details
 
getOwner() - Method in class ome.model.display.RenderingDef.Details
 
getOwner() - Method in class ome.model.display.Thumbnail.Details
 
getOwner() - Method in class ome.model.experiment.Experiment.Details
 
getOwner() - Method in class ome.model.experiment.MicrobeamManipulation.Details
 
getOwner() - Method in class ome.model.fs.Fileset.Details
 
getOwner() - Method in class ome.model.fs.FilesetEntry.Details
 
getOwner() - Method in class ome.model.fs.FilesetJobLink.Details
 
getOwner() - Method in interface ome.model.IDetails
 
getOwner() - Method in class ome.model.internal.Details
 
getOwner() - Method in class ome.model.internal.Link.Details
 
getOwner() - Method in class ome.model.jobs.Job.Details
 
getOwner() - Method in class ome.model.jobs.JobOriginalFileLink.Details
 
getOwner() - Method in class ome.model.meta.ExternalInfo.Details
 
getOwner() - Method in class ome.model.meta.GroupExperimenterMap
Simple field ome.model.meta.GroupExperimenterMap.owner (java.lang.Boolean)
getOwner() - Method in class ome.model.meta.Session
Many-to-one field ome.model.meta.Session.owner (ome.model.meta.Experimenter)
getOwner() - Method in class ome.model.roi.Roi.Details
 
getOwner() - Method in class ome.model.roi.Shape.Details
 
getOwner() - Method in class ome.model.screen.Plate.Details
 
getOwner() - Method in class ome.model.screen.PlateAcquisition.Details
 
getOwner() - Method in class ome.model.screen.Reagent.Details
 
getOwner() - Method in class ome.model.screen.Screen.Details
 
getOwner() - Method in class ome.model.screen.ScreenPlateLink.Details
 
getOwner() - Method in class ome.model.screen.Well.Details
 
getOwner() - Method in class ome.model.screen.WellReagentLink.Details
 
getOwner() - Method in class ome.model.screen.WellSample.Details
 
getOwner() - Method in class ome.model.stats.StatsInfo.Details
 
getOwner() - Method in class ome.security.basic.BasicEventContext
 
getOwner() - Method in class ome.security.basic.CurrentDetails
 
getOwner(Current) - Method in class omero.model.DetailsI
 
getOwner() - Method in class pojos.DataObject
Returns the owner of the object.
getOwnShares(boolean) - Method in interface ome.api.IShare
Gets all owned shares for the current Experimenter
getOwnShares(boolean) - Method in class ome.services.sharing.ShareBean
 
getOwnShares_async(AMD_IShare_getOwnShares, boolean, Current) - Method in class ome.services.blitz.impl.ShareI
 
getParameterTypes() - Method in class ome.security.basic.AllGroupsSecurityFilter
 
getParameterTypes() - Method in class ome.security.basic.OneGroupSecurityFilter
 
getParameterTypes() - Method in interface ome.security.SecurityFilter
Return a mapping of the hibernate types for each of the parameters that the condition takes.
getParameterTypes() - Method in class ome.security.SecurityFilterHolder
 
getParams() - Method in class ome.model.jobs.ParseJob
Simple field ome.model.jobs.ParseJob.params (byte[])
getParams(Long, String, Current) - Method in class ome.services.blitz.util.ParamsCache
Lookup a cached JobParams instance for the given key.
getParams_async(AMD_IScript_getParams, long, Current) - Method in class ome.services.blitz.impl.ScriptI
Get the Parameters of the script.
getParent() - Method in class ome.model.acquisition.FilterSetEmissionFilterLink
Many-to-one field ome.model.acquisition.FilterSetEmissionFilterLink.parent (ome.model.acquisition.FilterSet)
getParent() - Method in class ome.model.acquisition.FilterSetExcitationFilterLink
Many-to-one field ome.model.acquisition.FilterSetExcitationFilterLink.parent (ome.model.acquisition.FilterSet)
getParent() - Method in class ome.model.acquisition.LightPathEmissionFilterLink
Many-to-one field ome.model.acquisition.LightPathEmissionFilterLink.parent (ome.model.acquisition.LightPath)
getParent() - Method in class ome.model.acquisition.LightPathExcitationFilterLink
Many-to-one field ome.model.acquisition.LightPathExcitationFilterLink.parent (ome.model.acquisition.LightPath)
getParent() - Method in class ome.model.annotations.AnnotationAnnotationLink
Many-to-one field ome.model.annotations.AnnotationAnnotationLink.parent (ome.model.annotations.Annotation)
getParent() - Method in class ome.model.annotations.ChannelAnnotationLink
Many-to-one field ome.model.annotations.ChannelAnnotationLink.parent (ome.model.core.Channel)
getParent() - Method in class ome.model.annotations.DatasetAnnotationLink
Many-to-one field ome.model.annotations.DatasetAnnotationLink.parent (ome.model.containers.Dataset)
getParent() - Method in class ome.model.annotations.DetectorAnnotationLink
Many-to-one field ome.model.annotations.DetectorAnnotationLink.parent (ome.model.acquisition.Detector)
getParent() - Method in class ome.model.annotations.DichroicAnnotationLink
Many-to-one field ome.model.annotations.DichroicAnnotationLink.parent (ome.model.acquisition.Dichroic)
getParent() - Method in class ome.model.annotations.ExperimenterAnnotationLink
Many-to-one field ome.model.annotations.ExperimenterAnnotationLink.parent (ome.model.meta.Experimenter)
getParent() - Method in class ome.model.annotations.ExperimenterGroupAnnotationLink
Many-to-one field ome.model.annotations.ExperimenterGroupAnnotationLink.parent (ome.model.meta.ExperimenterGroup)
getParent() - Method in class ome.model.annotations.FilesetAnnotationLink
Many-to-one field ome.model.annotations.FilesetAnnotationLink.parent (ome.model.fs.Fileset)
getParent() - Method in class ome.model.annotations.FilterAnnotationLink
Many-to-one field ome.model.annotations.FilterAnnotationLink.parent (ome.model.acquisition.Filter)
getParent() - Method in class ome.model.annotations.ImageAnnotationLink
Many-to-one field ome.model.annotations.ImageAnnotationLink.parent (ome.model.core.Image)
getParent() - Method in class ome.model.annotations.InstrumentAnnotationLink
Many-to-one field ome.model.annotations.InstrumentAnnotationLink.parent (ome.model.acquisition.Instrument)
getParent() - Method in class ome.model.annotations.LightPathAnnotationLink
Many-to-one field ome.model.annotations.LightPathAnnotationLink.parent (ome.model.acquisition.LightPath)
getParent() - Method in class ome.model.annotations.LightSourceAnnotationLink
Many-to-one field ome.model.annotations.LightSourceAnnotationLink.parent (ome.model.acquisition.LightSource)
getParent() - Method in class ome.model.annotations.NamespaceAnnotationLink
Many-to-one field ome.model.annotations.NamespaceAnnotationLink.parent (ome.model.meta.Namespace)
getParent() - Method in class ome.model.annotations.NodeAnnotationLink
Many-to-one field ome.model.annotations.NodeAnnotationLink.parent (ome.model.meta.Node)
getParent() - Method in class ome.model.annotations.ObjectiveAnnotationLink
Many-to-one field ome.model.annotations.ObjectiveAnnotationLink.parent (ome.model.acquisition.Objective)
getParent() - Method in class ome.model.annotations.OriginalFileAnnotationLink
Many-to-one field ome.model.annotations.OriginalFileAnnotationLink.parent (ome.model.core.OriginalFile)
getParent() - Method in class ome.model.annotations.PlaneInfoAnnotationLink
Many-to-one field ome.model.annotations.PlaneInfoAnnotationLink.parent (ome.model.core.PlaneInfo)
getParent() - Method in class ome.model.annotations.PlateAcquisitionAnnotationLink
Many-to-one field ome.model.annotations.PlateAcquisitionAnnotationLink.parent (ome.model.screen.PlateAcquisition)
getParent() - Method in class ome.model.annotations.PlateAnnotationLink
Many-to-one field ome.model.annotations.PlateAnnotationLink.parent (ome.model.screen.Plate)
getParent() - Method in class ome.model.annotations.ProjectAnnotationLink
Many-to-one field ome.model.annotations.ProjectAnnotationLink.parent (ome.model.containers.Project)
getParent() - Method in class ome.model.annotations.ReagentAnnotationLink
Many-to-one field ome.model.annotations.ReagentAnnotationLink.parent (ome.model.screen.Reagent)
getParent() - Method in class ome.model.annotations.RoiAnnotationLink
Many-to-one field ome.model.annotations.RoiAnnotationLink.parent (ome.model.roi.Roi)
getParent() - Method in class ome.model.annotations.ScreenAnnotationLink
Many-to-one field ome.model.annotations.ScreenAnnotationLink.parent (ome.model.screen.Screen)
getParent() - Method in class ome.model.annotations.SessionAnnotationLink
Many-to-one field ome.model.annotations.SessionAnnotationLink.parent (ome.model.meta.Session)
getParent() - Method in class ome.model.annotations.ShapeAnnotationLink
Many-to-one field ome.model.annotations.ShapeAnnotationLink.parent (ome.model.roi.Shape)
getParent() - Method in class ome.model.annotations.WellAnnotationLink
Many-to-one field ome.model.annotations.WellAnnotationLink.parent (ome.model.screen.Well)
getParent() - Method in class ome.model.containers.DatasetImageLink
Many-to-one field ome.model.containers.DatasetImageLink.parent (ome.model.containers.Dataset)
getParent() - Method in class ome.model.containers.ProjectDatasetLink
Many-to-one field ome.model.containers.ProjectDatasetLink.parent (ome.model.containers.Project)
getParent() - Method in class ome.model.core.PixelsOriginalFileMap
Many-to-one field ome.model.core.PixelsOriginalFileMap.parent (ome.model.core.OriginalFile)
getParent() - Method in class ome.model.fs.FilesetJobLink
Many-to-one field ome.model.fs.FilesetJobLink.parent (ome.model.fs.Fileset)
getParent() - Method in interface ome.model.ILink
 
getParent() - Method in class ome.model.jobs.JobOriginalFileLink
Many-to-one field ome.model.jobs.JobOriginalFileLink.parent (ome.model.jobs.Job)
getParent() - Method in class ome.model.meta.GroupExperimenterMap
Many-to-one field ome.model.meta.GroupExperimenterMap.parent (ome.model.meta.ExperimenterGroup)
getParent() - Method in class ome.model.meta.ShareMember
Many-to-one field ome.model.meta.ShareMember.parent (ome.model.meta.Share)
getParent() - Method in class ome.model.screen.ScreenPlateLink
Many-to-one field ome.model.screen.ScreenPlateLink.parent (ome.model.screen.Screen)
getParent() - Method in class ome.model.screen.WellReagentLink
Many-to-one field ome.model.screen.WellReagentLink.parent (ome.model.screen.Well)
getParentFilePath() - Method in class pojos.ImageData
Returns the path to the file hosting the image.
getParentTransformer(Class) - Static method in class ome.services.query.Hierarchy
 
getPartial() - Method in class ome.model.core.Image
Simple field ome.model.core.Image.partial (java.lang.Boolean)
getPassword() - Method in class ome.system.Login
simple getter for the password passed into the constructor
getPasswordAuthentication() - Method in class ome.security.SmtpAuthenticator
 
getPasswordHash(Long) - Method in interface ome.util.SqlAction
 
getPasswordHash(Long) - Method in class ome.util.SqlAction.Impl
 
getPastConnections(long) - Method in interface ome.api.IShare
Gets previous connections to share.
getPastConnections(long) - Method in class ome.services.sharing.ShareBean
 
getPastConnections_async(AMD_IShare_getPastConnections, long, Current) - Method in class ome.services.blitz.impl.ShareI
 
getPath() - Method in class ome.io.bioformats.BfPixelBuffer
 
getPath() - Method in class ome.io.bioformats.BfPixelsWrapper
 
getPath() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
 
getPath() - Method in class ome.io.nio.AbstractBuffer
 
getPath() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
 
getPath() - Method in interface ome.io.nio.PixelBuffer
Retrieves the full path to this pixel buffer on disk
getPath() - Method in class ome.model.acquisition.OTF
Simple field ome.model.acquisition.OTF.path (java.lang.String)
getPath() - Method in class ome.model.core.OriginalFile
Simple field ome.model.core.OriginalFile.path (java.lang.String)
getPath(Matcher) - Method in class ome.services.graphs.GraphEntry
Deprecated.
 
getPath() - Method in class pojos.FileData
Returns the (relative) path of the file.
getPath() - Method in class pojos.OTFData
Returns the path.
getPathFor(long) - Method in class ome.services.blitz.repo.path.MakeNextDirectory
Get the subdirectories to create for the given index, the first directories to be created corresponding to index == 0.
getPathFrom(FsFile) - Method in class ome.services.blitz.repo.path.FsFile
Find the relative path of this path from a given parent.
getPathIterator(AffineTransform) - Method in class ome.util.math.geom2D.EllipseArea
Required by the Shape I/F.
getPathIterator(AffineTransform, double) - Method in class ome.util.math.geom2D.EllipseArea
Required by the Shape I/F.
getPathIterator(AffineTransform) - Method in class ome.util.math.geom2D.RectangleArea
Required by the Shape I/F.
getPathIterator(AffineTransform, double) - Method in class ome.util.math.geom2D.RectangleArea
Required by the Shape I/F.
getPaths() - Method in class ome.formats.importer.ImportCandidates
 
getPathSanitizer() - Method in class ome.services.blitz.repo.path.ServerFilePathTransformer
Get the string transformer that is used to make file-path components safe across platforms.
getPathToFile() - Method in class pojos.ImageData
Returns the path to the file.
getPerm1() - Method in class ome.model.internal.Permissions
 
getPerm1(Current) - Method in class omero.model.PermissionsI
 
getPermissions() - Method in class ome.model.acquisition.Detector.Details
 
getPermissions() - Method in class ome.model.acquisition.DetectorSettings.Details
 
getPermissions() - Method in class ome.model.acquisition.Dichroic.Details
 
getPermissions() - Method in class ome.model.acquisition.Filter.Details
 
getPermissions() - Method in class ome.model.acquisition.FilterSet.Details
 
getPermissions() - Method in class ome.model.acquisition.FilterSetEmissionFilterLink.Details
 
getPermissions() - Method in class ome.model.acquisition.FilterSetExcitationFilterLink.Details
 
getPermissions() - Method in class ome.model.acquisition.ImagingEnvironment.Details
 
getPermissions() - Method in class ome.model.acquisition.Instrument.Details
 
getPermissions() - Method in class ome.model.acquisition.LightPath.Details
 
getPermissions() - Method in class ome.model.acquisition.LightPathEmissionFilterLink.Details
 
getPermissions() - Method in class ome.model.acquisition.LightPathExcitationFilterLink.Details
 
getPermissions() - Method in class ome.model.acquisition.LightSettings.Details
 
getPermissions() - Method in class ome.model.acquisition.LightSource.Details
 
getPermissions() - Method in class ome.model.acquisition.Microscope.Details
 
getPermissions() - Method in class ome.model.acquisition.Objective.Details
 
getPermissions() - Method in class ome.model.acquisition.ObjectiveSettings.Details
 
getPermissions() - Method in class ome.model.acquisition.OTF.Details
 
getPermissions() - Method in class ome.model.acquisition.StageLabel.Details
 
getPermissions() - Method in class ome.model.acquisition.TransmittanceRange.Details
 
getPermissions() - Method in class ome.model.annotations.Annotation.Details
 
getPermissions() - Method in class ome.model.annotations.AnnotationAnnotationLink.Details
 
getPermissions() - Method in class ome.model.annotations.ChannelAnnotationLink.Details
 
getPermissions() - Method in class ome.model.annotations.DatasetAnnotationLink.Details
 
getPermissions() - Method in class ome.model.annotations.DetectorAnnotationLink.Details
 
getPermissions() - Method in class ome.model.annotations.DichroicAnnotationLink.Details
 
getPermissions() - Method in class ome.model.annotations.ExperimenterAnnotationLink.Details
 
getPermissions() - Method in class ome.model.annotations.ExperimenterGroupAnnotationLink.Details
 
getPermissions() - Method in class ome.model.annotations.FilesetAnnotationLink.Details
 
getPermissions() - Method in class ome.model.annotations.FilterAnnotationLink.Details
 
getPermissions() - Method in class ome.model.annotations.ImageAnnotationLink.Details
 
getPermissions() - Method in class ome.model.annotations.InstrumentAnnotationLink.Details
 
getPermissions() - Method in class ome.model.annotations.LightPathAnnotationLink.Details
 
getPermissions() - Method in class ome.model.annotations.LightSourceAnnotationLink.Details
 
getPermissions() - Method in class ome.model.annotations.NamespaceAnnotationLink.Details
 
getPermissions() - Method in class ome.model.annotations.NodeAnnotationLink.Details
 
getPermissions() - Method in class ome.model.annotations.ObjectiveAnnotationLink.Details
 
getPermissions() - Method in class ome.model.annotations.OriginalFileAnnotationLink.Details
 
getPermissions() - Method in class ome.model.annotations.PlaneInfoAnnotationLink.Details
 
getPermissions() - Method in class ome.model.annotations.PlateAcquisitionAnnotationLink.Details
 
getPermissions() - Method in class ome.model.annotations.PlateAnnotationLink.Details
 
getPermissions() - Method in class ome.model.annotations.ProjectAnnotationLink.Details
 
getPermissions() - Method in class ome.model.annotations.ReagentAnnotationLink.Details
 
getPermissions() - Method in class ome.model.annotations.RoiAnnotationLink.Details
 
getPermissions() - Method in class ome.model.annotations.ScreenAnnotationLink.Details
 
getPermissions() - Method in class ome.model.annotations.SessionAnnotationLink.Details
 
getPermissions() - Method in class ome.model.annotations.ShapeAnnotationLink.Details
 
getPermissions() - Method in class ome.model.annotations.WellAnnotationLink.Details
 
getPermissions() - Method in class ome.model.containers.Dataset.Details
 
getPermissions() - Method in class ome.model.containers.DatasetImageLink.Details
 
getPermissions() - Method in class ome.model.containers.Project.Details
 
getPermissions() - Method in class ome.model.containers.ProjectDatasetLink.Details
 
getPermissions() - Method in class ome.model.core.Channel.Details
 
getPermissions() - Method in class ome.model.core.Image.Details
 
getPermissions() - Method in class ome.model.core.LogicalChannel.Details
 
getPermissions() - Method in class ome.model.core.OriginalFile.Details
 
getPermissions() - Method in class ome.model.core.Pixels.Details
 
getPermissions() - Method in class ome.model.core.PixelsOriginalFileMap.Details
 
getPermissions() - Method in class ome.model.core.PlaneInfo.Details
 
getPermissions() - Method in class ome.model.display.ChannelBinding.Details
 
getPermissions() - Method in class ome.model.display.CodomainMapContext.Details
 
getPermissions() - Method in class ome.model.display.QuantumDef.Details
 
getPermissions() - Method in class ome.model.display.RenderingDef.Details
 
getPermissions() - Method in class ome.model.display.Thumbnail.Details
 
getPermissions() - Method in class ome.model.enums.AcquisitionMode.Details
 
getPermissions() - Method in class ome.model.enums.ArcType.Details
 
getPermissions() - Method in class ome.model.enums.Binning.Details
 
getPermissions() - Method in class ome.model.enums.ChecksumAlgorithm.Details
 
getPermissions() - Method in class ome.model.enums.ContrastMethod.Details
 
getPermissions() - Method in class ome.model.enums.Correction.Details
 
getPermissions() - Method in class ome.model.enums.DetectorType.Details
 
getPermissions() - Method in class ome.model.enums.DimensionOrder.Details
 
getPermissions() - Method in class ome.model.enums.EventType.Details
 
getPermissions() - Method in class ome.model.enums.ExperimentType.Details
 
getPermissions() - Method in class ome.model.enums.Family.Details
 
getPermissions() - Method in class ome.model.enums.FilamentType.Details
 
getPermissions() - Method in class ome.model.enums.FilterType.Details
 
getPermissions() - Method in class ome.model.enums.Format.Details
 
getPermissions() - Method in class ome.model.enums.Illumination.Details
 
getPermissions() - Method in class ome.model.enums.Immersion.Details
 
getPermissions() - Method in class ome.model.enums.LaserMedium.Details
 
getPermissions() - Method in class ome.model.enums.LaserType.Details
 
getPermissions() - Method in class ome.model.enums.Medium.Details
 
getPermissions() - Method in class ome.model.enums.MicrobeamManipulationType.Details
 
getPermissions() - Method in class ome.model.enums.MicroscopeType.Details
 
getPermissions() - Method in class ome.model.enums.PhotometricInterpretation.Details
 
getPermissions() - Method in class ome.model.enums.PixelsType.Details
 
getPermissions() - Method in class ome.model.enums.Pulse.Details
 
getPermissions() - Method in class ome.model.enums.RenderingModel.Details
 
getPermissions() - Method in class ome.model.experiment.Experiment.Details
 
getPermissions() - Method in class ome.model.experiment.MicrobeamManipulation.Details
 
getPermissions() - Method in class ome.model.fs.Fileset.Details
 
getPermissions() - Method in class ome.model.fs.FilesetEntry.Details
 
getPermissions() - Method in class ome.model.fs.FilesetJobLink.Details
 
getPermissions() - Method in interface ome.model.IDetails
 
getPermissions() - Method in class ome.model.internal.Details
Permissions is a component embedded into the Details component.
getPermissions() - Method in class ome.model.internal.Link.Details
 
getPermissions() - Method in class ome.model.jobs.Job.Details
 
getPermissions() - Method in class ome.model.jobs.JobOriginalFileLink.Details
 
getPermissions() - Method in class ome.model.jobs.JobStatus.Details
 
getPermissions() - Method in class ome.model.meta.DBPatch.Details
 
getPermissions() - Method in class ome.model.meta.Event.Details
 
getPermissions() - Method in class ome.model.meta.EventLog.Details
 
getPermissions() - Method in class ome.model.meta.Experimenter.Details
 
getPermissions() - Method in class ome.model.meta.ExperimenterGroup.Details
 
getPermissions() - Method in class ome.model.meta.ExternalInfo.Details
 
getPermissions() - Method in class ome.model.meta.GroupExperimenterMap.Details
 
getPermissions() - Method in class ome.model.meta.Namespace.Details
 
getPermissions() - Method in class ome.model.meta.Node.Details
 
getPermissions() - Method in class ome.model.meta.Session.Details
 
getPermissions() - Method in class ome.model.meta.ShareMember.Details
 
getPermissions() - Method in class ome.model.roi.Roi.Details
 
getPermissions() - Method in class ome.model.roi.Shape.Details
 
getPermissions() - Method in class ome.model.screen.Plate.Details
 
getPermissions() - Method in class ome.model.screen.PlateAcquisition.Details
 
getPermissions() - Method in class ome.model.screen.Reagent.Details
 
getPermissions() - Method in class ome.model.screen.Screen.Details
 
getPermissions() - Method in class ome.model.screen.ScreenPlateLink.Details
 
getPermissions() - Method in class ome.model.screen.Well.Details
 
getPermissions() - Method in class ome.model.screen.WellReagentLink.Details
 
getPermissions() - Method in class ome.model.screen.WellSample.Details
 
getPermissions() - Method in class ome.model.stats.StatsInfo.Details
 
getPermissions(Current) - Method in class omero.model.DetailsI
 
getPermissions() - Method in class pojos.DataObject
Returns the permission of the object.
getPermissionsForGroup(Long) - Method in class ome.security.basic.BasicEventContext
Never returns Permissions.DUMMY.
getPermissionsLevel() - Method in class pojos.PermissionData
Returns the permissions level.
getPhotometricInterpretation() - Method in class ome.model.core.LogicalChannel
Many-to-one field ome.model.core.LogicalChannel.photometricInterpretation (ome.model.enums.PhotometricInterpretation)
getPhysicalMemory() - Static method in class ome.services.util.JvmSettingsCheck
 
getPhysicalSizeX() - Method in class ome.model.core.Pixels
Enum-mapped unit-based field ome.model.core.Pixels.physicalSizeX (ome.model.units.Length)
getPhysicalSizeY() - Method in class ome.model.core.Pixels
Enum-mapped unit-based field ome.model.core.Pixels.physicalSizeY (ome.model.units.Length)
getPhysicalSizeZ() - Method in class ome.model.core.Pixels
Enum-mapped unit-based field ome.model.core.Pixels.physicalSizeZ (ome.model.units.Length)
getPinHoleSize() - Method in class ome.model.core.LogicalChannel
Enum-mapped unit-based field ome.model.core.LogicalChannel.pinHoleSize (ome.model.units.Length)
getPinholeSize(UnitsLength) - Method in class pojos.ChannelData
Returns the pin hole size of the channel.
getPinholeSize() - Method in class pojos.ChannelData
getPixelBuffer(Pixels) - Method in class ome.io.nio.PixelsService
Deprecated.
In the future callers should use the more descriptive PixelsService.getPixelBuffer(Pixels, boolean).
getPixelBuffer(Pixels, boolean) - Method in class ome.io.nio.PixelsService
Returns a pixel buffer for a given set of pixels.
getPixelIds() - Method in class ome.tools.RepositoryTask
This public method is used to return a list of pixel ids that require deletion from the disk repository.
getPixels() - Method in class ome.formats.importer.util.TinyImportFixture
 
getPixels() - Method in class ome.formats.OMEROImportFixture
Accessor for the created pixels.
getPixels() - Method in class ome.model.core.Channel
Many-to-one field ome.model.core.Channel.pixels (ome.model.core.Pixels)
getPixels() - Method in class ome.model.core.Image
returns pixels .
getPixels(int) - Method in class ome.model.core.Image
Gets the ome.model.core.Pixels at the given index.
getPixels() - Method in class ome.model.core.PlaneInfo
Many-to-one field ome.model.core.PlaneInfo.pixels (ome.model.core.Pixels)
getPixels() - Method in class ome.model.display.RenderingDef
Many-to-one field ome.model.display.RenderingDef.pixels (ome.model.core.Pixels)
getPixels() - Method in class ome.model.display.Thumbnail
Many-to-one field ome.model.display.Thumbnail.pixels (ome.model.core.Pixels)
getPixels() - Method in class ome.model.roi.Mask
Many-to-one field ome.model.roi.Mask.pixels (ome.model.core.Pixels)
getPixels(Long, ServiceFactory) - Method in class ome.services.pixeldata.PixelDataHandler
 
getPixels() - Method in class ome.services.RenderingBean
Implemented as specified by the RenderingEngine interface.
getPixels(long) - Method in class ome.services.ThumbnailCtx
Retrieves the Pixels object for a given Pixels ID.
getPixels() - Method in class omeis.providers.re.Renderer
Returns the object that allows to access the pixels raw data.
getPixels() - Method in interface omeis.providers.re.RenderingEngine
Returns the Pixels set the Rendering engine is for.
getPixels() - Method in class omero.util.RPSTileLoop
After saving the binary data, the update event of the Pixels instance will be updated and therefore need to be reloaded.
getPixels_async(AMD_RenderingEngine_getPixels, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
getPixelsBinDataBigEndian(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPixelsDimensionOrder(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPixelsFileMaps() - Method in class ome.model.core.OriginalFile
returns pixelsFileMaps .
getPixelsFileMaps() - Method in class ome.model.core.Pixels
returns pixelsFileMaps .
getPixelsFileMapsCountPerOwner() - Method in class ome.model.core.OriginalFile
If fetched, returns the count(*) of ome.model.core.PixelsOriginalFileMap that a user has.
getPixelsFileMapsCountPerOwner() - Method in class ome.model.core.Pixels
If fetched, returns the count(*) of ome.model.core.PixelsOriginalFileMap that a user has.
getPixelsId() - Method in interface ome.api.RawPixelsStore
Returns the current Pixels set identifier.
getPixelsId() - Method in exception ome.conditions.MissingPyramidException
 
getPixelsID(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPixelsId() - Method in class ome.services.RawPixelsBean
 
getPixelsId_async(AMD_RawPixelsStore_getPixelsId, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
getPixelsId_async(AMD_RawPixelsStore_getPixelsId, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
getPixelSizeX() - Method in class pojos.PixelsData
Deprecated.
getPixelSizeX(UnitsLength) - Method in class pojos.PixelsData
Returns the dimension of a pixel along the X-axis
getPixelSizeY() - Method in class pojos.PixelsData
Deprecated.
getPixelSizeY(UnitsLength) - Method in class pojos.PixelsData
Returns the dimension of a pixel along the Y-axis
getPixelSizeZ() - Method in class pojos.PixelsData
Deprecated.
getPixelSizeZ(UnitsLength) - Method in class pojos.PixelsData
Returns the dimension of a pixel along the Z-axis
getPixelsNamePathRepo(long) - Method in class ome.util.actions.PostgresSqlAction
 
getPixelsNamePathRepo(long) - Method in interface ome.util.SqlAction
Retrieves the name, path and repo for the given pixels set.
getPixelsPath() - Method in interface ome.api.RawPixelsStore
Returns the current Pixels path.
getPixelsPath(Long) - Method in class ome.io.nio.AbstractFileSystemService
Returns a numbered path relative to the root of this service, but is ignorant of FS and similar constructs.
getPixelsPath() - Method in class ome.services.RawPixelsBean
 
getPixelsPath_async(AMD_RawPixelsStore_getPixelsPath, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
getPixelsPath_async(AMD_RawPixelsStore_getPixelsPath, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
getPixelsPhysicalSizeX(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPixelsPhysicalSizeY(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPixelsPhysicalSizeZ(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPixelsService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
getPixelsService() - Method in class ome.system.ServiceFactory
 
getPixelsSizeC(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPixelsSizeT(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPixelsSizeX(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPixelsSizeY(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPixelsSizeZ(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPixelsTimeIncrement(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPixelsType() - Method in class ome.io.bioformats.BfPixelsWrapper
cgb - created from the methods below?
getPixelsType() - Method in class ome.model.acquisition.OTF
Many-to-one field ome.model.acquisition.OTF.pixelsType (ome.model.enums.PixelsType)
getPixelsType() - Method in class ome.model.core.Pixels
Many-to-one field ome.model.core.Pixels.pixelsType (ome.model.enums.PixelsType)
getPixelsType(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPixelsType() - Method in class omeis.providers.re.Renderer
Returns the pixels type.
getPixelsType() - Method in class pojos.OTFData
Returns the pixels type.
getPixelsTypeLowerBound(int) - Method in class ome.services.RenderingBean
Implemented as specified by the RenderingEngine interface.
getPixelsTypeLowerBound(int) - Method in class omeis.providers.re.Renderer
Returns the minimum value for that channels depending on the pixels type and the original range (globalmax, globalmin)
getPixelsTypeLowerBound(int) - Method in interface omeis.providers.re.RenderingEngine
Returns the minimum value for that channels depending on the pixels type and the original range (globalmax, globalmin)
getPixelsTypeLowerBound_async(AMD_RenderingEngine_getPixelsTypeLowerBound, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
getPixelsTypeMax() - Method in class omeis.providers.re.quantum.QuantumStrategy
Returns the upper bound of the pixels range or 0 if the value couldn't be set.
getPixelsTypeMin() - Method in class omeis.providers.re.quantum.QuantumStrategy
Returns the lower bound of the pixels range or 0 if the value couldn't be set.
getPixelsTypeUpperBound(int) - Method in class ome.services.RenderingBean
Implemented as specified by the RenderingEngine interface.
getPixelsTypeUpperBound(int) - Method in class omeis.providers.re.Renderer
Returns the maximum value for that channels depending on the pixels type and the original range (globalmax, globalmin)
getPixelsTypeUpperBound(int) - Method in interface omeis.providers.re.RenderingEngine
Returns the maximum value for that channels depending on the pixels type and the original range (globalmax, globalmin)
getPixelsTypeUpperBound_async(AMD_RenderingEngine_getPixelsTypeUpperBound, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
getPixelType() - Method in class pojos.PixelsData
Returns the pixels type.
getPixelValue(int) - Method in class ome.util.PixelData
Returns the pixel intensity value of the pixel at a given offset within the backing buffer.
getPixelValue(int, int) - Method in class omeis.providers.re.data.Plane2D
Returns the pixel intensity value of the pixel at (x1, x2).
getPixelValue(int) - Method in class omeis.providers.re.data.Plane2D
Returns the pixel intensity value of the pixel at a given offset within the backing buffer.
getPixelValueDirect(int) - Method in class ome.io.nio.ReorderedPixelData
Returns the pixel intensity value of the pixel at a given offset within the backing buffer.
getPixelValueDirect(int) - Method in class ome.util.PixelData
Returns the pixel intensity value of the pixel at a given offset within the backing buffer.
getPlane(int, int, int) - Method in interface ome.api.RawPixelsStore
 
getPlane(Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer
 
getPlane(Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPixelsWrapper
 
getPlane(Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
 
getPlane(Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
 
getPlane(Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer
Retrieves a particular 2D image plane from this pixel buffer.
getPlane(Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer
Implemented as specified by PixelBuffer I/F.
getPlane(int, int, int) - Method in class ome.services.RawPixelsBean
 
getPlane_async(AMD_RawPixelsStore_getPlane, int, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
getPlane_async(AMD_RawPixelsStore_getPlane, int, int, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
getPlaneCount(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPlaneCount() - Method in class pojos.ROIData
Returns the number of planes occupied by the ROI.
getPlaneDeltaT(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPlaneDimsAsString(PlaneDef) - Method in class omeis.providers.re.Renderer
Returns a string with the dimensions of the specified plane.
getPlaneDirect(Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPixelBuffer
 
getPlaneDirect(Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
 
getPlaneDirect(Integer, Integer, Integer, byte[]) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
 
getPlaneDirect(Integer, Integer, Integer, byte[]) - Method in interface ome.io.nio.PixelBuffer
Retrieves a particular 2D image plane from this pixel buffer.
getPlaneDirect(Integer, Integer, Integer, byte[]) - Method in class ome.io.nio.RomioPixelBuffer
Implemented as specified by PixelBuffer I/F.
getPlaneExposureTime(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPlaneInfo() - Method in class ome.model.core.Pixels
returns planeInfo .
getPlaneOffset(int, int, int) - Method in interface ome.api.RawPixelsStore
 
getPlaneOffset(Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer
 
getPlaneOffset(Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelsWrapper
 
getPlaneOffset(Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
 
getPlaneOffset(Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
 
getPlaneOffset(Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer
Retrieves the offset for a particular 2D image plane in this pixel buffer.
getPlaneOffset(Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer
Implemented as specified by PixelBuffer I/F.
getPlaneOffset(int, int, int) - Method in class ome.services.RawPixelsBean
 
getPlaneOffset_async(AMD_RawPixelsStore_getPlaneOffset, int, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
getPlaneOffset_async(AMD_RawPixelsStore_getPlaneOffset, int, int, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
getPlanePositionX(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPlanePositionY(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPlanePositionZ(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPlanePrevious() - Method in class ome.model.display.PlaneSlicingContext
Simple field ome.model.display.PlaneSlicingContext.planePrevious (java.lang.Integer)
getPlanePrevious() - Method in class omeis.providers.re.codomain.PlaneSlicingContext
Returns the value corresponding to the index of the bit-plane ranged just before the one selected.
getPlaneRegion(int, int, int, int, int) - Method in interface ome.api.RawPixelsStore
 
getPlaneRegion(Integer, Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer
 
getPlaneRegion(Integer, Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPixelsWrapper
 
getPlaneRegion(Integer, Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
 
getPlaneRegion(Integer, Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
 
getPlaneRegion(Integer, Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer
Retrieves a particular region of a 2D image plane from this pixel buffer.
getPlaneRegion(Integer, Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer
Implemented as specified by PixelBuffer I/F.
getPlaneRegion(int, int, int, int, int) - Method in class ome.services.RawPixelsBean
 
getPlaneRegion_async(AMD_RawPixelsStore_getPlaneRegion, int, int, int, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
getPlaneRegion_async(AMD_RawPixelsStore_getPlaneRegion, int, int, int, int, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
getPlaneRegionDirect(Integer, Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPixelBuffer
 
getPlaneRegionDirect(Integer, Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
 
getPlaneRegionDirect(Integer, Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
 
getPlaneRegionDirect(Integer, Integer, Integer, Integer, Integer, byte[]) - Method in interface ome.io.nio.PixelBuffer
Retrieves a region from a given plane directly.
getPlaneRegionDirect(Integer, Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.nio.RomioPixelBuffer
Implemented as specified by PixelBuffer I/F.
getPlaneSelected() - Method in class ome.model.display.PlaneSlicingContext
Simple field ome.model.display.PlaneSlicingContext.planeSelected (java.lang.Integer)
getPlaneSelected() - Method in class omeis.providers.re.codomain.PlaneSlicingContext
Returns the value corresponding to the index of the selected bit-plane.
getPlaneSize() - Method in interface ome.api.RawPixelsStore
delegates to PixelBuffer
getPlaneSize() - Method in class ome.io.bioformats.BfPixelBuffer
 
getPlaneSize() - Method in class ome.io.bioformats.BfPixelsWrapper
 
getPlaneSize() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
 
getPlaneSize() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
 
getPlaneSize() - Method in interface ome.io.nio.PixelBuffer
Retrieves the in memory size of a 2D image plane in this pixel buffer.
getPlaneSize() - Method in class ome.io.nio.RomioPixelBuffer
Implemented as specified by PixelBuffer I/F.
getPlaneSize() - Method in class ome.services.RawPixelsBean
 
getPlaneSize_async(AMD_RawPixelsStore_getPlaneSize, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
getPlaneSize_async(AMD_RawPixelsStore_getPlaneSize, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
getPlaneTheC(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPlaneTheT(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPlaneTheZ(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPlate() - Method in class ome.model.screen.PlateAcquisition
Many-to-one field ome.model.screen.PlateAcquisition.plate (ome.model.screen.Plate)
getPlate() - Method in class ome.model.screen.Well
Many-to-one field ome.model.screen.Well.plate (ome.model.screen.Plate)
getPlate() - Method in class pojos.WellData
Returns the plate containing this Well.
getPlateAcquisition() - Method in class ome.model.screen.WellSample
Many-to-one field ome.model.screen.WellSample.plateAcquisition (ome.model.screen.PlateAcquisition)
getPlateAcquisitions() - Method in class ome.model.screen.Plate
returns plateAcquisitions .
getPlateAcquisitions() - Method in class pojos.PlateData
Returns the plate acquisitions related to this plate.
getPlateLinks() - Method in class ome.model.screen.Screen
returns plateLinks .
getPlateLinksCountPerOwner() - Method in class ome.model.screen.Screen
If fetched, returns the count(*) of ome.model.screen.ScreenPlateLink that a user has.
getPlates() - Method in class pojos.ScreenData
Returns the plates contained in this screen.
getPlateType() - Method in class pojos.PlateData
Returns the type of plate e.g.
getPockelCell() - Method in class ome.model.acquisition.Laser
Simple field ome.model.acquisition.Laser.pockelCell (java.lang.Boolean)
getPockelCell() - Method in class pojos.ChannelData
Returns the Pockel cell settings.
getPockelCellSetting() - Method in class ome.model.core.LogicalChannel
Simple field ome.model.core.LogicalChannel.pockelCellSetting (java.lang.Integer)
getPoint(double) - Method in class ome.util.math.geom2D.Line
Returns the point of this line defined by k.
getPoint(double) - Method in class ome.util.math.geom2D.Segment
Returns the point of this line defined by k.
getPoints() - Method in class ome.model.roi.Polygon
Simple field ome.model.roi.Polygon.points (java.lang.String)
getPoints() - Method in class ome.model.roi.Polyline
Simple field ome.model.roi.Polyline.points (java.lang.String)
getPoints(long, Session) - Method in class ome.services.roi.GeomTool
 
getPoints() - Method in class ome.util.math.geom2D.EllipseArea
Implemented as specified by the PlaneArea I/F.
getPoints() - Method in interface ome.util.math.geom2D.PlaneArea
Returns an array of PlanePoint contained in the PlaneArea.
getPoints() - Method in class ome.util.math.geom2D.RectangleArea
Implemented as specified by the PlaneArea I/F.
getPoints() - Method in class pojos.PolygonData
Returns the points in the polygon.
getPoints() - Method in class pojos.PolylineData
Returns the points in the Polyline.
getPoints1() - Method in class pojos.PolygonData
Returns the points in the polygon.
getPoints1() - Method in class pojos.PolylineData
Returns the points in the Polyline.
getPoints2() - Method in class pojos.PolygonData
Returns the points in the polygon.
getPoints2() - Method in class pojos.PolylineData
Returns the points in the Polyline.
getPoints_async(AMD_IRoi_getPoints, long, Current) - Method in class ome.services.blitz.impl.RoiI
 
getPojoTypes() - Method in class ome.logic.TypesImpl
 
getPort() - Method in class ome.system.Server
simple getter for the port passed into the constructor or the default port if none.
getPositionX() - Method in class ome.model.acquisition.StageLabel
Enum-mapped unit-based field ome.model.acquisition.StageLabel.positionX (ome.model.units.Length)
getPositionX() - Method in class ome.model.core.PlaneInfo
Enum-mapped unit-based field ome.model.core.PlaneInfo.positionX (ome.model.units.Length)
getPositionX(UnitsLength) - Method in class pojos.ImageAcquisitionData
Returns the x-coordinate in the frame microscope.
getPositionX() - Method in class pojos.ImageAcquisitionData
getPositionX(UnitsLength) - Method in class pojos.WellSampleData
Returns the position X.
getPositionX() - Method in class pojos.WellSampleData
getPositionY() - Method in class ome.model.acquisition.StageLabel
Enum-mapped unit-based field ome.model.acquisition.StageLabel.positionY (ome.model.units.Length)
getPositionY() - Method in class ome.model.core.PlaneInfo
Enum-mapped unit-based field ome.model.core.PlaneInfo.positionY (ome.model.units.Length)
getPositionY(UnitsLength) - Method in class pojos.ImageAcquisitionData
Returns the y-coordinate in the frame microscope.
getPositionY() - Method in class pojos.ImageAcquisitionData
getPositionY(UnitsLength) - Method in class pojos.WellSampleData
Returns the position Y.
getPositionY() - Method in class pojos.WellSampleData
getPositionZ() - Method in class ome.model.acquisition.StageLabel
Enum-mapped unit-based field ome.model.acquisition.StageLabel.positionZ (ome.model.units.Length)
getPositionZ() - Method in class ome.model.core.PlaneInfo
Enum-mapped unit-based field ome.model.core.PlaneInfo.positionZ (ome.model.units.Length)
getPositionZ(UnitsLength) - Method in class pojos.ImageAcquisitionData
Returns the z-coordinate in the frame microscope.
getPositionZ() - Method in class pojos.ImageAcquisitionData
getPosX() - Method in class ome.model.screen.WellSample
Enum-mapped unit-based field ome.model.screen.WellSample.posX (ome.model.units.Length)
getPosY() - Method in class ome.model.screen.WellSample
Enum-mapped unit-based field ome.model.screen.WellSample.posY (ome.model.units.Length)
getPower() - Method in class ome.model.acquisition.LightSource
Enum-mapped unit-based field ome.model.acquisition.LightSource.power (ome.model.units.Power)
getPower(UnitsPower) - Method in class pojos.LightSourceData
Returns the power of the light source.
getPower() - Method in class pojos.LightSourceData
Deprecated.
getPrefix() - Method in class ome.system.ServiceFactory
used by ServiceFactory.getServiceByClass(Class) to find the correct service proxy in the ServiceFactory.ctx
getPrefix() - Method in class ome.tools.spring.InternalServiceFactory
 
getPrefix() - Method in class ome.tools.spring.ManagedServiceFactory
 
getPrepareStatementCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
getPreviousPatch() - Method in class ome.model.meta.DBPatch
Simple field ome.model.meta.DBPatch.previousPatch (java.lang.Integer)
getPreviousVersion() - Method in class ome.model.meta.DBPatch
Simple field ome.model.meta.DBPatch.previousVersion (java.lang.String)
getPrimaryChannel() - Method in class ome.model.core.Pixels
Gets the first element of channels which can be interpreted as the primary or default element in some situations.
getPrimaryChannelBinding() - Method in class ome.model.display.RenderingDef
Gets the first element of waveRendering which can be interpreted as the primary or default element in some situations.
getPrimaryCodomainMapContext() - Method in class ome.model.display.RenderingDef
Gets the first element of spatialDomainEnhancement which can be interpreted as the primary or default element in some situations.
getPrimaryFilesetEntry() - Method in class ome.model.fs.Fileset
Gets the first element of usedFiles which can be interpreted as the primary or default element in some situations.
getPrimaryFilesetJobLink() - Method in class ome.model.fs.Fileset
Gets the first element of jobLinks which can be interpreted as the primary or default element in some situations.
getPrimaryGroupExperimenterMap() - Method in class ome.model.meta.Experimenter
Gets the first element of groupExperimenterMap which can be interpreted as the primary or default element in some situations.
getPrimaryLightPathExcitationFilterLink() - Method in class ome.model.acquisition.LightPath
Gets the first element of excitationFilterLink which can be interpreted as the primary or default element in some situations.
getPrimaryPixels() - Method in class ome.model.core.Image
Gets the first element of pixels which can be interpreted as the primary or default element in some situations.
getPrimaryShape() - Method in class ome.model.roi.Roi
Gets the first element of shapes which can be interpreted as the primary or default element in some situations.
getPrimaryWellSample() - Method in class ome.model.screen.Well
Gets the first element of wellSamples which can be interpreted as the primary or default element in some situations.
getPrincipal(MethodInvocation) - Method in class ome.logic.HardWiredInterceptor
 
getPrincipal() - Method in class ome.security.basic.BasicEventContext
 
getPrincipal() - Method in class ome.services.util.ExecutionThread
 
getPrincipal() - Method in class omero.cmd.SessionI
 
getProcess() - Method in class ome.services.scripts.ScriptFileType
Return the import name of the process class which will be used to invoke scripts of this type.
getProcess(String) - Method in class ome.services.scripts.ScriptRepoHelper
Find an "omero.process..." property string for the given mimetype or return "" if none is found.
getProcessedIds(String) - Method in class ome.services.graphs.GraphState
Deprecated.
Get the set of ids which were actually processed.
getProject(long) - Method in class ome.formats.OMEROMetadataStoreClient
 
getProjections(IObject) - Method in class ome.services.search.FullText
 
getProjectionService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
getProjectionService() - Method in class ome.system.ServiceFactory
 
getProjectLinks() - Method in class ome.model.containers.Dataset
returns projectLinks .
getProjectLinksCountPerOwner() - Method in class ome.model.containers.Dataset
If fetched, returns the count(*) of ome.model.containers.ProjectDatasetLink that a user has.
getProjects() - Method in class ome.formats.OMEROMetadataStoreClient
 
getProjects() - Method in class pojos.DatasetData
Returns a set of projects containing the dataset.
getProjectsForDataset(long) - Method in interface ome.api.IAnalysis
 
getProjectsForUser(long) - Method in interface ome.api.IAnalysis
 
getProperties() - Method in class ome.security.auth.FilePasswordProvider
 
getProperties() - Method in class omero.client
Returns the active properties for this instance.
getProperty(String) - Method in class ome.system.OmeroContext
 
getProperty(String) - Method in class ome.system.PreferenceContext
Lookup method for getting access to the merged properties for this instance.
getProperty(String) - Method in class omero.client
Returns the property value for this key or the empty string if none.
getPropertyKind(String, String) - Method in class ome.services.graphs.GraphPathBean
Get what kind of property a specific class property is.
getPropertyMap() - Method in class omero.client
Returns all properties which are prefixed with "omero." or "Ice."
getPropertyMap(Properties) - Method in class omero.client
Returns all properties which are prefixed with "omero." or "Ice."
getProtocolDescription() - Method in class ome.model.screen.Screen
Simple field ome.model.screen.Screen.protocolDescription (java.lang.String)
getProtocolDescription() - Method in class pojos.ScreenData
Returns the description of the protocol.
getProtocolIdentifier() - Method in class ome.model.screen.Screen
Simple field ome.model.screen.Screen.protocolIdentifier (java.lang.String)
getProtocolIdentifier() - Method in class pojos.ScreenData
Returns the identifier of the protocol.
getProvider(ChecksumType) - Method in interface ome.util.checksum.ChecksumProviderFactory
Returns an implementation of ChecksumProvider depending on the specified ChecksumType.
getProvider(ChecksumType) - Method in class ome.util.checksum.ChecksumProviderFactoryImpl
 
getProxiedObject(T) - Static method in class ome.services.fulltext.BridgeHelper
Simpler wrapper to handle superclass proxy objects (e.g.
getProxy() - Method in class ome.services.blitz.impl.ScriptProcessI
 
getProxy(Current) - Method in class ome.services.blitz.repo.AbstractRepositoryI
 
getProxy() - Method in class ome.services.blitz.repo.ManagedImportProcessI
 
getProxy() - Method in interface ome.services.blitz.repo.ProcessContainer.Process
 
getProxy() - Method in class ome.services.blitz.util.RegisterServantMessage
 
getProxyOrNull(String, SessionControlPrx, Current) - Method in class ome.services.blitz.fire.Ring
Delegates to the Ring.redirector strategy configured for this instance.
getProxyOrNull(Redirector.Context, String, SessionControlPrx, Current) - Method in class ome.services.blitz.redirect.AbstractRedirector
Returns null early if the Current has already once been routed by a Redirector implementation, returns an existing session if it can be found, or returns a null.
getProxyOrNull(Redirector.Context, String, SessionControlPrx, Current) - Method in class ome.services.blitz.redirect.ConfigRedirector
Create or retrieve and returns a SessionPrx which the current method takes control of.
getProxyOrNull(Redirector.Context, String, SessionControlPrx, Current) - Method in class ome.services.blitz.redirect.NullRedirector
Always returns null
getProxyOrNull(Redirector.Context, String, SessionControlPrx, Current) - Method in interface ome.services.blitz.redirect.Redirector
Create or retrieve and returns a SessionPrx which the current method takes control of.
getProxyOrNull(Redirector.Context, String, SessionControlPrx, Current) - Method in class ome.services.blitz.redirect.ScaleRedirector
 
getPulse() - Method in class ome.model.acquisition.Laser
Many-to-one field ome.model.acquisition.Laser.pulse (ome.model.enums.Pulse)
getPump() - Method in class ome.model.acquisition.Laser
Many-to-one field ome.model.acquisition.Laser.pump (ome.model.acquisition.LightSource)
getQuantityClass() - Method in class ome.model.units.GenericEnumType
 
getQuantization() - Method in class ome.model.display.RenderingDef
Many-to-one field ome.model.display.RenderingDef.quantization (ome.model.display.QuantumDef)
getQuantumDef() - Method in class ome.services.RenderingBean
Implemented as specified by the RenderingEngine interface.
getQuantumDef() - Method in interface omeis.providers.re.RenderingEngine
Returns the quantization object.
getQuantumDef_async(AMD_RenderingEngine_getQuantumDef, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
getQuantumManager() - Method in class omeis.providers.re.Renderer
Returns the object that manages and allows to retrieve the objects that are used to quantize wavelength data.
getQueries() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
Get all executed query strings
getQueryCacheHitCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
getQueryCacheMissCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
getQueryCachePutCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
getQueryExecutionCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
getQueryExecutionMaxTime() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
getQueryExecutionMaxTimeQueryString() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
getQueryFactory() - Method in class ome.logic.AbstractLevel1Service
 
getQueryFactory() - Method in class ome.logic.AbstractLevel2Service
 
getQueryService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
getQueryService() - Method in class ome.services.mail.MailSender
 
getQueryService() - Method in class ome.system.ServiceFactory
 
getQueryStatistics(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
Query statistics from query string (HQL or SQL)
getQueryString() - Method in class ome.services.mail.ObjectMailSender
 
getRadiusX() - Method in class pojos.EllipseData
Returns the radius along the X-axis.
getRadiusY() - Method in class pojos.EllipseData
Returns the radius along the Y-axis.
getRating() - Method in class pojos.RatingAnnotationData
Returns the rating value.
getRawFileStore(long, CheckedPath, String, Current) - Method in interface ome.services.blitz.repo.RepositoryDao
Create a RawFileBean (i.e. an implementation of RawFileStore which can be passed to RepoRawFileStore for performing internal functions.
getRawFileStore(long, CheckedPath, String, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
 
getRdf() - Method in class ome.util.RdfPrinter
 
getReader() - Method in class ome.formats.importer.ImportContainer
Return the reader class name used for reading the contents of this import container.
getReader() - Method in interface ome.formats.model.IObjectContainerStore
Returns the current Bio-Formats reader that has been used to populate the container store.
getReader() - Method in class ome.formats.OMEROMetadataStoreClient
 
getReaderClass(Fileset, Current) - Method in class ome.services.blitz.repo.ManagedRepositoryI
Get the suggested BioFormats Reader for the given Fileset.
getReaderNames() - Static method in class ome.services.util.DBEnumCheck
 
getReaderType(String) - Method in class ome.formats.importer.ImportCandidates
Retrieve reader type for file specified in path
getReadOutRate() - Method in class ome.model.acquisition.DetectorSettings
Enum-mapped unit-based field ome.model.acquisition.DetectorSettings.readOutRate (ome.model.units.Frequency)
getReagentIdentifier() - Method in class ome.model.screen.Reagent
Simple field ome.model.screen.Reagent.reagentIdentifier (java.lang.String)
getReagentLinks() - Method in class ome.model.screen.Well
returns reagentLinks .
getReagentLinksCountPerOwner() - Method in class ome.model.screen.Well
If fetched, returns the count(*) of ome.model.screen.WellReagentLink that a user has.
getReagents() - Method in class ome.model.screen.Screen
returns reagents .
getReagentsCounts() - Method in class pojos.WellData
Returns the number of reagents linked to the object, key: id of the user, value: number of annotation.
getReagentSetDescripion() - Method in class pojos.ScreenData
Returns the description of the reagent set.
getReagentSetDescription() - Method in class ome.model.screen.Screen
Simple field ome.model.screen.Screen.reagentSetDescription (java.lang.String)
getReagentSetIdentifier() - Method in class ome.model.screen.Screen
Simple field ome.model.screen.Screen.reagentSetIdentifier (java.lang.String)
getReagentSetIdentifier() - Method in class pojos.ScreenData
Returns the identifier of the Reagent set.
getRed() - Method in class ome.model.core.Channel
Simple field ome.model.core.Channel.red (java.lang.Integer)
getRed() - Method in class ome.model.display.ChannelBinding
Simple field ome.model.display.ChannelBinding.red (java.lang.Integer)
getRed() - Method in class ome.model.screen.Well
Simple field ome.model.screen.Well.red (java.lang.Integer)
getRed() - Method in class pojos.WellData
Returns the red component of the color associated to the well, or -1.
getRedBand() - Method in class omeis.providers.re.RGBBuffer
Returns the data buffer for the red band.
getRedirect(Redirector.Context) - Method in class ome.services.blitz.redirect.AbstractRedirector
Returns the current redirect, to which all calls to #getProxyOrNull(String, Glacier2.SessionControlPrx, Ice.Current) will be pointed.
getRedValue(int) - Method in class omeis.providers.re.RGBAIntBuffer
Retrieves the Red value for a particular pixel index.
getRedValue(int) - Method in class omeis.providers.re.RGBBuffer
Retrieves the Red value for a particular pixel index.
getRedValue(int) - Method in class omeis.providers.re.RGBIntBuffer
Retrieves the Red value for a particular pixel index.
getRef() - Method in class ome.model.display.Thumbnail
Simple field ome.model.display.Thumbnail.ref (java.lang.String)
getReference() - Method in class pojos.ImageData
Returns the reference to the file to register.
getReferenceCache() - Method in interface ome.formats.model.IObjectContainerStore
Returns the current reference cache.
getReferenceCache() - Method in class ome.formats.OMEROMetadataStoreClient
 
getReferenceCount(String) - Method in interface ome.api.ISession
Retrieves the current reference count for the given uuid.
getReferenceCount(String) - Method in class ome.services.sessions.SessionBean
 
getReferenceCount(String) - Method in interface ome.services.sessions.SessionManager
Return the number of client which are presumed to be attached to this session or throw an exception if there's no such session.
getReferenceCount(String) - Method in class ome.services.sessions.SessionManagerImpl
 
getReferenceCount_async(AMD_ISession_getReferenceCount, String, Current) - Method in class ome.services.blitz.impl.SessionI
 
getReferenceStringCache() - Method in interface ome.formats.model.IObjectContainerStore
Returns the current string based reference cache.
getReferenceStringCache() - Method in class ome.formats.OMEROMetadataStoreClient
 
getRefPlateId() - Method in class pojos.PlateAcquisitionData
Returns the id of the plate of reference.
getRefractiveIndex() - Method in class ome.model.acquisition.ObjectiveSettings
Simple field ome.model.acquisition.ObjectiveSettings.refractiveIndex (java.lang.Double)
getRefractiveIndex() - Method in class pojos.ImageAcquisitionData
Returns the refractive index of the objective.
getRegion(int, long) - Method in interface ome.api.RawPixelsStore
 
getRegion(Integer, Long) - Method in class ome.io.bioformats.BfPixelBuffer
 
getRegion(Integer, Long, byte[]) - Method in class ome.io.bioformats.BfPixelsWrapper
 
getRegion(Integer, Long) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
 
getRegion(Integer, Long) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
 
getRegion(Integer, Long) - Method in interface ome.io.nio.PixelBuffer
Retrieves a region from this pixel buffer.
getRegion(Integer, Long) - Method in class ome.io.nio.RomioPixelBuffer
Implemented as specified by PixelBuffer I/F.
getRegion(int, long) - Method in class ome.services.RawPixelsBean
 
getRegion() - Method in class omeis.providers.re.data.PlaneDef
Returns the region to render.
getRegion_async(AMD_RawPixelsStore_getRegion, int, long, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
getRegion_async(AMD_RawPixelsStore_getRegion, int, long, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
getRegionDirect(Integer, Long, byte[]) - Method in class ome.io.bioformats.BfPixelBuffer
 
getRegionDirect(Integer, Long, byte[]) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
 
getRegionDirect(Integer, Long, byte[]) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
 
getRegionDirect(Integer, Long, byte[]) - Method in interface ome.io.nio.PixelBuffer
Retrieves a region from this pixel buffer directly.
getRegionDirect(Integer, Long, byte[]) - Method in class ome.io.nio.RomioPixelBuffer
Implemented as specified by PixelBuffer I/F.
getRegistry() - Method in class ome.services.blitz.repo.InternalRepositoryConfig
 
getRegistry() - Method in class ome.services.blitz.util.BlitzConfiguration
 
getRelatedTo() - Method in class ome.model.core.Pixels
Many-to-one field ome.model.core.Pixels.relatedTo (ome.model.core.Pixels)
getRelationship(String, String) - Method in interface ome.tools.hibernate.ExtendedMetadata
Walks both the #locksHolder and the #lockedByHolder data for "from" argument to see if there is any direct relationship to the "to" argument.
getRelationship(String, String) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
Walks both the ExtendedMetadata.Impl.locksHolder and the ExtendedMetadata.Impl.lockedByHolder data for "from" argument to see if there is any direct relationship to the "to" argument.
getRelativePath() - Method in class ome.services.blitz.repo.CheckedPath
Get the parent path of the entity to which this path corresponds.
getRenderingDef() - Method in class ome.model.display.ChannelBinding
Many-to-one field ome.model.display.ChannelBinding.renderingDef (ome.model.display.RenderingDef)
getRenderingDef() - Method in class ome.model.display.CodomainMapContext
Many-to-one field ome.model.display.CodomainMapContext.renderingDef (ome.model.display.RenderingDef)
getRenderingDef() - Method in class omeis.providers.re.Renderer
Returns the settings that define the transformation context.
getRenderingDefId() - Method in interface ome.api.ThumbnailStore
Return the id of the RenderingDef loaded in this instance.
getRenderingDefId() - Method in class ome.services.RenderingBean
 
getRenderingDefId() - Method in class ome.services.ThumbnailBean
 
getRenderingDefId() - Method in interface omeis.providers.re.RenderingEngine
Returns the id of the RederingDef loaded by either RenderingEngine.lookupRenderingDef(long) or RenderingEngine.loadRenderingDef(long).
getRenderingDefId_async(AMD_RenderingEngine_getRenderingDefId, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
getRenderingDefId_async(AMD_ThumbnailStore_getRenderingDefId, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
 
getRenderingSettings(long) - Method in interface ome.api.IRenderingSettings
Returns the default rendering settings for a given pixels for the current user.
getRenderingSettings(long) - Method in class ome.logic.RenderingSettingsImpl
Implemented as specified by the IRenderingSettings I/F
getRenderingSettings_async(AMD_IRenderingSettings_getRenderingSettings, long, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
 
getRenderingSettingsService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
getRenderingSettingsService() - Method in class ome.system.ServiceFactory
 
getRenderShapes() - Method in class omeis.providers.re.data.PlaneDef
Returns whether or not the shapes (masks) will be rendered.
getReorderedPixelOffset(int, int, int) - Static method in class ome.io.nio.ReorderedPixelData
Returns the re-ordered pixel offset.
getRepetitionRate() - Method in class ome.model.acquisition.Laser
Enum-mapped unit-based field ome.model.acquisition.Laser.repetitionRate (ome.model.units.Frequency)
getReplacement() - Method in class ome.model.internal.GraphHolder
a replacement is a managed entity instance which has the same primary key as this instance.
getRepositoryInfoService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
getRepositoryInfoService() - Method in class ome.system.ServiceFactory
 
getRepositorySpace() - Method in class ome.formats.OMEROMetadataStoreClient
 
getRepoUuid() - Method in class ome.services.blitz.repo.AbstractRepositoryI
 
getRepoUuid() - Method in class ome.services.blitz.repo.PublicRepositoryI
 
getRequest(Class<R>) - Method in class omero.cmd.graphs.GraphRequestFactory
Construct a request.
getRequest(Current) - Method in class omero.cmd.HandleI
 
getRequests() - Method in class omero.cmd.graphs.Preprocessor
Deprecated.
Returns a copy of the requests field or an empty list if null.
getRequiredPermissions() - Method in interface ome.services.graphs.GraphTraversal.Processor
 
getResolutionDescriptions() - Method in interface ome.api.RawPixelsStore
 
getResolutionDescriptions() - Method in class ome.io.bioformats.BfPixelBuffer
 
getResolutionDescriptions() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
 
getResolutionDescriptions() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
 
getResolutionDescriptions() - Method in interface ome.io.nio.PixelBuffer
Return a list of lists each of which has sizeX, sizeY for the resolution level matching the index of the outer index.
getResolutionDescriptions() - Method in class ome.io.nio.RomioPixelBuffer
 
getResolutionDescriptions() - Method in class ome.services.RawPixelsBean
 
getResolutionDescriptions() - Method in class ome.services.RenderingBean
 
getResolutionDescriptions() - Method in class omeis.providers.re.Renderer
Returns the image's size information per resolution level.
getResolutionDescriptions() - Method in interface omeis.providers.re.RenderingEngine
 
getResolutionDescriptions_async(AMD_PyramidService_getResolutionDescriptions, Current) - Method in class ome.services.blitz.impl.AbstractPyramidServant
 
getResolutionDescriptions_async(AMD_PyramidService_getResolutionDescriptions, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
getResolutionLevel() - Method in interface ome.api.RawPixelsStore
 
getResolutionLevel() - Method in class ome.io.bioformats.BfPixelBuffer
 
getResolutionLevel() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
 
getResolutionLevel() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
 
getResolutionLevel() - Method in interface ome.io.nio.PixelBuffer
Retrieves the active resolution level.
getResolutionLevel() - Method in class ome.io.nio.RomioPixelBuffer
 
getResolutionLevel() - Method in class ome.services.RawPixelsBean
 
getResolutionLevel() - Method in class ome.services.RenderingBean
 
getResolutionLevel() - Method in class omeis.providers.re.Renderer
Retrieves the active resolution level.
getResolutionLevel() - Method in interface omeis.providers.re.RenderingEngine
 
getResolutionLevel_async(AMD_PyramidService_getResolutionLevel, Current) - Method in class ome.services.blitz.impl.AbstractPyramidServant
 
getResolutionLevel_async(AMD_PyramidService_getResolutionLevel, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
getResolutionLevels() - Method in interface ome.api.RawPixelsStore
 
getResolutionLevels() - Method in class ome.io.bioformats.BfPixelBuffer
 
getResolutionLevels() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
 
getResolutionLevels() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
 
getResolutionLevels() - Method in interface ome.io.nio.PixelBuffer
Retrieves the number of resolution levels that the backing pixels pyramid contains.
getResolutionLevels() - Method in class ome.io.nio.RomioPixelBuffer
 
getResolutionLevels() - Method in class ome.services.RawPixelsBean
 
getResolutionLevels() - Method in class ome.services.RenderingBean
 
getResolutionLevels() - Method in class omeis.providers.re.Renderer
Retrieves the number of resolution levels that the backing pixels pyramid contains.
getResolutionLevels() - Method in interface omeis.providers.re.RenderingEngine
 
getResolutionLevels_async(AMD_PyramidService_getResolutionLevels, Current) - Method in class ome.services.blitz.impl.AbstractPyramidServant
 
getResolutionLevels_async(AMD_PyramidService_getResolutionLevels, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
getResponse() - Method in class ome.services.blitz.impl.commands.SaveI
 
getResponse() - Method in class ome.services.blitz.repo.ManagedImportRequestI
 
getResponse() - Method in class ome.services.blitz.repo.RawAccessRequestI
 
getResponse() - Method in class omero.cmd.admin.CurrentSessionsRequestI
 
getResponse() - Method in class omero.cmd.admin.ResetPasswordRequestI
 
getResponse() - Method in class omero.cmd.admin.UpdateSessionTimeoutRequestI
 
getResponse() - Method in class omero.cmd.basic.DoAllI
 
getResponse() - Method in class omero.cmd.basic.ListRequestsI
 
getResponse() - Method in class omero.cmd.basic.TimingI
 
getResponse() - Method in class omero.cmd.CmdCallbackI
Returns possibly null Response value.
getResponse() - Method in class omero.cmd.fs.ManageImageBinariesI
 
getResponse() - Method in class omero.cmd.fs.OriginalMetadataRequestI
 
getResponse() - Method in class omero.cmd.fs.UsedFilesRequestI
 
getResponse() - Method in class omero.cmd.graphs.Chgrp2I
 
getResponse() - Method in class omero.cmd.graphs.ChgrpFacadeI
Deprecated.
 
getResponse() - Method in class omero.cmd.graphs.ChgrpI
Deprecated.
 
getResponse() - Method in class omero.cmd.graphs.Chmod2I
 
getResponse() - Method in class omero.cmd.graphs.ChmodFacadeI
Deprecated.
 
getResponse() - Method in class omero.cmd.graphs.ChmodI
Deprecated.
 
getResponse() - Method in class omero.cmd.graphs.Chown2I
 
getResponse() - Method in class omero.cmd.graphs.ChownFacadeI
Deprecated.
 
getResponse() - Method in class omero.cmd.graphs.ChownI
Deprecated.
 
getResponse() - Method in class omero.cmd.graphs.Delete2I
 
getResponse() - Method in class omero.cmd.graphs.DeleteFacadeI
Deprecated.
 
getResponse() - Method in class omero.cmd.graphs.DeleteI
Deprecated.
 
getResponse() - Method in class omero.cmd.graphs.DiskUsageI
 
getResponse() - Method in class omero.cmd.graphs.GraphSpecListI
Deprecated.
 
getResponse() - Method in class omero.cmd.graphs.SkipHeadI
 
getResponse(Current) - Method in class omero.cmd.HandleI
 
getResponse() - Method in class omero.cmd.Helper
 
getResponse() - Method in interface omero.cmd.IRequest
Returns the current response value.
getResponse() - Method in class omero.cmd.mail.SendEmailRequestI
 
getResponses() - Method in class ome.services.blitz.impl.ProcessorCallbackI
Return the number of times this instance has been called in a thread safe manner.
getResults(int, Current) - Method in class ome.services.blitz.impl.ScriptProcessI
 
getResults() - Method in class ome.services.delete.QueryConstraints
 
getResults(ProcessPrx, Current) - Method in class omero.grid.InteractiveProcessorI
 
getResultSet() - Method in class ome.tools.hibernate.SqlArray
 
getResultSet(Map<String, Class<?>>) - Method in class ome.tools.hibernate.SqlArray
 
getResultSet(long, int) - Method in class ome.tools.hibernate.SqlArray
 
getResultSet(long, int, Map<String, Class<?>>) - Method in class ome.tools.hibernate.SqlArray
 
getResultsString(Object, IdentityHashMap<Object, String>) - Static method in class ome.services.util.ServiceHandler
public for testing purposes.
getResultTypes() - Method in class ome.logic.TypesImpl
 
getReverse() - Method in class ome.model.display.ReverseIntensityContext
Simple field ome.model.display.ReverseIntensityContext.reverse (java.lang.Boolean)
getRevision(Class) - Static method in class ome.system.Version
Parses the given class for its RevisionNumber annotation.
getRGBA(int) - Method in class ome.services.RenderingBean
Implemented as specified by the RenderingEngine interface.
getRGBA(int) - Method in interface omeis.providers.re.RenderingEngine
Returns a 4D-array representing the color associated to the specified channel.
getRGBA_async(AMD_RenderingEngine_getRGBA, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
getRing() - Method in class ome.services.blitz.util.BlitzConfiguration
 
getRoi() - Method in class ome.model.roi.Shape
Many-to-one field ome.model.roi.Shape.roi (ome.model.roi.Roi)
getROI() - Method in class pojos.util.ROIComponent
Returns all the ROI in the component as a list.
getROI() - Method in class pojos.util.UploadMask
Returns the ROIs created from uploading the images.
getROICoordinate() - Method in class pojos.ShapeData
Returns the ROICoordinate for the ShapeData.
getRoiIds() - Method in class ome.services.blitz.measurements.MeasurementStore
 
getRoiIds() - Method in interface ome.services.blitz.measurements.OmeroMeasurementStore
Returns the ids of all Roi instances created during the save method.
getRoiMeasurements_async(AMD_IRoi_getRoiMeasurements, long, RoiOptions, Current) - Method in class ome.services.blitz.impl.RoiI
 
getRois() - Method in class ome.model.core.Image
returns rois .
getRoiService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
getRoiStats_async(AMD_IRoi_getRoiStats, long, Current) - Method in class ome.services.blitz.impl.RoiI
 
getRoles() - Method in class ome.services.mail.MailSender
 
getRoles() - Method in class ome.services.util.DBUserCheck
 
getRoot() - Method in class ome.formats.OMEROMetadataStoreClient
 
getRoot() - Method in class ome.services.blitz.impl.OmeroMetadata
 
getRoot() - Method in class ome.services.graphs.AbstractHierarchyGraphSpec
Deprecated.
Return the root class for this hierarchy.
getRoot() - Method in class ome.services.graphs.AnnotationGraphSpec
Deprecated.
 
getRoot() - Method in class ome.services.graphs.LightSourceGraphSpec
Deprecated.
 
getRootFile() - Method in class ome.formats.importer.transfers.TransferState
Find original file represented by the managed repository that import is taking place to.
getRootId() - Method in class ome.system.Roles
 
getRootName() - Method in class ome.system.Roles
 
getRouter(Communicator) - Static method in class omero.client
Acquires the default router, and throws an exception if it is not of type {Glacier2.RouterPrx}.
getRow(int, int, int, int) - Method in interface ome.api.RawPixelsStore
 
getRow(Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer
 
getRow(Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPixelsWrapper
 
getRow(Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
 
getRow(Integer, Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
 
getRow(Integer, Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer
Retrieves a particular row or scanline from this pixel buffer.
getRow(Integer, Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer
Implemented as specified by PixelBuffer I/F.
getRow() - Method in class ome.model.screen.Well
Simple field ome.model.screen.Well.row (java.lang.Integer)
getRow(int, int, int, int) - Method in class ome.services.RawPixelsBean
 
getRow() - Method in class pojos.WellData
Returns the row used to indicate the location of the well on the grid.
getRow_async(AMD_RawPixelsStore_getRow, int, int, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
getRow_async(AMD_RawPixelsStore_getRow, int, int, int, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
getRowDirect(Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPixelBuffer
 
getRowDirect(Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
 
getRowDirect(Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
 
getRowDirect(Integer, Integer, Integer, Integer, byte[]) - Method in interface ome.io.nio.PixelBuffer
Retrieves a particular row or scanline from this pixel buffer.
getRowDirect(Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.nio.RomioPixelBuffer
Implemented as specified by PixelBuffer I/F.
getRowNamingConvention() - Method in class ome.model.screen.Plate
Simple field ome.model.screen.Plate.rowNamingConvention (java.lang.String)
getRowOffset(int, int, int, int) - Method in interface ome.api.RawPixelsStore
 
getRowOffset(Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer
 
getRowOffset(Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelsWrapper
 
getRowOffset(Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
 
getRowOffset(Integer, Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
 
getRowOffset(Integer, Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer
Retrieves the offset for a particular row or scanline in this pixel buffer.
getRowOffset(Integer, Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer
Implemented as specified by PixelBuffer I/F.
getRowOffset(int, int, int, int) - Method in class ome.services.RawPixelsBean
 
getRowOffset_async(AMD_RawPixelsStore_getRowOffset, int, int, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
getRowOffset_async(AMD_RawPixelsStore_getRowOffset, int, int, int, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
getRows() - Method in class ome.model.screen.Plate
Simple field ome.model.screen.Plate.rows (java.lang.Integer)
getRowSequenceIndex() - Method in class pojos.PlateData
Returns the index indicating how to label a row.
getRowSize() - Method in interface ome.api.RawPixelsStore
 
getRowSize() - Method in class ome.io.bioformats.BfPixelBuffer
 
getRowSize() - Method in class ome.io.bioformats.BfPixelsWrapper
 
getRowSize() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
 
getRowSize() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
 
getRowSize() - Method in interface ome.io.nio.PixelBuffer
Retrieves the in memory size of a row or scanline of pixels in this pixel buffer.
getRowSize() - Method in class ome.io.nio.RomioPixelBuffer
Implemented as specified by PixelBuffer I/F.
getRowSize() - Method in class ome.services.RawPixelsBean
 
getRowSize_async(AMD_RawPixelsStore_getRowSize, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
getRowSize_async(AMD_RawPixelsStore_getRowSize, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
getRx() - Method in class ome.model.roi.Ellipse
Simple field ome.model.roi.Ellipse.rx (java.lang.Double)
getRx() - Method in class ome.model.roi.Rect
Simple field ome.model.roi.Rect.rx (java.lang.Double)
getRy() - Method in class ome.model.roi.Ellipse
Simple field ome.model.roi.Ellipse.ry (java.lang.Double)
getSamplesPerPixel() - Method in class ome.model.core.LogicalChannel
Simple field ome.model.core.LogicalChannel.samplesPerPixel (java.lang.Integer)
getScale() - Method in class ome.model.meta.Node
Simple field ome.model.meta.Node.scale (java.lang.Integer)
getScalingFactor() - Method in class ome.io.nio.SimpleBackOff
 
getScheduledDeletes() - Method in class ome.services.delete.Deletion
Deprecated.
 
getScheduledFor() - Method in class ome.model.jobs.Job
Simple field ome.model.jobs.Job.scheduledFor (java.sql.Timestamp)
getScore(IObject) - Method in class ome.services.search.FullText
 
getScreen() - Method in class ome.model.screen.Reagent
Many-to-one field ome.model.screen.Reagent.screen (ome.model.screen.Screen)
getScreenLinks() - Method in class ome.model.screen.Plate
returns screenLinks .
getScreenLinksCountPerOwner() - Method in class ome.model.screen.Plate
If fetched, returns the count(*) of ome.model.screen.ScreenPlateLink that a user has.
getScreens() - Method in class ome.formats.OMEROMetadataStoreClient
 
getScreens() - Method in class pojos.PlateData
Returns a set of screens containing the plate.
getScriptDir() - Method in class ome.services.scripts.ScriptRepoHelper
Returns the actual root of this repository.
getScriptID_async(AMD_IScript_getScriptID, String, Current) - Method in class ome.services.blitz.impl.ScriptI
Get the id of the official script with given path.
getScriptRepository(Current) - Method in class ome.services.blitz.impl.SharedResourcesI
 
getScripts_async(AMD_IScript_getScripts, Current) - Method in class ome.services.blitz.impl.ScriptI
Get Scripts will return all the scripts by id and name available on the server.
getScriptService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
getScriptText_async(AMD_IScript_getScriptText, long, Current) - Method in class ome.services.blitz.impl.ScriptI
Return the script with the name to the user.
getScriptWithDetails_async(AMD_IScript_getScriptWithDetails, long, Current) - Method in class ome.services.blitz.impl.ScriptI
Return the script with the name to the user.
getSecondLevelCacheHitCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
getSecondLevelCacheMissCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
getSecondLevelCachePutCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
getSecondLevelCacheRegionNames() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
Get all second-level cache region names
getSecondLevelCacheStatistics(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
Second level cache statistics per region
getSecurityContexts(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
getSecurityRoles() - Method in interface ome.api.IAdmin
returns the active Roles in use by the server.
getSecurityRoles() - Method in class ome.logic.AdminImpl
 
getSecurityRoles() - Method in class ome.security.basic.BasicSecuritySystem
 
getSecurityRoles() - Method in interface ome.security.SecuritySystem
 
getSecurityRoles() - Method in class ome.security.SecuritySystemHolder
 
getSecurityRoles() - Method in class ome.security.sharing.SharingSecuritySystem
 
getSecurityRoles_async(AMD_IAdmin_getSecurityRoles, Current) - Method in class ome.services.blitz.impl.AdminI
 
getSecuritySystem() - Method in class ome.logic.AbstractLevel2Service
 
getSelectedFile() - Method in class ome.formats.importer.util.ErrorContainer
 
getSender() - Method in class ome.services.mail.MailUtil
Helper method that returns value of omero.mail.from.
getSerialNumber() - Method in class ome.model.acquisition.Detector
Simple field ome.model.acquisition.Detector.serialNumber (java.lang.String)
getSerialNumber() - Method in class ome.model.acquisition.Dichroic
Simple field ome.model.acquisition.Dichroic.serialNumber (java.lang.String)
getSerialNumber() - Method in class ome.model.acquisition.Filter
Simple field ome.model.acquisition.Filter.serialNumber (java.lang.String)
getSerialNumber() - Method in class ome.model.acquisition.FilterSet
Simple field ome.model.acquisition.FilterSet.serialNumber (java.lang.String)
getSerialNumber() - Method in class ome.model.acquisition.LightSource
Simple field ome.model.acquisition.LightSource.serialNumber (java.lang.String)
getSerialNumber() - Method in class ome.model.acquisition.Microscope
Simple field ome.model.acquisition.Microscope.serialNumber (java.lang.String)
getSerialNumber() - Method in class ome.model.acquisition.Objective
Simple field ome.model.acquisition.Objective.serialNumber (java.lang.String)
getSerialNumber() - Method in class pojos.DetectorData
Returns the serial number of the detector.
getSerialNumber() - Method in class pojos.DichroicData
Returns the serial number.
getSerialNumber() - Method in class pojos.FilterData
Returns the serial number.
getSerialNumber() - Method in class pojos.FilterSetData
Returns the serial number.
getSerialNumber() - Method in class pojos.LightSourceData
Returns the serial number of the light source.
getSerialNumber() - Method in class pojos.ObjectiveData
Returns the serial number of the objective.
getSeries() - Method in class ome.io.bioformats.BfPixelBuffer
Retrieves the current series of the underlying Bio-Formats reader.
getSeries(Pixels) - Method in class ome.io.nio.PixelsService
Retrieves the series for a given set of pixels.
getSeries() - Method in class ome.model.core.Image
Simple field ome.model.core.Image.series (java.lang.Integer)
getSeries() - Method in class pojos.ImageData
Returns the series.
getServant(Identity) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
getServant() - Method in class ome.services.blitz.util.RegisterServantMessage
 
getServantList() - Method in class omero.util.ServantHolder
 
getServerFileFromFsFile(FsFile) - Method in class ome.services.blitz.repo.path.ServerFilePathTransformer
Given a repository path, returns the corresponding server-local File.
getServerFileMimetype() - Method in class pojos.FileAnnotationData
Returns the file format as defined by the specification, corresponding to the file extension.
getServerPort() - Method in class ome.formats.importer.util.IniFileLoader
 
getServerTime() - Method in interface ome.api.IConfig
checks the current server for it's time.
getServerTime() - Method in class ome.logic.ConfigImpl
getServerTime_async(AMD_IConfig_getServerTime, Current) - Method in class ome.services.blitz.impl.ConfigI
 
getService() - Method in interface ome.services.util.Executor
Returns the ExecutorService assigned to this instance.
getService() - Method in class ome.services.util.Executor.Impl
 
getServiceByClass(Class<T>) - Method in class ome.system.ServiceFactory
looks up services based on the current prefix and the class name of the service type.
getServiceCleanups() - Method in class ome.security.basic.BasicEventContext
 
getServiceFactory() - Method in class ome.formats.OMEROMetadataStoreClient
Returns the currently active service factory.
getServiceFactory(MethodInvocation) - Method in class ome.logic.HardWiredInterceptor
 
getServiceFactory(String, String) - Method in class ome.services.blitz.fire.SessionManagerI
 
getServiceFactory(Identity) - Method in class ome.services.blitz.fire.SessionManagerI
 
getServiceFactory() - Method in class ome.services.blitz.impl.RawFileStoreI
 
getServiceFactory() - Method in class ome.services.blitz.util.FindServiceFactoryMessage
 
getServiceFactory() - Method in class omero.client
Deprecated. 
getServiceFactory() - Method in class omero.cmd.Helper
 
getServiceFactoryIdentity(Current) - Method in class ome.services.blitz.fire.SessionManagerI
 
getServiceInterface() - Method in class ome.logic.AdminImpl
 
getServiceInterface() - Method in class ome.logic.ConfigImpl
 
getServiceInterface() - Method in class ome.logic.LdapImpl
 
getServiceInterface() - Method in class ome.logic.MetadataImpl
Returns the Interface implemented by this class.
getServiceInterface() - Method in class ome.logic.PixelsImpl
Returns the interface this implementation is for.
getServiceInterface() - Method in class ome.logic.PojosImpl
Returns the Interface implemented by this class.
getServiceInterface() - Method in class ome.logic.QueryImpl
 
getServiceInterface() - Method in class ome.logic.RenderingSettingsImpl
Returns the interface this implementation is for.
getServiceInterface() - Method in class ome.logic.RepositoryInfoImpl
 
getServiceInterface() - Method in class ome.logic.TypesImpl
 
getServiceInterface() - Method in class ome.logic.UpdateImpl
 
getServiceInterface() - Method in class ome.services.delete.DeleteBean
 
getServiceInterface() - Method in class ome.services.JobBean
 
getServiceInterface() - Method in class ome.services.projection.ProjectionBean
Returns the interface this implementation is for.
getServiceInterface() - Method in class ome.services.RawFileBean
 
getServiceInterface() - Method in class ome.services.RawPixelsBean
 
getServiceInterface() - Method in class ome.services.RenderingBean
Returns the service corresponding to this class.
getServiceInterface() - Method in class ome.services.SearchBean
 
getServiceInterface() - Method in class ome.services.sessions.SessionBean
 
getServiceInterface() - Method in class ome.services.sharing.ShareBean
 
getServiceInterface() - Method in class ome.services.ThumbnailBean
 
getServiceInterface() - Method in interface ome.system.SelfConfigurableService
 
getServiceKey() - Method in class ome.services.blitz.util.ExpiredServantMessage
 
getSession(String) - Method in interface ome.api.ISession
Retrieves the session associated with this uuid, updating the last access time as well.
getSession() - Method in class ome.model.meta.Event
Many-to-one field ome.model.meta.Event.session (ome.model.meta.Session)
getSession(String) - Method in class ome.services.sessions.SessionBean
 
getSession() - Method in interface ome.services.sessions.SessionContext
 
getSession() - Method in class ome.services.sessions.SessionContextImpl
 
getSession() - Method in class ome.system.ServiceFactory
 
getSession() - Method in class ome.system.SessionInitializer
 
getSession() - Method in class ome.tools.hibernate.SessionFactory
Returns a session active for the current thread.
getSession() - Method in class omero.client
Returns the current active session or throws an exception if none has been created since the last client.closeSession()
getSession() - Method in class omero.cmd.Helper
 
getSession() - Method in class omero.model.DetailsI
 
getSession() - Method in class omero.util.RPSTileLoop
 
getSession() - Method in class omero.util.ServantHolder
 
getSession_async(AMD_ISession_getSession, String, Current) - Method in class ome.services.blitz.impl.SessionI
 
getSessionCloseCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
getSessionContext(String) - Method in class ome.services.sessions.state.SessionCache
Retrieve a session possibly raising either RemovedSessionException or SessionTimeoutException.
getSessionContext(String, boolean) - Method in class ome.services.sessions.state.SessionCache
Retrieve a session possibly raising either RemovedSessionException or SessionTimeoutException.
getSessionData() - Method in interface ome.services.sessions.SessionManager
Return all sessions that are active with associated possibly varing session data information.
getSessionData() - Method in class ome.services.sessions.SessionManagerImpl
 
getSessionData(String, boolean) - Method in class ome.services.sessions.state.SessionCache
Returns all the data contained in the internal implementation of this manger.
getSessionFactory() - Method in class ome.logic.AbstractLevel1Service
delegates to HibernateDaoSupport to get the current SessionFactory
getSessionId() - Method in class ome.services.messages.AbstractSessionMessage
 
getSessionId() - Method in class omero.client
Returns the UUID for the current session without making a remote call.
getSessionInitializer() - Method in class ome.system.ServiceFactory
 
getSessionOpenCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
getSessions() - Method in class ome.model.meta.Node
returns sessions .
getSessionService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
getSessionService() - Method in class ome.system.ServiceFactory
 
getSessionStats(String) - Method in interface ome.services.sessions.SessionManager
Return the SessionStats which are being counted for the given session or throw an exception if it has been removed.
getSessionStats(String) - Method in class ome.services.sessions.SessionManagerImpl
 
getSetting() - Method in interface ome.api.ILdap
Gets config value from properties.
getSetting() - Method in class ome.logic.LdapImpl
 
getSetting_async(AMD_ILdap_getSetting, Current) - Method in class ome.services.blitz.impl.LdapI
 
getSettings() - Method in class ome.model.core.Pixels
returns settings .
getSettings(long) - Method in class ome.services.ThumbnailCtx
Retrieves the RenderingDef object for a given Pixels ID.
getSha1() - Method in class ome.io.nio.RomioPixelBuffer
 
getSha1() - Method in class ome.model.core.Pixels
Simple field ome.model.core.Pixels.sha1 (java.lang.String)
getShape(int) - Method in class ome.model.roi.Roi
Gets the ome.model.roi.Shape at the given index.
getShapeCount() - Method in class pojos.ROIData
Returns the number of shapes in the ROI.
getShapeIds(long) - Method in class ome.util.actions.PostgresSqlAction
 
getShapeIds(long) - Method in interface ome.util.SqlAction
 
getShapeIds() - Method in class omeis.providers.re.data.PlaneDef
Returns whether or not the shapes (masks) will be rendered.
getShapes() - Method in class ome.model.roi.Roi
returns shapes .
getShapes(int, int) - Method in class pojos.ROIData
Returns the list of shapes on a given plane.
getShapeSettings() - Method in class pojos.ShapeData
Returns the settings associated to the shape.
getShapesInRange(ROICoordinate, ROICoordinate) - Method in class pojos.ROIData
Returns an iterator of the Shapes in the ROI in the range [start, end].
getShapeStats_async(AMD_IRoi_getShapeStats, long, Current) - Method in class ome.services.blitz.impl.RoiI
 
getShapeStatsList_async(AMD_IRoi_getShapeStatsList, List<Long>, Current) - Method in class ome.services.blitz.impl.RoiI
 
getShare(long) - Method in interface ome.api.IShare
Gets a share as a Session with all related: comments, members, fully loaded.
getShare(long) - Method in class ome.services.sharing.ShareBean
 
getShare_async(AMD_IShare_getShare, long, Current) - Method in class ome.services.blitz.impl.ShareI
 
getShareData(List<Long>) - Method in interface ome.util.SqlAction
Returns a map of Share ID to Share data blob.
getShareData(List<Long>) - Method in class ome.util.SqlAction.Impl
 
getShareIfAccessible(long) - Method in class ome.services.sharing.ShareBean
Loads share and checks it's owner and member data against the current context (owner/member/admin).
getShareIfAccessible(long, boolean, long) - Method in class ome.services.sharing.ShareStore
Loads share and checks its owner and member data against the current context (owner/member/admin).
getShares(long, boolean, boolean) - Method in class ome.services.sharing.BlobShareStore
 
getShares(long, boolean, boolean) - Method in class ome.services.sharing.ShareStore
 
getShareService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
getShareService() - Method in class ome.system.ServiceFactory
 
getSharesOwnedBy(Experimenter, boolean) - Method in interface ome.api.IShare
Gets all shares owned by the given Experimenter.
getSharesOwnedBy(Experimenter, boolean) - Method in class ome.services.sharing.ShareBean
 
getSharesOwnedBy_async(AMD_IShare_getSharesOwnedBy, Experimenter, boolean, Current) - Method in class ome.services.blitz.impl.ShareI
 
getSignificantBits() - Method in class ome.model.core.Pixels
Simple field ome.model.core.Pixels.significantBits (java.lang.Integer)
getSize() - Method in class ome.model.core.OriginalFile
Simple field ome.model.core.OriginalFile.size (java.lang.Long)
getSize() - Method in class ome.util.mem.CopiableArray
Returns the number of elements in the array.
getSizeC() - Method in class ome.io.bioformats.BfPixelBuffer
 
getSizeC() - Method in class ome.io.bioformats.BfPixelsWrapper
 
getSizeC() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
 
getSizeC() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
 
getSizeC() - Method in interface ome.io.nio.PixelBuffer
Delegates to Pixels.getSizeC().
getSizeC() - Method in class ome.io.nio.RomioPixelBuffer
Implemented as specified by PixelBuffer I/F.
getSizeC() - Method in class ome.model.core.Pixels
Simple field ome.model.core.Pixels.sizeC (java.lang.Integer)
getSizeC() - Method in class pojos.PixelsData
Returns the number of channels.
getSizeT() - Method in class ome.io.bioformats.BfPixelBuffer
 
getSizeT() - Method in class ome.io.bioformats.BfPixelsWrapper
 
getSizeT() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
 
getSizeT() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
 
getSizeT() - Method in interface ome.io.nio.PixelBuffer
Delegates to Pixels.getSizeT().
getSizeT() - Method in class ome.io.nio.RomioPixelBuffer
Implemented as specified by PixelBuffer I/F.
getSizeT() - Method in class ome.model.core.Pixels
Simple field ome.model.core.Pixels.sizeT (java.lang.Integer)
getSizeT() - Method in class pojos.PixelsData
Returns the number of time-points.
getSizeX() - Method in class ome.io.bioformats.BfPixelBuffer
 
getSizeX() - Method in class ome.io.bioformats.BfPixelsWrapper
 
getSizeX() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
 
getSizeX() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
 
getSizeX() - Method in interface ome.io.nio.PixelBuffer
Delegates to Pixels.getSizeX().
getSizeX() - Method in class ome.io.nio.RomioPixelBuffer
Implemented as specified by PixelBuffer I/F.
getSizeX() - Method in class ome.model.acquisition.OTF
Simple field ome.model.acquisition.OTF.sizeX (java.lang.Integer)
getSizeX() - Method in class ome.model.core.Pixels
Simple field ome.model.core.Pixels.sizeX (java.lang.Integer)
getSizeX() - Method in class ome.model.display.Thumbnail
Simple field ome.model.display.Thumbnail.sizeX (java.lang.Integer)
getSizeX() - Method in class pojos.OTFData
Returns the size along the X-axis.
getSizeX() - Method in class pojos.PixelsData
Returns the number of pixels along the X-axis.
getSizeX1() - Method in class omeis.providers.re.RGBBuffer
Returns the number of pixels on the X1-axis.
getSizeX2() - Method in class omeis.providers.re.RGBBuffer
Returns the number of pixels on the X2-axis.
getSizeY() - Method in class ome.io.bioformats.BfPixelBuffer
 
getSizeY() - Method in class ome.io.bioformats.BfPixelsWrapper
 
getSizeY() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
 
getSizeY() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
 
getSizeY() - Method in interface ome.io.nio.PixelBuffer
Delegates to Pixels.getSizeY().
getSizeY() - Method in class ome.io.nio.RomioPixelBuffer
Implemented as specified by PixelBuffer I/F.
getSizeY() - Method in class ome.model.acquisition.OTF
Simple field ome.model.acquisition.OTF.sizeY (java.lang.Integer)
getSizeY() - Method in class ome.model.core.Pixels
Simple field ome.model.core.Pixels.sizeY (java.lang.Integer)
getSizeY() - Method in class ome.model.display.Thumbnail
Simple field ome.model.display.Thumbnail.sizeY (java.lang.Integer)
getSizeY() - Method in class pojos.OTFData
Returns the size along the Y-axis.
getSizeY() - Method in class pojos.PixelsData
Returns the number of pixels along the Y-axis.
getSizeZ() - Method in class ome.io.bioformats.BfPixelBuffer
 
getSizeZ() - Method in class ome.io.bioformats.BfPixelsWrapper
 
getSizeZ() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
 
getSizeZ() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
 
getSizeZ() - Method in interface ome.io.nio.PixelBuffer
Delegates to Pixels.getSizeZ().
getSizeZ() - Method in class ome.io.nio.RomioPixelBuffer
Implemented as specified by PixelBuffer I/F.
getSizeZ() - Method in class ome.model.core.Pixels
Simple field ome.model.core.Pixels.sizeZ (java.lang.Integer)
getSizeZ() - Method in class pojos.PixelsData
Returns the number of pixels along the Z-axis.
getSkipHeadPolicyPerform(GraphPolicy, SetMultimap<String, Long>) - Static method in class omero.cmd.graphs.SkipHeadPolicy
Adjust an existing graph traversal policy so that for specific model objects permissions are not checked.
getSkipHeadPolicySkip(GraphPolicy, GraphPathBean, Collection<String>, GraphPolicy.Action, SetMultimap<String, Long>) - Static method in class omero.cmd.graphs.SkipHeadPolicy
Adjust an existing graph traversal policy so that orphaned model objects will always or never be included, according to their type.
getSlice() - Method in class omeis.providers.re.data.PlaneDef
Returns an identifier to tell which kind of plane this object identifies.
getSnapshot() - Method in class ome.system.metrics.DefaultHistogram
 
getSnapshot() - Method in interface ome.system.metrics.Histogram
 
getSource() - Method in class ome.model.roi.Roi
Many-to-one field ome.model.roi.Roi.source (ome.model.core.OriginalFile)
getSourceObject(LSID) - Method in interface ome.formats.model.IObjectContainerStore
Retrieves an OMERO Blitz source object for a given LSID.
getSourceObject(LSID) - Method in class ome.formats.OMEROMetadataStoreClient
 
getSourceObjects(Class<T>) - Method in interface ome.formats.model.IObjectContainerStore
Retrieves all OMERO Blitz source objects of a given class.
getSourceObjects(Class<T>) - Method in class ome.formats.OMEROMetadataStoreClient
 
getSpatialDomainEnhancement() - Method in class ome.model.display.RenderingDef
returns spatialDomainEnhancement .
getSql() - Method in class omero.cmd.Helper
 
getSqlAction() - Method in class ome.services.util.Executor.SimpleWork
 
getSQLJoin(String, String, String, String) - Method in interface ome.tools.hibernate.ExtendedMetadata
provides the link between two tables similar to {link ExtendedMetadata.getRelationship(String, String).
getSQLJoin(String, String, String, String) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
Note: this implementation does not yet take into account the mapping of joined subclasses like Job->UpdateJob.
getStack(int, int) - Method in interface ome.api.RawPixelsStore
 
getStack(Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer
 
getStack(Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPixelsWrapper
 
getStack(Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
 
getStack(Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
 
getStack(Integer, Integer) - Method in interface ome.io.nio.PixelBuffer
Retrieves the the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel buffer.
getStack(Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer
Implemented as specified by PixelBuffer I/F.
getStack(int, int) - Method in class ome.services.RawPixelsBean
 
getStack_async(AMD_RawPixelsStore_getStack, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
getStack_async(AMD_RawPixelsStore_getStack, int, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
getStackDirect(Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPixelBuffer
 
getStackDirect(Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
 
getStackDirect(Integer, Integer, byte[]) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
 
getStackDirect(Integer, Integer, byte[]) - Method in interface ome.io.nio.PixelBuffer
Retrieves the the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel buffer.
getStackDirect(Integer, Integer, byte[]) - Method in class ome.io.nio.RomioPixelBuffer
Implemented as specified by PixelBuffer I/F.
getStackOffset(int, int) - Method in interface ome.api.RawPixelsStore
 
getStackOffset(Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer
 
getStackOffset(Integer, Integer) - Method in class ome.io.bioformats.BfPixelsWrapper
 
getStackOffset(Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
 
getStackOffset(Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
 
getStackOffset(Integer, Integer) - Method in interface ome.io.nio.PixelBuffer
Retrieves the offset for the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel buffer.
getStackOffset(Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer
Implemented as specified by PixelBuffer I/F.
getStackOffset(int, int) - Method in class ome.services.RawPixelsBean
 
getStackOffset_async(AMD_RawPixelsStore_getStackOffset, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
getStackOffset_async(AMD_RawPixelsStore_getStackOffset, int, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
getStackSize() - Method in interface ome.api.RawPixelsStore
 
getStackSize() - Method in class ome.io.bioformats.BfPixelBuffer
 
getStackSize() - Method in class ome.io.bioformats.BfPixelsWrapper
 
getStackSize() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
 
getStackSize() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
 
getStackSize() - Method in interface ome.io.nio.PixelBuffer
Retrieves the in memory size of the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel buffer.
getStackSize() - Method in class ome.io.nio.RomioPixelBuffer
Implemented as specified by PixelBuffer I/F.
getStackSize() - Method in class ome.services.RawPixelsBean
 
getStackSize_async(AMD_RawPixelsStore_getStackSize, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
getStackSize_async(AMD_RawPixelsStore_getStackSize, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
getStackTrace(Throwable) - Static method in class ome.formats.importer.util.ErrorHandler
Return stack trace from throwable
getStageLabel() - Method in class ome.model.core.Image
Many-to-one field ome.model.core.Image.stageLabel (ome.model.acquisition.StageLabel)
getStageLabelId() - Method in class pojos.ImageAcquisitionData
Returns the id of the StageLabel or -1 if not already linked to the image.
getStart() - Method in class ome.services.delete.Deletion
Deprecated.
 
getStarted() - Method in class ome.model.jobs.Job
Simple field ome.model.jobs.Job.started (java.sql.Timestamp)
getStarted() - Method in class ome.model.meta.Session
Simple field ome.model.meta.Session.started (java.sql.Timestamp)
getStartFrom(Response) - Method in class omero.cmd.graphs.Chgrp2I
 
getStartFrom(Response) - Method in class omero.cmd.graphs.Chmod2I
 
getStartFrom(Response) - Method in class omero.cmd.graphs.Chown2I
 
getStartFrom(Response) - Method in class omero.cmd.graphs.Delete2I
 
getStartFrom(Response) - Method in interface omero.cmd.graphs.WrappableRequest
From the response of the head-skipping request, determine which model objects are the targets of the operation.
getStartTime() - Method in class ome.model.screen.PlateAcquisition
Simple field ome.model.screen.PlateAcquisition.startTime (java.sql.Timestamp)
getStartTime() - Method in class ome.parameters.Parameters
 
getStartTime() - Method in class omero.sys.ParametersI
Returns the value of the start time parameter.
getStartTime() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
getStartTime() - Method in class pojos.PlateAcquisitionData
Returns the time when the first image was collected.
getStartTime() - Method in class pojos.WellSampleData
Returns the time at which the field was acquired.
getStatefulServiceCount() - Method in class ome.services.blitz.impl.ServiceFactoryI
NB: Much of the logic here is similar to SessionI.doClose and should be pushed down.
getStatefulServiceCount() - Method in class omero.util.ServantHolder
 
getStatefulServices() - Method in class omero.client
Returns all active StatefulServiceInterface proxies.
getStaticDisableHistory() - Method in class ome.formats.importer.ImportConfig
 
getStaticDisableHistory() - Method in class ome.formats.importer.util.IniFileLoader
 
getStats() - Method in class ome.security.basic.BasicEventContext
 
getStats() - Method in class ome.security.basic.CurrentDetails
 
getStats(List<Long>) - Method in class ome.services.roi.GeomTool
 
getStats() - Method in class omeis.providers.re.Renderer
Returns a RenderingStats object that the rendering strategy can use to track performance.
getStats() - Method in class omeis.providers.re.RenderingStats
Returns a stats report ready to be written to the log file.
getStatsInfo() - Method in class ome.model.core.Channel
Many-to-one field ome.model.core.Channel.statsInfo (ome.model.stats.StatsInfo)
getStatus() - Method in class ome.formats.importer.util.ErrorContainer
return the error status
getStatus() - Method in class ome.model.jobs.Job
Many-to-one field ome.model.jobs.Job.status (ome.model.jobs.JobStatus)
getStatus() - Method in class ome.model.meta.Event
Simple field ome.model.meta.Event.status (java.lang.String)
getStatus() - Method in class ome.model.screen.Plate
Simple field ome.model.screen.Plate.status (java.lang.String)
getStatus() - Method in class ome.model.screen.Well
Simple field ome.model.screen.Well.status (java.lang.String)
getStatus() - Method in class omero.cmd.CmdCallbackI
Returns possibly null Status value.
getStatus(Current) - Method in class omero.cmd.HandleI
 
getStatus() - Method in class omero.cmd.Helper
 
getStatus() - Method in class pojos.PlateData
Returns the status of the plate.
getStatus() - Method in class pojos.WellData
Returns the status of the well.
getStatusOrThrow() - Method in class omero.cmd.CmdCallbackI
 
getStdDev() - Method in class ome.system.metrics.DefaultSnapshot
 
getStdDev() - Method in interface ome.system.metrics.Snapshot
 
getStep(int) - Method in class ome.services.graphs.GraphState
Deprecated.
 
getStepProvidingCompleteResponse() - Method in class omero.cmd.graphs.Chgrp2I
 
getStepProvidingCompleteResponse() - Method in class omero.cmd.graphs.Chmod2I
 
getStepProvidingCompleteResponse() - Method in class omero.cmd.graphs.Chown2I
 
getStepProvidingCompleteResponse() - Method in class omero.cmd.graphs.Delete2I
 
getStepProvidingCompleteResponse() - Method in interface omero.cmd.graphs.WrappableRequest
Get the step of this request that suffices for assembling the request's response.
getSteps() - Method in class ome.services.delete.Deletion
Deprecated.
 
getSteps() - Method in class omero.cmd.Helper
 
getStop() - Method in class ome.services.delete.Deletion
Deprecated.
 
getStore() - Method in class ome.services.fulltext.SimpleLuceneOptions
 
getStrategy(QuantumDef, Pixels) - Method in class omeis.providers.re.quantum.QuantumFactory
Returns a strategy to carry out the quantization process whose context is defined by pd.
getStride() - Method in class omeis.providers.re.data.PlaneDef
Returns the stride.
getString(String) - Static method in class ome.util.actions.PsqlStrings
 
getStroke() - Method in class pojos.ShapeSettingsData
Returns the color of the stroke.
getStrokeColor() - Method in class ome.model.roi.Shape
Simple field ome.model.roi.Shape.strokeColor (java.lang.Integer)
getStrokeDashArray() - Method in class ome.model.roi.Shape
Simple field ome.model.roi.Shape.strokeDashArray (java.lang.String)
getStrokeDashArray() - Method in class pojos.ShapeSettingsData
Returns the stroke dashes.
getStrokeDashOffset() - Method in class ome.model.roi.Shape
Simple field ome.model.roi.Shape.strokeDashOffset (java.lang.Integer)
getStrokeLineCap() - Method in class ome.model.roi.Shape
Simple field ome.model.roi.Shape.strokeLineCap (java.lang.String)
getStrokeLineJoin() - Method in class ome.model.roi.Shape
Simple field ome.model.roi.Shape.strokeLineJoin (java.lang.String)
getStrokeMiterLimit() - Method in class ome.model.roi.Shape
Simple field ome.model.roi.Shape.strokeMiterLimit (java.lang.Integer)
getStrokeWidth() - Method in class ome.model.roi.Shape
Enum-mapped unit-based field ome.model.roi.Shape.strokeWidth (ome.model.units.Length)
getStrokeWidth() - Method in class pojos.ShapeSettingsData
getStrokeWidth(UnitsLength) - Method in class pojos.ShapeSettingsData
Returns the stroke's width (or 1 px if it's not set or <= 0)
getSubclassesOf(String) - Method in class ome.services.graphs.GraphPathBean
Get the subclasses of the given class, if any.
getSubclassesOfReflexive(String) - Method in class ome.services.graphs.GraphPathBean
Get the name of this class and of its mapped subclasses.
getSubjectPrefix() - Method in class ome.services.mail.MailSender
 
getSubmitted() - Method in class ome.model.jobs.Job
Simple field ome.model.jobs.Job.submitted (java.sql.Timestamp)
getSubSpec() - Method in class ome.services.graphs.GraphEntry
Deprecated.
 
getSubtypeValue(int, int, Object) - Method in class ome.tools.hibernate.ExtendedMetadata.Locks
uses the ClassMetadata for this ExtendedMetadata.Locks tp retrieve the component value.
getSuccessfulTransactionCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
getSuperclassesOf(String) - Method in class ome.services.graphs.GraphPathBean
Get the superclasses of the given class, if any.
getSuperclassesOfReflexive(String) - Method in class ome.services.graphs.GraphPathBean
Get the name of this class and of its mapped superclasses.
getSuperSpec() - Method in class ome.services.graphs.BaseGraphSpec
Deprecated.
 
getSuperSpec() - Method in class ome.services.graphs.GraphEntry
Deprecated.
 
getSuperSpec() - Method in interface ome.services.graphs.GraphSpec
Deprecated.
Specification of where this GraphSpec is attached under another .
getSupportedMetadataLevels() - Method in class ome.formats.importer.OMEROWrapper
 
getSymbol() - Method in enum ome.model.enums.UnitsElectricPotential
 
getSymbol() - Method in enum ome.model.enums.UnitsFrequency
 
getSymbol() - Method in enum ome.model.enums.UnitsLength
 
getSymbol() - Method in enum ome.model.enums.UnitsPower
 
getSymbol() - Method in enum ome.model.enums.UnitsPressure
 
getSymbol() - Method in enum ome.model.enums.UnitsTemperature
 
getSymbol() - Method in enum ome.model.enums.UnitsTime
 
getSymbol() - Method in interface ome.model.units.UnitEnum
 
getSymbol(Current) - Method in class omero.model.ElectricPotentialI
 
getSymbol(Current) - Method in class omero.model.FrequencyI
 
getSymbol(Current) - Method in class omero.model.LengthI
 
getSymbol(Current) - Method in class omero.model.PowerI
 
getSymbol(Current) - Method in class omero.model.PressureI
 
getSymbol(Current) - Method in class omero.model.TemperatureI
 
getSymbol(Current) - Method in class omero.model.TimeI
 
getSystemGroupId() - Method in class ome.system.Roles
 
getSystemGroupName() - Method in class ome.system.Roles
 
getT() - Method in class omeis.providers.re.data.PlaneDef
Returns the timepoint.
getT() - Method in class pojos.ShapeData
Returns the time-point.
getTable() - Method in class ome.services.blitz.measurements.MeasurementStore
 
getTable() - Method in interface ome.services.blitz.measurements.OmeroMeasurementStore
Returns the Table proxy which is in use by this service.
getTable_async(AMD_IRoi_getTable, long, Current) - Method in class ome.services.blitz.impl.RoiI
 
getTagAnnotationCount() - Method in class ome.services.blitz.impl.OmeroMetadata
 
getTagAnnotationDescription(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getTagAnnotationID(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getTagAnnotationNamespace(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getTagAnnotationValue(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getTagDescription() - Method in class pojos.TagAnnotationData
Returns the description of the tag.
getTagDescriptions() - Method in class pojos.TagAnnotationData
Returns the descriptions linked to that tag.
getTaggedObjectsCount(Set<Long>, Parameters) - Method in interface ome.api.IMetadata
Returns a map whose key is a tag's id and the value the number of Projects, Datasets, and Images linked to that tag.
getTaggedObjectsCount(Set<Long>, Parameters) - Method in class ome.logic.MetadataImpl
Implemented as specified by the IMetadata I/F
getTaggedObjectsCount_async(AMD_IMetadata_getTaggedObjectsCount, List<Long>, Parameters, Current) - Method in class ome.services.blitz.impl.MetadataI
 
getTags() - Method in class pojos.TagAnnotationData
Returns the collection of tags related to this tag.
getTagValue() - Method in class pojos.TagAnnotationData
Returns the text of the tag.
getTarget() - Method in class ome.formats.importer.ImportContainer
 
getTarget(Class<T>, long) - Method in class ome.formats.OMEROMetadataStoreClient
Helper method to retrieve an object from iQuery
getTarget() - Method in class ome.services.blitz.repo.ManagedImportLocationI
Return the server-side CheckedPath instance which can be passed to a Bio-Formats reader.
getTargetType(String) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
Returns the IObject type which a given field points to.
getTempDir() - Method in class omero.util.TempFileManager
Returns the directory under which all temporary files and folders will be created.
gettempdir() - Static method in class omero.util.TempFileManager
getTemperature() - Method in class ome.model.acquisition.ImagingEnvironment
Enum-mapped unit-based field ome.model.acquisition.ImagingEnvironment.temperature (ome.model.units.Temperature)
getTemperature(UnitsTemperature) - Method in class pojos.ImageAcquisitionData
Returns the temperature in Celcius.
getTemperature() - Method in class pojos.ImageAcquisitionData
getTemplatePrefix() - Method in class ome.model.fs.Fileset
Simple field ome.model.fs.Fileset.templatePrefix (java.lang.String)
getTerm() - Method in class pojos.TermAnnotationData
Returns the term.
getTermAnnotationCount() - Method in class ome.services.blitz.impl.OmeroMetadata
 
getTermAnnotationDescription(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getTermAnnotationID(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getTermAnnotationNamespace(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getTermAnnotationValue(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getTermDescription() - Method in class pojos.TermAnnotationData
Returns the description of the term.
getTermValue() - Method in class ome.model.annotations.TermAnnotation
Simple field ome.model.annotations.TermAnnotation.termValue (java.lang.String)
getTermVector() - Method in class ome.services.fulltext.SimpleLuceneOptions
 
getTestIds() - Method in class ome.tools.RepositoryTask
Private method used for testing only.
getText() - Method in class pojos.EllipseData
Returns the text of the shape.
getText() - Method in class pojos.LineData
Returns the text of the shape.
getText() - Method in class pojos.MaskData
Returns the text of the shape.
getText() - Method in class pojos.PointData
Returns the text of the shape.
getText() - Method in class pojos.PolygonData
Returns the text of the shape.
getText() - Method in class pojos.PolylineData
Returns the text of the shape.
getText() - Method in class pojos.RectangleData
Returns the text of the shape.
getText() - Method in class pojos.TextData
Returns the text of the shape.
getText() - Method in class pojos.TextualAnnotationData
Returns the text of this annotation.
getText() - Method in class pojos.XMLAnnotationData
Returns the text of this annotation.
getTextValue() - Method in class ome.model.annotations.TextAnnotation
Simple field ome.model.annotations.TextAnnotation.textValue (java.lang.String)
getTextValue() - Method in class ome.model.roi.Ellipse
Simple field ome.model.roi.Ellipse.textValue (java.lang.String)
getTextValue() - Method in class ome.model.roi.Label
Simple field ome.model.roi.Label.textValue (java.lang.String)
getTextValue() - Method in class ome.model.roi.Line
Simple field ome.model.roi.Line.textValue (java.lang.String)
getTextValue() - Method in class ome.model.roi.Mask
Simple field ome.model.roi.Mask.textValue (java.lang.String)
getTextValue() - Method in class ome.model.roi.Path
Simple field ome.model.roi.Path.textValue (java.lang.String)
getTextValue() - Method in class ome.model.roi.Point
Simple field ome.model.roi.Point.textValue (java.lang.String)
getTextValue() - Method in class ome.model.roi.Polygon
Simple field ome.model.roi.Polygon.textValue (java.lang.String)
getTextValue() - Method in class ome.model.roi.Polyline
Simple field ome.model.roi.Polyline.textValue (java.lang.String)
getTextValue() - Method in class ome.model.roi.Rect
Simple field ome.model.roi.Rect.textValue (java.lang.String)
getTheC() - Method in class ome.model.core.PlaneInfo
Simple field ome.model.core.PlaneInfo.theC (java.lang.Integer)
getTheC() - Method in class ome.model.roi.Shape
Simple field ome.model.roi.Shape.theC (java.lang.Integer)
getTheT() - Method in class ome.model.core.PlaneInfo
Simple field ome.model.core.PlaneInfo.theT (java.lang.Integer)
getTheT() - Method in class ome.model.roi.Shape
Simple field ome.model.roi.Shape.theT (java.lang.Integer)
getTheZ() - Method in class ome.model.core.PlaneInfo
Simple field ome.model.core.PlaneInfo.theZ (java.lang.Integer)
getTheZ() - Method in class ome.model.roi.Shape
Simple field ome.model.roi.Shape.theZ (java.lang.Integer)
getThis() - Method in interface ome.services.util.Executor.StatefulWork
 
getThis(MethodInvocation) - Method in class ome.tools.hibernate.SessionHandler
 
getThreadIdentifier() - Static method in class ome.util.Utils
Returns a String which can be used to correlate log messages.
getThumbnail(Integer, Integer) - Method in interface ome.api.ThumbnailStore
Retrieves a thumbnail for a pixels set using a given set of rendering settings (RenderingDef).
getThumbnail(Thumbnail) - Method in class ome.io.nio.ThumbnailService
Return byte array of Thumbnail
getThumbnail(Thumbnail, byte[]) - Method in class ome.io.nio.ThumbnailService
Return byte array of Thumbnail, providing byte array
getThumbnail(Integer, Integer) - Method in class ome.services.ThumbnailBean
 
getThumbnail_async(AMD_ThumbnailStore_getThumbnail, RInt, RInt, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
 
getThumbnailByLongestSide(Integer) - Method in interface ome.api.ThumbnailStore
Retrieves a thumbnail for a pixels set using a given set of rendering settings (RenderingDef).
getThumbnailByLongestSide(Integer) - Method in class ome.services.ThumbnailBean
 
getThumbnailByLongestSide_async(AMD_ThumbnailStore_getThumbnailByLongestSide, RInt, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
 
getThumbnailByLongestSideDirect(Integer) - Method in interface ome.api.ThumbnailStore
Retrieves a thumbnail for a pixels set using a given set of rendering settings (RenderingDef).
getThumbnailByLongestSideDirect(Integer) - Method in class ome.services.ThumbnailBean
 
getThumbnailByLongestSideDirect_async(AMD_ThumbnailStore_getThumbnailByLongestSideDirect, RInt, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
 
getThumbnailByLongestSideSet(Integer, Set<Long>) - Method in interface ome.api.ThumbnailStore
Retrieves a number of thumbnails for pixels sets using given sets of rendering settings (RenderingDef).
getThumbnailByLongestSideSet(Integer, Set<Long>) - Method in class ome.services.ThumbnailBean
 
getThumbnailByLongestSideSet_async(AMD_ThumbnailStore_getThumbnailByLongestSideSet, RInt, List<Long>, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
 
getThumbnailDirect(Integer, Integer) - Method in interface ome.api.ThumbnailStore
Retrieves a thumbnail for a pixels set using a given set of rendering settings (RenderingDef).
getThumbnailDirect(Integer, Integer) - Method in class ome.services.ThumbnailBean
 
getThumbnailDirect_async(AMD_ThumbnailStore_getThumbnailDirect, RInt, RInt, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
 
getThumbnailExists(Thumbnail) - Method in class ome.io.nio.ThumbnailService
Returns whether or not a thumbnail exists on disk.
getThumbnailForSectionByLongestSideDirect(int, int, Integer) - Method in interface ome.api.ThumbnailStore
Retrieves a thumbnail for a pixels set using a given set of rendering settings (RenderingDef) for a particular section.
getThumbnailForSectionByLongestSideDirect(int, int, Integer) - Method in class ome.services.ThumbnailBean
 
getThumbnailForSectionByLongestSideDirect_async(AMD_ThumbnailStore_getThumbnailForSectionByLongestSideDirect, int, int, RInt, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
 
getThumbnailForSectionDirect(int, int, Integer, Integer) - Method in interface ome.api.ThumbnailStore
Retrieves a thumbnail for a pixels set using a given set of rendering settings (RenderingDef) for a particular section.
getThumbnailForSectionDirect(int, int, Integer, Integer) - Method in class ome.services.ThumbnailBean
 
getThumbnailForSectionDirect_async(AMD_ThumbnailStore_getThumbnailForSectionDirect, int, int, RInt, RInt, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
 
getThumbnailIds() - Method in class ome.tools.RepositoryTask
This public method is used to return a list of thumbnail ids that require deletion from the disk repository.
getThumbnailLength(Thumbnail) - Method in class ome.io.nio.ThumbnailService
Returns length of Thumbnail on disk
getThumbnailOutputStream(Thumbnail) - Method in class ome.io.nio.ThumbnailService
Return FileOutputStream of Thumbnail
getThumbnailPath(Long) - Method in class ome.io.nio.AbstractFileSystemService
Returns a numbered path relative to the root of this service, but is ignorant of FS and similar constructs.
getThumbnails() - Method in class ome.model.core.Pixels
returns thumbnails .
getThumbnailSet(Integer, Integer, Set<Long>) - Method in interface ome.api.ThumbnailStore
Retrieves a number of thumbnails for pixels sets using given sets of rendering settings (RenderingDef).
getThumbnailSet(Integer, Integer, Set<Long>) - Method in class ome.services.ThumbnailBean
 
getThumbnailSet_async(AMD_ThumbnailStore_getThumbnailSet, RInt, RInt, List<Long>, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
 
getTie(Identity) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
getTile(int, int, int, int, int, int, int) - Method in interface ome.api.RawPixelsStore
 
getTile(Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer
 
getTile(int, int, int, int, int, int, int, byte[]) - Method in class ome.io.bioformats.BfPixelsWrapper
 
getTile(Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
 
getTile(Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
 
getTile(Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer
Retrieves a tile from this pixel buffer.
getTile(Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer
 
getTile(int, int, int, int, int, int, int) - Method in class ome.services.RawPixelsBean
 
getTile(int, int, int, int, int, int, int) - Method in class omero.util.RPSTileData
 
getTile(int, int, int, int, int, int, int) - Method in interface omero.util.TileData
 
getTile_async(AMD_RawPixelsStore_getTile, int, int, int, int, int, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
getTile_async(AMD_RawPixelsStore_getTile, int, int, int, int, int, int, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
getTileDirect(Integer, Integer, Integer, Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPixelBuffer
 
getTileDirect(Integer, Integer, Integer, Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
 
getTileDirect(Integer, Integer, Integer, Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
 
getTileDirect(Integer, Integer, Integer, Integer, Integer, Integer, Integer, byte[]) - Method in interface ome.io.nio.PixelBuffer
Retrieves a tile from this pixel buffer.
getTileDirect(Integer, Integer, Integer, Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.nio.RomioPixelBuffer
 
getTileHeight() - Method in class ome.io.nio.ConfiguredTileSizes
 
getTileHeight() - Method in interface ome.io.nio.TileSizes
 
getTileSize() - Method in interface ome.api.RawPixelsStore
 
getTileSize(Long) - Method in class ome.formats.OMEROMetadataStoreClient
Retrieves the suggested tile size for a pixels set.
getTileSize() - Method in class ome.io.bioformats.BfPixelBuffer
 
getTileSize() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
 
getTileSize() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
 
getTileSize() - Method in interface ome.io.nio.PixelBuffer
Retrieves the tile size for the pixel store.
getTileSize() - Method in class ome.io.nio.RomioPixelBuffer
 
getTileSize() - Method in class ome.services.RawPixelsBean
 
getTileSize() - Method in class ome.services.RenderingBean
 
getTileSize() - Method in class omeis.providers.re.Renderer
Retrieves the tile size for the pixel store.
getTileSize() - Method in interface omeis.providers.re.RenderingEngine
 
getTileSize_async(AMD_PyramidService_getTileSize, Current) - Method in class ome.services.blitz.impl.AbstractPyramidServant
 
getTileSize_async(AMD_PyramidService_getTileSize, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
getTileWidth() - Method in class ome.io.nio.ConfiguredTileSizes
 
getTileWidth() - Method in interface ome.io.nio.TileSizes
 
getTime() - Method in class ome.model.meta.Event
Simple field ome.model.meta.Event.time (java.sql.Timestamp)
getTime() - Method in class pojos.TimeAnnotationData
Returns the time value.
getTimeIncrement() - Method in class ome.model.core.Pixels
Enum-mapped unit-based field ome.model.core.Pixels.timeIncrement (ome.model.units.Time)
getTimelineService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
getTimepoint(int) - Method in interface ome.api.RawPixelsStore
 
getTimepoint(Integer) - Method in class ome.io.bioformats.BfPixelBuffer
 
getTimepoint(Integer, byte[]) - Method in class ome.io.bioformats.BfPixelsWrapper
 
getTimepoint(Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
 
getTimepoint(Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
 
getTimepoint(Integer) - Method in interface ome.io.nio.PixelBuffer
Retrieves the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel buffer.
getTimepoint(Integer) - Method in class ome.io.nio.RomioPixelBuffer
Implemented as specified by PixelBuffer I/F.
getTimepoint() - Method in class ome.model.screen.WellSample
Simple field ome.model.screen.WellSample.timepoint (java.sql.Timestamp)
getTimepoint(int) - Method in class ome.services.RawPixelsBean
 
getTimePoint() - Method in class pojos.ROICoordinate
Returns the timepoint.
getTimepoint_async(AMD_RawPixelsStore_getTimepoint, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
getTimepoint_async(AMD_RawPixelsStore_getTimepoint, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
getTimepointDirect(Integer, byte[]) - Method in class ome.io.bioformats.BfPixelBuffer
 
getTimepointDirect(Integer, byte[]) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
 
getTimepointDirect(Integer, byte[]) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
 
getTimepointDirect(Integer, byte[]) - Method in interface ome.io.nio.PixelBuffer
Retrieves the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel buffer.
getTimepointDirect(Integer, byte[]) - Method in class ome.io.nio.RomioPixelBuffer
Implemented as specified by PixelBuffer I/F.
getTimepointOffset(int) - Method in interface ome.api.RawPixelsStore
 
getTimepointOffset(Integer) - Method in class ome.io.bioformats.BfPixelBuffer
 
getTimepointOffset(Integer) - Method in class ome.io.bioformats.BfPixelsWrapper
 
getTimepointOffset(Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
 
getTimepointOffset(Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
 
getTimepointOffset(Integer) - Method in interface ome.io.nio.PixelBuffer
Retrieves the in memory size of the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel buffer.
getTimepointOffset(Integer) - Method in class ome.io.nio.RomioPixelBuffer
Implemented as specified by PixelBuffer I/F.
getTimepointOffset(int) - Method in class ome.services.RawPixelsBean
 
getTimepointOffset_async(AMD_RawPixelsStore_getTimepointOffset, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
getTimepointOffset_async(AMD_RawPixelsStore_getTimepointOffset, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
getTimepointSize() - Method in interface ome.api.RawPixelsStore
 
getTimepointSize() - Method in class ome.io.bioformats.BfPixelBuffer
 
getTimepointSize() - Method in class ome.io.bioformats.BfPixelsWrapper
 
getTimepointSize() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
 
getTimepointSize() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
 
getTimepointSize() - Method in interface ome.io.nio.PixelBuffer
Retrieves the in memory size of the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel buffer.
getTimepointSize() - Method in class ome.io.nio.RomioPixelBuffer
Implemented as specified by PixelBuffer I/F.
getTimepointSize() - Method in class ome.services.RawPixelsBean
 
getTimepointSize_async(AMD_RawPixelsStore_getTimepointSize, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
getTimepointSize_async(AMD_RawPixelsStore_getTimepointSize, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
getTimestampAnnotationCount() - Method in class ome.services.blitz.impl.OmeroMetadata
 
getTimestampAnnotationDescription(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getTimestampAnnotationID(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getTimestampAnnotationNamespace(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getTimestampAnnotationValue(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getTimeToIdle() - Method in class ome.model.meta.Session
Simple field ome.model.meta.Session.timeToIdle (java.lang.Long)
getTimeToLive() - Method in class ome.model.meta.Session
Simple field ome.model.meta.Session.timeToLive (java.lang.Long)
getTimeValue() - Method in class ome.model.annotations.TimestampAnnotation
Simple field ome.model.annotations.TimestampAnnotation.timeValue (java.sql.Timestamp)
getToken() - Method in class ome.formats.importer.util.ErrorContainer
 
getTokenUrl() - Method in class ome.formats.importer.ImportConfig
 
getTooSimilarFiles(Set<File>) - Method in class ome.services.blitz.repo.path.ClientFilePathTransformer
Get the files that are too similarly named.
getTopicManager() - Method in class ome.services.blitz.util.BlitzConfiguration
 
getTotalFoundCount() - Method in class ome.services.graphs.GraphState
Deprecated.
Return the total number of ids loaded into this instance.
getTotalProcessedCount() - Method in class ome.services.graphs.GraphState
Deprecated.
Return the total number of ids which were processed.
getTotalSize() - Method in interface ome.api.RawPixelsStore
 
getTotalSize() - Method in class ome.io.bioformats.BfPixelBuffer
 
getTotalSize() - Method in class ome.io.bioformats.BfPixelsWrapper
 
getTotalSize() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
 
getTotalSize() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
 
getTotalSize() - Method in interface ome.io.nio.PixelBuffer
Retrieves the in memory size of the entire pixel buffer.
getTotalSize() - Method in class ome.io.nio.RomioPixelBuffer
Implemented as specified by PixelBuffer I/F.
getTotalSize() - Method in class ome.services.RawPixelsBean
 
getTotalSize(IObject) - Method in class ome.services.search.FullText
 
getTotalSize_async(AMD_RawPixelsStore_getTotalSize, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
getTotalSize_async(AMD_RawPixelsStore_getTotalSize, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
getTransactionAttribute(Method, Class) - Method in class ome.services.sharing.ShareRestrictionTransactionAttributeSource
 
getTransactionAttribute(Method, Class) - Method in class ome.tools.spring.ForceTransactionAttributeSource
 
getTransactionCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
getTransform() - Method in class ome.model.roi.Shape
Simple field ome.model.roi.Shape.transform (java.lang.String)
getTransform() - Method in class pojos.ShapeData
Returns the transformation.
getTransmittance() - Method in class ome.model.acquisition.TransmittanceRange
Simple field ome.model.acquisition.TransmittanceRange.transmittance (java.lang.Double)
getTransmittance() - Method in class pojos.FilterData
Returns the cut out tolerance value or -1.
getTransmittanceRange() - Method in class ome.model.acquisition.Filter
Many-to-one field ome.model.acquisition.Filter.transmittanceRange (ome.model.acquisition.TransmittanceRange)
getTuneable() - Method in class ome.model.acquisition.Laser
Simple field ome.model.acquisition.Laser.tuneable (java.lang.Boolean)
getType() - Method in class ome.model.acquisition.Arc
Many-to-one field ome.model.acquisition.Arc.type (ome.model.enums.ArcType)
getType() - Method in class ome.model.acquisition.Detector
Many-to-one field ome.model.acquisition.Detector.type (ome.model.enums.DetectorType)
getType() - Method in class ome.model.acquisition.Filament
Many-to-one field ome.model.acquisition.Filament.type (ome.model.enums.FilamentType)
getType() - Method in class ome.model.acquisition.Filter
Many-to-one field ome.model.acquisition.Filter.type (ome.model.enums.FilterType)
getType() - Method in class ome.model.acquisition.Laser
Many-to-one field ome.model.acquisition.Laser.type (ome.model.enums.LaserType)
getType() - Method in class ome.model.acquisition.Microscope
Many-to-one field ome.model.acquisition.Microscope.type (ome.model.enums.MicroscopeType)
getType() - Method in class ome.model.experiment.Experiment
Many-to-one field ome.model.experiment.Experiment.type (ome.model.enums.ExperimentType)
getType() - Method in class ome.model.experiment.MicrobeamManipulation
Many-to-one field ome.model.experiment.MicrobeamManipulation.type (ome.model.enums.MicrobeamManipulationType)
getType() - Method in class ome.model.jobs.Job
Simple field ome.model.jobs.Job.type (java.lang.String)
getType() - Method in class ome.model.meta.Event
Many-to-one field ome.model.meta.Event.type (ome.model.enums.EventType)
getType() - Method in class ome.model.screen.Screen
Simple field ome.model.screen.Screen.type (java.lang.String)
getType() - Method in class ome.model.screen.Well
Simple field ome.model.screen.Well.type (java.lang.String)
getType(MethodInvocation) - Method in class ome.tools.hibernate.EventMethodInterceptor.DisableAction
 
getType() - Method in class pojos.DetectorData
Returns the type of the detector.
getType() - Method in class pojos.FilterData
Returns the type.
getType() - Method in class pojos.LightSourceData
Returns the type of light.
getTypes() - Method in class ome.security.policy.BasePolicy
 
getTypes() - Method in interface ome.security.policy.Policy
Each Policy should tell the PolicyService which types of IObject instances it cares about.
getTypes(ExtendedMetadata) - Method in class ome.services.graphs.AbstractHierarchyGraphSpec
Deprecated.
Returns all the types that are known for this hierarchy.
getTypes(ExtendedMetadata) - Method in class ome.services.graphs.AnnotationGraphSpec
Deprecated.
 
getTypes(ExtendedMetadata) - Method in class ome.services.graphs.LightSourceGraphSpec
Deprecated.
 
getTypesService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
getTypesService() - Method in class ome.system.ServiceFactory
 
getUIBounds() - Method in class ome.formats.importer.ImportConfig
 
getUIBounds() - Method in class ome.formats.importer.util.IniFileLoader
 
getUndeletedFiles() - Method in class ome.services.delete.Deletion
Deprecated.
 
getUndeletedFiles() - Method in class ome.services.delete.files.AbstractFileDeletions
 
getUndeletedFiles() - Method in class ome.services.delete.files.FileDeleter
 
getUnique() - Method in class omero.sys.ParametersI
 
getUnit() - Method in class ome.model.units.ElectricPotential
Many-to-one field ome.model.units.ElectricPotential.unit (ome.model.enums.UnitsElectricPotential).
getUnit() - Method in class ome.model.units.Frequency
Many-to-one field ome.model.units.Frequency.unit (ome.model.enums.UnitsFrequency).
getUnit() - Method in class ome.model.units.Length
Many-to-one field ome.model.units.Length.unit (ome.model.enums.UnitsLength).
getUnit() - Method in class ome.model.units.Power
Many-to-one field ome.model.units.Power.unit (ome.model.enums.UnitsPower).
getUnit() - Method in class ome.model.units.Pressure
Many-to-one field ome.model.units.Pressure.unit (ome.model.enums.UnitsPressure).
getUnit() - Method in class ome.model.units.Temperature
Many-to-one field ome.model.units.Temperature.unit (ome.model.enums.UnitsTemperature).
getUnit() - Method in class ome.model.units.Time
Many-to-one field ome.model.units.Time.unit (ome.model.enums.UnitsTime).
getUnit() - Method in interface ome.model.units.Unit
 
getUnit(Current) - Method in class omero.model.ElectricPotentialI
 
getUnit(Current) - Method in class omero.model.FrequencyI
 
getUnit(Current) - Method in class omero.model.LengthI
 
getUnit(Current) - Method in class omero.model.PowerI
 
getUnit(Current) - Method in class omero.model.PressureI
 
getUnit(Current) - Method in class omero.model.TemperatureI
 
getUnit(Current) - Method in class omero.model.TimeI
 
getUntied(Identity) - Method in class omero.util.ServantHolder
 
getUp() - Method in class ome.model.meta.Node
Simple field ome.model.meta.Node.up (java.sql.Timestamp)
getUpdated() - Method in class pojos.DataObject
Returns the updated time of the object.
getUpdateEvent() - Method in class ome.model.acquisition.Detector.Details
 
getUpdateEvent() - Method in class ome.model.acquisition.DetectorSettings.Details
 
getUpdateEvent() - Method in class ome.model.acquisition.Dichroic.Details
 
getUpdateEvent() - Method in class ome.model.acquisition.Filter.Details
 
getUpdateEvent() - Method in class ome.model.acquisition.FilterSet.Details
 
getUpdateEvent() - Method in class ome.model.acquisition.FilterSetEmissionFilterLink.Details
 
getUpdateEvent() - Method in class ome.model.acquisition.FilterSetExcitationFilterLink.Details
 
getUpdateEvent() - Method in class ome.model.acquisition.ImagingEnvironment.Details
 
getUpdateEvent() - Method in class ome.model.acquisition.Instrument.Details
 
getUpdateEvent() - Method in class ome.model.acquisition.LightPath.Details
 
getUpdateEvent() - Method in class ome.model.acquisition.LightPathEmissionFilterLink.Details
 
getUpdateEvent() - Method in class ome.model.acquisition.LightPathExcitationFilterLink.Details
 
getUpdateEvent() - Method in class ome.model.acquisition.LightSettings.Details
 
getUpdateEvent() - Method in class ome.model.acquisition.LightSource.Details
 
getUpdateEvent() - Method in class ome.model.acquisition.Microscope.Details
 
getUpdateEvent() - Method in class ome.model.acquisition.Objective.Details
 
getUpdateEvent() - Method in class ome.model.acquisition.ObjectiveSettings.Details
 
getUpdateEvent() - Method in class ome.model.acquisition.OTF.Details
 
getUpdateEvent() - Method in class ome.model.acquisition.StageLabel.Details
 
getUpdateEvent() - Method in class ome.model.acquisition.TransmittanceRange.Details
 
getUpdateEvent() - Method in class ome.model.annotations.Annotation.Details
 
getUpdateEvent() - Method in class ome.model.annotations.AnnotationAnnotationLink.Details
 
getUpdateEvent() - Method in class ome.model.annotations.ChannelAnnotationLink.Details
 
getUpdateEvent() - Method in class ome.model.annotations.DatasetAnnotationLink.Details
 
getUpdateEvent() - Method in class ome.model.annotations.DetectorAnnotationLink.Details
 
getUpdateEvent() - Method in class ome.model.annotations.DichroicAnnotationLink.Details
 
getUpdateEvent() - Method in class ome.model.annotations.ExperimenterAnnotationLink.Details
 
getUpdateEvent() - Method in class ome.model.annotations.ExperimenterGroupAnnotationLink.Details
 
getUpdateEvent() - Method in class ome.model.annotations.FilesetAnnotationLink.Details
 
getUpdateEvent() - Method in class ome.model.annotations.FilterAnnotationLink.Details
 
getUpdateEvent() - Method in class ome.model.annotations.ImageAnnotationLink.Details
 
getUpdateEvent() - Method in class ome.model.annotations.InstrumentAnnotationLink.Details
 
getUpdateEvent() - Method in class ome.model.annotations.LightPathAnnotationLink.Details
 
getUpdateEvent() - Method in class ome.model.annotations.LightSourceAnnotationLink.Details
 
getUpdateEvent() - Method in class ome.model.annotations.NamespaceAnnotationLink.Details
 
getUpdateEvent() - Method in class ome.model.annotations.NodeAnnotationLink.Details
 
getUpdateEvent() - Method in class ome.model.annotations.ObjectiveAnnotationLink.Details
 
getUpdateEvent() - Method in class ome.model.annotations.OriginalFileAnnotationLink.Details
 
getUpdateEvent() - Method in class ome.model.annotations.PlaneInfoAnnotationLink.Details
 
getUpdateEvent() - Method in class ome.model.annotations.PlateAcquisitionAnnotationLink.Details
 
getUpdateEvent() - Method in class ome.model.annotations.PlateAnnotationLink.Details
 
getUpdateEvent() - Method in class ome.model.annotations.ProjectAnnotationLink.Details
 
getUpdateEvent() - Method in class ome.model.annotations.ReagentAnnotationLink.Details
 
getUpdateEvent() - Method in class ome.model.annotations.RoiAnnotationLink.Details
 
getUpdateEvent() - Method in class ome.model.annotations.ScreenAnnotationLink.Details
 
getUpdateEvent() - Method in class ome.model.annotations.SessionAnnotationLink.Details
 
getUpdateEvent() - Method in class ome.model.annotations.ShapeAnnotationLink.Details
 
getUpdateEvent() - Method in class ome.model.annotations.WellAnnotationLink.Details
 
getUpdateEvent() - Method in class ome.model.containers.Dataset.Details
 
getUpdateEvent() - Method in class ome.model.containers.DatasetImageLink.Details
 
getUpdateEvent() - Method in class ome.model.containers.Project.Details
 
getUpdateEvent() - Method in class ome.model.containers.ProjectDatasetLink.Details
 
getUpdateEvent() - Method in class ome.model.core.Channel.Details
 
getUpdateEvent() - Method in class ome.model.core.Image.Details
 
getUpdateEvent() - Method in class ome.model.core.LogicalChannel.Details
 
getUpdateEvent() - Method in class ome.model.core.OriginalFile.Details
 
getUpdateEvent() - Method in class ome.model.core.Pixels.Details
 
getUpdateEvent() - Method in class ome.model.core.PixelsOriginalFileMap.Details
 
getUpdateEvent() - Method in class ome.model.core.PlaneInfo.Details
 
getUpdateEvent() - Method in class ome.model.display.ChannelBinding.Details
 
getUpdateEvent() - Method in class ome.model.display.CodomainMapContext.Details
 
getUpdateEvent() - Method in class ome.model.display.QuantumDef.Details
 
getUpdateEvent() - Method in class ome.model.display.RenderingDef.Details
 
getUpdateEvent() - Method in class ome.model.display.Thumbnail.Details
 
getUpdateEvent() - Method in class ome.model.experiment.Experiment.Details
 
getUpdateEvent() - Method in class ome.model.experiment.MicrobeamManipulation.Details
 
getUpdateEvent() - Method in class ome.model.fs.Fileset.Details
 
getUpdateEvent() - Method in class ome.model.fs.FilesetEntry.Details
 
getUpdateEvent() - Method in class ome.model.fs.FilesetJobLink.Details
 
getUpdateEvent() - Method in class ome.model.internal.Details
 
getUpdateEvent() - Method in class ome.model.internal.Link.Details
 
getUpdateEvent() - Method in class ome.model.jobs.Job.Details
 
getUpdateEvent() - Method in class ome.model.jobs.JobOriginalFileLink.Details
 
getUpdateEvent() - Method in class ome.model.meta.ExternalInfo.Details
Overrides Details.getUpdateEvent() to always return null.
getUpdateEvent() - Method in class ome.model.roi.Roi.Details
 
getUpdateEvent() - Method in class ome.model.roi.Shape.Details
 
getUpdateEvent() - Method in class ome.model.screen.Plate.Details
 
getUpdateEvent() - Method in class ome.model.screen.PlateAcquisition.Details
 
getUpdateEvent() - Method in class ome.model.screen.Reagent.Details
 
getUpdateEvent() - Method in class ome.model.screen.Screen.Details
 
getUpdateEvent() - Method in class ome.model.screen.ScreenPlateLink.Details
 
getUpdateEvent() - Method in class ome.model.screen.Well.Details
 
getUpdateEvent() - Method in class ome.model.screen.WellReagentLink.Details
 
getUpdateEvent() - Method in class ome.model.screen.WellSample.Details
 
getUpdateEvent() - Method in class ome.model.stats.StatsInfo.Details
 
getUpdateEvent(Current) - Method in class omero.model.DetailsI
 
getUpdateService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
getUpdateService() - Method in class ome.system.ServiceFactory
 
getUpgradeUrl() - Method in class ome.system.UpgradeCheck
 
getUploader() - Method in class ome.formats.importer.transfers.TransferState
Return the RawFileStorePrx instance for this index.
getUploader(String) - Method in class ome.formats.importer.transfers.TransferState
Return the RawFileStorePrx instance for this index setting the mode if not null.
getUploader(int, Current) - Method in class ome.services.blitz.repo.ManagedImportProcessI
 
getUploaderUrl() - Method in class ome.formats.importer.ImportConfig
 
getUploadOffset(int, Current) - Method in class ome.services.blitz.repo.ManagedImportProcessI
 
getUploadTimeLeft() - Method in class ome.formats.importer.transfers.TransferState
 
getUploadTimeLeft() - Method in class ome.formats.importer.util.ProportionalTimeEstimatorImpl
 
getUploadTimeLeft() - Method in interface ome.formats.importer.util.TimeEstimator
Return the estimated time left in milliseconds based on the calls to start and stop methods.
getUploadUrl() - Method in class ome.formats.importer.util.ErrorContainer
 
getUpperLimit() - Method in class ome.model.display.PlaneSlicingContext
Simple field ome.model.display.PlaneSlicingContext.upperLimit (java.lang.Integer)
getUpperLimit() - Method in class omeis.providers.re.codomain.PlaneSlicingContext
Returns the constant level for bit-planes > planeSelected w.r.t the higher-order bits.
getUsageFraction() - Method in interface ome.api.IRepositoryInfo
This method returns a double of the used space divided by the free space.
getUsageFraction() - Method in class ome.logic.RepositoryInfoImpl
Deprecated.
getUsageFraction_async(AMD_IRepositoryInfo_getUsageFraction, Current) - Method in class ome.services.blitz.impl.RepositoryInfoI
 
getUsedFilePaths() - Method in class pojos.FilesetData
Returns the collection of file paths used for importing the files (in case of in-place imports these are the targets of the (sym)links)
getUsedFiles(String) - Method in class ome.formats.importer.ImportCandidates
Return string of files used by container item at path
getUsedFiles() - Method in class ome.formats.importer.ImportContainer
Return a list of file names that belong to this import container.
getUsedFiles() - Method in class ome.model.fs.Fileset
returns usedFiles .
getUsedFilesTotalSize() - Method in class ome.formats.importer.ImportContainer
Returns the total size in bytes (based on File.length()) of all files in this import container.
getUsedSpaceInKilobytes() - Method in interface ome.api.IRepositoryInfo
This method returns the total space in bytes for this file system including nested subdirectories.
getUsedSpaceInKilobytes() - Method in class ome.logic.RepositoryInfoImpl
Deprecated.
getUsedSpaceInKilobytes_async(AMD_IRepositoryInfo_getUsedSpaceInKilobytes, Current) - Method in class ome.services.blitz.impl.RepositoryInfoI
 
getUseQuaqua() - Method in class ome.formats.importer.ImportConfig
 
getUseQuaqua() - Method in class ome.formats.importer.util.IniFileLoader
 
getUserAgent() - Method in class ome.model.meta.Session
Simple field ome.model.meta.Session.userAgent (java.lang.String)
getUserAttribute(String) - Method in class ome.security.auth.LdapConfig
 
getUserDisableHistory() - Method in class ome.formats.importer.ImportConfig
 
getUserDisableHistory() - Method in class ome.formats.importer.util.IniFileLoader
 
getUserEmail(String) - Method in class ome.services.mail.MailSender
 
getUserEmailsByGroup(long) - Method in interface ome.util.SqlAction
Load all the non-empty email addresses for users in a given group.
getUserEmailsByGroup(long) - Method in class ome.util.SqlAction.Impl
 
getUserFilter() - Method in class ome.security.auth.LdapConfig
 
getUserFullPath() - Method in class ome.formats.importer.ImportConfig
 
getUserFullPath() - Method in class ome.formats.importer.util.IniFileLoader
 
getUserGroupId() - Method in class ome.system.Roles
 
getUserGroupName() - Method in class ome.system.Roles
 
getUserGroups(String) - Method in interface ome.util.SqlAction
 
getUserGroups(String) - Method in class ome.util.SqlAction.Impl
 
getUserId() - Method in class ome.services.ThumbnailCtx
Retrieves the current user ID to use for queries.
getUserId(String) - Method in interface ome.util.SqlAction
Get the user's ID
getUserId(String) - Method in class ome.util.SqlAction.Impl
 
getUserImages(Parameters) - Method in interface ome.api.IContainer
Retrieve a user's images.
getUserImages(Parameters) - Method in class ome.logic.PojosImpl
Implemented as specified by the IContainer I/F
getUserImages_async(AMD_IContainer_getUserImages, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI
 
getUserInstitution(long, Current) - Method in interface ome.services.blitz.repo.RepositoryDao
Get the current user's institution.
getUserInstitution(long, ServiceFactory) - Method in interface ome.services.blitz.repo.RepositoryDao
Get the current user's institution.
getUserInstitution(long, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
 
getUserInstitution(long, ServiceFactory) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
 
getUserIP() - Method in class ome.model.meta.Session
Simple field ome.model.meta.Session.userIP (java.lang.String)
getUsername() - Method in class ome.model.jobs.Job
Simple field ome.model.jobs.Job.username (java.lang.String)
getUsername(long) - Method in interface ome.util.SqlAction
Get the user's name
getUsername(long) - Method in class ome.util.SqlAction.Impl
 
getUserName() - Method in class pojos.ExperimenterData
Returns the last name of the experimenter.
getUserPasswordHash(Long) - Method in class ome.security.auth.PasswordUtil
 
getUserPixels() - Method in class ome.formats.importer.ImportContainer
 
getUserRoles(Experimenter) - Method in interface ome.api.local.LocalAdmin
Finds the group names for all groups for which the given Experimenter is a member.
getUserRoles(Experimenter) - Method in class ome.logic.AdminImpl
 
getUserRoles() - Method in interface ome.services.sessions.SessionContext
 
getUserRoles() - Method in class ome.services.sessions.SessionContextImpl
 
getUserRoles(String) - Method in interface ome.services.sessions.SessionManager
 
getUserRoles(String) - Method in class ome.services.sessions.SessionManagerImpl
 
getUserScripts_async(AMD_IScript_getUserScripts, List<IObject>, Current) - Method in class ome.services.blitz.impl.ScriptI
 
getUserSettingsDirectory() - Method in class ome.formats.importer.ImportConfig
 
getUserSettingsDirectory() - Method in class ome.formats.importer.util.IniFileLoader
 
getUserSpecifiedAnnotations() - Method in interface ome.formats.model.IObjectContainerStore
Returns the user specified annotations.
getUserSpecifiedAnnotations() - Method in class ome.formats.OMEROMetadataStoreClient
 
getUserSpecifiedDescription() - Method in class ome.formats.importer.ImportContainer
Retrieves the current custom image/plate description string.
getUserSpecifiedDescription() - Method in interface ome.formats.model.IObjectContainerStore
Returns the user specified image/plate description.
getUserSpecifiedDescription() - Method in class ome.formats.OMEROMetadataStoreClient
 
getUserSpecifiedImageName() - Method in class ome.formats.OMEROMetadataStoreClient
 
getUserSpecifiedName() - Method in class ome.formats.importer.ImportContainer
Retrieves the current custom image/plate name string.
getUserSpecifiedName() - Method in interface ome.formats.model.IObjectContainerStore
Returns the user specified image/plate name.
getUserSpecifiedName() - Method in class ome.formats.OMEROMetadataStoreClient
 
getUserSpecifiedPhysicalPixelSizes() - Method in interface ome.formats.model.IObjectContainerStore
Returns the user specified physical pixel sizes.
getUserSpecifiedPhysicalPixelSizes() - Method in class ome.formats.OMEROMetadataStoreClient
 
getUserSpecifiedTarget() - Method in interface ome.formats.model.IObjectContainerStore
Returns the user specified linkage target (usually a Dataset for Images and a Screen for Plates).
getUserSpecifiedTarget() - Method in class ome.formats.OMEROMetadataStoreClient
 
getUuid() - Method in class ome.model.meta.ExternalInfo
Simple field ome.model.meta.ExternalInfo.uuid (java.lang.String)
getUuid() - Method in class ome.model.meta.Node
Simple field ome.model.meta.Node.uuid (java.lang.String)
getUuid() - Method in class ome.model.meta.Session
Simple field ome.model.meta.Session.uuid (java.lang.String)
getUuid() - Method in class ome.services.db.DatabaseIdentity
 
getUuid() - Method in class ome.services.scripts.ScriptRepoHelper
Uuid of this repository.
getUuid() - Method in class ome.services.sessions.events.ChangeSecurityContextEvent
 
getValue() - Method in exception ome.formats.enums.EnumerationException
 
getValue() - Method in enum ome.formats.Index
 
getValue(Class<? extends IObject>, int) - Method in class ome.formats.OMEXMLModelComparator
Assigns a value to a particular class based on its location in the OME-XML hierarchy.
getValue() - Method in class ome.model.enums.AcquisitionMode
Simple field ome.model.enums.AcquisitionMode.value (java.lang.String)
getValue() - Method in class ome.model.enums.ArcType
Simple field ome.model.enums.ArcType.value (java.lang.String)
getValue() - Method in class ome.model.enums.Binning
Simple field ome.model.enums.Binning.value (java.lang.String)
getValue() - Method in class ome.model.enums.ChecksumAlgorithm
Simple field ome.model.enums.ChecksumAlgorithm.value (java.lang.String)
getValue() - Method in class ome.model.enums.ContrastMethod
Simple field ome.model.enums.ContrastMethod.value (java.lang.String)
getValue() - Method in class ome.model.enums.Correction
Simple field ome.model.enums.Correction.value (java.lang.String)
getValue() - Method in class ome.model.enums.DetectorType
Simple field ome.model.enums.DetectorType.value (java.lang.String)
getValue() - Method in class ome.model.enums.DimensionOrder
Simple field ome.model.enums.DimensionOrder.value (java.lang.String)
getValue() - Method in class ome.model.enums.EventType
Simple field ome.model.enums.EventType.value (java.lang.String)
getValue() - Method in class ome.model.enums.ExperimentType
Simple field ome.model.enums.ExperimentType.value (java.lang.String)
getValue() - Method in class ome.model.enums.Family
Simple field ome.model.enums.Family.value (java.lang.String)
getValue() - Method in class ome.model.enums.FilamentType
Simple field ome.model.enums.FilamentType.value (java.lang.String)
getValue() - Method in class ome.model.enums.FilterType
Simple field ome.model.enums.FilterType.value (java.lang.String)
getValue() - Method in class ome.model.enums.Format
Simple field ome.model.enums.Format.value (java.lang.String)
getValue() - Method in class ome.model.enums.Illumination
Simple field ome.model.enums.Illumination.value (java.lang.String)
getValue() - Method in class ome.model.enums.Immersion
Simple field ome.model.enums.Immersion.value (java.lang.String)
getValue() - Method in class ome.model.enums.LaserMedium
Simple field ome.model.enums.LaserMedium.value (java.lang.String)
getValue() - Method in class ome.model.enums.LaserType
Simple field ome.model.enums.LaserType.value (java.lang.String)
getValue() - Method in class ome.model.enums.Medium
Simple field ome.model.enums.Medium.value (java.lang.String)
getValue() - Method in class ome.model.enums.MicrobeamManipulationType
Simple field ome.model.enums.MicrobeamManipulationType.value (java.lang.String)
getValue() - Method in class ome.model.enums.MicroscopeType
Simple field ome.model.enums.MicroscopeType.value (java.lang.String)
getValue() - Method in class ome.model.enums.PhotometricInterpretation
Simple field ome.model.enums.PhotometricInterpretation.value (java.lang.String)
getValue() - Method in class ome.model.enums.PixelsType
Simple field ome.model.enums.PixelsType.value (java.lang.String)
getValue() - Method in class ome.model.enums.Pulse
Simple field ome.model.enums.Pulse.value (java.lang.String)
getValue() - Method in class ome.model.enums.RenderingModel
Simple field ome.model.enums.RenderingModel.value (java.lang.String)
getValue() - Method in interface ome.model.IEnum
the single String value associated with this instance.
getValue() - Method in class ome.model.internal.NamedValue
 
getValue() - Method in class ome.model.jobs.JobStatus
Simple field ome.model.jobs.JobStatus.value (java.lang.String)
getValue() - Method in class ome.model.units.ElectricPotential
value of this unit-field.
getValue() - Method in class ome.model.units.Frequency
value of this unit-field.
getValue() - Method in class ome.model.units.Length
value of this unit-field.
getValue() - Method in class ome.model.units.Power
value of this unit-field.
getValue() - Method in class ome.model.units.Pressure
value of this unit-field.
getValue() - Method in class ome.model.units.Temperature
value of this unit-field.
getValue() - Method in class ome.model.units.Time
value of this unit-field.
getValue() - Method in interface ome.model.units.Unit
 
getValue(double) - Method in class ome.system.metrics.DefaultSnapshot
 
getValue(double) - Method in interface ome.system.metrics.Snapshot
 
getValue(Current) - Method in class omero.model.ElectricPotentialI
 
getValue(Current) - Method in class omero.model.FrequencyI
 
getValue(Current) - Method in class omero.model.LengthI
 
getValue(Current) - Method in class omero.model.PowerI
 
getValue(Current) - Method in class omero.model.PressureI
 
getValue(Current) - Method in class omero.model.TemperatureI
 
getValue(Current) - Method in class omero.model.TimeI
 
getValue() - Method in class pojos.BooleanAnnotationData
Returns the text of this annotation.
getValues() - Method in class ome.system.metrics.DefaultSnapshot
 
getValues() - Method in interface ome.system.metrics.Snapshot
 
getVectorEffect() - Method in class ome.model.roi.Shape
Simple field ome.model.roi.Shape.vectorEffect (java.lang.String)
getVersion() - Method in interface ome.api.IConfig
Provides the release version.
getVersion() - Method in class ome.logic.ConfigImpl
getVersion() - Method in class ome.model.acquisition.Detector
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.acquisition.DetectorSettings
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.acquisition.Dichroic
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.acquisition.Filter
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.acquisition.FilterSet
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.acquisition.FilterSetEmissionFilterLink
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.acquisition.FilterSetExcitationFilterLink
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.acquisition.ImagingEnvironment
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.acquisition.Instrument
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.acquisition.LightPath
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.acquisition.LightPathEmissionFilterLink
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.acquisition.LightPathExcitationFilterLink
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.acquisition.LightSettings
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.acquisition.LightSource
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.acquisition.Microscope
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.acquisition.Objective
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.acquisition.ObjectiveSettings
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.acquisition.OTF
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.acquisition.StageLabel
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.acquisition.TransmittanceRange
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.annotations.Annotation
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.annotations.AnnotationAnnotationLink
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.annotations.ChannelAnnotationLink
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.annotations.DatasetAnnotationLink
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.annotations.DetectorAnnotationLink
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.annotations.DichroicAnnotationLink
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.annotations.ExperimenterAnnotationLink
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.annotations.ExperimenterGroupAnnotationLink
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.annotations.FilesetAnnotationLink
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.annotations.FilterAnnotationLink
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.annotations.ImageAnnotationLink
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.annotations.InstrumentAnnotationLink
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.annotations.LightPathAnnotationLink
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.annotations.LightSourceAnnotationLink
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.annotations.NamespaceAnnotationLink
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.annotations.NodeAnnotationLink
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.annotations.ObjectiveAnnotationLink
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.annotations.OriginalFileAnnotationLink
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.annotations.PlaneInfoAnnotationLink
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.annotations.PlateAcquisitionAnnotationLink
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.annotations.PlateAnnotationLink
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.annotations.ProjectAnnotationLink
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.annotations.ReagentAnnotationLink
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.annotations.RoiAnnotationLink
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.annotations.ScreenAnnotationLink
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.annotations.SessionAnnotationLink
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.annotations.ShapeAnnotationLink
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.annotations.WellAnnotationLink
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.containers.Dataset
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.containers.DatasetImageLink
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.containers.Project
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.containers.ProjectDatasetLink
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.core.Channel
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.core.Image
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.core.LogicalChannel
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.core.OriginalFile
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.core.Pixels
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.core.PixelsOriginalFileMap
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.core.PlaneInfo
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.display.ChannelBinding
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.display.CodomainMapContext
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.display.QuantumDef
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.display.RenderingDef
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.display.Thumbnail
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.experiment.Experiment
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.experiment.MicrobeamManipulation
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.fs.Fileset
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.fs.FilesetEntry
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.fs.FilesetJobLink
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in interface ome.model.IMutable
optimistic-lock version.
getVersion() - Method in class ome.model.internal.Link
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.jobs.Job
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.jobs.JobOriginalFileLink
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.meta.Experimenter
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.meta.ExperimenterGroup
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.meta.GroupExperimenterMap
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.meta.Namespace
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.meta.Node
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.meta.Session
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.meta.ShareMember
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.roi.Roi
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.roi.Shape
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.screen.Plate
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.screen.PlateAcquisition
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.screen.Reagent
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.screen.Screen
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.screen.ScreenPlateLink
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.screen.Well
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.screen.WellReagentLink
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.screen.WellSample
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class ome.model.stats.StatsInfo
This version number is controlled by the database for optimisitic locking.
getVersion() - Method in class pojos.DataObject
Returns the version of the object if the object is immutable, false otherwise.
getVersion_async(AMD_IConfig_getVersion, Current) - Method in class ome.services.blitz.impl.ConfigI
 
getVersionInfo() - Method in class ome.model.jobs.MetadataImportJob
 
getVersionInfo() - Method in class ome.model.jobs.UploadJob
 
getVersionNote() - Method in class ome.formats.importer.util.IniFileLoader
 
getVersionNumber() - Method in class ome.formats.importer.ImportConfig
 
getVersionNumber() - Method in class ome.formats.importer.util.IniFileLoader
 
getVisibility() - Method in class ome.model.roi.Shape
Simple field ome.model.roi.Shape.visibility (java.lang.Boolean)
getVisibility() - Method in class ome.system.Preference
 
getVoltage() - Method in class ome.model.acquisition.Detector
Enum-mapped unit-based field ome.model.acquisition.Detector.voltage (ome.model.units.ElectricPotential)
getVoltage() - Method in class ome.model.acquisition.DetectorSettings
Enum-mapped unit-based field ome.model.acquisition.DetectorSettings.voltage (ome.model.units.ElectricPotential)
getVoltage(UnitsElectricPotential) - Method in class pojos.DetectorData
Returns the voltage of the detector.
getVoltage() - Method in class pojos.DetectorData
getWarmUpFactor() - Method in class ome.io.nio.SimpleBackOff
 
getWarning() - Method in class ome.services.delete.Deletion
Deprecated.
 
getWarning() - Method in class ome.services.delete.files.FileDeleter
 
getWaveIncrement() - Method in class ome.model.core.Pixels
Simple field ome.model.core.Pixels.waveIncrement (java.lang.Integer)
getWavelength() - Method in class ome.model.acquisition.Laser
Enum-mapped unit-based field ome.model.acquisition.Laser.wavelength (ome.model.units.Length)
getWavelength() - Method in class ome.model.acquisition.LightSettings
Enum-mapped unit-based field ome.model.acquisition.LightSettings.wavelength (ome.model.units.Length)
getWavelength() - Method in exception omeis.providers.re.quantum.QuantizationException
Returns the index of the wavelength that couldn't be rendered.
getWaveRendering() - Method in class ome.model.display.RenderingDef
returns waveRendering .
getWaveStart() - Method in class ome.model.core.Pixels
Simple field ome.model.core.Pixels.waveStart (java.lang.Integer)
getWell() - Method in class ome.model.screen.WellSample
Many-to-one field ome.model.screen.WellSample.well (ome.model.screen.Well)
getWellLinks() - Method in class ome.model.screen.Reagent
returns wellLinks .
getWellLinksCountPerOwner() - Method in class ome.model.screen.Reagent
If fetched, returns the count(*) of ome.model.screen.WellReagentLink that a user has.
getWellOriginX() - Method in class ome.model.screen.Plate
Enum-mapped unit-based field ome.model.screen.Plate.wellOriginX (ome.model.units.Length)
getWellOriginX(UnitsLength) - Method in class pojos.PlateData
Returns the x-coordinate in 2D-space of the well.
getWellOriginX() - Method in class pojos.PlateData
Deprecated.
getWellOriginY() - Method in class ome.model.screen.Plate
Enum-mapped unit-based field ome.model.screen.Plate.wellOriginY (ome.model.units.Length)
getWellOriginY(UnitsLength) - Method in class pojos.PlateData
Returns the y-coordinate in 2D-space of the well.
getWellOriginY() - Method in class pojos.PlateData
Deprecated.
getWells() - Method in class ome.model.screen.Plate
returns wells .
getWellSample() - Method in class ome.model.screen.PlateAcquisition
returns wellSample .
getWellSample(int) - Method in class ome.model.screen.Well
Gets the ome.model.screen.WellSample at the given index.
getWellSamples() - Method in class ome.model.core.Image
returns wellSamples .
getWellSamples() - Method in class ome.model.screen.Well
returns wellSamples .
getWellSamples() - Method in class pojos.WellData
Returns the well samples linked to the well.
getWellType() - Method in class pojos.WellData
Returns a human readable identifier for the screening status e.g. empty, positive control, etc.
getWidth() - Method in class ome.model.roi.Mask
Simple field ome.model.roi.Mask.width (java.lang.Double)
getWidth() - Method in class ome.model.roi.Rect
Simple field ome.model.roi.Rect.width (java.lang.Double)
getWidth() - Method in class omeis.providers.re.data.RegionDef
Returns the width of the region.
getWidth() - Method in class pojos.MaskData
Returns the width of the mask.
getWidth() - Method in class pojos.RectangleData
Returns the width untransformed rectangle.
getWindowEnd() - Method in class omeis.providers.re.quantum.QuantumStrategy
Returns the upper bound of the input interval.
getWindowStart() - Method in class omeis.providers.re.quantum.QuantumStrategy
Returns the lower bound of the input interval.
getWorkingDistance() - Method in class ome.model.acquisition.Objective
Enum-mapped unit-based field ome.model.acquisition.Objective.workingDistance (ome.model.units.Length)
getWorkingDistance(UnitsLength) - Method in class pojos.ObjectiveData
Returns the working distance.
getWorkingDistance() - Method in class pojos.ObjectiveData
getWritingMode() - Method in class ome.model.roi.Label
Simple field ome.model.roi.Label.writingMode (java.lang.String)
getX() - Method in class ome.model.roi.Label
Simple field ome.model.roi.Label.x (java.lang.Double)
getX() - Method in class ome.model.roi.Mask
Simple field ome.model.roi.Mask.x (java.lang.Double)
getX() - Method in class ome.model.roi.Rect
Simple field ome.model.roi.Rect.x (java.lang.Double)
getX() - Method in class omeis.providers.re.data.PlaneDef
Returns the index of the plane in the set identified by this object.
getX() - Method in class omeis.providers.re.data.RegionDef
Returns the x-coordinate of the top-left corner.
getX() - Method in class pojos.EllipseData
Returns the x-coordinate of the center of the ellipse.
getX() - Method in class pojos.MaskData
Returns the x-coordinate of the top-left corner of the mask.
getX() - Method in class pojos.PointData
Returns the x-coordinate of the shape.
getX() - Method in class pojos.RectangleData
Returns the x-coordinate of the top-left corner of an untransformed rectangle.
getX() - Method in class pojos.TextData
Returns the x-coordinate text field.
getX1() - Method in class ome.model.roi.Line
Simple field ome.model.roi.Line.x1 (java.lang.Double)
getX1() - Method in class pojos.LineData
Returns the x-coordinate of the starting point of an untransformed line.
getX2() - Method in class ome.model.roi.Line
Simple field ome.model.roi.Line.x2 (java.lang.Double)
getX2() - Method in class pojos.LineData
Returns the x-coordinate of the end point of an untransformed line.
getXend() - Method in class ome.model.display.ContrastStretchingContext
Simple field ome.model.display.ContrastStretchingContext.xend (java.lang.Integer)
getXEnd() - Method in class omeis.providers.re.codomain.ContrastStretchingContext
Returns the x-coordinate of the pEnd point.
getXMLAnnotationCount() - Method in class ome.services.blitz.impl.OmeroMetadata
 
getXMLAnnotationDescription(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getXMLAnnotationID(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getXMLAnnotationNamespace(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getXMLAnnotationValue(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getXstart() - Method in class ome.model.display.ContrastStretchingContext
Simple field ome.model.display.ContrastStretchingContext.xstart (java.lang.Integer)
getXStart() - Method in class omeis.providers.re.codomain.ContrastStretchingContext
Returns the x-coordinate of the pStart point.
getY() - Method in class ome.model.roi.Label
Simple field ome.model.roi.Label.y (java.lang.Double)
getY() - Method in class ome.model.roi.Mask
Simple field ome.model.roi.Mask.y (java.lang.Double)
getY() - Method in class ome.model.roi.Rect
Simple field ome.model.roi.Rect.y (java.lang.Double)
getY() - Method in class omeis.providers.re.data.PlaneDef
Returns the index of the plane in the set identified by this object.
getY() - Method in class omeis.providers.re.data.RegionDef
Returns the y-coordinate of the top-left corner.
getY() - Method in class pojos.EllipseData
Returns the y-coordinate of the center of the ellipse.
getY() - Method in class pojos.MaskData
Returns the y-coordinate of the top-left corner of the mask.
getY() - Method in class pojos.PointData
Returns the y coordinate of the shape.
getY() - Method in class pojos.RectangleData
Returns the y-coordinate of the top-left corner of an untransformed rectangle.
getY() - Method in class pojos.TextData
Returns the y-coordinate text field.
getY1() - Method in class ome.model.roi.Line
Simple field ome.model.roi.Line.y1 (java.lang.Double)
getY1() - Method in class pojos.LineData
Returns the y-coordinate of the starting point of an untransformed line.
getY2() - Method in class ome.model.roi.Line
Simple field ome.model.roi.Line.y2 (java.lang.Double)
getY2() - Method in class pojos.LineData
Returns the y-coordinate of the end point of an untransformed line.
getYend() - Method in class ome.model.display.ContrastStretchingContext
Simple field ome.model.display.ContrastStretchingContext.yend (java.lang.Integer)
getYEnd() - Method in class omeis.providers.re.codomain.ContrastStretchingContext
Returns the y-coordinate of the pEnd point.
getYstart() - Method in class ome.model.display.ContrastStretchingContext
Simple field ome.model.display.ContrastStretchingContext.ystart (java.lang.Integer)
getYStart() - Method in class omeis.providers.re.codomain.ContrastStretchingContext
Returns the y-coordinate of the pStart point.
getZ() - Method in class omeis.providers.re.data.PlaneDef
Returns the index of the plane in the set identified by this object.
getZ() - Method in class pojos.ShapeData
Returns the z-section.
getZoom() - Method in class ome.model.acquisition.Detector
Simple field ome.model.acquisition.Detector.zoom (java.lang.Double)
getZoom() - Method in class ome.model.acquisition.DetectorSettings
Simple field ome.model.acquisition.DetectorSettings.zoom (java.lang.Double)
getZoom() - Method in class pojos.DetectorData
Returns the offset of the detector.
getZSection() - Method in class pojos.ROICoordinate
Returns the z-section.
globalMax - Variable in class ome.model.stats.StatsInfo
 
GLOBALMAX - Static variable in class ome.model.stats.StatsInfo
 
globalMin - Variable in class ome.model.stats.StatsInfo
 
GLOBALMIN - Static variable in class ome.model.stats.StatsInfo
 
GlobalMulticaster - Class in ome.services.messages
Global ApplicationEventMulticaster which can be used to integrate parent and child OmeroContext instances.
GlobalMulticaster() - Constructor for class ome.services.messages.GlobalMulticaster
Keeps track of which instance this is.
glyphOrientationVertical - Variable in class ome.model.roi.Label
 
GLYPHORIENTATIONVERTICAL - Static variable in class ome.model.roi.Label
 
grant(Permissions.Role, Permissions.Right...) - Method in class ome.model.internal.Permissions
turns on the rights for the given role.
grantAll(Permissions) - Method in class ome.model.internal.Permissions
takes a permissions instance and ORs it with the current instance.
granted(int, int) - Method in class omero.model.PermissionsI
 
GraphConstraintException - Exception in ome.services.graphs
Deprecated.
will be removed in OMERO 5.2, so use the new graphs implementation
GraphConstraintException(String, HashMultimap<String, Long>) - Constructor for exception ome.services.graphs.GraphConstraintException
Deprecated.
 
GraphEntry - Class in ome.services.graphs
Deprecated.
will be removed in OMERO 5.2, so use the new graphs implementation
GraphEntry(GraphSpec, String) - Constructor for class ome.services.graphs.GraphEntry
Deprecated.
 
GraphEntry(GraphSpec, String, GraphEntry) - Constructor for class ome.services.graphs.GraphEntry
Deprecated.
 
GraphException - Exception in ome.services.graphs
Exception which will be thrown by activities within GraphSpec implementations.
GraphException(String) - Constructor for exception ome.services.graphs.GraphException
 
graphException(GraphException, long, long) - Method in class omero.cmd.Helper
Deprecated.
GraphHolder - Class in ome.model.internal
holds information regarding the graph to which an IObject belongs.
GraphHolder() - Constructor for class ome.model.internal.GraphHolder
 
GraphOpts - Class in ome.services.graphs
Deprecated.
will be removed in OMERO 5.3, so use the new graphs implementation
GraphOpts() - Constructor for class ome.services.graphs.GraphOpts
Deprecated.
 
GraphOpts.Op - Enum in ome.services.graphs
Deprecated.
 
GraphPathBean - Class in ome.services.graphs
The graph path bean holds the Hiberate object mapping and assists navigation thereof.
GraphPathBean() - Constructor for class ome.services.graphs.GraphPathBean
 
GraphPathReport - Class in ome.services.graphs
A standalone tool for producing a summary of the Hibernate object mapping for our Sphinx documentation.
GraphPathReport() - Constructor for class ome.services.graphs.GraphPathReport
 
GraphPolicy - Class in ome.services.graphs
A policy guides how to traverse the graph.
GraphPolicy() - Constructor for class ome.services.graphs.GraphPolicy
 
GraphPolicy.Ability - Enum in ome.services.graphs
Abilities that the user may have to operate upon model objects.
GraphPolicy.Action - Enum in ome.services.graphs
The action to take on an object instance.
GraphPolicy.Details - Class in ome.services.graphs
A tuple noting the state of a mapped object instance in the current graph traversal.
GraphPolicy.Orphan - Enum in ome.services.graphs
If an object instance has any GraphPolicy.Action.EXCLUDEd parents that would prevent it from being orphaned.
GraphPolicyRule - Class in ome.services.graphs
A graph policy rule specifies a component of a GraphPolicy.
GraphPolicyRule() - Constructor for class ome.services.graphs.GraphPolicyRule
 
GraphPolicyRulePredicate - Interface in ome.services.graphs
A plug-in for graph policy rule matches whereby an object may be matched against named values.
GraphRequestFactory - Class in omero.cmd.graphs
Create request objects that are executed using the GraphPathBean.
GraphRequestFactory(ACLVoter, Roles, SystemTypes, GraphPathBean, Deletion, Map<Class<? extends Request>, List<String>>, Map<Class<? extends Request>, List<GraphPolicyRule>>, List<String>, Set<String>, boolean) - Constructor for class omero.cmd.graphs.GraphRequestFactory
Construct a new graph request factory.
GraphSpec - Interface in ome.services.graphs
Deprecated.
will be removed in OMERO 5.2, so use the new graphs implementation
GraphSpecListI - Class in omero.cmd.graphs
Deprecated.
will be removed in OMERO 5.2, so use the new graphs implementation
GraphSpecListI(OmeroContext) - Constructor for class omero.cmd.graphs.GraphSpecListI
Deprecated.
 
GraphSpecPostProcessor - Class in ome.services.graphs
Deprecated.
will be removed in OMERO 5.2, so use the new graphs implementation
GraphSpecPostProcessor() - Constructor for class ome.services.graphs.GraphSpecPostProcessor
Deprecated.
 
GraphState - Class in ome.services.graphs
Deprecated.
will be removed in OMERO 5.2, so use the new graphs implementation
GraphState(EventContext, GraphStepFactory, SqlAction, Session, GraphSpec) - Constructor for class ome.services.graphs.GraphState
Deprecated.
 
GraphStep - Class in ome.services.graphs
Deprecated.
will be removed in OMERO 5.2, so use the new graphs implementation
GraphStep(ExtendedMetadata, int, List<GraphStep>, GraphSpec, GraphEntry, long[]) - Constructor for class ome.services.graphs.GraphStep
Deprecated.
 
GraphStep.Callback - Interface in ome.services.graphs
Deprecated.
 
GraphStepFactory - Interface in ome.services.graphs
Deprecated.
will be removed in OMERO 5.2, so use the new graphs implementation
GraphSteps - Class in ome.services.graphs
Deprecated.
will be removed in OMERO 5.2, so use the new graphs implementation
GraphSteps(List<GraphStep>) - Constructor for class ome.services.graphs.GraphSteps
Deprecated.
 
GraphTables - Class in ome.services.graphs
Deprecated.
will be removed in OMERO 5.2, so use the new graphs implementation
GraphTables() - Constructor for class ome.services.graphs.GraphTables
Deprecated.
 
GraphTraversal - Class in ome.services.graphs
An alternative implementation of model object graph traversal, relying on SELECTing in advance for making decisions, instead of rolling back to savepoints to recover from failed attempts to act.
GraphTraversal(Session, EventContext, ACLVoter, SystemTypes, GraphPathBean, SetMultimap<String, String>, GraphPolicy, GraphTraversal.Processor) - Constructor for class ome.services.graphs.GraphTraversal
Construct a new instance of a graph traversal manager.
GraphTraversal.PlanExecutor - Interface in ome.services.graphs
Executor that allows callers to actually perform the planned action.
GraphTraversal.Processor - Interface in ome.services.graphs
Executes the planned operation.
GraphUtil - Class in omero.cmd.graphs
Static utility methods for model graph operations.
GraphUtil() - Constructor for class omero.cmd.graphs.GraphUtil
 
graphValidation(Session) - Method in class ome.services.graphs.GraphStep
Deprecated.
Immediately we check that an object moved from GroupA to GroupB is no longer pointed at by any objects in GroupA via foreign key constraints.
green - Variable in class ome.model.core.Channel
 
GREEN - Static variable in class ome.model.core.Channel
 
green - Variable in class ome.model.display.ChannelBinding
 
GREEN - Static variable in class ome.model.display.ChannelBinding
 
green - Variable in class ome.model.screen.Well
 
GREEN - Static variable in class ome.model.screen.Well
 
GREEN_INDEX - Static variable in class ome.formats.model.ColorsFactory
Index of the red component of a color.
GREEN_INDEX - Static variable in class omeis.providers.re.ColorsFactory
Index of the red component of a color.
GREEN_TEXT - Static variable in class ome.formats.model.ChannelProcessor
Name of the green component when it is a graphics image.
group - Variable in class ome.formats.importer.ImportConfig
 
GROUP - Static variable in class ome.model.internal.Details
 
group - Variable in class ome.model.meta.Share
 
GROUP - Static variable in class ome.model.meta.Share
 
group(long) - Method in class ome.parameters.Filter
 
group() - Method in class ome.parameters.Filter
 
group() - Method in class ome.parameters.Parameters
 
group - Variable in class ome.system.Principal
 
GROUP_COLLAB_READ - Static variable in class ome.formats.importer.ImportEvent
 
GROUP_COLLAB_READ_LINK - Static variable in class ome.formats.importer.ImportEvent
 
GROUP_EXPERIMENTER_MAP - Static variable in class pojos.ExperimenterData
Identifies the Experimenter#GROUPEXPERIMENTERMAP field.
GROUP_EXPERIMENTER_MAP - Static variable in class pojos.GroupData
Identifies the ExperimenterGroup#GROUPEXPERIMENTERMAP field.
GROUP_FILTER - Static variable in class ome.model.acquisition.Arc
 
GROUP_FILTER - Static variable in class ome.model.acquisition.Detector
 
GROUP_FILTER - Static variable in class ome.model.acquisition.DetectorSettings
 
GROUP_FILTER - Static variable in class ome.model.acquisition.Dichroic
 
GROUP_FILTER - Static variable in class ome.model.acquisition.Filament
 
GROUP_FILTER - Static variable in class ome.model.acquisition.Filter
 
GROUP_FILTER - Static variable in class ome.model.acquisition.FilterSet
 
GROUP_FILTER - Static variable in class ome.model.acquisition.FilterSetEmissionFilterLink
 
GROUP_FILTER - Static variable in class ome.model.acquisition.FilterSetExcitationFilterLink
 
GROUP_FILTER - Static variable in class ome.model.acquisition.GenericExcitationSource
 
GROUP_FILTER - Static variable in class ome.model.acquisition.ImagingEnvironment
 
GROUP_FILTER - Static variable in class ome.model.acquisition.Instrument
 
GROUP_FILTER - Static variable in class ome.model.acquisition.Laser
 
GROUP_FILTER - Static variable in class ome.model.acquisition.LightEmittingDiode
 
GROUP_FILTER - Static variable in class ome.model.acquisition.LightPath
 
GROUP_FILTER - Static variable in class ome.model.acquisition.LightPathEmissionFilterLink
 
GROUP_FILTER - Static variable in class ome.model.acquisition.LightPathExcitationFilterLink
 
GROUP_FILTER - Static variable in class ome.model.acquisition.LightSettings
 
GROUP_FILTER - Static variable in class ome.model.acquisition.LightSource
 
GROUP_FILTER - Static variable in class ome.model.acquisition.Microscope
 
GROUP_FILTER - Static variable in class ome.model.acquisition.Objective
 
GROUP_FILTER - Static variable in class ome.model.acquisition.ObjectiveSettings
 
GROUP_FILTER - Static variable in class ome.model.acquisition.OTF
 
GROUP_FILTER - Static variable in class ome.model.acquisition.StageLabel
 
GROUP_FILTER - Static variable in class ome.model.acquisition.TransmittanceRange
 
GROUP_FILTER - Static variable in class ome.model.annotations.Annotation
 
GROUP_FILTER - Static variable in class ome.model.annotations.AnnotationAnnotationLink
 
GROUP_FILTER - Static variable in class ome.model.annotations.BasicAnnotation
 
GROUP_FILTER - Static variable in class ome.model.annotations.BooleanAnnotation
 
GROUP_FILTER - Static variable in class ome.model.annotations.ChannelAnnotationLink
 
GROUP_FILTER - Static variable in class ome.model.annotations.CommentAnnotation
 
GROUP_FILTER - Static variable in class ome.model.annotations.DatasetAnnotationLink
 
GROUP_FILTER - Static variable in class ome.model.annotations.DetectorAnnotationLink
 
GROUP_FILTER - Static variable in class ome.model.annotations.DichroicAnnotationLink
 
GROUP_FILTER - Static variable in class ome.model.annotations.DoubleAnnotation
 
GROUP_FILTER - Static variable in class ome.model.annotations.ExperimenterAnnotationLink
 
GROUP_FILTER - Static variable in class ome.model.annotations.ExperimenterGroupAnnotationLink
 
GROUP_FILTER - Static variable in class ome.model.annotations.FileAnnotation
 
GROUP_FILTER - Static variable in class ome.model.annotations.FilesetAnnotationLink
 
GROUP_FILTER - Static variable in class ome.model.annotations.FilterAnnotationLink
 
GROUP_FILTER - Static variable in class ome.model.annotations.ImageAnnotationLink
 
GROUP_FILTER - Static variable in class ome.model.annotations.InstrumentAnnotationLink
 
GROUP_FILTER - Static variable in class ome.model.annotations.LightPathAnnotationLink
 
GROUP_FILTER - Static variable in class ome.model.annotations.LightSourceAnnotationLink
 
GROUP_FILTER - Static variable in class ome.model.annotations.ListAnnotation
 
GROUP_FILTER - Static variable in class ome.model.annotations.LongAnnotation
 
GROUP_FILTER - Static variable in class ome.model.annotations.MapAnnotation
 
GROUP_FILTER - Static variable in class ome.model.annotations.NamespaceAnnotationLink
 
GROUP_FILTER - Static variable in class ome.model.annotations.NodeAnnotationLink
 
GROUP_FILTER - Static variable in class ome.model.annotations.NumericAnnotation
 
GROUP_FILTER - Static variable in class ome.model.annotations.ObjectiveAnnotationLink
 
GROUP_FILTER - Static variable in class ome.model.annotations.OriginalFileAnnotationLink
 
GROUP_FILTER - Static variable in class ome.model.annotations.PlaneInfoAnnotationLink
 
GROUP_FILTER - Static variable in class ome.model.annotations.PlateAcquisitionAnnotationLink
 
GROUP_FILTER - Static variable in class ome.model.annotations.PlateAnnotationLink
 
GROUP_FILTER - Static variable in class ome.model.annotations.ProjectAnnotationLink
 
GROUP_FILTER - Static variable in class ome.model.annotations.ReagentAnnotationLink
 
GROUP_FILTER - Static variable in class ome.model.annotations.RoiAnnotationLink
 
GROUP_FILTER - Static variable in class ome.model.annotations.ScreenAnnotationLink
 
GROUP_FILTER - Static variable in class ome.model.annotations.SessionAnnotationLink
 
GROUP_FILTER - Static variable in class ome.model.annotations.ShapeAnnotationLink
 
GROUP_FILTER - Static variable in class ome.model.annotations.TagAnnotation
 
GROUP_FILTER - Static variable in class ome.model.annotations.TermAnnotation
 
GROUP_FILTER - Static variable in class ome.model.annotations.TextAnnotation
 
GROUP_FILTER - Static variable in class ome.model.annotations.TimestampAnnotation
 
GROUP_FILTER - Static variable in class ome.model.annotations.TypeAnnotation
 
GROUP_FILTER - Static variable in class ome.model.annotations.WellAnnotationLink
 
GROUP_FILTER - Static variable in class ome.model.annotations.XmlAnnotation
 
GROUP_FILTER - Static variable in class ome.model.containers.Dataset
 
GROUP_FILTER - Static variable in class ome.model.containers.DatasetImageLink
 
GROUP_FILTER - Static variable in class ome.model.containers.Project
 
GROUP_FILTER - Static variable in class ome.model.containers.ProjectDatasetLink
 
GROUP_FILTER - Static variable in class ome.model.core.Channel
 
GROUP_FILTER - Static variable in class ome.model.core.Image
 
GROUP_FILTER - Static variable in class ome.model.core.LogicalChannel
 
GROUP_FILTER - Static variable in class ome.model.core.OriginalFile
 
GROUP_FILTER - Static variable in class ome.model.core.Pixels
 
GROUP_FILTER - Static variable in class ome.model.core.PixelsOriginalFileMap
 
GROUP_FILTER - Static variable in class ome.model.core.PlaneInfo
 
GROUP_FILTER - Static variable in class ome.model.display.ChannelBinding
 
GROUP_FILTER - Static variable in class ome.model.display.CodomainMapContext
 
GROUP_FILTER - Static variable in class ome.model.display.ContrastStretchingContext
 
GROUP_FILTER - Static variable in class ome.model.display.PlaneSlicingContext
 
GROUP_FILTER - Static variable in class ome.model.display.QuantumDef
 
GROUP_FILTER - Static variable in class ome.model.display.RenderingDef
 
GROUP_FILTER - Static variable in class ome.model.display.ReverseIntensityContext
 
GROUP_FILTER - Static variable in class ome.model.display.Thumbnail
 
GROUP_FILTER - Static variable in class ome.model.experiment.Experiment
 
GROUP_FILTER - Static variable in class ome.model.experiment.MicrobeamManipulation
 
GROUP_FILTER - Static variable in class ome.model.fs.Fileset
 
GROUP_FILTER - Static variable in class ome.model.fs.FilesetEntry
 
GROUP_FILTER - Static variable in class ome.model.fs.FilesetJobLink
 
GROUP_FILTER - Static variable in class ome.model.internal.Link
 
GROUP_FILTER - Static variable in class ome.model.jobs.ImportJob
 
GROUP_FILTER - Static variable in class ome.model.jobs.IndexingJob
 
GROUP_FILTER - Static variable in class ome.model.jobs.IntegrityCheckJob
 
GROUP_FILTER - Static variable in class ome.model.jobs.Job
 
GROUP_FILTER - Static variable in class ome.model.jobs.JobOriginalFileLink
 
GROUP_FILTER - Static variable in class ome.model.jobs.MetadataImportJob
 
GROUP_FILTER - Static variable in class ome.model.jobs.ParseJob
 
GROUP_FILTER - Static variable in class ome.model.jobs.PixelDataJob
 
GROUP_FILTER - Static variable in class ome.model.jobs.ScriptJob
 
GROUP_FILTER - Static variable in class ome.model.jobs.ThumbnailGenerationJob
 
GROUP_FILTER - Static variable in class ome.model.jobs.UploadJob
 
GROUP_FILTER - Static variable in class ome.model.meta.ExternalInfo
 
GROUP_FILTER - Static variable in class ome.model.roi.Ellipse
 
GROUP_FILTER - Static variable in class ome.model.roi.Label
 
GROUP_FILTER - Static variable in class ome.model.roi.Line
 
GROUP_FILTER - Static variable in class ome.model.roi.Mask
 
GROUP_FILTER - Static variable in class ome.model.roi.Path
 
GROUP_FILTER - Static variable in class ome.model.roi.Point
 
GROUP_FILTER - Static variable in class ome.model.roi.Polygon
 
GROUP_FILTER - Static variable in class ome.model.roi.Polyline
 
GROUP_FILTER - Static variable in class ome.model.roi.Rect
 
GROUP_FILTER - Static variable in class ome.model.roi.Roi
 
GROUP_FILTER - Static variable in class ome.model.roi.Shape
 
GROUP_FILTER - Static variable in class ome.model.screen.Plate
 
GROUP_FILTER - Static variable in class ome.model.screen.PlateAcquisition
 
GROUP_FILTER - Static variable in class ome.model.screen.Reagent
 
GROUP_FILTER - Static variable in class ome.model.screen.Screen
 
GROUP_FILTER - Static variable in class ome.model.screen.ScreenPlateLink
 
GROUP_FILTER - Static variable in class ome.model.screen.Well
 
GROUP_FILTER - Static variable in class ome.model.screen.WellReagentLink
 
GROUP_FILTER - Static variable in class ome.model.screen.WellSample
 
GROUP_FILTER - Static variable in class ome.model.stats.StatsInfo
 
GROUP_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.acquisition.Detector
 
GROUP_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.acquisition.Dichroic
 
GROUP_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.acquisition.Filter
 
GROUP_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.acquisition.Instrument
 
GROUP_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.acquisition.LightPath
 
GROUP_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.acquisition.LightSource
 
GROUP_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.acquisition.Objective
 
GROUP_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.annotations.Annotation
 
GROUP_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.containers.Dataset
 
GROUP_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.containers.Project
 
GROUP_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.core.Channel
 
GROUP_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.core.Image
 
GROUP_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.core.OriginalFile
 
GROUP_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.core.PlaneInfo
 
GROUP_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.fs.Fileset
 
GROUP_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.meta.Experimenter
 
GROUP_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.meta.ExperimenterGroup
 
GROUP_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.meta.Namespace
 
GROUP_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.meta.Node
 
GROUP_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.meta.Session
 
GROUP_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.roi.Roi
 
GROUP_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.roi.Shape
 
GROUP_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.screen.Plate
 
GROUP_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.screen.PlateAcquisition
 
GROUP_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.screen.Reagent
 
GROUP_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.screen.Screen
 
GROUP_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.screen.Well
 
GROUP_FILTER_CHANNELS - Static variable in class ome.model.core.LogicalChannel
 
GROUP_FILTER_CHANNELS - Static variable in class ome.model.core.Pixels
 
GROUP_FILTER_DATASETLINKS - Static variable in class ome.model.containers.Project
 
GROUP_FILTER_DATASETLINKS - Static variable in class ome.model.core.Image
 
GROUP_FILTER_DETECTOR - Static variable in class ome.model.acquisition.Instrument
 
GROUP_FILTER_DICHROIC - Static variable in class ome.model.acquisition.Instrument
 
GROUP_FILTER_EMISSIONFILTERLINK - Static variable in class ome.model.acquisition.Filter
 
GROUP_FILTER_EMISSIONFILTERLINK - Static variable in class ome.model.acquisition.FilterSet
 
GROUP_FILTER_EMISSIONFILTERLINK - Static variable in class ome.model.acquisition.LightPath
 
GROUP_FILTER_EXCITATIONFILTERLINK - Static variable in class ome.model.acquisition.Filter
 
GROUP_FILTER_EXCITATIONFILTERLINK - Static variable in class ome.model.acquisition.FilterSet
 
GROUP_FILTER_EXCITATIONFILTERLINK - Static variable in class ome.model.acquisition.LightPath
 
GROUP_FILTER_FILESETENTRIES - Static variable in class ome.model.core.OriginalFile
 
GROUP_FILTER_FILTER - Static variable in class ome.model.acquisition.Instrument
 
GROUP_FILTER_FILTERSET - Static variable in class ome.model.acquisition.Instrument
 
GROUP_FILTER_IMAGELINKS - Static variable in class ome.model.containers.Dataset
 
GROUP_FILTER_IMAGES - Static variable in class ome.model.fs.Fileset
 
GROUP_FILTER_JOBLINKS - Static variable in class ome.model.fs.Fileset
 
GROUP_FILTER_LIGHTSOURCE - Static variable in class ome.model.acquisition.Instrument
 
GROUP_FILTER_LIGHTSOURCESETTINGS - Static variable in class ome.model.experiment.MicrobeamManipulation
 
GROUP_FILTER_MICROBEAMMANIPULATION - Static variable in class ome.model.experiment.Experiment
 
GROUP_FILTER_OBJECTIVE - Static variable in class ome.model.acquisition.Instrument
 
GROUP_FILTER_ORIGINALFILELINKS - Static variable in class ome.model.jobs.Job
 
GROUP_FILTER_OTF - Static variable in class ome.model.acquisition.Instrument
 
GROUP_FILTER_PIXELS - Static variable in class ome.model.core.Image
 
GROUP_FILTER_PIXELSFILEMAPS - Static variable in class ome.model.core.OriginalFile
 
GROUP_FILTER_PIXELSFILEMAPS - Static variable in class ome.model.core.Pixels
 
GROUP_FILTER_PLANEINFO - Static variable in class ome.model.core.Pixels
 
GROUP_FILTER_PLATEACQUISITIONS - Static variable in class ome.model.screen.Plate
 
GROUP_FILTER_PLATELINKS - Static variable in class ome.model.screen.Screen
 
GROUP_FILTER_PROJECTLINKS - Static variable in class ome.model.containers.Dataset
 
GROUP_FILTER_REAGENTLINKS - Static variable in class ome.model.screen.Well
 
GROUP_FILTER_REAGENTS - Static variable in class ome.model.screen.Screen
 
GROUP_FILTER_ROIS - Static variable in class ome.model.core.Image
 
GROUP_FILTER_SCREENLINKS - Static variable in class ome.model.screen.Plate
 
GROUP_FILTER_SETTINGS - Static variable in class ome.model.core.Pixels
 
GROUP_FILTER_SHAPES - Static variable in class ome.model.roi.Roi
 
GROUP_FILTER_SPATIALDOMAINENHANCEMENT - Static variable in class ome.model.display.RenderingDef
 
GROUP_FILTER_THUMBNAILS - Static variable in class ome.model.core.Pixels
 
GROUP_FILTER_USEDFILES - Static variable in class ome.model.fs.Fileset
 
GROUP_FILTER_WAVERENDERING - Static variable in class ome.model.display.RenderingDef
 
GROUP_FILTER_WELLLINKS - Static variable in class ome.model.screen.Reagent
 
GROUP_FILTER_WELLS - Static variable in class ome.model.screen.Plate
 
GROUP_FILTER_WELLSAMPLE - Static variable in class ome.model.screen.PlateAcquisition
 
GROUP_FILTER_WELLSAMPLES - Static variable in class ome.model.core.Image
 
GROUP_FILTER_WELLSAMPLES - Static variable in class ome.model.screen.Well
 
GROUP_ID - Static variable in class ome.parameters.Parameters
named parameter "groupId".
GROUP_IMMUTABLE - Static variable in class ome.model.internal.Permissions
R_R___ : user and group can only read
GROUP_PRIVATE - Static variable in class ome.formats.importer.ImportEvent
 
GROUP_PRIVATE - Static variable in class ome.model.internal.Permissions
RWRW__ : user and group can read and write
GROUP_PUBLIC - Static variable in class ome.formats.importer.ImportEvent
 
GROUP_READABLE - Static variable in class ome.model.internal.Permissions
RWR___ : user can read and write, group can read
GROUP_SUDO_NS - Static variable in class ome.services.sessions.SessionManagerImpl
 
GROUP_SYSTEM - Static variable in class ome.formats.importer.ImportEvent
 
GROUP_WRITEABLE - Static variable in class ome.model.internal.Permissions
RWRWR_ : user and group can read and write, world can read
GroupAttributeMapper - Class in ome.security.auth
 
GroupAttributeMapper(LdapConfig) - Constructor for class ome.security.auth.GroupAttributeMapper
 
GroupChmodStrategy - Class in ome.security.basic
ChmodStrategy which only permits modifying the permissions on groups.
GroupChmodStrategy(BasicACLVoter, SessionFactory, SqlAction, ExtendedMetadata) - Constructor for class ome.security.basic.GroupChmodStrategy
 
groupContext(Long, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
Creates a copy of the Current.ctx map and if groupId is not null, sets the "omero.group" key to be a string version of the id.
GroupContextMapper - Class in ome.security.auth
Specialized OME ExperimenterGroup context mapper.
GroupContextMapper(LdapConfig, String) - Constructor for class ome.security.auth.GroupContextMapper
 
GroupContextMapper(LdapConfig, String, String) - Constructor for class ome.security.auth.GroupContextMapper
 
GroupData - Class in pojos
The data that makes up an OME Group along with the various members of the Group
GroupData() - Constructor for class pojos.GroupData
Creates a new instance.
GroupData(ExperimenterGroup) - Constructor for class pojos.GroupData
Creates a new instance.
groupExperimenterMap - Variable in class ome.model.meta.Experimenter
 
GROUPEXPERIMENTERMAP - Static variable in class ome.model.meta.Experimenter
 
groupExperimenterMap - Variable in class ome.model.meta.ExperimenterGroup
 
GROUPEXPERIMENTERMAP - Static variable in class ome.model.meta.ExperimenterGroup
 
GroupExperimenterMap - Class in ome.model.meta
 
GroupExperimenterMap() - Constructor for class ome.model.meta.GroupExperimenterMap
 
GroupExperimenterMap(Long) - Constructor for class ome.model.meta.GroupExperimenterMap
 
GroupExperimenterMap(Long, boolean) - Constructor for class ome.model.meta.GroupExperimenterMap
Main constructor.
GroupExperimenterMap(IObject, IObject, Boolean) - Constructor for class ome.model.meta.GroupExperimenterMap
 
GroupExperimenterMap.Details - Class in ome.model.meta
 
GroupExperimenterMap.Details() - Constructor for class ome.model.meta.GroupExperimenterMap.Details
 
GroupExperimenterMap.Details(Object[]) - Constructor for class ome.model.meta.GroupExperimenterMap.Details
 
groupId - Variable in class ome.services.graphs.GraphPolicy.Details
the ID of the object's ExperimenterGroup, or null if the object does not have a group
groupId - Variable in class ome.util.SqlAction.DeleteLog
 
groupInfo(SqlAction) - Method in class ome.services.graphs.BaseGraphSpec
Deprecated.
 
groupInfo(SqlAction) - Method in interface ome.services.graphs.GraphSpec
Deprecated.
Like GraphSpec.load(Session) uses the current table and id information to look up information on the given target.
groupInfoFor(String, long) - Method in interface ome.util.SqlAction
Return a mostly unloaded ExperimenterGroup object containing only the id, name, and permissions.
groupInfoFor(String, long) - Method in class ome.util.SqlAction.Impl
 
groupname - Variable in class ome.model.jobs.Job
 
GROUPNAME - Static variable in class ome.model.jobs.Job
 
groupnameFilter(String) - Method in class ome.security.auth.LdapConfig
 
GroupPredicate - Class in ome.services.graphs
A predicate that allows group=system and similar to be used in graph policy rule matches.
GroupPredicate(Roles) - Constructor for class ome.services.graphs.GroupPredicate
Construct a new group predicate.
groupProxy(Long) - Method in interface ome.api.local.LocalAdmin
returns a possibly uninitialized proxy for the given group id.
groupProxy(String) - Method in interface ome.api.local.LocalAdmin
returns a possibly uninitialized proxy for the given group name.
groupProxy(Long) - Method in class ome.logic.AdminImpl
 
groupProxy(String) - Method in class ome.logic.AdminImpl
 
groupRestrictions(IObject) - Method in class ome.security.policy.BinaryAccessPolicy
 
groups(String, LdapConfig, LdapOperations, RoleProvider, AttributeSet) - Method in class ome.security.auth.AttributeNewUserGroupBean
 
groups(String, LdapConfig, LdapOperations, RoleProvider, AttributeSet) - Method in interface ome.security.auth.NewUserGroupBean
 
groups(String, LdapConfig, LdapOperations, RoleProvider, AttributeSet) - Method in class ome.security.auth.OrgUnitNewUserGroupBean
 
groups(String, LdapConfig, LdapOperations, RoleProvider, AttributeSet) - Method in class ome.security.auth.QueryNewUserGroupBean
 
GroupSecurityViolation - Exception in ome.conditions
Extension of SecurityViolation which signifies that the violation in question goes against the group-based permissions introduced in 4.2.
GroupSecurityViolation(String) - Constructor for exception ome.conditions.GroupSecurityViolation
 
groupsLed - Variable in class ome.services.sessions.SessionManager.CreationRequest
 
grp(long) - Method in class ome.parameters.Parameters
 
grp(RLong) - Method in class omero.sys.ParametersI
Sets the value of the group parameter.
GUEST - Static variable in class ome.system.Login
CopyOfLogin constant which has username and password values set to null and other values set to their default.
GUEST - Static variable in class pojos.GroupData
Identifies the Guest group.

H

handle(IObject) - Method in interface ome.formats.model.handler.ModelObjectHandler
Attempt to handle the model object of this type.
handle - Variable in class ome.services.blitz.repo.ManagedImportRequestI
Set by ManagedImportProcessI when verifyUpload has been called.
Handle - Class in ome.util.mem
Provides the basic machinery to share the same logical state across objects with different identities.
Handle(Copiable) - Constructor for class ome.util.mem.Handle
Subclasses use this constructor to specify the Body instance this handle will be paired up with.
handle - Variable in class omero.cmd.CmdCallbackI
Proxy passed to this instance on creation.
handle(int, int) - Method in interface omero.model.SmartShape.PointCallback
 
handleAnnotated(IAnnotated, Document, LuceneOptions) - Method in class ome.services.fulltext.bridges.TablesBridge
Responsible for iterating over any attached OMERO.tables and registering all appropriate row objects for later processing.
handleAnnotation(Annotation, TablesBridge.RowProcessor) - Method in class ome.services.fulltext.bridges.TablesBridge
Detects if the given annotation contains an OMERO.table and if so, passes it off for further processing.
handleCallbackException(Exception) - Method in class omero.cmd.SessionI
Reusable method for logging an exception that occurs on one-way communication with clients during callback notification.
handleContextRefreshedEvent(ContextRefreshedEvent) - Method in class ome.security.policy.DefaultPolicyService
Loads all Policy instances from the context, and uses them to initialize this PolicyService.
handleContextRefreshedEvent(ContextRefreshedEvent) - Method in class ome.services.blitz.util.CheckAllJobs
 
handleContextRefreshedEvent(ContextRefreshedEvent) - Method in class ome.services.graphs.GraphPathBean
The application context after refresh should contain a usable Hibernate session factory.
handleContextRefreshedEvent(ContextRefreshedEvent) - Method in class ome.services.mail.ServerUpMailSender
 
handleContextRefreshedEvent(ContextRefreshedEvent) - Method in class ome.services.scripts.ScriptRepoHelper
Loads all ScriptFileType instances from the context, and uses them to initialize all scripts in the repo.
handleContextRefreshedEvent(ContextRefreshedEvent) - Method in class ome.services.util.NamespaceCheck
 
handleContextRefreshedEvent(ContextRefreshedEvent) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
Listener method which waits for a ContextRefreshedEvent and then extracts the SessionFactory from the ApplicationContext and pases it to ExtendedMetadata.Impl.setSessionFactory(SessionFactory).
handleContextRefreshedEvent(ContextRefreshedEvent) - Method in class ome.tools.spring.OnContextRefreshedEventListener
 
handleEventLog(FullTextSession, EventLog) - Method in class ome.services.fulltext.FullTextIndexer
 
handleEventLog(EventLog, Session, ServiceFactory) - Method in class ome.services.pixeldata.PixelDataHandler
Handles only single elements from the PersistentEventLogLoader in order to keep transactions short and safe.
handleException(Throwable) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
handleException(Throwable, OmeroContext) - Method in class omero.util.IceMapper
 
HandleFactory - Class in omero.cmd
SPIOrthogonal interface hierarchy of types for working with the Request hierarchy.
HandleFactory(long) - Constructor for class omero.cmd.HandleFactory
 
handleFile(File, int, Collection) - Method in class ome.formats.importer.ImportCandidates
Handle a file import
handleHdf5(String, TablesBridge.RowProcessor) - Method in class ome.services.fulltext.bridges.TablesBridge
Process a single OMERO.tables file.
HandleI - Class in omero.cmd
Servant for the handle proxy from the Command API.
HandleI(int) - Constructor for class omero.cmd.HandleI
Create a HandleI in the State#CREATED state with the given cancel timeout in milliseconds.
HandleI.Cancel - Exception in omero.cmd
Signals that HandleI.run() has noticed that HandleI.state wants a cancellation or that the Request implementation wishes to stop execution.
HandleI.Cancel(String) - Constructor for exception omero.cmd.HandleI.Cancel
 
handleImage(Image, Document, LuceneOptions) - Method in class ome.services.fulltext.bridges.TablesBridge
Processes any annotations attached to the following types which contain this image: Plate, Dataset
handleInput(Class<?>, Object) - Method in class omero.util.IceMapper
 
handleLsid(IObject) - Method in class ome.services.blitz.impl.OmeroMetadata
 
handleMissingPyramid(Pixels, String) - Method in class ome.io.nio.PixelsService
If the outer loop should continue, this method returns successfully; otherwise it throws a MissingPyramidException.
handleMissingStatsInfo(Pixels) - Method in class ome.io.nio.PixelsService
If the outer loop should continue, this method returns successfully; otherwise it throws a MissingPyramidException.
handleOptions(int, String[]) - Method in class ome.services.graphs.AbstractHierarchyGraphSpec
Deprecated.
Called once per loop iteration throw rawOptions during AbstractHierarchyGraphSpec.initialize(long, String, Map)
handleOptions(int, String[]) - Method in class ome.services.graphs.AnnotationGraphSpec
Deprecated.
 
handleOptions(int, String[]) - Method in class ome.services.graphs.LightSourceGraphSpec
Deprecated.
 
handleOutput(Class, Object) - Method in class omero.util.IceMapper
 
handlePotentialPgArrayJarError(UncategorizedSQLException) - Method in class ome.util.actions.PostgresSqlAction
If postgresql is installed with an older jdbc jar that is on the bootstrap classpath, then it's possible that the use of pgarrays will fail (I think).
handler - Variable in class ome.formats.importer.cli.CommandLineImporter
ErrorHandler which is also responsible for uploading files
handleRingShutdown(Redirector.Context, String) - Method in class ome.services.blitz.redirect.ConfigRedirector
 
handleRingShutdown(Redirector.Context, String) - Method in class ome.services.blitz.redirect.NullRedirector
Does nothing.
handleRingShutdown(Redirector.Context, String) - Method in interface ome.services.blitz.redirect.Redirector
Gives the Redirector a chance to remove the current Ring when it is being shutdown.
handleRingShutdown(Redirector.Context, String) - Method in class ome.services.blitz.redirect.ScaleRedirector
Nothing needs to be done on shutdown, since the Ring implementation will properly disable the Node table queried during the next call to Redirector.getProxyOrNull(Context, String, Glacier2.SessionControlPrx, Ice.Current)
handleServerError(Throwable, OmeroContext) - Method in class omero.util.IceMapper
wraps any non-ServerError returned by IceMapper.handleException(Throwable, OmeroContext) in an InternalException.
HardlinkFileTransfer - Class in ome.formats.importer.transfers
Local-only file transfer mechanism which makes use of hard-linking.
HardlinkFileTransfer() - Constructor for class ome.formats.importer.transfers.HardlinkFileTransfer
 
HardWiredInterceptor - Class in ome.logic
Extension point for interceptors which should be compiled in from third-party code.
HardWiredInterceptor() - Constructor for class ome.logic.HardWiredInterceptor
 
hasAlias(String) - Method in class ome.system.Preference
 
hasDectector() - Method in class pojos.ChannelAcquisitionData
Returns true if there is a detector for that channel, false otherwise.
hasEmissionData(ChannelData) - Static method in class ome.formats.model.ColorsFactory
Returns true if the channel has emission metadata, false otherwise.
hasEmissionData(LogicalChannel) - Static method in class omeis.providers.re.ColorsFactory
Returns true if the channel has emission metadata, false otherwise.
hasFilter() - Method in class pojos.ChannelAcquisitionData
Returns true if there is a filter set linked to the channel false otherwise.
hash - Variable in class ome.model.core.OriginalFile
 
HASH - Static variable in class ome.model.core.OriginalFile
 
hash - Variable in class ome.security.auth.ConfigurablePasswordProvider
Hash implementation to use for encoding passwords to check and changed passwords.
hash - Variable in class ome.services.blitz.repo.CheckedPath
 
hash() - Method in class ome.services.blitz.repo.CheckedPath
 
hash() - Method in class ome.services.scripts.RepoFile.FsFile
 
hash() - Method in class ome.services.scripts.RepoFile
 
hashCode() - Method in class ome.model.internal.NamedValue
 
hashCode() - Method in class ome.model.units.ElectricPotential
 
hashCode() - Method in class ome.model.units.Frequency
 
hashCode(Object) - Method in class ome.model.units.GenericEnumType
 
hashCode() - Method in class ome.model.units.Length
 
hashCode() - Method in class ome.model.units.Power
 
hashCode() - Method in class ome.model.units.Pressure
 
hashCode() - Method in class ome.model.units.Temperature
 
hashCode() - Method in class ome.model.units.Time
 
hashCode() - Method in class ome.parameters.QueryParameter
 
hashCode() - Method in class ome.services.blitz.repo.CheckedPath
On Windows systems the calculation is not case-sensitive.
hashCode() - Method in class ome.services.blitz.repo.path.FsFile
hashCode() - Method in class ome.tools.FileSystem
Public hashcode implementation based on String hash() return
hashCode(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
 
hashCode() - Method in class ome.util.LSID
 
hashCode() - Method in class ome.util.math.geom2D.Line
Overridden to reflect equality of abstract values (data object) as opposite to object identity.
hashCode() - Method in class ome.util.math.geom2D.PlanePoint
Overridden to reflect equality of abstract values (data object) as opposite to object identity.
hashCode() - Method in class ome.util.math.geom2D.Segment
Overridden to reflect equality of abstract values (data object) as opposite to object identity.
hashCode() - Method in class omeis.providers.re.data.PlaneDef
Overridden to reflect equality of abstract values (data object) as opposite to object identity.
hashCode() - Method in class omero.cmd.graphs.Preprocessor.GraphModifyTarget
Deprecated.
 
hashCode() - Method in class omero.model.ElectricPotentialI
 
hashCode() - Method in class omero.model.FrequencyI
 
hashCode() - Method in class omero.model.LengthI
 
hashCode() - Method in class omero.model.PowerI
 
hashCode() - Method in class omero.model.PressureI
 
hashCode() - Method in class omero.model.TemperatureI
 
hashCode() - Method in class omero.model.TimeI
 
hashCode() - Method in class pojos.ROICoordinate
Calculate the hashCode for the data, The hashcode is generated by bitshifting z by ZTBITSPLIT bits and adding t.
hasher - Variable in class ome.model.core.OriginalFile
 
HASHER - Static variable in class ome.model.core.OriginalFile
 
hasher() - Method in class ome.services.scripts.RepoFile.FsFile
 
hasher() - Method in class ome.services.scripts.RepoFile
 
hasIris() - Method in class pojos.ObjectiveData
Returns a boolean flag if the value has been set, null otherwise.
hasLightPath() - Method in class pojos.ChannelAcquisitionData
Returns true if there is a light path described for that channel, false otherwise.
hasMetadata(long) - Method in class ome.services.ThumbnailCtx
Whether or not thumbnail metadata is available for a given Pixels ID.
hasNext() - Method in interface ome.api.Search
Returns true if another call to Search.next() is valid.
hasNext() - Method in class ome.services.eventlogs.EventLogLoader
Tests for available objects.
hasNext() - Method in class ome.services.eventlogs.EventLogQueue
Checks if either any Entry instances are available or tries to load them if not.
hasNext() - Method in class ome.services.graphs.BaseGraphSpec.SubSpecIterator
Deprecated.
 
hasNext() - Method in class ome.services.SearchBean
 
hasNext() - Method in class ome.util.EmptyIterator
 
hasNext_async(AMD_Search_hasNext, Current) - Method in class ome.services.blitz.impl.SearchI
 
hasntSeen(Object) - Method in class ome.util.ContextFilter
 
hasntSeen(Object) - Method in class omero.util.IceMapper
 
hasOpticalAxisAveraged() - Method in class pojos.OTFData
Returns a boolean flag if the value has been set
hasPassword(MethodInvocation) - Method in class ome.logic.HardWiredInterceptor
 
hasPassword(String) - Method in class ome.security.auth.ConfigurablePasswordProvider
Always returns false, override with specific logic.
hasPassword(String) - Method in class ome.security.auth.FilePasswordProvider
 
hasPassword(String) - Method in class ome.security.auth.JdbcPasswordProvider
 
hasPassword(String) - Method in class ome.security.auth.LdapPasswordProvider
Only returns if the user is already in the database and has a DN value in the password table.
hasPassword(String) - Method in interface ome.security.auth.PasswordProvider
Returns true if this provider considers itself responsible for the given user name.
hasPassword(String) - Method in class ome.security.auth.PasswordProviders
 
hasPassword(String) - Method in class ome.security.auth.providers.LdapPasswordProvider431
Only returns if the user is already in the database and has a DN value in the password table.
hasPrivilegedToken(IObject) - Method in class ome.security.basic.BasicSecuritySystem
See {@link TokenHolder#hasPrivilegedToken(IObject)
hasPrivilegedToken(IObject) - Method in class ome.security.basic.TokenHolder
 
hasPrivilegedToken(IObject) - Method in interface ome.security.SecuritySystem
checks that the IObject argument has been granted a Token by the SecuritySystem.
hasPrivilegedToken(IObject) - Method in class ome.security.SecuritySystemHolder
 
hasPrivilegedToken(IObject) - Method in class ome.security.sharing.SharingSecuritySystem
 
hasPump() - Method in class pojos.LightSourceData
Returns true if the light source is a laser with a pump, false otherwise.
hasReference(LSID, LSID) - Method in interface ome.formats.model.IObjectContainerStore
Checks to see if there is currently an active reference for two LSIDs.
hasReference(LSID, LSID) - Method in class ome.formats.OMEROMetadataStoreClient
 
hasReplacement(Object) - Method in class ome.tools.hibernate.UpdateFilter
 
hasSavepoint() - Method in class ome.services.graphs.GraphStep
Deprecated.
 
hasSession() - Method in class ome.system.SessionInitializer
 
hasSettings(long) - Method in class ome.services.ThumbnailCtx
Whether or not settings are available for a given Pixels ID.
hasShapes - Variable in class ome.services.roi.GeomTool
 
hasStats() - Method in class pojos.ChannelData
Returns true if the channel has some channel information false otherwise.
hasSubtypes(int) - Method in class ome.tools.hibernate.ExtendedMetadata.Locks
returns true if this offset points to a field which is an embedded component.
hasToken() - Method in class ome.model.internal.GraphHolder
tests if this GraphHolder contains a Token reference.
hasUnicodeUnits() - Method in interface ome.util.SqlAction
 
hasUnicodeUnits() - Method in class ome.util.SqlAction.Impl
 
height - Variable in class ome.model.roi.Mask
 
HEIGHT - Static variable in class ome.model.roi.Mask
 
height - Variable in class ome.model.roi.Rect
 
HEIGHT - Static variable in class ome.model.roi.Rect
 
help(String[]) - Static method in class prefs
Returns a help string array.
Helper - Class in ome.services.blitz.measurements
Parallel type hierarchy to Column to facilitate (and speed-up) working with columns without adding methods to the slice definitions.
Helper() - Constructor for class ome.services.blitz.measurements.Helper
 
helper - Variable in class ome.services.blitz.repo.RawAccessRequestI
 
helper - Variable in class omero.cmd.admin.CurrentSessionsRequestI
 
helper - Variable in class omero.cmd.admin.UpdateSessionTimeoutRequestI
 
Helper - Class in omero.cmd
Helper object for all omero.cmd implementations.
Helper(Request, Status, SqlAction, Session, ServiceFactory) - Constructor for class omero.cmd.Helper
 
HibernateUtils - Class in ome.tools.hibernate
contains methods for reloading unloaded entities and nulled collections as well as determining the index of certain properties in a dehydrated Hiberante array.
HibernateUtils() - Constructor for class ome.tools.hibernate.HibernateUtils
 
Hidden - Annotation Type in ome.annotations
annotation which specifies that a method parameter (e.g. a password) must be hidden from logging output.
Hierarchy - Class in ome.services.query
single-point of entry for walking of OME container hierarchies.
Hierarchy() - Constructor for class ome.services.query.Hierarchy
 
HierarchyNavigator - Class in ome.services.query
Query the database for relationships between model objects.
HierarchyNavigator(IQuery) - Constructor for class ome.services.query.HierarchyNavigator
Construct a new hierarchy navigator.
hierarchyNavigator - Variable in class omero.cmd.graphs.Preprocessor
Deprecated.
 
HierarchyNavigatorWrap<T,E> - Class in ome.services.query
Convenience class for creating versions of HierarchyNavigator with different model object representations.
HierarchyNavigatorWrap(IQuery) - Constructor for class ome.services.query.HierarchyNavigatorWrap
 
HierarchyTransformations - Class in ome.tools
 
HierarchyTransformations() - Constructor for class ome.tools.HierarchyTransformations
 
hints - Variable in class ome.services.SVGRasterizer
The transcoder hints.
histogram(Object, String) - Method in class ome.system.metrics.DefaultMetrics
 
Histogram - Interface in ome.system.metrics
Thin wrapper around Histogram
histogram(Object, String) - Method in interface ome.system.metrics.Metrics
 
histogram(Object, String) - Method in class ome.system.metrics.NullMetrics
 
holder - Variable in class ome.services.blitz.impl.AbstractAmdServant
 
holder - Variable in class omero.cmd.SessionI
 
hostname - Variable in class ome.formats.importer.ImportConfig
 
HqlQuery - Class in ome.services.search
HqlQuery(SearchValues, String, Parameters) - Constructor for class ome.services.search.HqlQuery
 
HTM - Static variable in class pojos.FileAnnotationData
Identifies the HTM file formats.
HTML - Static variable in class pojos.FileAnnotationData
Identifies the HTML file formats.
HtmlMessenger - Class in ome.formats.importer.util
This class allows you to submit a URL and a String hash map of key-value pairs to be posted to the URL in question.
HtmlMessenger(String, Map<String, String>) - Constructor for class ome.formats.importer.util.HtmlMessenger
Instantiate messenger
HtmlMessengerException - Exception in ome.formats.importer.util
 
HtmlMessengerException(String, Exception) - Constructor for exception ome.formats.importer.util.HtmlMessengerException
Creates a new instance.
HtmlMessengerException(String) - Constructor for exception ome.formats.importer.util.HtmlMessengerException
Creates a new instance.
humidity - Variable in class ome.model.acquisition.ImagingEnvironment
 
HUMIDITY - Static variable in class ome.model.acquisition.ImagingEnvironment
 

I

IAdmin - Interface in ome.api
Administration interface providing access to admin-only functionality as well as JMX-based server access and selected user functions.
IAnalysis - Interface in ome.api
Provides access to the model objects involved in analysis.
IAnnotated - Interface in ome.model
 
IAnnotationLink - Interface in ome.model
extension of ILink for marking links whose child field is an Annotation.
ic - Variable in class ome.services.sharing.ShareStore
 
ice_exception(Exception) - Method in class ome.services.blitz.repo.PublicRepositoryI.AMD_submit
 
ice_postUnmarshal() - Method in class omero.model.PermissionsI
Called as Ice converts from a binary stream to a PermissionsI object.
ice_response(HandlePrx) - Method in class ome.services.blitz.repo.PublicRepositoryI.AMD_submit
 
IceMapper - Class in omero.util
Responsible for the mapping of ome.* types to omero.* types and back again.
IceMapper() - Constructor for class omero.util.IceMapper
 
IceMapper(IceMapper.ReturnMapping) - Constructor for class omero.util.IceMapper
 
IceMapper.ReturnMapping - Interface in omero.util
 
IceMethodInvoker - Class in ome.services.blitz.util
Method-cache primed either with an ServiceInterface instance or with a Class with generic type ServiceInterface.
IceMethodInvoker(ServiceInterface, OmeroContext) - Constructor for class ome.services.blitz.util.IceMethodInvoker
Create an IceMethodInvoker instance using the Class of the passed argument to call IceMethodInvoker#IceMethodInvoker(Class).
IceMethodInvoker(Class<S>, OmeroContext) - Constructor for class ome.services.blitz.util.IceMethodInvoker
Creates an IceMethodInvoker instance by using reflection on the Class argument.
IceUtil - Class in ome.services.util
Methods for working with Ice.
IceUtil() - Constructor for class ome.services.util.IceUtil
 
icMap - Variable in class ome.formats.importer.util.ErrorHandler
Host information about the file and its corresponding import candidate.
IConfig - Interface in ome.api
Access to server configuration.
IContainer - Interface in ome.api
Provides methods for dealing with the core "Pojos" of OME.
ID - Static variable in class ome.model.acquisition.Detector
 
id - Variable in class ome.model.acquisition.Detector
 
ID - Static variable in class ome.model.acquisition.DetectorSettings
 
id - Variable in class ome.model.acquisition.DetectorSettings
 
ID - Static variable in class ome.model.acquisition.Dichroic
 
id - Variable in class ome.model.acquisition.Dichroic
 
ID - Static variable in class ome.model.acquisition.Filter
 
id - Variable in class ome.model.acquisition.Filter
 
ID - Static variable in class ome.model.acquisition.FilterSet
 
id - Variable in class ome.model.acquisition.FilterSet
 
ID - Static variable in class ome.model.acquisition.FilterSetEmissionFilterLink
 
id - Variable in class ome.model.acquisition.FilterSetEmissionFilterLink
 
ID - Static variable in class ome.model.acquisition.FilterSetExcitationFilterLink
 
id - Variable in class ome.model.acquisition.FilterSetExcitationFilterLink
 
ID - Static variable in class ome.model.acquisition.ImagingEnvironment
 
id - Variable in class ome.model.acquisition.ImagingEnvironment
 
ID - Static variable in class ome.model.acquisition.Instrument
 
id - Variable in class ome.model.acquisition.Instrument
 
ID - Static variable in class ome.model.acquisition.LightPath
 
id - Variable in class ome.model.acquisition.LightPath
 
ID - Static variable in class ome.model.acquisition.LightPathEmissionFilterLink
 
id - Variable in class ome.model.acquisition.LightPathEmissionFilterLink
 
ID - Static variable in class ome.model.acquisition.LightPathExcitationFilterLink
 
id - Variable in class ome.model.acquisition.LightPathExcitationFilterLink
 
ID - Static variable in class ome.model.acquisition.LightSettings
 
id - Variable in class ome.model.acquisition.LightSettings
 
ID - Static variable in class ome.model.acquisition.LightSource
 
id - Variable in class ome.model.acquisition.LightSource
 
ID - Static variable in class ome.model.acquisition.Microscope
 
id - Variable in class ome.model.acquisition.Microscope
 
ID - Static variable in class ome.model.acquisition.Objective
 
id - Variable in class ome.model.acquisition.Objective
 
ID - Static variable in class ome.model.acquisition.ObjectiveSettings
 
id - Variable in class ome.model.acquisition.ObjectiveSettings
 
ID - Static variable in class ome.model.acquisition.OTF
 
id - Variable in class ome.model.acquisition.OTF
 
ID - Static variable in class ome.model.acquisition.StageLabel
 
id - Variable in class ome.model.acquisition.StageLabel
 
ID - Static variable in class ome.model.acquisition.TransmittanceRange
 
id - Variable in class ome.model.acquisition.TransmittanceRange
 
ID - Static variable in class ome.model.annotations.Annotation
 
id - Variable in class ome.model.annotations.Annotation
 
ID - Static variable in class ome.model.annotations.AnnotationAnnotationLink
 
id - Variable in class ome.model.annotations.AnnotationAnnotationLink
 
ID - Static variable in class ome.model.annotations.ChannelAnnotationLink
 
id - Variable in class ome.model.annotations.ChannelAnnotationLink
 
ID - Static variable in class ome.model.annotations.DatasetAnnotationLink
 
id - Variable in class ome.model.annotations.DatasetAnnotationLink
 
ID - Static variable in class ome.model.annotations.DetectorAnnotationLink
 
id - Variable in class ome.model.annotations.DetectorAnnotationLink
 
ID - Static variable in class ome.model.annotations.DichroicAnnotationLink
 
id - Variable in class ome.model.annotations.DichroicAnnotationLink
 
ID - Static variable in class ome.model.annotations.ExperimenterAnnotationLink
 
id - Variable in class ome.model.annotations.ExperimenterAnnotationLink
 
ID - Static variable in class ome.model.annotations.ExperimenterGroupAnnotationLink
 
id - Variable in class ome.model.annotations.ExperimenterGroupAnnotationLink
 
ID - Static variable in class ome.model.annotations.FilesetAnnotationLink
 
id - Variable in class ome.model.annotations.FilesetAnnotationLink
 
ID - Static variable in class ome.model.annotations.FilterAnnotationLink
 
id - Variable in class ome.model.annotations.FilterAnnotationLink
 
ID - Static variable in class ome.model.annotations.ImageAnnotationLink
 
id - Variable in class ome.model.annotations.ImageAnnotationLink
 
ID - Static variable in class ome.model.annotations.InstrumentAnnotationLink
 
id - Variable in class ome.model.annotations.InstrumentAnnotationLink
 
ID - Static variable in class ome.model.annotations.LightPathAnnotationLink
 
id - Variable in class ome.model.annotations.LightPathAnnotationLink
 
ID - Static variable in class ome.model.annotations.LightSourceAnnotationLink
 
id - Variable in class ome.model.annotations.LightSourceAnnotationLink
 
ID - Static variable in class ome.model.annotations.NamespaceAnnotationLink
 
id - Variable in class ome.model.annotations.NamespaceAnnotationLink
 
ID - Static variable in class ome.model.annotations.NodeAnnotationLink
 
id - Variable in class ome.model.annotations.NodeAnnotationLink
 
ID - Static variable in class ome.model.annotations.ObjectiveAnnotationLink
 
id - Variable in class ome.model.annotations.ObjectiveAnnotationLink
 
ID - Static variable in class ome.model.annotations.OriginalFileAnnotationLink
 
id - Variable in class ome.model.annotations.OriginalFileAnnotationLink
 
ID - Static variable in class ome.model.annotations.PlaneInfoAnnotationLink
 
id - Variable in class ome.model.annotations.PlaneInfoAnnotationLink
 
ID - Static variable in class ome.model.annotations.PlateAcquisitionAnnotationLink
 
id - Variable in class ome.model.annotations.PlateAcquisitionAnnotationLink
 
ID - Static variable in class ome.model.annotations.PlateAnnotationLink
 
id - Variable in class ome.model.annotations.PlateAnnotationLink
 
ID - Static variable in class ome.model.annotations.ProjectAnnotationLink
 
id - Variable in class ome.model.annotations.ProjectAnnotationLink
 
ID - Static variable in class ome.model.annotations.ReagentAnnotationLink
 
id - Variable in class ome.model.annotations.ReagentAnnotationLink
 
ID - Static variable in class ome.model.annotations.RoiAnnotationLink
 
id - Variable in class ome.model.annotations.RoiAnnotationLink
 
ID - Static variable in class ome.model.annotations.ScreenAnnotationLink
 
id - Variable in class ome.model.annotations.ScreenAnnotationLink
 
ID - Static variable in class ome.model.annotations.SessionAnnotationLink
 
id - Variable in class ome.model.annotations.SessionAnnotationLink
 
ID - Static variable in class ome.model.annotations.ShapeAnnotationLink
 
id - Variable in class ome.model.annotations.ShapeAnnotationLink
 
ID - Static variable in class ome.model.annotations.WellAnnotationLink
 
id - Variable in class ome.model.annotations.WellAnnotationLink
 
ID - Static variable in class ome.model.containers.Dataset
 
id - Variable in class ome.model.containers.Dataset
 
ID - Static variable in class ome.model.containers.DatasetImageLink
 
id - Variable in class ome.model.containers.DatasetImageLink
 
ID - Static variable in class ome.model.containers.Project
 
id - Variable in class ome.model.containers.Project
 
ID - Static variable in class ome.model.containers.ProjectDatasetLink
 
id - Variable in class ome.model.containers.ProjectDatasetLink
 
ID - Static variable in class ome.model.core.Channel
 
id - Variable in class ome.model.core.Channel
 
ID - Static variable in class ome.model.core.Image
 
id - Variable in class ome.model.core.Image
 
ID - Static variable in class ome.model.core.LogicalChannel
 
id - Variable in class ome.model.core.LogicalChannel
 
ID - Static variable in class ome.model.core.OriginalFile
 
id - Variable in class ome.model.core.OriginalFile
 
ID - Static variable in class ome.model.core.Pixels
 
id - Variable in class ome.model.core.Pixels
 
ID - Static variable in class ome.model.core.PixelsOriginalFileMap
 
id - Variable in class ome.model.core.PixelsOriginalFileMap
 
ID - Static variable in class ome.model.core.PlaneInfo
 
id - Variable in class ome.model.core.PlaneInfo
 
ID - Static variable in class ome.model.display.ChannelBinding
 
id - Variable in class ome.model.display.ChannelBinding
 
ID - Static variable in class ome.model.display.CodomainMapContext
 
id - Variable in class ome.model.display.CodomainMapContext
 
ID - Static variable in class ome.model.display.QuantumDef
 
id - Variable in class ome.model.display.QuantumDef
 
ID - Static variable in class ome.model.display.RenderingDef
 
id - Variable in class ome.model.display.RenderingDef
 
ID - Static variable in class ome.model.display.Thumbnail
 
id - Variable in class ome.model.display.Thumbnail
 
ID - Static variable in class ome.model.enums.AcquisitionMode
 
id - Variable in class ome.model.enums.AcquisitionMode
 
ID - Static variable in class ome.model.enums.ArcType
 
id - Variable in class ome.model.enums.ArcType
 
ID - Static variable in class ome.model.enums.Binning
 
id - Variable in class ome.model.enums.Binning
 
ID - Static variable in class ome.model.enums.ChecksumAlgorithm
 
id - Variable in class ome.model.enums.ChecksumAlgorithm
 
ID - Static variable in class ome.model.enums.ContrastMethod
 
id - Variable in class ome.model.enums.ContrastMethod
 
ID - Static variable in class ome.model.enums.Correction
 
id - Variable in class ome.model.enums.Correction
 
ID - Static variable in class ome.model.enums.DetectorType
 
id - Variable in class ome.model.enums.DetectorType
 
ID - Static variable in class ome.model.enums.DimensionOrder
 
id - Variable in class ome.model.enums.DimensionOrder
 
ID - Static variable in class ome.model.enums.EventType
 
id - Variable in class ome.model.enums.EventType
 
ID - Static variable in class ome.model.enums.ExperimentType
 
id - Variable in class ome.model.enums.ExperimentType
 
ID - Static variable in class ome.model.enums.Family
 
id - Variable in class ome.model.enums.Family
 
ID - Static variable in class ome.model.enums.FilamentType
 
id - Variable in class ome.model.enums.FilamentType
 
ID - Static variable in class ome.model.enums.FilterType
 
id - Variable in class ome.model.enums.FilterType
 
ID - Static variable in class ome.model.enums.Format
 
id - Variable in class ome.model.enums.Format
 
ID - Static variable in class ome.model.enums.Illumination
 
id - Variable in class ome.model.enums.Illumination
 
ID - Static variable in class ome.model.enums.Immersion
 
id - Variable in class ome.model.enums.Immersion
 
ID - Static variable in class ome.model.enums.LaserMedium
 
id - Variable in class ome.model.enums.LaserMedium
 
ID - Static variable in class ome.model.enums.LaserType
 
id - Variable in class ome.model.enums.LaserType
 
ID - Static variable in class ome.model.enums.Medium
 
id - Variable in class ome.model.enums.Medium
 
ID - Static variable in class ome.model.enums.MicrobeamManipulationType
 
id - Variable in class ome.model.enums.MicrobeamManipulationType
 
ID - Static variable in class ome.model.enums.MicroscopeType
 
id - Variable in class ome.model.enums.MicroscopeType
 
ID - Static variable in class ome.model.enums.PhotometricInterpretation
 
id - Variable in class ome.model.enums.PhotometricInterpretation
 
ID - Static variable in class ome.model.enums.PixelsType
 
id - Variable in class ome.model.enums.PixelsType
 
ID - Static variable in class ome.model.enums.Pulse
 
id - Variable in class ome.model.enums.Pulse
 
ID - Static variable in class ome.model.enums.RenderingModel
 
id - Variable in class ome.model.enums.RenderingModel
 
ID - Static variable in class ome.model.experiment.Experiment
 
id - Variable in class ome.model.experiment.Experiment
 
ID - Static variable in class ome.model.experiment.MicrobeamManipulation
 
id - Variable in class ome.model.experiment.MicrobeamManipulation
 
ID - Static variable in class ome.model.fs.Fileset
 
id - Variable in class ome.model.fs.Fileset
 
ID - Static variable in class ome.model.fs.FilesetEntry
 
id - Variable in class ome.model.fs.FilesetEntry
 
ID - Static variable in class ome.model.fs.FilesetJobLink
 
id - Variable in class ome.model.fs.FilesetJobLink
 
ID - Static variable in class ome.model.internal.Link
 
id - Variable in class ome.model.internal.Link
 
ID - Static variable in class ome.model.jobs.Job
 
id - Variable in class ome.model.jobs.Job
 
ID - Static variable in class ome.model.jobs.JobOriginalFileLink
 
id - Variable in class ome.model.jobs.JobOriginalFileLink
 
ID - Static variable in class ome.model.jobs.JobStatus
 
id - Variable in class ome.model.jobs.JobStatus
 
ID - Static variable in class ome.model.meta.DBPatch
 
id - Variable in class ome.model.meta.DBPatch
 
ID - Static variable in class ome.model.meta.Event
 
id - Variable in class ome.model.meta.Event
 
ID - Static variable in class ome.model.meta.EventLog
 
id - Variable in class ome.model.meta.EventLog
 
ID - Static variable in class ome.model.meta.Experimenter
 
id - Variable in class ome.model.meta.Experimenter
 
ID - Static variable in class ome.model.meta.ExperimenterGroup
 
id - Variable in class ome.model.meta.ExperimenterGroup
 
ID - Static variable in class ome.model.meta.ExternalInfo
 
id - Variable in class ome.model.meta.ExternalInfo
 
ID - Static variable in class ome.model.meta.GroupExperimenterMap
 
id - Variable in class ome.model.meta.GroupExperimenterMap
 
ID - Static variable in class ome.model.meta.Namespace
 
id - Variable in class ome.model.meta.Namespace
 
ID - Static variable in class ome.model.meta.Node
 
id - Variable in class ome.model.meta.Node
 
ID - Static variable in class ome.model.meta.Session
 
id - Variable in class ome.model.meta.Session
 
ID - Static variable in class ome.model.meta.ShareMember
 
id - Variable in class ome.model.meta.ShareMember
 
ID - Static variable in class ome.model.roi.Roi
 
id - Variable in class ome.model.roi.Roi
 
ID - Static variable in class ome.model.roi.Shape
 
id - Variable in class ome.model.roi.Shape
 
ID - Static variable in class ome.model.screen.Plate
 
id - Variable in class ome.model.screen.Plate
 
ID - Static variable in class ome.model.screen.PlateAcquisition
 
id - Variable in class ome.model.screen.PlateAcquisition
 
ID - Static variable in class ome.model.screen.Reagent
 
id - Variable in class ome.model.screen.Reagent
 
ID - Static variable in class ome.model.screen.Screen
 
id - Variable in class ome.model.screen.Screen
 
ID - Static variable in class ome.model.screen.ScreenPlateLink
 
id - Variable in class ome.model.screen.ScreenPlateLink
 
ID - Static variable in class ome.model.screen.Well
 
id - Variable in class ome.model.screen.Well
 
ID - Static variable in class ome.model.screen.WellReagentLink
 
id - Variable in class ome.model.screen.WellReagentLink
 
ID - Static variable in class ome.model.screen.WellSample
 
id - Variable in class ome.model.screen.WellSample
 
ID - Static variable in class ome.model.stats.StatsInfo
 
id - Variable in class ome.model.stats.StatsInfo
 
ID - Static variable in class ome.parameters.Parameters
named parameter "id".
id - Variable in class ome.services.blitz.repo.CheckedPath
 
id - Variable in class ome.services.blitz.util.FindServiceFactoryMessage
 
id - Variable in class ome.services.graphs.BaseGraphSpec
Deprecated.
The id of the root type which will be processed.
id - Variable in class ome.services.graphs.GraphStep
Deprecated.
The actual id to be processed as opposed to GraphEntry.getId() which is the id of the root object.
IdBlock - Class in ome.util
CBlock implementation which collects ids from IObjects
IdBlock() - Constructor for class ome.util.IdBlock
 
IDelete - Interface in ome.api
Provides simplifed methods for deleting instances from the database.
identical(Permissions) - Method in class ome.model.internal.Permissions
two Permissions instances are identical if they have the same bit representation.
IdentityMapContext - Class in omeis.providers.re.codomain
An empty context for the identity map.
IdentityMapContext() - Constructor for class omeis.providers.re.codomain.IdentityMapContext
 
idEqual(IObject, IObject) - Static method in class ome.tools.hibernate.HibernateUtils
returns true under the following circumstatnces: both arguments are null, or both arguments are identical (==), or both arguments have the same id value(equals)
IDetails - Interface in ome.model
simple interface for Details; currently unused.
idOnly - Variable in class ome.services.search.SearchValues
 
IDS - Static variable in class ome.parameters.Parameters
named parameter "ids".
ids(Criteria) - Method in class ome.services.search.SearchAction
 
ids(QueryBuilder, String) - Method in class ome.services.search.SearchAction
 
idsInDb() - Method in class ome.services.scripts.ScriptRepoHelper
 
idsInDb(SqlAction) - Method in class ome.services.scripts.ScriptRepoHelper
 
idToUuid(long) - Method in class ome.services.sharing.ShareBean
 
idx - Variable in class ome.services.graphs.GraphStep
Deprecated.
Location of this step in GraphState.steps.
IEnum - Interface in ome.model
interface for all domain enumarations.
IFD_TAG_PLANE_NUMBER - Static variable in class ome.io.bioformats.OmeroPixelsPyramidWriter
TIFF tag we're using to store the Bio-Formats plane number.
IFD_TAG_SERIES - Static variable in class ome.io.bioformats.OmeroPixelsPyramidWriter
TIFF tag we're using to store the Bio-Formats series.
IGlobal - Interface in ome.model
marker interface for all global types, which have no Details fields other than permissions.
ignoreAnnotator(String, Object...) - Method in class ome.formats.OMEROMetadataStoreClient
For all cases of an annotator being ignore (WARN).
ignoreInsecure(String, Object...) - Method in class ome.formats.OMEROMetadataStoreClient
Called when saving a property to OMERO would result in a SecurityViolation (DEBUG).
ignoreMissing(String, Object...) - Method in class ome.formats.OMEROMetadataStoreClient
Called when a property is missing from the OMERO model (WARN).
ignoreUnknown - Variable in class ome.security.auth.ConfigurablePasswordProvider
If true, this implementation should return a null on #checkPassword(String, String) if the user is unknown, otherwise a Boolean.FALSE.
ignoreUnneeded(String, Object...) - Method in class ome.formats.OMEROMetadataStoreClient
Called when a property is not needed in OMERO since the data can be gotten elsewhere, as in directly from the file itself (DEBUG).
ignoreUnsupported(String, Object...) - Method in class ome.formats.OMEROMetadataStoreClient
Called when a property is not expected in a file to be imported.
IGraphModifyRequest - Interface in omero.cmd.graphs
Deprecated.
will be removed in OMERO 5.3, so use the new graphs implementation
IHandle - Interface in omero.cmd
SPIOrthogonal interface hierarchy of types for working with the Request hierarchy.
ILdap - Interface in ome.api
Administration interface providing access to admin-only functionality as well as JMX-based server access and selected user functions.
ILink - Interface in ome.model
extension of IObject for building object hierarchies.
IllegalArgumentException - Exception in omero
 
IllegalArgumentException(String) - Constructor for exception omero.IllegalArgumentException
 
illumination - Variable in class ome.model.core.LogicalChannel
 
ILLUMINATION - Static variable in class ome.model.core.LogicalChannel
 
Illumination - Class in ome.model.enums
 
Illumination() - Constructor for class ome.model.enums.Illumination
 
Illumination(Long) - Constructor for class ome.model.enums.Illumination
 
Illumination(Long, boolean) - Constructor for class ome.model.enums.Illumination
Main constructor.
Illumination(String) - Constructor for class ome.model.enums.Illumination
 
Illumination.Details - Class in ome.model.enums
 
Illumination.Details() - Constructor for class ome.model.enums.Illumination.Details
 
Illumination.Details(Object[]) - Constructor for class ome.model.enums.Illumination.Details
 
Image - Class in ome.model.core
These filter definitions are used by the security system to eliminate non-readable objects from queries.
Image() - Constructor for class ome.model.core.Image
 
Image(Long) - Constructor for class ome.model.core.Image
 
Image(Long, boolean) - Constructor for class ome.model.core.Image
Main constructor.
Image(String) - Constructor for class ome.model.core.Image
 
image - Variable in class ome.model.core.Pixels
 
IMAGE - Static variable in class ome.model.core.Pixels
 
image - Variable in class ome.model.roi.Roi
 
IMAGE - Static variable in class ome.model.roi.Roi
 
image - Variable in class ome.model.screen.WellSample
 
IMAGE - Static variable in class ome.model.screen.WellSample
 
IMAGE - Static variable in class pojos.PixelsData
Identifies the Pixels#IMAGE field.
Image.Details - Class in ome.model.core
 
Image.Details() - Constructor for class ome.model.core.Image.Details
 
Image.Details(Object[]) - Constructor for class ome.model.core.Image.Details
 
IMAGE_DESCRIPTION - Static variable in class ome.io.bioformats.OmeroPixelsPyramidWriter
Current TIFF image comment for OMERO pixels pyramid TIFFs.
IMAGE_LINKS - Static variable in class pojos.DatasetData
Identifies the Dataset#IMAGELINKS field.
IMAGE_QUERY - Static variable in class ome.services.delete.DeleteBean
Loads an Image graph including: Pixels, Channel, LogicalChannel, StatsInfo, PlaneInfo, Thumbnails, file maps, OriginalFiles, and Settings
ImageAcquisitionData - Class in pojos
Object hosting the acquisition metadata.
ImageAcquisitionData(Image) - Constructor for class pojos.ImageAcquisitionData
Creates a new instance.
ImageAnnotationLink - Class in ome.model.annotations
These filter definitions are used by the security system to eliminate non-readable objects from queries.
ImageAnnotationLink() - Constructor for class ome.model.annotations.ImageAnnotationLink
 
ImageAnnotationLink(Long) - Constructor for class ome.model.annotations.ImageAnnotationLink
 
ImageAnnotationLink(Long, boolean) - Constructor for class ome.model.annotations.ImageAnnotationLink
Main constructor.
ImageAnnotationLink(IObject, IObject) - Constructor for class ome.model.annotations.ImageAnnotationLink
 
ImageAnnotationLink.Details - Class in ome.model.annotations
 
ImageAnnotationLink.Details() - Constructor for class ome.model.annotations.ImageAnnotationLink.Details
 
ImageAnnotationLink.Details(Object[]) - Constructor for class ome.model.annotations.ImageAnnotationLink.Details
 
imageCount - Variable in class ome.formats.importer.ImportSize
 
ImageData - Class in pojos
The data that makes up an OME Image along with links to its Pixels, enclosing Datasets, and the Experimenter that owns this Image.
ImageData() - Constructor for class pojos.ImageData
Creates a new instance.
ImageData(Image) - Constructor for class pojos.ImageData
Creates a new instance.
imageDescription - Variable in class ome.model.jobs.ImportJob
 
IMAGEDESCRIPTION - Static variable in class ome.model.jobs.ImportJob
 
imageID - Variable in class loci.ome.io.OMECredentials
 
imageLinks - Variable in class ome.model.containers.Dataset
 
IMAGELINKS - Static variable in class ome.model.containers.Dataset
 
IMAGELINKSCOUNTPEROWNER - Static variable in class ome.model.containers.Dataset
 
imageName - Variable in class ome.model.jobs.ImportJob
 
IMAGENAME - Static variable in class ome.model.jobs.ImportJob
 
ImageNameMetadataStore - Class in ome.formats
Stores all Image names consumed by the interface.
ImageNameMetadataStore() - Constructor for class ome.formats.ImageNameMetadataStore
 
images - Variable in class ome.model.fs.Fileset
 
IMAGES - Static variable in class ome.model.fs.Fileset
 
ImageUtil - Class in ome.util
Provides helper methods for performing various things on image data.
ImageUtil() - Constructor for class ome.util.ImageUtil
 
ImagingEnvironment - Class in ome.model.acquisition
These filter definitions are used by the security system to eliminate non-readable objects from queries.
ImagingEnvironment() - Constructor for class ome.model.acquisition.ImagingEnvironment
 
ImagingEnvironment(Long) - Constructor for class ome.model.acquisition.ImagingEnvironment
 
ImagingEnvironment(Long, boolean) - Constructor for class ome.model.acquisition.ImagingEnvironment
Main constructor.
imagingEnvironment - Variable in class ome.model.core.Image
 
IMAGINGENVIRONMENT - Static variable in class ome.model.core.Image
 
ImagingEnvironment.Details - Class in ome.model.acquisition
 
ImagingEnvironment.Details() - Constructor for class ome.model.acquisition.ImagingEnvironment.Details
 
ImagingEnvironment.Details(Object[]) - Constructor for class ome.model.acquisition.ImagingEnvironment.Details
 
ImagingEnvironment_AirPressure - Static variable in class ome.formats.model.UnitsFactory
 
ImagingEnvironment_Temperature - Static variable in class ome.formats.model.UnitsFactory
 
IMetadata - Interface in ome.api
Provides method to interact with acquisition metadata and annotations.
img - Variable in class ome.services.SVGRasterizer
The image that represents the SVG document.
immersion - Variable in class ome.model.acquisition.Objective
 
IMMERSION - Static variable in class ome.model.acquisition.Objective
 
Immersion - Class in ome.model.enums
 
Immersion() - Constructor for class ome.model.enums.Immersion
 
Immersion(Long) - Constructor for class ome.model.enums.Immersion
 
Immersion(Long, boolean) - Constructor for class ome.model.enums.Immersion
Main constructor.
Immersion(String) - Constructor for class ome.model.enums.Immersion
 
Immersion.Details - Class in ome.model.enums
 
Immersion.Details() - Constructor for class ome.model.enums.Immersion.Details
 
Immersion.Details(Object[]) - Constructor for class ome.model.enums.Immersion.Details
 
IMPORT_LOG_MIMETYPE - Static variable in class ome.services.blitz.repo.PublicRepositoryI
media type for import logs
ImportCandidates - Class in ome.formats.importer
Utility class which given any File object will determine the correct number and members of a given import.
ImportCandidates(OMEROWrapper, String[], IObserver) - Constructor for class ome.formats.importer.ImportCandidates
ImportCandidates(int, OMEROWrapper, String[], IObserver) - Constructor for class ome.formats.importer.ImportCandidates
Main constructor which iterates over all the paths calling DirectoryWalker.walk(File, Collection) and permitting a descent to the given depth.
importCandidates(ImportConfig, ImportCandidates) - Method in class ome.formats.importer.ImportLibrary
Primary user method for importing a number
ImportCandidates.CANCEL - Exception in ome.formats.importer
Marker exception raised if the ImportCandidates.SCANNING.cancel() method is called by an IObserver instance.
ImportCandidates.CANCEL() - Constructor for exception ome.formats.importer.ImportCandidates.CANCEL
 
ImportCandidates.SCANNING - Class in ome.formats.importer
Event raised during a pass through the directory structure given to ImportCandidates.
ImportCandidates.SCANNING(File, int, int, int) - Constructor for class ome.formats.importer.ImportCandidates.SCANNING
 
ImportConfig - Class in ome.formats.importer
Utility class which configures the Import.
ImportConfig() - Constructor for class ome.formats.importer.ImportConfig
Simplest constructor which use calls ImportConfig.ImportConfig(File) with null.
ImportConfig(File) - Constructor for class ome.formats.importer.ImportConfig
Calls ImportConfig.ImportConfig(Preferences, IniFileLoader, Properties) with user preferences, a local PreferenceContext, an IniFileLoader initialized with the given argument, and System.getProperties().
ImportConfig(Preferences, IniFileLoader, Properties) - Constructor for class ome.formats.importer.ImportConfig
Complete constructor.
ImportConfig.AnnotationListValue - Class in ome.formats.importer
 
ImportConfig.AnnotationListValue(String, ImportConfig, List<Annotation>) - Constructor for class ome.formats.importer.ImportConfig.AnnotationListValue
 
ImportConfig.BoolValue - Class in ome.formats.importer
 
ImportConfig.BoolValue(String, ImportConfig, boolean) - Constructor for class ome.formats.importer.ImportConfig.BoolValue
 
ImportConfig.DoubleArrayValue - Class in ome.formats.importer
 
ImportConfig.DoubleArrayValue(String, ImportConfig, Double[]) - Constructor for class ome.formats.importer.ImportConfig.DoubleArrayValue
 
ImportConfig.FileValue - Class in ome.formats.importer
 
ImportConfig.FileValue(String, ImportConfig) - Constructor for class ome.formats.importer.ImportConfig.FileValue
 
ImportConfig.IntValue - Class in ome.formats.importer
 
ImportConfig.IntValue(String, ImportConfig, int) - Constructor for class ome.formats.importer.ImportConfig.IntValue
 
ImportConfig.IntValue(String, ImportConfig, int, String) - Constructor for class ome.formats.importer.ImportConfig.IntValue
 
ImportConfig.LongValue - Class in ome.formats.importer
 
ImportConfig.LongValue(String, ImportConfig, Long) - Constructor for class ome.formats.importer.ImportConfig.LongValue
 
ImportConfig.PassValue - Class in ome.formats.importer
 
ImportConfig.PassValue(String, ImportConfig) - Constructor for class ome.formats.importer.ImportConfig.PassValue
 
ImportConfig.StrValue - Class in ome.formats.importer
 
ImportConfig.StrValue(String, ImportConfig) - Constructor for class ome.formats.importer.ImportConfig.StrValue
 
ImportConfig.StrValue(String, ImportConfig, String) - Constructor for class ome.formats.importer.ImportConfig.StrValue
 
ImportConfig.StrValue(String, ImportConfig, String, String) - Constructor for class ome.formats.importer.ImportConfig.StrValue
 
ImportConfig.Value<T> - Class in ome.formats.importer
Container which thread-safely makes a generic configuration value available, without requiring getters and setters.
ImportConfig.VersionInfo - Enum in ome.formats.importer
Keys for fileset version information entries.
ImportContainer - Class in ome.formats.importer
 
ImportContainer(File, IObject, Double[], String, String[], Boolean) - Constructor for class ome.formats.importer.ImportContainer
 
ImportContainer(ImportConfig, File, IObject, Double[], String, String[], Boolean) - Constructor for class ome.formats.importer.ImportContainer
 
ImportEvent - Class in ome.formats.importer
Simple event base-class used by IObservable and IObserver implementations.
ImportEvent() - Constructor for class ome.formats.importer.ImportEvent
 
ImportEvent.ADD - Class in ome.formats.importer
 
ImportEvent.ADD() - Constructor for class ome.formats.importer.ImportEvent.ADD
 
ImportEvent.BEGIN_POST_PROCESS - Class in ome.formats.importer
 
ImportEvent.BEGIN_POST_PROCESS(int, ImportContainer, IObject, Long, int, ImportSize) - Constructor for class ome.formats.importer.ImportEvent.BEGIN_POST_PROCESS
 
ImportEvent.BEGIN_SAVE_TO_DB - Class in ome.formats.importer
 
ImportEvent.BEGIN_SAVE_TO_DB(int, ImportContainer, IObject, Long, int, ImportSize) - Constructor for class ome.formats.importer.ImportEvent.BEGIN_SAVE_TO_DB
 
ImportEvent.COUNT_EVENT - Class in ome.formats.importer
 
ImportEvent.DATA_STORED - Class in ome.formats.importer
 
ImportEvent.DATA_STORED(int, ImportContainer, IObject, Long, int, ImportSize) - Constructor for class ome.formats.importer.ImportEvent.DATA_STORED
 
ImportEvent.DATASET_STORED - Class in ome.formats.importer
 
ImportEvent.DATASET_STORED(int, ImportContainer, IObject, Long, int, ImportSize, Integer, Integer) - Constructor for class ome.formats.importer.ImportEvent.DATASET_STORED
 
ImportEvent.DEBUG_SEND - Class in ome.formats.importer
 
ImportEvent.DEBUG_SEND(boolean, boolean) - Constructor for class ome.formats.importer.ImportEvent.DEBUG_SEND
 
ImportEvent.END_POST_PROCESS - Class in ome.formats.importer
 
ImportEvent.END_POST_PROCESS(int, ImportContainer, IObject, Long, int, ImportSize) - Constructor for class ome.formats.importer.ImportEvent.END_POST_PROCESS
 
ImportEvent.END_SAVE_TO_DB - Class in ome.formats.importer
 
ImportEvent.END_SAVE_TO_DB(int, ImportContainer, IObject, Long, int, ImportSize) - Constructor for class ome.formats.importer.ImportEvent.END_SAVE_TO_DB
 
ImportEvent.ERRORS_COMPLETE - Class in ome.formats.importer
 
ImportEvent.ERRORS_COMPLETE() - Constructor for class ome.formats.importer.ImportEvent.ERRORS_COMPLETE
 
ImportEvent.ERRORS_FAILED - Class in ome.formats.importer
 
ImportEvent.ERRORS_FAILED() - Constructor for class ome.formats.importer.ImportEvent.ERRORS_FAILED
 
ImportEvent.ERRORS_PENDING - Class in ome.formats.importer
 
ImportEvent.ERRORS_PENDING() - Constructor for class ome.formats.importer.ImportEvent.ERRORS_PENDING
 
ImportEvent.FILE_UPLOAD_BYTES - Class in ome.formats.importer
 
ImportEvent.FILE_UPLOAD_BYTES(String, int, int, Long, Long, Long, Exception) - Constructor for class ome.formats.importer.ImportEvent.FILE_UPLOAD_BYTES
 
ImportEvent.FILE_UPLOAD_CANCELLED - Class in ome.formats.importer
 
ImportEvent.FILE_UPLOAD_CANCELLED(String, int, int, Long, Long, Exception) - Constructor for class ome.formats.importer.ImportEvent.FILE_UPLOAD_CANCELLED
 
ImportEvent.FILE_UPLOAD_COMPLETE - Class in ome.formats.importer
 
ImportEvent.FILE_UPLOAD_COMPLETE(String, int, int, Long, Long, Exception) - Constructor for class ome.formats.importer.ImportEvent.FILE_UPLOAD_COMPLETE
 
ImportEvent.FILE_UPLOAD_ERROR - Class in ome.formats.importer
 
ImportEvent.FILE_UPLOAD_ERROR(String, int, int, Long, Long, Exception) - Constructor for class ome.formats.importer.ImportEvent.FILE_UPLOAD_ERROR
 
ImportEvent.FILE_UPLOAD_EVENT - Class in ome.formats.importer
 
ImportEvent.FILE_UPLOAD_FAILED - Class in ome.formats.importer
 
ImportEvent.FILE_UPLOAD_FAILED(String, int, int, Long, Long, Exception) - Constructor for class ome.formats.importer.ImportEvent.FILE_UPLOAD_FAILED
 
ImportEvent.FILE_UPLOAD_FINISHED - Class in ome.formats.importer
 
ImportEvent.FILE_UPLOAD_FINISHED(String, int, int, Long, Long, Exception) - Constructor for class ome.formats.importer.ImportEvent.FILE_UPLOAD_FINISHED
 
ImportEvent.FILE_UPLOAD_STARTED - Class in ome.formats.importer
 
ImportEvent.FILE_UPLOAD_STARTED(String, int, int, Long, Long, Exception) - Constructor for class ome.formats.importer.ImportEvent.FILE_UPLOAD_STARTED
 
ImportEvent.FILESET_EXCLUSION - Class in ome.formats.importer
 
ImportEvent.FILESET_EXCLUSION(String, int, int) - Constructor for class ome.formats.importer.ImportEvent.FILESET_EXCLUSION
 
ImportEvent.FILESET_UPLOAD_END - Class in ome.formats.importer
 
ImportEvent.FILESET_UPLOAD_END(String, int, int, Long, Long, String[], List<String>, Map<Integer, String>, Exception) - Constructor for class ome.formats.importer.ImportEvent.FILESET_UPLOAD_END
 
ImportEvent.FILESET_UPLOAD_PREPARATION - Class in ome.formats.importer
 
ImportEvent.FILESET_UPLOAD_PREPARATION(String, int, int, Long, Long, Exception) - Constructor for class ome.formats.importer.ImportEvent.FILESET_UPLOAD_PREPARATION
 
ImportEvent.FILESET_UPLOAD_START - Class in ome.formats.importer
 
ImportEvent.FILESET_UPLOAD_START(String, int, int, Long, Long, Exception) - Constructor for class ome.formats.importer.ImportEvent.FILESET_UPLOAD_START
 
ImportEvent.IMPORT_ARCHIVING - Class in ome.formats.importer
 
ImportEvent.IMPORT_ARCHIVING(int, ImportContainer, IObject, Long, int, ImportSize) - Constructor for class ome.formats.importer.ImportEvent.IMPORT_ARCHIVING
 
ImportEvent.IMPORT_DONE - Class in ome.formats.importer
 
ImportEvent.IMPORT_DONE(int, ImportContainer, IObject, Long, int, ImportSize, List<Pixels>, Fileset, List<IObject>) - Constructor for class ome.formats.importer.ImportEvent.IMPORT_DONE
 
ImportEvent.IMPORT_OVERLAYS - Class in ome.formats.importer
 
ImportEvent.IMPORT_OVERLAYS(int, ImportContainer, IObject, Long, int, ImportSize) - Constructor for class ome.formats.importer.ImportEvent.IMPORT_OVERLAYS
 
ImportEvent.IMPORT_PROCESSING - Class in ome.formats.importer
 
ImportEvent.IMPORT_PROCESSING(int, ImportContainer, IObject, Long, int, ImportSize) - Constructor for class ome.formats.importer.ImportEvent.IMPORT_PROCESSING
 
ImportEvent.IMPORT_STARTED - Class in ome.formats.importer
 
ImportEvent.IMPORT_STARTED(int, ImportContainer, IObject, Long, int, ImportSize, Integer, Integer, Long) - Constructor for class ome.formats.importer.ImportEvent.IMPORT_STARTED
 
ImportEvent.IMPORT_STEP - Class in ome.formats.importer
 
ImportEvent.IMPORT_STEP(int, int, int) - Constructor for class ome.formats.importer.ImportEvent.IMPORT_STEP
 
ImportEvent.IMPORT_SUMMARY - Class in ome.formats.importer
 
ImportEvent.IMPORT_SUMMARY(long, int) - Constructor for class ome.formats.importer.ImportEvent.IMPORT_SUMMARY
 
ImportEvent.LOADED_IMAGE - Class in ome.formats.importer
 
ImportEvent.LOADED_IMAGE(String, Integer, Integer, Integer) - Constructor for class ome.formats.importer.ImportEvent.LOADED_IMAGE
 
ImportEvent.LOADING_IMAGE - Class in ome.formats.importer
 
ImportEvent.LOADING_IMAGE(String, Integer, Integer, Integer) - Constructor for class ome.formats.importer.ImportEvent.LOADING_IMAGE
 
ImportEvent.LOGGED_IN - Class in ome.formats.importer
 
ImportEvent.LOGGED_IN() - Constructor for class ome.formats.importer.ImportEvent.LOGGED_IN
 
ImportEvent.LOGGED_OUT - Class in ome.formats.importer
 
ImportEvent.LOGGED_OUT() - Constructor for class ome.formats.importer.ImportEvent.LOGGED_OUT
 
ImportEvent.METADATA_IMPORTED - Class in ome.formats.importer
 
ImportEvent.METADATA_IMPORTED(int, ImportContainer, IObject, Long, int, ImportSize, Integer, Integer, Long) - Constructor for class ome.formats.importer.ImportEvent.METADATA_IMPORTED
 
ImportEvent.METADATA_PROCESSED - Class in ome.formats.importer
 
ImportEvent.METADATA_PROCESSED(int, ImportContainer, IObject, Long, int, ImportSize, Integer, Integer, Long) - Constructor for class ome.formats.importer.ImportEvent.METADATA_PROCESSED
 
ImportEvent.OBJECTS_RETURNED - Class in ome.formats.importer
 
ImportEvent.OBJECTS_RETURNED(int, ImportContainer, IObject, Long, int, ImportSize, Integer, Integer, Long) - Constructor for class ome.formats.importer.ImportEvent.OBJECTS_RETURNED
 
ImportEvent.PIXELDATA_PROCESSED - Class in ome.formats.importer
 
ImportEvent.PIXELDATA_PROCESSED(int, ImportContainer, IObject, Long, int, ImportSize, Integer, Integer, Long) - Constructor for class ome.formats.importer.ImportEvent.PIXELDATA_PROCESSED
 
ImportEvent.POST_UPLOAD_EVENT - Class in ome.formats.importer
 
ImportEvent.POST_UPLOAD_EVENT(int, ImportContainer, IObject, Long, int, ImportSize, Integer, Integer, Long) - Constructor for class ome.formats.importer.ImportEvent.POST_UPLOAD_EVENT
 
ImportEvent.PROGRESS_EVENT - Class in ome.formats.importer
 
ImportEvent.PROGRESS_EVENT(int, ImportContainer, IObject, Long, int, ImportSize, Integer, Integer) - Constructor for class ome.formats.importer.ImportEvent.PROGRESS_EVENT
 
ImportEvent.REIMPORT - Class in ome.formats.importer
 
ImportEvent.REIMPORT() - Constructor for class ome.formats.importer.ImportEvent.REIMPORT
 
ImportEvent.THUMBNAILS_GENERATED - Class in ome.formats.importer
 
ImportEvent.THUMBNAILS_GENERATED(int, ImportContainer, IObject, Long, int, ImportSize, Integer, Integer, Long) - Constructor for class ome.formats.importer.ImportEvent.THUMBNAILS_GENERATED
 
importFileset(Fileset, ImportSettings, Current) - Method in class ome.services.blitz.repo.ManagedRepositoryI
Return a template based directory path.
ImportFixture - Class in ome.formats.importer
test fixture for importing files without a GUI.
ImportFixture(OMEROMetadataStoreClient, OMEROWrapper) - Constructor for class ome.formats.importer.ImportFixture
 
importImage(ImportContainer, int, int, int) - Method in class ome.formats.importer.ImportLibrary
Perform an image import uploading files if necessary.
ImportJob - Class in ome.model.jobs
 
ImportJob() - Constructor for class ome.model.jobs.ImportJob
 
ImportJob(Long) - Constructor for class ome.model.jobs.ImportJob
 
ImportJob(Long, boolean) - Constructor for class ome.model.jobs.ImportJob
Main constructor.
ImportJob(String, String) - Constructor for class ome.model.jobs.ImportJob
 
ImportLibrary - Class in ome.formats.importer
support class for the proper usage of OMEROMetadataStoreClient and FormatReader instances.
ImportLibrary(OMEROMetadataStoreClient, OMEROWrapper) - Constructor for class ome.formats.importer.ImportLibrary
The default implementation of FileTransfer performs a no-op and therefore need not have FileTransfer#afterTransfer(int, File[]) as with the ImportLibrary.ImportLibrary(OMEROMetadataStoreClient, OMEROWrapper, FileTransfer) constructor.
ImportLibrary(OMEROMetadataStoreClient, OMEROWrapper, FileTransfer) - Constructor for class ome.formats.importer.ImportLibrary
The library will not close the client instance.
ImportLibrary(OMEROMetadataStoreClient, OMEROWrapper, FileTransfer, int) - Constructor for class ome.formats.importer.ImportLibrary
 
ImportLibrary(OMEROMetadataStoreClient, OMEROWrapper, FileTransfer, List<FileExclusion>, int) - Constructor for class ome.formats.importer.ImportLibrary
 
ImportLibrary.ImportCallback - Class in ome.formats.importer
 
ImportLibrary.ImportCallback(ImportProcessPrx, HandlePrx, ImportContainer) - Constructor for class ome.formats.importer.ImportLibrary.ImportCallback
 
importMetadata(MetadataImportJob) - Method in class ome.services.blitz.repo.ManagedImportRequestI
Uses the OMEROMetadataStoreClient to save all metadata for the current image provided.
importPaths(List<String>, Current) - Method in class ome.services.blitz.repo.ManagedRepositoryI
 
ImportSize - Class in ome.formats.importer
Calculates the various dimensions of an image from a Pixels instance.
ImportSize(String, Pixels, String) - Constructor for class ome.formats.importer.ImportSize
 
importTime - Variable in class ome.formats.importer.ImportEvent.IMPORT_SUMMARY
 
IMutable - Interface in ome.model
interface for all mutable domain objects.
in(String[]) - Method in class ome.util.PixelData
Returns whether or not the pixel data type is is one of the elements in an array.
in(PixelsType, String[]) - Static method in class omeis.providers.re.data.PlaneFactory
A static helper method to check if a type is one of the elements in an array.
inc() - Method in interface ome.system.metrics.Counter
 
inc() - Method in class ome.system.metrics.DefaultCounter
 
include(int) - Method in class ome.tools.hibernate.ExtendedMetadata.Locks
returns true if this offset points to a field which may contain an IObject instance
increment() - Method in class ome.services.sessions.SessionContext.Count
Increment the current reference count and return the new value atomically.
increment(int) - Method in class ome.services.sessions.stats.LongCounter
 
index - Variable in class ome.formats.importer.ImportEvent.COUNT_EVENT
 
index - Variable in class ome.formats.importer.ImportEvent.PROGRESS_EVENT
 
Index - Enum in ome.formats
 
index(IndexingJob) - Method in class ome.services.blitz.repo.ManagedImportRequestI
 
index(String, String[]) - Static method in class ome.tools.hibernate.HibernateUtils
 
indexAllEvents() - Static method in class ome.services.fulltext.Main
 
indexByClass(Set<String>) - Static method in class ome.services.fulltext.Main
 
indexer - Variable in class ome.services.fulltext.FullTextThread
 
indexFullDb() - Static method in class ome.services.fulltext.Main
 
IndexingJob - Class in ome.model.jobs
 
IndexingJob() - Constructor for class ome.model.jobs.IndexingJob
 
IndexingJob(Long) - Constructor for class ome.model.jobs.IndexingJob
 
IndexingJob(Long, boolean) - Constructor for class ome.model.jobs.IndexingJob
Main constructor.
indexObject(IObject) - Method in interface ome.api.IUpdate
Initiates full-text indexing for the given object.
indexObject(IObject) - Method in class ome.logic.UpdateImpl
 
indexObject_async(AMD_IUpdate_indexObject, IObject, Current) - Method in class ome.services.blitz.impl.UpdateI
 
info(String, Object...) - Method in class omero.cmd.Helper
 
IniFileLoader - Class in ome.formats.importer.util
This class loads in the default importer.ini file (or one specified from the command line when starting the app)
IniFileLoader(File) - Constructor for class ome.formats.importer.util.IniFileLoader
Load given file
init(String, boolean) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
 
init(ObjectAdapter, String) - Method in class ome.services.blitz.fire.Ring
Typically called from within BlitzConfiguration after the communicator and adapter have been properly setup.
init(Helper) - Method in class ome.services.blitz.impl.commands.SaveI
 
init(String) - Method in class ome.services.blitz.repo.FileMaker
 
init(Helper) - Method in class ome.services.blitz.repo.ManagedImportRequestI
 
init(Helper) - Method in class ome.services.blitz.repo.RawAccessRequestI
 
init() - Static method in class ome.services.fulltext.Main
 
init() - Method in class ome.services.sessions.SessionManagerImpl
Initialization method called by the Spring run-time to acquire an initial Session.
init() - Method in class ome.services.sharing.ShareStore
Calls ShareStore.doInit() within a transaction with a session available to all HibernateTemplate callbacks.
init(Helper) - Method in class omero.cmd.admin.CurrentSessionsRequestI
 
init(Helper) - Method in class omero.cmd.admin.ResetPasswordRequestI
 
init(Helper) - Method in class omero.cmd.admin.UpdateSessionTimeoutRequestI
 
init(Helper) - Method in class omero.cmd.basic.DoAllI
 
init(Helper) - Method in class omero.cmd.basic.ListRequestsI
 
init(Helper) - Method in class omero.cmd.basic.TimingI
 
init(Helper) - Method in class omero.cmd.fs.ManageImageBinariesI
 
init(Helper) - Method in class omero.cmd.fs.OriginalMetadataRequestI
 
init(Helper) - Method in class omero.cmd.fs.UsedFilesRequestI
 
init(Helper) - Method in class omero.cmd.graphs.Chgrp2I
 
init(Helper) - Method in class omero.cmd.graphs.ChgrpFacadeI
Deprecated.
 
init(Helper) - Method in class omero.cmd.graphs.ChgrpI
Deprecated.
 
init() - Method in class omero.cmd.graphs.ChildOptionI
Initialize this child option instance.
init(Helper) - Method in class omero.cmd.graphs.Chmod2I
 
init(Helper) - Method in class omero.cmd.graphs.ChmodFacadeI
Deprecated.
 
init(Helper) - Method in class omero.cmd.graphs.ChmodI
Deprecated.
 
init(Helper) - Method in class omero.cmd.graphs.Chown2I
 
init(Helper) - Method in class omero.cmd.graphs.ChownFacadeI
Deprecated.
 
init(Helper) - Method in class omero.cmd.graphs.ChownI
Deprecated.
 
init(Helper) - Method in class omero.cmd.graphs.Delete2I
 
init(Helper) - Method in class omero.cmd.graphs.DeleteFacadeI
Deprecated.
 
init(Helper) - Method in class omero.cmd.graphs.DeleteI
Deprecated.
 
init(Helper) - Method in class omero.cmd.graphs.DiskUsageI
 
init(Helper) - Method in class omero.cmd.graphs.GraphSpecListI
Deprecated.
 
init(Helper) - Method in class omero.cmd.graphs.SkipHeadI
 
init(Helper) - Method in interface omero.cmd.IRequest
Method called within the transaction boundaries before any processing occurs.
init(Helper) - Method in class omero.cmd.mail.SendEmailRequestI
 
initFile(String) - Method in class loci.ome.io.OmeroReader
 
initFile(String) - Method in class ome.services.formats.OmeroReader
 
INITIAL_DELAY - Static variable in class ome.logic.RepositoryInfoImpl
Time (2 minutes) between successive calls to RepositoryInfoImpl.sanityCheckRepository() needed to trigger an actual call to RepositoryInfoImpl.getUsageFraction()
INITIAL_FREE_PHYSICAL_MEMORY - Static variable in class ome.services.util.JvmSettingsCheck
FreePhysicalMemorySize value from the OperatingSystem JMX bean at startup.
initializationDone() - Method in class omero.cmd.CmdCallbackI
Subclasses which must perform their own initialization before CmdCallbackI.onFinished(Response, Status, Current) is called should call CmdCallbackI.initializationDone() once that setup is complete.
initialize(Object) - Method in interface ome.api.local.LocalQuery
Uses the Hibernate static method initialize to prepare an object for shipping over the wire.
initialize(ServiceFactoryPrx) - Method in class ome.formats.OMEROMetadataStoreClient
Initializes the MetadataStore with an already logged in, ready to go service factory.
initialize(client) - Method in class ome.formats.OMEROMetadataStoreClient
Initializes the MetadataStore with an already logged in, ready to go service factory.
initialize(String, String, String, int) - Method in class ome.formats.OMEROMetadataStoreClient
Initializes the MetadataStore taking string parameters to feed to the OMERO Blitz client object.
initialize(String, String, String, int, boolean) - Method in class ome.formats.OMEROMetadataStoreClient
Initializes the MetadataStore taking string parameters to feed to the OMERO Blitz client object.
initialize(String, String, String, int, Long, boolean) - Method in class ome.formats.OMEROMetadataStoreClient
Initializes the MetadataStore taking string parameters to feed to the OMERO Blitz client object.
initialize(String, int, String) - Method in class ome.formats.OMEROMetadataStoreClient
Initializes the MetadataStore by joining an existing session.
initialize(String, int, String, boolean) - Method in class ome.formats.OMEROMetadataStoreClient
Initializes the MetadataStore by joining an existing session.
initialize(ServiceFactoryPrx, List<Pixels>, List<Long>) - Method in class ome.formats.OverlayMetadataStore
Initializes the metadata store implementation.
initialize(Object) - Method in class ome.logic.QueryImpl
 
initialize(Session) - Method in class ome.services.blitz.impl.OmeroMetadata
 
initialize(String[], String[], Class[], Map<String, Object>) - Method in class ome.services.blitz.measurements.MeasurementStore
 
initialize(String[], String[], Class[], Map<String, Object>) - Method in interface ome.services.blitz.measurements.OmeroMeasurementStore
 
initialize(FileMaker, Long, String) - Method in class ome.services.blitz.repo.PublicRepositoryI
Called by the internal repository once initialization has taken place.
initialize() - Method in class ome.services.eventlogs.EventLogQueue
Do nothing.
initialize() - Method in class ome.services.eventlogs.PersistentEventLogLoader
Called when the configuration database does not contain a valid current_id.
initialize() - Method in class ome.services.fulltext.PersistentEventLogLoader
Called when the configuration database does not contain a valid current_id.
initialize(long, String, Map<String, String>) - Method in class ome.services.graphs.AbstractHierarchyGraphSpec
Deprecated.
In order to allow subclasses like the AnnotationGraphSpec to make use of this method, hooks have been added.
initialize(long, String, Map<String, String>) - Method in class ome.services.graphs.BaseGraphSpec
Deprecated.
 
initialize(long, String, Map<String, String>) - Method in class ome.services.graphs.GraphEntry
Deprecated.
Called during GraphSpec.initialize(long, String, Map) to give the entry a chance to modify its #op based on the options and to initialize subspecs.
initialize(long, String, Map<String, String>) - Method in interface ome.services.graphs.GraphSpec
Deprecated.
Called as each action is started.
initialize() - Method in class ome.services.pixeldata.PersistentEventLogLoader
 
initialize(Identity, IRequest, Map<String, String>) - Method in class omero.cmd.HandleI
 
initialize(Identity, IRequest, Map<String, String>) - Method in interface omero.cmd.IHandle
Must be called on all instances exactly once before processing.
initializeQuery(FullTextQuery) - Method in class ome.services.search.FullText
Allows settings offset and limit on the query.
initializeReader() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
If the pyramid file exists (which the constructor guarantees) then we assume that even if a lock file is present, that it's no longer valid.
initializeRedirect(Redirector.Context, String) - Method in class ome.services.blitz.redirect.AbstractRedirector
Set the new redirect value if null, or if the uuid is null or empty, then the existing redirect will be removed.
initializeUserAttributes(MethodInvocation, ServiceFactory, Principal, AtomicBoolean) - Static method in class ome.logic.HardWiredInterceptor
Adds the given environment context objects to the ReflectiveMethodInvocation.getUserAttributes() Map for lookup in subclasses
initializeWriter(String, String, boolean, int, int) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
Initializes the writer.
initialPoll() - Method in class omero.cmd.CmdCallbackI
Called at the end of construction to check a race condition.
initPixelsRange(Pixels) - Method in class omeis.providers.re.metadata.StatsFactory
Determines the minimum and maximum corresponding to the passed pixels.
inMemoryCache(String) - Method in interface ome.services.sessions.SessionManager
Returns after possibly creating an in-memory cache which can be used throughout the session.
inMemoryCache(String) - Method in class ome.services.sessions.SessionManagerImpl
 
inMemoryCache(String) - Method in class ome.services.sessions.state.SessionCache
 
InMemoryPlanarPixelBuffer - Class in ome.io.nio
Class implementation of the PixelBuffer interface for in memory planar pixel data.
InMemoryPlanarPixelBuffer(Pixels, byte[][][][]) - Constructor for class ome.io.nio.InMemoryPlanarPixelBuffer
Constructs an in memory pixel buffer based on a defined dimensionality.
INNER_JOIN - Static variable in class ome.services.query.Query
imported constant for ease of use
input - Variable in class ome.services.SVGRasterizer
The transcoder input.
inputEnd - Variable in class ome.model.display.ChannelBinding
 
INPUTEND - Static variable in class ome.model.display.ChannelBinding
 
inputEnvironment(String) - Method in interface ome.services.sessions.SessionManager
Returns a copy of the input environment.
inputEnvironment(String) - Method in class ome.services.sessions.SessionManagerImpl
 
inputStart - Variable in class ome.model.display.ChannelBinding
 
INPUTSTART - Static variable in class ome.model.display.ChannelBinding
 
insertEntity(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
insertFormat(String) - Method in class ome.util.actions.PostgresSqlAction
 
insertFormat(String) - Method in interface ome.util.SqlAction
 
insertFormatSql - Static variable in class ome.util.actions.PostgresSqlAction
 
insertLogs(List<Object[]>) - Method in class ome.util.actions.PostgresSqlAction
 
insertLogs(List<Object[]>) - Method in interface ome.util.SqlAction
 
insertRows(PersistentCollection, Serializable, SessionImplementor) - Method in class ome.util.CountCollectionPersister
 
insertSession(Map<String, Object>) - Method in class ome.util.actions.PostgresSqlAction
 
insertSession(Map<String, Object>) - Method in interface ome.util.SqlAction
 
INSIGHT_PUBLISHED_NS - Static variable in class pojos.BooleanAnnotationData
The name space used to indicate that the tag is used a tag set.
INSIGHT_RATING_NS - Static variable in class pojos.RatingAnnotationData
The name space used to identify the archived annotation linked to a set of pixels.
INSIGHT_TAGSET_NS - Static variable in class pojos.TagAnnotationData
The name space used to indicate that the tag is used a tag set.
InstanceProvider - Interface in ome.formats.model
An instance provider, whose job is to make OMERO Blitz classes available to a consumer based on a set of criteria.
instantiate(String, EntityMode, Serializable) - Method in class ome.security.basic.OmeroInterceptor
default logic, but we may want to use them eventually for dependency-injection.
institution - Variable in class ome.model.meta.Experimenter
 
INSTITUTION - Static variable in class ome.model.meta.Experimenter
 
INSTITUTION - Static variable in class pojos.ExperimenterData
Identifies the Experimenter#INSTITUTION field.
instrument - Variable in class ome.model.acquisition.Detector
 
INSTRUMENT - Static variable in class ome.model.acquisition.Detector
 
instrument - Variable in class ome.model.acquisition.Dichroic
 
INSTRUMENT - Static variable in class ome.model.acquisition.Dichroic
 
instrument - Variable in class ome.model.acquisition.Filter
 
INSTRUMENT - Static variable in class ome.model.acquisition.Filter
 
instrument - Variable in class ome.model.acquisition.FilterSet
 
INSTRUMENT - Static variable in class ome.model.acquisition.FilterSet
 
Instrument - Class in ome.model.acquisition
These filter definitions are used by the security system to eliminate non-readable objects from queries.
Instrument() - Constructor for class ome.model.acquisition.Instrument
 
Instrument(Long) - Constructor for class ome.model.acquisition.Instrument
 
Instrument(Long, boolean) - Constructor for class ome.model.acquisition.Instrument
Main constructor.
instrument - Variable in class ome.model.acquisition.LightSource
 
INSTRUMENT - Static variable in class ome.model.acquisition.LightSource
 
instrument - Variable in class ome.model.acquisition.Objective
 
INSTRUMENT - Static variable in class ome.model.acquisition.Objective
 
instrument - Variable in class ome.model.acquisition.OTF
 
INSTRUMENT - Static variable in class ome.model.acquisition.OTF
 
instrument - Variable in class ome.model.core.Image
 
INSTRUMENT - Static variable in class ome.model.core.Image
 
Instrument.Details - Class in ome.model.acquisition
 
Instrument.Details() - Constructor for class ome.model.acquisition.Instrument.Details
 
Instrument.Details(Object[]) - Constructor for class ome.model.acquisition.Instrument.Details
 
InstrumentAnnotationLink - Class in ome.model.annotations
These filter definitions are used by the security system to eliminate non-readable objects from queries.
InstrumentAnnotationLink() - Constructor for class ome.model.annotations.InstrumentAnnotationLink
 
InstrumentAnnotationLink(Long) - Constructor for class ome.model.annotations.InstrumentAnnotationLink
 
InstrumentAnnotationLink(Long, boolean) - Constructor for class ome.model.annotations.InstrumentAnnotationLink
Main constructor.
InstrumentAnnotationLink(IObject, IObject) - Constructor for class ome.model.annotations.InstrumentAnnotationLink
 
InstrumentAnnotationLink.Details - Class in ome.model.annotations
 
InstrumentAnnotationLink.Details() - Constructor for class ome.model.annotations.InstrumentAnnotationLink.Details
 
InstrumentAnnotationLink.Details(Object[]) - Constructor for class ome.model.annotations.InstrumentAnnotationLink.Details
 
InstrumentData - Class in pojos
Hosts the instrument used to capture an image.
InstrumentData(Instrument) - Constructor for class pojos.InstrumentData
Creates a new instance.
InstrumentProcessor - Class in ome.formats.model
Processes the members of an Instrument (Objective, OTF, Arc Laser and Filament) and ensures that the Instrument containers are present in the container cache, adding them if they are missing.
InstrumentProcessor() - Constructor for class ome.formats.model.InstrumentProcessor
 
Int(long) - Static method in class ome.model.units.Conversion
Static helper for creating Conversion.Int instances.
Int(String) - Static method in class ome.model.units.Conversion
Static helper for creating Conversion.Int instances.
INT - Static variable in class ome.util.PixelData
Identifies the type used to store pixel values.
INT - Static variable in class omeis.providers.re.data.PlaneFactory
Identifies the type used to store pixel values.
INT16 - Static variable in class omeis.providers.re.data.PlaneFactory
Identifies the INT16 data type used to store pixel values, as per OME spec.
INT16_TYPE - Static variable in class pojos.PixelsData
Identifies the type used to store pixel values.
INT32 - Static variable in class omeis.providers.re.data.PlaneFactory
Identifies the INT32 data type used to store pixel values, as per OME spec.
INT32_TYPE - Static variable in class pojos.PixelsData
Identifies the type used to store pixel values.
INT8 - Static variable in class omeis.providers.re.data.PlaneFactory
Identifies the INT8 data type used to store pixel values, as per OME spec.
INT8_TYPE - Static variable in class pojos.PixelsData
Identifies the type used to store pixel values.
INTEGER(Connection, List<Integer>) - Method in interface ome.tools.hibernate.ListAsSQLArrayUserType.ArrayFactory
 
integration - Variable in class ome.model.acquisition.DetectorSettings
 
INTEGRATION - Static variable in class ome.model.acquisition.DetectorSettings
 
IntegrityCheckJob - Class in ome.model.jobs
 
IntegrityCheckJob() - Constructor for class ome.model.jobs.IntegrityCheckJob
 
IntegrityCheckJob(Long) - Constructor for class ome.model.jobs.IntegrityCheckJob
 
IntegrityCheckJob(Long, boolean) - Constructor for class ome.model.jobs.IntegrityCheckJob
Main constructor.
InteractiveProcessorI - Class in omero.grid
Processor implementation which delegates to an omero.grid.Processor servant.
InteractiveProcessorI(Principal, SessionManager, Executor, ProcessorPrx, Job, long, SessionControlPrx, ParamsCache, ParamsHelper, ScriptRepoHelper, Current) - Constructor for class omero.grid.InteractiveProcessorI
 
interceptor - Variable in class ome.security.basic.BasicSecuritySystem
 
internalDelete(IObject, UpdateFilter, Session) - Method in class ome.logic.UpdateImpl
 
InternalException - Exception in ome.conditions
Catchall for unknown server exceptions.
InternalException(String) - Constructor for exception ome.conditions.InternalException
 
internalForm(Permissions) - Static method in class ome.util.Utils
Returns the internal representation of a Permissions object.
internalMerge(IObject, UpdateFilter, Session) - Method in class ome.logic.UpdateImpl
Note if we use anything other than merge here, functionality from ome.tools.hibernate.MergeEventListener needs to be moved to UpdateFilter or to another event listener.
InternalMessage - Class in ome.util.messages
InternalMessage(Object) - Constructor for class ome.util.messages.InternalMessage
Sole constructor which takes the "source" of this EventObject.
internalMkdir(CheckedPath) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
This method should only be used by the register public method in order to guarantee that the DB is kept in sync with the file system.
internalMoveToCommonSpace(IObject) - Method in interface ome.api.local.LocalAdmin
Unconditionally move an object into the user group (usually id=1).
internalMoveToCommonSpace(IObject) - Method in class ome.logic.AdminImpl
Helpers which unconditionally moves the object to the common space.
InternalRepositoryConfig - Class in ome.services.blitz.repo
Simple configuration class which is created via repository.xml Spring configuration file after the OMERO.repository context is loaded.
InternalRepositoryConfig(String) - Constructor for class ome.services.blitz.repo.InternalRepositoryConfig
 
InternalRepositoryI - Class in ome.services.blitz.repo
Standalone repository service.
InternalRepositoryI(ObjectAdapter, Registry, Executor, Principal, String, PublicRepositoryI) - Constructor for class ome.services.blitz.repo.InternalRepositoryI
 
internalSave(IObject, ReloadFilter, Session) - Method in class ome.logic.UpdateImpl
Note if we use anything other than merge here, functionality from ome.tools.hibernate.MergeEventListener needs to be moved to UpdateFilter or to another event listener.
internalServantConfig(Object) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
internalServantConfig(Object) - Method in class omero.cmd.SessionI
 
InternalServiceFactory - Class in ome.tools.spring
subclass of ome.system.ServiceFactory which retrieves unmanaged ("internal") service-instances.
InternalServiceFactory() - Constructor for class ome.tools.spring.InternalServiceFactory
default construtor
InternalServiceFactory(OmeroContext) - Constructor for class ome.tools.spring.InternalServiceFactory
 
internalSession - Variable in class ome.services.sessions.SessionManagerImpl
Internal SessionContext created during SessionManagerImpl.init() which is used for all method calls internal to the session manager (see execute* methods)
Intersection - Class in ome.services.search
Intersection SearchAction which combines two other search actions into one logical unit, e.g.
Intersection(SearchValues, SearchAction, SearchAction) - Constructor for class ome.services.search.Intersection
 
intersects(double, double, double, double) - Method in class ome.util.math.geom2D.EllipseArea
Required by the Shape I/F.
intersects(Rectangle2D) - Method in class ome.util.math.geom2D.EllipseArea
Required by the Shape I/F.
intersects(double, double, double, double) - Method in class ome.util.math.geom2D.RectangleArea
Required by the Shape I/F.
intersects(Rectangle2D) - Method in class ome.util.math.geom2D.RectangleArea
Required by the Shape I/F.
intervalEnd - Variable in class omeis.providers.re.codomain.CodomainMapContext
The upper bound of the codomain interval.
intervalStart - Variable in class omeis.providers.re.codomain.CodomainMapContext
The lower bound of the codomain interval.
InThreadThrottlingStrategy - Class in ome.services.throttling
Throttling implementation which uses the calling server Thread for execution.
InThreadThrottlingStrategy(CurrentDetails) - Constructor for class ome.services.throttling.InThreadThrottlingStrategy
 
invalidate(String) - Method in class ome.util.Validation
 
invalidateConnection(long, Experimenter) - Method in interface ome.api.IShare
Makes the connection invalid for share for specifiec user.
invalidateConnection(long, Experimenter) - Method in class ome.services.sharing.ShareBean
 
invalidateConnection_async(AMD_IShare_invalidateConnection, long, Experimenter, Current) - Method in class ome.services.blitz.impl.ShareI
 
invalidateCurrentEventContext() - Method in class ome.security.basic.CurrentDetails
It suffices to set the Details to a new instance to make this context unusable.
invalidateEventContext() - Method in class ome.security.basic.BasicSecuritySystem
 
invalidateEventContext() - Method in interface ome.security.SecuritySystem
Clears the content of the EventContextso that the SecuritySystem will no longer return true for SecuritySystem.isReady().
invalidateEventContext() - Method in class ome.security.SecuritySystemHolder
 
invalidateEventContext() - Method in class ome.security.sharing.SharingSecuritySystem
 
InvalidQueryException - Exception in ome.util.search
Exception to indicate that the query string was invalid
InvalidQueryException() - Constructor for exception ome.util.search.InvalidQueryException
 
InvalidQueryException(String, Throwable) - Constructor for exception ome.util.search.InvalidQueryException
 
InvalidQueryException(String) - Constructor for exception ome.util.search.InvalidQueryException
 
InvalidQueryException(Throwable) - Constructor for exception ome.util.search.InvalidQueryException
 
invertPDI(Set<Image>, CBlock<T>) - Static method in class ome.tools.HierarchyTransformations
 
invoke(MethodInvocation) - Method in class ome.security.basic.BasicSecurityWiring
Wraps all OMERO invocations with login/logout semantics.
invoke(MethodInvocation) - Method in class ome.security.basic.EventHandler
invocation interceptor for prepairing this Thread for execution and subsequently reseting it.
invoke(MethodInvocation) - Method in class ome.security.basic.NullEventHandler
 
invoke(MethodInvocation) - Method in class ome.services.blitz.fire.AopContextInitializer
 
invoke(Object, Current, IceMapper, Object...) - Method in class ome.services.blitz.util.IceMethodInvoker
Calls the method named in Current.operation with the arguments provided mapped via the IceMapper instance.
invoke(MethodInvocation) - Method in class ome.services.util.ServiceHandler
 
invoke(MethodInvocation) - Method in class ome.tools.hibernate.EventMethodInterceptor
 
invoke(MethodInvocation) - Method in class ome.tools.hibernate.ProxyCleanupFilter.Interceptor
 
invoke(MethodInvocation) - Method in class ome.tools.hibernate.SessionFactory
Wraps all invocations to Session to prevent certain usages.
invoke(MethodInvocation) - Method in class ome.tools.hibernate.SessionHandler
delegates to HibernateInterceptor or manages sessions internally, based on the type of service.
invoke(MethodInvocation) - Method in class ome.util.SqlAction.LoggingSqlAction
 
invoke(MethodInvocation) - Method in class omero.cmd.CallContext
 
invoker - Variable in class ome.services.blitz.impl.AbstractAmdServant
If a service is provided, then an invoker will be created to cache all of its methods.
IObject - Interface in ome.model
central model interface.
IObjectClassQuery - Class in ome.services.query
simple query subclass which uses the Parameters.CLASS parameter value to create a Criteria and then adds Expression instances based on all other parameter names.
IObjectClassQuery(Parameters) - Constructor for class ome.services.query.IObjectClassQuery
 
IObjectContainerStore - Interface in ome.formats.model
An object that handles the storage and manipulation of IObject containers and their references.
iObjectType - Variable in class ome.services.graphs.GraphStep
Deprecated.
Type of object which is being processed, using during GraphState#release(String) to send an EventLogMessage.
IObservable - Interface in ome.formats.importer
 
IObserver - Interface in ome.formats.importer
 
ip - Variable in class ome.services.sessions.SessionManager.CreationRequest
 
IPixels - Interface in ome.api
Metadata gateway for the RenderingEngine and clients.
iPixels - Variable in class ome.services.projection.ProjectionBean
Reference to the service used to retrieve the pixels metadata.
IProcessManager - Interface in ome.services.procs
Manages asynchronous processing logic for all Job instances created
IProjection - Interface in ome.api
Provides methods for performing projections of Pixels sets.
IQuery - Interface in ome.api
Provides methods for directly querying object graphs.
iQuery - Variable in class ome.logic.AbstractLevel2Service
 
iQuery - Variable in class ome.services.AbstractStatefulBean
 
iQuery - Variable in class ome.services.query.HierarchyNavigator
available query service
IQueryEnumProvider - Class in ome.formats.enums
An enumeration provider which uses IQuery and a cache to fulfill the contract of an EnumerationProvider.
IQueryEnumProvider(IQueryPrx) - Constructor for class ome.formats.enums.IQueryEnumProvider
Default IQuery based enumeration provider constructor.
IRenderingSettings - Interface in ome.api
Provides method to apply rendering settings to a collection of images.
IRepositoryInfo - Interface in ome.api
Provides methods for obtaining information for server repository disk space allocation.
IRequest - Interface in omero.cmd
SPI Orthogonal interface hierarchy of types for working with the Request hierarchy.
iris - Variable in class ome.model.acquisition.Objective
 
IRIS - Static variable in class ome.model.acquisition.Objective
 
is_admin - Static variable in class ome.security.basic.AllGroupsSecurityFilter
 
is_adminorpi - Static variable in interface ome.security.SecurityFilter
 
is_nonprivate - Static variable in interface ome.security.SecurityFilter
 
IS_ROOT_USER - Variable in class ome.system.Roles
 
is_share - Static variable in interface ome.security.SecurityFilter
 
IS_SYSTEM_GROUP - Variable in class ome.system.Roles
 
IS_USER_GROUP - Variable in class ome.system.Roles
 
isAbstract - Variable in class ome.services.graphs.AbstractHierarchyGraphSpec
Deprecated.
Whether or not the type of types[i] is abstract.
isAcceptable(List<String>) - Method in class ome.services.blitz.repo.path.MakeNextDirectory
If the circumstances (filesystem, etc.) are such that it is okay to use the given subdirectories.
isAccepted(boolean, String, String, Current) - Method in class ome.services.blitz.impl.ProcessorCallbackI
Deprecated.
isAcquisitionData() - Method in class ome.parameters.Parameters
 
isActive() - Method in class ome.security.basic.BasicMethodSecurity
isActive() - Method in interface ome.security.MethodSecurity
Indicates whether or not method security is active.
isActive() - Method in interface ome.services.procs.Process
 
isActive() - Method in class ome.services.procs.ProcessSkeleton
 
isActive(int) - Method in class ome.services.RenderingBean
Implemented as specified by the RenderingEngine interface.
isActive(int) - Method in interface omeis.providers.re.RenderingEngine
Returns true if the channel is mapped, false otherwise.
isActive() - Method in class pojos.ExperimenterData
Returns true if the experimenter is active, false otherwise.
isActive_async(AMD_RenderingEngine_isActive, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
isAdjustedAfterReview(GraphPolicy.Details) - Method in class omero.cmd.graphs.BaseGraphPolicyAdjuster
An opportunity to adjust each model object after the graph policy reviews it.
isAdjustedBeforeReview(GraphPolicy.Details) - Method in class omero.cmd.graphs.BaseGraphPolicyAdjuster
An opportunity to adjust each model object before the graph policy reviews it.
isAdmin - Variable in class ome.system.SimpleEventContext
 
isAdminOrPi(EventContext) - Method in class ome.security.basic.AbstractSecurityFilter
 
isAllowLeadingWildcard() - Method in interface ome.api.Search
Returns the current leading-wildcard setting.
isAllowLeadingWildcard() - Method in class ome.services.SearchBean
 
isAllowLeadingWildcard_async(AMD_Search_isAllowLeadingWildcard, Current) - Method in class ome.services.blitz.impl.SearchI
 
isAlphalessRendering() - Method in class omeis.providers.re.Optimizations
Returns true if the alphaless rendering optimization is enabled, and false if it is not.
isArchived() - Method in class pojos.ImageData
Returns true if the image has been archived, false otherwise.
isAutoCloseEnabled() - Method in class ome.tools.hibernate.CurrentSessionContext
 
IScale - Interface in ome.api
Provides methods for performing scaling (change of the image size through interpolation or other means) on BufferedImages.
isCancelled() - Method in class omero.cmd.CmdCallbackI
Returns whether Status::CANCELLED is contained in the flags variable of the Status instance.
isCaseSensitive() - Method in interface ome.api.Search
Returns the current case sensitivity setting.
isCaseSensitive() - Method in class ome.services.SearchBean
 
isCaseSensitive_async(AMD_Search_isCaseSensitive, Current) - Method in class ome.services.blitz.impl.SearchI
 
isCheckPermissions - Variable in class ome.services.graphs.GraphPolicy.Details
if the user's permissions for the object should be checked before the GraphTraversal.Processor acts upon it
isClientObject() - Method in class pojos.ShapeData
Returns true if the object one that has been created client side.
isClientSide() - Method in class pojos.ROIData
Returns true if the object a client-side object, false otherwise.
isCondition(String) - Method in class ome.services.graphs.GraphPolicy
Check if a condition has been set.
isCondition(String) - Method in class omero.cmd.graphs.BaseGraphPolicyAdjuster
 
IsConstant() - Method in class omeis.providers.re.codomain.PlaneSlicingContext
Returns the type of bit-planes mapping.
isCurrentUserAdmin() - Method in class ome.services.sessions.SessionContextImpl
 
isCurrentUserAdmin() - Method in interface ome.system.EventContext
 
isCurrentUserAdmin() - Method in class ome.system.SimpleEventContext
 
isDb() - Method in class ome.system.Preference
 
isDebugConsole() - Method in class ome.formats.importer.util.IniFileLoader
 
isDebugUI() - Method in class ome.formats.importer.util.IniFileLoader
 
isDetectorSettingsDirty() - Method in class pojos.ChannelAcquisitionData
Returns true if the detector settings has been updated, false otherwise.
isDirectory() - Method in class ome.services.blitz.repo.CheckedPath
 
isDirectory() - Method in class pojos.FileData
Returns true if the file is a directory, false otherwise.
isDirty() - Method in class pojos.DataObject
Returns true if setter value has modified the value of the stored IObject, false otherwise.
isDisabled(String) - Method in class ome.security.basic.BasicSecuritySystem
 
isDisabled(String) - Method in class ome.security.basic.CurrentDetails
 
isDisabled(String) - Method in interface ome.security.SecuritySystem
checks if the listed id is disabled for the current Thread.
isDisabled(String) - Method in class ome.security.SecuritySystemHolder
 
isDisabled(String) - Method in class ome.security.sharing.SharingSecuritySystem
 
isDisallow(boolean[], int) - Static method in class ome.model.internal.Permissions
 
isDisallow(int, Current) - Method in class omero.model.PermissionsI
 
isDisallowAnnotate() - Method in class ome.model.internal.Permissions
 
isDisallowDelete() - Method in class ome.model.internal.Permissions
 
isDisallowEdit() - Method in class ome.model.internal.Permissions
 
isDisallowLink() - Method in class ome.model.internal.Permissions
 
isDiskSpaceChecking() - Method in class ome.services.RawFileBean
getter disk overflow checking
isDiskSpaceChecking() - Method in class ome.services.RawPixelsBean
 
isDiskSpaceChecking() - Method in class ome.services.ThumbnailBean
 
isEmpty() - Method in class ome.services.query.Definitions
 
isEmptyEventContext() - Method in class ome.security.sharing.SharingSecuritySystem
 
isEnabled() - Method in class ome.security.auth.LdapConfig
 
isEnabled() - Method in class ome.services.mail.MailSender
 
isEncryptedConnection() - Method in class ome.formats.OMEROMetadataStoreClient
 
isEndTime() - Method in class omero.sys.ParametersI
Returns true if the map contains the end time parameter, false otherwise.
isError(SqlAction.DeleteLog) - Method in class ome.services.messages.DeleteLogMessage
 
ISession - Interface in ome.api
Start here: Session creation service for OMERO.
isExceptionThrown() - Method in class ome.system.UpgradeCheck
 
isExperimenter() - Method in class ome.parameters.Parameters
 
isExperimenter() - Method in class omero.sys.ParametersI
Returns true if the filter contains and ownerId parameter, false otherwise.
isExtendedGraphCritical(Set<Long>) - Method in class ome.services.ThumbnailCtx
Whether or not we're extended graph critical for a given set of dimension pools.
isf - Variable in class ome.services.util.Executor.Impl
 
isFailure() - Method in class omero.cmd.CmdCallbackI
Returns whether Status::FAILURE is contained in the flags variable of the Status instance.
isFileInRepo(String, long, Set<String>) - Method in class ome.util.SqlAction.Impl
 
isFileInRepo(String, long, Set<String>) - Method in interface ome.util.SqlAction
 
isFiltered(String) - Method in class ome.model.internal.Details
Was this collection filtered during creation?
isFloat() - Method in interface ome.api.RawPixelsStore
 
isFloat() - Method in class ome.io.bioformats.BfPixelBuffer
 
isFloat() - Method in class ome.io.bioformats.BfPixelsWrapper
 
isFloat() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
 
isFloat() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
 
isFloat() - Method in interface ome.io.nio.PixelBuffer
Returns whether or not the pixel buffer has floating point pixels.
isFloat() - Method in class ome.io.nio.RomioPixelBuffer
Implemented as specified by PixelBuffer I/F.
isFloat() - Method in class ome.services.RawPixelsBean
 
isFloat - Variable in class ome.util.PixelData
If the data is floating point.
isFloat() - Method in class ome.util.PixelData
Returns whether or not the data is floating point.
isFloat_async(AMD_RawPixelsStore_isFloat, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
isFloat_async(AMD_RawPixelsStore_isFloat, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
isFontBold() - Method in class pojos.ShapeSettingsData
Returns true if it is bold, false otherwise.
isFontItalic() - Method in class pojos.ShapeSettingsData
Returns true if it is italic, false otherwise.
isForce() - Method in class ome.services.graphs.GraphOpts
Deprecated.
 
isFSImage() - Method in class pojos.ImageData
Returns true is the image has been imported the new import strategy known as FS import, false if imported using the previous import approach (data duplication).
isGranted(Permissions.Role, Permissions.Right) - Method in class ome.model.internal.Permissions
tests that a given Permissions.Role has the given Permissions.Right.
isGranted(Permissions.Role, Permissions.Right) - Static method in class ome.security.basic.AllGroupsSecurityFilter
 
isGraphCritical(Details) - Method in class ome.security.basic.BasicSecuritySystem
 
isGraphCritical(Details) - Method in class ome.security.basic.CurrentDetails
 
isGraphCritical(Details) - Method in interface ome.security.SecuritySystem
Determines if the current security context has the possibility of corrupting consistent graphs.
isGraphCritical(Details) - Method in class ome.security.SecuritySystemHolder
 
isGraphCritical(Details) - Method in class ome.security.sharing.SharingSecuritySystem
 
isGraphsWrap() - Method in class omero.cmd.graphs.GraphRequestFactory
 
isGroup() - Method in class ome.parameters.Parameters
 
isGroup() - Method in class omero.sys.ParametersI
Returns true if the filter contains an groupId, false otherwise.
isGroupAnnotate(Current) - Method in class omero.model.PermissionsI
 
isGroupAnnotate() - Method in class pojos.PermissionData
Returns true if the group has annotate access i.e.
isGroupRead(Current) - Method in class omero.model.PermissionsI
 
isGroupRead() - Method in class pojos.PermissionData
Returns true if the group has read access i.e.
isGroupWrite(Current) - Method in class omero.model.PermissionsI
 
isGroupWrite() - Method in class pojos.PermissionData
Returns true if the group has write access i.e.
isHard() - Method in class ome.services.messages.stats.AbstractStatsMessage
 
IShare - Interface in ome.api
Provides method for sharing - collaboration process for images, datasets, projects.
isHidden() - Method in class pojos.FileData
Returns true if the file is hidden, false otherwise.
isIgnoreCaseLookup() - Method in interface ome.security.auth.RoleProvider
 
isIgnoreCaseLookup() - Method in class ome.security.auth.SimpleRoleProvider
 
isImagingEnvironmentDirty() - Method in class pojos.ImageAcquisitionData
Returns true if the StageLabel has been updated, false otherwise.
isImmutable(Object) - Method in class omero.util.IceMapper
 
isIncludeType(Class<? extends IObject>) - Method in class omero.cmd.graphs.ChildOptionI
Test if this child option adjusts graph traversal policy for the given child object class.
isInProgress() - Method in interface ome.api.ThumbnailStore
This returns the last available in progress state for a thumbnail.
isInProgress() - Method in class ome.services.ThumbnailBean
 
isInProgress_async(AMD_ThumbnailStore_isInProgress, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
 
isInRepo(long) - Method in class ome.services.scripts.ScriptRepoHelper
 
isInRepo(SqlAction, long) - Method in class ome.services.scripts.ScriptRepoHelper
 
isInSystemGroup(Long) - Method in class ome.security.SystemTypes
 
isInSystemGroup(Details) - Method in class ome.security.SystemTypes
 
isInUserGroup(Long) - Method in class ome.security.SystemTypes
 
isInUserGroup(Details) - Method in class ome.security.SystemTypes
 
isKeep() - Method in class ome.services.graphs.GraphEntry
Deprecated.
 
isLast(int) - Method in class omero.cmd.Helper
Returns true if this is the last step for the given request.
isLDAP() - Method in class pojos.ExperimenterData
Returns true if the user is connected via LDAP.
isLdapExperimenter(Long) - Method in class ome.util.SqlAction.Impl
 
isLdapExperimenter(Long) - Method in interface ome.util.SqlAction
Checks whether the specified experimenter ID has the ldap flag set.
isLeaves() - Method in class ome.parameters.Parameters
 
isLegalFsFile(FsFile) - Method in class ome.services.blitz.repo.path.ServerFilePathTransformer
Test if the given FsFile has been properly sanitized by the client.
isLeicaReader() - Method in class ome.formats.importer.OMEROWrapper
 
isLifetime() - Method in class pojos.ImageData
Returns true if the image is a lifetime image, false otherwise.
isLightSourceSettingsDirty() - Method in class pojos.ChannelAcquisitionData
Returns true if the light source settings has been updated, false otherwise.
isLinux() - Static method in class ome.services.blitz.util.CurrentPlatform
 
isLittleEndian() - Method in class ome.io.bioformats.BfPixelBuffer
Delegates to IFormatReader.isLittleEndian().
isLoaded() - Method in class ome.model.acquisition.Detector
 
isLoaded() - Method in class ome.model.acquisition.DetectorSettings
 
isLoaded() - Method in class ome.model.acquisition.Dichroic
 
isLoaded() - Method in class ome.model.acquisition.Filter
 
isLoaded() - Method in class ome.model.acquisition.FilterSet
 
isLoaded() - Method in class ome.model.acquisition.FilterSetEmissionFilterLink
 
isLoaded() - Method in class ome.model.acquisition.FilterSetExcitationFilterLink
 
isLoaded() - Method in class ome.model.acquisition.ImagingEnvironment
 
isLoaded() - Method in class ome.model.acquisition.Instrument
 
isLoaded() - Method in class ome.model.acquisition.LightPath
 
isLoaded() - Method in class ome.model.acquisition.LightPathEmissionFilterLink
 
isLoaded() - Method in class ome.model.acquisition.LightPathExcitationFilterLink
 
isLoaded() - Method in class ome.model.acquisition.LightSettings
 
isLoaded() - Method in class ome.model.acquisition.LightSource
 
isLoaded() - Method in class ome.model.acquisition.Microscope
 
isLoaded() - Method in class ome.model.acquisition.Objective
 
isLoaded() - Method in class ome.model.acquisition.ObjectiveSettings
 
isLoaded() - Method in class ome.model.acquisition.OTF
 
isLoaded() - Method in class ome.model.acquisition.StageLabel
 
isLoaded() - Method in class ome.model.acquisition.TransmittanceRange
 
isLoaded() - Method in class ome.model.annotations.Annotation
 
isLoaded() - Method in class ome.model.annotations.AnnotationAnnotationLink
 
isLoaded() - Method in class ome.model.annotations.ChannelAnnotationLink
 
isLoaded() - Method in class ome.model.annotations.DatasetAnnotationLink
 
isLoaded() - Method in class ome.model.annotations.DetectorAnnotationLink
 
isLoaded() - Method in class ome.model.annotations.DichroicAnnotationLink
 
isLoaded() - Method in class ome.model.annotations.ExperimenterAnnotationLink
 
isLoaded() - Method in class ome.model.annotations.ExperimenterGroupAnnotationLink
 
isLoaded() - Method in class ome.model.annotations.FilesetAnnotationLink
 
isLoaded() - Method in class ome.model.annotations.FilterAnnotationLink
 
isLoaded() - Method in class ome.model.annotations.ImageAnnotationLink
 
isLoaded() - Method in class ome.model.annotations.InstrumentAnnotationLink
 
isLoaded() - Method in class ome.model.annotations.LightPathAnnotationLink
 
isLoaded() - Method in class ome.model.annotations.LightSourceAnnotationLink
 
isLoaded() - Method in class ome.model.annotations.NamespaceAnnotationLink
 
isLoaded() - Method in class ome.model.annotations.NodeAnnotationLink
 
isLoaded() - Method in class ome.model.annotations.ObjectiveAnnotationLink
 
isLoaded() - Method in class ome.model.annotations.OriginalFileAnnotationLink
 
isLoaded() - Method in class ome.model.annotations.PlaneInfoAnnotationLink
 
isLoaded() - Method in class ome.model.annotations.PlateAcquisitionAnnotationLink
 
isLoaded() - Method in class ome.model.annotations.PlateAnnotationLink
 
isLoaded() - Method in class ome.model.annotations.ProjectAnnotationLink
 
isLoaded() - Method in class ome.model.annotations.ReagentAnnotationLink
 
isLoaded() - Method in class ome.model.annotations.RoiAnnotationLink
 
isLoaded() - Method in class ome.model.annotations.ScreenAnnotationLink
 
isLoaded() - Method in class ome.model.annotations.SessionAnnotationLink
 
isLoaded() - Method in class ome.model.annotations.ShapeAnnotationLink
 
isLoaded() - Method in class ome.model.annotations.WellAnnotationLink
 
isLoaded() - Method in class ome.model.containers.Dataset
 
isLoaded() - Method in class ome.model.containers.DatasetImageLink
 
isLoaded() - Method in class ome.model.containers.Project
 
isLoaded() - Method in class ome.model.containers.ProjectDatasetLink
 
isLoaded() - Method in class ome.model.core.Channel
 
isLoaded() - Method in class ome.model.core.Image
 
isLoaded() - Method in class ome.model.core.LogicalChannel
 
isLoaded() - Method in class ome.model.core.OriginalFile
 
isLoaded() - Method in class ome.model.core.Pixels
 
isLoaded() - Method in class ome.model.core.PixelsOriginalFileMap
 
isLoaded() - Method in class ome.model.core.PlaneInfo
 
isLoaded() - Method in class ome.model.display.ChannelBinding
 
isLoaded() - Method in class ome.model.display.CodomainMapContext
 
isLoaded() - Method in class ome.model.display.QuantumDef
 
isLoaded() - Method in class ome.model.display.RenderingDef
 
isLoaded() - Method in class ome.model.display.Thumbnail
 
isLoaded() - Method in class ome.model.enums.AcquisitionMode
 
isLoaded() - Method in class ome.model.enums.ArcType
 
isLoaded() - Method in class ome.model.enums.Binning
 
isLoaded() - Method in class ome.model.enums.ChecksumAlgorithm
 
isLoaded() - Method in class ome.model.enums.ContrastMethod
 
isLoaded() - Method in class ome.model.enums.Correction
 
isLoaded() - Method in class ome.model.enums.DetectorType
 
isLoaded() - Method in class ome.model.enums.DimensionOrder
 
isLoaded() - Method in class ome.model.enums.EventType
 
isLoaded() - Method in class ome.model.enums.ExperimentType
 
isLoaded() - Method in class ome.model.enums.Family
 
isLoaded() - Method in class ome.model.enums.FilamentType
 
isLoaded() - Method in class ome.model.enums.FilterType
 
isLoaded() - Method in class ome.model.enums.Format
 
isLoaded() - Method in class ome.model.enums.Illumination
 
isLoaded() - Method in class ome.model.enums.Immersion
 
isLoaded() - Method in class ome.model.enums.LaserMedium
 
isLoaded() - Method in class ome.model.enums.LaserType
 
isLoaded() - Method in class ome.model.enums.Medium
 
isLoaded() - Method in class ome.model.enums.MicrobeamManipulationType
 
isLoaded() - Method in class ome.model.enums.MicroscopeType
 
isLoaded() - Method in class ome.model.enums.PhotometricInterpretation
 
isLoaded() - Method in class ome.model.enums.PixelsType
 
isLoaded() - Method in class ome.model.enums.Pulse
 
isLoaded() - Method in class ome.model.enums.RenderingModel
 
isLoaded() - Method in class ome.model.experiment.Experiment
 
isLoaded() - Method in class ome.model.experiment.MicrobeamManipulation
 
isLoaded() - Method in class ome.model.fs.Fileset
 
isLoaded() - Method in class ome.model.fs.FilesetEntry
 
isLoaded() - Method in class ome.model.fs.FilesetJobLink
 
isLoaded() - Method in class ome.model.internal.Link
 
isLoaded() - Method in interface ome.model.IObject
transient field (not stored in the DB) which specifies whether this object has been loaded from the DB or is only a wrapper around the ID.
isLoaded() - Method in class ome.model.jobs.Job
 
isLoaded() - Method in class ome.model.jobs.JobOriginalFileLink
 
isLoaded() - Method in class ome.model.jobs.JobStatus
 
isLoaded() - Method in class ome.model.meta.DBPatch
 
isLoaded() - Method in class ome.model.meta.Event
 
isLoaded() - Method in class ome.model.meta.EventLog
 
isLoaded() - Method in class ome.model.meta.Experimenter
 
isLoaded() - Method in class ome.model.meta.ExperimenterGroup
 
isLoaded() - Method in class ome.model.meta.ExternalInfo
 
isLoaded() - Method in class ome.model.meta.GroupExperimenterMap
 
isLoaded() - Method in class ome.model.meta.Namespace
 
isLoaded() - Method in class ome.model.meta.Node
 
isLoaded() - Method in class ome.model.meta.Session
 
isLoaded() - Method in class ome.model.meta.ShareMember
 
isLoaded() - Method in class ome.model.roi.Roi
 
isLoaded() - Method in class ome.model.roi.Shape
 
isLoaded() - Method in class ome.model.screen.Plate
 
isLoaded() - Method in class ome.model.screen.PlateAcquisition
 
isLoaded() - Method in class ome.model.screen.Reagent
 
isLoaded() - Method in class ome.model.screen.Screen
 
isLoaded() - Method in class ome.model.screen.ScreenPlateLink
 
isLoaded() - Method in class ome.model.screen.Well
 
isLoaded() - Method in class ome.model.screen.WellReagentLink
 
isLoaded() - Method in class ome.model.screen.WellSample
 
isLoaded() - Method in class ome.model.stats.StatsInfo
 
isLoaded() - Method in class pojos.DataObject
Returns true if the object is loaded, false otherwise.
isLockedByOthers() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
 
isMacOSX() - Static method in class ome.services.blitz.util.CurrentPlatform
 
isMatch(GraphPolicy.Details, String) - Method in interface ome.services.graphs.GraphPolicyRulePredicate
If this predicate is satisfied by the given object.
isMatch(GraphPolicy.Details, String) - Method in class ome.services.graphs.GroupPredicate
 
isMatch(GraphPolicy.Details, String) - Method in class ome.services.graphs.PermissionsPredicate
 
isMemberOfGroup(long) - Method in class pojos.ExperimenterData
Checks if supplied group id matches any group to which the current experimenter belongs to.
isMergedBatches() - Method in interface ome.api.Search
Returns the current merged-batches setting.
isMergedBatches() - Method in class ome.services.SearchBean
 
isMergedBatches_async(AMD_Search_isMergedBatches, Current) - Method in class ome.services.blitz.impl.SearchI
 
isMinMaxSet() - Method in class ome.formats.importer.OMEROWrapper
 
isModified() - Method in class ome.services.AbstractStatefulBean
 
isModified() - Method in class ome.services.RawFileBean
Extends the check of the AbstractStatefulBean.modified flag performed by super with an additional check of the actual file size against the value stored in the database
isMovieFile() - Method in class pojos.FileAnnotationData
Returns true if it is a movie file.
isMutable() - Method in class ome.model.units.GenericEnumType
 
isMutable() - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
 
isNoiseReduction() - Method in class omeis.providers.re.metadata.StatsFactory
Returns true if the flag is on, false otherwise.
isNonPrivate(EventContext) - Method in class ome.security.basic.AbstractSecurityFilter
 
isNull() - Method in class ome.services.graphs.GraphEntry
Deprecated.
 
isNullablePrimitive(Class<?>) - Static method in class omero.util.IceMapper
 
isObjectiveSettingsDirty() - Method in class pojos.ImageAcquisitionData
Returns true if the objective settings has been updated, false otherwise.
isOMERO - Variable in class loci.ome.io.OMECredentials
 
isOrphan() - Method in class ome.parameters.Parameters
 
isOverrideKeep(int, QueryBuilder, String) - Method in class ome.services.graphs.AbstractHierarchyGraphSpec
Deprecated.
If BaseGraphSpec.overrideKeep() returns true for a subclass, then this method will likely want to (at least sometimes) return a true value.
isOverrideKeep(int, QueryBuilder, String) - Method in class ome.services.graphs.AnnotationGraphSpec
Deprecated.
 
isOverrideKeep(int, QueryBuilder, String) - Method in class ome.services.graphs.LightSourceGraphSpec
Deprecated.
 
isOwnerOrSupervisor(IObject) - Method in class ome.security.basic.BasicSecuritySystem
tests whether or not the current user is either the owner of this entity, or the superivsor of this entity, for example as root or as group owner.
isOwnerOrSupervisor(IObject) - Method in class ome.security.basic.CurrentDetails
 
isPagination() - Method in class ome.parameters.Parameters
 
isPagination() - Method in class omero.sys.ParametersI
Returns true if the filter contains a limit OR a offset, false otherwise.
isPasswordRequired(Long) - Method in class ome.security.auth.PasswordUtil
Returns a boolean based on the supplied user ID and system property setting.
isPixelsTypeSigned() - Method in class ome.services.RenderingBean
Implemented as specified by the RenderingEngine interface.
isPixelsTypeSigned() - Method in class omeis.providers.re.Renderer
Returns true if the pixels type is signed, false otherwise.
isPixelsTypeSigned() - Method in interface omeis.providers.re.RenderingEngine
Returns true if the pixels type is signed, false otherwise.
isPixelsTypeSigned_async(AMD_RenderingEngine_isPixelsTypeSigned, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
isPrefs() - Method in class ome.system.Preference
 
isPrimaryColorEnabled() - Method in class omeis.providers.re.Optimizations
Returns true if the primary color optimization is enabled, and false if it is not.
isPrimitive(Class<?>) - Method in class omero.util.IceMapper
 
isPropertyAccessible(String, String) - Method in class ome.services.graphs.GraphPathBean
Find if the given property can be accessed.
isProxyAccepted(boolean, String, ProcessorPrx, Current) - Method in class ome.services.blitz.impl.ProcessorCallbackI
Callback method called by the remote processor instance.
isReadOnly() - Method in class ome.services.sessions.SessionContextImpl
 
isReadOnly() - Method in interface ome.system.EventContext
 
isReadOnly - Variable in class ome.system.SimpleEventContext
 
isReadOnly() - Method in class ome.system.SimpleEventContext
 
isReadOnly() - Method in class pojos.ShapeData
Returns true if the object a read-only object, false otherwise.
isReady() - Method in class ome.security.basic.BasicSecuritySystem
isReady() - Method in class ome.security.basic.CurrentDetails
Checks if the current Thread has non-null Experimenter, Event, and ExperimenterGroup, required for proper functioning of the security system.
isReady() - Method in interface ome.security.SecuritySystem
checks if this SecuritySystem instance is in a valid state.
isReady() - Method in class ome.security.SecuritySystemHolder
 
isReady() - Method in class ome.security.sharing.SharingSecuritySystem
 
isReap() - Method in class ome.services.graphs.GraphEntry
Deprecated.
 
isRestricted(IObject) - Method in class ome.security.policy.BasePolicy
 
isRestricted(IObject) - Method in class ome.security.policy.BinaryAccessPolicy
 
isRestricted(String, IObject) - Method in class ome.security.policy.DefaultPolicyService
 
isRestricted(IObject) - Method in interface ome.security.policy.Policy
Checks whether or not this instance would throw a SecurityViolation if the same instance were passed to Policy.checkRestriction(IObject).
isRestricted(String, IObject) - Method in interface ome.security.policy.PolicyService
Ask each configured Policy instance with the given name argument if it considers the restriction active for the given IObject argument.
isRestricted(String, Current) - Method in class omero.model.PermissionsI
 
isRetry() - Method in class ome.io.messages.MissingPyramidMessage
 
isReturnUnloaded() - Method in interface ome.api.Search
Returns the current return-unloaded setting.
isReturnUnloaded() - Method in class ome.services.SearchBean
 
isReturnUnloaded_async(AMD_Search_isReturnUnloaded, Current) - Method in class ome.services.blitz.impl.SearchI
 
isRoot - Variable in class ome.services.blitz.repo.CheckedPath
 
isRootUser(Experimenter) - Method in class ome.system.Roles
 
isSecure() - Method in class omero.client
Specifies whether or not this client was created via a call to client.createClient(boolean) with a boolean of false.
isSend(int) - Method in class ome.formats.importer.util.ErrorHandler
Check if files need sending at error container index
isSet(Permissions.Flag) - Method in class ome.model.internal.Permissions
tests that a given Permissions.Flag is set.
isShare(EventContext) - Method in class ome.security.basic.AbstractSecurityFilter
 
isSigned() - Method in interface ome.api.RawPixelsStore
 
isSigned() - Method in class ome.io.bioformats.BfPixelBuffer
 
isSigned() - Method in class ome.io.bioformats.BfPixelsWrapper
 
isSigned() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
 
isSigned() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
 
isSigned() - Method in interface ome.io.nio.PixelBuffer
Returns whether or not the pixel buffer has signed pixels.
isSigned() - Method in class ome.io.nio.RomioPixelBuffer
Implemented as specified by PixelBuffer I/F.
isSigned() - Method in class ome.services.RawPixelsBean
 
isSigned - Variable in class ome.util.PixelData
If the data is signed.
isSigned() - Method in class ome.util.PixelData
Returns whether or not the data is signed.
isSigned_async(AMD_RawPixelsStore_isSigned, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
isSigned_async(AMD_RawPixelsStore_isSigned, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
isSingleton() - Method in class ome.security.basic.EventListenersFactoryBean
being a singleton implies that this FactoryBean will only ever create one instance.
isSoft() - Method in class ome.services.graphs.GraphEntry
Deprecated.
 
isSPWReader() - Method in class ome.formats.importer.OMEROWrapper
 
isStageLabelDirty() - Method in class pojos.ImageAcquisitionData
Returns true if the position has been updated, false otherwise.
isStartTime() - Method in class omero.sys.ParametersI
Returns true if the map contains the start time parameter, false otherwise.
isStatisticsEnabled() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
Are statistics logged
isStopSet() - Method in class ome.services.eventlogs.EventLogLoader
Returns true if the stop flag has been set on this instance.
isSyncOnLogin() - Method in class ome.security.auth.LdapConfig
 
isSystemGroup(ExperimenterGroup) - Method in class ome.system.Roles
 
isSystemType(Class<? extends IObject>) - Method in class ome.security.basic.BasicSecuritySystem
classes which cannot be created by regular users.
isSystemType(Class<? extends IObject>) - Method in interface ome.security.SecuritySystem
checks if instances of the given type are "System-Types".
isSystemType(Class<? extends IObject>) - Method in class ome.security.SecuritySystemHolder
 
isSystemType(Class<? extends IObject>) - Method in class ome.security.sharing.SharingSecuritySystem
 
isSystemType(Class<?>) - Method in class ome.security.SystemTypes
classes which cannot be created by regular users.
isTargetNamespace(String) - Method in class omero.cmd.graphs.ChildOptionI
Test if this child option adjusts graph traversal policy for child objects that are annotations in the given namespace.
isThisType(String, boolean) - Method in class loci.ome.io.OmeroReader
 
isThisType(String, boolean) - Method in class ome.io.bioformats.OmeroPixelsPyramidReader
 
isThisType(String, boolean) - Method in class ome.services.formats.OmeroReader
 
isThisType(RandomAccessInputStream) - Method in class ome.services.formats.OmeroReader
 
isThreadSafe() - Method in class ome.services.messages.AbstractSessionMessage
 
isThreadSafe() - Method in class ome.util.messages.InternalMessage
Returns true if this message can safely be passed to another Thread.
isThumbnailCached(long) - Method in class ome.services.ThumbnailCtx
Checks to see if a thumbnail is in the on disk cache or not.
isTransient(Object) - Method in class ome.security.basic.OmeroInterceptor
 
isTypeSigned(PixelsType) - Static method in class omeis.providers.re.data.PlaneFactory
A static helper method to retrieve pixel byte signage.
isUnique() - Method in class ome.parameters.Filter
check uniqueness for this query.
isUnique() - Method in class ome.parameters.Parameters
 
isUnknown() - Static method in class ome.services.blitz.util.CurrentPlatform
 
isUnloaded(Object) - Static method in class ome.tools.hibernate.HibernateUtils
 
isUpgradeNeeded() - Method in class ome.formats.importer.ImportConfig
Check online to see if this is the current version
isUpgradeNeeded() - Method in class ome.system.UpgradeCheck
 
isUseProjections() - Method in interface ome.api.Search
Returns the current use-projection setting.
isUseProjections() - Method in class ome.services.SearchBean
 
isUseProjections_async(AMD_Search_isUseProjections, Current) - Method in class ome.services.blitz.impl.SearchI
 
isUserAnnotate(Current) - Method in class omero.model.PermissionsI
 
isUserGroup(ExperimenterGroup) - Method in class ome.system.Roles
 
isUserRead(Current) - Method in class omero.model.PermissionsI
 
isUserRead() - Method in class pojos.PermissionData
Returns true if the user has read access, false otherwise.
isUserWrite(Current) - Method in class omero.model.PermissionsI
 
isUserWrite() - Method in class pojos.PermissionData
Returns true if the user has write access, false otherwise.
isValid() - Method in class ome.model.acquisition.Arc
 
isValid() - Method in class ome.model.acquisition.Detector
 
isValid() - Method in class ome.model.acquisition.DetectorSettings
 
isValid() - Method in class ome.model.acquisition.Dichroic
 
isValid() - Method in class ome.model.acquisition.Filament
 
isValid() - Method in class ome.model.acquisition.Filter
 
isValid() - Method in class ome.model.acquisition.FilterSet
 
isValid() - Method in class ome.model.acquisition.FilterSetEmissionFilterLink
 
isValid() - Method in class ome.model.acquisition.FilterSetExcitationFilterLink
 
isValid() - Method in class ome.model.acquisition.GenericExcitationSource
 
isValid() - Method in class ome.model.acquisition.ImagingEnvironment
 
isValid() - Method in class ome.model.acquisition.Instrument
 
isValid() - Method in class ome.model.acquisition.Laser
 
isValid() - Method in class ome.model.acquisition.LightEmittingDiode
 
isValid() - Method in class ome.model.acquisition.LightPath
 
isValid() - Method in class ome.model.acquisition.LightPathEmissionFilterLink
 
isValid() - Method in class ome.model.acquisition.LightPathExcitationFilterLink
 
isValid() - Method in class ome.model.acquisition.LightSettings
 
isValid() - Method in class ome.model.acquisition.LightSource
 
isValid() - Method in class ome.model.acquisition.Microscope
 
isValid() - Method in class ome.model.acquisition.Objective
 
isValid() - Method in class ome.model.acquisition.ObjectiveSettings
 
isValid() - Method in class ome.model.acquisition.OTF
 
isValid() - Method in class ome.model.acquisition.StageLabel
 
isValid() - Method in class ome.model.acquisition.TransmittanceRange
 
isValid() - Method in class ome.model.annotations.Annotation
 
isValid() - Method in class ome.model.annotations.AnnotationAnnotationLink
 
isValid() - Method in class ome.model.annotations.BasicAnnotation
 
isValid() - Method in class ome.model.annotations.BooleanAnnotation
 
isValid() - Method in class ome.model.annotations.ChannelAnnotationLink
 
isValid() - Method in class ome.model.annotations.CommentAnnotation
 
isValid() - Method in class ome.model.annotations.DatasetAnnotationLink
 
isValid() - Method in class ome.model.annotations.DetectorAnnotationLink
 
isValid() - Method in class ome.model.annotations.DichroicAnnotationLink
 
isValid() - Method in class ome.model.annotations.DoubleAnnotation
 
isValid() - Method in class ome.model.annotations.ExperimenterAnnotationLink
 
isValid() - Method in class ome.model.annotations.ExperimenterGroupAnnotationLink
 
isValid() - Method in class ome.model.annotations.FileAnnotation
 
isValid() - Method in class ome.model.annotations.FilesetAnnotationLink
 
isValid() - Method in class ome.model.annotations.FilterAnnotationLink
 
isValid() - Method in class ome.model.annotations.ImageAnnotationLink
 
isValid() - Method in class ome.model.annotations.InstrumentAnnotationLink
 
isValid() - Method in class ome.model.annotations.LightPathAnnotationLink
 
isValid() - Method in class ome.model.annotations.LightSourceAnnotationLink
 
isValid() - Method in class ome.model.annotations.ListAnnotation
 
isValid() - Method in class ome.model.annotations.LongAnnotation
 
isValid() - Method in class ome.model.annotations.MapAnnotation
 
isValid() - Method in class ome.model.annotations.NamespaceAnnotationLink
 
isValid() - Method in class ome.model.annotations.NodeAnnotationLink
 
isValid() - Method in class ome.model.annotations.NumericAnnotation
 
isValid() - Method in class ome.model.annotations.ObjectiveAnnotationLink
 
isValid() - Method in class ome.model.annotations.OriginalFileAnnotationLink
 
isValid() - Method in class ome.model.annotations.PlaneInfoAnnotationLink
 
isValid() - Method in class ome.model.annotations.PlateAcquisitionAnnotationLink
 
isValid() - Method in class ome.model.annotations.PlateAnnotationLink
 
isValid() - Method in class ome.model.annotations.ProjectAnnotationLink
 
isValid() - Method in class ome.model.annotations.ReagentAnnotationLink
 
isValid() - Method in class ome.model.annotations.RoiAnnotationLink
 
isValid() - Method in class ome.model.annotations.ScreenAnnotationLink
 
isValid() - Method in class ome.model.annotations.SessionAnnotationLink
 
isValid() - Method in class ome.model.annotations.ShapeAnnotationLink
 
isValid() - Method in class ome.model.annotations.TagAnnotation
 
isValid() - Method in class ome.model.annotations.TermAnnotation
 
isValid() - Method in class ome.model.annotations.TextAnnotation
 
isValid() - Method in class ome.model.annotations.TimestampAnnotation
 
isValid() - Method in class ome.model.annotations.TypeAnnotation
 
isValid() - Method in class ome.model.annotations.WellAnnotationLink
 
isValid() - Method in class ome.model.annotations.XmlAnnotation
 
isValid() - Method in class ome.model.containers.Dataset
 
isValid() - Method in class ome.model.containers.DatasetImageLink
 
isValid() - Method in class ome.model.containers.Project
 
isValid() - Method in class ome.model.containers.ProjectDatasetLink
 
isValid() - Method in class ome.model.core.Channel
 
isValid() - Method in class ome.model.core.Image
 
isValid() - Method in class ome.model.core.LogicalChannel
 
isValid() - Method in class ome.model.core.OriginalFile
 
isValid() - Method in class ome.model.core.Pixels
 
isValid() - Method in class ome.model.core.PixelsOriginalFileMap
 
isValid() - Method in class ome.model.core.PlaneInfo
 
isValid() - Method in class ome.model.display.ChannelBinding
 
isValid() - Method in class ome.model.display.CodomainMapContext
 
isValid() - Method in class ome.model.display.ContrastStretchingContext
 
isValid() - Method in class ome.model.display.PlaneSlicingContext
 
isValid() - Method in class ome.model.display.QuantumDef
 
isValid() - Method in class ome.model.display.RenderingDef
 
isValid() - Method in class ome.model.display.ReverseIntensityContext
 
isValid() - Method in class ome.model.display.Thumbnail
 
isValid() - Method in class ome.model.enums.AcquisitionMode
 
isValid() - Method in class ome.model.enums.ArcType
 
isValid() - Method in class ome.model.enums.Binning
 
isValid() - Method in class ome.model.enums.ChecksumAlgorithm
 
isValid() - Method in class ome.model.enums.ContrastMethod
 
isValid() - Method in class ome.model.enums.Correction
 
isValid() - Method in class ome.model.enums.DetectorType
 
isValid() - Method in class ome.model.enums.DimensionOrder
 
isValid() - Method in class ome.model.enums.EventType
 
isValid() - Method in class ome.model.enums.ExperimentType
 
isValid() - Method in class ome.model.enums.Family
 
isValid() - Method in class ome.model.enums.FilamentType
 
isValid() - Method in class ome.model.enums.FilterType
 
isValid() - Method in class ome.model.enums.Format
 
isValid() - Method in class ome.model.enums.Illumination
 
isValid() - Method in class ome.model.enums.Immersion
 
isValid() - Method in class ome.model.enums.LaserMedium
 
isValid() - Method in class ome.model.enums.LaserType
 
isValid() - Method in class ome.model.enums.Medium
 
isValid() - Method in class ome.model.enums.MicrobeamManipulationType
 
isValid() - Method in class ome.model.enums.MicroscopeType
 
isValid() - Method in class ome.model.enums.PhotometricInterpretation
 
isValid() - Method in class ome.model.enums.PixelsType
 
isValid() - Method in class ome.model.enums.Pulse
 
isValid() - Method in class ome.model.enums.RenderingModel
 
isValid() - Method in class ome.model.experiment.Experiment
 
isValid() - Method in class ome.model.experiment.MicrobeamManipulation
 
isValid() - Method in class ome.model.fs.Fileset
 
isValid() - Method in class ome.model.fs.FilesetEntry
 
isValid() - Method in class ome.model.fs.FilesetJobLink
 
isValid() - Method in class ome.model.internal.Link
 
isValid() - Method in interface ome.model.IObject
calls the class-specific validator for this instance and returns the value from Validation.isValid()
isValid() - Method in class ome.model.jobs.ImportJob
 
isValid() - Method in class ome.model.jobs.IndexingJob
 
isValid() - Method in class ome.model.jobs.IntegrityCheckJob
 
isValid() - Method in class ome.model.jobs.Job
 
isValid() - Method in class ome.model.jobs.JobOriginalFileLink
 
isValid() - Method in class ome.model.jobs.JobStatus
 
isValid() - Method in class ome.model.jobs.MetadataImportJob
 
isValid() - Method in class ome.model.jobs.ParseJob
 
isValid() - Method in class ome.model.jobs.PixelDataJob
 
isValid() - Method in class ome.model.jobs.ScriptJob
 
isValid() - Method in class ome.model.jobs.ThumbnailGenerationJob
 
isValid() - Method in class ome.model.jobs.UploadJob
 
isValid() - Method in class ome.model.meta.DBPatch
 
isValid() - Method in class ome.model.meta.Event
 
isValid() - Method in class ome.model.meta.EventLog
 
isValid() - Method in class ome.model.meta.Experimenter
 
isValid() - Method in class ome.model.meta.ExperimenterGroup
 
isValid() - Method in class ome.model.meta.ExternalInfo
 
isValid() - Method in class ome.model.meta.GroupExperimenterMap
 
isValid() - Method in class ome.model.meta.Namespace
 
isValid() - Method in class ome.model.meta.Node
 
isValid() - Method in class ome.model.meta.Session
 
isValid() - Method in class ome.model.meta.Share
 
isValid() - Method in class ome.model.meta.ShareMember
 
isValid() - Method in class ome.model.roi.Ellipse
 
isValid() - Method in class ome.model.roi.Label
 
isValid() - Method in class ome.model.roi.Line
 
isValid() - Method in class ome.model.roi.Mask
 
isValid() - Method in class ome.model.roi.Path
 
isValid() - Method in class ome.model.roi.Point
 
isValid() - Method in class ome.model.roi.Polygon
 
isValid() - Method in class ome.model.roi.Polyline
 
isValid() - Method in class ome.model.roi.Rect
 
isValid() - Method in class ome.model.roi.Roi
 
isValid() - Method in class ome.model.roi.Shape
 
isValid() - Method in class ome.model.screen.Plate
 
isValid() - Method in class ome.model.screen.PlateAcquisition
 
isValid() - Method in class ome.model.screen.Reagent
 
isValid() - Method in class ome.model.screen.Screen
 
isValid() - Method in class ome.model.screen.ScreenPlateLink
 
isValid() - Method in class ome.model.screen.Well
 
isValid() - Method in class ome.model.screen.WellReagentLink
 
isValid() - Method in class ome.model.screen.WellSample
 
isValid() - Method in class ome.model.stats.StatsInfo
 
isValid() - Method in class ome.util.Validation
 
isVisible() - Method in class pojos.ShapeData
Returns true if the shape is visible, false otherwise.
isVoid(Current) - Method in class ome.services.blitz.util.IceMethodInvoker
Checks for a void return type, which is needed to know what type of ice_response() method to invoke.
isVoid - Variable in class ome.services.throttling.Task
 
isVoid() - Method in class omero.util.IceMapper
Returns true only if the current mapping is the IceMapper.VOID mapping.
isWindows() - Method in class ome.formats.importer.transfers.AbstractFileTransfer
Uses os.name to determine whether or not this JVM is running under Windows.
isWindows() - Static method in class ome.services.blitz.util.CurrentPlatform
 
isWorldAnnotate(Current) - Method in class omero.model.PermissionsI
 
isWorldRead(Current) - Method in class omero.model.PermissionsI
 
isWorldRead() - Method in class pojos.PermissionData
Returns true if the world has read access, false otherwise.
isWorldWrite(Current) - Method in class omero.model.PermissionsI
 
isWorldWrite() - Method in class pojos.PermissionData
Returns true if the world has write access, false otherwise.
isWrapperArray(Class<?>) - Static method in class omero.util.IceMapper
 
isWrite() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
Whether or not this instance is in writing-mode.
isXYPlanar() - Method in class omeis.providers.re.data.Plane2D
Returns true if the plane is an XY-plane, false otherwise.
itemCount - Variable in class ome.model.meta.Share
 
ITEMCOUNT - Static variable in class ome.model.meta.Share
 
iterate() - Method in class ome.services.scripts.ScriptRepoHelper
 
iterateAnnotationLinks() - Method in class ome.model.acquisition.Detector
should be used rather than accessing the annotationLinks set directly.
iterateAnnotationLinks() - Method in class ome.model.acquisition.Dichroic
should be used rather than accessing the annotationLinks set directly.
iterateAnnotationLinks() - Method in class ome.model.acquisition.Filter
should be used rather than accessing the annotationLinks set directly.
iterateAnnotationLinks() - Method in class ome.model.acquisition.Instrument
should be used rather than accessing the annotationLinks set directly.
iterateAnnotationLinks() - Method in class ome.model.acquisition.LightPath
should be used rather than accessing the annotationLinks set directly.
iterateAnnotationLinks() - Method in class ome.model.acquisition.LightSource
should be used rather than accessing the annotationLinks set directly.
iterateAnnotationLinks() - Method in class ome.model.acquisition.Objective
should be used rather than accessing the annotationLinks set directly.
iterateAnnotationLinks() - Method in class ome.model.annotations.Annotation
should be used rather than accessing the annotationLinks set directly.
iterateAnnotationLinks() - Method in class ome.model.containers.Dataset
should be used rather than accessing the annotationLinks set directly.
iterateAnnotationLinks() - Method in class ome.model.containers.Project
should be used rather than accessing the annotationLinks set directly.
iterateAnnotationLinks() - Method in class ome.model.core.Channel
should be used rather than accessing the annotationLinks set directly.
iterateAnnotationLinks() - Method in class ome.model.core.Image
should be used rather than accessing the annotationLinks set directly.
iterateAnnotationLinks() - Method in class ome.model.core.OriginalFile
should be used rather than accessing the annotationLinks set directly.
iterateAnnotationLinks() - Method in class ome.model.core.PlaneInfo
should be used rather than accessing the annotationLinks set directly.
iterateAnnotationLinks() - Method in class ome.model.fs.Fileset
should be used rather than accessing the annotationLinks set directly.
iterateAnnotationLinks() - Method in interface ome.model.IAnnotated
 
iterateAnnotationLinks() - Method in class ome.model.meta.Experimenter
should be used rather than accessing the annotationLinks set directly.
iterateAnnotationLinks() - Method in class ome.model.meta.ExperimenterGroup
should be used rather than accessing the annotationLinks set directly.
iterateAnnotationLinks() - Method in class ome.model.meta.Namespace
should be used rather than accessing the annotationLinks set directly.
iterateAnnotationLinks() - Method in class ome.model.meta.Node
should be used rather than accessing the annotationLinks set directly.
iterateAnnotationLinks() - Method in class ome.model.meta.Session
should be used rather than accessing the annotationLinks set directly.
iterateAnnotationLinks() - Method in class ome.model.roi.Roi
should be used rather than accessing the annotationLinks set directly.
iterateAnnotationLinks() - Method in class ome.model.roi.Shape
should be used rather than accessing the annotationLinks set directly.
iterateAnnotationLinks() - Method in class ome.model.screen.Plate
should be used rather than accessing the annotationLinks set directly.
iterateAnnotationLinks() - Method in class ome.model.screen.PlateAcquisition
should be used rather than accessing the annotationLinks set directly.
iterateAnnotationLinks() - Method in class ome.model.screen.Reagent
should be used rather than accessing the annotationLinks set directly.
iterateAnnotationLinks() - Method in class ome.model.screen.Screen
should be used rather than accessing the annotationLinks set directly.
iterateAnnotationLinks() - Method in class ome.model.screen.Well
should be used rather than accessing the annotationLinks set directly.
iterateChannels() - Method in class ome.model.core.LogicalChannel
should be used rather than accessing the channels set directly.
iterateChannels() - Method in class ome.model.core.Pixels
should be used rather than accessing the channels set directly.
iterateDatasetLinks() - Method in class ome.model.containers.Project
should be used rather than accessing the datasetLinks set directly.
iterateDatasetLinks() - Method in class ome.model.core.Image
should be used rather than accessing the datasetLinks set directly.
iterateDetector() - Method in class ome.model.acquisition.Instrument
should be used rather than accessing the detector set directly.
iterateDichroic() - Method in class ome.model.acquisition.Instrument
should be used rather than accessing the dichroic set directly.
iterateEmissionFilterLink() - Method in class ome.model.acquisition.Filter
should be used rather than accessing the emissionFilterLink set directly.
iterateEmissionFilterLink() - Method in class ome.model.acquisition.FilterSet
should be used rather than accessing the emissionFilterLink set directly.
iterateEmissionFilterLink() - Method in class ome.model.acquisition.LightPath
should be used rather than accessing the emissionFilterLink set directly.
iterateEvents() - Method in class ome.model.meta.Session
should be used rather than accessing the events set directly.
iterateExcitationFilterLink() - Method in class ome.model.acquisition.Filter
should be used rather than accessing the excitationFilterLink set directly.
iterateExcitationFilterLink() - Method in class ome.model.acquisition.FilterSet
should be used rather than accessing the excitationFilterLink set directly.
iterateExcitationFilterLink() - Method in class ome.model.acquisition.LightPath
should be used rather than accessing the excitationFilterLink set directly.
iterateFilesetEntries() - Method in class ome.model.core.OriginalFile
should be used rather than accessing the filesetEntries set directly.
iterateFilter() - Method in class ome.model.acquisition.Instrument
should be used rather than accessing the filter set directly.
iterateFilterSet() - Method in class ome.model.acquisition.Instrument
should be used rather than accessing the filterSet set directly.
iterateGroupExperimenterMap() - Method in class ome.model.meta.Experimenter
should be used rather than accessing the groupExperimenterMap set directly.
iterateGroupExperimenterMap() - Method in class ome.model.meta.ExperimenterGroup
should be used rather than accessing the groupExperimenterMap set directly.
iterateImageLinks() - Method in class ome.model.containers.Dataset
should be used rather than accessing the imageLinks set directly.
iterateImages() - Method in class ome.model.fs.Fileset
should be used rather than accessing the images set directly.
iterateJobLinks() - Method in class ome.model.fs.Fileset
should be used rather than accessing the jobLinks set directly.
iterateLightSource() - Method in class ome.model.acquisition.Instrument
should be used rather than accessing the lightSource set directly.
iterateLightSourceSettings() - Method in class ome.model.experiment.MicrobeamManipulation
should be used rather than accessing the lightSourceSettings set directly.
iterateLogs() - Method in class ome.model.meta.Event
should be used rather than accessing the logs set directly.
iterateMicrobeamManipulation() - Method in class ome.model.experiment.Experiment
should be used rather than accessing the microbeamManipulation set directly.
iterateObjective() - Method in class ome.model.acquisition.Instrument
should be used rather than accessing the objective set directly.
iterateOriginalFileLinks() - Method in class ome.model.jobs.Job
should be used rather than accessing the originalFileLinks set directly.
iterateOtf() - Method in class ome.model.acquisition.Instrument
should be used rather than accessing the otf set directly.
iteratePixels() - Method in class ome.model.core.Image
should be used rather than accessing the pixels set directly.
iteratePixelsFileMaps() - Method in class ome.model.core.OriginalFile
should be used rather than accessing the pixelsFileMaps set directly.
iteratePixelsFileMaps() - Method in class ome.model.core.Pixels
should be used rather than accessing the pixelsFileMaps set directly.
iteratePlaneInfo() - Method in class ome.model.core.Pixels
should be used rather than accessing the planeInfo set directly.
iteratePlateAcquisitions() - Method in class ome.model.screen.Plate
should be used rather than accessing the plateAcquisitions set directly.
iteratePlateLinks() - Method in class ome.model.screen.Screen
should be used rather than accessing the plateLinks set directly.
iterateProjectLinks() - Method in class ome.model.containers.Dataset
should be used rather than accessing the projectLinks set directly.
iterateReagentLinks() - Method in class ome.model.screen.Well
should be used rather than accessing the reagentLinks set directly.
iterateReagents() - Method in class ome.model.screen.Screen
should be used rather than accessing the reagents set directly.
iterateRois() - Method in class ome.model.core.Image
should be used rather than accessing the rois set directly.
iterateScreenLinks() - Method in class ome.model.screen.Plate
should be used rather than accessing the screenLinks set directly.
iterateSessions() - Method in class ome.model.meta.Node
should be used rather than accessing the sessions set directly.
iterateSettings() - Method in class ome.model.core.Pixels
should be used rather than accessing the settings set directly.
iterateShapes() - Method in class ome.model.roi.Roi
should be used rather than accessing the shapes set directly.
iterateSpatialDomainEnhancement() - Method in class ome.model.display.RenderingDef
should be used rather than accessing the spatialDomainEnhancement set directly.
iterateThumbnails() - Method in class ome.model.core.Pixels
should be used rather than accessing the thumbnails set directly.
iterateUsedFiles() - Method in class ome.model.fs.Fileset
should be used rather than accessing the usedFiles set directly.
iterateWaveRendering() - Method in class ome.model.display.RenderingDef
should be used rather than accessing the waveRendering set directly.
iterateWellLinks() - Method in class ome.model.screen.Reagent
should be used rather than accessing the wellLinks set directly.
iterateWells() - Method in class ome.model.screen.Plate
should be used rather than accessing the wells set directly.
iterateWellSample() - Method in class ome.model.screen.PlateAcquisition
should be used rather than accessing the wellSample set directly.
iterateWellSamples() - Method in class ome.model.core.Image
should be used rather than accessing the wellSamples set directly.
iterateWellSamples() - Method in class ome.model.screen.Well
should be used rather than accessing the wellSamples set directly.
iterator() - Method in class ome.services.eventlogs.EventLogLoader
 
ITypes - Interface in ome.api
Access to reflective type information.
IUpdate - Interface in ome.api
Provides methods for directly updating object graphs.
iUpdate - Variable in class ome.logic.AbstractLevel2Service
 
iUpdate - Variable in class ome.services.AbstractStatefulBean
 

J

JavaImageScalingService - Class in ome.logic
Provides methods for scaling buffered images using Java Image Scaling.
JavaImageScalingService() - Constructor for class ome.logic.JavaImageScalingService
 
JAVASSIST_IDENTIFIER - Static variable in class ome.util.Utils
 
javaType - Variable in class ome.util.PixelData
The pixels type as it would be represented in Java.
javaType() - Method in class ome.util.PixelData
Returns the Java type that has the same byte width of the pixel data.
JdbcHashedPasswordProvider - Class in ome.security.auth
Central PasswordProvider which uses the "password" table in the central OMERO database.
JdbcHashedPasswordProvider(PasswordUtil) - Constructor for class ome.security.auth.JdbcHashedPasswordProvider
 
JdbcHashedPasswordProvider(PasswordUtil, boolean) - Constructor for class ome.security.auth.JdbcHashedPasswordProvider
 
JdbcPasswordProvider - Class in ome.security.auth
Central PasswordProvider which uses the "password" table in the central OMERO database.
JdbcPasswordProvider(PasswordUtil) - Constructor for class ome.security.auth.JdbcPasswordProvider
 
JdbcPasswordProvider(PasswordUtil, boolean) - Constructor for class ome.security.auth.JdbcPasswordProvider
 
JdbcPasswordProvider(PasswordUtil, boolean, boolean) - Constructor for class ome.security.auth.JdbcPasswordProvider
 
Job - Class in ome.model.jobs
These filter definitions are used by the security system to eliminate non-readable objects from queries.
Job() - Constructor for class ome.model.jobs.Job
 
Job(Long) - Constructor for class ome.model.jobs.Job
 
Job(Long, boolean) - Constructor for class ome.model.jobs.Job
Main constructor.
Job(String, String, String, String, JobStatus, Timestamp, Timestamp) - Constructor for class ome.model.jobs.Job
 
job(ServiceFactory, long) - Method in class ome.services.procs.ProcessManager.Work
 
Job.Details - Class in ome.model.jobs
 
Job.Details() - Constructor for class ome.model.jobs.Job.Details
 
Job.Details(Object[]) - Constructor for class ome.model.jobs.Job.Details
 
JobBean - Class in ome.services
Provides methods for submitting asynchronous tasks.
JobBean() - Constructor for class ome.services.JobBean
default constructor
jobError() - Method in interface ome.api.JobHandle
Returns true if the Job has thrown an error.
jobError() - Method in class ome.services.JobBean
 
jobError_async(AMD_JobHandle_jobError, Current) - Method in class ome.services.blitz.impl.JobHandleI
 
jobFinished() - Method in interface ome.api.JobHandle
 
jobFinished() - Method in class ome.services.JobBean
 
jobFinished_async(AMD_JobHandle_jobFinished, Current) - Method in class ome.services.blitz.impl.JobHandleI
 
JobHandle - Interface in ome.api
Allows submission of asynchronous jobs.
JobHandleI - Class in ome.services.blitz.impl
Implementation of the JobHandle service.
JobHandleI(JobHandle, BlitzExecutor) - Constructor for class ome.services.blitz.impl.JobHandleI
 
jobLinks - Variable in class ome.model.fs.Fileset
 
JOBLINKS - Static variable in class ome.model.fs.Fileset
 
JOBLINKSCOUNTPEROWNER - Static variable in class ome.model.fs.Fileset
 
jobMessage() - Method in interface ome.api.JobHandle
 
jobMessage() - Method in class ome.services.JobBean
 
jobMessage_async(AMD_JobHandle_jobMessage, Current) - Method in class ome.services.blitz.impl.JobHandleI
 
JobOriginalFileLink - Class in ome.model.jobs
These filter definitions are used by the security system to eliminate non-readable objects from queries.
JobOriginalFileLink() - Constructor for class ome.model.jobs.JobOriginalFileLink
 
JobOriginalFileLink(Long) - Constructor for class ome.model.jobs.JobOriginalFileLink
 
JobOriginalFileLink(Long, boolean) - Constructor for class ome.model.jobs.JobOriginalFileLink
Main constructor.
JobOriginalFileLink(IObject, IObject) - Constructor for class ome.model.jobs.JobOriginalFileLink
 
JobOriginalFileLink.Details - Class in ome.model.jobs
 
JobOriginalFileLink.Details() - Constructor for class ome.model.jobs.JobOriginalFileLink.Details
 
JobOriginalFileLink.Details(Object[]) - Constructor for class ome.model.jobs.JobOriginalFileLink.Details
 
jobRunning() - Method in interface ome.api.JobHandle
Returns true if the Job is running, i.e. has an attached Process.
jobRunning() - Method in class ome.services.JobBean
 
jobRunning_async(AMD_JobHandle_jobRunning, Current) - Method in class ome.services.blitz.impl.JobHandleI
 
jobStatus() - Method in interface ome.api.JobHandle
 
JobStatus - Class in ome.model.jobs
 
JobStatus() - Constructor for class ome.model.jobs.JobStatus
 
JobStatus(Long) - Constructor for class ome.model.jobs.JobStatus
 
JobStatus(Long, boolean) - Constructor for class ome.model.jobs.JobStatus
Main constructor.
JobStatus(String) - Constructor for class ome.model.jobs.JobStatus
 
jobStatus() - Method in class ome.services.JobBean
 
JobStatus.Details - Class in ome.model.jobs
 
JobStatus.Details() - Constructor for class ome.model.jobs.JobStatus.Details
 
JobStatus.Details(Object[]) - Constructor for class ome.model.jobs.JobStatus.Details
 
jobStatus_async(AMD_JobHandle_jobStatus, Current) - Method in class ome.services.blitz.impl.JobHandleI
 
join(QueryBuilder, String, String, String, String) - Method in class ome.services.graphs.BaseGraphSpec
Deprecated.
Used to generate a join statement on the QueryBuilder making use of {@link ExtendedMetadata#getRelationship(String, String).
join(String) - Method in interface ome.services.sessions.SessionCallback
 
join(String) - Method in class ome.services.sessions.SessionCallback.SimpleCloseCallback
 
join(String, String, boolean, boolean) - Method in class ome.tools.hibernate.QueryBuilder
 
join(String...) - Static method in class prefs
Joins all the String arguments given into a single String (joined with " "), and returns that String as the first element of a new array.
joinChildren(Criteria, Class, int) - Static method in class ome.services.query.Hierarchy
 
joinDataset(QueryBuilder, String, String) - Method in class ome.services.graphs.BaseGraphSpec
Deprecated.
 
joinParents(Criteria, Class, int) - Static method in class ome.services.query.Hierarchy
 
joinPlate(QueryBuilder, String, String) - Method in class ome.services.graphs.BaseGraphSpec
Deprecated.
 
joinSession(String) - Method in class omero.client
Uses the given session uuid as name and password to rejoin a running session.
JvmSettingsCheck - Class in ome.services.util
Hook run by the context which prints out JVM-related information, primarily Java version, max heap size and available processors.
JvmSettingsCheck() - Constructor for class ome.services.util.JvmSettingsCheck
 

K

keepAlive(ServiceInterfacePrx, Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
Currently ignoring the individual proxies
keepAllAlive(ServiceInterfacePrx[], Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
key - Variable in enum ome.formats.importer.ImportConfig.VersionInfo
the map key corresponding to this instance
key(String) - Method in class ome.security.auth.AttributeSet
 
key - Variable in class ome.services.eventlogs.PersistentEventLogLoader
Key used to look configuration value; 'name'
KeyAndTrustStoreConfiguration - Class in ome.security
Calls System.setProperty(String, String) for the "javax.net.ssl" properties needed to configure a trust store and a keystore for the Java process.
KeyAndTrustStoreConfiguration() - Constructor for class ome.security.KeyAndTrustStoreConfiguration
 
keys() - Method in class ome.services.sharing.BlobShareStore
 
keys() - Method in class ome.services.sharing.ShareStore
 
keys(String[]) - Static method in class prefs
keySet() - Method in class ome.parameters.Parameters
the Set of all names which would would return a non-null value from Parameters.get(String)
keySet() - Method in class ome.services.query.Definitions
 
keywords - Variable in class ome.model.meta.Namespace
 
KEYWORDS - Static variable in class ome.model.meta.Namespace
 
keywords - Variable in class ome.model.roi.Roi
 
KEYWORDS - Static variable in class ome.model.roi.Roi
 
kill(Current) - Method in class ome.services.blitz.impl.ScriptProcessI
 
killSession() - Method in class omero.client
Calls ISession.closeSession(omero.model.Session) until the returned reference count is greater than zero.
knownManagers() - Method in class ome.services.blitz.fire.Ring
 

L

Label - Class in ome.model.roi
 
Label() - Constructor for class ome.model.roi.Label
 
Label(Long) - Constructor for class ome.model.roi.Label
 
Label(Long, boolean) - Constructor for class ome.model.roi.Label
Main constructor.
Laser - Class in ome.model.acquisition
 
Laser() - Constructor for class ome.model.acquisition.Laser
 
Laser(Long) - Constructor for class ome.model.acquisition.Laser
 
Laser(Long, boolean) - Constructor for class ome.model.acquisition.Laser
Main constructor.
Laser(LaserType, LaserMedium) - Constructor for class ome.model.acquisition.Laser
 
LASER - Static variable in class pojos.LightSourceData
Indicates that the light source is a laser.
Laser_RepetitionRate - Static variable in class ome.formats.model.UnitsFactory
 
Laser_Wavelength - Static variable in class ome.formats.model.UnitsFactory
 
laserMedium - Variable in class ome.model.acquisition.Laser
 
LASERMEDIUM - Static variable in class ome.model.acquisition.Laser
 
LaserMedium - Class in ome.model.enums
 
LaserMedium() - Constructor for class ome.model.enums.LaserMedium
 
LaserMedium(Long) - Constructor for class ome.model.enums.LaserMedium
 
LaserMedium(Long, boolean) - Constructor for class ome.model.enums.LaserMedium
Main constructor.
LaserMedium(String) - Constructor for class ome.model.enums.LaserMedium
 
LaserMedium.Details - Class in ome.model.enums
 
LaserMedium.Details() - Constructor for class ome.model.enums.LaserMedium.Details
 
LaserMedium.Details(Object[]) - Constructor for class ome.model.enums.LaserMedium.Details
 
LaserType - Class in ome.model.enums
 
LaserType() - Constructor for class ome.model.enums.LaserType
 
LaserType(Long) - Constructor for class ome.model.enums.LaserType
 
LaserType(Long, boolean) - Constructor for class ome.model.enums.LaserType
Main constructor.
LaserType(String) - Constructor for class ome.model.enums.LaserType
 
LaserType.Details - Class in ome.model.enums
 
LaserType.Details() - Constructor for class ome.model.enums.LaserType.Details
 
LaserType.Details(Object[]) - Constructor for class ome.model.enums.LaserType.Details
 
lastEventLog() - Method in class ome.services.eventlogs.EventLogLoader
 
lastModified() - Method in class pojos.FileData
Returns when the file was last modified.
lastName - Variable in class ome.model.meta.Experimenter
 
LASTNAME - Static variable in class ome.model.meta.Experimenter
 
LASTNAME - Static variable in class pojos.ExperimenterData
Identifies the Experimenter#LASTNAME field.
lastPlane() - Method in class pojos.ROIData
Returns the last plane that the ROI ends on.
lastresultsAsWorkingGroup() - Method in class ome.services.SearchBean
 
launchProcessing() - Method in class ome.formats.OMEROMetadataStoreClient
 
ldap - Variable in class ome.model.meta.Experimenter
 
LDAP - Static variable in class ome.model.meta.Experimenter
 
ldap - Variable in class ome.model.meta.ExperimenterGroup
 
LDAP - Static variable in class ome.model.meta.ExperimenterGroup
 
LdapConfig - Class in ome.security.auth
Static methods for dealing with LDAP (DN) and the "password" table.
LdapConfig(boolean, String, String, String, String, String) - Constructor for class ome.security.auth.LdapConfig
Sets LdapConfig.syncOnLogin to false and LdapConfig.base to null.
LdapConfig(boolean, String, String, String, String, String, boolean) - Constructor for class ome.security.auth.LdapConfig
Sets LdapConfig.base to null.
LdapConfig(boolean, String, String, String, String, String, boolean, String) - Constructor for class ome.security.auth.LdapConfig
LdapConfig(boolean, String, String, String, String, String, boolean, String, String) - Constructor for class ome.security.auth.LdapConfig
Base constructor which stores all LdapConfig.parse(String) and stores all values for later lookup.
LdapI - Class in ome.services.blitz.impl
Implementation of the ILdap service.
LdapI(ILdap, BlitzExecutor) - Constructor for class ome.services.blitz.impl.LdapI
 
LdapImpl - Class in ome.logic
Provides methods for administering user accounts, passwords, as well as methods which require special privileges.
LdapImpl(ContextSource, LdapOperations, Roles, LdapConfig, RoleProvider, SqlAction) - Constructor for class ome.logic.LdapImpl
 
LdapImpl.GroupLoader - Class in ome.logic
Data class which stores the state of the NewUserGroupBean and NewUserGroupOwnerBean operations.
LdapPasswordProvider - Class in ome.security.auth
LDAP PasswordProvider which can create users on request to synchronize with an LDAP directory.
LdapPasswordProvider(PasswordUtil, LdapImpl) - Constructor for class ome.security.auth.LdapPasswordProvider
 
LdapPasswordProvider(PasswordUtil, LdapImpl, boolean) - Constructor for class ome.security.auth.LdapPasswordProvider
 
LdapPasswordProvider431 - Class in ome.security.auth.providers
LDAP PasswordProvider which can create users on request to synchronize with an LDAP directory.
LdapPasswordProvider431(PasswordUtil, LdapImpl) - Constructor for class ome.security.auth.providers.LdapPasswordProvider431
 
LdapPasswordProvider431(PasswordUtil, LdapImpl, boolean) - Constructor for class ome.security.auth.providers.LdapPasswordProvider431
 
ldapUtil - Variable in class ome.logic.AdminImpl
 
ldapUtil - Variable in class ome.security.auth.LdapPasswordProvider
 
ldapUtil - Variable in class ome.security.auth.providers.LdapPasswordProvider431
 
leader_of_groups - Static variable in class ome.security.basic.AllGroupsSecurityFilter
 
leaderOfGroups - Variable in class ome.system.SimpleEventContext
 
leadingWildcard - Variable in class ome.services.search.SearchValues
 
leaves - Variable in class ome.parameters.Options
 
leaves() - Method in class ome.parameters.Parameters
 
leaves() - Method in class omero.sys.ParametersI
Sets the leaf parameter to true.
LEFT_JOIN - Static variable in class ome.services.query.Query
imported constant for ease of use
LegacyRepositoryI - Class in ome.services.blitz.repo
Repository which makes the ${omero.data.dir} directory available via the standard Repository API.
LegacyRepositoryI(ObjectAdapter, Registry, Executor, Principal, String, PublicRepositoryI) - Constructor for class ome.services.blitz.repo.LegacyRepositoryI
 
LegacyRepositoryI(ObjectAdapter, Registry, Executor, Principal, FileMaker, PublicRepositoryI) - Constructor for class ome.services.blitz.repo.LegacyRepositoryI
 
legacyUtil - Variable in class ome.security.auth.ConfigurablePasswordProvider
Possibly null PasswordUtil instance which will be used as a fallback for password checks if the ConfigurablePasswordProvider.util instance fails.
Length - Class in ome.model.units
class storing both a Length and a unit for that Length (e.g. m, in, ly, etc.) encapsulated in a UnitsLength instance.
Length() - Constructor for class ome.model.units.Length
Deprecated.
Length(double, String) - Constructor for class ome.model.units.Length
 
Length(double, UnitsLength) - Constructor for class ome.model.units.Length
 
Length(double, Unit<Length>) - Constructor for class ome.model.units.Length
 
Length(Length) - Constructor for class ome.model.units.Length
 
length() - Method in class ome.services.scripts.RepoFile.FsFile
 
length() - Method in class ome.services.scripts.RepoFile
 
length - Variable in class ome.util.mem.ReadOnlyByteArray
The length of the slice.
LengthI - Class in omero.model
Blitz wrapper around the Length class.
LengthI() - Constructor for class omero.model.LengthI
 
LengthI(double, UnitsLength) - Constructor for class omero.model.LengthI
 
LengthI(double, Unit<Length>) - Constructor for class omero.model.LengthI
 
LengthI(Length, Unit<Length>) - Constructor for class omero.model.LengthI
Copy constructor that converts the given Length based on the given ome-xml enum
LengthI(double, UnitsLength) - Constructor for class omero.model.LengthI
Copy constructor that converts the given Length based on the given ome.model enum
LengthI(Length, String) - Constructor for class omero.model.LengthI
Copy constructor that converts the given Length based on the given enum string.
LengthI(Length, UnitsLength) - Constructor for class omero.model.LengthI
Copy constructor that converts between units if possible.
LengthI(Length) - Constructor for class omero.model.LengthI
Convert a Bio-Formats Length to an OMERO Length.
lensNA - Variable in class ome.model.acquisition.Objective
 
LENSNA - Static variable in class ome.model.acquisition.Objective
 
LEVEL_FIVE - Static variable in class pojos.RatingAnnotationData
Indicates the object is rated with five stars.
LEVEL_FOUR - Static variable in class pojos.RatingAnnotationData
Indicates the object is rated with four stars.
LEVEL_ONE - Static variable in class pojos.RatingAnnotationData
Indicates the object is rated with one star.
LEVEL_THREE - Static variable in class pojos.RatingAnnotationData
Indicates the object is rated with three stars.
LEVEL_TWO - Static variable in class pojos.RatingAnnotationData
Indicates the object is rated with two stars.
LEVEL_ZERO - Static variable in class pojos.RatingAnnotationData
Indicates the object is not rated.
library - Variable in class ome.formats.importer.cli.CommandLineImporter
Base importer library, this is what we actually use to import.
lies(PlanePoint) - Method in class ome.util.math.geom2D.Line
Tells whether the specified point lies on this line.
lies(PlanePoint, boolean) - Method in class ome.util.math.geom2D.Line
Tells whether the specified point lies on this line and within the specified orientation.
lies(double, double) - Method in class ome.util.math.geom2D.Segment
Tells whether a specified point lies on this line.
LIGHT_EMITTING_DIODE - Static variable in class pojos.LightSourceData
Indicates that the light source is a light emitting diode.
LightEmittingDiode - Class in ome.model.acquisition
 
LightEmittingDiode() - Constructor for class ome.model.acquisition.LightEmittingDiode
 
LightEmittingDiode(Long) - Constructor for class ome.model.acquisition.LightEmittingDiode
 
LightEmittingDiode(Long, boolean) - Constructor for class ome.model.acquisition.LightEmittingDiode
Main constructor.
LightPath - Class in ome.model.acquisition
These filter definitions are used by the security system to eliminate non-readable objects from queries.
LightPath() - Constructor for class ome.model.acquisition.LightPath
 
LightPath(Long) - Constructor for class ome.model.acquisition.LightPath
 
LightPath(Long, boolean) - Constructor for class ome.model.acquisition.LightPath
Main constructor.
lightPath - Variable in class ome.model.core.LogicalChannel
 
LIGHTPATH - Static variable in class ome.model.core.LogicalChannel
 
LightPath.Details - Class in ome.model.acquisition
 
LightPath.Details() - Constructor for class ome.model.acquisition.LightPath.Details
 
LightPath.Details(Object[]) - Constructor for class ome.model.acquisition.LightPath.Details
 
LightPathAnnotationLink - Class in ome.model.annotations
These filter definitions are used by the security system to eliminate non-readable objects from queries.
LightPathAnnotationLink() - Constructor for class ome.model.annotations.LightPathAnnotationLink
 
LightPathAnnotationLink(Long) - Constructor for class ome.model.annotations.LightPathAnnotationLink
 
LightPathAnnotationLink(Long, boolean) - Constructor for class ome.model.annotations.LightPathAnnotationLink
Main constructor.
LightPathAnnotationLink(IObject, IObject) - Constructor for class ome.model.annotations.LightPathAnnotationLink
 
LightPathAnnotationLink.Details - Class in ome.model.annotations
 
LightPathAnnotationLink.Details() - Constructor for class ome.model.annotations.LightPathAnnotationLink.Details
 
LightPathAnnotationLink.Details(Object[]) - Constructor for class ome.model.annotations.LightPathAnnotationLink.Details
 
LightPathData - Class in pojos
Object hosting a light path.
LightPathData(LightPath) - Constructor for class pojos.LightPathData
Creates a new instance.
LightPathEmissionFilterLink - Class in ome.model.acquisition
These filter definitions are used by the security system to eliminate non-readable objects from queries.
LightPathEmissionFilterLink() - Constructor for class ome.model.acquisition.LightPathEmissionFilterLink
 
LightPathEmissionFilterLink(Long) - Constructor for class ome.model.acquisition.LightPathEmissionFilterLink
 
LightPathEmissionFilterLink(Long, boolean) - Constructor for class ome.model.acquisition.LightPathEmissionFilterLink
Main constructor.
LightPathEmissionFilterLink(IObject, IObject) - Constructor for class ome.model.acquisition.LightPathEmissionFilterLink
 
LightPathEmissionFilterLink.Details - Class in ome.model.acquisition
 
LightPathEmissionFilterLink.Details() - Constructor for class ome.model.acquisition.LightPathEmissionFilterLink.Details
 
LightPathEmissionFilterLink.Details(Object[]) - Constructor for class ome.model.acquisition.LightPathEmissionFilterLink.Details
 
LightPathExcitationFilterLink - Class in ome.model.acquisition
These filter definitions are used by the security system to eliminate non-readable objects from queries.
LightPathExcitationFilterLink() - Constructor for class ome.model.acquisition.LightPathExcitationFilterLink
 
LightPathExcitationFilterLink(Long) - Constructor for class ome.model.acquisition.LightPathExcitationFilterLink
 
LightPathExcitationFilterLink(Long, boolean) - Constructor for class ome.model.acquisition.LightPathExcitationFilterLink
Main constructor.
LightPathExcitationFilterLink(IObject, IObject) - Constructor for class ome.model.acquisition.LightPathExcitationFilterLink
 
LightPathExcitationFilterLink.Details - Class in ome.model.acquisition
 
LightPathExcitationFilterLink.Details() - Constructor for class ome.model.acquisition.LightPathExcitationFilterLink.Details
 
LightPathExcitationFilterLink.Details(Object[]) - Constructor for class ome.model.acquisition.LightPathExcitationFilterLink.Details
 
LightSettings - Class in ome.model.acquisition
These filter definitions are used by the security system to eliminate non-readable objects from queries.
LightSettings() - Constructor for class ome.model.acquisition.LightSettings
 
LightSettings(Long) - Constructor for class ome.model.acquisition.LightSettings
 
LightSettings(Long, boolean) - Constructor for class ome.model.acquisition.LightSettings
Main constructor.
LightSettings(LightSource) - Constructor for class ome.model.acquisition.LightSettings
 
LightSettings.Details - Class in ome.model.acquisition
 
LightSettings.Details() - Constructor for class ome.model.acquisition.LightSettings.Details
 
LightSettings.Details(Object[]) - Constructor for class ome.model.acquisition.LightSettings.Details
 
lightSource - Variable in class ome.model.acquisition.Instrument
 
LIGHTSOURCE - Static variable in class ome.model.acquisition.Instrument
 
lightSource - Variable in class ome.model.acquisition.LightSettings
 
LIGHTSOURCE - Static variable in class ome.model.acquisition.LightSettings
 
LightSource - Class in ome.model.acquisition
These filter definitions are used by the security system to eliminate non-readable objects from queries.
LightSource() - Constructor for class ome.model.acquisition.LightSource
 
LightSource(Long) - Constructor for class ome.model.acquisition.LightSource
 
LightSource(Long, boolean) - Constructor for class ome.model.acquisition.LightSource
Main constructor.
LightSource(Instrument) - Constructor for class ome.model.acquisition.LightSource
 
LightSource.Details - Class in ome.model.acquisition
 
LightSource.Details() - Constructor for class ome.model.acquisition.LightSource.Details
 
LightSource.Details(Object[]) - Constructor for class ome.model.acquisition.LightSource.Details
 
LightSource_Power - Static variable in class ome.formats.model.UnitsFactory
 
LightSourceAnnotationLink - Class in ome.model.annotations
These filter definitions are used by the security system to eliminate non-readable objects from queries.
LightSourceAnnotationLink() - Constructor for class ome.model.annotations.LightSourceAnnotationLink
 
LightSourceAnnotationLink(Long) - Constructor for class ome.model.annotations.LightSourceAnnotationLink
 
LightSourceAnnotationLink(Long, boolean) - Constructor for class ome.model.annotations.LightSourceAnnotationLink
Main constructor.
LightSourceAnnotationLink(IObject, IObject) - Constructor for class ome.model.annotations.LightSourceAnnotationLink
 
LightSourceAnnotationLink.Details - Class in ome.model.annotations
 
LightSourceAnnotationLink.Details() - Constructor for class ome.model.annotations.LightSourceAnnotationLink.Details
 
LightSourceAnnotationLink.Details(Object[]) - Constructor for class ome.model.annotations.LightSourceAnnotationLink.Details
 
LightSourceData - Class in pojos
Object hosting a light source: filament, arc, laser or light emitting diode
LightSourceData(LightSource) - Constructor for class pojos.LightSourceData
Creates a new instance.
LightSourceGraphSpec - Class in ome.services.graphs
Deprecated.
will be removed in OMERO 5.2, so use the new graphs implementation
LightSourceGraphSpec(List<String>) - Constructor for class ome.services.graphs.LightSourceGraphSpec
Deprecated.
Creates a new instance.
lightSourceSettings - Variable in class ome.model.core.LogicalChannel
 
LIGHTSOURCESETTINGS - Static variable in class ome.model.core.LogicalChannel
 
lightSourceSettings - Variable in class ome.model.experiment.MicrobeamManipulation
 
LIGHTSOURCESETTINGS - Static variable in class ome.model.experiment.MicrobeamManipulation
 
LightSourceSettings_Wavelength - Static variable in class ome.formats.model.UnitsFactory
 
limit - Variable in class ome.parameters.Filter
 
Line - Class in ome.model.roi
 
Line() - Constructor for class ome.model.roi.Line
 
Line(Long) - Constructor for class ome.model.roi.Line
 
Line(Long, boolean) - Constructor for class ome.model.roi.Line
Main constructor.
Line - Class in ome.util.math.geom2D
An orientated line in the Euclidean space R2.
Line(PlanePoint, PlanePoint) - Constructor for class ome.util.math.geom2D.Line
Creates a new object to represent the line passing through the o and p points.
Line(PlanePoint, PlanePoint, PlanePoint) - Constructor for class ome.util.math.geom2D.Line
Creates a new object to represent the line passing through o and having direction pq.
LINE_CAP_BUTT - Static variable in class pojos.ShapeSettingsData
The Butt descriptor.
LINE_CAP_ROUND - Static variable in class pojos.ShapeSettingsData
The Round descriptor.
LINE_CAP_SQUARE - Static variable in class pojos.ShapeSettingsData
The Square descriptor.
LINEAR - Static variable in class omeis.providers.re.quantum.QuantumFactory
Flag to select a linear map for the quantization process.
LineData - Class in pojos
Represents a line in the Euclidean space R2.
LineData(Shape) - Constructor for class pojos.LineData
Creates a new instance.
LineData() - Constructor for class pojos.LineData
Create a new instance of LineData, creating a new LineI Object.
LineData(double, double, double, double) - Constructor for class pojos.LineData
Create a new instance of the LineData,
link(ILink[], Parameters) - Method in interface ome.api.IContainer
Convenience method for creating links.
link(ILink[], Parameters) - Method in class ome.logic.PojosImpl
Implemented as specified by the IContainer I/F
link(FilterSet, Filter) - Method in class ome.model.acquisition.FilterSetEmissionFilterLink
 
link(FilterSet, Filter) - Method in class ome.model.acquisition.FilterSetExcitationFilterLink
 
link(LightPath, Filter) - Method in class ome.model.acquisition.LightPathEmissionFilterLink
 
link(LightPath, Filter) - Method in class ome.model.acquisition.LightPathExcitationFilterLink
 
link(Annotation, Annotation) - Method in class ome.model.annotations.AnnotationAnnotationLink
 
link(Channel, Annotation) - Method in class ome.model.annotations.ChannelAnnotationLink
 
link(Dataset, Annotation) - Method in class ome.model.annotations.DatasetAnnotationLink
 
link(Detector, Annotation) - Method in class ome.model.annotations.DetectorAnnotationLink
 
link(Dichroic, Annotation) - Method in class ome.model.annotations.DichroicAnnotationLink
 
link(Experimenter, Annotation) - Method in class ome.model.annotations.ExperimenterAnnotationLink
 
link(ExperimenterGroup, Annotation) - Method in class ome.model.annotations.ExperimenterGroupAnnotationLink
 
link(Fileset, Annotation) - Method in class ome.model.annotations.FilesetAnnotationLink
 
link(Filter, Annotation) - Method in class ome.model.annotations.FilterAnnotationLink
 
link(Image, Annotation) - Method in class ome.model.annotations.ImageAnnotationLink
 
link(Instrument, Annotation) - Method in class ome.model.annotations.InstrumentAnnotationLink
 
link(LightPath, Annotation) - Method in class ome.model.annotations.LightPathAnnotationLink
 
link(LightSource, Annotation) - Method in class ome.model.annotations.LightSourceAnnotationLink
 
link(Namespace, Annotation) - Method in class ome.model.annotations.NamespaceAnnotationLink
 
link(Node, Annotation) - Method in class ome.model.annotations.NodeAnnotationLink
 
link(Objective, Annotation) - Method in class ome.model.annotations.ObjectiveAnnotationLink
 
link(OriginalFile, Annotation) - Method in class ome.model.annotations.OriginalFileAnnotationLink
 
link(PlaneInfo, Annotation) - Method in class ome.model.annotations.PlaneInfoAnnotationLink
 
link(PlateAcquisition, Annotation) - Method in class ome.model.annotations.PlateAcquisitionAnnotationLink
 
link(Plate, Annotation) - Method in class ome.model.annotations.PlateAnnotationLink
 
link(Project, Annotation) - Method in class ome.model.annotations.ProjectAnnotationLink
 
link(Reagent, Annotation) - Method in class ome.model.annotations.ReagentAnnotationLink
 
link(Roi, Annotation) - Method in class ome.model.annotations.RoiAnnotationLink
 
link(Screen, Annotation) - Method in class ome.model.annotations.ScreenAnnotationLink
 
link(Session, Annotation) - Method in class ome.model.annotations.SessionAnnotationLink
 
link(Shape, Annotation) - Method in class ome.model.annotations.ShapeAnnotationLink
 
link(Well, Annotation) - Method in class ome.model.annotations.WellAnnotationLink
 
link(Dataset, Image) - Method in class ome.model.containers.DatasetImageLink
 
link(Project, Dataset) - Method in class ome.model.containers.ProjectDatasetLink
 
link(OriginalFile, Pixels) - Method in class ome.model.core.PixelsOriginalFileMap
 
link(Fileset, Job) - Method in class ome.model.fs.FilesetJobLink
 
Link - Class in ome.model.internal
These filter definitions are used by the security system to eliminate non-readable objects from queries.
Link() - Constructor for class ome.model.internal.Link
 
Link(Long) - Constructor for class ome.model.internal.Link
 
Link(Long, boolean) - Constructor for class ome.model.internal.Link
Main constructor.
link(Job, OriginalFile) - Method in class ome.model.jobs.JobOriginalFileLink
 
link(ExperimenterGroup, Experimenter) - Method in class ome.model.meta.GroupExperimenterMap
 
link(Share, Experimenter) - Method in class ome.model.meta.ShareMember
 
link(Screen, Plate) - Method in class ome.model.screen.ScreenPlateLink
 
link(Well, Reagent) - Method in class ome.model.screen.WellReagentLink
 
Link.Details - Class in ome.model.internal
 
Link.Details() - Constructor for class ome.model.internal.Link.Details
 
Link.Details(Object[]) - Constructor for class ome.model.internal.Link.Details
 
link_async(AMD_IContainer_link, List<IObject>, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI
 
linkAnnotation(Annotation) - Method in class ome.model.acquisition.Detector
Adds a ome.model.annotations.DetectorAnnotationLink to annotationLinks .
linkAnnotation(Annotation) - Method in class ome.model.acquisition.Dichroic
Adds a ome.model.annotations.DichroicAnnotationLink to annotationLinks .
linkAnnotation(Annotation) - Method in class ome.model.acquisition.Filter
Adds a ome.model.annotations.FilterAnnotationLink to annotationLinks .
linkAnnotation(Annotation) - Method in class ome.model.acquisition.Instrument
Adds a ome.model.annotations.InstrumentAnnotationLink to annotationLinks .
linkAnnotation(Annotation) - Method in class ome.model.acquisition.LightPath
Adds a ome.model.annotations.LightPathAnnotationLink to annotationLinks .
linkAnnotation(Annotation) - Method in class ome.model.acquisition.LightSource
Adds a ome.model.annotations.LightSourceAnnotationLink to annotationLinks .
linkAnnotation(Annotation) - Method in class ome.model.acquisition.Objective
Adds a ome.model.annotations.ObjectiveAnnotationLink to annotationLinks .
linkAnnotation(Annotation) - Method in class ome.model.annotations.Annotation
Adds a ome.model.annotations.AnnotationAnnotationLink to annotationLinks .
linkAnnotation(Annotation) - Method in class ome.model.containers.Dataset
Adds a ome.model.annotations.DatasetAnnotationLink to annotationLinks .
linkAnnotation(Annotation) - Method in class ome.model.containers.Project
Adds a ome.model.annotations.ProjectAnnotationLink to annotationLinks .
linkAnnotation(Annotation) - Method in class ome.model.core.Channel
Adds a ome.model.annotations.ChannelAnnotationLink to annotationLinks .
linkAnnotation(Annotation) - Method in class ome.model.core.Image
Adds a ome.model.annotations.ImageAnnotationLink to annotationLinks .
linkAnnotation(Annotation) - Method in class ome.model.core.OriginalFile
Adds a ome.model.annotations.OriginalFileAnnotationLink to annotationLinks .
linkAnnotation(Annotation) - Method in class ome.model.core.PlaneInfo
Adds a ome.model.annotations.PlaneInfoAnnotationLink to annotationLinks .
linkAnnotation(Annotation) - Method in class ome.model.fs.Fileset
Adds a ome.model.annotations.FilesetAnnotationLink to annotationLinks .
linkAnnotation(Annotation) - Method in interface ome.model.IAnnotated
 
linkAnnotation(Annotation) - Method in class ome.model.meta.Experimenter
Adds a ome.model.annotations.ExperimenterAnnotationLink to annotationLinks .
linkAnnotation(Annotation) - Method in class ome.model.meta.ExperimenterGroup
Adds a ome.model.annotations.ExperimenterGroupAnnotationLink to annotationLinks .
linkAnnotation(Annotation) - Method in class ome.model.meta.Namespace
Adds a ome.model.annotations.NamespaceAnnotationLink to annotationLinks .
linkAnnotation(Annotation) - Method in class ome.model.meta.Node
Adds a ome.model.annotations.NodeAnnotationLink to annotationLinks .
linkAnnotation(Annotation) - Method in class ome.model.meta.Session
Adds a ome.model.annotations.SessionAnnotationLink to annotationLinks .
linkAnnotation(Annotation) - Method in class ome.model.roi.Roi
Adds a ome.model.annotations.RoiAnnotationLink to annotationLinks .
linkAnnotation(Annotation) - Method in class ome.model.roi.Shape
Adds a ome.model.annotations.ShapeAnnotationLink to annotationLinks .
linkAnnotation(Annotation) - Method in class ome.model.screen.Plate
Adds a ome.model.annotations.PlateAnnotationLink to annotationLinks .
linkAnnotation(Annotation) - Method in class ome.model.screen.PlateAcquisition
Adds a ome.model.annotations.PlateAcquisitionAnnotationLink to annotationLinks .
linkAnnotation(Annotation) - Method in class ome.model.screen.Reagent
Adds a ome.model.annotations.ReagentAnnotationLink to annotationLinks .
linkAnnotation(Annotation) - Method in class ome.model.screen.Screen
Adds a ome.model.annotations.ScreenAnnotationLink to annotationLinks .
linkAnnotation(Annotation) - Method in class ome.model.screen.Well
Adds a ome.model.annotations.WellAnnotationLink to annotationLinks .
linkDataset(Dataset) - Method in class ome.model.containers.Project
Adds a ome.model.containers.ProjectDatasetLink to datasetLinks .
linkDataset(Dataset) - Method in class ome.model.core.Image
Adds a ome.model.containers.DatasetImageLink to datasetLinks .
linkedAnnotationIterator() - Method in class ome.model.acquisition.Detector
provides an iterator over the parent values of the annotationLinks.
linkedAnnotationIterator() - Method in class ome.model.acquisition.Dichroic
provides an iterator over the parent values of the annotationLinks.
linkedAnnotationIterator() - Method in class ome.model.acquisition.Filter
provides an iterator over the parent values of the annotationLinks.
linkedAnnotationIterator() - Method in class ome.model.acquisition.Instrument
provides an iterator over the parent values of the annotationLinks.
linkedAnnotationIterator() - Method in class ome.model.acquisition.LightPath
provides an iterator over the parent values of the annotationLinks.
linkedAnnotationIterator() - Method in class ome.model.acquisition.LightSource
provides an iterator over the parent values of the annotationLinks.
linkedAnnotationIterator() - Method in class ome.model.acquisition.Objective
provides an iterator over the parent values of the annotationLinks.
linkedAnnotationIterator() - Method in class ome.model.annotations.Annotation
provides an iterator over the parent values of the annotationLinks.
linkedAnnotationIterator() - Method in class ome.model.containers.Dataset
provides an iterator over the parent values of the annotationLinks.
linkedAnnotationIterator() - Method in class ome.model.containers.Project
provides an iterator over the parent values of the annotationLinks.
linkedAnnotationIterator() - Method in class ome.model.core.Channel
provides an iterator over the parent values of the annotationLinks.
linkedAnnotationIterator() - Method in class ome.model.core.Image
provides an iterator over the parent values of the annotationLinks.
linkedAnnotationIterator() - Method in class ome.model.core.OriginalFile
provides an iterator over the parent values of the annotationLinks.
linkedAnnotationIterator() - Method in class ome.model.core.PlaneInfo
provides an iterator over the parent values of the annotationLinks.
linkedAnnotationIterator() - Method in class ome.model.fs.Fileset
provides an iterator over the parent values of the annotationLinks.
linkedAnnotationIterator() - Method in interface ome.model.IAnnotated
 
linkedAnnotationIterator() - Method in class ome.model.meta.Experimenter
provides an iterator over the parent values of the annotationLinks.
linkedAnnotationIterator() - Method in class ome.model.meta.ExperimenterGroup
provides an iterator over the parent values of the annotationLinks.
linkedAnnotationIterator() - Method in class ome.model.meta.Namespace
provides an iterator over the parent values of the annotationLinks.
linkedAnnotationIterator() - Method in class ome.model.meta.Node
provides an iterator over the parent values of the annotationLinks.
linkedAnnotationIterator() - Method in class ome.model.meta.Session
provides an iterator over the parent values of the annotationLinks.
linkedAnnotationIterator() - Method in class ome.model.roi.Roi
provides an iterator over the parent values of the annotationLinks.
linkedAnnotationIterator() - Method in class ome.model.roi.Shape
provides an iterator over the parent values of the annotationLinks.
linkedAnnotationIterator() - Method in class ome.model.screen.Plate
provides an iterator over the parent values of the annotationLinks.
linkedAnnotationIterator() - Method in class ome.model.screen.PlateAcquisition
provides an iterator over the parent values of the annotationLinks.
linkedAnnotationIterator() - Method in class ome.model.screen.Reagent
provides an iterator over the parent values of the annotationLinks.
linkedAnnotationIterator() - Method in class ome.model.screen.Screen
provides an iterator over the parent values of the annotationLinks.
linkedAnnotationIterator() - Method in class ome.model.screen.Well
provides an iterator over the parent values of the annotationLinks.
linkedAnnotationList() - Method in class ome.model.acquisition.Detector
produces a List-copy of the underlying collection.
linkedAnnotationList() - Method in class ome.model.acquisition.Dichroic
produces a List-copy of the underlying collection.
linkedAnnotationList() - Method in class ome.model.acquisition.Filter
produces a List-copy of the underlying collection.
linkedAnnotationList() - Method in class ome.model.acquisition.Instrument
produces a List-copy of the underlying collection.
linkedAnnotationList() - Method in class ome.model.acquisition.LightPath
produces a List-copy of the underlying collection.
linkedAnnotationList() - Method in class ome.model.acquisition.LightSource
produces a List-copy of the underlying collection.
linkedAnnotationList() - Method in class ome.model.acquisition.Objective
produces a List-copy of the underlying collection.
linkedAnnotationList() - Method in class ome.model.annotations.Annotation
produces a List-copy of the underlying collection.
linkedAnnotationList() - Method in class ome.model.containers.Dataset
produces a List-copy of the underlying collection.
linkedAnnotationList() - Method in class ome.model.containers.Project
produces a List-copy of the underlying collection.
linkedAnnotationList() - Method in class ome.model.core.Channel
produces a List-copy of the underlying collection.
linkedAnnotationList() - Method in class ome.model.core.Image
produces a List-copy of the underlying collection.
linkedAnnotationList() - Method in class ome.model.core.OriginalFile
produces a List-copy of the underlying collection.
linkedAnnotationList() - Method in class ome.model.core.PlaneInfo
produces a List-copy of the underlying collection.
linkedAnnotationList() - Method in class ome.model.fs.Fileset
produces a List-copy of the underlying collection.
linkedAnnotationList() - Method in interface ome.model.IAnnotated
 
linkedAnnotationList() - Method in class ome.model.meta.Experimenter
produces a List-copy of the underlying collection.
linkedAnnotationList() - Method in class ome.model.meta.ExperimenterGroup
produces a List-copy of the underlying collection.
linkedAnnotationList() - Method in class ome.model.meta.Namespace
produces a List-copy of the underlying collection.
linkedAnnotationList() - Method in class ome.model.meta.Node
produces a List-copy of the underlying collection.
linkedAnnotationList() - Method in class ome.model.meta.Session
produces a List-copy of the underlying collection.
linkedAnnotationList() - Method in class ome.model.roi.Roi
produces a List-copy of the underlying collection.
linkedAnnotationList() - Method in class ome.model.roi.Shape
produces a List-copy of the underlying collection.
linkedAnnotationList() - Method in class ome.model.screen.Plate
produces a List-copy of the underlying collection.
linkedAnnotationList() - Method in class ome.model.screen.PlateAcquisition
produces a List-copy of the underlying collection.
linkedAnnotationList() - Method in class ome.model.screen.Reagent
produces a List-copy of the underlying collection.
linkedAnnotationList() - Method in class ome.model.screen.Screen
produces a List-copy of the underlying collection.
linkedAnnotationList() - Method in class ome.model.screen.Well
produces a List-copy of the underlying collection.
linkedDatasetIterator() - Method in class ome.model.containers.Project
provides an iterator over the parent values of the datasetLinks.
linkedDatasetIterator() - Method in class ome.model.core.Image
provides an iterator over the child values of the datasetLinks.
linkedDatasetList() - Method in class ome.model.containers.Project
produces a List-copy of the underlying collection.
linkedDatasetList() - Method in class ome.model.core.Image
produces a List-copy of the underlying collection.
linkedEmissionFilterIterator() - Method in class ome.model.acquisition.Filter
provides an iterator over the child values of the emissionFilterLink.
linkedEmissionFilterIterator() - Method in class ome.model.acquisition.FilterSet
provides an iterator over the parent values of the emissionFilterLink.
linkedEmissionFilterIterator() - Method in class ome.model.acquisition.LightPath
provides an iterator over the parent values of the emissionFilterLink.
linkedEmissionFilterList() - Method in class ome.model.acquisition.Filter
produces a List-copy of the underlying collection.
linkedEmissionFilterList() - Method in class ome.model.acquisition.FilterSet
produces a List-copy of the underlying collection.
linkedEmissionFilterList() - Method in class ome.model.acquisition.LightPath
produces a List-copy of the underlying collection.
linkedExcitationFilterIterator() - Method in class ome.model.acquisition.Filter
provides an iterator over the child values of the excitationFilterLink.
linkedExcitationFilterIterator() - Method in class ome.model.acquisition.FilterSet
provides an iterator over the parent values of the excitationFilterLink.
linkedExcitationFilterIterator() - Method in class ome.model.acquisition.LightPath
provides an iterator over the parent values of the excitationFilterLink.
linkedExcitationFilterList() - Method in class ome.model.acquisition.Filter
produces a List-copy of the underlying collection.
linkedExcitationFilterList() - Method in class ome.model.acquisition.FilterSet
produces a List-copy of the underlying collection.
linkedExcitationFilterList() - Method in class ome.model.acquisition.LightPath
produces a List-copy of the underlying collection.
linkedExperimenterGroupIterator() - Method in class ome.model.meta.Experimenter
provides an iterator over the child values of the groupExperimenterMap.
linkedExperimenterGroupList() - Method in class ome.model.meta.Experimenter
produces a List-copy of the underlying collection.
linkedExperimenterIterator() - Method in class ome.model.meta.ExperimenterGroup
provides an iterator over the parent values of the groupExperimenterMap.
linkedExperimenterList() - Method in class ome.model.meta.ExperimenterGroup
produces a List-copy of the underlying collection.
linkedImageIterator() - Method in class ome.model.containers.Dataset
provides an iterator over the parent values of the imageLinks.
linkedImageList() - Method in class ome.model.containers.Dataset
produces a List-copy of the underlying collection.
linkedJobIterator() - Method in class ome.model.fs.Fileset
provides an iterator over the parent values of the jobLinks.
linkedJobList() - Method in class ome.model.fs.Fileset
produces a List-copy of the underlying collection.
linkedOriginalFileIterator() - Method in class ome.model.core.Pixels
provides an iterator over the child values of the pixelsFileMaps.
linkedOriginalFileIterator() - Method in class ome.model.jobs.Job
provides an iterator over the parent values of the originalFileLinks.
linkedOriginalFileList() - Method in class ome.model.core.Pixels
produces a List-copy of the underlying collection.
linkedOriginalFileList() - Method in class ome.model.jobs.Job
produces a List-copy of the underlying collection.
linkedPixelsIterator() - Method in class ome.model.core.OriginalFile
provides an iterator over the parent values of the pixelsFileMaps.
linkedPixelsList() - Method in class ome.model.core.OriginalFile
produces a List-copy of the underlying collection.
linkedPlateIterator() - Method in class ome.model.screen.Screen
provides an iterator over the parent values of the plateLinks.
linkedPlateList() - Method in class ome.model.screen.Screen
produces a List-copy of the underlying collection.
linkedProjectIterator() - Method in class ome.model.containers.Dataset
provides an iterator over the child values of the projectLinks.
linkedProjectList() - Method in class ome.model.containers.Dataset
produces a List-copy of the underlying collection.
linkedReagentIterator() - Method in class ome.model.screen.Well
provides an iterator over the parent values of the reagentLinks.
linkedReagentList() - Method in class ome.model.screen.Well
produces a List-copy of the underlying collection.
linkedScreenIterator() - Method in class ome.model.screen.Plate
provides an iterator over the child values of the screenLinks.
linkedScreenList() - Method in class ome.model.screen.Plate
produces a List-copy of the underlying collection.
linkedWellIterator() - Method in class ome.model.screen.Reagent
provides an iterator over the child values of the wellLinks.
linkedWellList() - Method in class ome.model.screen.Reagent
produces a List-copy of the underlying collection.
linkEmissionFilter(FilterSet) - Method in class ome.model.acquisition.Filter
Adds a ome.model.acquisition.FilterSetEmissionFilterLink to emissionFilterLink .
linkEmissionFilter(Filter) - Method in class ome.model.acquisition.FilterSet
Adds a ome.model.acquisition.FilterSetEmissionFilterLink to emissionFilterLink .
linkEmissionFilter(Filter) - Method in class ome.model.acquisition.LightPath
Adds a ome.model.acquisition.LightPathEmissionFilterLink to emissionFilterLink .
linkExcitationFilter(FilterSet) - Method in class ome.model.acquisition.Filter
Adds a ome.model.acquisition.FilterSetExcitationFilterLink to excitationFilterLink .
linkExcitationFilter(Filter) - Method in class ome.model.acquisition.FilterSet
Adds a ome.model.acquisition.FilterSetExcitationFilterLink to excitationFilterLink .
linkExcitationFilter(Filter) - Method in class ome.model.acquisition.LightPath
Adds a ome.model.acquisition.LightPathExcitationFilterLink to excitationFilterLink .
linkExperimenter(Experimenter) - Method in class ome.model.meta.ExperimenterGroup
Adds a ome.model.meta.GroupExperimenterMap to groupExperimenterMap .
linkExperimenterGroup(ExperimenterGroup) - Method in class ome.model.meta.Experimenter
Adds a ome.model.meta.GroupExperimenterMap to groupExperimenterMap .
linkGroupAndUser(ExperimenterGroup, Experimenter, boolean) - Method in class ome.security.auth.SimpleRoleProvider
 
linkImage(Image) - Method in class ome.model.containers.Dataset
Adds a ome.model.containers.DatasetImageLink to imageLinks .
linkJob(Job) - Method in class ome.model.fs.Fileset
Adds a ome.model.fs.FilesetJobLink to jobLinks .
linkOriginalFile(OriginalFile) - Method in class ome.model.core.Pixels
Adds a ome.model.core.PixelsOriginalFileMap to pixelsFileMaps .
linkOriginalFile(OriginalFile) - Method in class ome.model.jobs.Job
Adds a ome.model.jobs.JobOriginalFileLink to originalFileLinks .
linkPixels(Pixels) - Method in class ome.model.core.OriginalFile
Adds a ome.model.core.PixelsOriginalFileMap to pixelsFileMaps .
linkPlate(Plate) - Method in class ome.model.screen.Screen
Adds a ome.model.screen.ScreenPlateLink to plateLinks .
linkProject(Project) - Method in class ome.model.containers.Dataset
Adds a ome.model.containers.ProjectDatasetLink to projectLinks .
linkReagent(Reagent) - Method in class ome.model.screen.Well
Adds a ome.model.screen.WellReagentLink to reagentLinks .
LINKRESTRICTION - Static variable in class ome.model.internal.Permissions
 
linkScreen(Screen) - Method in class ome.model.screen.Plate
Adds a ome.model.screen.ScreenPlateLink to screenLinks .
linkWell(Well) - Method in class ome.model.screen.Reagent
Adds a ome.model.screen.WellReagentLink to wellLinks .
list(String, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
 
list(List<Obj>) - Method in class ome.services.sharing.ShareBean
 
listActiveRestrictions(IObject) - Method in class ome.security.policy.DefaultPolicyService
 
listActiveRestrictions(IObject) - Method in interface ome.security.policy.PolicyService
Return all identifier strings as would be passed as the first argument to PolicyService.isRestricted(String, IObject) or PolicyService.checkRestriction(String, IObject) which considers itself active for the given argument.
listAllRestrictions() - Method in class ome.security.policy.DefaultPolicyService
 
listAllRestrictions() - Method in interface ome.security.policy.PolicyService
Return all configured identifier strings as would be passed as the first argument to PolicyService.isRestricted(String, IObject) or PolicyService.checkRestriction(String, IObject).
ListAnnotation - Class in ome.model.annotations
 
ListAnnotation() - Constructor for class ome.model.annotations.ListAnnotation
 
ListAnnotation(Long) - Constructor for class ome.model.annotations.ListAnnotation
 
ListAnnotation(Long, boolean) - Constructor for class ome.model.annotations.ListAnnotation
Main constructor.
ListAsSQLArrayUserType<T> - Class in ome.tools.hibernate
Hibernate type to store Lists of primitives using SQL ARRAY.
ListAsSQLArrayUserType() - Constructor for class ome.tools.hibernate.ListAsSQLArrayUserType
 
ListAsSQLArrayUserType.ArrayFactory - Interface in ome.tools.hibernate
 
ListAsSQLArrayUserType.BOOLEAN - Class in ome.tools.hibernate
To use, define : hibernate.property type="ome.tools.hibernate.ListAsSQLArrayUserType$BOOLEAN" hibernate.column name="fieldName" sql-type="bool[]"
ListAsSQLArrayUserType.BOOLEAN() - Constructor for class ome.tools.hibernate.ListAsSQLArrayUserType.BOOLEAN
 
ListAsSQLArrayUserType.DATE - Class in ome.tools.hibernate
To use, define : hibernate.property type="ome.tools.hibernate.ListAsSQLArrayUserType$DATE" hibernate.column name="fieldName" sql-type="timestamp[]"
ListAsSQLArrayUserType.DATE() - Constructor for class ome.tools.hibernate.ListAsSQLArrayUserType.DATE
 
ListAsSQLArrayUserType.DOUBLE - Class in ome.tools.hibernate
To use, define : hibernate.property type="ome.tools.hibernate.ListAsSQLArrayUserType$DOUBLE" hibernate.column name="fieldName" sql-type="float8[]"
ListAsSQLArrayUserType.DOUBLE() - Constructor for class ome.tools.hibernate.ListAsSQLArrayUserType.DOUBLE
 
ListAsSQLArrayUserType.ENUM<E extends Enum<E>> - Class in ome.tools.hibernate
Warning, this one is special.
ListAsSQLArrayUserType.ENUM(E[]) - Constructor for class ome.tools.hibernate.ListAsSQLArrayUserType.ENUM
 
ListAsSQLArrayUserType.FLOAT - Class in ome.tools.hibernate
To use, define : hibernate.property type="ome.tools.hibernate.ListAsSQLArrayUserType$FLOAT" hibernate.column name="fieldName" sql-type="real[]"
ListAsSQLArrayUserType.FLOAT() - Constructor for class ome.tools.hibernate.ListAsSQLArrayUserType.FLOAT
 
ListAsSQLArrayUserType.INTEGER - Class in ome.tools.hibernate
To use, define : hibernate.property type="ome.tools.hibernate.ListAsSQLArrayUserType$INTEGER" hibernate.column name="fieldName" sql-type="int[]"
ListAsSQLArrayUserType.INTEGER() - Constructor for class ome.tools.hibernate.ListAsSQLArrayUserType.INTEGER
 
ListAsSQLArrayUserType.STRING - Class in ome.tools.hibernate
To use, define : hibernate.property type="ome.tools.hibernate.ListAsSQLArrayUserType$STRING" hibernate.column name="fieldName" sql-type="text[]"
ListAsSQLArrayUserType.STRING() - Constructor for class ome.tools.hibernate.ListAsSQLArrayUserType.STRING
 
ListAsSQLArrayUserType.STRING2 - Class in ome.tools.hibernate
To use, define : hibernate.property type="ome.tools.hibernate.ListAsSQLArrayUserType$STRING2" hibernate.column name="fieldName" sql-type="text[]" Added by Josh
ListAsSQLArrayUserType.STRING2() - Constructor for class ome.tools.hibernate.ListAsSQLArrayUserType.STRING2
 
listChecksumAlgorithms(Current) - Method in class ome.services.blitz.repo.ManagedRepositoryI
 
listFiles(String, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
 
listImports(Current) - Method in class ome.services.blitz.repo.ManagedRepositoryI
 
LISTOBJECTARRAY_TO_RTYPESEQSEQ - Static variable in class omero.util.IceMapper
 
listProcesses(Collection<Long>) - Method in class ome.services.blitz.repo.ProcessContainer
 
ListRequestsI - Class in omero.cmd.basic
 
ListRequestsI(OmeroContext) - Constructor for class omero.cmd.basic.ListRequestsI
 
listSqlTypes() - Static method in enum ome.model.units.UNITS
 
ln(double, double, double, double) - Method in class ome.services.roi.GeomTool
 
load() - Method in class ome.formats.importer.ImportConfig.Value
Loads properties from various locations.
load(FileDeleter.Type) - Method in class ome.services.delete.files.FileDeleter
Lookup the ids which are scheduled for deletion.
load(FileDeleter.Type) - Method in class ome.services.delete.files.FileDeleterGraphState
Deprecated.
Lookup the ids which are scheduled for deletion from the GraphState.
load(List<Object[]>) - Method in class ome.services.eventlogs.EventLogQueue
 
load(Long, String, Long, String, Integer) - Method in class ome.services.eventlogs.EventLogQueue
Guarantees that the given arguments are available somewhere in the queue returning true if they were newly added.
load(Session) - Method in class ome.services.graphs.BaseGraphSpec
Deprecated.
 
load(Session) - Method in interface ome.services.graphs.GraphSpec
Deprecated.
Loads the object that this spec points to.
load() - Method in class ome.services.RenderingBean
Implemented as specified by the RenderingEngine interface.
load(long, boolean) - Method in class ome.services.scripts.ScriptRepoHelper
 
load(long, Session, SqlAction, boolean) - Method in class ome.services.scripts.ScriptRepoHelper
 
load() - Method in class ome.services.util.DBUserCheck
 
load() - Method in interface omeis.providers.re.RenderingEngine
Creates a instance of the rendering engine.
load() - Method in class omero.cmd.graphs.ChmodI
Deprecated.
 
load(String[]) - Static method in class prefs
Loads a profile from Properties files, or properly formatted System.in input if no files are given.
load_async(AMD_RenderingEngine_load, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
load_nowarn(String[]) - Static method in class prefs
Performs the same actions as prefs.load(String[]) but does not throw prefs.CONFLICT if a key already exists.
loadAll() - Method in class ome.formats.importer.ImportConfig
Loads all the values for which it makes sense to have a preferences values.
loadAll(boolean) - Method in class ome.services.scripts.ScriptRepoHelper
Walks all files in the repository (via ScriptRepoHelper.iterate() and adds them if not found in the database.
loadAllMetadata(long) - Method in class ome.services.ThumbnailCtx
Retrieves all thumbnail metadata available in the database for a given Pixels ID.
loadAndPrepareMetadata(Set<Long>, int) - Method in class ome.services.ThumbnailCtx
Bulk loads and prepares metadata for a group of pixels sets.
loadAndPrepareMetadata(Set<Long>, Dimension) - Method in class ome.services.ThumbnailCtx
Bulk loads and prepares metadata for a group of pixels sets.
loadAndPrepareMetadata(Set<Long>, Dimension, boolean) - Method in class ome.services.ThumbnailCtx
Bulk loads and prepares metadata for a group of pixels sets.
loadAndPrepareRenderingSettings(Set<Long>) - Method in class ome.services.ThumbnailCtx
Bulk loads a set of rendering settings for a group of pixels sets and prepares our internal data structures.
loadAndPrepareRenderingSettings(long, long) - Method in class ome.services.ThumbnailCtx
Loads and prepares a rendering settings for a Pixels ID and RenderingDef ID.
loadAnnotation(Set<Long>) - Method in interface ome.api.IMetadata
Loads the specified annotations.
loadAnnotation(Set<Long>) - Method in class ome.logic.MetadataImpl
Implemented as specified by the IMetadata I/F
loadAnnotation_async(AMD_IMetadata_loadAnnotation, List<Long>, Current) - Method in class ome.services.blitz.impl.MetadataI
 
loadAnnotations(Class<T>, Set<Long>, Set<String>, Set<Long>, Parameters) - Method in interface ome.api.IMetadata
Loads all the annotations of given types, that have been attached to the specified rootNodes for the specified annotatorIds.
loadAnnotations(Class<T>, Set<Long>, Set<String>, Set<Long>, Parameters) - Method in class ome.logic.MetadataImpl
Implemented as specified by the IMetadata I/F
loadAnnotations_async(AMD_IMetadata_loadAnnotations, String, List<Long>, List<String>, List<Long>, Parameters, Current) - Method in class ome.services.blitz.impl.MetadataI
 
loadAnnotationsUsedNotOwned(Class, long) - Method in interface ome.api.IMetadata
Loads the annotations of a given type used by the specified user but not owned by the user.
loadAnnotationsUsedNotOwned(Class, long) - Method in class ome.logic.MetadataImpl
Implemented as specified by the IMetadata I/F
loadAnnotationsUsedNotOwned_async(AMD_IMetadata_loadAnnotationsUsedNotOwned, String, long, Current) - Method in class ome.services.blitz.impl.MetadataI
 
loadChannelAcquisitionData(Set<Long>) - Method in interface ome.api.IMetadata
Loads the logical channels and the acquisition metadata related to them.
loadChannelAcquisitionData(Set<Long>) - Method in class ome.logic.MetadataImpl
Implemented as specified by the IMetadata I/F
loadChannelAcquisitionData_async(AMD_IMetadata_loadChannelAcquisitionData, List<Long>, Current) - Method in class ome.services.blitz.impl.MetadataI
 
loadCollection(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
loadContainerHierarchy(Class<T>, Set<Long>, Parameters) - Method in interface ome.api.IContainer
Retrieves hierarchy trees rooted by a given node (unless orphan is specified -- See below) This method also retrieves the Experimenters linked to the objects in the tree.
loadContainerHierarchy(Class, Set, Parameters) - Method in class ome.logic.PojosImpl
Implemented as specified by the IContainer I/F
loadContainerHierarchy_async(AMD_IContainer_loadContainerHierarchy, String, List<Long>, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI
 
loaded - Variable in class ome.services.blitz.fire.SessionManagerI
 
loadedObjects(int) - Method in class ome.services.sessions.stats.DelegatingStats
 
loadedObjects(int) - Method in class ome.services.sessions.stats.NullSessionStats
 
loadedObjects(int) - Method in interface ome.services.sessions.stats.SessionStats
 
loadedObjects(int) - Method in class ome.services.sessions.stats.SimpleSessionStats
 
loadEntity(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
loader - Variable in class ome.services.eventlogs.EventLogFailure
 
loader - Variable in class ome.services.fulltext.FullTextIndexer
 
loader - Variable in class ome.services.pixeldata.PixelDataHandler
 
loadEventContext(boolean) - Method in class ome.security.basic.BasicSecuritySystem
 
loadEventContext(boolean, boolean) - Method in class ome.security.basic.BasicSecuritySystem
 
loadEventContext(boolean) - Method in interface ome.security.SecuritySystem
Prepares the current EventContext instance with the current Principal.
loadEventContext(boolean) - Method in class ome.security.SecuritySystemHolder
 
loadEventContext(boolean) - Method in class ome.security.sharing.SharingSecuritySystem
 
loadFileAnnotation() - Method in class omero.cmd.fs.OriginalMetadataRequestI
loadFileset() - Method in class omero.cmd.fs.OriginalMetadataRequestI
Searches for a Fileset attached to this Image, and if present, uses Bio-Formats to parse the metadata into the OriginalMetadataResponse instance.
loadFilesets(List<Long>, Current) - Method in interface ome.services.blitz.repo.RepositoryDao
Load filesets by id.
loadFilesets(List<Long>, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
 
loadGui() - Method in class ome.formats.importer.ImportConfig
Loads gui specific values for which it makes sense to have a preferences values.
loadInstrument(long) - Method in interface ome.api.IMetadata
Loads the instrument and its components i.e. detectors, objectives, etc.
loadInstrument(long) - Method in class ome.logic.MetadataImpl
Implemented as specified by the IMetadata I/F
loadInstrument_async(AMD_IMetadata_loadInstrument, long, Current) - Method in class ome.services.blitz.impl.MetadataI
 
loadLdapGroups(String, DistinguishedName) - Method in class ome.logic.LdapImpl
Deprecated.
loadLogFile() - Method in class ome.formats.importer.ImportLibrary.ImportCallback
 
loadLogFiles(Class<? extends IObject>, Set<Long>) - Method in interface ome.api.IMetadata
Find the original file IDs for the import logs corresponding to the given Image or Fileset IDs.
loadLogFiles(Class<? extends IObject>, Set<Long>) - Method in class ome.logic.MetadataImpl
 
loadLogFiles_async(AMD_IMetadata_loadLogFiles, String, List<Long>, Current) - Method in class ome.services.blitz.impl.MetadataI
 
loadMeasuredRois(Session, long, long) - Method in class ome.services.blitz.impl.RoiI
 
loadMembers(ShareData) - Method in class ome.services.sharing.ShareBean
 
loadOriginalFile(RawFileStorePrx) - Method in class ome.formats.importer.ImportLibrary
Use RawFileStorePrx.getFileId() in order to load the OriginalFile that the service argument is acting on.
loadPermissions(Session) - Method in class ome.security.basic.BasicEventContext
 
loadPermissions(Session) - Method in class ome.security.basic.CurrentDetails
loadRenderingDef(long) - Method in class ome.services.RenderingBean
Implemented as specified by the RenderingEngine interface.
loadRenderingDef(long) - Method in interface omeis.providers.re.RenderingEngine
Loads a specific set of rendering settings that does not necessarily have to be linked to the given Pixels set.
loadRenderingDef_async(AMD_RenderingEngine_loadRenderingDef, long, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
loadRndSettings(long) - Method in interface ome.api.IPixels
Loads a specific set of rendering settings with the following objects pre-linked: renderingDef.quantization renderingDef.model renderingDef.waveRendering renderingDef.waveRendering.color renderingDef.waveRendering.family renderingDef.spatialDomainEnhancement
loadRndSettings(long) - Method in class ome.logic.PixelsImpl
Implemented as specified by the IPixels I/F.
loadRndSettings_async(AMD_IPixels_loadRndSettings, long, Current) - Method in class ome.services.blitz.impl.PixelsI
 
loadScripts(ServiceFactory, Parameters) - Method in class ome.services.scripts.ScriptFinder
Load all scripts that match the name, hash, and format for script
loadSpecifiedAnnotations(Class, Set<String>, Set<String>, Parameters) - Method in interface ome.api.IMetadata
Loads all the annotations of a given type.
loadSpecifiedAnnotations(Class, Set<String>, Set<String>, Parameters) - Method in class ome.logic.MetadataImpl
Implemented as specified by the IMetadata I/F
loadSpecifiedAnnotations_async(AMD_IMetadata_loadSpecifiedAnnotations, String, List<String>, List<String>, Parameters, Current) - Method in class ome.services.blitz.impl.MetadataI
 
loadSpecifiedAnnotationsLinkedTo(Class, Set<String>, Set<String>, Class, Set<Long>, Parameters) - Method in interface ome.api.IMetadata
Loads the annotations of a given type linked to the specified objects.
loadSpecifiedAnnotationsLinkedTo(Class, Set<String>, Set<String>, Class, Set<Long>, Parameters) - Method in class ome.logic.MetadataImpl
Implemented as specified by the IMetadata I/F
loadSpecifiedAnnotationsLinkedTo_async(AMD_IMetadata_loadSpecifiedAnnotationsLinkedTo, String, List<String>, List<String>, String, List<Long>, Parameters, Current) - Method in class ome.services.blitz.impl.MetadataI
 
loadTagContent(Set<Long>, Parameters) - Method in interface ome.api.IMetadata
Loads the Tag Set if the id is specified otherwise loads all the Tag Set.
loadTagContent(Set<Long>, Parameters) - Method in class ome.logic.MetadataImpl
Implemented as specified by the IMetadata I/F
loadTagContent_async(AMD_IMetadata_loadTagContent, List<Long>, Parameters, Current) - Method in class ome.services.blitz.impl.MetadataI
 
loadTagSets(Parameters) - Method in interface ome.api.IMetadata
Loads all the tag Sets.
loadTagSets(Parameters) - Method in class ome.logic.MetadataImpl
Implemented as specified by the IMetadata I/F
loadTagSets_async(AMD_IMetadata_loadTagSets, Parameters, Current) - Method in class ome.services.blitz.impl.MetadataI
 
local(AbstractRepositoryI, PublicRepositoryI, Current) - Method in class ome.services.blitz.repo.RawAccessRequestI
Method called locally to the repository during RawAccessRequestI.rawAccess().
LocalAdmin - Interface in ome.api.local
Provides local (internal) extensions for administration
LocalCompress - Interface in ome.api.local
Provides methods for performing scaling (change of the image size through interpolation or other means) on BufferedImages.
LocalConfig - Interface in ome.api.local
Provides local (internal) extensions for configuration.
LocalQuery - Interface in ome.api.local
Provides local (internal) extensions for querying
localQuery - Variable in class ome.logic.UpdateImpl
 
LocalShare - Interface in ome.api.local
Provides local (internal) extensions for shares
LocalUpdate - Interface in ome.api.local
Provides local (internal) extensions for updating
loci.ome.io - package loci.ome.io
OME I/O: a library for OME database import, upload and download.
loci.ome.io.services - package loci.ome.io.services
 
lock() - Static method in class ome.util.DetailsFieldBridge
 
locked - Variable in class ome.model.roi.Shape
 
LOCKED - Static variable in class ome.model.roi.Shape
 
LockTimeout - Exception in ome.conditions
Server could not acquire necessary lock.
LockTimeout(String, long, int) - Constructor for exception ome.conditions.LockTimeout
 
log - Variable in class ome.formats.importer.exclusions.AbstractFileExclusion
 
log - Variable in class ome.formats.importer.transfers.AbstractFileTransfer
 
log - Variable in class ome.formats.importer.util.ErrorHandler
 
log - Variable in class ome.security.auth.ConfigurablePasswordProvider
 
log - Variable in class ome.security.basic.AbstractSecurityFilter
 
log(String) - Method in class ome.security.basic.OmeroInterceptor
 
log - Variable in class ome.services.blitz.impl.AbstractAmdServant
 
log - Variable in class ome.services.blitz.redirect.AbstractRedirector
 
log - Static variable in class ome.services.delete.DeleteBean
 
log - Variable in class ome.services.eventlogs.EventLogFailure
 
log - Variable in class ome.services.eventlogs.EventLogLoader
 
log - Variable in class ome.services.fulltext.BridgeHelper
 
log(String) - Method in class ome.services.graphs.GraphEntry
Deprecated.
Similar to GraphEntry.toString() but used to
log - Variable in class ome.services.mail.MailSender
 
log - Variable in class ome.services.roi.GeomTool
 
log - Variable in class ome.services.roi.PixelData
 
log - Variable in class ome.services.scripts.ScriptFinder
 
log - Variable in class ome.services.scripts.ScriptRepoHelper
 
log - Static variable in class ome.services.sharing.ShareBean
 
log - Variable in class ome.services.sharing.ShareStore
 
log - Variable in class ome.services.throttling.AbstractThrottlingStrategy
 
log - Static variable in class ome.services.util.DBEnumCheck
 
log - Static variable in class ome.services.util.DBPatchCheck
 
log - Static variable in class ome.services.util.DBUserCheck
 
log - Static variable in class ome.services.util.JvmSettingsCheck
 
log - Static variable in class ome.services.util.NamespaceCheck
 
log - Static variable in class ome.services.util.ServerDirectoryCheck
 
log - Static variable in class ome.services.util.ServerVersionCheck
 
log(String) - Method in class ome.tools.hibernate.EventMethodInterceptor
 
log - Static variable in class ome.util.ModelMapper
 
log - Variable in class ome.util.SqlAction.Impl
 
log - Static variable in class ome.util.Validation
 
log - Static variable in class ome.util.Validator
 
log - Variable in class omero.util.ObjectFactoryRegistry
 
LOG_FILE_NS - Static variable in class pojos.FileAnnotationData
The name space used to indicate that the FileAnnotation is an import log file.
LOGARITHMIC - Static variable in class omeis.providers.re.quantum.QuantumFactory
Flag to select a logarithmic map for the quantization process.
LogarithmicMap - Class in omeis.providers.re.quantum
This class implements the QuantumMap interface.
LogarithmicMap() - Constructor for class omeis.providers.re.quantum.LogarithmicMap
 
LOGFILE - Static variable in class ome.formats.importer.util.IniFileLoader
Public in order to configure LogAppenderProxy, but then the value might as well be configured in the log4j.properties file
logFile - Variable in class ome.services.blitz.repo.ManagedImportLocationI
 
logFileId - Variable in class ome.formats.importer.ImportEvent.POST_UPLOAD_EVENT
 
logger() - Method in class ome.services.fulltext.BridgeHelper
 
LOGGER - Static variable in class ome.services.util.DBUnicodeUnitsCheck
 
LoggingImportMonitor - Class in ome.formats.importer.cli
Basic import process monitor that writes information to the log.
LoggingImportMonitor() - Constructor for class ome.formats.importer.cli.LoggingImportMonitor
 
logicalChannel - Variable in class ome.model.core.Channel
 
LOGICALCHANNEL - Static variable in class ome.model.core.Channel
 
LogicalChannel - Class in ome.model.core
These filter definitions are used by the security system to eliminate non-readable objects from queries.
LogicalChannel() - Constructor for class ome.model.core.LogicalChannel
 
LogicalChannel(Long) - Constructor for class ome.model.core.LogicalChannel
 
LogicalChannel(Long, boolean) - Constructor for class ome.model.core.LogicalChannel
Main constructor.
LogicalChannel.Details - Class in ome.model.core
 
LogicalChannel.Details() - Constructor for class ome.model.core.LogicalChannel.Details
 
LogicalChannel.Details(Object[]) - Constructor for class ome.model.core.LogicalChannel.Details
 
login(Principal) - Method in class ome.security.basic.BasicSecuritySystem
 
login(Principal) - Method in class ome.security.basic.CurrentDetails
 
login(BasicEventContext) - Method in class ome.security.basic.CurrentDetails
Login method which can be used by the security system to replace the existing BasicEventContext.
login(Principal) - Method in interface ome.security.basic.PrincipalHolder
Add a new principal context to the stack.
login(BasicEventContext) - Method in interface ome.security.basic.PrincipalHolder
Allow logging in directly with an event context.
login(Principal) - Method in interface ome.security.SecuritySystem
stores this Principal instance in the current thread context for authenticating and authorizing all actions.
login(Principal) - Method in class ome.security.SecuritySystemHolder
 
login(Principal) - Method in class ome.security.sharing.SharingSecuritySystem
 
Login - Class in ome.system
Provides simplified handling of login properties when creating a ServiceFactory.
Login(String, String) - Constructor for class ome.system.Login
standard constructor which leaves OMERO_GROUP and OMERO_EVENT null.
Login(String, String, String, String) - Constructor for class ome.system.Login
extended constructor.
loginAttempt(String, Boolean) - Method in class ome.security.auth.ConfigurablePasswordProvider
 
LoginAttemptListener - Class in ome.security.auth
Listens for any LoginAttemptMessage.
LoginAttemptListener(int, long) - Constructor for class ome.security.auth.LoginAttemptListener
 
LoginAttemptMessage - Class in ome.services.messages
Published when any check is performed against a password.
LoginAttemptMessage(Object, String, Boolean) - Constructor for class ome.services.messages.LoginAttemptMessage
 
logout() - Method in class ome.formats.OMEROMetadataStoreClient
Destroys the sessionFactory and closes the client.
logout() - Method in class ome.security.basic.BasicSecuritySystem
 
logout() - Method in class ome.security.basic.CurrentDetails
 
logout() - Method in interface ome.security.basic.PrincipalHolder
Pop the last created principal context and return the number of active contexts remaining.
logout() - Method in interface ome.security.SecuritySystem
clears the top Principal instance from the current thread context.
logout() - Method in class ome.security.SecuritySystemHolder
 
logout() - Method in class ome.security.sharing.SharingSecuritySystem
 
logPhase(String) - Method in class ome.services.graphs.GraphStep
Deprecated.
 
logResults(int) - Method in class ome.services.graphs.GraphStep
Deprecated.
 
logs - Variable in class ome.model.meta.Event
 
LOGS - Static variable in class ome.model.meta.Event
 
logSummary() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
log in info level the main statistics
logVersionInfo(String) - Method in class ome.formats.OMEROMetadataStoreClient
 
LONG - Static variable in class ome.util.PixelData
Identifies the type used to store pixel values.
LONG - Static variable in class omeis.providers.re.data.PlaneFactory
Identifies the type used to store pixel values.
LongAnnotation - Class in ome.model.annotations
 
LongAnnotation() - Constructor for class ome.model.annotations.LongAnnotation
 
LongAnnotation(Long) - Constructor for class ome.model.annotations.LongAnnotation
 
LongAnnotation(Long, boolean) - Constructor for class ome.model.annotations.LongAnnotation
Main constructor.
LongAnnotationData - Class in pojos
Wraps a long annotation.
LongAnnotationData(long) - Constructor for class pojos.LongAnnotationData
Creates a new instance.
LongAnnotationData() - Constructor for class pojos.LongAnnotationData
Creates a new instance.
LongAnnotationData(LongAnnotation) - Constructor for class pojos.LongAnnotationData
Creates a new instance.
LongCounter - Class in ome.services.sessions.stats
Counter object which increments an internal long by some integer value, and according to some strategy publishes an InternalMessage subclass.
LongCounter(int) - Constructor for class ome.services.sessions.stats.LongCounter
 
longValue - Variable in class ome.model.annotations.LongAnnotation
 
LONGVALUE - Static variable in class ome.model.annotations.LongAnnotation
 
lookup(ParamsCache.Key) - Method in class ome.services.blitz.util.ParamsCache
Called by the LoadingCache when a cache-miss occurs.
lookup() - Method in class ome.services.eventlogs.EventLogQueue
 
lookup(long) - Method in class ome.services.procs.ProcessorSkeleton
 
lookup(String, Parameters) - Method in class ome.services.query.ClassQuerySource
 
lookup(String, Parameters) - Method in class ome.services.query.NullQuerySource
 
lookup(String, Parameters) - Method in class ome.services.query.QueryFactory
 
lookup(String, Parameters) - Method in class ome.services.query.QuerySource
map the queryID argument to some Query instance (including null).
lookup(String, Parameters) - Method in class ome.services.query.StringQuerySource
 
lookup(String, ApplicationContext) - Method in class ome.system.OmeroContext.Locator
uses ContextSingletonBeanFactoryLocator.createDefinition(java.lang.String, java.lang.String) and ContextSingletonBeanFactoryLocator.initializeDefinition(org.springframework.beans.factory.BeanFactory) to create a new context from a given definition.
lookupAll() - Method in class ome.services.blitz.util.ParamsCache
Called from a Quartz cron trigger for periodically reloading all scripts.
lookupClusterNodes() - Method in class ome.services.blitz.fire.Registry.Impl
 
lookupClusterNodes() - Method in interface ome.services.blitz.fire.Registry
Returns all found cluster nodes or null if something goes wrong during lookup (null QueryPrx for example)
lookupExperimenter(String) - Method in interface ome.api.IAdmin
look up an Experimenter and all related groups by name.
lookupExperimenter(String) - Method in class ome.logic.AdminImpl
 
lookupExperimenter_async(AMD_IAdmin_lookupExperimenter, String, Current) - Method in class ome.services.blitz.impl.AdminI
 
lookupExperimenters() - Method in interface ome.api.IAdmin
Looks up all experimenters present and all related groups.
lookupExperimenters() - Method in class ome.logic.AdminImpl
 
lookupExperimenters_async(AMD_IAdmin_lookupExperimenters, Current) - Method in class ome.services.blitz.impl.AdminI
 
lookupGroup(String) - Method in interface ome.api.IAdmin
look up an ExperimenterGroup and all contained users by name.
lookupGroup(String) - Method in class ome.logic.AdminImpl
 
lookupGroup_async(AMD_IAdmin_lookupGroup, String, Current) - Method in class ome.services.blitz.impl.AdminI
 
lookupGroups() - Method in interface ome.api.IAdmin
Looks up all groups present and all related experimenters.
lookupGroups() - Method in class ome.logic.AdminImpl
 
lookupGroups_async(AMD_IAdmin_lookupGroups, Current) - Method in class ome.services.blitz.impl.AdminI
 
lookupLdapAuthExperimenter(long) - Method in interface ome.api.IAdmin
Looks up experimenters who uses LDAP authentication (has set dn on password table).
lookupLdapAuthExperimenter(long) - Method in class ome.logic.AdminImpl
 
lookupLdapAuthExperimenter(Long) - Method in class ome.logic.LdapImpl
Queries the LDAP server and returns the DN for the specified OMERO user ID.
lookupLdapAuthExperimenter_async(AMD_IAdmin_lookupLdapAuthExperimenter, long, Current) - Method in class ome.services.blitz.impl.AdminI
 
lookupLdapAuthExperimenters() - Method in interface ome.api.IAdmin
Looks up all id of experimenters who uses LDAP authentication (has set dn on password table).
lookupLdapAuthExperimenters() - Method in class ome.logic.AdminImpl
 
lookupLdapAuthExperimenters() - Method in class ome.logic.LdapImpl
Queries the LDAP server and returns the DN for all OMERO users that have the ldap flag enabled.
lookupLdapAuthExperimenters_async(AMD_IAdmin_lookupLdapAuthExperimenters, Current) - Method in class ome.services.blitz.impl.AdminI
 
lookupManagedRepository() - Method in class ome.formats.importer.ImportLibrary
Retrieves the first managed repository from the list of current active repositories.
lookupMonitorServers() - Method in class ome.services.blitz.fire.Registry.Impl
 
lookupMonitorServers() - Method in interface ome.services.blitz.fire.Registry
 
lookupPixels(long) - Method in class ome.services.RenderingBean
Implemented as specified by the RenderingEngine interface.
lookupPixels(long) - Method in interface omeis.providers.re.RenderingEngine
Loads the Pixels set this Rendering Engine is for.
lookupPixels_async(AMD_RenderingEngine_lookupPixels, long, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
lookupProcessors() - Method in class ome.services.blitz.fire.Registry.Impl
 
lookupProcessors() - Method in interface ome.services.blitz.fire.Registry
 
lookupRenderingDef(long) - Method in class ome.services.RenderingBean
Implemented as specified by the RenderingEngine interface.
lookupRenderingDef(long) - Method in interface omeis.providers.re.RenderingEngine
Loads the rendering settings associated to the specified pixels set.
lookupRenderingDef_async(AMD_RenderingEngine_lookupRenderingDef, long, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
lookupRepositories() - Method in class ome.services.blitz.fire.Registry.Impl
 
lookupRepositories() - Method in interface ome.services.blitz.fire.Registry
 
lookupSymbol(UnitsElectricPotential) - Static method in class omero.model.ElectricPotentialI
 
lookupSymbol(UnitsFrequency) - Static method in class omero.model.FrequencyI
 
lookupSymbol(UnitsLength) - Static method in class omero.model.LengthI
 
lookupSymbol(UnitsPower) - Static method in class omero.model.PowerI
 
lookupSymbol(UnitsPressure) - Static method in class omero.model.PressureI
 
lookupSymbol(UnitsTemperature) - Static method in class omero.model.TemperatureI
 
lookupSymbol(UnitsTime) - Static method in class omero.model.TimeI
 
lookupTable - Variable in class ome.model.core.Channel
 
LOOKUPTABLE - Static variable in class ome.model.core.Channel
 
lookupTable - Variable in class ome.model.display.ChannelBinding
 
LOOKUPTABLE - Static variable in class ome.model.display.ChannelBinding
 
lookupTables() - Method in class ome.services.blitz.fire.Registry.Impl
 
lookupTables() - Method in interface ome.services.blitz.fire.Registry
 
loop(int, long) - Method in class omero.cmd.CmdCallbackI
Calls block(long) "loops" number of times with the "ms" argument.
loop - Variable in class omero.util.RPSTileData
 
lotNumber - Variable in class ome.model.acquisition.Detector
 
LOTNUMBER - Static variable in class ome.model.acquisition.Detector
 
lotNumber - Variable in class ome.model.acquisition.Dichroic
 
LOTNUMBER - Static variable in class ome.model.acquisition.Dichroic
 
lotNumber - Variable in class ome.model.acquisition.Filter
 
LOTNUMBER - Static variable in class ome.model.acquisition.Filter
 
lotNumber - Variable in class ome.model.acquisition.FilterSet
 
LOTNUMBER - Static variable in class ome.model.acquisition.FilterSet
 
lotNumber - Variable in class ome.model.acquisition.LightSource
 
LOTNUMBER - Static variable in class ome.model.acquisition.LightSource
 
lotNumber - Variable in class ome.model.acquisition.Microscope
 
LOTNUMBER - Static variable in class ome.model.acquisition.Microscope
 
lotNumber - Variable in class ome.model.acquisition.Objective
 
LOTNUMBER - Static variable in class ome.model.acquisition.Objective
 
lowerLimit - Variable in class ome.model.display.PlaneSlicingContext
 
LOWERLIMIT - Static variable in class ome.model.display.PlaneSlicingContext
 
lowestEntityId - Variable in class ome.services.pixeldata.PersistentEventLogLoader
The lowest entity id from a single dataPerUser set.
lsid - Variable in class ome.model.meta.ExternalInfo
 
LSID - Static variable in class ome.model.meta.ExternalInfo
 
lsid(Class, long) - Method in class ome.services.db.DatabaseIdentity
 
lsid(Class, long, long) - Method in class ome.services.db.DatabaseIdentity
 
lsid(String, String) - Method in class ome.services.db.DatabaseIdentity
 
lsid(String, String, String) - Method in class ome.services.db.DatabaseIdentity
 
LSID - Class in ome.util
This class represents an LSID as used by the OME-XML data model.
LSID(Class, int...) - Constructor for class ome.util.LSID
Default constructor.
LSID(String) - Constructor for class ome.util.LSID
Constructor for non-standard LSIDs.
LSID(String, boolean) - Constructor for class ome.util.LSID
Constructor for standard LSIDs that should be parsed.
LsidUtils - Class in ome.tools.lsid
 
LsidUtils() - Constructor for class ome.tools.lsid.LsidUtils
 
LuceneQueryBuilder - Class in ome.util.search
Utility class for building lucene queries

Example:
Fields to search for: 'name', 'description'
Input query: a b AND c AND d f

will be transformed to this lucene expression:
name:a description:a name:f description:f ((name:b description:b) AND (name:c description:c) AND (name:d description:d))

LuceneQueryBuilder() - Constructor for class ome.util.search.LuceneQueryBuilder
 

M

mailSender - Variable in class ome.logic.AdminImpl
 
MailSender - Class in ome.services.mail
Basic bean with setter injection that can be used as a base class for other senders.
MailSender() - Constructor for class ome.services.mail.MailSender
 
mailSender - Variable in class ome.services.mail.MailUtil
 
MailUtil - Class in ome.services.mail
Methods for dealing with the preparation of JavaMail MIME messages.
MailUtil(String, JavaMailSender) - Constructor for class ome.services.mail.MailUtil
 
mailUtil - Variable in class ome.services.sharing.ShareBean
 
main(String[]) - Static method in class loci.ome.io.OmeroReader
A simple command line tool for downloading images from OMERO.
main(String[]) - Static method in class ome.formats.importer.cli.CommandLineImporter
Command line application entry point which parses CLI arguments and passes them into the importer.
main(String[]) - Static method in class ome.security.auth.PasswordUtil
Main method which takes exactly one argument, passes it to PasswordUtil.preparePassword(String) and prints the results on System.out.
main(String[]) - Static method in class ome.services.blitz.Entry
Entry point to the server.
main(String[]) - Static method in class ome.services.blitz.Status
Uses the passed args to create an Communicator.
Main - Class in ome.services.fulltext
Commandline entry-point for various full text actions.
Main() - Constructor for class ome.services.fulltext.Main
 
main(String[]) - Static method in class ome.services.fulltext.Main
 
main(String[]) - Static method in class ome.services.graphs.GraphPathReport
Generate a Sphinx report of OMERO Hibernate entities.
main(String[]) - Static method in class ome.services.sharing.BlobShareStore
 
main(String[]) - Static method in class ome.services.util.JvmSettingsCheck
 
main(String[]) - Static method in class ome.tools.FileSystem
 
main(String[]) - Static method in class omero.cmd.fs.OriginalMetadataRequestI
 
main(String[]) - Static method in class omero.util.TempFileManager
Command-line interface to the global TempFileManager instance ( #manger).
main(String[]) - Static method in class prefs
Entry point to the prefs command line too.
makeAdjustedCurrent(Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
 
makeCheckedDirs(LinkedList<CheckedPath>, boolean, Session, ServiceFactory, SqlAction, EventContext) - Method in class ome.services.blitz.repo.ManagedRepositoryI
Checks for the top-level user directory restriction before calling PublicRepositoryI#makeCheckedDirs(LinkedList, boolean, Current)
makeCheckedDirs(LinkedList<CheckedPath>, boolean, Session, ServiceFactory, SqlAction, EventContext) - Method in class ome.services.blitz.repo.PublicRepositoryI
Internal method to be used by subclasses to perform any extra checks on the listed of CheckedPath instances before allowing the creation of directories.
makeDir(String, boolean, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
Create a nested path in the repository.
makeDir(CheckedPath, boolean, Session, ServiceFactory, SqlAction, EventContext) - Method in class ome.services.blitz.repo.PublicRepositoryI
 
makeDirs(PublicRepositoryI, List<CheckedPath>, boolean, Current) - Method in interface ome.services.blitz.repo.RepositoryDao
Create a number of directories in a single transaction, using the PublicRepositoryI instance as a callback for implementation specific logic.
makeDirs(PublicRepositoryI, List<CheckedPath>, boolean, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
 
makeElectricPotential(double, Unit<ElectricPotential>) - Static method in class ome.formats.model.UnitsFactory
 
makeElectricPotential(double, UnitsElectricPotential) - Static method in class ome.formats.model.UnitsFactory
 
makeElectricPotentialUnitXML(String) - Static method in class ome.formats.model.UnitsFactory
 
makeElectricPotentialUnitXML(String) - Static method in class ome.model.units.ElectricPotential
 
makeElectricPotentialXML(double, String) - Static method in class ome.formats.model.UnitsFactory
 
makeElectricPotentialXML(double, String) - Static method in class ome.model.units.ElectricPotential
 
makeFactory(client) - Static method in class omero.model.DetailsI
 
makeFactory(client) - Static method in class omero.model.ElectricPotentialI
 
makeFactory(client) - Static method in class omero.model.FrequencyI
 
makeFactory(client) - Static method in class omero.model.LengthI
 
makeFactory(client) - Static method in class omero.model.PowerI
 
makeFactory(client) - Static method in class omero.model.PressureI
 
makeFactory(client) - Static method in class omero.model.TemperatureI
 
makeFactory(client) - Static method in class omero.model.TimeI
 
makeFrequency(double, Unit<Frequency>) - Static method in class ome.formats.model.UnitsFactory
 
makeFrequency(double, UnitsFrequency) - Static method in class ome.formats.model.UnitsFactory
 
makeFrequencyUnitXML(String) - Static method in class ome.formats.model.UnitsFactory
 
makeFrequencyUnitXML(String) - Static method in class ome.model.units.Frequency
 
makeFrequencyXML(double, String) - Static method in class ome.formats.model.UnitsFactory
 
makeFrequencyXML(double, String) - Static method in class ome.model.units.Frequency
 
makeLength(double, Unit<Length>) - Static method in class ome.formats.model.UnitsFactory
 
makeLength(double, UnitsLength) - Static method in class ome.formats.model.UnitsFactory
 
makeLengthUnitXML(String) - Static method in class ome.formats.model.UnitsFactory
 
makeLengthUnitXML(String) - Static method in class ome.model.units.Length
 
makeLengthXML(double, String) - Static method in class ome.formats.model.UnitsFactory
 
makeLengthXML(double, String) - Static method in class ome.model.units.Length
 
makeNew(int) - Method in class ome.util.mem.CopiableArray
Creates a new array of the speficied size.
MakeNextDirectory - Class in ome.services.blitz.repo.path
Abstracts a pattern for using repository template path directories in {@link ManagedRepositoryI.TemplateDirectoryCreator): pinpoint the next directory to use, then try to use it while watching for conflicts from other similar threads.
MakeNextDirectory() - Constructor for class ome.services.blitz.repo.path.MakeNextDirectory
 
MakePathComponentSafe - Class in ome.services.blitz.repo.path
 
MakePathComponentSafe(FilePathRestrictions...) - Constructor for class ome.services.blitz.repo.path.MakePathComponentSafe
 
makePower(double, Unit<Power>) - Static method in class ome.formats.model.UnitsFactory
 
makePower(double, UnitsPower) - Static method in class ome.formats.model.UnitsFactory
 
makePowerUnitXML(String) - Static method in class ome.formats.model.UnitsFactory
 
makePowerUnitXML(String) - Static method in class ome.model.units.Power
 
makePowerXML(double, String) - Static method in class ome.formats.model.UnitsFactory
 
makePowerXML(double, String) - Static method in class ome.model.units.Power
 
makePressure(double, Unit<Pressure>) - Static method in class ome.formats.model.UnitsFactory
 
makePressure(double, UnitsPressure) - Static method in class ome.formats.model.UnitsFactory
 
makePressureUnitXML(String) - Static method in class ome.formats.model.UnitsFactory
 
makePressureUnitXML(String) - Static method in class ome.model.units.Pressure
 
makePressureXML(double, String) - Static method in class ome.formats.model.UnitsFactory
 
makePressureXML(double, String) - Static method in class ome.model.units.Pressure
 
makePyramid(Pixels) - Method in class ome.io.nio.PixelsService
Creates a pixels pyramid for a given set of pixels.
makeTemperature(double, Unit<Temperature>) - Static method in class ome.formats.model.UnitsFactory
 
makeTemperature(double, UnitsTemperature) - Static method in class ome.formats.model.UnitsFactory
 
makeTemperatureUnitXML(String) - Static method in class ome.formats.model.UnitsFactory
 
makeTemperatureUnitXML(String) - Static method in class ome.model.units.Temperature
 
makeTemperatureXML(double, String) - Static method in class ome.formats.model.UnitsFactory
 
makeTemperatureXML(double, String) - Static method in class ome.model.units.Temperature
 
makeTime(double, Unit<Time>) - Static method in class ome.formats.model.UnitsFactory
 
makeTime(double, UnitsTime) - Static method in class ome.formats.model.UnitsFactory
 
makeTimeUnitXML(String) - Static method in class ome.formats.model.UnitsFactory
 
makeTimeUnitXML(String) - Static method in class ome.model.units.Time
 
makeTimeXML(double, String) - Static method in class ome.formats.model.UnitsFactory
 
makeTimeXML(double, String) - Static method in class ome.model.units.Time
 
makeXMLQuantity(double, String) - Static method in class omero.model.ElectricPotentialI
 
makeXMLQuantity(double, String) - Static method in class omero.model.FrequencyI
 
makeXMLQuantity(double, String) - Static method in class omero.model.LengthI
 
makeXMLQuantity(double, String) - Static method in class omero.model.PowerI
 
makeXMLQuantity(double, String) - Static method in class omero.model.PressureI
 
makeXMLQuantity(double, String) - Static method in class omero.model.TemperatureI
 
makeXMLQuantity(double, String) - Static method in class omero.model.TimeI
 
makeXMLUnit(String) - Static method in class omero.model.ElectricPotentialI
 
makeXMLUnit(String) - Static method in class omero.model.FrequencyI
 
makeXMLUnit(String) - Static method in class omero.model.LengthI
 
makeXMLUnit(String) - Static method in class omero.model.PowerI
 
makeXMLUnit(String) - Static method in class omero.model.PressureI
 
makeXMLUnit(String) - Static method in class omero.model.TemperatureI
 
makeXMLUnit(String) - Static method in class omero.model.TimeI
 
MANAGED_CONTEXT - Static variable in class ome.system.OmeroContext
identifier for an OmeroContext configured in classpath*:beanRefContext.xml for use by server-side processes.
managedEvent(boolean, IObject, Details, Details, Details) - Method in class ome.security.basic.OmeroInterceptor
 
managedExternalInfo(boolean, IObject, Details, Details, Details) - Method in class ome.security.basic.OmeroInterceptor
responsible for guaranteeing that external info is not modified by any users, including rot.
managedGroup(boolean, IObject, Details, Details, Details, BasicEventContext) - Method in class ome.security.basic.OmeroInterceptor
 
ManagedImportLocationI - Class in ome.services.blitz.repo
Server-side implementation of ImportLocation for also storing the CheckedPath instances for each used file.
ManagedImportLocationI() - Constructor for class ome.services.blitz.repo.ManagedImportLocationI
 
ManagedImportProcessI - Class in ome.services.blitz.repo
Represents a single import within a defined-session all running server-side.
ManagedImportProcessI(ManagedRepositoryI, Fileset, ImportLocation, ImportSettings, Current) - Constructor for class ome.services.blitz.repo.ManagedImportProcessI
Create and register a servant for servicing the import process within a managed repository.
ManagedImportRequestI - Class in ome.services.blitz.repo
Wrapper around FilesetJobLink instances which need to be handled on the server-side.
ManagedImportRequestI(Registry, TileSizes, RepositoryDao, OMEROWrapper, String) - Constructor for class ome.services.blitz.repo.ManagedImportRequestI
 
managedOwner(boolean, IObject, Details, Details, Details, BasicEventContext) - Method in class ome.security.basic.OmeroInterceptor
 
ManagedRepositoryI - Class in ome.services.blitz.repo
Extension of the PublicRepository API which only manages files under ${omero.data.dir}/ManagedRepository.
ManagedRepositoryI(String, RepositoryDao) - Constructor for class ome.services.blitz.repo.ManagedRepositoryI
Creates a ProcessContainer internally that will not be managed by background threads.
ManagedRepositoryI(String, RepositoryDao, ProcessContainer, ChecksumProviderFactory, String, String, String, Roles) - Constructor for class ome.services.blitz.repo.ManagedRepositoryI
 
ManagedServiceFactory - Class in ome.tools.spring
subclass of ome.system.ServiceFactory which retrieves managed service-instances.
ManagedServiceFactory() - Constructor for class ome.tools.spring.ManagedServiceFactory
 
ManageImageBinariesI - Class in omero.cmd.fs
Workflow for converting attached original images into OMERO5+ filesets.
ManageImageBinariesI(PixelsService, ACLVoter) - Constructor for class omero.cmd.fs.ManageImageBinariesI
 
manager - Variable in class ome.services.util.ExecutionThread
 
manager - Variable in class omero.cmd.admin.CurrentSessionsRequestI
 
manager - Variable in class omero.cmd.admin.UpdateSessionTimeoutRequestI
 
managerOrNull() - Method in class ome.services.blitz.fire.TopicManager.Impl
 
ManualFlushHibernateTemplate - Class in ome.tools.spring
 
ManualFlushHibernateTemplate() - Constructor for class ome.tools.spring.ManualFlushHibernateTemplate
 
manufacturer - Variable in class ome.model.acquisition.Detector
 
MANUFACTURER - Static variable in class ome.model.acquisition.Detector
 
manufacturer - Variable in class ome.model.acquisition.Dichroic
 
MANUFACTURER - Static variable in class ome.model.acquisition.Dichroic
 
manufacturer - Variable in class ome.model.acquisition.Filter
 
MANUFACTURER - Static variable in class ome.model.acquisition.Filter
 
manufacturer - Variable in class ome.model.acquisition.FilterSet
 
MANUFACTURER - Static variable in class ome.model.acquisition.FilterSet
 
manufacturer - Variable in class ome.model.acquisition.LightSource
 
MANUFACTURER - Static variable in class ome.model.acquisition.LightSource
 
manufacturer - Variable in class ome.model.acquisition.Microscope
 
MANUFACTURER - Static variable in class ome.model.acquisition.Microscope
 
manufacturer - Variable in class ome.model.acquisition.Objective
 
MANUFACTURER - Static variable in class ome.model.acquisition.Objective
 
map() - Method in class ome.formats.importer.ImportConfig
 
map - Variable in class ome.model.acquisition.GenericExcitationSource
 
MAP - Static variable in class ome.model.acquisition.GenericExcitationSource
 
map - Variable in class ome.model.acquisition.ImagingEnvironment
 
MAP - Static variable in class ome.model.acquisition.ImagingEnvironment
 
map(List<String>) - Method in class ome.services.blitz.impl.MetadataI
 
map(String) - Method in class ome.services.blitz.impl.MetadataI
 
map(Map<String, List<Long>>) - Method in class ome.services.sharing.ShareBean
 
map(Filterable) - Method in class ome.util.ModelMapper
 
map(Collection) - Method in class ome.util.ModelMapper
 
map(Map) - Method in class ome.util.ModelMapper
 
map() - Method in class omero.sys.ParametersI
Deprecated.
map(Filterable[]) - Method in class omero.util.IceMapper
 
MapAnnotation - Class in ome.model.annotations
 
MapAnnotation() - Constructor for class ome.model.annotations.MapAnnotation
 
MapAnnotation(Long) - Constructor for class ome.model.annotations.MapAnnotation
 
MapAnnotation(Long, boolean) - Constructor for class ome.model.annotations.MapAnnotation
Main constructor.
MapAnnotationData - Class in pojos
 
MapAnnotationData(MapAnnotation) - Constructor for class pojos.MapAnnotationData
 
MapAnnotationData() - Constructor for class pojos.MapAnnotationData
 
MapAnnotationSubethaListener - Class in ome.services.mail
Basic SimpleMessageListener which stores all received emails as MapAnnotation instances belong to root with the namespace MapAnnotationSubethaListener.NAMESPACE.
MapAnnotationSubethaListener(Executor, Principal) - Constructor for class ome.services.mail.MapAnnotationSubethaListener
 
MapAnnotationSubethaListener(Executor, String) - Constructor for class ome.services.mail.MapAnnotationSubethaListener
 
mapFlexServer(String, String) - Method in class ome.formats.importer.util.IniFileLoader
Append keep to server map
mapFromAttributes(Attributes) - Method in class ome.security.auth.GroupAttributeMapper
 
mapFromContext(Object) - Method in class ome.security.auth.GroupContextMapper
 
mapFromContext(Object) - Method in class ome.security.auth.OmeroModelContextMapper
 
mapFromContext(Object) - Method in class ome.security.auth.PersonContextMapper
 
MapPut - Class in ome.util
Simple bean which calls "map.put(key, object)" on {@link InitializingBean#afterPropertiesSet().
MapPut() - Constructor for class ome.util.MapPut
 
mapReturnValue(IceMapper, Object) - Method in class ome.services.blitz.impl.RoiI.RoiResultMapReturnMapper
 
mapReturnValue(IceMapper, Object) - Method in class ome.services.blitz.impl.RoiI.RoiResultReturnMapper
 
mapReturnValue(Object) - Method in class omero.util.IceMapper
Convert the given Object via the set IceMapper.ReturnMapping.
mapReturnValue(IceMapper, Object) - Method in interface omero.util.IceMapper.ReturnMapping
 
mapRow(ResultSet, int) - Method in class ome.util.SqlAction.DeleteLog
 
mapRow(ResultSet, int) - Method in class ome.util.SqlAction.IdRowMapper
 
mapRow(ResultSet, int) - Method in class ome.util.SqlAction.StringRowMapper
 
mapUserGroups() - Method in class ome.formats.OMEROMetadataStoreClient
Maps the user's groups for use by ScreenLogin.registerGroup() Also strips system groups from this map
mapValue - Variable in class ome.model.annotations.MapAnnotation
 
MAPVALUE - Static variable in class ome.model.annotations.MapAnnotation
 
markAndSweep() - Method in class ome.services.db.SelfCorrectingDataSource
First removes all entries in SelfCorrectingDataSource.errorTimes that are older than some given time and then uses the remaining number of errors to determine the backoff : (#^1/2)*1000 milliseconds.
markModified() - Method in class ome.services.blitz.repo.CheckedPath
Mark this existing file as having been modified at the present moment.
Mask - Class in ome.model.roi
 
Mask() - Constructor for class ome.model.roi.Mask
 
Mask(Long) - Constructor for class ome.model.roi.Mask
 
Mask(Long, boolean) - Constructor for class ome.model.roi.Mask
Main constructor.
MaskData - Class in pojos
Represents an Mask in the Euclidean space R2.
MaskData(Shape) - Constructor for class pojos.MaskData
Creates a new instance.
MaskData() - Constructor for class pojos.MaskData
Creates a new instance of MaskData.
MaskData(double, double, double, double, byte[]) - Constructor for class pojos.MaskData
Creates a new instance of the MaskData.
matches(Class, Class) - Static method in class ome.services.blitz.util.ApiConsistencyCheck
Defines what Class types match.
matches(String, String) - Method in class ome.services.messages.EventLogsMessage
 
matches(File) - Method in class ome.services.scripts.RepoFile
 
MAX - Static variable in class omeis.providers.re.quantum.QuantumStrategy
Maximum value (255) allowed for the upper bound of the codomain interval.
MAX_CHANNELS - Static variable in class omeis.providers.re.Renderer
The maximum number of channels.
MAX_IN_SIZE - Static variable in class ome.util.SqlAction.Impl
 
maxFileSize - Variable in class ome.services.fulltext.FileParser
 
maximum - Variable in class ome.util.PixelData
The maximum pixel value for the pixels type of the pixel data.
MAXIMUM_BUFFER_SIZE - Static variable in class ome.io.nio.RomioPixelBuffer
Default maximum buffer size for planar data transfer. (1MB)
MAXIMUM_INTENSITY - Static variable in interface ome.api.IProjection
Maximum intensity projection (MIP)
maximumFieldCount - Variable in class ome.model.screen.PlateAcquisition
 
MAXIMUMFIELDCOUNT - Static variable in class ome.model.screen.PlateAcquisition
 
maxUserTimeToIdle - Variable in class ome.services.sessions.SessionManagerImpl
 
maxUserTimeToLive - Variable in class ome.services.sessions.SessionManagerImpl
 
mayHaveMapProperties(Class<? extends IObject>) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
 
mayHaveMapProperties(Class<? extends IObject>) - Method in interface ome.tools.hibernate.ExtendedMetadata
Check if an object of this class may have map properties.
MD5ChecksumProviderImpl - Class in ome.util.checksum
An implementation of the ChecksumProvider interface using MD5 as the message digest algorithm.
MD5ChecksumProviderImpl() - Constructor for class ome.util.checksum.MD5ChecksumProviderImpl
 
MEAN_INTENSITY - Static variable in interface ome.api.IProjection
Mean intensity projection
MEASUREMENT_NS - Static variable in class pojos.FileAnnotationData
The name space used to indicate that the FileAnnotation is a Measurement file.
MeasurementStore - Class in ome.services.blitz.measurements
Parser API implementation for storing result measurements from SPW companion files as ROIs and OMERO.tables.
MeasurementStore(LocalUpdate, TablePrx) - Constructor for class ome.services.blitz.measurements.MeasurementStore
 
medium - Variable in class ome.model.acquisition.ObjectiveSettings
 
MEDIUM - Static variable in class ome.model.acquisition.ObjectiveSettings
 
Medium - Class in ome.model.enums
 
Medium() - Constructor for class ome.model.enums.Medium
 
Medium(Long) - Constructor for class ome.model.enums.Medium
 
Medium(Long, boolean) - Constructor for class ome.model.enums.Medium
Main constructor.
Medium(String) - Constructor for class ome.model.enums.Medium
 
Medium.Details - Class in ome.model.enums
 
Medium.Details() - Constructor for class ome.model.enums.Medium.Details
 
Medium.Details(Object[]) - Constructor for class ome.model.enums.Medium.Details
 
member_of_groups - Static variable in class ome.security.basic.AllGroupsSecurityFilter
 
memberOfGroups - Variable in class ome.system.SimpleEventContext
 
MEMOIZER_WAIT - Static variable in class ome.io.nio.PixelsService
Default of 100 ms for PixelsService.memoizerWait
memoizerDirectory - Variable in class ome.io.nio.PixelsService
Location where cached data from the Memoizer should be stored.
memoizerWait - Variable in class ome.io.nio.PixelsService
Time in ms. which setId must take before a file is memoized
MERGE_EVENT - Static variable in class ome.security.basic.MergeEventListener
 
mergedBatches - Variable in class ome.services.search.SearchValues
 
MergeEventListener - Class in ome.security.basic
responsible for responding to merge events. in particular in load/re-loading certain types to make use by clients easier.
MergeEventListener(CurrentDetails, TokenHolder) - Constructor for class ome.security.basic.MergeEventListener
main constructor.
message - Variable in exception ome.io.nio.PixelBufferException
 
message - Variable in class ome.model.jobs.Job
 
MESSAGE - Static variable in class ome.model.jobs.Job
 
message - Variable in class ome.model.meta.DBPatch
 
MESSAGE - Static variable in class ome.model.meta.DBPatch
 
message - Variable in class ome.model.meta.Session
 
MESSAGE - Static variable in class ome.model.meta.Session
 
message - Variable in exception ome.services.graphs.GraphException
 
message() - Method in class ome.services.sessions.stats.LongCounter
 
message() - Method in class ome.services.sessions.stats.MethodCounter
 
message() - Method in class ome.services.sessions.stats.ObjectsReadCounter
 
message() - Method in class ome.services.sessions.stats.ObjectsWrittenCounter
 
message() - Method in class ome.services.sessions.stats.SessionsCreatedCounter
 
MessageException - Exception in ome.util.messages
Message which wraps a Throwable instance since OmeroContext.publishEvent(org.springframework.context.ApplicationEvent) cannot throw a checked exception.
MessageException(String, Throwable) - Constructor for exception ome.util.messages.MessageException
Create an instance.
meta - Variable in class ome.services.roi.PixelData
 
metadata - Variable in class ome.logic.AbstractLevel2Service
 
METADATA_LEVEL - Static variable in class ome.formats.importer.ImportCandidates
 
MetadataI - Class in ome.services.blitz.impl
Implementation of the IMetadata service.
MetadataI(IMetadata, BlitzExecutor) - Constructor for class ome.services.blitz.impl.MetadataI
Creates a new instance.
MetadataImpl - Class in ome.logic
Implement the IMetadata I/F.
MetadataImpl() - Constructor for class ome.logic.MetadataImpl
 
MetadataImportJob - Class in ome.model.jobs
 
MetadataImportJob() - Constructor for class ome.model.jobs.MetadataImportJob
 
MetadataImportJob(Long) - Constructor for class ome.model.jobs.MetadataImportJob
 
MetadataImportJob(Long, boolean) - Constructor for class ome.model.jobs.MetadataImportJob
Main constructor.
MetadataStoreI - Class in ome.services.blitz.impl
 
MetadataStoreI(BlitzExecutor, PopulateRoiJob, SqlAction, OriginalFilesService, String) - Constructor for class ome.services.blitz.impl.MetadataStoreI
 
methodCount() - Method in class ome.services.sessions.stats.DelegatingStats
 
methodCount() - Method in class ome.services.sessions.stats.NullSessionStats
 
methodCount() - Method in interface ome.services.sessions.stats.SessionStats
 
methodCount() - Method in class ome.services.sessions.stats.SimpleSessionStats
 
MethodCounter - Class in ome.services.sessions.stats
Counter for active methods for a given session.
MethodCounter(int) - Constructor for class ome.services.sessions.stats.MethodCounter
 
methodHardLimit - Variable in class ome.services.sessions.stats.CounterFactory
 
methodIn() - Method in class ome.services.sessions.stats.DelegatingStats
 
methodIn() - Method in class ome.services.sessions.stats.NullSessionStats
 
methodIn() - Method in interface ome.services.sessions.stats.SessionStats
 
methodIn() - Method in class ome.services.sessions.stats.SimpleSessionStats
 
methodology - Variable in class ome.model.core.Pixels
 
METHODOLOGY - Static variable in class ome.model.core.Pixels
 
METHODOLOGY_STRINGS - Static variable in interface ome.api.IProjection
Methodology strings
methodOut() - Method in class ome.services.sessions.stats.DelegatingStats
 
methodOut() - Method in class ome.services.sessions.stats.NullSessionStats
 
methodOut() - Method in interface ome.services.sessions.stats.SessionStats
 
methodOut() - Method in class ome.services.sessions.stats.SimpleSessionStats
 
methodSecurity - Variable in class ome.security.basic.BasicSecurityWiring
 
MethodSecurity - Interface in ome.security
Interface which allows security interceptors to check if a method should be executable for a given user.
MethodStatsMessage - Class in ome.services.messages.stats
Published when more than the specified number of active method calls is reached.
MethodStatsMessage(Object, long) - Constructor for class ome.services.messages.stats.MethodStatsMessage
 
Metrics - Interface in ome.system.metrics
Thin-interface around com.codahale.metrics.Metrics.
microbeamManipulation - Variable in class ome.model.acquisition.LightSettings
 
MICROBEAMMANIPULATION - Static variable in class ome.model.acquisition.LightSettings
 
microbeamManipulation - Variable in class ome.model.experiment.Experiment
 
MICROBEAMMANIPULATION - Static variable in class ome.model.experiment.Experiment
 
MicrobeamManipulation - Class in ome.model.experiment
These filter definitions are used by the security system to eliminate non-readable objects from queries.
MicrobeamManipulation() - Constructor for class ome.model.experiment.MicrobeamManipulation
 
MicrobeamManipulation(Long) - Constructor for class ome.model.experiment.MicrobeamManipulation
 
MicrobeamManipulation(Long, boolean) - Constructor for class ome.model.experiment.MicrobeamManipulation
Main constructor.
MicrobeamManipulation(MicrobeamManipulationType, Experiment) - Constructor for class ome.model.experiment.MicrobeamManipulation
 
MicrobeamManipulation.Details - Class in ome.model.experiment
 
MicrobeamManipulation.Details() - Constructor for class ome.model.experiment.MicrobeamManipulation.Details
 
MicrobeamManipulation.Details(Object[]) - Constructor for class ome.model.experiment.MicrobeamManipulation.Details
 
MicrobeamManipulationType - Class in ome.model.enums
 
MicrobeamManipulationType() - Constructor for class ome.model.enums.MicrobeamManipulationType
 
MicrobeamManipulationType(Long) - Constructor for class ome.model.enums.MicrobeamManipulationType
 
MicrobeamManipulationType(Long, boolean) - Constructor for class ome.model.enums.MicrobeamManipulationType
Main constructor.
MicrobeamManipulationType(String) - Constructor for class ome.model.enums.MicrobeamManipulationType
 
MicrobeamManipulationType.Details - Class in ome.model.enums
 
MicrobeamManipulationType.Details() - Constructor for class ome.model.enums.MicrobeamManipulationType.Details
 
MicrobeamManipulationType.Details(Object[]) - Constructor for class ome.model.enums.MicrobeamManipulationType.Details
 
microscope - Variable in class ome.model.acquisition.Instrument
 
MICROSCOPE - Static variable in class ome.model.acquisition.Instrument
 
Microscope - Class in ome.model.acquisition
These filter definitions are used by the security system to eliminate non-readable objects from queries.
Microscope() - Constructor for class ome.model.acquisition.Microscope
 
Microscope(Long) - Constructor for class ome.model.acquisition.Microscope
 
Microscope(Long, boolean) - Constructor for class ome.model.acquisition.Microscope
Main constructor.
Microscope(MicroscopeType) - Constructor for class ome.model.acquisition.Microscope
 
Microscope.Details - Class in ome.model.acquisition
 
Microscope.Details() - Constructor for class ome.model.acquisition.Microscope.Details
 
Microscope.Details(Object[]) - Constructor for class ome.model.acquisition.Microscope.Details
 
MicroscopeType - Class in ome.model.enums
 
MicroscopeType() - Constructor for class ome.model.enums.MicroscopeType
 
MicroscopeType(Long) - Constructor for class ome.model.enums.MicroscopeType
 
MicroscopeType(Long, boolean) - Constructor for class ome.model.enums.MicroscopeType
Main constructor.
MicroscopeType(String) - Constructor for class ome.model.enums.MicroscopeType
 
MicroscopeType.Details - Class in ome.model.enums
 
MicroscopeType.Details() - Constructor for class ome.model.enums.MicroscopeType.Details
 
MicroscopeType.Details(Object[]) - Constructor for class ome.model.enums.MicroscopeType.Details
 
middleName - Variable in class ome.model.meta.Experimenter
 
MIDDLENAME - Static variable in class ome.model.meta.Experimenter
 
MIDDLENAME - Static variable in class pojos.ExperimenterData
Identifies the Experimenter#MIDDLENAME field.
mime - Variable in class ome.services.blitz.repo.CheckedPath
 
mimetype - Variable in class ome.model.core.OriginalFile
 
MIMETYPE - Static variable in class ome.model.core.OriginalFile
 
mimeType - Variable in class ome.model.display.Thumbnail
 
MIMETYPE - Static variable in class ome.model.display.Thumbnail
 
mimetype(String, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
Get the mimetype for a file.
MIN - Static variable in class omeis.providers.re.quantum.QuantumStrategy
Minimum value (0) allowed for the lower bound of the codomain interval.
minimum - Variable in class ome.util.PixelData
The minimum pixel value for the pixels type of the pixel data.
minMaxSet - Variable in class ome.formats.importer.OMEROWrapper
 
MissingPyramidException - Exception in ome.conditions
 
MissingPyramidException(String, long, long) - Constructor for exception ome.conditions.MissingPyramidException
 
MissingPyramidMessage - Class in ome.io.messages
Published when an request is made for a pixels pyramid when the file does not yet exist.
MissingPyramidMessage(Object, long) - Constructor for class ome.io.messages.MissingPyramidMessage
 
MissingStatsInfoMessage - Class in ome.io.messages
Published when an request is made for a pixels pyramid when the file does not yet contain channel statistics.
MissingStatsInfoMessage(Object, long) - Constructor for class ome.io.messages.MissingStatsInfoMessage
 
mkdir() - Method in class ome.services.blitz.repo.CheckedPath
Create this directory on the underlying filesystem.
mkdirs() - Method in class ome.services.blitz.repo.CheckedPath
Create this directory, and parents if necessary, on the underlying filesystem.
mode - Variable in class ome.model.core.LogicalChannel
 
MODE - Static variable in class ome.model.core.LogicalChannel
 
model - Variable in class ome.model.acquisition.Detector
 
MODEL - Static variable in class ome.model.acquisition.Detector
 
model - Variable in class ome.model.acquisition.Dichroic
 
MODEL - Static variable in class ome.model.acquisition.Dichroic
 
model - Variable in class ome.model.acquisition.Filter
 
MODEL - Static variable in class ome.model.acquisition.Filter
 
model - Variable in class ome.model.acquisition.FilterSet
 
MODEL - Static variable in class ome.model.acquisition.FilterSet
 
model - Variable in class ome.model.acquisition.LightSource
 
MODEL - Static variable in class ome.model.acquisition.LightSource
 
model - Variable in class ome.model.acquisition.Microscope
 
MODEL - Static variable in class ome.model.acquisition.Microscope
 
model - Variable in class ome.model.acquisition.Objective
 
MODEL - Static variable in class ome.model.acquisition.Objective
 
model - Variable in class ome.model.display.RenderingDef
 
MODEL - Static variable in class ome.model.display.RenderingDef
 
model2target - Variable in class ome.util.ModelMapper
 
MODEL_GREYSCALE - Static variable in class omeis.providers.re.Renderer
Identifies the type used to store model values.
MODEL_HSB - Static variable in class omeis.providers.re.Renderer
Identifies the type used to store model values.
MODEL_RGB - Static variable in class omeis.providers.re.Renderer
Identifies the type used to store model values.
ModelBased - Interface in ome.model
used for reverse mapping.
ModelException - Exception in ome.formats.model
Exception thrown when there is an object instantiation error or error processing the model.
ModelException(String) - Constructor for exception ome.formats.model.ModelException
Default constructor.
ModelException(String, Class<? extends IObject>, Exception) - Constructor for exception ome.formats.model.ModelException
Default constructor.
ModelMapper - Class in ome.util
 
ModelMapper() - Constructor for class ome.util.ModelMapper
 
ModelObjectHandler - Interface in ome.formats.model.handler
A model object handler whose purpose is to provide extra logic, such as enumeration not-null constraint fulfilment.
ModelObjectHandlerFactory - Class in ome.formats.model.handler
Factory for all available model handlers.
ModelObjectHandlerFactory(EnumerationProvider) - Constructor for class ome.formats.model.handler.ModelObjectHandlerFactory
Default constructor.
ModelObjectSequencer - Class in ome.services.graphs
OMERO model objects sometimes must be processed in a specific order.
ModelObjectSequencer() - Constructor for class ome.services.graphs.ModelObjectSequencer
 
ModelProcessor - Interface in ome.formats.model
An object which performs post-processing on an IObjectContainerStore.
modificationCheck() - Method in class ome.services.scripts.ScriptRepoHelper
Checks if
modified - Variable in class ome.services.AbstractStatefulBean
True if any write operation took place on this bean.
modified() - Method in class ome.services.AbstractStatefulBean
 
modifiedStart - Variable in class ome.services.search.SearchValues
 
modifiedStop - Variable in class ome.services.search.SearchValues
 
MODULO_NS - Static variable in class pojos.XMLAnnotationData
The name space used to identify modulo concept.
more() - Method in class ome.services.eventlogs.AllEntitiesPseudoLogLoader
Returns the number of classes which are still unprocessed as a proxy for how much is left to process.
more() - Method in class ome.services.eventlogs.AllEventsLogLoader
 
more() - Method in class ome.services.eventlogs.EventLogLoader
Should return an estimate of how many more EventLog instances are available for processing.
more() - Method in class ome.services.eventlogs.EventLogQueue
In general, EventLogQueue will intend to use much larger batch sizes, and so further loops should likely not be attempted.
more() - Method in class ome.services.eventlogs.PersistentEventLogLoader
 
MoveFileTransfer - Class in ome.formats.importer.transfers
Local-only file transfer mechanism which makes use of hard-linking followed by the deletion of the original source file.
MoveFileTransfer() - Constructor for class ome.formats.importer.transfers.MoveFileTransfer
 
moveToCommonSpace(IObject...) - Method in interface ome.api.IAdmin
Moves the given objects into the "user" group to make them visible and linkable from all security contexts.
moveToCommonSpace(IObject...) - Method in class ome.logic.AdminImpl
 
moveToCommonSpace_async(AMD_IAdmin_moveToCommonSpace, List<IObject>, Current) - Method in class ome.services.blitz.impl.AdminI
 
MOVIE_MPEG_NS - Static variable in interface ome.api.IMetadata
The name space used to indicate that the FileAnnotation is an MPEG file.
MOVIE_NS - Static variable in class pojos.FileAnnotationData
The name space used to indicate that the FileAnnotation is a movie.
MOVIE_QT_NS - Static variable in interface ome.api.IMetadata
The name space used to indicate that the FileAnnotation is an QT file.
MOVIE_WMV_NS - Static variable in interface ome.api.IMetadata
The name space used to indicate that the FileAnnotation is an WMV file.
MS_EXCEL - Static variable in class pojos.FileAnnotationData
Identifies the Excel file formats.
MS_POWER_POINT - Static variable in class pojos.FileAnnotationData
Identifies the Power point file formats.
MS_POWER_POINT_SHOW - Static variable in class pojos.FileAnnotationData
Identifies the Power point file formats.
MS_POWER_POINT_X - Static variable in class pojos.FileAnnotationData
Identifies the Power point file formats.
MS_WORD - Static variable in class pojos.FileAnnotationData
Identifies the Word file formats.
MS_WORD_X - Static variable in class pojos.FileAnnotationData
Identifies the Word file formats.
mtime - Variable in class ome.model.core.OriginalFile
 
MTIME - Static variable in class ome.model.core.OriginalFile
 
Mul(Conversion...) - Static method in class ome.model.units.Conversion
Static helper for creating Conversion.Mul instances.
multicastEvent(ApplicationEvent) - Method in class ome.services.messages.GlobalMulticaster
Multicast only if this instance was the first created.
MultiImageData - Class in pojos
Handle image file composed of multiples files e.g. lei.
MultiImageData(OriginalFile) - Constructor for class pojos.MultiImageData
Creates a new instance.
multivalued - Variable in class ome.model.meta.Namespace
 
MULTIVALUED - Static variable in class ome.model.meta.Namespace
 
Murmur128ChecksumProviderImpl - Class in ome.util.checksum
An implementation of the ChecksumProvider interface using Murmur3_128 as the hash algorithm.
Murmur128ChecksumProviderImpl() - Constructor for class ome.util.checksum.Murmur128ChecksumProviderImpl
 
Murmur32ChecksumProviderImpl - Class in ome.util.checksum
An implementation of the ChecksumProvider interface using Murmur3_32 as the hash algorithm.
Murmur32ChecksumProviderImpl() - Constructor for class ome.util.checksum.Murmur32ChecksumProviderImpl
 
mustEdit() - Method in class ome.services.blitz.repo.CheckedPath
 
mustExist() - Method in class ome.services.blitz.repo.CheckedPath
Checks for existence of the original path, throwing an exception if not present.
mutex - Variable in class ome.system.SessionInitializer
 
myFilterCondition() - Method in class ome.security.basic.AllGroupsSecurityFilter
 
myFilterCondition() - Method in class ome.security.basic.OneGroupSecurityFilter
 
MySeqGenerator - Class in ome.tools.hibernate
http://www.hibernate.org/296.html
MySeqGenerator() - Constructor for class ome.tools.hibernate.MySeqGenerator
 

N

name - Variable in class ome.model.acquisition.StageLabel
 
NAME - Static variable in class ome.model.acquisition.StageLabel
 
name - Variable in class ome.model.annotations.Annotation
 
NAME - Static variable in class ome.model.annotations.Annotation
 
name - Variable in class ome.model.containers.Dataset
 
NAME - Static variable in class ome.model.containers.Dataset
 
name - Variable in class ome.model.containers.Project
 
NAME - Static variable in class ome.model.containers.Project
 
name - Variable in class ome.model.core.Image
 
NAME - Static variable in class ome.model.core.Image
 
name - Variable in class ome.model.core.LogicalChannel
 
NAME - Static variable in class ome.model.core.LogicalChannel
 
name - Variable in class ome.model.core.OriginalFile
 
NAME - Static variable in class ome.model.core.OriginalFile
 
name - Variable in class ome.model.display.RenderingDef
 
NAME - Static variable in class ome.model.display.RenderingDef
 
name - Variable in class ome.model.meta.ExperimenterGroup
 
NAME - Static variable in class ome.model.meta.ExperimenterGroup
 
name - Variable in class ome.model.meta.Namespace
 
NAME - Static variable in class ome.model.meta.Namespace
 
name - Variable in class ome.model.roi.Roi
 
NAME - Static variable in class ome.model.roi.Roi
 
name - Variable in class ome.model.screen.Plate
 
NAME - Static variable in class ome.model.screen.Plate
 
name - Variable in class ome.model.screen.PlateAcquisition
 
NAME - Static variable in class ome.model.screen.PlateAcquisition
 
name - Variable in class ome.model.screen.Reagent
 
NAME - Static variable in class ome.model.screen.Reagent
 
name - Variable in class ome.model.screen.Screen
 
NAME - Static variable in class ome.model.screen.Screen
 
name - Variable in class ome.parameters.QueryParameter
 
NAME - Static variable in class ome.security.policy.BinaryAccessPolicy
This string can also be found in the Constants.ice file in the blitz package.
name - Variable in enum ome.services.blitz.repo.path.FilePathRestrictionInstance
 
name - Variable in class ome.services.query.QueryParameterDef
name of this parameter.
name - Variable in class ome.services.scripts.RepoFile.FsFile
 
name - Variable in class ome.system.Principal
 
name - Variable in class ome.util.SqlAction.DeleteLog
 
NAME - Static variable in class pojos.DatasetData
Identifies the Dataset#NAME field.
NAME - Static variable in class pojos.GroupData
Identifies the ExperimenterGroup#NAME field.
NAME - Static variable in class pojos.ImageData
Identifies the Image#NAME field.
NAME - Static variable in class pojos.PlateData
Identifies the Plate#NAME field.
NAME - Static variable in class pojos.ProjectData
Identifies the Project#NAME field.
NAME - Static variable in class pojos.ScreenData
Identifies the Screen#NAME field.
nameById(long) - Method in interface ome.security.auth.RoleProvider
 
nameById(long) - Method in class ome.security.auth.SimpleRoleProvider
 
NamedValue - Class in ome.model.internal
class to store a single value in an ordered list.
NamedValue() - Constructor for class ome.model.internal.NamedValue
Deprecated.
NamedValue(String, String) - Constructor for class ome.model.internal.NamedValue
 
Namespace - Class in ome.model.meta
 
Namespace() - Constructor for class ome.model.meta.Namespace
 
Namespace(Long) - Constructor for class ome.model.meta.Namespace
 
Namespace(Long, boolean) - Constructor for class ome.model.meta.Namespace
Main constructor.
Namespace(String) - Constructor for class ome.model.meta.Namespace
 
NAMESPACE - Static variable in class ome.services.mail.MapAnnotationSubethaListener
 
Namespace.Details - Class in ome.model.meta
 
Namespace.Details() - Constructor for class ome.model.meta.Namespace.Details
 
Namespace.Details(Object[]) - Constructor for class ome.model.meta.Namespace.Details
 
NamespaceAnnotationLink - Class in ome.model.annotations
These filter definitions are used by the security system to eliminate non-readable objects from queries.
NamespaceAnnotationLink() - Constructor for class ome.model.annotations.NamespaceAnnotationLink
 
NamespaceAnnotationLink(Long) - Constructor for class ome.model.annotations.NamespaceAnnotationLink
 
NamespaceAnnotationLink(Long, boolean) - Constructor for class ome.model.annotations.NamespaceAnnotationLink
Main constructor.
NamespaceAnnotationLink(IObject, IObject) - Constructor for class ome.model.annotations.NamespaceAnnotationLink
 
NamespaceAnnotationLink.Details - Class in ome.model.annotations
 
NamespaceAnnotationLink.Details() - Constructor for class ome.model.annotations.NamespaceAnnotationLink.Details
 
NamespaceAnnotationLink.Details(Object[]) - Constructor for class ome.model.annotations.NamespaceAnnotationLink.Details
 
NamespaceCheck - Class in ome.services.util
Hook run by the context.
NamespaceCheck(Executor, String, Roles) - Constructor for class ome.services.util.NamespaceCheck
 
namespaces - Variable in class ome.model.roi.Roi
 
NAMESPACES - Static variable in class ome.model.roi.Roi
 
ndFilter - Variable in class ome.model.core.LogicalChannel
 
NDFILTER - Static variable in class ome.model.core.LogicalChannel
 
neededRight(Class<?>, Class<?>) - Method in class ome.security.basic.OmeroInterceptor
The default right need for a linkage is WRITE If however, this is only an annotation or only a viewing, then less permission is needed.
needsInit() - Method in class ome.services.blitz.repo.FileMaker
 
needsSanityCheck() - Method in class ome.logic.RepositoryInfoImpl
Calculates based on the cached usage and the elapsed time whether or not a real RepositoryInfoImpl.sanityCheckRepository() should be calculated.
newBlueColor() - Static method in class ome.formats.model.ColorsFactory
Creates a new Blue Color object.
newBlueColor() - Static method in class omeis.providers.re.ColorsFactory
Creates a new Blue Color object.
newCurrent(Identity, String, ObjectAdapter, String) - Static method in class omero.cmd.SessionI
 
newCurrent(Identity, String) - Method in class omero.cmd.SessionI
 
newEvent(Session, EventType, TokenHolder) - Method in class ome.security.basic.CurrentDetails
 
newGreenColor() - Static method in class ome.formats.model.ColorsFactory
Creates a new Green Color object.
newGreenColor() - Static method in class omeis.providers.re.ColorsFactory
Creates a new Green Color object.
newGreyColor() - Static method in class ome.formats.model.ColorsFactory
Creates a new Grey Color object.
newGreyColor() - Static method in class omeis.providers.re.ColorsFactory
Creates a new Grey Color object.
newInstance() - Method in class ome.model.acquisition.Arc
 
newInstance() - Method in class ome.model.acquisition.Detector.Details
 
newInstance() - Method in class ome.model.acquisition.Detector
 
newInstance() - Method in class ome.model.acquisition.DetectorSettings.Details
 
newInstance() - Method in class ome.model.acquisition.DetectorSettings
 
newInstance() - Method in class ome.model.acquisition.Dichroic.Details
 
newInstance() - Method in class ome.model.acquisition.Dichroic
 
newInstance() - Method in class ome.model.acquisition.Filament
 
newInstance() - Method in class ome.model.acquisition.Filter.Details
 
newInstance() - Method in class ome.model.acquisition.Filter
 
newInstance() - Method in class ome.model.acquisition.FilterSet.Details
 
newInstance() - Method in class ome.model.acquisition.FilterSet
 
newInstance() - Method in class ome.model.acquisition.FilterSetEmissionFilterLink.Details
 
newInstance() - Method in class ome.model.acquisition.FilterSetEmissionFilterLink
 
newInstance() - Method in class ome.model.acquisition.FilterSetExcitationFilterLink.Details
 
newInstance() - Method in class ome.model.acquisition.FilterSetExcitationFilterLink
 
newInstance() - Method in class ome.model.acquisition.GenericExcitationSource
 
newInstance() - Method in class ome.model.acquisition.ImagingEnvironment.Details
 
newInstance() - Method in class ome.model.acquisition.ImagingEnvironment
 
newInstance() - Method in class ome.model.acquisition.Instrument.Details
 
newInstance() - Method in class ome.model.acquisition.Instrument
 
newInstance() - Method in class ome.model.acquisition.Laser
 
newInstance() - Method in class ome.model.acquisition.LightEmittingDiode
 
newInstance() - Method in class ome.model.acquisition.LightPath.Details
 
newInstance() - Method in class ome.model.acquisition.LightPath
 
newInstance() - Method in class ome.model.acquisition.LightPathEmissionFilterLink.Details
 
newInstance() - Method in class ome.model.acquisition.LightPathEmissionFilterLink
 
newInstance() - Method in class ome.model.acquisition.LightPathExcitationFilterLink.Details
 
newInstance() - Method in class ome.model.acquisition.LightPathExcitationFilterLink
 
newInstance() - Method in class ome.model.acquisition.LightSettings.Details
 
newInstance() - Method in class ome.model.acquisition.LightSettings
 
newInstance() - Method in class ome.model.acquisition.LightSource.Details
 
newInstance() - Method in class ome.model.acquisition.Microscope.Details
 
newInstance() - Method in class ome.model.acquisition.Microscope
 
newInstance() - Method in class ome.model.acquisition.Objective.Details
 
newInstance() - Method in class ome.model.acquisition.Objective
 
newInstance() - Method in class ome.model.acquisition.ObjectiveSettings.Details
 
newInstance() - Method in class ome.model.acquisition.ObjectiveSettings
 
newInstance() - Method in class ome.model.acquisition.OTF.Details
 
newInstance() - Method in class ome.model.acquisition.OTF
 
newInstance() - Method in class ome.model.acquisition.StageLabel.Details
 
newInstance() - Method in class ome.model.acquisition.StageLabel
 
newInstance() - Method in class ome.model.acquisition.TransmittanceRange.Details
 
newInstance() - Method in class ome.model.acquisition.TransmittanceRange
 
newInstance() - Method in class ome.model.annotations.Annotation.Details
 
newInstance() - Method in class ome.model.annotations.AnnotationAnnotationLink.Details
 
newInstance() - Method in class ome.model.annotations.AnnotationAnnotationLink
 
newInstance() - Method in class ome.model.annotations.BooleanAnnotation
 
newInstance() - Method in class ome.model.annotations.ChannelAnnotationLink.Details
 
newInstance() - Method in class ome.model.annotations.ChannelAnnotationLink
 
newInstance() - Method in class ome.model.annotations.CommentAnnotation
 
newInstance() - Method in class ome.model.annotations.DatasetAnnotationLink.Details
 
newInstance() - Method in class ome.model.annotations.DatasetAnnotationLink
 
newInstance() - Method in class ome.model.annotations.DetectorAnnotationLink.Details
 
newInstance() - Method in class ome.model.annotations.DetectorAnnotationLink
 
newInstance() - Method in class ome.model.annotations.DichroicAnnotationLink.Details
 
newInstance() - Method in class ome.model.annotations.DichroicAnnotationLink
 
newInstance() - Method in class ome.model.annotations.DoubleAnnotation
 
newInstance() - Method in class ome.model.annotations.ExperimenterAnnotationLink.Details
 
newInstance() - Method in class ome.model.annotations.ExperimenterAnnotationLink
 
newInstance() - Method in class ome.model.annotations.ExperimenterGroupAnnotationLink.Details
 
newInstance() - Method in class ome.model.annotations.ExperimenterGroupAnnotationLink
 
newInstance() - Method in class ome.model.annotations.FileAnnotation
 
newInstance() - Method in class ome.model.annotations.FilesetAnnotationLink.Details
 
newInstance() - Method in class ome.model.annotations.FilesetAnnotationLink
 
newInstance() - Method in class ome.model.annotations.FilterAnnotationLink.Details
 
newInstance() - Method in class ome.model.annotations.FilterAnnotationLink
 
newInstance() - Method in class ome.model.annotations.ImageAnnotationLink.Details
 
newInstance() - Method in class ome.model.annotations.ImageAnnotationLink
 
newInstance() - Method in class ome.model.annotations.InstrumentAnnotationLink.Details
 
newInstance() - Method in class ome.model.annotations.InstrumentAnnotationLink
 
newInstance() - Method in class ome.model.annotations.LightPathAnnotationLink.Details
 
newInstance() - Method in class ome.model.annotations.LightPathAnnotationLink
 
newInstance() - Method in class ome.model.annotations.LightSourceAnnotationLink.Details
 
newInstance() - Method in class ome.model.annotations.LightSourceAnnotationLink
 
newInstance() - Method in class ome.model.annotations.ListAnnotation
 
newInstance() - Method in class ome.model.annotations.LongAnnotation
 
newInstance() - Method in class ome.model.annotations.MapAnnotation
 
newInstance() - Method in class ome.model.annotations.NamespaceAnnotationLink.Details
 
newInstance() - Method in class ome.model.annotations.NamespaceAnnotationLink
 
newInstance() - Method in class ome.model.annotations.NodeAnnotationLink.Details
 
newInstance() - Method in class ome.model.annotations.NodeAnnotationLink
 
newInstance() - Method in class ome.model.annotations.ObjectiveAnnotationLink.Details
 
newInstance() - Method in class ome.model.annotations.ObjectiveAnnotationLink
 
newInstance() - Method in class ome.model.annotations.OriginalFileAnnotationLink.Details
 
newInstance() - Method in class ome.model.annotations.OriginalFileAnnotationLink
 
newInstance() - Method in class ome.model.annotations.PlaneInfoAnnotationLink.Details
 
newInstance() - Method in class ome.model.annotations.PlaneInfoAnnotationLink
 
newInstance() - Method in class ome.model.annotations.PlateAcquisitionAnnotationLink.Details
 
newInstance() - Method in class ome.model.annotations.PlateAcquisitionAnnotationLink
 
newInstance() - Method in class ome.model.annotations.PlateAnnotationLink.Details
 
newInstance() - Method in class ome.model.annotations.PlateAnnotationLink
 
newInstance() - Method in class ome.model.annotations.ProjectAnnotationLink.Details
 
newInstance() - Method in class ome.model.annotations.ProjectAnnotationLink
 
newInstance() - Method in class ome.model.annotations.ReagentAnnotationLink.Details
 
newInstance() - Method in class ome.model.annotations.ReagentAnnotationLink
 
newInstance() - Method in class ome.model.annotations.RoiAnnotationLink.Details
 
newInstance() - Method in class ome.model.annotations.RoiAnnotationLink
 
newInstance() - Method in class ome.model.annotations.ScreenAnnotationLink.Details
 
newInstance() - Method in class ome.model.annotations.ScreenAnnotationLink
 
newInstance() - Method in class ome.model.annotations.SessionAnnotationLink.Details
 
newInstance() - Method in class ome.model.annotations.SessionAnnotationLink
 
newInstance() - Method in class ome.model.annotations.ShapeAnnotationLink.Details
 
newInstance() - Method in class ome.model.annotations.ShapeAnnotationLink
 
newInstance() - Method in class ome.model.annotations.TagAnnotation
 
newInstance() - Method in class ome.model.annotations.TermAnnotation
 
newInstance() - Method in class ome.model.annotations.TimestampAnnotation
 
newInstance() - Method in class ome.model.annotations.WellAnnotationLink.Details
 
newInstance() - Method in class ome.model.annotations.WellAnnotationLink
 
newInstance() - Method in class ome.model.annotations.XmlAnnotation
 
newInstance() - Method in class ome.model.containers.Dataset.Details
 
newInstance() - Method in class ome.model.containers.Dataset
 
newInstance() - Method in class ome.model.containers.DatasetImageLink.Details
 
newInstance() - Method in class ome.model.containers.DatasetImageLink
 
newInstance() - Method in class ome.model.containers.Project.Details
 
newInstance() - Method in class ome.model.containers.Project
 
newInstance() - Method in class ome.model.containers.ProjectDatasetLink.Details
 
newInstance() - Method in class ome.model.containers.ProjectDatasetLink
 
newInstance() - Method in class ome.model.core.Channel.Details
 
newInstance() - Method in class ome.model.core.Channel
 
newInstance() - Method in class ome.model.core.Image.Details
 
newInstance() - Method in class ome.model.core.Image
 
newInstance() - Method in class ome.model.core.LogicalChannel.Details
 
newInstance() - Method in class ome.model.core.LogicalChannel
 
newInstance() - Method in class ome.model.core.OriginalFile.Details
 
newInstance() - Method in class ome.model.core.OriginalFile
 
newInstance() - Method in class ome.model.core.Pixels.Details
 
newInstance() - Method in class ome.model.core.Pixels
 
newInstance() - Method in class ome.model.core.PixelsOriginalFileMap.Details
 
newInstance() - Method in class ome.model.core.PixelsOriginalFileMap
 
newInstance() - Method in class ome.model.core.PlaneInfo.Details
 
newInstance() - Method in class ome.model.core.PlaneInfo
 
newInstance() - Method in class ome.model.display.ChannelBinding.Details
 
newInstance() - Method in class ome.model.display.ChannelBinding
 
newInstance() - Method in class ome.model.display.CodomainMapContext.Details
 
newInstance() - Method in class ome.model.display.ContrastStretchingContext
 
newInstance() - Method in class ome.model.display.PlaneSlicingContext
 
newInstance() - Method in class ome.model.display.QuantumDef.Details
 
newInstance() - Method in class ome.model.display.QuantumDef
 
newInstance() - Method in class ome.model.display.RenderingDef.Details
 
newInstance() - Method in class ome.model.display.RenderingDef
 
newInstance() - Method in class ome.model.display.ReverseIntensityContext
 
newInstance() - Method in class ome.model.display.Thumbnail.Details
 
newInstance() - Method in class ome.model.display.Thumbnail
 
newInstance() - Method in class ome.model.enums.AcquisitionMode.Details
 
newInstance() - Method in class ome.model.enums.AcquisitionMode
 
newInstance() - Method in class ome.model.enums.ArcType.Details
 
newInstance() - Method in class ome.model.enums.ArcType
 
newInstance() - Method in class ome.model.enums.Binning.Details
 
newInstance() - Method in class ome.model.enums.Binning
 
newInstance() - Method in class ome.model.enums.ChecksumAlgorithm.Details
 
newInstance() - Method in class ome.model.enums.ChecksumAlgorithm
 
newInstance() - Method in class ome.model.enums.ContrastMethod.Details
 
newInstance() - Method in class ome.model.enums.ContrastMethod
 
newInstance() - Method in class ome.model.enums.Correction.Details
 
newInstance() - Method in class ome.model.enums.Correction
 
newInstance() - Method in class ome.model.enums.DetectorType.Details
 
newInstance() - Method in class ome.model.enums.DetectorType
 
newInstance() - Method in class ome.model.enums.DimensionOrder.Details
 
newInstance() - Method in class ome.model.enums.DimensionOrder
 
newInstance() - Method in class ome.model.enums.EventType.Details
 
newInstance() - Method in class ome.model.enums.EventType
 
newInstance() - Method in class ome.model.enums.ExperimentType.Details
 
newInstance() - Method in class ome.model.enums.ExperimentType
 
newInstance() - Method in class ome.model.enums.Family.Details
 
newInstance() - Method in class ome.model.enums.Family
 
newInstance() - Method in class ome.model.enums.FilamentType.Details
 
newInstance() - Method in class ome.model.enums.FilamentType
 
newInstance() - Method in class ome.model.enums.FilterType.Details
 
newInstance() - Method in class ome.model.enums.FilterType
 
newInstance() - Method in class ome.model.enums.Format.Details
 
newInstance() - Method in class ome.model.enums.Format
 
newInstance() - Method in class ome.model.enums.Illumination.Details
 
newInstance() - Method in class ome.model.enums.Illumination
 
newInstance() - Method in class ome.model.enums.Immersion.Details
 
newInstance() - Method in class ome.model.enums.Immersion
 
newInstance() - Method in class ome.model.enums.LaserMedium.Details
 
newInstance() - Method in class ome.model.enums.LaserMedium
 
newInstance() - Method in class ome.model.enums.LaserType.Details
 
newInstance() - Method in class ome.model.enums.LaserType
 
newInstance() - Method in class ome.model.enums.Medium.Details
 
newInstance() - Method in class ome.model.enums.Medium
 
newInstance() - Method in class ome.model.enums.MicrobeamManipulationType.Details
 
newInstance() - Method in class ome.model.enums.MicrobeamManipulationType
 
newInstance() - Method in class ome.model.enums.MicroscopeType.Details
 
newInstance() - Method in class ome.model.enums.MicroscopeType
 
newInstance() - Method in class ome.model.enums.PhotometricInterpretation.Details
 
newInstance() - Method in class ome.model.enums.PhotometricInterpretation
 
newInstance() - Method in class ome.model.enums.PixelsType.Details
 
newInstance() - Method in class ome.model.enums.PixelsType
 
newInstance() - Method in class ome.model.enums.Pulse.Details
 
newInstance() - Method in class ome.model.enums.Pulse
 
newInstance() - Method in class ome.model.enums.RenderingModel.Details
 
newInstance() - Method in class ome.model.enums.RenderingModel
 
newInstance() - Method in class ome.model.experiment.Experiment.Details
 
newInstance() - Method in class ome.model.experiment.Experiment
 
newInstance() - Method in class ome.model.experiment.MicrobeamManipulation.Details
 
newInstance() - Method in class ome.model.experiment.MicrobeamManipulation
 
newInstance() - Method in class ome.model.fs.Fileset.Details
 
newInstance() - Method in class ome.model.fs.Fileset
 
newInstance() - Method in class ome.model.fs.FilesetEntry.Details
 
newInstance() - Method in class ome.model.fs.FilesetEntry
 
newInstance() - Method in class ome.model.fs.FilesetJobLink.Details
 
newInstance() - Method in class ome.model.fs.FilesetJobLink
 
newInstance() - Method in class ome.model.internal.Details
 
newInstance() - Method in class ome.model.internal.Link.Details
 
newInstance() - Method in class ome.model.internal.Link
 
newInstance() - Method in class ome.model.jobs.ImportJob
 
newInstance() - Method in class ome.model.jobs.IndexingJob
 
newInstance() - Method in class ome.model.jobs.IntegrityCheckJob
 
newInstance() - Method in class ome.model.jobs.Job.Details
 
newInstance() - Method in class ome.model.jobs.JobOriginalFileLink.Details
 
newInstance() - Method in class ome.model.jobs.JobOriginalFileLink
 
newInstance() - Method in class ome.model.jobs.JobStatus.Details
 
newInstance() - Method in class ome.model.jobs.JobStatus
 
newInstance() - Method in class ome.model.jobs.MetadataImportJob
 
newInstance() - Method in class ome.model.jobs.ParseJob
 
newInstance() - Method in class ome.model.jobs.PixelDataJob
 
newInstance() - Method in class ome.model.jobs.ScriptJob
 
newInstance() - Method in class ome.model.jobs.ThumbnailGenerationJob
 
newInstance() - Method in class ome.model.jobs.UploadJob
 
newInstance() - Method in class ome.model.meta.DBPatch.Details
 
newInstance() - Method in class ome.model.meta.DBPatch
 
newInstance() - Method in class ome.model.meta.Event.Details
 
newInstance() - Method in class ome.model.meta.Event
 
newInstance() - Method in class ome.model.meta.EventLog.Details
 
newInstance() - Method in class ome.model.meta.EventLog
 
newInstance() - Method in class ome.model.meta.Experimenter.Details
 
newInstance() - Method in class ome.model.meta.Experimenter
 
newInstance() - Method in class ome.model.meta.ExperimenterGroup.Details
 
newInstance() - Method in class ome.model.meta.ExperimenterGroup
 
newInstance() - Method in class ome.model.meta.ExternalInfo.Details
 
newInstance() - Method in class ome.model.meta.ExternalInfo
 
newInstance() - Method in class ome.model.meta.GroupExperimenterMap.Details
 
newInstance() - Method in class ome.model.meta.GroupExperimenterMap
 
newInstance() - Method in class ome.model.meta.Namespace.Details
 
newInstance() - Method in class ome.model.meta.Namespace
 
newInstance() - Method in class ome.model.meta.Node.Details
 
newInstance() - Method in class ome.model.meta.Node
 
newInstance() - Method in class ome.model.meta.Session.Details
 
newInstance() - Method in class ome.model.meta.Session
 
newInstance() - Method in class ome.model.meta.Share
 
newInstance() - Method in class ome.model.meta.ShareMember.Details
 
newInstance() - Method in class ome.model.meta.ShareMember
 
newInstance() - Method in class ome.model.roi.Ellipse
 
newInstance() - Method in class ome.model.roi.Label
 
newInstance() - Method in class ome.model.roi.Line
 
newInstance() - Method in class ome.model.roi.Mask
 
newInstance() - Method in class ome.model.roi.Path
 
newInstance() - Method in class ome.model.roi.Point
 
newInstance() - Method in class ome.model.roi.Polygon
 
newInstance() - Method in class ome.model.roi.Polyline
 
newInstance() - Method in class ome.model.roi.Rect
 
newInstance() - Method in class ome.model.roi.Roi.Details
 
newInstance() - Method in class ome.model.roi.Roi
 
newInstance() - Method in class ome.model.roi.Shape.Details
 
newInstance() - Method in class ome.model.screen.Plate.Details
 
newInstance() - Method in class ome.model.screen.Plate
 
newInstance() - Method in class ome.model.screen.PlateAcquisition.Details
 
newInstance() - Method in class ome.model.screen.PlateAcquisition
 
newInstance() - Method in class ome.model.screen.Reagent.Details
 
newInstance() - Method in class ome.model.screen.Reagent
 
newInstance() - Method in class ome.model.screen.Screen.Details
 
newInstance() - Method in class ome.model.screen.Screen
 
newInstance() - Method in class ome.model.screen.ScreenPlateLink.Details
 
newInstance() - Method in class ome.model.screen.ScreenPlateLink
 
newInstance() - Method in class ome.model.screen.Well.Details
 
newInstance() - Method in class ome.model.screen.Well
 
newInstance() - Method in class ome.model.screen.WellReagentLink.Details
 
newInstance() - Method in class ome.model.screen.WellReagentLink
 
newInstance() - Method in class ome.model.screen.WellSample.Details
 
newInstance() - Method in class ome.model.screen.WellSample
 
newInstance() - Method in class ome.model.stats.StatsInfo.Details
 
newInstance() - Method in class ome.model.stats.StatsInfo
 
newlyEnabledFilters - Variable in class ome.services.query.Query
the set of filters that is being or has been enabled for this Query.
newOMEROReader() - Method in interface loci.ome.io.services.OMEReaderWriterService
Creates a new OMERO IFormatReader implementation.
newOMEROReader() - Method in class loci.ome.io.services.OMEReaderWriterServiceImpl
 
newOMEROWriter() - Method in class loci.ome.io.services.OMEReaderWriterServiceImpl
 
newRedColor() - Static method in class ome.formats.model.ColorsFactory
Creates a new Red Color object.
newRedColor() - Static method in class omeis.providers.re.ColorsFactory
Creates a new Red Color object.
newTable(long, String, Current) - Method in class ome.services.blitz.impl.SharedResourcesI
 
newTransientDetails(IObject) - Method in class ome.security.basic.BasicSecuritySystem
 
newTransientDetails(IObject) - Method in class ome.security.basic.OmeroInterceptor
 
newTransientDetails(IObject, Details) - Method in class ome.security.basic.OmeroInterceptor
Like OmeroInterceptor.newTransientDetails(IObject) but allows passing in a newDetails object with possibly pre-set values.
newTransientDetails(IObject) - Method in interface ome.security.SecuritySystem
creates a new secure details for transient entities.
newTransientDetails(IObject) - Method in class ome.security.SecuritySystemHolder
 
newTransientDetails(IObject) - Method in class ome.security.sharing.SharingSecuritySystem
 
NewUserGroupBean - Interface in ome.security.auth
Strategy for finding the appropriate groups for a given user in LDAP.
NewUserGroupOwnerBean - Interface in ome.security.auth
Strategy for finding the appropriate group owners for a given user in LDAP.
newWhiteColor() - Static method in class ome.formats.model.ColorsFactory
Creates a new White Color object.
newWhiteColor() - Static method in class omeis.providers.re.ColorsFactory
Creates a new White Color object.
next() - Method in interface ome.api.Search
Returns the next entity from the current query.
next() - Method in class ome.services.eventlogs.EventLogLoader
Returns the current EventLogLoader.log instance which may be loaded by a call to EventLogLoader.hasNext() if necessary.
next() - Method in class ome.services.eventlogs.EventLogQueue
Return a wrapped version of Data#next() which could possibly be null.
next() - Method in class ome.services.graphs.BaseGraphSpec.SubSpecIterator
Deprecated.
 
next() - Method in class ome.services.SearchBean
 
next() - Method in class ome.util.EmptyIterator
 
next_async(AMD_Search_next, Current) - Method in class ome.services.blitz.impl.SearchI
 
nextEventLog(long) - Method in class ome.services.eventlogs.EventLogLoader
Returns the EventLog with the next id after the given argument or null if none exists.
nextPixelsDataLogForRepo(String, long, int) - Method in class ome.util.SqlAction.Impl
 
nextPixelsDataLogForRepo(String, long, int) - Method in interface ome.util.SqlAction
Returns arrays of longs for the following SQL return values: experimenter, eventlog, entityid as pixels, rownumber The oldest N eventlogs with action = "PIXELDATA" and entitytype = "ome.model.core.Pixels" is found per user and returned.
nextSessionId() - Method in class ome.util.actions.PostgresSqlAction
 
nextSessionId() - Method in interface ome.util.SqlAction
 
nextValue(String, int) - Method in class ome.util.actions.PostgresSqlAction
 
nextValue(String, int) - Method in interface ome.util.SqlAction
The implementation of this method guarantees that even if the current transaction fails that the value found will not be used by another transaction.
noAcquisitionData() - Method in class omero.sys.ParametersI
Sets the acquisition data parameter to false.
Node - Class in ome.model.meta
 
Node() - Constructor for class ome.model.meta.Node
 
Node(Long) - Constructor for class ome.model.meta.Node
 
Node(Long, boolean) - Constructor for class ome.model.meta.Node
Main constructor.
Node(String, String, Timestamp) - Constructor for class ome.model.meta.Node
 
node - Variable in class ome.model.meta.Session
 
NODE - Static variable in class ome.model.meta.Session
 
Node.Details - Class in ome.model.meta
 
Node.Details() - Constructor for class ome.model.meta.Node.Details
 
Node.Details(Object[]) - Constructor for class ome.model.meta.Node.Details
 
NodeAnnotationLink - Class in ome.model.annotations
These filter definitions are used by the security system to eliminate non-readable objects from queries.
NodeAnnotationLink() - Constructor for class ome.model.annotations.NodeAnnotationLink
 
NodeAnnotationLink(Long) - Constructor for class ome.model.annotations.NodeAnnotationLink
 
NodeAnnotationLink(Long, boolean) - Constructor for class ome.model.annotations.NodeAnnotationLink
Main constructor.
NodeAnnotationLink(IObject, IObject) - Constructor for class ome.model.annotations.NodeAnnotationLink
 
NodeAnnotationLink.Details - Class in ome.model.annotations
 
NodeAnnotationLink.Details() - Constructor for class ome.model.annotations.NodeAnnotationLink.Details
 
NodeAnnotationLink.Details(Object[]) - Constructor for class ome.model.annotations.NodeAnnotationLink.Details
 
nodeId(String) - Method in class ome.util.actions.PostgresSqlAction
 
nodeId(String) - Method in interface ome.util.SqlAction
 
nodeProxyQuery(Redirector.Context, String, String) - Method in class ome.services.blitz.redirect.AbstractRedirector
 
NOISE_REDUCTION - Static variable in class omeis.providers.re.quantum.QuantumFactory
Default value.
noiseReduction - Variable in class ome.model.display.ChannelBinding
 
NOISEREDUCTION - Static variable in class ome.model.display.ChannelBinding
 
noLeaves() - Method in class ome.parameters.Parameters
 
noLeaves() - Method in class omero.sys.ParametersI
Sets the leaf parameter to false.
nominalMagnification - Variable in class ome.model.acquisition.Objective
 
NOMINALMAGNIFICATION - Static variable in class ome.model.acquisition.Objective
 
noOrphan() - Method in class ome.parameters.Parameters
 
noOrphan() - Method in class omero.sys.ParametersI
Sets the orphan parameter to false.
noPage() - Method in class omero.sys.ParametersI
Nulls both the Filter.limit and Filter.offset values.
norm(String) - Static method in class ome.services.scripts.RepoFile
Somewhat complicated method to turn any path into a unique like path rooted at "/".
norm() - Method in class ome.util.math.geom2D.PlanePoint
Calculates the Euclidian norm of this vector.
normalize() - Method in class ome.util.math.geom2D.PlanePoint
Calculates the unit vector of this vector, provided this is not the null vector.
noStatsInfo - Variable in class ome.formats.importer.ImportConfig
 
not() - Method in interface ome.api.Search
Applies the next by* method to the previous by* method, so that a call Search.hasNext(), Search.next(), or Search.results() sees only the intersection of the two calls.
not() - Method in class ome.services.SearchBean
 
not_async(AMD_Search_not, Current) - Method in class ome.services.blitz.impl.SearchI
 
notAnnotatedBy(Details) - Method in interface ome.api.Search
Restricts entities by who has not annotated them with an Annotation matching the other filters.
notAnnotatedBy - Variable in class ome.services.search.SearchValues
 
notAnnotatedBy(Details) - Method in class ome.services.SearchBean
 
notAnnotatedBy_async(AMD_Search_notAnnotatedBy, Details, Current) - Method in class ome.services.blitz.impl.SearchI
 
noteDetails(Session, IObject, String, long) - Method in class ome.services.graphs.GraphPolicy
Any model object about which policy may be asked is first passed to #noteDetails(IObject, String, long) before #review(Map, Details, Map, Set).
noteDetails(Session, IObject, String, long) - Method in interface ome.services.graphs.GraphPolicyRulePredicate
Once this instance is submitted to GraphPolicy#registerPredicate(GraphPolicyPredicate) then this method is called by GraphPolicy.noteDetails(org.hibernate.Session, IObject, String, long).
noteDetails(Session, IObject, String, long) - Method in class ome.services.graphs.GroupPredicate
 
noteDetails(Session, IObject, String, long) - Method in class ome.services.graphs.PermissionsPredicate
 
noteDetails(Session, IObject, String, long) - Method in class omero.cmd.graphs.BaseGraphPolicyAdjuster
 
notifications(String) - Method in class ome.services.sessions.SessionManagerImpl
 
notifyCallbacks() - Method in class omero.cmd.HandleI
Calls the proper notification on all callbacks based on the current HandleI.state.
notifyElementEvicted(Ehcache, Element) - Method in class ome.services.sessions.state.CacheListener
 
notifyElementExpired(Ehcache, Element) - Method in class ome.services.sessions.state.CacheListener
 
notifyElementPut(Ehcache, Element) - Method in class ome.services.sessions.state.CacheListener
 
notifyElementRemoved(Ehcache, Element) - Method in class ome.services.sessions.state.CacheListener
 
notifyElementUpdated(Ehcache, Element) - Method in class ome.services.sessions.state.CacheListener
 
notifyMembersOfShare(long, String, String, boolean) - Method in interface ome.api.IShare
Notify via email selected members of share.
notifyMembersOfShare(long, String, String, boolean) - Method in class ome.services.sharing.ShareBean
 
notifyMembersOfShare_async(AMD_IShare_notifyMembersOfShare, long, String, String, boolean, Current) - Method in class ome.services.blitz.impl.ShareI
 
notifyObservers(ImportEvent) - Method in class ome.formats.importer.ImportLibrary
 
notifyObservers(ImportEvent) - Method in interface ome.formats.importer.IObservable
Notify observers of event
notifyObservers(ImportEvent) - Method in class ome.formats.importer.util.ClientKeepAlive
 
notifyObservers(ImportEvent) - Method in class ome.formats.importer.util.ErrorHandler
 
notifyObservers(ImportEvent) - Method in class ome.formats.importer.util.FileUploader
 
notifyRemoveAll(Ehcache) - Method in class ome.services.sessions.state.CacheListener
 
NotNull - Annotation Type in ome.annotations
annotation used for determining the types of a Set
notNull(String[]) - Static method in class prefs
Returns an empty array if the argument is null.
notNullOrLikeOrEqual(QueryBuilder, String, Class, Object, boolean, boolean) - Static method in class ome.services.search.SearchAction
 
notNullOrLikeOrEqual(String, Class, Object, boolean, boolean) - Static method in class ome.services.search.SearchAction
 
notOwnedBy(Details) - Method in interface ome.api.Search
Uses the Details.getOwner() and Details.getGroup() information to restrict the entities which will be returned.
notOwnedBy - Variable in class ome.services.search.SearchValues
 
notOwnedBy(Details) - Method in class ome.services.SearchBean
 
notOwnedBy_async(AMD_Search_notOwnedBy, Details, Current) - Method in class ome.services.blitz.impl.SearchI
 
noUnique() - Method in class omero.sys.ParametersI
 
now() - Method in class ome.util.actions.PostgresSqlAction
 
now() - Method in interface ome.util.SqlAction
 
ns - Variable in class ome.model.annotations.Annotation
 
NS - Static variable in class ome.model.annotations.Annotation
 
NS_CLIENT_CREATED - Static variable in class pojos.MapAnnotationData
The name space used to identify MapAnnotations created be the user
NS_COMMENT - Static variable in class ome.services.sharing.ShareBean
 
NS_ENABLED - Static variable in class ome.services.sharing.ShareBean
 
NS_IMPORTER_ARCHIVED - Static variable in interface ome.api.IMetadata
The name space indicating that the Boolean annotation indicated if an archived image is imported with the image.
NS_INSIGHT_RATING - Static variable in interface ome.api.IMetadata
The name space indicating that the Long annotation is a rating annotation i.e. an integer in the interval [0, 5].
NS_INSIGHT_TAG_SET - Static variable in interface ome.api.IMetadata
The name space indicating that the tag is used a tag set.
nsExcludes - Static variable in class ome.services.graphs.AnnotationGraphSpec
Deprecated.
Collection of namespace values (defined as AnnotationGraphSpec.nsIncludes) which will be omitted from processing by default.
NSEXPERIMENTERPHOTO - Static variable in class ome.logic.AdminImpl
 
nsIncludes - Static variable in class ome.services.graphs.AnnotationGraphSpec
Deprecated.
Collection of namespace values (or LIKE values if they contain '%' or '?')
NULL_PLANE_SIZE - Static variable in class ome.io.nio.PixelsService
Null plane size constant.
NULL_RENDERER - Static variable in class ome.services.RenderingBean
Message if the rendering engine is not ready.
nullDetails() - Method in class pojos.DataObject
Returns true if the details are null otherwise false otherwise.
NullEventHandler - Class in ome.security.basic
Provides only the bare minimum of functionality to allow methods to succeed.
NullEventHandler(SecuritySystem, SessionFactory) - Constructor for class ome.security.basic.NullEventHandler
 
NullMetrics - Class in ome.system.metrics
No-op version of Metrics
NullMetrics() - Constructor for class ome.system.metrics.NullMetrics
 
nullPlane - Static variable in class ome.io.nio.PixelsService
Null plane byte array.
nullProperties(String, String, Collection<Long>) - Method in interface ome.services.graphs.GraphTraversal.Processor
Null the given property of the indicated instances.
nullProperties(String, String, Collection<Long>) - Method in class omero.cmd.graphs.BaseGraphTraversalProcessor
 
NullQuerySource - Class in ome.services.query
always returns null for any id.
NullQuerySource() - Constructor for class ome.services.query.NullQuerySource
 
NullRedirector - Class in ome.services.blitz.redirect
Redirector implementation to effectively disable redirects.
NullRedirector() - Constructor for class ome.services.blitz.redirect.NullRedirector
 
nullSafe(Integer) - Method in class pojos.DataObject
 
nullSafe(RInt) - Method in class pojos.DataObject
 
nullSafe(Long) - Method in class pojos.DataObject
 
nullSafe(Double) - Method in class pojos.DataObject
 
nullSafe(Float) - Method in class pojos.DataObject
 
nullSafe(RFloat) - Method in class pojos.DataObject
 
nullSafe(RDouble) - Method in class pojos.DataObject
 
nullSafe(Length) - Method in class pojos.DataObject
 
nullSafeDouble(Double) - Method in class ome.util.ModelMapper
 
nullSafeFloat(Float) - Method in class ome.util.ModelMapper
 
nullSafeGet(ResultSet, String[], Object) - Method in class ome.model.units.GenericEnumType
 
nullSafeGet(ResultSet, String[], Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
 
nullSafeGroupId(IObject) - Static method in class ome.tools.hibernate.HibernateUtils
returns the id of the group of this entity, or null if: (1) the object is null, (2) the Details is null, (3) the group is null.
nullSafeInt(Integer) - Method in class ome.util.ModelMapper
 
nullSafeLong(Long) - Method in class ome.util.ModelMapper
 
nullSafeOwnerId(IObject) - Static method in class ome.tools.hibernate.HibernateUtils
returns the id of the owner of this entity, or null if: (1) the object is null, (2) the Details is null, (3) the owner is null.
nullSafeSet(PreparedStatement, Object, int) - Method in class ome.model.units.GenericEnumType
 
nullSafeSet(PreparedStatement, Object, int) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
 
NullSessionStats - Class in ome.services.sessions.stats
Implementation of SimpleStats which does nothing.
NullSessionStats() - Constructor for class ome.services.sessions.stats.NullSessionStats
 
numberOfSubtypes(int) - Method in class ome.tools.hibernate.ExtendedMetadata.Locks
returns the number of subtypes for iterating over this secondary array.
numDone - Variable in class ome.formats.importer.ImportEvent.COUNT_EVENT
 
numDone - Variable in class ome.formats.importer.ImportEvent.PROGRESS_EVENT
 
NumericAnnotation - Class in ome.model.annotations
 
NumericAnnotation() - Constructor for class ome.model.annotations.NumericAnnotation
 
NumericAnnotation(Long) - Constructor for class ome.model.annotations.NumericAnnotation
 
NumericAnnotation(Long, boolean) - Constructor for class ome.model.annotations.NumericAnnotation
Main constructor.
numFiles - Variable in class ome.formats.importer.ImportCandidates.SCANNING
 
numOfDirectories - Variable in class ome.formats.importer.ImportConfig
 
numThreads - Variable in class ome.services.pixeldata.PersistentEventLogLoader
 

O

OBJECT_TO_RTYPE - Static variable in class omero.util.IceMapper
 
OBJECTARRAY_TO_RTYPESEQ - Static variable in class omero.util.IceMapper
 
ObjectFactoryRegistry - Class in omero.util
SPI type picked up from the Spring configuration and given a chance to register all its ObjectFactory instances with the Communicator.
ObjectFactoryRegistry() - Constructor for class omero.util.ObjectFactoryRegistry
 
ObjectFactoryRegistry.ObjectFactory - Class in omero.util
 
ObjectFactoryRegistry.ObjectFactory(String) - Constructor for class omero.util.ObjectFactoryRegistry.ObjectFactory
 
objective - Variable in class ome.model.acquisition.Instrument
 
OBJECTIVE - Static variable in class ome.model.acquisition.Instrument
 
Objective - Class in ome.model.acquisition
These filter definitions are used by the security system to eliminate non-readable objects from queries.
Objective() - Constructor for class ome.model.acquisition.Objective
 
Objective(Long) - Constructor for class ome.model.acquisition.Objective
 
Objective(Long, boolean) - Constructor for class ome.model.acquisition.Objective
Main constructor.
Objective(Immersion, Correction, Instrument) - Constructor for class ome.model.acquisition.Objective
 
objective - Variable in class ome.model.acquisition.ObjectiveSettings
 
OBJECTIVE - Static variable in class ome.model.acquisition.ObjectiveSettings
 
objective - Variable in class ome.model.acquisition.OTF
 
OBJECTIVE - Static variable in class ome.model.acquisition.OTF
 
Objective.Details - Class in ome.model.acquisition
 
Objective.Details() - Constructor for class ome.model.acquisition.Objective.Details
 
Objective.Details(Object[]) - Constructor for class ome.model.acquisition.Objective.Details
 
Objective_WorkingDistance - Static variable in class ome.formats.model.UnitsFactory
 
ObjectiveAnnotationLink - Class in ome.model.annotations
These filter definitions are used by the security system to eliminate non-readable objects from queries.
ObjectiveAnnotationLink() - Constructor for class ome.model.annotations.ObjectiveAnnotationLink
 
ObjectiveAnnotationLink(Long) - Constructor for class ome.model.annotations.ObjectiveAnnotationLink
 
ObjectiveAnnotationLink(Long, boolean) - Constructor for class ome.model.annotations.ObjectiveAnnotationLink
Main constructor.
ObjectiveAnnotationLink(IObject, IObject) - Constructor for class ome.model.annotations.ObjectiveAnnotationLink
 
ObjectiveAnnotationLink.Details - Class in ome.model.annotations
 
ObjectiveAnnotationLink.Details() - Constructor for class ome.model.annotations.ObjectiveAnnotationLink.Details
 
ObjectiveAnnotationLink.Details(Object[]) - Constructor for class ome.model.annotations.ObjectiveAnnotationLink.Details
 
ObjectiveData - Class in pojos
Hosts an objective used to capture an image.
ObjectiveData(Objective) - Constructor for class pojos.ObjectiveData
Creates a new instance.
ObjectiveSettings - Class in ome.model.acquisition
These filter definitions are used by the security system to eliminate non-readable objects from queries.
ObjectiveSettings() - Constructor for class ome.model.acquisition.ObjectiveSettings
 
ObjectiveSettings(Long) - Constructor for class ome.model.acquisition.ObjectiveSettings
 
ObjectiveSettings(Long, boolean) - Constructor for class ome.model.acquisition.ObjectiveSettings
Main constructor.
ObjectiveSettings(Objective) - Constructor for class ome.model.acquisition.ObjectiveSettings
 
objectiveSettings - Variable in class ome.model.core.Image
 
OBJECTIVESETTINGS - Static variable in class ome.model.core.Image
 
ObjectiveSettings.Details - Class in ome.model.acquisition
 
ObjectiveSettings.Details() - Constructor for class ome.model.acquisition.ObjectiveSettings.Details
 
ObjectiveSettings.Details(Object[]) - Constructor for class ome.model.acquisition.ObjectiveSettings.Details
 
ObjectMailSender - Class in ome.services.mail
When an EventLogMessage of the specified type and kind is received, an email is sent to all users which are returned by a given query.
ObjectMailSender() - Constructor for class ome.services.mail.ObjectMailSender
 
objects - Variable in class ome.formats.importer.ImportEvent.IMPORT_DONE
 
objects - Variable in class ome.services.messages.ReindexMessage
 
ObjectsReadCounter - Class in ome.services.sessions.stats
Counter for all the objects read in a session.
ObjectsReadCounter(int) - Constructor for class ome.services.sessions.stats.ObjectsReadCounter
 
objectsReadHardLimit - Variable in class ome.services.sessions.stats.CounterFactory
 
ObjectsReadStatsMessage - Class in ome.services.messages.stats
Published when some limit in user/group/session activity has been reached.
ObjectsReadStatsMessage(Object, long) - Constructor for class ome.services.messages.stats.ObjectsReadStatsMessage
 
ObjectsWrittenCounter - Class in ome.services.sessions.stats
Counter for all the objects read in a session.
ObjectsWrittenCounter(int) - Constructor for class ome.services.sessions.stats.ObjectsWrittenCounter
 
objectsWrittenHardLimit - Variable in class ome.services.sessions.stats.CounterFactory
 
ObjectsWrittenStatsMessage - Class in ome.services.messages.stats
 
ObjectsWrittenStatsMessage(Object, long) - Constructor for class ome.services.messages.stats.ObjectsWrittenStatsMessage
 
observers - Variable in class ome.formats.importer.util.ErrorHandler
 
obtainProxy(String, Redirector.Context, String, SessionControlPrx, Current) - Method in class ome.services.blitz.redirect.AbstractRedirector
 
obToImageCache - Variable in class ome.services.sharing.BlobShareStore
 
offset - Variable in class ome.parameters.Filter
 
offset - Variable in class ome.util.mem.ReadOnlyByteArray
Marks the start of the slice.
offsetValue - Variable in class ome.model.acquisition.Detector
 
OFFSETVALUE - Static variable in class ome.model.acquisition.Detector
 
offsetValue - Variable in class ome.model.acquisition.DetectorSettings
 
OFFSETVALUE - Static variable in class ome.model.acquisition.DetectorSettings
 
ome.annotations - package ome.annotations
Runtime source annotation package for the OMERO server This includes classes that annotate source code and check metadata at runtime for server API calls.
ome.api - package ome.api
Contains the central verbs of the Omero System.
ome.api.local - package ome.api.local
Non-client service API for OMERO This includes interfaces for the local administration of the OMERO server.
ome.conditions - package ome.conditions
Forms the basis of all Omero exception hierarchies.
ome.conditions.acl - package ome.conditions.acl
Exceptions thrown due to access control violations.
ome.formats - package ome.formats
 
ome.formats.enums - package ome.formats.enums
 
ome.formats.enums.handler - package ome.formats.enums.handler
 
ome.formats.importer - package ome.formats.importer
 
ome.formats.importer.cli - package ome.formats.importer.cli
 
ome.formats.importer.exclusions - package ome.formats.importer.exclusions
mechanism for determing which potential filesets should be excluded from import.
ome.formats.importer.transfers - package ome.formats.importer.transfers
mechanism for shipping client-side files to the server-side.
ome.formats.importer.util - package ome.formats.importer.util
 
ome.formats.model - package ome.formats.model
 
ome.formats.model.handler - package ome.formats.model.handler
 
ome.io.bioformats - package ome.io.bioformats
 
ome.io.messages - package ome.io.messages
 
ome.io.nio - package ome.io.nio
New Input/Output handling for the OMERO server This includes interfaces/classes for the input and output handling of data within the OMERO server.
ome.logic - package ome.logic
The central repository of implementations which will be accessible through this server.
ome.model - package ome.model
Central interfaces in the Omero object model.
ome.model.acquisition - package ome.model.acquisition
 
ome.model.annotations - package ome.model.annotations
 
ome.model.containers - package ome.model.containers
 
ome.model.core - package ome.model.core
 
ome.model.display - package ome.model.display
 
ome.model.enums - package ome.model.enums
 
ome.model.experiment - package ome.model.experiment
 
ome.model.fs - package ome.model.fs
 
ome.model.internal - package ome.model.internal
Contains non-code-generated model objects.
ome.model.jobs - package ome.model.jobs
 
ome.model.meta - package ome.model.meta
 
ome.model.roi - package ome.model.roi
 
ome.model.screen - package ome.model.screen
 
ome.model.stats - package ome.model.stats
 
ome.model.units - package ome.model.units
 
ome.parameters - package ome.parameters
Contains necessary parameters for various API methods throughout OMERO.
ome.security - package ome.security
JBoss and OMERO security handling This includes classes that provide security for the execution and usage of the OMERO server on a JBoss platform.
ome.security.auth - package ome.security.auth
 
ome.security.auth.providers - package ome.security.auth.providers
 
ome.security.basic - package ome.security.basic
Basic OMERO security contextual classes Basic classes that provide security context objects necessary to secure the implementation of the OMERO server on a JBoss platform.
ome.security.policy - package ome.security.policy
Extensible service and security policies which can influence whether a user, group, or other agent can perform a certain action.
ome.security.sharing - package ome.security.sharing
 
ome.services - package ome.services
Base services package for OMERO API services This includes classes that implement OMERO API services described as interfaces in the OMERO Common component.
ome.services.blitz - package ome.services.blitz
 
ome.services.blitz.fire - package ome.services.blitz.fire
 
ome.services.blitz.impl - package ome.services.blitz.impl
 
ome.services.blitz.impl.commands - package ome.services.blitz.impl.commands
 
ome.services.blitz.measurements - package ome.services.blitz.measurements
 
ome.services.blitz.redirect - package ome.services.blitz.redirect
 
ome.services.blitz.repo - package ome.services.blitz.repo
 
ome.services.blitz.repo.path - package ome.services.blitz.repo.path
 
ome.services.blitz.util - package ome.services.blitz.util
 
ome.services.chgrp - package ome.services.chgrp
 
ome.services.chown - package ome.services.chown
 
ome.services.db - package ome.services.db
 
ome.services.delete - package ome.services.delete
Implementations of the ome.api.IDelete service.
ome.services.delete.files - package ome.services.delete.files
 
ome.services.eventlogs - package ome.services.eventlogs
 
ome.services.export - package ome.services.export
Helpers for implementing the necessary interfaces from Bio-Formats for mapping OMERO objects (ome.model.*) to OME-XML and OME-TIFF
ome.services.formats - package ome.services.formats
 
ome.services.fulltext - package ome.services.fulltext
All necessary classes for background indexing of metadata and attached binary files.
ome.services.fulltext.bridges - package ome.services.fulltext.bridges
Custom FieldBridge implementations which can be configured to be run on each indexing activity.
ome.services.graphs - package ome.services.graphs
Server classes for handling complicated graphs of model objects.
ome.services.mail - package ome.services.mail
General mail services.
ome.services.messages - package ome.services.messages
Message implementations used throughout the server for internal communication.
ome.services.messages.stats - package ome.services.messages.stats
 
ome.services.pixeldata - package ome.services.pixeldata
 
ome.services.procs - package ome.services.procs
Internal process and process management This includes interfaces and classes that provide thread process management for internal processes critical to the operation of the OMERO server.
ome.services.procs.scripts - package ome.services.procs.scripts
Script processor infrastructure.
ome.services.projection - package ome.services.projection
 
ome.services.query - package ome.services.query
facilitates the creation of Hibernate Queries and Criteria.
ome.services.roi - package ome.services.roi
 
ome.services.scheduler - package ome.services.scheduler
 
ome.services.scripts - package ome.services.scripts
 
ome.services.search - package ome.services.search
Internal search implementation classes.
ome.services.sessions - package ome.services.sessions
 
ome.services.sessions.events - package ome.services.sessions.events
 
ome.services.sessions.state - package ome.services.sessions.state
 
ome.services.sessions.stats - package ome.services.sessions.stats
 
ome.services.sharing - package ome.services.sharing
ome.api.IShare support infrastructure.
ome.services.throttling - package ome.services.throttling
 
ome.services.util - package ome.services.util
Helper classes to support OMERO service beans Instead of abstract classes, IOC methods and dependency injection is used to provide service interception for the Service (binary) bean classes.
ome.system - package ome.system
Provides the necessary container structure for the entire Omero system.
ome.system.metrics - package ome.system.metrics
General metrics registry for use by all server-side components.
ome.tools - package ome.tools
OMERO Server Utility and Spring/Hibernate Tools Classes/Interfaces that implement File, Hibernate, Spring, Annotation, Hierarchy, etc. method mechanics for the OMERO server Related Documentation For more information, please see: TODO
ome.tools.hibernate - package ome.tools.hibernate
Hibernate specific tools for the OMERO Server Classes/Interfaces that implement Hibernate method mechanics for the OMERO server Related Documentation For more information, please see: TODO
ome.tools.lsid - package ome.tools.lsid
Life Science Identifier (LSID) tools Classes/Interfaces that manage conversions and creation of LSID unique identifiers Related Documentation For more information, please see: TODO
ome.tools.spring - package ome.tools.spring
OMERO Server tools specific to Spring Classes/Interfaces that implement AOP, Post-processing injection, session flushing, and factory management.
ome.util - package ome.util
Utilities for all of OMERO.
ome.util.actions - package ome.util.actions
 
ome.util.checksum - package ome.util.checksum
 
ome.util.logback - package ome.util.logback
 
ome.util.math.geom2D - package ome.util.math.geom2D
Plane geometry data structures for OMERO This includes a several implementations of various two dimensional simple geometry classes to represent these structures within the OMERO system.
ome.util.mem - package ome.util.mem
Dynamic object instance and state management for OMERO This includes various implementations of copy and clonable operations.
ome.util.messages - package ome.util.messages
Messages package for specialized exception handling for OMERO.
ome.util.search - package ome.util.search
 
OMECredentials - Class in loci.ome.io
Stores credentials for logging into an OME/OMERO server.
OMECredentials(String, String, String) - Constructor for class loci.ome.io.OMECredentials
 
OMECredentials(String) - Constructor for class loci.ome.io.OMECredentials
Get credentials from a string.
omeis.providers.re - package omeis.providers.re
Red-Green-Blue (RGB) data structures and Image Rendering Service This package provides basic data structures to represent an RGB pixel set and provide a service for the rendering of this pixel set.
omeis.providers.re.codomain - package omeis.providers.re.codomain
Provides codomain pixel set data structures for Maps and Contexts.
omeis.providers.re.data - package omeis.providers.re.data
Provides classes needed to define XY planes within a dynamic 3D context.
omeis.providers.re.metadata - package omeis.providers.re.metadata
 
omeis.providers.re.quantum - package omeis.providers.re.quantum
 
omeName - Variable in class ome.model.meta.Experimenter
 
OMENAME - Static variable in class ome.model.meta.Experimenter
 
OMENAME - Static variable in class pojos.ExperimenterData
Identifies the Experimenter#OMENAME field.
OMEReaderWriterService - Interface in loci.ome.io.services
 
OMEReaderWriterServiceImpl - Class in loci.ome.io.services
 
OMEReaderWriterServiceImpl() - Constructor for class loci.ome.io.services.OMEReaderWriterServiceImpl
 
omero - package omero
 
omero.cmd - package omero.cmd
 
omero.cmd.admin - package omero.cmd.admin
 
omero.cmd.basic - package omero.cmd.basic
 
omero.cmd.fs - package omero.cmd.fs
 
omero.cmd.graphs - package omero.cmd.graphs
 
omero.cmd.mail - package omero.cmd.mail
 
omero.grid - package omero.grid
 
omero.model - package omero.model
 
omero.sys - package omero.sys
 
omero.util - package omero.util
 
OMERO_EMISSION_FILTER_SUFFIX - Static variable in class ome.formats.OMEROMetadataStoreClient
Emission filter LSID suffix.
OMERO_EVENT - Static variable in class ome.system.Login
Java property name for use in configuration of client login.
OMERO_EXCITATION_FILTER_SUFFIX - Static variable in class ome.formats.OMEROMetadataStoreClient
Excitation filter LSID suffix.
OMERO_GROUP - Static variable in class ome.system.Login
Java property name for use in configuration of client login.
OMERO_HOST - Static variable in class ome.system.Server
Java property name for use in configuration of the client connection.
OMERO_PASS - Static variable in class ome.system.Login
Java property name for use in configuration of client login.
OMERO_PORT - Static variable in class ome.system.Server
Java property name for use in configuration of the client connection.
OMERO_TABLE - Variable in class ome.services.fulltext.bridges.TablesBridge
Mimetype set on OriginalFile.mimetype (or in previous version, OriginalFile.format.value).
OMERO_USER - Static variable in class ome.system.Login
Java property name for use in configuration of client login.
omeroClass(String, boolean) - Static method in class omero.util.IceMapper
 
OmeroContext - Class in ome.system
Provides static access for the creation of singleton and non-singleton application contexts.
OmeroContext(String) - Constructor for class ome.system.OmeroContext
 
OmeroContext(String[]) - Constructor for class ome.system.OmeroContext
 
OmeroContext(String[], boolean) - Constructor for class ome.system.OmeroContext
 
OmeroContext(String[], ApplicationContext) - Constructor for class ome.system.OmeroContext
 
OmeroContext(String[], boolean, ApplicationContext) - Constructor for class ome.system.OmeroContext
 
OmeroContext.Locator - Class in ome.system
provides access to the protected methods of ContextSingletonBeanFactoryLocator which cannot be used externally.
OmeroContext.Locator() - Constructor for class ome.system.OmeroContext.Locator
 
omeroDataDir - Variable in class ome.services.blitz.impl.MetadataStoreI
 
omeroDataDir - Variable in class ome.services.OmeroFilePathResolver
The server's OMERO data directory.
OmeroFilePathResolver - Class in ome.services
OMERO server based resolver for file paths.
OmeroFilePathResolver(SqlAction, String) - Constructor for class ome.services.OmeroFilePathResolver
Constructor.
OMEROImportFixture - Class in ome.formats
test fixture for importing files without a GUI.
OMEROImportFixture(OMEROMetadataStoreClient, OMEROWrapper) - Constructor for class ome.formats.OMEROImportFixture
 
OmeroInterceptor - Class in ome.security.basic
implements Interceptor for controlling various aspects of the Hibernate runtime.
OmeroInterceptor(Roles, SystemTypes, ExtendedMetadata, CurrentDetails, TokenHolder, SessionStats) - Constructor for class ome.security.basic.OmeroInterceptor
 
OmeroMeasurementStore - Interface in ome.services.blitz.measurements
Sub-interface of MeasurementStore with extended life-cycle methods for handling exceptions during saving the measurements to multiple stores.
OmeroMetadata - Class in ome.services.blitz.impl
An implementation for MetadataStore and MetadataRetrieve that knows how to read and write the OMERO object model.
OmeroMetadata(DatabaseIdentity) - Constructor for class ome.services.blitz.impl.OmeroMetadata
 
OMEROMetadataStore - Class in ome.formats
An OMERO metadata store.
OMEROMetadataStore() - Constructor for class ome.formats.OMEROMetadataStore
Empty constructor for testing purposes.
OMEROMetadataStore(ServiceFactory, SqlAction) - Constructor for class ome.formats.OMEROMetadataStore
Creates a new instance.
OMEROMetadataStoreClient - Class in ome.formats
Client side implementation of the Bio-Formats MetadataStore.
OMEROMetadataStoreClient() - Constructor for class ome.formats.OMEROMetadataStoreClient
 
OMEROMetadataStoreClientRoot - Class in ome.formats
MetadataRoot implementation for the client side implementation of the Bio-Formats MetadataStore.
OMEROMetadataStoreClientRoot() - Constructor for class ome.formats.OMEROMetadataStoreClientRoot
Default constructor.
OMEROMetadataStoreClientRoot(List<Pixels>) - Constructor for class ome.formats.OMEROMetadataStoreClientRoot
Copy constructor.
OmeroModelContextMapper - Class in ome.security.auth
Parent class for any OMERO model-to-LDAP mappers.
OmeroModelContextMapper(LdapConfig, String, String) - Constructor for class ome.security.auth.OmeroModelContextMapper
 
OmeroPixelsPyramidReader - Class in ome.io.bioformats
File format reader for OMERO pixels pyramid files.
OmeroPixelsPyramidReader() - Constructor for class ome.io.bioformats.OmeroPixelsPyramidReader
 
OmeroPixelsPyramidWriter - Class in ome.io.bioformats
File format writer for OMERO pixels pyramid files.
OmeroPixelsPyramidWriter() - Constructor for class ome.io.bioformats.OmeroPixelsPyramidWriter
 
OmeroReader - Class in loci.ome.io
Implementation of IFormatReader for use in export from an OMERO Beta 4.2.x database.
OmeroReader() - Constructor for class loci.ome.io.OmeroReader
 
OmeroReader - Class in ome.services.formats
Implementation of IFormatReader for use in export.
OmeroReader(RawPixelsStore, Pixels) - Constructor for class ome.services.formats.OmeroReader
 
OmeroReader(RawPixelsStorePrx, Pixels) - Constructor for class ome.services.formats.OmeroReader
 
OMEROWrapper - Class in ome.formats.importer
 
OMEROWrapper(ImportConfig) - Constructor for class ome.formats.importer.OMEROWrapper
Wrapper for bio-formats
OMEROWrapper(ImportConfig, long, File) - Constructor for class ome.formats.importer.OMEROWrapper
 
OMEXMLModelComparator - Class in ome.formats
This comparator takes into account the OME-XML data model hierarchy and uses that to define equivalence.
OMEXMLModelComparator() - Constructor for class ome.formats.OMEXMLModelComparator
 
onAddError(ErrorContainer, String) - Method in class ome.formats.importer.util.ErrorHandler
Action to take on adding an error to container
onApplicationEvent(LoginAttemptMessage) - Method in class ome.security.auth.LoginAttemptListener
 
onApplicationEvent(EventLogMessage) - Method in class ome.security.basic.BasicSecuritySystem
 
onApplicationEvent(ContextMessage) - Method in class ome.security.basic.EventHandler
If a ContextMessage is received, then we either need to add a ContextMessage.Push login to the stack or ContextMessage.Pop remove one.
onApplicationEvent(InternalMessage) - Method in class ome.services.blitz.fire.SessionManagerI
 
onApplicationEvent(ApplicationEvent) - Method in class ome.services.blitz.fire.TopicManager.Impl
 
onApplicationEvent(InternalMessage) - Method in class ome.services.blitz.repo.AbstractRepositoryI
 
onApplicationEvent(UserSignalMessage) - Method in class ome.services.db.SelfCorrectingDataSource
Handles the USR1 posix signal by calling close on the underlying data source via reflection.
onApplicationEvent(ApplicationEvent) - Method in class ome.services.eventlogs.EventLogLoader
 
onApplicationEvent(ApplicationEvent) - Method in class ome.services.eventlogs.EventLogQueue
 
onApplicationEvent(ApplicationEvent) - Method in class ome.services.fulltext.ParserSession
 
onApplicationEvent(ApplicationEvent) - Method in class ome.services.fulltext.PersistentEventLogLoader
 
onApplicationEvent(LoginAttemptMessage) - Method in class ome.services.mail.FailedLoginMailSender
 
onApplicationEvent(EventLogsMessage) - Method in class ome.services.mail.ObjectMailSender
 
onApplicationEvent(ShutdownMessage) - Method in class ome.services.mail.ServerDownMailSender
 
onApplicationEvent(MissingPyramidMessage) - Method in class ome.services.pixeldata.PixelDataThread
Called in the main server (Blitz-0) in order to create a PIXELDATA EventLog which will get processed by PixelData-0.
onApplicationEvent(ContextRefreshedEvent) - Method in class ome.services.scheduler.SchedulerFactoryBean
 
onApplicationEvent(ApplicationEvent) - Method in class ome.services.sessions.SessionManagerImpl
 
onApplicationEvent(ApplicationEvent) - Method in class ome.services.throttling.AbstractThrottlingStrategy
 
onApplicationEvent(ApplicationEvent) - Method in class ome.services.util.ServiceHandler
 
onApplicationEvent(ContextRefreshedEvent) - Method in class ome.tools.spring.OnContextRefreshedEventListener
 
onBoundaries(double, double) - Method in class ome.util.math.geom2D.EllipseArea
Implemented as specified by the PlaneArea I/F.
onBoundaries(double, double) - Method in interface ome.util.math.geom2D.PlaneArea
Controls if a specified point is on the boundary of the PlaneArea.
onBoundaries(double, double) - Method in class ome.util.math.geom2D.RectangleArea
Implemented as specified by the PlaneArea I/F.
onCancel() - Method in class ome.formats.importer.util.ErrorHandler
action to take on cancel
onCollectionRecreate(Object, Serializable) - Method in class ome.security.basic.OmeroInterceptor
 
onCollectionRemove(Object, Serializable) - Method in class ome.security.basic.OmeroInterceptor
 
onCollectionUpdate(Object, Serializable) - Method in class ome.security.basic.OmeroInterceptor
 
OnContextRefreshedEventListener - Class in ome.tools.spring
ApplicationListener which only listens for ContextRefreshedEvent and only responds to the first one.
OnContextRefreshedEventListener() - Constructor for class ome.tools.spring.OnContextRefreshedEventListener
 
OnContextRefreshedEventListener(boolean, int) - Constructor for class ome.tools.spring.OnContextRefreshedEventListener
 
onDelete(Object, Serializable, Object[], String[], Type[]) - Method in class ome.security.basic.OmeroInterceptor
default logic
onDiskCache(String) - Method in interface ome.services.sessions.SessionManager
Returns after possibly creating an on-disk cache which can be used throughout the session.
onDiskCache(String) - Method in class ome.services.sessions.SessionManagerImpl
 
onDiskCache(String) - Method in class ome.services.sessions.state.SessionCache
 
onegroup - Variable in class ome.security.SecurityFilterHolder
 
OneGroupSecurityFilter - Class in ome.security.basic
overrides FilterDefinitionFactoryBean in order to construct our security filter in code and not in XML.
OneGroupSecurityFilter() - Constructor for class ome.security.basic.OneGroupSecurityFilter
default constructor which calls all the necessary setters for this FactoryBean.
OneGroupSecurityFilter(Roles) - Constructor for class ome.security.basic.OneGroupSecurityFilter
 
onException(Exception) - Method in class ome.formats.importer.util.ErrorHandler
Action to take on exception
onExecutionException(ExecutionException) - Method in class ome.services.pixeldata.PixelDataThread
Basic handling just logs at ERROR level.
onFinished(Response, Status, Current) - Method in class ome.formats.importer.ImportLibrary.ImportCallback
Overridden to handle the end of the process.
onFinished(Response, Status, Current) - Method in class omero.cmd.CmdCallbackI
Method intended to be overridden by subclasses.
onFinishedDone() - Method in class omero.cmd.CmdCallbackI
 
onFlushDirty(Object, Serializable, Object[], Object[], String[], Type[]) - Method in class ome.security.basic.OmeroInterceptor
onHeartbeat(Runnable) - Method in class omero.client
 
onLoad(Object, Serializable, Object[], String[], Type[]) - Method in class ome.security.basic.OmeroInterceptor
default logic.
onlyAnnotatedBetween(Timestamp, Timestamp) - Method in interface ome.api.Search
Restricts entities by the time in which any annotation (which matches the other filters) was added them.
onlyAnnotatedBetween(Timestamp, Timestamp) - Method in class ome.services.SearchBean
 
onlyAnnotatedBetween_async(AMD_Search_onlyAnnotatedBetween, RTime, RTime, Current) - Method in class ome.services.blitz.impl.SearchI
 
onlyAnnotatedBy(Details) - Method in interface ome.api.Search
Restricts entities by who has annotated them with an Annotation matching the other filters.
onlyAnnotatedBy(Details) - Method in class ome.services.SearchBean
 
onlyAnnotatedBy_async(AMD_Search_onlyAnnotatedBy, Details, Current) - Method in class ome.services.blitz.impl.SearchI
 
onlyAnnotatedWith(Class...) - Method in interface ome.api.Search
Restricts entities to having an Annotation of all the given types.
onlyAnnotatedWith - Variable in class ome.services.search.SearchValues
 
onlyAnnotatedWith(Class...) - Method in class ome.services.SearchBean
 
onlyAnnotatedWith_async(AMD_Search_onlyAnnotatedWith, List<String>, Current) - Method in class ome.services.blitz.impl.SearchI
 
onlyCreatedBetween(Timestamp, Timestamp) - Method in interface ome.api.Search
Restricts the time between which an entity may have been created.
onlyCreatedBetween(Timestamp, Timestamp) - Method in class ome.services.SearchBean
 
onlyCreatedBetween_async(AMD_Search_onlyCreatedBetween, RTime, RTime, Current) - Method in class ome.services.blitz.impl.SearchI
 
onlyIds(Long...) - Method in interface ome.api.Search
Restricts the set of ids which will be checked.
onlyIds - Variable in class ome.services.search.SearchValues
 
onlyIds(Long...) - Method in class ome.services.SearchBean
 
onlyIds_async(AMD_Search_onlyIds, List<Long>, Current) - Method in class ome.services.blitz.impl.SearchI
 
onlyModifiedBetween(Timestamp, Timestamp) - Method in interface ome.api.Search
Restricts the time between which an entity may have last been modified.
onlyModifiedBetween(Timestamp, Timestamp) - Method in class ome.services.SearchBean
 
onlyModifiedBetween_async(AMD_Search_onlyModifiedBetween, RTime, RTime, Current) - Method in class ome.services.blitz.impl.SearchI
 
onlyOwnedBy(Details) - Method in interface ome.api.Search
Uses the Details.getOwner() and Details.getGroup() information to restrict the entities which will be returned.
onlyOwnedBy(Details) - Method in class ome.services.SearchBean
 
onlyOwnedBy_async(AMD_Search_onlyOwnedBy, Details, Current) - Method in class ome.services.blitz.impl.SearchI
 
onlyPermissionsChanged(Details, Details) - Static method in class ome.tools.hibernate.HibernateUtils
 
onlyType(Class<T>) - Method in interface ome.api.Search
Restricts the search to a single type.
onlyType(Class<T>) - Method in class ome.services.SearchBean
 
onlyType_async(AMD_Search_onlyType, String, Current) - Method in class ome.services.blitz.impl.SearchI
 
onlyTypes(Class<T>...) - Method in interface ome.api.Search
Restricts searches to a set of types.
onlyTypes - Variable in class ome.services.search.SearchValues
 
onlyTypes(Class<T>...) - Method in class ome.services.SearchBean
 
onlyTypes_async(AMD_Search_onlyTypes, List<String>, Current) - Method in class ome.services.blitz.impl.SearchI
 
onMerge(MergeEvent) - Method in class ome.security.basic.MergeEventListener
 
onMerge(MergeEvent, Map) - Method in class ome.security.basic.MergeEventListener
 
onNotSending(int, String) - Method in class ome.formats.importer.util.ErrorHandler
 
onPostDelete(PostDeleteEvent) - Method in class ome.security.ACLEventListener
unused
onPostDelete(PostDeleteEvent) - Method in class ome.security.basic.EventLogListener
 
onPostInsert(PostInsertEvent) - Method in class ome.security.ACLEventListener
unused
onPostInsert(PostInsertEvent) - Method in class ome.security.basic.EventLogListener
 
onPostLoad(PostLoadEvent) - Method in class ome.security.ACLEventListener
catches all load events after the fact, and tests the current users permissions to read that object.
onPostProcess(List<GraphStep>) - Method in class ome.services.graphs.AbstractStepFactory
Deprecated.
 
onPostUpdate(PostUpdateEvent) - Method in class ome.security.ACLEventListener
unused
onPostUpdate(PostUpdateEvent) - Method in class ome.security.basic.EventLogListener
 
onPreDelete(PreDeleteEvent) - Method in class ome.security.ACLEventListener
 
onPreInsert(PreInsertEvent) - Method in class ome.security.ACLEventListener
 
onPreLoad(PreLoadEvent) - Method in class ome.security.ACLEventListener
unused
onPrepareStatement(String) - Method in class ome.security.basic.OmeroInterceptor
 
onPreUpdate(PreUpdateEvent) - Method in class ome.security.ACLEventListener
 
onPreUpdate(PreUpdateEvent) - Method in class ome.security.basic.UpdateEventListener
updates the update event field of an IObject instance.
onRefresh() - Method in class ome.system.OmeroContext
 
onRefresh(RefreshEvent) - Method in class ome.tools.hibernate.ReloadingRefreshEventListener
 
onRefresh(RefreshEvent, Map) - Method in class ome.tools.hibernate.ReloadingRefreshEventListener
 
onRelease(Class<IObject>, Set<Long>) - Method in class ome.services.chgrp.ChgrpStep
Deprecated.
 
onRelease(Class<IObject>, Set<Long>) - Method in class ome.services.chown.ChownStep
Deprecated.
 
onRelease(Class<IObject>, Set<Long>) - Method in class ome.services.delete.DeleteStep
Deprecated.
 
onRelease(Class<IObject>, Set<Long>) - Method in class ome.services.export.ExporterStep
Deprecated.
 
onRelease(Class<IObject>, Set<Long>) - Method in class ome.services.graphs.GraphStep
Deprecated.
 
onSave(Object, Serializable, Object[], String[], Type[]) - Method in class ome.security.basic.OmeroInterceptor
onSaveOrUpdate(SaveOrUpdateEvent) - Method in class ome.security.basic.SaveEventListener
 
onSending(int) - Method in class ome.formats.importer.util.ErrorHandler
 
onSent(int) - Method in class ome.formats.importer.util.ErrorHandler
 
onSessionClosed(Runnable) - Method in class omero.client
 
onSetOmeroContext(OmeroContext) - Method in class ome.services.blitz.impl.AbstractAmdServant
To be overridden by subclasses.
onSetOmeroContext(OmeroContext) - Method in class ome.services.blitz.impl.MetadataStoreI
 
onShutdown(Runnable) - Method in class omero.client
 
onUpdate(IObservable, ImportEvent) - Method in class ome.formats.importer.cli.ErrorHandler
 
onUpdate(IObservable, ImportEvent) - Method in class ome.formats.importer.util.ErrorHandler
abstract on update method
onWindowChange() - Method in class omeis.providers.re.quantum.BinaryMaskQuantizer
 
onWindowChange() - Method in class omeis.providers.re.quantum.Quantization_32_bit
The input window size changed, re-map the values.
onWindowChange() - Method in class omeis.providers.re.quantum.Quantization_8_16_bit
The input window size changed, rebuild the LUT.
onWindowChange() - Method in class omeis.providers.re.quantum.Quantization_float
The input window size changed, re-map the values.
onWindowChange() - Method in class omeis.providers.re.quantum.QuantumStrategy
Notifies when the input interval has changed or the mapping strategy has changed.
openBytes(int, byte[], int, int, int, int) - Method in class loci.ome.io.OmeroReader
 
openBytes(int, byte[], int, int, int, int) - Method in class ome.services.formats.OmeroReader
 
openPlane2D(String, int, byte[]) - Method in class ome.formats.importer.OMEROWrapper
Obtains an object which represents a given sub-image of a plane within the file.
openPlane2D(String, int, byte[], int, int, int, int) - Method in class ome.formats.importer.OMEROWrapper
Obtains an object which represents a given sub-image of a plane within the file.
openSession() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
openTable(OriginalFile, Current) - Method in class ome.services.blitz.impl.SharedResourcesI
 
opticalAxisAveraged - Variable in class ome.model.acquisition.OTF
 
OPTICALAXISAVERAGED - Static variable in class ome.model.acquisition.OTF
 
optimisticFailure(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
OptimisticLockException - Exception in ome.conditions
Signifies that another user has updated or deleted a given object, more specifically a query of the form : "<action> where id = ?
OptimisticLockException(String) - Constructor for exception ome.conditions.OptimisticLockException
 
Optimizations - Class in omeis.providers.re
A container for any potential optimizations that the renderer can enable based on the data and rendering settings it has been fed.
Optimizations() - Constructor for class omeis.providers.re.Optimizations
 
optional - Variable in class ome.services.query.QueryParameterDef
whether or not this QueryParameter can be omitted or its value null.
optionallyNullField(Session, Long) - Method in class ome.services.graphs.GraphStep
Deprecated.
 
optionalNullBuilder() - Method in class ome.services.graphs.GraphStep
Deprecated.
 
Options - Class in ome.parameters
Simple options container.
Options() - Constructor for class ome.parameters.Options
 
options - Variable in class ome.services.graphs.BaseGraphSpec
Deprecated.
Options passed to the #initialize(long, Map) method, which may be used during GraphState.execute(int) to alter behavior.
optSource - Variable in class ome.services.graphs.AbstractHierarchyGraphSpec
Deprecated.
Key from the options map which was the source of the rawOption value of the same index.
or() - Method in interface ome.api.Search
Applies the next by* method to the previous by* method, so that a call Search.hasNext(), Search.next(), or Search.results() sees only the union of the two calls.
or() - Method in class ome.services.SearchBean
 
or(String) - Method in class ome.tools.hibernate.QueryBuilder
Appends "or" plus your string unless this is the first where-spec in which case it is simply appended.
or_async(AMD_Search_or, Current) - Method in class ome.services.blitz.impl.SearchI
 
order(String, boolean) - Method in class ome.tools.hibernate.QueryBuilder
 
orderBy - Variable in class ome.services.search.SearchValues
 
orderByAscending(String) - Static method in class ome.services.search.SearchAction
 
orderByPath(String) - Static method in class ome.services.search.SearchAction
 
org.hibernate.stat - package org.hibernate.stat
 
OrgUnitNewUserGroupBean - Class in ome.security.auth
Handles the ":ou:" specifier from etc/omero.properties by adding the user to a group named by the final organizational unit.
OrgUnitNewUserGroupBean(DistinguishedName) - Constructor for class ome.security.auth.OrgUnitNewUserGroupBean
 
origin - Variable in class ome.util.math.geom2D.Line
The origin point of the line.
ORIGINAL_METADATA_NAME - Static variable in class pojos.FileAnnotationData
The default name for the original metadata file.
OriginalFile - Class in ome.model.core
These filter definitions are used by the security system to eliminate non-readable objects from queries.
OriginalFile() - Constructor for class ome.model.core.OriginalFile
 
OriginalFile(Long) - Constructor for class ome.model.core.OriginalFile
 
OriginalFile(Long, boolean) - Constructor for class ome.model.core.OriginalFile
Main constructor.
OriginalFile(String, String) - Constructor for class ome.model.core.OriginalFile
 
originalFile - Variable in class ome.model.fs.FilesetEntry
 
ORIGINALFILE - Static variable in class ome.model.fs.FilesetEntry
 
OriginalFile.Details - Class in ome.model.core
 
OriginalFile.Details() - Constructor for class ome.model.core.OriginalFile.Details
 
OriginalFile.Details(Object[]) - Constructor for class ome.model.core.OriginalFile.Details
 
OriginalFileAnnotationLink - Class in ome.model.annotations
These filter definitions are used by the security system to eliminate non-readable objects from queries.
OriginalFileAnnotationLink() - Constructor for class ome.model.annotations.OriginalFileAnnotationLink
 
OriginalFileAnnotationLink(Long) - Constructor for class ome.model.annotations.OriginalFileAnnotationLink
 
OriginalFileAnnotationLink(Long, boolean) - Constructor for class ome.model.annotations.OriginalFileAnnotationLink
Main constructor.
OriginalFileAnnotationLink(IObject, IObject) - Constructor for class ome.model.annotations.OriginalFileAnnotationLink
 
OriginalFileAnnotationLink.Details - Class in ome.model.annotations
 
OriginalFileAnnotationLink.Details() - Constructor for class ome.model.annotations.OriginalFileAnnotationLink.Details
 
OriginalFileAnnotationLink.Details(Object[]) - Constructor for class ome.model.annotations.OriginalFileAnnotationLink.Details
 
OriginalFileDeletions - Class in ome.services.delete.files
Deletes all repository files immediately.
OriginalFileDeletions(AbstractFileSystemService, Set<Long>, OmeroContext) - Constructor for class ome.services.delete.files.OriginalFileDeletions
 
originalFileLinks - Variable in class ome.model.jobs.Job
 
ORIGINALFILELINKS - Static variable in class ome.model.jobs.Job
 
ORIGINALFILELINKSCOUNTPEROWNER - Static variable in class ome.model.jobs.Job
 
OriginalFilesService - Class in ome.io.nio
Raw file service which provides access to FileBuffers.
OriginalFilesService(String) - Constructor for class ome.io.nio.OriginalFilesService
Constructor
OriginalMetadataRequestI - Class in omero.cmd.fs
Original metadata loader, handling both pre-FS and post-FS data.
OriginalMetadataRequestI(PixelsService) - Constructor for class omero.cmd.fs.OriginalMetadataRequestI
 
originalSize - Variable in class ome.services.graphs.AbstractStepFactory
Deprecated.
 
originX1 - Variable in class ome.util.math.geom2D.Segment
The origin of the segment's first element.
originX2 - Variable in class ome.util.math.geom2D.Segment
The origin of the segment's first element.
orphan - Variable in class ome.parameters.Options
 
orphan() - Method in class ome.parameters.Parameters
 
orphan - Variable in class ome.services.graphs.GraphPolicy.Details
the current orphan state of the object, may be mutated by Policy#review(Map, Details, Map, Set); applies only if GraphPolicy.Details.action is GraphPolicy.Action.EXCLUDE
orphan() - Method in class omero.sys.ParametersI
Sets the orphan parameter to true.
osf - Variable in class ome.logic.AdminImpl
 
otf - Variable in class ome.model.acquisition.Instrument
 
OTF - Static variable in class ome.model.acquisition.Instrument
 
OTF - Class in ome.model.acquisition
These filter definitions are used by the security system to eliminate non-readable objects from queries.
OTF() - Constructor for class ome.model.acquisition.OTF
 
OTF(Long) - Constructor for class ome.model.acquisition.OTF
 
OTF(Long, boolean) - Constructor for class ome.model.acquisition.OTF
Main constructor.
OTF(Integer, Integer, Boolean, PixelsType, String, Objective, Instrument) - Constructor for class ome.model.acquisition.OTF
 
otf - Variable in class ome.model.core.LogicalChannel
 
OTF - Static variable in class ome.model.core.LogicalChannel
 
OTF.Details - Class in ome.model.acquisition
 
OTF.Details() - Constructor for class ome.model.acquisition.OTF.Details
 
OTF.Details(Object[]) - Constructor for class ome.model.acquisition.OTF.Details
 
OTFData - Class in pojos
Hosts an OTF.
OTFData(OTF) - Constructor for class pojos.OTFData
Creates a new instance.
outputEnvironment(String) - Method in interface ome.services.sessions.SessionManager
Returns a copy of the output environment.
outputEnvironment(String) - Method in class ome.services.sessions.SessionManagerImpl
 
OverlayMetadataStore - Class in ome.formats
Client side metadata store implementation that only deals with overlays.
OverlayMetadataStore() - Constructor for class ome.formats.OverlayMetadataStore
 
override(String[], Object) - Method in class ome.security.basic.EventListenersFactoryBean
calls override for each key
override(String, Object) - Method in class ome.security.basic.EventListenersFactoryBean
first re-initializes the list for key, and then adds object
overrideKeep() - Method in class ome.services.graphs.AnnotationGraphSpec
Deprecated.
Returns true to prevent skipping of the entire subspec if there were any "excludes" passed in with the options.
overrideKeep() - Method in class ome.services.graphs.BaseGraphSpec
Deprecated.
Always returns false.
overrideKeep() - Method in interface ome.services.graphs.GraphSpec
Deprecated.
For some GraphSpec type/option combinations, a "KEEP" setting may need to be overridden.
overrideKeep() - Method in class ome.services.graphs.LightSourceGraphSpec
Deprecated.
 
overrides() - Method in class ome.security.basic.EventListenersFactoryBean
 
OverUsageException - Exception in ome.conditions
More specific ApiUsageException, in that the current use of the OMERO API could overwhelm the server and has been blocked.
OverUsageException(String) - Constructor for exception ome.conditions.OverUsageException
 
own(String) - Method in class ome.services.db.DatabaseIdentity
 
ownedBy - Variable in class ome.services.search.SearchValues
 
OWNER - Static variable in class ome.model.internal.Details
 
owner - Variable in class ome.model.meta.GroupExperimenterMap
 
OWNER - Static variable in class ome.model.meta.GroupExperimenterMap
 
owner - Variable in class ome.model.meta.Session
 
OWNER - Static variable in class ome.model.meta.Session
 
owner(long) - Method in class ome.parameters.Filter
 
owner() - Method in class ome.parameters.Filter
 
owner() - Method in class ome.parameters.Parameters
 
OWNER_FILTER - Static variable in class ome.model.acquisition.Arc
 
OWNER_FILTER - Static variable in class ome.model.acquisition.Detector
 
OWNER_FILTER - Static variable in class ome.model.acquisition.DetectorSettings
 
OWNER_FILTER - Static variable in class ome.model.acquisition.Dichroic
 
OWNER_FILTER - Static variable in class ome.model.acquisition.Filament
 
OWNER_FILTER - Static variable in class ome.model.acquisition.Filter
 
OWNER_FILTER - Static variable in class ome.model.acquisition.FilterSet
 
OWNER_FILTER - Static variable in class ome.model.acquisition.FilterSetEmissionFilterLink
 
OWNER_FILTER - Static variable in class ome.model.acquisition.FilterSetExcitationFilterLink
 
OWNER_FILTER - Static variable in class ome.model.acquisition.GenericExcitationSource
 
OWNER_FILTER - Static variable in class ome.model.acquisition.ImagingEnvironment
 
OWNER_FILTER - Static variable in class ome.model.acquisition.Instrument
 
OWNER_FILTER - Static variable in class ome.model.acquisition.Laser
 
OWNER_FILTER - Static variable in class ome.model.acquisition.LightEmittingDiode
 
OWNER_FILTER - Static variable in class ome.model.acquisition.LightPath
 
OWNER_FILTER - Static variable in class ome.model.acquisition.LightPathEmissionFilterLink
 
OWNER_FILTER - Static variable in class ome.model.acquisition.LightPathExcitationFilterLink
 
OWNER_FILTER - Static variable in class ome.model.acquisition.LightSettings
 
OWNER_FILTER - Static variable in class ome.model.acquisition.LightSource
 
OWNER_FILTER - Static variable in class ome.model.acquisition.Microscope
 
OWNER_FILTER - Static variable in class ome.model.acquisition.Objective
 
OWNER_FILTER - Static variable in class ome.model.acquisition.ObjectiveSettings
 
OWNER_FILTER - Static variable in class ome.model.acquisition.OTF
 
OWNER_FILTER - Static variable in class ome.model.acquisition.StageLabel
 
OWNER_FILTER - Static variable in class ome.model.acquisition.TransmittanceRange
 
OWNER_FILTER - Static variable in class ome.model.annotations.Annotation
 
OWNER_FILTER - Static variable in class ome.model.annotations.AnnotationAnnotationLink
 
OWNER_FILTER - Static variable in class ome.model.annotations.BasicAnnotation
 
OWNER_FILTER - Static variable in class ome.model.annotations.BooleanAnnotation
 
OWNER_FILTER - Static variable in class ome.model.annotations.ChannelAnnotationLink
 
OWNER_FILTER - Static variable in class ome.model.annotations.CommentAnnotation
 
OWNER_FILTER - Static variable in class ome.model.annotations.DatasetAnnotationLink
 
OWNER_FILTER - Static variable in class ome.model.annotations.DetectorAnnotationLink
 
OWNER_FILTER - Static variable in class ome.model.annotations.DichroicAnnotationLink
 
OWNER_FILTER - Static variable in class ome.model.annotations.DoubleAnnotation
 
OWNER_FILTER - Static variable in class ome.model.annotations.ExperimenterAnnotationLink
 
OWNER_FILTER - Static variable in class ome.model.annotations.ExperimenterGroupAnnotationLink
 
OWNER_FILTER - Static variable in class ome.model.annotations.FileAnnotation
 
OWNER_FILTER - Static variable in class ome.model.annotations.FilesetAnnotationLink
 
OWNER_FILTER - Static variable in class ome.model.annotations.FilterAnnotationLink
 
OWNER_FILTER - Static variable in class ome.model.annotations.ImageAnnotationLink
 
OWNER_FILTER - Static variable in class ome.model.annotations.InstrumentAnnotationLink
 
OWNER_FILTER - Static variable in class ome.model.annotations.LightPathAnnotationLink
 
OWNER_FILTER - Static variable in class ome.model.annotations.LightSourceAnnotationLink
 
OWNER_FILTER - Static variable in class ome.model.annotations.ListAnnotation
 
OWNER_FILTER - Static variable in class ome.model.annotations.LongAnnotation
 
OWNER_FILTER - Static variable in class ome.model.annotations.MapAnnotation
 
OWNER_FILTER - Static variable in class ome.model.annotations.NamespaceAnnotationLink
 
OWNER_FILTER - Static variable in class ome.model.annotations.NodeAnnotationLink
 
OWNER_FILTER - Static variable in class ome.model.annotations.NumericAnnotation
 
OWNER_FILTER - Static variable in class ome.model.annotations.ObjectiveAnnotationLink
 
OWNER_FILTER - Static variable in class ome.model.annotations.OriginalFileAnnotationLink
 
OWNER_FILTER - Static variable in class ome.model.annotations.PlaneInfoAnnotationLink
 
OWNER_FILTER - Static variable in class ome.model.annotations.PlateAcquisitionAnnotationLink
 
OWNER_FILTER - Static variable in class ome.model.annotations.PlateAnnotationLink
 
OWNER_FILTER - Static variable in class ome.model.annotations.ProjectAnnotationLink
 
OWNER_FILTER - Static variable in class ome.model.annotations.ReagentAnnotationLink
 
OWNER_FILTER - Static variable in class ome.model.annotations.RoiAnnotationLink
 
OWNER_FILTER - Static variable in class ome.model.annotations.ScreenAnnotationLink
 
OWNER_FILTER - Static variable in class ome.model.annotations.SessionAnnotationLink
 
OWNER_FILTER - Static variable in class ome.model.annotations.ShapeAnnotationLink
 
OWNER_FILTER - Static variable in class ome.model.annotations.TagAnnotation
 
OWNER_FILTER - Static variable in class ome.model.annotations.TermAnnotation
 
OWNER_FILTER - Static variable in class ome.model.annotations.TextAnnotation
 
OWNER_FILTER - Static variable in class ome.model.annotations.TimestampAnnotation
 
OWNER_FILTER - Static variable in class ome.model.annotations.TypeAnnotation
 
OWNER_FILTER - Static variable in class ome.model.annotations.WellAnnotationLink
 
OWNER_FILTER - Static variable in class ome.model.annotations.XmlAnnotation
 
OWNER_FILTER - Static variable in class ome.model.containers.Dataset
 
OWNER_FILTER - Static variable in class ome.model.containers.DatasetImageLink
 
OWNER_FILTER - Static variable in class ome.model.containers.Project
 
OWNER_FILTER - Static variable in class ome.model.containers.ProjectDatasetLink
 
OWNER_FILTER - Static variable in class ome.model.core.Channel
 
OWNER_FILTER - Static variable in class ome.model.core.Image
 
OWNER_FILTER - Static variable in class ome.model.core.LogicalChannel
 
OWNER_FILTER - Static variable in class ome.model.core.OriginalFile
 
OWNER_FILTER - Static variable in class ome.model.core.Pixels
 
OWNER_FILTER - Static variable in class ome.model.core.PixelsOriginalFileMap
 
OWNER_FILTER - Static variable in class ome.model.core.PlaneInfo
 
OWNER_FILTER - Static variable in class ome.model.display.ChannelBinding
 
OWNER_FILTER - Static variable in class ome.model.display.CodomainMapContext
 
OWNER_FILTER - Static variable in class ome.model.display.ContrastStretchingContext
 
OWNER_FILTER - Static variable in class ome.model.display.PlaneSlicingContext
 
OWNER_FILTER - Static variable in class ome.model.display.QuantumDef
 
OWNER_FILTER - Static variable in class ome.model.display.RenderingDef
 
OWNER_FILTER - Static variable in class ome.model.display.ReverseIntensityContext
 
OWNER_FILTER - Static variable in class ome.model.display.Thumbnail
 
OWNER_FILTER - Static variable in class ome.model.experiment.Experiment
 
OWNER_FILTER - Static variable in class ome.model.experiment.MicrobeamManipulation
 
OWNER_FILTER - Static variable in class ome.model.fs.Fileset
 
OWNER_FILTER - Static variable in class ome.model.fs.FilesetEntry
 
OWNER_FILTER - Static variable in class ome.model.fs.FilesetJobLink
 
OWNER_FILTER - Static variable in class ome.model.internal.Link
 
OWNER_FILTER - Static variable in class ome.model.jobs.ImportJob
 
OWNER_FILTER - Static variable in class ome.model.jobs.IndexingJob
 
OWNER_FILTER - Static variable in class ome.model.jobs.IntegrityCheckJob
 
OWNER_FILTER - Static variable in class ome.model.jobs.Job
 
OWNER_FILTER - Static variable in class ome.model.jobs.JobOriginalFileLink
 
OWNER_FILTER - Static variable in class ome.model.jobs.MetadataImportJob
 
OWNER_FILTER - Static variable in class ome.model.jobs.ParseJob
 
OWNER_FILTER - Static variable in class ome.model.jobs.PixelDataJob
 
OWNER_FILTER - Static variable in class ome.model.jobs.ScriptJob
 
OWNER_FILTER - Static variable in class ome.model.jobs.ThumbnailGenerationJob
 
OWNER_FILTER - Static variable in class ome.model.jobs.UploadJob
 
OWNER_FILTER - Static variable in class ome.model.meta.ExternalInfo
 
OWNER_FILTER - Static variable in class ome.model.roi.Ellipse
 
OWNER_FILTER - Static variable in class ome.model.roi.Label
 
OWNER_FILTER - Static variable in class ome.model.roi.Line
 
OWNER_FILTER - Static variable in class ome.model.roi.Mask
 
OWNER_FILTER - Static variable in class ome.model.roi.Path
 
OWNER_FILTER - Static variable in class ome.model.roi.Point
 
OWNER_FILTER - Static variable in class ome.model.roi.Polygon
 
OWNER_FILTER - Static variable in class ome.model.roi.Polyline
 
OWNER_FILTER - Static variable in class ome.model.roi.Rect
 
OWNER_FILTER - Static variable in class ome.model.roi.Roi
 
OWNER_FILTER - Static variable in class ome.model.roi.Shape
 
OWNER_FILTER - Static variable in class ome.model.screen.Plate
 
OWNER_FILTER - Static variable in class ome.model.screen.PlateAcquisition
 
OWNER_FILTER - Static variable in class ome.model.screen.Reagent
 
OWNER_FILTER - Static variable in class ome.model.screen.Screen
 
OWNER_FILTER - Static variable in class ome.model.screen.ScreenPlateLink
 
OWNER_FILTER - Static variable in class ome.model.screen.Well
 
OWNER_FILTER - Static variable in class ome.model.screen.WellReagentLink
 
OWNER_FILTER - Static variable in class ome.model.screen.WellSample
 
OWNER_FILTER - Static variable in class ome.model.stats.StatsInfo
 
OWNER_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.acquisition.Detector
 
OWNER_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.acquisition.Dichroic
 
OWNER_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.acquisition.Filter
 
OWNER_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.acquisition.Instrument
 
OWNER_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.acquisition.LightPath
 
OWNER_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.acquisition.LightSource
 
OWNER_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.acquisition.Objective
 
OWNER_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.annotations.Annotation
 
OWNER_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.containers.Dataset
 
OWNER_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.containers.Project
 
OWNER_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.core.Channel
 
OWNER_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.core.Image
 
OWNER_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.core.OriginalFile
 
OWNER_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.core.PlaneInfo
 
OWNER_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.fs.Fileset
 
OWNER_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.meta.Experimenter
 
OWNER_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.meta.ExperimenterGroup
 
OWNER_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.meta.Namespace
 
OWNER_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.meta.Node
 
OWNER_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.meta.Session
 
OWNER_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.roi.Roi
 
OWNER_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.roi.Shape
 
OWNER_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.screen.Plate
 
OWNER_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.screen.PlateAcquisition
 
OWNER_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.screen.Reagent
 
OWNER_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.screen.Screen
 
OWNER_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.screen.Well
 
OWNER_FILTER_CHANNELS - Static variable in class ome.model.core.LogicalChannel
 
OWNER_FILTER_CHANNELS - Static variable in class ome.model.core.Pixels
 
OWNER_FILTER_DATASETLINKS - Static variable in class ome.model.containers.Project
 
OWNER_FILTER_DATASETLINKS - Static variable in class ome.model.core.Image
 
OWNER_FILTER_DETECTOR - Static variable in class ome.model.acquisition.Instrument
 
OWNER_FILTER_DICHROIC - Static variable in class ome.model.acquisition.Instrument
 
OWNER_FILTER_EMISSIONFILTERLINK - Static variable in class ome.model.acquisition.Filter
 
OWNER_FILTER_EMISSIONFILTERLINK - Static variable in class ome.model.acquisition.FilterSet
 
OWNER_FILTER_EMISSIONFILTERLINK - Static variable in class ome.model.acquisition.LightPath
 
OWNER_FILTER_EXCITATIONFILTERLINK - Static variable in class ome.model.acquisition.Filter
 
OWNER_FILTER_EXCITATIONFILTERLINK - Static variable in class ome.model.acquisition.FilterSet
 
OWNER_FILTER_EXCITATIONFILTERLINK - Static variable in class ome.model.acquisition.LightPath
 
OWNER_FILTER_FILESETENTRIES - Static variable in class ome.model.core.OriginalFile
 
OWNER_FILTER_FILTER - Static variable in class ome.model.acquisition.Instrument
 
OWNER_FILTER_FILTERSET - Static variable in class ome.model.acquisition.Instrument
 
OWNER_FILTER_IMAGELINKS - Static variable in class ome.model.containers.Dataset
 
OWNER_FILTER_IMAGES - Static variable in class ome.model.fs.Fileset
 
OWNER_FILTER_JOBLINKS - Static variable in class ome.model.fs.Fileset
 
OWNER_FILTER_LIGHTSOURCE - Static variable in class ome.model.acquisition.Instrument
 
OWNER_FILTER_LIGHTSOURCESETTINGS - Static variable in class ome.model.experiment.MicrobeamManipulation
 
OWNER_FILTER_MICROBEAMMANIPULATION - Static variable in class ome.model.experiment.Experiment
 
OWNER_FILTER_OBJECTIVE - Static variable in class ome.model.acquisition.Instrument
 
OWNER_FILTER_ORIGINALFILELINKS - Static variable in class ome.model.jobs.Job
 
OWNER_FILTER_OTF - Static variable in class ome.model.acquisition.Instrument
 
OWNER_FILTER_PIXELS - Static variable in class ome.model.core.Image
 
OWNER_FILTER_PIXELSFILEMAPS - Static variable in class ome.model.core.OriginalFile
 
OWNER_FILTER_PIXELSFILEMAPS - Static variable in class ome.model.core.Pixels
 
OWNER_FILTER_PLANEINFO - Static variable in class ome.model.core.Pixels
 
OWNER_FILTER_PLATEACQUISITIONS - Static variable in class ome.model.screen.Plate
 
OWNER_FILTER_PLATELINKS - Static variable in class ome.model.screen.Screen
 
OWNER_FILTER_PROJECTLINKS - Static variable in class ome.model.containers.Dataset
 
OWNER_FILTER_REAGENTLINKS - Static variable in class ome.model.screen.Well
 
OWNER_FILTER_REAGENTS - Static variable in class ome.model.screen.Screen
 
OWNER_FILTER_ROIS - Static variable in class ome.model.core.Image
 
OWNER_FILTER_SCREENLINKS - Static variable in class ome.model.screen.Plate
 
OWNER_FILTER_SETTINGS - Static variable in class ome.model.core.Pixels
 
OWNER_FILTER_SHAPES - Static variable in class ome.model.roi.Roi
 
OWNER_FILTER_SPATIALDOMAINENHANCEMENT - Static variable in class ome.model.display.RenderingDef
 
OWNER_FILTER_THUMBNAILS - Static variable in class ome.model.core.Pixels
 
OWNER_FILTER_USEDFILES - Static variable in class ome.model.fs.Fileset
 
OWNER_FILTER_WAVERENDERING - Static variable in class ome.model.display.RenderingDef
 
OWNER_FILTER_WELLLINKS - Static variable in class ome.model.screen.Reagent
 
OWNER_FILTER_WELLS - Static variable in class ome.model.screen.Plate
 
OWNER_FILTER_WELLSAMPLE - Static variable in class ome.model.screen.PlateAcquisition
 
OWNER_FILTER_WELLSAMPLES - Static variable in class ome.model.core.Image
 
OWNER_FILTER_WELLSAMPLES - Static variable in class ome.model.screen.Well
 
OWNER_ID - Static variable in class ome.parameters.Parameters
named parameter "ownerId".
ownerId - Variable in class ome.services.graphs.GraphPolicy.Details
the ID of the object's Experimenter, or null if the object does not have an owner
ownerId - Variable in class ome.util.SqlAction.DeleteLog
 
ownerOfGroups(String, LdapConfig, LdapOperations, RoleProvider, AttributeSet) - Method in interface ome.security.auth.NewUserGroupOwnerBean
 
ownerOfGroups(String, LdapConfig, LdapOperations, RoleProvider, AttributeSet) - Method in class ome.security.auth.QueryNewUserGroupBean
 
ownerOrGroup(Class, Criteria) - Method in class ome.services.search.SearchAction
 
ownerOrGroup(Class, QueryBuilder, String) - Method in class ome.services.search.SearchAction
 
ownerOrGroupFilters(Session, String[], String[]) - Method in class ome.services.query.Query
standard filter used by many subclasses which uses the PojoOptions#isExperimenter() and PojoOptions#isGroup() booleans to see if a filter should be turned on.
ownParts() - Method in class ome.services.graphs.GraphEntry
Deprecated.
Returns the size of GraphEntry.parts and GraphEntry.path combined.

P

page(Integer, Integer) - Method in class ome.parameters.Filter
 
page(Integer, Integer) - Method in class ome.parameters.Parameters
 
page(int, int) - Method in class omero.sys.ParametersI
Sets both the Filter.limit and Filter.offset values by wrapping the arguments in RInt and passing the values to ParametersI.page(RInt, RInt)
page(RInt, RInt) - Method in class omero.sys.ParametersI
Creates a Filter if necessary and sets both Filter.limit and Filter.offset.
paginate(Integer, Integer) - Method in class ome.parameters.Parameters
 
param(int, Object) - Method in class ome.tools.hibernate.QueryBuilder
 
param(String, Object) - Method in class ome.tools.hibernate.QueryBuilder
 
Parameters - Class in ome.parameters
container object for QueryParameter and Filter instances.
Parameters() - Constructor for class ome.parameters.Parameters
default constructor.
Parameters(Filter) - Constructor for class ome.parameters.Parameters
Filter constructor.
Parameters(Parameters) - Constructor for class ome.parameters.Parameters
copy constructor.
Parameters(QueryParameter[]) - Constructor for class ome.parameters.Parameters
copy constructor.
ParametersI - Class in omero.sys
Helper subclass of Parameters for simplifying method parameter creation.
ParametersI() - Constructor for class omero.sys.ParametersI
Default constructor creates the ParametersI.map() instance to prevent later NullPointerExceptions.
ParametersI(Map<String, RType>) - Constructor for class omero.sys.ParametersI
Uses (and does not copy) the given Map as the named parameter store in this instance.
paramList(String, Collection) - Method in class ome.tools.hibernate.QueryBuilder
 
params - Variable in class ome.model.jobs.ParseJob
 
PARAMS - Static variable in class ome.model.jobs.ParseJob
 
params - Variable in class ome.services.query.Query
container of QueryParameter instances.
params(Parameters) - Method in class ome.tools.hibernate.QueryBuilder
 
params() - Method in class omero.cmd.graphs.ChmodI
Deprecated.
 
params(String...) - Method in class omero.cmd.Helper
Converts pairs of values from the varargs list into a map.
params(Current) - Method in class omero.grid.InteractiveProcessorI
 
ParamsCache - Class in ome.services.blitz.util
Caching replacement of ParamsHelper which maintains an OriginalFile ID+SHA1-to-JobParams mapping in memory rather than storing ParseJob instances in the database.
ParamsCache(Registry, Roles, ScriptRepoHelper, String) - Constructor for class ome.services.blitz.util.ParamsCache
 
ParamsHelper - Class in omero.grid
 
ParamsHelper(ParamsHelper.Acquirer, Executor, Principal) - Constructor for class omero.grid.ParamsHelper
 
ParamsHelper.Acquirer - Interface in omero.grid
Interface added in order to allow ParamHelper instances to use methods from SharedResourcesI.
parent - Variable in class ome.model.acquisition.FilterSetEmissionFilterLink
 
PARENT - Static variable in class ome.model.acquisition.FilterSetEmissionFilterLink
 
parent() - Method in class ome.model.acquisition.FilterSetEmissionFilterLink
 
parent - Variable in class ome.model.acquisition.FilterSetExcitationFilterLink
 
PARENT - Static variable in class ome.model.acquisition.FilterSetExcitationFilterLink
 
parent() - Method in class ome.model.acquisition.FilterSetExcitationFilterLink
 
parent - Variable in class ome.model.acquisition.LightPathEmissionFilterLink
 
PARENT - Static variable in class ome.model.acquisition.LightPathEmissionFilterLink
 
parent() - Method in class ome.model.acquisition.LightPathEmissionFilterLink
 
parent - Variable in class ome.model.acquisition.LightPathExcitationFilterLink
 
PARENT - Static variable in class ome.model.acquisition.LightPathExcitationFilterLink
 
parent() - Method in class ome.model.acquisition.LightPathExcitationFilterLink
 
parent - Variable in class ome.model.annotations.AnnotationAnnotationLink
 
PARENT - Static variable in class ome.model.annotations.AnnotationAnnotationLink
 
parent() - Method in class ome.model.annotations.AnnotationAnnotationLink
 
parent - Variable in class ome.model.annotations.ChannelAnnotationLink
 
PARENT - Static variable in class ome.model.annotations.ChannelAnnotationLink
 
parent() - Method in class ome.model.annotations.ChannelAnnotationLink
 
parent - Variable in class ome.model.annotations.DatasetAnnotationLink
 
PARENT - Static variable in class ome.model.annotations.DatasetAnnotationLink
 
parent() - Method in class ome.model.annotations.DatasetAnnotationLink
 
parent - Variable in class ome.model.annotations.DetectorAnnotationLink
 
PARENT - Static variable in class ome.model.annotations.DetectorAnnotationLink
 
parent() - Method in class ome.model.annotations.DetectorAnnotationLink
 
parent - Variable in class ome.model.annotations.DichroicAnnotationLink
 
PARENT - Static variable in class ome.model.annotations.DichroicAnnotationLink
 
parent() - Method in class ome.model.annotations.DichroicAnnotationLink
 
parent - Variable in class ome.model.annotations.ExperimenterAnnotationLink
 
PARENT - Static variable in class ome.model.annotations.ExperimenterAnnotationLink
 
parent() - Method in class ome.model.annotations.ExperimenterAnnotationLink
 
parent - Variable in class ome.model.annotations.ExperimenterGroupAnnotationLink
 
PARENT - Static variable in class ome.model.annotations.ExperimenterGroupAnnotationLink
 
parent() - Method in class ome.model.annotations.ExperimenterGroupAnnotationLink
 
parent - Variable in class ome.model.annotations.FilesetAnnotationLink
 
PARENT - Static variable in class ome.model.annotations.FilesetAnnotationLink
 
parent() - Method in class ome.model.annotations.FilesetAnnotationLink
 
parent - Variable in class ome.model.annotations.FilterAnnotationLink
 
PARENT - Static variable in class ome.model.annotations.FilterAnnotationLink
 
parent() - Method in class ome.model.annotations.FilterAnnotationLink
 
parent - Variable in class ome.model.annotations.ImageAnnotationLink
 
PARENT - Static variable in class ome.model.annotations.ImageAnnotationLink
 
parent() - Method in class ome.model.annotations.ImageAnnotationLink
 
parent - Variable in class ome.model.annotations.InstrumentAnnotationLink
 
PARENT - Static variable in class ome.model.annotations.InstrumentAnnotationLink
 
parent() - Method in class ome.model.annotations.InstrumentAnnotationLink
 
parent - Variable in class ome.model.annotations.LightPathAnnotationLink
 
PARENT - Static variable in class ome.model.annotations.LightPathAnnotationLink
 
parent() - Method in class ome.model.annotations.LightPathAnnotationLink
 
parent - Variable in class ome.model.annotations.LightSourceAnnotationLink
 
PARENT - Static variable in class ome.model.annotations.LightSourceAnnotationLink
 
parent() - Method in class ome.model.annotations.LightSourceAnnotationLink
 
parent - Variable in class ome.model.annotations.NamespaceAnnotationLink
 
PARENT - Static variable in class ome.model.annotations.NamespaceAnnotationLink
 
parent() - Method in class ome.model.annotations.NamespaceAnnotationLink
 
parent - Variable in class ome.model.annotations.NodeAnnotationLink
 
PARENT - Static variable in class ome.model.annotations.NodeAnnotationLink
 
parent() - Method in class ome.model.annotations.NodeAnnotationLink
 
parent - Variable in class ome.model.annotations.ObjectiveAnnotationLink
 
PARENT - Static variable in class ome.model.annotations.ObjectiveAnnotationLink
 
parent() - Method in class ome.model.annotations.ObjectiveAnnotationLink
 
parent - Variable in class ome.model.annotations.OriginalFileAnnotationLink
 
PARENT - Static variable in class ome.model.annotations.OriginalFileAnnotationLink
 
parent() - Method in class ome.model.annotations.OriginalFileAnnotationLink
 
parent - Variable in class ome.model.annotations.PlaneInfoAnnotationLink
 
PARENT - Static variable in class ome.model.annotations.PlaneInfoAnnotationLink
 
parent() - Method in class ome.model.annotations.PlaneInfoAnnotationLink
 
parent - Variable in class ome.model.annotations.PlateAcquisitionAnnotationLink
 
PARENT - Static variable in class ome.model.annotations.PlateAcquisitionAnnotationLink
 
parent() - Method in class ome.model.annotations.PlateAcquisitionAnnotationLink
 
parent - Variable in class ome.model.annotations.PlateAnnotationLink
 
PARENT - Static variable in class ome.model.annotations.PlateAnnotationLink
 
parent() - Method in class ome.model.annotations.PlateAnnotationLink
 
parent - Variable in class ome.model.annotations.ProjectAnnotationLink
 
PARENT - Static variable in class ome.model.annotations.ProjectAnnotationLink
 
parent() - Method in class ome.model.annotations.ProjectAnnotationLink
 
parent - Variable in class ome.model.annotations.ReagentAnnotationLink
 
PARENT - Static variable in class ome.model.annotations.ReagentAnnotationLink
 
parent() - Method in class ome.model.annotations.ReagentAnnotationLink
 
parent - Variable in class ome.model.annotations.RoiAnnotationLink
 
PARENT - Static variable in class ome.model.annotations.RoiAnnotationLink
 
parent() - Method in class ome.model.annotations.RoiAnnotationLink
 
parent - Variable in class ome.model.annotations.ScreenAnnotationLink
 
PARENT - Static variable in class ome.model.annotations.ScreenAnnotationLink
 
parent() - Method in class ome.model.annotations.ScreenAnnotationLink
 
parent - Variable in class ome.model.annotations.SessionAnnotationLink
 
PARENT - Static variable in class ome.model.annotations.SessionAnnotationLink
 
parent() - Method in class ome.model.annotations.SessionAnnotationLink
 
parent - Variable in class ome.model.annotations.ShapeAnnotationLink
 
PARENT - Static variable in class ome.model.annotations.ShapeAnnotationLink
 
parent() - Method in class ome.model.annotations.ShapeAnnotationLink
 
parent - Variable in class ome.model.annotations.WellAnnotationLink
 
PARENT - Static variable in class ome.model.annotations.WellAnnotationLink
 
parent() - Method in class ome.model.annotations.WellAnnotationLink
 
parent - Variable in class ome.model.containers.DatasetImageLink
 
PARENT - Static variable in class ome.model.containers.DatasetImageLink
 
parent() - Method in class ome.model.containers.DatasetImageLink
 
parent - Variable in class ome.model.containers.ProjectDatasetLink
 
PARENT - Static variable in class ome.model.containers.ProjectDatasetLink
 
parent() - Method in class ome.model.containers.ProjectDatasetLink
 
parent - Variable in class ome.model.core.PixelsOriginalFileMap
 
PARENT - Static variable in class ome.model.core.PixelsOriginalFileMap
 
parent() - Method in class ome.model.core.PixelsOriginalFileMap
 
parent - Variable in class ome.model.fs.FilesetJobLink
 
PARENT - Static variable in class ome.model.fs.FilesetJobLink
 
parent() - Method in class ome.model.fs.FilesetJobLink
 
parent - Variable in class ome.model.jobs.JobOriginalFileLink
 
PARENT - Static variable in class ome.model.jobs.JobOriginalFileLink
 
parent() - Method in class ome.model.jobs.JobOriginalFileLink
 
parent - Variable in class ome.model.meta.GroupExperimenterMap
 
PARENT - Static variable in class ome.model.meta.GroupExperimenterMap
 
parent() - Method in class ome.model.meta.GroupExperimenterMap
 
parent - Variable in class ome.model.meta.ShareMember
 
PARENT - Static variable in class ome.model.meta.ShareMember
 
parent() - Method in class ome.model.meta.ShareMember
 
parent - Variable in class ome.model.screen.ScreenPlateLink
 
PARENT - Static variable in class ome.model.screen.ScreenPlateLink
 
parent() - Method in class ome.model.screen.ScreenPlateLink
 
parent - Variable in class ome.model.screen.WellReagentLink
 
PARENT - Static variable in class ome.model.screen.WellReagentLink
 
parent() - Method in class ome.model.screen.WellReagentLink
 
parent() - Method in class ome.services.blitz.repo.CheckedPath
Returns a new CheckedPath using File.getParent() and passing in all other values.
parent - Variable in class ome.services.graphs.GraphStep
Deprecated.
Final member of GraphStep.stack which is the direct ancestor of this step.
parse(String[]) - Static method in class ome.logic.HardWiredInterceptor
Produces a List of instantiated interceptors from a list of HardWiredInterceptor subclass names.
parse(String) - Method in class ome.security.auth.LdapConfig
 
parse(OriginalFile, OriginalFilesService, Map<String, FileParser>) - Method in class ome.services.fulltext.BridgeHelper
Attempts to parse the given OriginalFile.
parse(File) - Method in class ome.services.fulltext.FileParser
Uses FileParser.doParse(File) to create manageable chunks of a file for indexing.
parse(String[], String[], String[]) - Static method in class ome.services.search.SomeMustNone
 
parse(ShareData) - Method in class ome.services.sharing.ShareStore
 
parse(long, byte[]) - Method in class ome.services.sharing.ShareStore
 
parseAndSetInt(InitializationData, String, int) - Method in class omero.client
 
parseAwtPath(String) - Static method in class omero.model.SmartShape.Util
 
parseData(String, int, ImportSize) - Method in class ome.services.blitz.repo.ManagedImportRequestI
Parse the binary data to generate min/max values and allow an md to be calculated.
parseField(String) - Static method in class ome.tools.lsid.LsidUtils
takes a field identifier as code-generated in each IObject class and produces a back-end useable name.
parseFilter(Criteria, Filter) - Method in class ome.logic.QueryImpl
responsible for applying the information provided in a Filter to a org.hibernate.Critieria instance.
parseFlexMaps(Preferences) - Method in class ome.formats.importer.util.IniFileLoader
Parse Flex reader server maps
parseIndexes() - Method in class ome.util.LSID
Attempts to parse and return the indexes for the LSID parsed from the LSID's string representation.
parseJavaClass() - Method in class ome.util.LSID
Attempts to parse and return the concrete Java class for the LSID from the LSID's string representation.
ParseJob - Class in ome.model.jobs
 
ParseJob() - Constructor for class ome.model.jobs.ParseJob
 
ParseJob(Long) - Constructor for class ome.model.jobs.ParseJob
 
ParseJob(Long, boolean) - Constructor for class ome.model.jobs.ParseJob
Main constructor.
parseOriginalMetadataTxt(File) - Method in class omero.cmd.fs.OriginalMetadataRequestI
Read the given INI-style file and populate the maps with the properties from the corresponding sections.
parsePoints(String) - Static method in class loci.ome.io.OmeroReader
Parse Points String obtained from convertPoints and extract Coordinates as String
parsePoints(String) - Static method in class omero.model.SmartShape.Util
 
parsePointsToIntegerList(String) - Method in class pojos.ShapeData
Parses the points list from the string to a list of integer objects.
parsePointsToPath(String, boolean) - Static method in class omero.model.SmartShape.Util
 
parsePointsToPoint2DList(String) - Method in class pojos.ShapeData
Parses the points list from the string to a list of point2d objects.
parseResults(String[], GraphEntry, List<List<Long>>) - Method in class ome.services.graphs.BaseGraphSpec
Deprecated.
 
ParserOpenFileMessage - Class in ome.services.messages
A trivial copy of RegisterServiceCleanupMessage with a different name so that we can catch files opened during search indexing and close them at the end of parsing.
ParserOpenFileMessage(Object, Object) - Constructor for class ome.services.messages.ParserOpenFileMessage
 
parsers - Variable in class ome.services.fulltext.FullTextBridge
 
parserSession - Variable in class ome.services.fulltext.FullTextIndexer
 
ParserSession - Class in ome.services.fulltext
Provides a session for file parsing by the search indexer
ParserSession() - Constructor for class ome.services.fulltext.ParserSession
 
parseRules(GraphPathBean, Collection<GraphPolicyRule>) - Static method in class ome.services.graphs.GraphPolicyRule
Convert the text-based rules as specified in the configuration metadata into a policy applicable in model object graph traversal.
parseStream(InputStream) - Method in class ome.services.mail.MapAnnotationSubethaListener
 
parseString(String) - Static method in class ome.model.internal.Permissions
 
parseType(String) - Static method in class ome.tools.lsid.LsidUtils
takes a field identifier as code-generated in each IObject class and produces a back-end useable type name.
partial - Variable in class ome.model.core.Image
 
PARTIAL - Static variable in class ome.model.core.Image
 
passesFilter(Session, Details, EventContext) - Method in class ome.security.basic.AllGroupsSecurityFilter
tests that the Details argument passes the security test that this filter defines.
passesFilter(Session, Details, EventContext) - Method in class ome.security.basic.OneGroupSecurityFilter
tests that the Details argument passes the security test that this filter defines.
passesFilter(Session, Details, EventContext) - Method in interface ome.security.SecurityFilter
tests that the Details argument passes the security test that this filter defines.
passesFilter(Session, Details, EventContext) - Method in class ome.security.SecurityFilterHolder
 
passivate() - Method in interface ome.api.StatefulServiceInterface
Perform whatever passivation is possible or throw an exception.
passivate() - Method in class ome.services.JobBean
Does nothing.
passivate() - Method in class ome.services.RawFileBean
 
passivate() - Method in class ome.services.RawPixelsBean
 
passivate() - Method in class ome.services.RenderingBean
 
passivate() - Method in class ome.services.SearchBean
 
passivate() - Method in class ome.services.ThumbnailBean
 
passivate_async(AMD_StatefulServiceInterface_passivate, Current) - Method in class ome.services.blitz.impl.AbstractAmdServant
 
passivate_async(AMD_StatefulServiceInterface_passivate, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
passivationNotAllowed() - Method in class ome.services.util.BeanHelper
 
password - Variable in class loci.ome.io.OMECredentials
 
password - Variable in class ome.formats.importer.ImportConfig
 
PasswordChangeException - Exception in ome.security.auth
Caught exception thrown from PasswordProvider.changePassword(String, String) to allow read-only implementations to refuse an action.
PasswordChangeException(String) - Constructor for exception ome.security.auth.PasswordChangeException
 
passwordDigest(String) - Method in class ome.security.auth.PasswordUtil
Creates an MD5 hash of the given clear text and base64 encodes it.
passwordDigest(Long, String, boolean) - Method in class ome.security.auth.PasswordUtil
 
passwordProvider - Variable in class ome.logic.AdminImpl
 
PasswordProvider - Interface in ome.security.auth
Authentication interface responsible for checking and changing passwords.
PasswordProviders - Class in ome.security.auth
Composite class which delegates to each of the configured providers in turn.
PasswordProviders(PasswordProvider...) - Constructor for class ome.security.auth.PasswordProviders
 
PasswordProviders(AtomicBoolean, PasswordProvider...) - Constructor for class ome.security.auth.PasswordProviders
 
passwordUtil - Variable in class ome.logic.AdminImpl
 
PasswordUtil - Class in ome.security.auth
Static methods for dealing with password hashes and the "password" table.
PasswordUtil(SqlAction) - Constructor for class ome.security.auth.PasswordUtil
 
PasswordUtil(SqlAction, boolean) - Constructor for class ome.security.auth.PasswordUtil
 
PasswordUtil(SqlAction, Charset) - Constructor for class ome.security.auth.PasswordUtil
 
PasswordUtil(SqlAction, boolean, Charset) - Constructor for class ome.security.auth.PasswordUtil
 
PasswordUtil(SqlAction, Roles, boolean) - Constructor for class ome.security.auth.PasswordUtil
 
PasswordUtil(SqlAction, Roles, boolean, Charset) - Constructor for class ome.security.auth.PasswordUtil
 
PasswordUtil.METHOD - Enum in ome.security.auth
 
PasswordUtility - Interface in ome.security.auth
Extension interface to PasswordProvider for methods which may or may not be available from a provider implementation.
path - Variable in class ome.model.acquisition.OTF
 
PATH - Static variable in class ome.model.acquisition.OTF
 
path - Variable in class ome.model.core.OriginalFile
 
PATH - Static variable in class ome.model.core.OriginalFile
 
Path - Class in ome.model.roi
 
Path() - Constructor for class ome.model.roi.Path
 
Path(Long) - Constructor for class ome.model.roi.Path
 
Path(Long, boolean) - Constructor for class ome.model.roi.Path
Main constructor.
path(String) - Method in class ome.services.graphs.GraphEntry
Deprecated.
 
path - Variable in class ome.services.scripts.RepoFile.FsFile
 
path - Variable in class ome.util.SqlAction.DeleteLog
 
pathMsg - Variable in class ome.services.graphs.GraphStep
Deprecated.
String representation of the path to this GraphEntry used for logging.
PDF - Static variable in class pojos.FileAnnotationData
Identifies the PDF file formats.
PdfParser - Class in ome.services.fulltext
FileParser for "application/pdf" files using PDFBox.
PdfParser() - Constructor for class ome.services.fulltext.PdfParser
 
perform(int, boolean) - Method in class ome.services.graphs.GraphState
Deprecated.
 
Period - Class in ome.parameters
parameter which defines the ordering as well as the start and offset for a List-valued result set.
Period(int, int) - Constructor for class ome.parameters.Period
 
PermissionData - Class in pojos
Simple data object to wrap a Permissions instance.
PermissionData() - Constructor for class pojos.PermissionData
Creates a new instance.
PermissionData(Permissions) - Constructor for class pojos.PermissionData
Creates a new instance.
PermissionMismatchGroupSecurityViolation - Exception in ome.conditions
Extension of GroupSecurityViolation signalling that an object has a permission which does not match the group permissions.
PermissionMismatchGroupSecurityViolation(String) - Constructor for exception ome.conditions.PermissionMismatchGroupSecurityViolation
 
permissions(Class<T>) - Method in class ome.logic.TypesImpl
 
PERMISSIONS - Static variable in class ome.model.internal.Details
 
Permissions - Class in ome.model.internal
class responsible for storing all Right/Role-based information for entities as well as various flags for the containing Details instance.
Permissions() - Constructor for class ome.model.internal.Permissions
simple contructor.
Permissions(Permissions) - Constructor for class ome.model.internal.Permissions
copy constructor.
permissions - Variable in class ome.services.graphs.GraphPolicy.Details
the current permissions on the object
Permissions.Flag - Enum in ome.model.internal
Currently unused.
Permissions.Right - Enum in ome.model.internal
enumeration of granted rights.
Permissions.Role - Enum in ome.model.internal
enumeration of currently active roles.
PERMISSIONS_GROUP_READ - Static variable in class pojos.GroupData
Indicates that the group is Group i.e.
PERMISSIONS_GROUP_READ_LINK - Static variable in class pojos.GroupData
Indicates that the group is Group i.e.
PERMISSIONS_GROUP_READ_LINK_SHORT_TEXT - Static variable in class pojos.GroupData
Indicates that the group is Group i.e.
PERMISSIONS_GROUP_READ_LINK_TEXT - Static variable in class pojos.GroupData
Indicates that the group is Group i.e.
PERMISSIONS_GROUP_READ_SHORT_TEXT - Static variable in class pojos.GroupData
Indicates that the group is Group i.e.
PERMISSIONS_GROUP_READ_TEXT - Static variable in class pojos.GroupData
Indicates that the group is Group i.e.
PERMISSIONS_GROUP_READ_WRITE - Static variable in class pojos.GroupData
Indicates that the group is Group i.e.
PERMISSIONS_GROUP_READ_WRITE_SHORT_TEXT - Static variable in class pojos.GroupData
Indicates that the group is Group i.e.
PERMISSIONS_GROUP_READ_WRITE_TEXT - Static variable in class pojos.GroupData
Indicates that the group is Group i.e.
PERMISSIONS_PRIVATE - Static variable in class pojos.GroupData
Indicates that the group is Private i.e.
PERMISSIONS_PRIVATE_TEXT - Static variable in class pojos.GroupData
Indicates that the group is Private i.e.
PERMISSIONS_PUBLIC_READ - Static variable in class pojos.GroupData
Indicates that the group is Public i.e.
PERMISSIONS_PUBLIC_READ_TEXT - Static variable in class pojos.GroupData
Indicates that the group is Public i.e.
PERMISSIONS_PUBLIC_READ_WRITE - Static variable in class pojos.GroupData
Indicates that the group is Public i.e.
PERMISSIONS_PUBLIC_READ_WRITE_TEXT - Static variable in class pojos.GroupData
Indicates that the group is Public i.e.
permissionsClause(EventContext, QueryBuilder, boolean) - Method in class ome.services.graphs.BaseGraphSpec
Deprecated.
Appends a clause to the QueryBuilder based on the current user.
PermissionsI - Class in omero.model
Blitz wrapper around the Permissions class.
PermissionsI() - Constructor for class omero.model.PermissionsI
 
PermissionsI(String) - Constructor for class omero.model.PermissionsI
 
PermissionsI(PermissionsI) - Constructor for class omero.model.PermissionsI
 
PermissionsI(Permissions) - Constructor for class omero.model.PermissionsI
 
PermissionsPredicate - Class in ome.services.graphs
A predicate that allows perms=rwr--- and similar to be used in graph policy rule matches.
PermissionsPredicate() - Constructor for class ome.services.graphs.PermissionsPredicate
 
PermissionsVerifierI - Class in ome.services.blitz.fire
 
PermissionsVerifierI(Ring, SessionManager, Executor, String) - Constructor for class ome.services.blitz.fire.PermissionsVerifierI
 
PermitAll - Annotation Type in ome.annotations
Security annotation which allows a method to be called by all users regardless of their status.
PERMS_FILTER - Static variable in class ome.model.acquisition.Arc
 
PERMS_FILTER - Static variable in class ome.model.acquisition.Detector
 
PERMS_FILTER - Static variable in class ome.model.acquisition.DetectorSettings
 
PERMS_FILTER - Static variable in class ome.model.acquisition.Dichroic
 
PERMS_FILTER - Static variable in class ome.model.acquisition.Filament
 
PERMS_FILTER - Static variable in class ome.model.acquisition.Filter
 
PERMS_FILTER - Static variable in class ome.model.acquisition.FilterSet
 
PERMS_FILTER - Static variable in class ome.model.acquisition.FilterSetEmissionFilterLink
 
PERMS_FILTER - Static variable in class ome.model.acquisition.FilterSetExcitationFilterLink
 
PERMS_FILTER - Static variable in class ome.model.acquisition.GenericExcitationSource
 
PERMS_FILTER - Static variable in class ome.model.acquisition.ImagingEnvironment
 
PERMS_FILTER - Static variable in class ome.model.acquisition.Instrument
 
PERMS_FILTER - Static variable in class ome.model.acquisition.Laser
 
PERMS_FILTER - Static variable in class ome.model.acquisition.LightEmittingDiode
 
PERMS_FILTER - Static variable in class ome.model.acquisition.LightPath
 
PERMS_FILTER - Static variable in class ome.model.acquisition.LightPathEmissionFilterLink
 
PERMS_FILTER - Static variable in class ome.model.acquisition.LightPathExcitationFilterLink
 
PERMS_FILTER - Static variable in class ome.model.acquisition.LightSettings
 
PERMS_FILTER - Static variable in class ome.model.acquisition.LightSource
 
PERMS_FILTER - Static variable in class ome.model.acquisition.Microscope
 
PERMS_FILTER - Static variable in class ome.model.acquisition.Objective
 
PERMS_FILTER - Static variable in class ome.model.acquisition.ObjectiveSettings
 
PERMS_FILTER - Static variable in class ome.model.acquisition.OTF
 
PERMS_FILTER - Static variable in class ome.model.acquisition.StageLabel
 
PERMS_FILTER - Static variable in class ome.model.acquisition.TransmittanceRange
 
PERMS_FILTER - Static variable in class ome.model.annotations.Annotation
 
PERMS_FILTER - Static variable in class ome.model.annotations.AnnotationAnnotationLink
 
PERMS_FILTER - Static variable in class ome.model.annotations.BasicAnnotation
 
PERMS_FILTER - Static variable in class ome.model.annotations.BooleanAnnotation
 
PERMS_FILTER - Static variable in class ome.model.annotations.ChannelAnnotationLink
 
PERMS_FILTER - Static variable in class ome.model.annotations.CommentAnnotation
 
PERMS_FILTER - Static variable in class ome.model.annotations.DatasetAnnotationLink
 
PERMS_FILTER - Static variable in class ome.model.annotations.DetectorAnnotationLink
 
PERMS_FILTER - Static variable in class ome.model.annotations.DichroicAnnotationLink
 
PERMS_FILTER - Static variable in class ome.model.annotations.DoubleAnnotation
 
PERMS_FILTER - Static variable in class ome.model.annotations.ExperimenterAnnotationLink
 
PERMS_FILTER - Static variable in class ome.model.annotations.ExperimenterGroupAnnotationLink
 
PERMS_FILTER - Static variable in class ome.model.annotations.FileAnnotation
 
PERMS_FILTER - Static variable in class ome.model.annotations.FilesetAnnotationLink
 
PERMS_FILTER - Static variable in class ome.model.annotations.FilterAnnotationLink
 
PERMS_FILTER - Static variable in class ome.model.annotations.ImageAnnotationLink
 
PERMS_FILTER - Static variable in class ome.model.annotations.InstrumentAnnotationLink
 
PERMS_FILTER - Static variable in class ome.model.annotations.LightPathAnnotationLink
 
PERMS_FILTER - Static variable in class ome.model.annotations.LightSourceAnnotationLink
 
PERMS_FILTER - Static variable in class ome.model.annotations.ListAnnotation
 
PERMS_FILTER - Static variable in class ome.model.annotations.LongAnnotation
 
PERMS_FILTER - Static variable in class ome.model.annotations.MapAnnotation
 
PERMS_FILTER - Static variable in class ome.model.annotations.NamespaceAnnotationLink
 
PERMS_FILTER - Static variable in class ome.model.annotations.NodeAnnotationLink
 
PERMS_FILTER - Static variable in class ome.model.annotations.NumericAnnotation
 
PERMS_FILTER - Static variable in class ome.model.annotations.ObjectiveAnnotationLink
 
PERMS_FILTER - Static variable in class ome.model.annotations.OriginalFileAnnotationLink
 
PERMS_FILTER - Static variable in class ome.model.annotations.PlaneInfoAnnotationLink
 
PERMS_FILTER - Static variable in class ome.model.annotations.PlateAcquisitionAnnotationLink
 
PERMS_FILTER - Static variable in class ome.model.annotations.PlateAnnotationLink
 
PERMS_FILTER - Static variable in class ome.model.annotations.ProjectAnnotationLink
 
PERMS_FILTER - Static variable in class ome.model.annotations.ReagentAnnotationLink
 
PERMS_FILTER - Static variable in class ome.model.annotations.RoiAnnotationLink
 
PERMS_FILTER - Static variable in class ome.model.annotations.ScreenAnnotationLink
 
PERMS_FILTER - Static variable in class ome.model.annotations.SessionAnnotationLink
 
PERMS_FILTER - Static variable in class ome.model.annotations.ShapeAnnotationLink
 
PERMS_FILTER - Static variable in class ome.model.annotations.TagAnnotation
 
PERMS_FILTER - Static variable in class ome.model.annotations.TermAnnotation
 
PERMS_FILTER - Static variable in class ome.model.annotations.TextAnnotation
 
PERMS_FILTER - Static variable in class ome.model.annotations.TimestampAnnotation
 
PERMS_FILTER - Static variable in class ome.model.annotations.TypeAnnotation
 
PERMS_FILTER - Static variable in class ome.model.annotations.WellAnnotationLink
 
PERMS_FILTER - Static variable in class ome.model.annotations.XmlAnnotation
 
PERMS_FILTER - Static variable in class ome.model.containers.Dataset
 
PERMS_FILTER - Static variable in class ome.model.containers.DatasetImageLink
 
PERMS_FILTER - Static variable in class ome.model.containers.Project
 
PERMS_FILTER - Static variable in class ome.model.containers.ProjectDatasetLink
 
PERMS_FILTER - Static variable in class ome.model.core.Channel
 
PERMS_FILTER - Static variable in class ome.model.core.Image
 
PERMS_FILTER - Static variable in class ome.model.core.LogicalChannel
 
PERMS_FILTER - Static variable in class ome.model.core.OriginalFile
 
PERMS_FILTER - Static variable in class ome.model.core.Pixels
 
PERMS_FILTER - Static variable in class ome.model.core.PixelsOriginalFileMap
 
PERMS_FILTER - Static variable in class ome.model.core.PlaneInfo
 
PERMS_FILTER - Static variable in class ome.model.display.ChannelBinding
 
PERMS_FILTER - Static variable in class ome.model.display.CodomainMapContext
 
PERMS_FILTER - Static variable in class ome.model.display.ContrastStretchingContext
 
PERMS_FILTER - Static variable in class ome.model.display.PlaneSlicingContext
 
PERMS_FILTER - Static variable in class ome.model.display.QuantumDef
 
PERMS_FILTER - Static variable in class ome.model.display.RenderingDef
 
PERMS_FILTER - Static variable in class ome.model.display.ReverseIntensityContext
 
PERMS_FILTER - Static variable in class ome.model.display.Thumbnail
 
PERMS_FILTER - Static variable in class ome.model.experiment.Experiment
 
PERMS_FILTER - Static variable in class ome.model.experiment.MicrobeamManipulation
 
PERMS_FILTER - Static variable in class ome.model.fs.Fileset
 
PERMS_FILTER - Static variable in class ome.model.fs.FilesetEntry
 
PERMS_FILTER - Static variable in class ome.model.fs.FilesetJobLink
 
PERMS_FILTER - Static variable in class ome.model.internal.Link
 
PERMS_FILTER - Static variable in class ome.model.jobs.ImportJob
 
PERMS_FILTER - Static variable in class ome.model.jobs.IndexingJob
 
PERMS_FILTER - Static variable in class ome.model.jobs.IntegrityCheckJob
 
PERMS_FILTER - Static variable in class ome.model.jobs.Job
 
PERMS_FILTER - Static variable in class ome.model.jobs.JobOriginalFileLink
 
PERMS_FILTER - Static variable in class ome.model.jobs.MetadataImportJob
 
PERMS_FILTER - Static variable in class ome.model.jobs.ParseJob
 
PERMS_FILTER - Static variable in class ome.model.jobs.PixelDataJob
 
PERMS_FILTER - Static variable in class ome.model.jobs.ScriptJob
 
PERMS_FILTER - Static variable in class ome.model.jobs.ThumbnailGenerationJob
 
PERMS_FILTER - Static variable in class ome.model.jobs.UploadJob
 
PERMS_FILTER - Static variable in class ome.model.meta.ExternalInfo
 
PERMS_FILTER - Static variable in class ome.model.roi.Ellipse
 
PERMS_FILTER - Static variable in class ome.model.roi.Label
 
PERMS_FILTER - Static variable in class ome.model.roi.Line
 
PERMS_FILTER - Static variable in class ome.model.roi.Mask
 
PERMS_FILTER - Static variable in class ome.model.roi.Path
 
PERMS_FILTER - Static variable in class ome.model.roi.Point
 
PERMS_FILTER - Static variable in class ome.model.roi.Polygon
 
PERMS_FILTER - Static variable in class ome.model.roi.Polyline
 
PERMS_FILTER - Static variable in class ome.model.roi.Rect
 
PERMS_FILTER - Static variable in class ome.model.roi.Roi
 
PERMS_FILTER - Static variable in class ome.model.roi.Shape
 
PERMS_FILTER - Static variable in class ome.model.screen.Plate
 
PERMS_FILTER - Static variable in class ome.model.screen.PlateAcquisition
 
PERMS_FILTER - Static variable in class ome.model.screen.Reagent
 
PERMS_FILTER - Static variable in class ome.model.screen.Screen
 
PERMS_FILTER - Static variable in class ome.model.screen.ScreenPlateLink
 
PERMS_FILTER - Static variable in class ome.model.screen.Well
 
PERMS_FILTER - Static variable in class ome.model.screen.WellReagentLink
 
PERMS_FILTER - Static variable in class ome.model.screen.WellSample
 
PERMS_FILTER - Static variable in class ome.model.stats.StatsInfo
 
PERMS_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.acquisition.Detector
 
PERMS_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.acquisition.Dichroic
 
PERMS_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.acquisition.Filter
 
PERMS_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.acquisition.Instrument
 
PERMS_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.acquisition.LightPath
 
PERMS_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.acquisition.LightSource
 
PERMS_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.acquisition.Objective
 
PERMS_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.annotations.Annotation
 
PERMS_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.containers.Dataset
 
PERMS_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.containers.Project
 
PERMS_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.core.Channel
 
PERMS_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.core.Image
 
PERMS_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.core.OriginalFile
 
PERMS_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.core.PlaneInfo
 
PERMS_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.fs.Fileset
 
PERMS_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.meta.Experimenter
 
PERMS_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.meta.ExperimenterGroup
 
PERMS_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.meta.Namespace
 
PERMS_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.meta.Node
 
PERMS_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.meta.Session
 
PERMS_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.roi.Roi
 
PERMS_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.roi.Shape
 
PERMS_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.screen.Plate
 
PERMS_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.screen.PlateAcquisition
 
PERMS_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.screen.Reagent
 
PERMS_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.screen.Screen
 
PERMS_FILTER_ANNOTATIONLINKS - Static variable in class ome.model.screen.Well
 
PERMS_FILTER_CHANNELS - Static variable in class ome.model.core.LogicalChannel
 
PERMS_FILTER_CHANNELS - Static variable in class ome.model.core.Pixels
 
PERMS_FILTER_DATASETLINKS - Static variable in class ome.model.containers.Project
 
PERMS_FILTER_DATASETLINKS - Static variable in class ome.model.core.Image
 
PERMS_FILTER_DETECTOR - Static variable in class ome.model.acquisition.Instrument
 
PERMS_FILTER_DICHROIC - Static variable in class ome.model.acquisition.Instrument
 
PERMS_FILTER_EMISSIONFILTERLINK - Static variable in class ome.model.acquisition.Filter
 
PERMS_FILTER_EMISSIONFILTERLINK - Static variable in class ome.model.acquisition.FilterSet
 
PERMS_FILTER_EMISSIONFILTERLINK - Static variable in class ome.model.acquisition.LightPath
 
PERMS_FILTER_EXCITATIONFILTERLINK - Static variable in class ome.model.acquisition.Filter
 
PERMS_FILTER_EXCITATIONFILTERLINK - Static variable in class ome.model.acquisition.FilterSet
 
PERMS_FILTER_EXCITATIONFILTERLINK - Static variable in class ome.model.acquisition.LightPath
 
PERMS_FILTER_FILESETENTRIES - Static variable in class ome.model.core.OriginalFile
 
PERMS_FILTER_FILTER - Static variable in class ome.model.acquisition.Instrument
 
PERMS_FILTER_FILTERSET - Static variable in class ome.model.acquisition.Instrument
 
PERMS_FILTER_IMAGELINKS - Static variable in class ome.model.containers.Dataset
 
PERMS_FILTER_IMAGES - Static variable in class ome.model.fs.Fileset
 
PERMS_FILTER_JOBLINKS - Static variable in class ome.model.fs.Fileset
 
PERMS_FILTER_LIGHTSOURCE - Static variable in class ome.model.acquisition.Instrument
 
PERMS_FILTER_LIGHTSOURCESETTINGS - Static variable in class ome.model.experiment.MicrobeamManipulation
 
PERMS_FILTER_MICROBEAMMANIPULATION - Static variable in class ome.model.experiment.Experiment
 
PERMS_FILTER_OBJECTIVE - Static variable in class ome.model.acquisition.Instrument
 
PERMS_FILTER_ORIGINALFILELINKS - Static variable in class ome.model.jobs.Job
 
PERMS_FILTER_OTF - Static variable in class ome.model.acquisition.Instrument
 
PERMS_FILTER_PIXELS - Static variable in class ome.model.core.Image
 
PERMS_FILTER_PIXELSFILEMAPS - Static variable in class ome.model.core.OriginalFile
 
PERMS_FILTER_PIXELSFILEMAPS - Static variable in class ome.model.core.Pixels
 
PERMS_FILTER_PLANEINFO - Static variable in class ome.model.core.Pixels
 
PERMS_FILTER_PLATEACQUISITIONS - Static variable in class ome.model.screen.Plate
 
PERMS_FILTER_PLATELINKS - Static variable in class ome.model.screen.Screen
 
PERMS_FILTER_PROJECTLINKS - Static variable in class ome.model.containers.Dataset
 
PERMS_FILTER_REAGENTLINKS - Static variable in class ome.model.screen.Well
 
PERMS_FILTER_REAGENTS - Static variable in class ome.model.screen.Screen
 
PERMS_FILTER_ROIS - Static variable in class ome.model.core.Image
 
PERMS_FILTER_SCREENLINKS - Static variable in class ome.model.screen.Plate
 
PERMS_FILTER_SETTINGS - Static variable in class ome.model.core.Pixels
 
PERMS_FILTER_SHAPES - Static variable in class ome.model.roi.Roi
 
PERMS_FILTER_SPATIALDOMAINENHANCEMENT - Static variable in class ome.model.display.RenderingDef
 
PERMS_FILTER_THUMBNAILS - Static variable in class ome.model.core.Pixels
 
PERMS_FILTER_USEDFILES - Static variable in class ome.model.fs.Fileset
 
PERMS_FILTER_WAVERENDERING - Static variable in class ome.model.display.RenderingDef
 
PERMS_FILTER_WELLLINKS - Static variable in class ome.model.screen.Reagent
 
PERMS_FILTER_WELLS - Static variable in class ome.model.screen.Plate
 
PERMS_FILTER_WELLSAMPLE - Static variable in class ome.model.screen.PlateAcquisition
 
PERMS_FILTER_WELLSAMPLES - Static variable in class ome.model.core.Image
 
PERMS_FILTER_WELLSAMPLES - Static variable in class ome.model.screen.Well
 
PerSessionStats - Class in ome.services.sessions.stats
Delegates to a SessionStats which is acquired on every method invocation.
PerSessionStats(CurrentDetails) - Constructor for class ome.services.sessions.stats.PerSessionStats
 
PersistentEventLogLoader - Class in ome.services.eventlogs
EventLogLoader implementation which keeps tracks of the last EventLog instance, and always provides the next unindexed instance.
PersistentEventLogLoader() - Constructor for class ome.services.eventlogs.PersistentEventLogLoader
 
PersistentEventLogLoader - Class in ome.services.fulltext
EventLogLoader implementation which keeps tracks of the last EventLog instance, and always provides the next unindexed instance.
PersistentEventLogLoader() - Constructor for class ome.services.fulltext.PersistentEventLogLoader
 
PersistentEventLogLoader - Class in ome.services.pixeldata
EventLogLoader implementation which keeps tracks of the last EventLog instance, and always provides the next unindexed instance.
PersistentEventLogLoader(String, int) - Constructor for class ome.services.pixeldata.PersistentEventLogLoader
 
persistLogFile(OriginalFile, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
Deprecated.
PersonContextMapper - Class in ome.security.auth
Specialized OME Experimenter context mapper.
PersonContextMapper(LdapConfig, String) - Constructor for class ome.security.auth.PersonContextMapper
 
PersonContextMapper(LdapConfig, String, String) - Constructor for class ome.security.auth.PersonContextMapper
 
PerThreadStats - Class in ome.services.sessions.stats
Delegates to a SessionStats which is acquired on every method invocation.
PerThreadStats(CurrentDetails) - Constructor for class ome.services.sessions.stats.PerThreadStats
 
PHOTOMETRIC_MONOCHROME - Static variable in class omeis.providers.re.Renderer
Identifies the type used to store photometric interpretation values.
photometricInterpretation - Variable in class ome.model.core.LogicalChannel
 
PHOTOMETRICINTERPRETATION - Static variable in class ome.model.core.LogicalChannel
 
PhotometricInterpretation - Class in ome.model.enums
 
PhotometricInterpretation() - Constructor for class ome.model.enums.PhotometricInterpretation
 
PhotometricInterpretation(Long) - Constructor for class ome.model.enums.PhotometricInterpretation
 
PhotometricInterpretation(Long, boolean) - Constructor for class ome.model.enums.PhotometricInterpretation
Main constructor.
PhotometricInterpretation(String) - Constructor for class ome.model.enums.PhotometricInterpretation
 
PhotometricInterpretation.Details - Class in ome.model.enums
 
PhotometricInterpretation.Details() - Constructor for class ome.model.enums.PhotometricInterpretation.Details
 
PhotometricInterpretation.Details(Object[]) - Constructor for class ome.model.enums.PhotometricInterpretation.Details
 
physicalSizeX - Variable in class ome.model.core.Pixels
 
PHYSICALSIZEX - Static variable in class ome.model.core.Pixels
 
physicalSizeY - Variable in class ome.model.core.Pixels
 
PHYSICALSIZEY - Static variable in class ome.model.core.Pixels
 
physicalSizeZ - Variable in class ome.model.core.Pixels
 
PHYSICALSIZEZ - Static variable in class ome.model.core.Pixels
 
pid() - Method in class omero.util.TempFileManager
Returns some representation of the current process's id
ping() - Method in class ome.formats.OMEROMetadataStoreClient
Pings all registered OMERO Blitz proxies.
ping() - Method in class ome.services.blitz.repo.ManagedImportProcessI
 
ping() - Method in interface ome.services.blitz.repo.ProcessContainer.Process
 
pingAll() - Method in class ome.services.blitz.repo.ProcessContainer
Called periodically by quartz to keep the sessions alive.
pinHoleSize - Variable in class ome.model.core.LogicalChannel
 
PINHOLESIZE - Static variable in class ome.model.core.LogicalChannel
 
PixelBuffer - Interface in ome.io.nio
This interface declares the I/O responsibilities of a buffer, file or otherwise, that contains a 5-dimensional Pixel array (XYZCT).
PixelBufferException - Exception in ome.io.nio
 
PixelBufferException(String) - Constructor for exception ome.io.nio.PixelBufferException
 
pixelData(PixelDataJob) - Method in class ome.services.blitz.repo.ManagedImportRequestI
 
PixelData - Class in ome.services.roi
Strategy for loading and optionally caching pixel data.
PixelData(PixelsService, IPixels) - Constructor for class ome.services.roi.PixelData
 
PixelData - Class in ome.util
Represents a block of pixel data.
PixelData(String, ByteBuffer) - Constructor for class ome.util.PixelData
Default constructor.
PixelDataHandler - Class in ome.services.pixeldata
Simple action which can be done in an asynchronous thread in order to process PIXELDATA event logs.
PixelDataHandler(EventLogLoader, PixelsService) - Constructor for class ome.services.pixeldata.PixelDataHandler
 
PixelDataJob - Class in ome.model.jobs
 
PixelDataJob() - Constructor for class ome.model.jobs.PixelDataJob
 
PixelDataJob(Long) - Constructor for class ome.model.jobs.PixelDataJob
 
PixelDataJob(Long, boolean) - Constructor for class ome.model.jobs.PixelDataJob
Main constructor.
PixelDataThread - Class in ome.services.pixeldata
 
PixelDataThread(SessionManager, Executor, PixelDataHandler, String) - Constructor for class ome.services.pixeldata.PixelDataThread
Uses default Principal for processing
PixelDataThread(SessionManager, Executor, PixelDataHandler, String, int) - Constructor for class ome.services.pixeldata.PixelDataThread
Uses default Principal for processing and a NullMetrics instance.
PixelDataThread(SessionManager, Executor, PixelDataHandler, Principal, String, int) - Constructor for class ome.services.pixeldata.PixelDataThread
Calculates PixelDataThread.performProcessing based on the existence of the "pixelDataTrigger" and passes all parameters to the main ctor passing a NullMetrics as necessary.
PixelDataThread(SessionManager, Executor, PixelDataHandler, String, int, Metrics) - Constructor for class ome.services.pixeldata.PixelDataThread
Calculates PixelDataThread.performProcessing based on the existence of the "pixelDataTrigger" and passes all parameters to the main ctor.
PixelDataThread(SessionManager, Executor, PixelDataHandler, Principal, String, int, Metrics) - Constructor for class ome.services.pixeldata.PixelDataThread
Calculates PixelDataThread.performProcessing based on the existence of the "pixelDataTrigger" and passes all parameters to the main ctor.
PixelDataThread(boolean, SessionManager, Executor, PixelDataHandler, Principal, String, int) - Constructor for class ome.services.pixeldata.PixelDataThread
Calls main constructor with NullMetrics.
PixelDataThread(boolean, SessionManager, Executor, PixelDataHandler, Principal, String, int, Metrics) - Constructor for class ome.services.pixeldata.PixelDataThread
Main constructor.
pixels - Variable in class ome.formats.importer.ImportEvent.IMPORT_DONE
 
pixels - Variable in class ome.formats.importer.ImportSize
 
pixels - Variable in class ome.model.core.Channel
 
PIXELS - Static variable in class ome.model.core.Channel
 
pixels - Variable in class ome.model.core.Image
 
PIXELS - Static variable in class ome.model.core.Image
 
Pixels - Class in ome.model.core
These filter definitions are used by the security system to eliminate non-readable objects from queries.
Pixels() - Constructor for class ome.model.core.Pixels
 
Pixels(Long) - Constructor for class ome.model.core.Pixels
 
Pixels(Long, boolean) - Constructor for class ome.model.core.Pixels
Main constructor.
Pixels(Image, PixelsType, Integer, Integer, Integer, Integer, Integer, String, DimensionOrder) - Constructor for class ome.model.core.Pixels
 
pixels - Variable in class ome.model.core.PlaneInfo
 
PIXELS - Static variable in class ome.model.core.PlaneInfo
 
pixels - Variable in class ome.model.display.RenderingDef
 
PIXELS - Static variable in class ome.model.display.RenderingDef
 
pixels - Variable in class ome.model.display.Thumbnail
 
PIXELS - Static variable in class ome.model.display.Thumbnail
 
pixels - Variable in class ome.model.roi.Mask
 
PIXELS - Static variable in class ome.model.roi.Mask
 
pixels(String, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
 
pixels - Variable in class omeis.providers.re.quantum.QuantumStrategy
The pixels this strategy is for.
pixels - Variable in class omero.util.RPSTileLoop
Instance will be replaced on RawPixelsStorePrx.save()
PIXELS - Static variable in class pojos.ImageData
Identifies the Image#PIXELS field.
Pixels.Details - Class in ome.model.core
 
Pixels.Details() - Constructor for class ome.model.core.Pixels.Details
 
Pixels.Details(Object[]) - Constructor for class ome.model.core.Pixels.Details
 
PIXELS_PATH - Static variable in class ome.io.nio.AbstractFileSystemService
 
Pixels_PhysicalSizeX - Static variable in class ome.formats.model.UnitsFactory
 
Pixels_PhysicalSizeY - Static variable in class ome.formats.model.UnitsFactory
 
Pixels_PhysicalSizeZ - Static variable in class ome.formats.model.UnitsFactory
 
Pixels_TimeIncrement - Static variable in class ome.formats.model.UnitsFactory
 
pixelsData - Variable in class ome.logic.RenderingSettingsImpl
Reference to the service used to retrieve the pixels data.
PixelsData - Class in pojos
The data that makes up an OME Pixels object along with a back pointer to the Image that owns this Pixels.
PixelsData() - Constructor for class pojos.PixelsData
Creates a new instance.
PixelsData(Pixels) - Constructor for class pojos.PixelsData
Creates a new instance.
PixelsFileDeletions - Class in ome.services.delete.files
Registers the given file paths as well as other Pixel-related files like Pyramids for later deletion via #deleteLocal(java.util.Map).
PixelsFileDeletions(AbstractFileSystemService, Set<Long>) - Constructor for class ome.services.delete.files.PixelsFileDeletions
 
pixelsFileMaps - Variable in class ome.model.core.OriginalFile
 
PIXELSFILEMAPS - Static variable in class ome.model.core.OriginalFile
 
pixelsFileMaps - Variable in class ome.model.core.Pixels
 
PIXELSFILEMAPS - Static variable in class ome.model.core.Pixels
 
PIXELSFILEMAPSCOUNTPEROWNER - Static variable in class ome.model.core.OriginalFile
 
PIXELSFILEMAPSCOUNTPEROWNER - Static variable in class ome.model.core.Pixels
 
PixelsI - Class in ome.services.blitz.impl
Implementation of the IPixels service.
PixelsI(IPixels, BlitzExecutor) - Constructor for class ome.services.blitz.impl.PixelsI
 
pixelsID - Variable in exception ome.conditions.MissingPyramidException
 
pixelsID - Variable in class ome.io.messages.MissingPyramidMessage
 
PixelsImpl - Class in ome.logic
implementation of the Pixels service interface.
PixelsImpl() - Constructor for class ome.logic.PixelsImpl
 
pixelsMetadata - Variable in class ome.logic.RenderingSettingsImpl
Reference to the service used to retrieve the pixels metadata.
PixelsOriginalFileMap - Class in ome.model.core
These filter definitions are used by the security system to eliminate non-readable objects from queries.
PixelsOriginalFileMap() - Constructor for class ome.model.core.PixelsOriginalFileMap
 
PixelsOriginalFileMap(Long) - Constructor for class ome.model.core.PixelsOriginalFileMap
 
PixelsOriginalFileMap(Long, boolean) - Constructor for class ome.model.core.PixelsOriginalFileMap
Main constructor.
PixelsOriginalFileMap(IObject, IObject) - Constructor for class ome.model.core.PixelsOriginalFileMap
 
PixelsOriginalFileMap.Details - Class in ome.model.core
 
PixelsOriginalFileMap.Details() - Constructor for class ome.model.core.PixelsOriginalFileMap.Details
 
PixelsOriginalFileMap.Details(Object[]) - Constructor for class ome.model.core.PixelsOriginalFileMap.Details
 
PixelsProcessor - Class in ome.formats.model
Processes the pixels sets of an IObjectContainerStore and ensures that the physical pixel dimensions are updated if they were specified by the user.
PixelsProcessor() - Constructor for class ome.formats.model.PixelsProcessor
 
PixelsService - Class in ome.io.nio
 
PixelsService(String) - Constructor for class ome.io.nio.PixelsService
Constructor.
PixelsService(String, FilePathResolver) - Constructor for class ome.io.nio.PixelsService
Constructor.
PixelsService(String, FilePathResolver, BackOff, TileSizes, IQuery) - Constructor for class ome.io.nio.PixelsService
Constructor.
PixelsService(String, long, FilePathResolver, BackOff, TileSizes, IQuery) - Constructor for class ome.io.nio.PixelsService
Call #PixelsService(String, File, long, FilePathResolver, BackOff, TileSizes) with PixelsService.MEMOIZER_WAIT.
PixelsService(String, File, FilePathResolver, BackOff, TileSizes, IQuery) - Constructor for class ome.io.nio.PixelsService
Call #PixelsService(String, File, long, FilePathResolver, BackOff, TileSizes) with PixelsService.MEMOIZER_WAIT.
PixelsService(String, File, long, FilePathResolver, BackOff, TileSizes, IQuery) - Constructor for class ome.io.nio.PixelsService
 
pixelsService - Variable in class ome.services.pixeldata.PixelDataHandler
 
pixelsService - Variable in class ome.services.projection.ProjectionBean
Reference to the service used to retrieve the pixels data.
pixelsType - Variable in class ome.model.acquisition.OTF
 
PIXELSTYPE - Static variable in class ome.model.acquisition.OTF
 
pixelsType - Variable in class ome.model.core.Pixels
 
PIXELSTYPE - Static variable in class ome.model.core.Pixels
 
PixelsType - Class in ome.model.enums
 
PixelsType() - Constructor for class ome.model.enums.PixelsType
 
PixelsType(Long) - Constructor for class ome.model.enums.PixelsType
 
PixelsType(Long, boolean) - Constructor for class ome.model.enums.PixelsType
Main constructor.
PixelsType(String) - Constructor for class ome.model.enums.PixelsType
 
pixelsType - Variable in class ome.util.PixelData
Type of the pixel data.
PixelsType.Details - Class in ome.model.enums
 
PixelsType.Details() - Constructor for class ome.model.enums.PixelsType.Details
 
PixelsType.Details(Object[]) - Constructor for class ome.model.enums.PixelsType.Details
 
pixId - Variable in class ome.formats.importer.ImportEvent.PROGRESS_EVENT
 
pixToImageCache - Variable in class ome.services.sharing.BlobShareStore
 
Plane2D - Class in omeis.providers.re.data
 
Plane2D(PlaneDef, Pixels, PixelData) - Constructor for class omeis.providers.re.data.Plane2D
Constructor that sub-classes must call.
Plane_DeltaT - Static variable in class ome.formats.model.UnitsFactory
 
Plane_ExposureTime - Static variable in class ome.formats.model.UnitsFactory
 
Plane_PositionX - Static variable in class ome.formats.model.UnitsFactory
 
Plane_PositionY - Static variable in class ome.formats.model.UnitsFactory
 
Plane_PositionZ - Static variable in class ome.formats.model.UnitsFactory
 
PlaneArea - Interface in ome.util.math.geom2D
Interface that all areas of the Euclidean space R2 must implement.
planeDef - Variable in class omeis.providers.re.data.Plane2D
The type of plane.
PlaneDef - Class in omeis.providers.re.data
Identifies a 2D-plane in the XYZ moving frame of the 3D stack.
PlaneDef(int, int) - Constructor for class omeis.providers.re.data.PlaneDef
Creates a new instance.
PlaneFactory - Class in omeis.providers.re.data
Encapsulates access to the image raw data.
PlaneFactory() - Constructor for class omeis.providers.re.data.PlaneFactory
 
planeInfo - Variable in class ome.model.core.Pixels
 
PLANEINFO - Static variable in class ome.model.core.Pixels
 
PlaneInfo - Class in ome.model.core
These filter definitions are used by the security system to eliminate non-readable objects from queries.
PlaneInfo() - Constructor for class ome.model.core.PlaneInfo
 
PlaneInfo(Long) - Constructor for class ome.model.core.PlaneInfo
 
PlaneInfo(Long, boolean) - Constructor for class ome.model.core.PlaneInfo
Main constructor.
PlaneInfo(Pixels, Integer, Integer, Integer) - Constructor for class ome.model.core.PlaneInfo
 
PlaneInfo.Details - Class in ome.model.core
 
PlaneInfo.Details() - Constructor for class ome.model.core.PlaneInfo.Details
 
PlaneInfo.Details(Object[]) - Constructor for class ome.model.core.PlaneInfo.Details
 
PlaneInfoAnnotationLink - Class in ome.model.annotations
These filter definitions are used by the security system to eliminate non-readable objects from queries.
PlaneInfoAnnotationLink() - Constructor for class ome.model.annotations.PlaneInfoAnnotationLink
 
PlaneInfoAnnotationLink(Long) - Constructor for class ome.model.annotations.PlaneInfoAnnotationLink
 
PlaneInfoAnnotationLink(Long, boolean) - Constructor for class ome.model.annotations.PlaneInfoAnnotationLink
Main constructor.
PlaneInfoAnnotationLink(IObject, IObject) - Constructor for class ome.model.annotations.PlaneInfoAnnotationLink
 
PlaneInfoAnnotationLink.Details - Class in ome.model.annotations
 
PlaneInfoAnnotationLink.Details() - Constructor for class ome.model.annotations.PlaneInfoAnnotationLink.Details
 
PlaneInfoAnnotationLink.Details(Object[]) - Constructor for class ome.model.annotations.PlaneInfoAnnotationLink.Details
 
PlaneInfoProcessor - Class in ome.formats.model
Processes the plane info sets of an IObjectContainerStore and removes entities of this rapidly exploding object that have no metadata populated.
PlaneInfoProcessor() - Constructor for class ome.formats.model.PlaneInfoProcessor
 
PlanePoint - Class in ome.util.math.geom2D
Represents a point in the Euclidean space R2.
PlanePoint(double, double) - Constructor for class ome.util.math.geom2D.PlanePoint
Creates a new instance.
planePrevious - Variable in class ome.model.display.PlaneSlicingContext
 
PLANEPREVIOUS - Static variable in class ome.model.display.PlaneSlicingContext
 
planes - Variable in class ome.services.formats.OmeroReader
 
planeSelected - Variable in class ome.model.display.PlaneSlicingContext
 
PLANESELECTED - Static variable in class ome.model.display.PlaneSlicingContext
 
PlaneSlicingContext - Class in ome.model.display
 
PlaneSlicingContext() - Constructor for class ome.model.display.PlaneSlicingContext
 
PlaneSlicingContext(Long) - Constructor for class ome.model.display.PlaneSlicingContext
 
PlaneSlicingContext(Long, boolean) - Constructor for class ome.model.display.PlaneSlicingContext
Main constructor.
PlaneSlicingContext(Integer, Integer, Integer, Integer, Boolean) - Constructor for class ome.model.display.PlaneSlicingContext
 
PlaneSlicingContext - Class in omeis.providers.re.codomain
We consider that the image is composed of eight 1-bit planes ranging from bit-plane 0 for the least significant bit to bit-plane 7 for the most significant bit.
PlaneSlicingContext(int, int, boolean) - Constructor for class omeis.providers.re.codomain.PlaneSlicingContext
Creates a new instance.
planOperation(Session, SetMultimap<String, Long>, boolean, boolean) - Method in class ome.services.graphs.GraphTraversal
Traverse model object graph to determine steps for the proposed operation.
planOperation(Session, Collection<? extends IObject>, boolean, boolean) - Method in class ome.services.graphs.GraphTraversal
Traverse model object graph to determine steps for the proposed operation.
Plate - Class in ome.model.screen
These filter definitions are used by the security system to eliminate non-readable objects from queries.
Plate() - Constructor for class ome.model.screen.Plate
 
Plate(Long) - Constructor for class ome.model.screen.Plate
 
Plate(Long, boolean) - Constructor for class ome.model.screen.Plate
Main constructor.
Plate(String) - Constructor for class ome.model.screen.Plate
 
plate - Variable in class ome.model.screen.PlateAcquisition
 
PLATE - Static variable in class ome.model.screen.PlateAcquisition
 
plate - Variable in class ome.model.screen.Well
 
PLATE - Static variable in class ome.model.screen.Well
 
Plate.Details - Class in ome.model.screen
 
Plate.Details() - Constructor for class ome.model.screen.Plate.Details
 
Plate.Details(Object[]) - Constructor for class ome.model.screen.Plate.Details
 
PLATE_LINKS - Static variable in class pojos.ScreenData
Identifies the Screen#PLATELINKS field.
Plate_WellOriginX - Static variable in class ome.formats.model.UnitsFactory
 
Plate_WellOriginY - Static variable in class ome.formats.model.UnitsFactory
 
PlateAcquisition - Class in ome.model.screen
These filter definitions are used by the security system to eliminate non-readable objects from queries.
PlateAcquisition() - Constructor for class ome.model.screen.PlateAcquisition
 
PlateAcquisition(Long) - Constructor for class ome.model.screen.PlateAcquisition
 
PlateAcquisition(Long, boolean) - Constructor for class ome.model.screen.PlateAcquisition
Main constructor.
PlateAcquisition(Plate) - Constructor for class ome.model.screen.PlateAcquisition
 
plateAcquisition - Variable in class ome.model.screen.WellSample
 
PLATEACQUISITION - Static variable in class ome.model.screen.WellSample
 
PlateAcquisition.Details - Class in ome.model.screen
 
PlateAcquisition.Details() - Constructor for class ome.model.screen.PlateAcquisition.Details
 
PlateAcquisition.Details(Object[]) - Constructor for class ome.model.screen.PlateAcquisition.Details
 
PlateAcquisitionAnnotationLink - Class in ome.model.annotations
These filter definitions are used by the security system to eliminate non-readable objects from queries.
PlateAcquisitionAnnotationLink() - Constructor for class ome.model.annotations.PlateAcquisitionAnnotationLink
 
PlateAcquisitionAnnotationLink(Long) - Constructor for class ome.model.annotations.PlateAcquisitionAnnotationLink
 
PlateAcquisitionAnnotationLink(Long, boolean) - Constructor for class ome.model.annotations.PlateAcquisitionAnnotationLink
Main constructor.
PlateAcquisitionAnnotationLink(IObject, IObject) - Constructor for class ome.model.annotations.PlateAcquisitionAnnotationLink
 
PlateAcquisitionAnnotationLink.Details - Class in ome.model.annotations
 
PlateAcquisitionAnnotationLink.Details() - Constructor for class ome.model.annotations.PlateAcquisitionAnnotationLink.Details
 
PlateAcquisitionAnnotationLink.Details(Object[]) - Constructor for class ome.model.annotations.PlateAcquisitionAnnotationLink.Details
 
PlateAcquisitionData - Class in pojos
The data that makes up an OME PlateAcquisition.
PlateAcquisitionData() - Constructor for class pojos.PlateAcquisitionData
Creates a new instance.
PlateAcquisitionData(PlateAcquisition) - Constructor for class pojos.PlateAcquisitionData
Creates a new instance.
plateAcquisitions - Variable in class ome.model.screen.Plate
 
PLATEACQUISITIONS - Static variable in class ome.model.screen.Plate
 
PlateAnnotationLink - Class in ome.model.annotations
These filter definitions are used by the security system to eliminate non-readable objects from queries.
PlateAnnotationLink() - Constructor for class ome.model.annotations.PlateAnnotationLink
 
PlateAnnotationLink(Long) - Constructor for class ome.model.annotations.PlateAnnotationLink
 
PlateAnnotationLink(Long, boolean) - Constructor for class ome.model.annotations.PlateAnnotationLink
Main constructor.
PlateAnnotationLink(IObject, IObject) - Constructor for class ome.model.annotations.PlateAnnotationLink
 
PlateAnnotationLink.Details - Class in ome.model.annotations
 
PlateAnnotationLink.Details() - Constructor for class ome.model.annotations.PlateAnnotationLink.Details
 
PlateAnnotationLink.Details(Object[]) - Constructor for class ome.model.annotations.PlateAnnotationLink.Details
 
PlateData - Class in pojos
The data that makes up an OME Plate along with links to its contained Well and enclosing Screen as well as the Experimenter that owns this Plate.
PlateData() - Constructor for class pojos.PlateData
Creates a new instance.
PlateData(Plate) - Constructor for class pojos.PlateData
Creates a new instance.
PLATEIMAGES_QUERY - Static variable in class ome.services.delete.DeleteBean
 
plateLinks - Variable in class ome.model.screen.Screen
 
PLATELINKS - Static variable in class ome.model.screen.Screen
 
PLATELINKSCOUNTPEROWNER - Static variable in class ome.model.screen.Screen
 
pockelCell - Variable in class ome.model.acquisition.Laser
 
POCKELCELL - Static variable in class ome.model.acquisition.Laser
 
pockelCellSetting - Variable in class ome.model.core.LogicalChannel
 
POCKELCELLSETTING - Static variable in class ome.model.core.LogicalChannel
 
Point - Class in ome.model.roi
 
Point() - Constructor for class ome.model.roi.Point
 
Point(Long) - Constructor for class ome.model.roi.Point
 
Point(Long, boolean) - Constructor for class ome.model.roi.Point
Main constructor.
PointData - Class in pojos
Represents a point in the Euclidean space R2.
PointData(Shape) - Constructor for class pojos.PointData
Creates a new instance.
PointData() - Constructor for class pojos.PointData
Create a new instance of PointData, creating a new pointI Object.
PointData(double, double) - Constructor for class pojos.PointData
Create a new instance of the PointData,
points - Variable in class ome.model.roi.Polygon
 
POINTS - Static variable in class ome.model.roi.Polygon
 
points - Variable in class ome.model.roi.Polyline
 
POINTS - Static variable in class ome.model.roi.Polyline
 
points(double, double, double, double) - Static method in class omero.model.SmartShape.Util
Returns the four corner points of a rectangle
pointsByBoundingBox(Shape, Rectangle2D, SmartShape.PointCallback) - Static method in class omero.model.SmartShape.Util
 
pointsToPath(List<Point>, boolean) - Static method in class omero.model.SmartShape.Util
 
pojos - package pojos
 
pojos.util - package pojos.util
 
PojosFindAnnotationsQueryDefinition - Class in ome.services.query
 
PojosFindAnnotationsQueryDefinition(Parameters) - Constructor for class ome.services.query.PojosFindAnnotationsQueryDefinition
 
PojosFindHierarchiesQueryDefinition - Class in ome.services.query
walks up the hierarchy tree starting at Image nodes while fetching various information.
PojosFindHierarchiesQueryDefinition(Parameters) - Constructor for class ome.services.query.PojosFindHierarchiesQueryDefinition
 
PojosGetImagesByOptionsQueryDefinition - Class in ome.services.query
 
PojosGetImagesByOptionsQueryDefinition(Parameters) - Constructor for class ome.services.query.PojosGetImagesByOptionsQueryDefinition
 
PojosGetImagesQueryDefinition - Class in ome.services.query
 
PojosGetImagesQueryDefinition(Parameters) - Constructor for class ome.services.query.PojosGetImagesQueryDefinition
 
PojosGetUserImagesQueryDefinition - Class in ome.services.query
 
PojosGetUserImagesQueryDefinition(Parameters) - Constructor for class ome.services.query.PojosGetUserImagesQueryDefinition
 
PojosImpl - Class in ome.logic
implementation of the Pojos service interface.
PojosImpl() - Constructor for class ome.logic.PojosImpl
 
PojosLoadHierarchyQueryDefinition - Class in ome.services.query
 
PojosLoadHierarchyQueryDefinition(Parameters) - Constructor for class ome.services.query.PojosLoadHierarchyQueryDefinition
 
Policy - Interface in ome.security.policy
Strategy to permit the flexible restriction of certain actions throughout OMERO.
policyService - Variable in class ome.security.basic.BasicACLVoter
 
policyService - Variable in class ome.security.basic.BasicSecuritySystem
 
PolicyService - Interface in ome.security.policy
Internal service containing a number of configured Policy instances.
poll(Current) - Method in class ome.services.blitz.impl.ScriptProcessI
 
poll() - Method in class omero.cmd.CmdCallbackI
Calls HandlePrx.getResponse() in order to check for a non-null value.
Polygon - Class in ome.model.roi
 
Polygon() - Constructor for class ome.model.roi.Polygon
 
Polygon(Long) - Constructor for class ome.model.roi.Polygon
 
Polygon(Long, boolean) - Constructor for class ome.model.roi.Polygon
Main constructor.
PolygonData - Class in pojos
Represents an Polygon shape in the Euclidean space R2.
PolygonData(Shape) - Constructor for class pojos.PolygonData
Creates a new instance.
PolygonData() - Constructor for class pojos.PolygonData
Creates a new instance of PolygonData.
PolygonData(List<Point2D.Double>, List<Point2D.Double>, List<Point2D.Double>, List<Integer>) - Constructor for class pojos.PolygonData
Creates a new instance of the PolygonData, set the points in the polygon.
Polyline - Class in ome.model.roi
 
Polyline() - Constructor for class ome.model.roi.Polyline
 
Polyline(Long) - Constructor for class ome.model.roi.Polyline
 
Polyline(Long, boolean) - Constructor for class ome.model.roi.Polyline
Main constructor.
PolylineData - Class in pojos
Represents an Polyline shape in the Euclidean space R2.
PolylineData(Shape) - Constructor for class pojos.PolylineData
Creates a new instance.
PolylineData() - Constructor for class pojos.PolylineData
Creates a new instance of polyline, creating a new PolylineI Object.
PolylineData(List<Point2D.Double>, List<Point2D.Double>, List<Point2D.Double>, List<Integer>) - Constructor for class pojos.PolylineData
Create a new instance of the PolylineData, set the points in the polyline.
POLYNOMIAL - Static variable in class omeis.providers.re.quantum.QuantumFactory
Flag to select a polynomial map for the quantization process.
PolynomialMap - Class in omeis.providers.re.quantum
This class implements the QuantumMap interface.
PolynomialMap() - Constructor for class omeis.providers.re.quantum.PolynomialMap
 
pop(GraphOpts) - Method in class ome.services.graphs.GraphEntry
Deprecated.
 
pop() - Method in class ome.services.graphs.GraphOpts
Deprecated.
 
pop(GraphOpts) - Method in class ome.services.graphs.GraphStep
Deprecated.
 
pop() - Method in class ome.services.pixeldata.PersistentEventLogLoader
 
pop(List<IObject>) - Method in class ome.services.SearchBean
Wrapper method which should be called on all results for the user.
pop(Object) - Method in class ome.util.ContextFilter
 
pop(String[]) - Static method in class prefs
Creates a new subarray from the argument, effectively popping off the first element.
popRoi - Variable in class ome.services.blitz.impl.MetadataStoreI
 
populateMinMax(double[][][]) - Method in class ome.formats.OMEROMetadataStore
Synchronize the minimum and maximum intensity values with those specified by the client and save them in the DB.
populateMinMax() - Method in class ome.formats.OMEROMetadataStoreClient
Sends all the minimums and maximums for all images processed so far to the server.
populateMinMax_async(AMD_MetadataStore_populateMinMax, double[][][], Current) - Method in class ome.services.blitz.impl.MetadataStoreI
 
PopulateRoiJob - Class in ome.services.roi
Start-up task which guarantees that lib/python/populateroi.py is added as a script to the server.
PopulateRoiJob(Roles, String, Executor) - Constructor for class ome.services.roi.PopulateRoiJob
 
PopulateRoiJob(Roles, String, Executor, File) - Constructor for class ome.services.roi.PopulateRoiJob
 
PopulateRoiJob(Roles, Principal, Executor, File) - Constructor for class ome.services.roi.PopulateRoiJob
 
port - Variable in class loci.ome.io.OMECredentials
 
port - Variable in class ome.formats.importer.ImportConfig
 
positionX - Variable in class ome.model.acquisition.StageLabel
 
POSITIONX - Static variable in class ome.model.acquisition.StageLabel
 
positionX - Variable in class ome.model.core.PlaneInfo
 
POSITIONX - Static variable in class ome.model.core.PlaneInfo
 
positionY - Variable in class ome.model.acquisition.StageLabel
 
POSITIONY - Static variable in class ome.model.acquisition.StageLabel
 
positionY - Variable in class ome.model.core.PlaneInfo
 
POSITIONY - Static variable in class ome.model.core.PlaneInfo
 
positionZ - Variable in class ome.model.acquisition.StageLabel
 
POSITIONZ - Static variable in class ome.model.acquisition.StageLabel
 
positionZ - Variable in class ome.model.core.PlaneInfo
 
POSITIONZ - Static variable in class ome.model.core.PlaneInfo
 
postClose(Current) - Method in class ome.services.blitz.impl.AbstractCloseableAmdServant
Should not throw any exceptions which should be detected by clients since it is called in a finally block after the client thread has been released.
postClose(Current) - Method in class ome.services.blitz.impl.AbstractPyramidServant
 
postClose(Current) - Method in class ome.services.blitz.impl.ExporterI
 
postClose(Current) - Method in class ome.services.blitz.impl.JobHandleI
 
postClose(Current) - Method in class ome.services.blitz.impl.MetadataStoreI
 
postClose(Current) - Method in class ome.services.blitz.impl.RawFileStoreI
 
postClose(Current) - Method in class ome.services.blitz.impl.SearchI
 
postClose(Current) - Method in class ome.services.blitz.impl.SharedResourcesI
 
postClose(Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
 
postClose(Current) - Method in class ome.services.blitz.repo.ManagedImportProcessI
 
postClose(Current) - Method in class ome.services.blitz.repo.RepoRawFileStoreI
 
postFlush(Iterator) - Method in class ome.security.basic.OmeroInterceptor
 
PostgresqlDialect - Class in ome.util
select i from Image i where i.id in (:ids) becomes select i from Image i where i.id in (select id from temp_ids());
PostgresqlDialect() - Constructor for class ome.util.PostgresqlDialect
 
PostgresSqlAction - Class in ome.util.actions
 
PostgresSqlAction(SimpleJdbcOperations) - Constructor for class ome.util.actions.PostgresSqlAction
 
postProcess() - Method in class ome.formats.OMEROMetadataStoreClient
Post processes the internal structure of the client side MetadataStore.
postProcess() - Method in class ome.io.bioformats.OmeroPixelsPyramidWriter
Performs re-compression post processing on the pixel pyramid.
postProcess(IObject) - Method in interface ome.security.ACLVoter
Gives the ACLVoter instance a chance to act on the IObject after the transaction but before finishing the AOP stack.
postProcess(IObject) - Method in class ome.security.basic.BasicACLVoter
 
postProcess(IObject) - Method in class ome.security.CompositeACLVoter
 
postProcess(IObject) - Method in class ome.security.sharing.SharingACLVoter
 
postProcess(List<GraphStep>) - Method in class ome.services.export.ExporterStepFactory
Deprecated.
 
postProcess(List<GraphStep>) - Method in class ome.services.graphs.AbstractStepFactory
Deprecated.
 
postProcess(ListableBeanFactory) - Method in class ome.services.graphs.BaseGraphSpec
Deprecated.
 
postProcess(ListableBeanFactory) - Method in class ome.services.graphs.GraphEntry
Deprecated.
Load the spec which has the same name as this entry, but do not load the spec if the name matches GraphEntry.name.
postProcess(ListableBeanFactory) - Method in interface ome.services.graphs.GraphSpec
Deprecated.
Gives all specs a chance to reference subspecs.
postProcess(List<GraphStep>) - Method in interface ome.services.graphs.GraphStepFactory
Deprecated.
Gives the GraphStepFactory a chance to add pre or post-steps for validation and similar activities.
postProcess_async(AMD_MetadataStore_postProcess, Current) - Method in class ome.services.blitz.impl.MetadataStoreI
Called after some number of Passes the #savedPixels to a background processor for further work.
postProcessAfterInitialization(Object, String) - Method in class ome.services.blitz.util.ApiConsistencyCheck
 
postProcessAfterInitialization(Object, String) - Method in class ome.services.graphs.GraphSpecPostProcessor
Deprecated.
 
postProcessBeanFactory(ConfigurableListableBeanFactory) - Method in class ome.system.PreferenceContext
 
postProcessBeforeInitialization(Object, String) - Method in class ome.services.blitz.util.ApiConsistencyCheck
No-op
postProcessBeforeInitialization(Object, String) - Method in class ome.services.graphs.GraphSpecPostProcessor
Deprecated.
 
postProcessOptions() - Method in class ome.services.graphs.AbstractHierarchyGraphSpec
Deprecated.
If any options exist, this method will be called to finalize any of the processing done by AbstractHierarchyGraphSpec.handleOptions(int, String[]).
postProcessOptions() - Method in class ome.services.graphs.AnnotationGraphSpec
Deprecated.
 
postProcessOptions() - Method in class ome.services.graphs.LightSourceGraphSpec
Deprecated.
 
posX - Variable in class ome.model.screen.WellSample
 
POSX - Static variable in class ome.model.screen.WellSample
 
posY - Variable in class ome.model.screen.WellSample
 
POSY - Static variable in class ome.model.screen.WellSample
 
Pow(long, int) - Static method in class ome.model.units.Conversion
Static helper for creating Conversion.Pow instances.
power - Variable in class ome.model.acquisition.LightSource
 
POWER - Static variable in class ome.model.acquisition.LightSource
 
Power - Class in ome.model.units
class storing both a Power and a unit for that Power (e.g. m, in, ly, etc.) encapsulated in a UnitsPower instance.
Power() - Constructor for class ome.model.units.Power
Deprecated.
Power(double, String) - Constructor for class ome.model.units.Power
 
Power(double, UnitsPower) - Constructor for class ome.model.units.Power
 
Power(double, Unit<Power>) - Constructor for class ome.model.units.Power
 
Power(Power) - Constructor for class ome.model.units.Power
 
PowerI - Class in omero.model
Blitz wrapper around the Power class.
PowerI() - Constructor for class omero.model.PowerI
 
PowerI(double, UnitsPower) - Constructor for class omero.model.PowerI
 
PowerI(double, Unit<Power>) - Constructor for class omero.model.PowerI
 
PowerI(Power, Unit<Power>) - Constructor for class omero.model.PowerI
Copy constructor that converts the given Power based on the given ome-xml enum
PowerI(double, UnitsPower) - Constructor for class omero.model.PowerI
Copy constructor that converts the given Power based on the given ome.model enum
PowerI(Power, String) - Constructor for class omero.model.PowerI
Copy constructor that converts the given Power based on the given enum string.
PowerI(Power, UnitsPower) - Constructor for class omero.model.PowerI
Copy constructor that converts between units if possible.
PowerI(Power) - Constructor for class omero.model.PowerI
Convert a Bio-Formats Length to an OMERO Length.
preClose(Current) - Method in class ome.services.blitz.impl.AbstractCloseableAmdServant
 
preClose(Current) - Method in class ome.services.blitz.impl.AbstractPyramidServant
 
preClose(Current) - Method in class ome.services.blitz.impl.ExporterI
 
preClose(Current) - Method in class ome.services.blitz.impl.JobHandleI
 
preClose(Current) - Method in class ome.services.blitz.impl.MetadataStoreI
 
preClose(Current) - Method in class ome.services.blitz.impl.RawFileStoreI
 
preClose(Current) - Method in class ome.services.blitz.impl.SearchI
 
preClose(Current) - Method in class ome.services.blitz.impl.SharedResourcesI
 
preClose(Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
 
preClose(Current) - Method in class ome.services.blitz.repo.ManagedImportProcessI
 
preClose(Current) - Method in class ome.services.blitz.repo.RepoRawFileStoreI
 
predicates - Variable in class ome.services.graphs.GraphPolicy
The predicates that have been registered with GraphPolicy.registerPredicate(GraphPolicyRulePredicate).
Preference - Class in ome.system
Definition of a server configuration variable ("preference") along with its mutability, visibility, aliases and other important information.
Preference() - Constructor for class ome.system.Preference
By default, configures this instance for PropertyPlaceholderConfigurer.SYSTEM_PROPERTIES_MODE_OVERRIDE as well as ignoring unfound resources.
Preference(String, boolean, Preference.Visibility, String[]) - Constructor for class ome.system.Preference
 
Preference.Visibility - Enum in ome.system
 
PreferenceContext - Class in ome.system
Central configuration for OMERO properties from (in order): Any injected Properties instances Java System.getProperties() Any configured property files As of OMERO 4.2, server configurations are not stored in Java's Preferences API but in an IceGrid xml file under etc/grid of the server installation.
PreferenceContext() - Constructor for class ome.system.PreferenceContext
By default, configures this instance for PropertyPlaceholderConfigurer.SYSTEM_PROPERTIES_MODE_OVERRIDE as well as ignoring unfound resources.
preFlush(Iterator) - Method in class ome.security.basic.OmeroInterceptor
 
prefs - Class in <Unnamed>
Command-line (and static) utility for working with the omero.prefs Preferences node in order to store Java properties-file like values on a user basis.
prefs() - Constructor for class prefs
 
prepare(Set<Long>) - Method in interface ome.api.RawPixelsStore
Prepares the stateful service with a cache of loaded Pixels objects.
prepare(Map<Integer, Image>) - Method in class ome.formats.OMEROMetadataStoreClient
Prepares the metadata store using existing metadata that has been pre-registered by OMERO.fs.
prepare(Set<Long>) - Method in class ome.services.RawPixelsBean
 
prepare_async(AMD_RawPixelsStore_prepare, List<Long>, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
prepare_async(AMD_RawPixelsStore_prepare, List<Long>, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
prepareLookups(String, String, Collection<Long>) - Method in class ome.services.query.HierarchyNavigator
Batch bulk database queries to prime the cache for HierarchyNavigator.doLookup(String, String, Long).
prepareLookups(T, Collection<E>) - Method in class ome.services.query.HierarchyNavigatorWrap
Batch bulk database queries to prime the cache for HierarchyNavigatorWrap.doLookup(Object, Object).
preparePassword(String) - Method in class ome.security.auth.PasswordUtil
 
preparePassword(Long, String, boolean) - Method in class ome.security.auth.PasswordUtil
 
preparePixelsStore(List<Long>) - Method in class ome.formats.OMEROMetadataStoreClient
Prepares the server side RawPixelsStore.
prepareReload() - Method in class ome.services.sessions.SessionManagerImpl
 
prepareSaltedPassword(Long, String) - Method in class ome.security.auth.PasswordUtil
 
prepareSession(long, long, long) - Method in class ome.util.actions.PostgresSqlAction
 
prepareSession(long, long, long) - Method in interface ome.util.SqlAction
Stores the current event context information in a temporary table so that triggers can make use of them.
prepareStatement() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
prepend(String, Object...) - Method in class ome.security.basic.EventListenersFactoryBean
adds the objects to the existing list identified by key.
Preprocessor - Class in omero.cmd.graphs
Deprecated.
will be removed in OMERO 5.2, so use the new graphs implementation
Preprocessor(List<Request>, Helper) - Constructor for class omero.cmd.graphs.Preprocessor
Deprecated.
 
Preprocessor(List<Request>, HierarchyNavigatorWrap<Preprocessor.TargetType, Preprocessor.GraphModifyTarget>) - Constructor for class omero.cmd.graphs.Preprocessor
Deprecated.
 
Preprocessor.GraphModifyTarget - Class in omero.cmd.graphs
Deprecated.
A tuple of target type and target ID.
Preprocessor.GraphModifyTarget(Preprocessor.TargetType, long) - Constructor for class omero.cmd.graphs.Preprocessor.GraphModifyTarget
Deprecated.
Construct a target type-ID tuple.
Preprocessor.TargetType - Enum in omero.cmd.graphs
Deprecated.
The types of target for which we care about adjusting graph operation requests.
Pressure - Class in ome.model.units
class storing both a Pressure and a unit for that Pressure (e.g. m, in, ly, etc.) encapsulated in a UnitsPressure instance.
Pressure() - Constructor for class ome.model.units.Pressure
Deprecated.
Pressure(double, String) - Constructor for class ome.model.units.Pressure
 
Pressure(double, UnitsPressure) - Constructor for class ome.model.units.Pressure
 
Pressure(double, Unit<Pressure>) - Constructor for class ome.model.units.Pressure
 
Pressure(Pressure) - Constructor for class ome.model.units.Pressure
 
PressureI - Class in omero.model
Blitz wrapper around the Pressure class.
PressureI() - Constructor for class omero.model.PressureI
 
PressureI(double, UnitsPressure) - Constructor for class omero.model.PressureI
 
PressureI(double, Unit<Pressure>) - Constructor for class omero.model.PressureI
 
PressureI(Pressure, Unit<Pressure>) - Constructor for class omero.model.PressureI
Copy constructor that converts the given Pressure based on the given ome-xml enum
PressureI(double, UnitsPressure) - Constructor for class omero.model.PressureI
Copy constructor that converts the given Pressure based on the given ome.model enum
PressureI(Pressure, String) - Constructor for class omero.model.PressureI
Copy constructor that converts the given Pressure based on the given enum string.
PressureI(Pressure, UnitsPressure) - Constructor for class omero.model.PressureI
Copy constructor that converts between units if possible.
PressureI(Pressure) - Constructor for class omero.model.PressureI
Convert a Bio-Formats Length to an OMERO Length.
previewImageDelete(long, boolean) - Method in interface ome.api.IDelete
Returns all entities which would be deleted by a call to IDelete.deleteImage(long, boolean).
previewImageDelete(long, boolean) - Method in class ome.services.delete.DeleteBean
This uses DeleteBean.IMAGE_QUERY to load all the subordinate metadata of the Image which will be deleted.
previousContext(int) - Method in class ome.util.ContextFilter
 
previousPatch - Variable in class ome.model.meta.DBPatch
 
PREVIOUSPATCH - Static variable in class ome.model.meta.DBPatch
 
previousVersion - Variable in class ome.model.meta.DBPatch
 
PREVIOUSVERSION - Static variable in class ome.model.meta.DBPatch
 
primaryColorEnabled - Variable in class omeis.providers.re.Optimizations
The channel bindings are only "primary" colors.
Primitive - Interface in ome.model.internal
marker interface for all non-filterable types.
PRIMITIVE - Static variable in class omero.util.IceMapper
 
PRIMITIVE_FILTERABLE_COLLECTION_MAP - Static variable in class omero.util.IceMapper
 
PRIMITIVE_MAP - Static variable in class omero.util.IceMapper
 
principal - Variable in class ome.services.blitz.fire.Ring
 
principal() - Method in class ome.services.blitz.fire.Ring
 
principal() - Method in interface ome.services.blitz.redirect.Redirector.Context
Principal instance which can be used for internal calls the Executor.
principal - Variable in class ome.services.blitz.repo.RepositoryDaoImpl
 
principal - Variable in class ome.services.sessions.SessionManager.CreationRequest
 
principal - Variable in class ome.services.util.ExecutionThread
 
principal() - Method in class ome.services.util.Executor.Impl
 
principal() - Method in interface ome.services.util.Executor
Returns a Principal representing your current session or null, if none is active.
Principal - Class in ome.system
implementation of Principal.
Principal(String) - Constructor for class ome.system.Principal
Creates a Principal with null group and event type.
Principal(String, String, String) - Constructor for class ome.system.Principal
 
principal - Variable in class ome.system.SessionInitializer
Principal given by the user
principal - Variable in class omero.cmd.SessionI
 
principalHolder - Variable in class ome.security.basic.BasicSecurityWiring
 
PrincipalHolder - Interface in ome.security.basic
Stack of active Principal instances.
principalHolder - Variable in class ome.services.sessions.SessionManagerImpl
 
principalHolder - Variable in class ome.services.util.Executor.Impl
 
print() - Method in class ome.formats.importer.ImportCandidates
Prints the "standard" representation of the groups, which is parsed by other software layers.
print(String[]) - Static method in class prefs
Prints the arg array and returns an empty array (for exit purposes)
printDebug(String[]) - Static method in class prefs
Delegates to prefs.printErr(String[]) iff prefs.DEBUG is true.
printErr(String[]) - Static method in class prefs
Prints the arg array and returns the input array (for exit purposes)
printLine() - Method in class ome.formats.importer.transfers.AbstractExecFileTransfer
 
printLine() - Method in class ome.formats.importer.transfers.AbstractFileTransfer
 
printThrowable(Throwable) - Method in class ome.util.SqlAction.Impl
 
PRIVATE - Static variable in class ome.model.internal.Permissions
an immutable Permissions instance with permissions only for the object owner..
process(IObjectContainerStore) - Method in class ome.formats.model.ChannelProcessor
Processes the OMERO client side metadata store.
process(IObjectContainerStore) - Method in class ome.formats.model.InstrumentProcessor
Processes the OMERO client side metadata store.
process(IObjectContainerStore) - Method in interface ome.formats.model.ModelProcessor
Processes the an IObjectContainerStore.
process(IObjectContainerStore) - Method in class ome.formats.model.PixelsProcessor
Processes the OMERO client side metadata store.
process(IObjectContainerStore) - Method in class ome.formats.model.PlaneInfoProcessor
Processes the OMERO client side metadata store.
process(IObjectContainerStore) - Method in class ome.formats.model.ReferenceProcessor
 
process(IObjectContainerStore) - Method in class ome.formats.model.ShapeProcessor
Processes the OMERO client side metadata store.
process(IObjectContainerStore) - Method in class ome.formats.model.TargetProcessor
Processes the OMERO client side metadata store.
process(IObjectContainerStore) - Method in class ome.formats.model.WellProcessor
Processes the OMERO client side metadata store.
process(Long, ServiceFactory, Session) - Method in class ome.services.pixeldata.PixelDataHandler
Here we assume that our log loader will only return us the proper types, since we are using the specific type defined in this package.
Process - Interface in ome.services.procs
 
process(long) - Method in interface ome.services.procs.Processor
 
process(long) - Method in class ome.services.procs.ProcessorSkeleton
 
process(Job) - Method in class ome.services.procs.ProcessorSkeleton
 
process() - Method in class omero.cmd.graphs.Preprocessor
Deprecated.
Preprocess the list of requests.
process - Variable in class omero.grid.ProcessCallbackI
Proxy passed to this instance on creation.
ProcessCallback - Interface in ome.services.procs
 
ProcessCallbackI - Class in omero.grid
 
ProcessCallbackI(client, ProcessPrx) - Constructor for class omero.grid.ProcessCallbackI
 
ProcessCallbackI(client, ProcessPrx, boolean) - Constructor for class omero.grid.ProcessCallbackI
 
ProcessCallbackI(ObjectAdapter, String, ProcessPrx) - Constructor for class omero.grid.ProcessCallbackI
 
ProcessCallbackI(ObjectAdapter, String, ProcessPrx, boolean) - Constructor for class omero.grid.ProcessCallbackI
 
ProcessCallbackI.Action - Enum in omero.grid
 
processCancelled(Process) - Method in class ome.services.JobBean
 
processCancelled(Process) - Method in interface ome.services.procs.ProcessCallback
 
processCancelled(boolean, Current) - Method in class omero.grid.ProcessCallbackI
 
ProcessContainer - Class in ome.services.blitz.repo
Helper class for holding the individual ManagedImportProcessI instances created by ManagedRepositoryI.
ProcessContainer() - Constructor for class ome.services.blitz.repo.ProcessContainer
 
ProcessContainer.Process - Interface in ome.services.blitz.repo
 
processFinished(Process) - Method in class ome.services.JobBean
 
processFinished(Process) - Method in interface ome.services.procs.ProcessCallback
 
processFinished(int, Current) - Method in class omero.grid.ProcessCallbackI
 
processInstances(String, Collection<Long>) - Method in interface ome.services.graphs.GraphTraversal.Processor
Process the given instances.
processKilled(boolean, Current) - Method in class omero.grid.ProcessCallbackI
 
ProcessManager - Class in ome.services.procs
 
ProcessManager(SessionManager, SecuritySystem, Executor, Processor...) - Constructor for class ome.services.procs.ProcessManager
main constructor which takes a non-null array of Processor instances as its only argument.
ProcessManager.Work - Class in ome.services.procs
Task performed by the ProcessManager on each invocation of ExecutionThread.run().
ProcessManager.Work(SecuritySystem, Processor...) - Constructor for class ome.services.procs.ProcessManager.Work
 
processor() - Method in interface ome.services.procs.Process
 
Processor - Interface in ome.services.procs
 
processor() - Method in class ome.services.procs.ProcessSkeleton
 
ProcessorCallbackI - Class in ome.services.blitz.impl
Callback used to lookup active processors via IceStorm.
ProcessorCallbackI(ServiceFactoryI) - Constructor for class ome.services.blitz.impl.ProcessorCallbackI
Simplified constructor used to see if any usermode processor is active for either the current group or the current user.
ProcessorCallbackI(ServiceFactoryI, ResultHolder<ProcessorPrx>, Job) - Constructor for class ome.services.blitz.impl.ProcessorCallbackI
Primary constructor.
processors - Variable in class ome.services.procs.ProcessManager.Work
processors available for processing.
ProcessorSkeleton - Class in ome.services.procs
 
ProcessorSkeleton() - Constructor for class ome.services.procs.ProcessorSkeleton
 
ProcessSkeleton - Class in ome.services.procs
 
ProcessSkeleton(Processor) - Constructor for class ome.services.procs.ProcessSkeleton
 
processTargets() - Method in class ome.services.graphs.GraphTraversal
Prepare to process the targeted model objects.
procMap - Variable in class ome.services.procs.ProcessManager.Work
Map of all active processes.
Project - Class in ome.model.containers
These filter definitions are used by the security system to eliminate non-readable objects from queries.
Project() - Constructor for class ome.model.containers.Project
 
Project(Long) - Constructor for class ome.model.containers.Project
 
Project(Long, boolean) - Constructor for class ome.model.containers.Project
Main constructor.
Project(String) - Constructor for class ome.model.containers.Project
 
Project.Details - Class in ome.model.containers
 
Project.Details() - Constructor for class ome.model.containers.Project.Details
 
Project.Details(Object[]) - Constructor for class ome.model.containers.Project.Details
 
PROJECT_LINKS - Static variable in class pojos.DatasetData
Identifies the Dataset#PROJECTLINKS field.
ProjectAnnotationLink - Class in ome.model.annotations
These filter definitions are used by the security system to eliminate non-readable objects from queries.
ProjectAnnotationLink() - Constructor for class ome.model.annotations.ProjectAnnotationLink
 
ProjectAnnotationLink(Long) - Constructor for class ome.model.annotations.ProjectAnnotationLink
 
ProjectAnnotationLink(Long, boolean) - Constructor for class ome.model.annotations.ProjectAnnotationLink
Main constructor.
ProjectAnnotationLink(IObject, IObject) - Constructor for class ome.model.annotations.ProjectAnnotationLink
 
ProjectAnnotationLink.Details - Class in ome.model.annotations
 
ProjectAnnotationLink.Details() - Constructor for class ome.model.annotations.ProjectAnnotationLink.Details
 
ProjectAnnotationLink.Details(Object[]) - Constructor for class ome.model.annotations.ProjectAnnotationLink.Details
 
ProjectData - Class in pojos
The data that makes up an OME Project along with links to its contained Datasets and the Experimenter that owns this Project.
ProjectData() - Constructor for class pojos.ProjectData
Creates a new instance.
ProjectData(Project) - Constructor for class pojos.ProjectData
Creates a new instance.
ProjectDatasetLink - Class in ome.model.containers
These filter definitions are used by the security system to eliminate non-readable objects from queries.
ProjectDatasetLink() - Constructor for class ome.model.containers.ProjectDatasetLink
 
ProjectDatasetLink(Long) - Constructor for class ome.model.containers.ProjectDatasetLink
 
ProjectDatasetLink(Long, boolean) - Constructor for class ome.model.containers.ProjectDatasetLink
Main constructor.
ProjectDatasetLink(IObject, IObject) - Constructor for class ome.model.containers.ProjectDatasetLink
 
ProjectDatasetLink.Details - Class in ome.model.containers
 
ProjectDatasetLink.Details() - Constructor for class ome.model.containers.ProjectDatasetLink.Details
 
ProjectDatasetLink.Details(Object[]) - Constructor for class ome.model.containers.ProjectDatasetLink.Details
 
projection(String, Parameters) - Method in interface ome.api.IQuery
Return a list of Java Object instances (not IObject instances).
projection(String, Parameters) - Method in class ome.logic.QueryImpl
 
projection_async(AMD_IQuery_projection, String, Parameters, Current) - Method in class ome.services.blitz.impl.QueryI
 
ProjectionBean - Class in ome.services.projection
Implements projection functionality for Pixels sets as declared in IProjection.
ProjectionBean() - Constructor for class ome.services.projection.ProjectionBean
 
ProjectionI - Class in ome.services.blitz.impl
Implementation of the IProjection service.
ProjectionI(ServiceInterface, BlitzExecutor) - Constructor for class ome.services.blitz.impl.ProjectionI
 
projectLinks - Variable in class ome.model.containers.Dataset
 
PROJECTLINKS - Static variable in class ome.model.containers.Dataset
 
PROJECTLINKSCOUNTPEROWNER - Static variable in class ome.model.containers.Dataset
 
projectPixels(long, PixelsType, int, int, int, List<Integer>, int, int, int, String) - Method in interface ome.api.IProjection
Performs a projection through selected optical sections and optical sections for a given set of time points of a Pixels set.
projectPixels(long, PixelsType, int, int, int, List<Integer>, int, int, int, String) - Method in class ome.services.projection.ProjectionBean
 
projectPixels_async(AMD_IProjection_projectPixels, long, PixelsType, ProjectionType, int, int, List<Integer>, int, int, int, String, Current) - Method in class ome.services.blitz.impl.ProjectionI
 
projectStack(long, PixelsType, int, int, int, int, int, int) - Method in interface ome.api.IProjection
Performs a projection through the optical sections of a particular wavelength at a given time point of a Pixels set.
projectStack(long, PixelsType, int, int, int, int, int, int) - Method in class ome.services.projection.ProjectionBean
 
projectStack_async(AMD_IProjection_projectStack, long, PixelsType, ProjectionType, int, int, int, int, int, Current) - Method in class ome.services.blitz.impl.ProjectionI
 
ProjectWithImageNameBridge - Class in ome.services.fulltext.bridges
Example custom FieldBridge implementation which parses all Image names from a Project and inserts them into the index for that Project.
ProjectWithImageNameBridge() - Constructor for class ome.services.fulltext.bridges.ProjectWithImageNameBridge
 
prompt(ImportConfig.Value, String, boolean) - Method in class ome.formats.importer.ImportConfig
Build prompt
propagateHiddenValues(IObject, IObject) - Method in class ome.security.basic.MergeEventListener
 
ProportionalTimeEstimatorImpl - Class in ome.formats.importer.util
Class implementing the TimeEstimator interface.
ProportionalTimeEstimatorImpl(long) - Constructor for class ome.formats.importer.util.ProportionalTimeEstimatorImpl
Creates a new object of this class with a defined internal buffer size.
protocolDescription - Variable in class ome.model.screen.Screen
 
PROTOCOLDESCRIPTION - Static variable in class ome.model.screen.Screen
 
protocolIdentifier - Variable in class ome.model.screen.Screen
 
PROTOCOLIDENTIFIER - Static variable in class ome.model.screen.Screen
 
proxy() - Method in class ome.model.acquisition.Arc
 
proxy() - Method in class ome.model.acquisition.Detector
 
proxy() - Method in class ome.model.acquisition.DetectorSettings
 
proxy() - Method in class ome.model.acquisition.Dichroic
 
proxy() - Method in class ome.model.acquisition.Filament
 
proxy() - Method in class ome.model.acquisition.Filter
 
proxy() - Method in class ome.model.acquisition.FilterSet
 
proxy() - Method in class ome.model.acquisition.FilterSetEmissionFilterLink
 
proxy() - Method in class ome.model.acquisition.FilterSetExcitationFilterLink
 
proxy() - Method in class ome.model.acquisition.GenericExcitationSource
 
proxy() - Method in class ome.model.acquisition.ImagingEnvironment
 
proxy() - Method in class ome.model.acquisition.Instrument
 
proxy() - Method in class ome.model.acquisition.Laser
 
proxy() - Method in class ome.model.acquisition.LightEmittingDiode
 
proxy() - Method in class ome.model.acquisition.LightPath
 
proxy() - Method in class ome.model.acquisition.LightPathEmissionFilterLink
 
proxy() - Method in class ome.model.acquisition.LightPathExcitationFilterLink
 
proxy() - Method in class ome.model.acquisition.LightSettings
 
proxy() - Method in class ome.model.acquisition.Microscope
 
proxy() - Method in class ome.model.acquisition.Objective
 
proxy() - Method in class ome.model.acquisition.ObjectiveSettings
 
proxy() - Method in class ome.model.acquisition.OTF
 
proxy() - Method in class ome.model.acquisition.StageLabel
 
proxy() - Method in class ome.model.acquisition.TransmittanceRange
 
proxy() - Method in class ome.model.annotations.AnnotationAnnotationLink
 
proxy() - Method in class ome.model.annotations.BooleanAnnotation
 
proxy() - Method in class ome.model.annotations.ChannelAnnotationLink
 
proxy() - Method in class ome.model.annotations.CommentAnnotation
 
proxy() - Method in class ome.model.annotations.DatasetAnnotationLink
 
proxy() - Method in class ome.model.annotations.DetectorAnnotationLink
 
proxy() - Method in class ome.model.annotations.DichroicAnnotationLink
 
proxy() - Method in class ome.model.annotations.DoubleAnnotation
 
proxy() - Method in class ome.model.annotations.ExperimenterAnnotationLink
 
proxy() - Method in class ome.model.annotations.ExperimenterGroupAnnotationLink
 
proxy() - Method in class ome.model.annotations.FileAnnotation
 
proxy() - Method in class ome.model.annotations.FilesetAnnotationLink
 
proxy() - Method in class ome.model.annotations.FilterAnnotationLink
 
proxy() - Method in class ome.model.annotations.ImageAnnotationLink
 
proxy() - Method in class ome.model.annotations.InstrumentAnnotationLink
 
proxy() - Method in class ome.model.annotations.LightPathAnnotationLink
 
proxy() - Method in class ome.model.annotations.LightSourceAnnotationLink
 
proxy() - Method in class ome.model.annotations.ListAnnotation
 
proxy() - Method in class ome.model.annotations.LongAnnotation
 
proxy() - Method in class ome.model.annotations.MapAnnotation
 
proxy() - Method in class ome.model.annotations.NamespaceAnnotationLink
 
proxy() - Method in class ome.model.annotations.NodeAnnotationLink
 
proxy() - Method in class ome.model.annotations.ObjectiveAnnotationLink
 
proxy() - Method in class ome.model.annotations.OriginalFileAnnotationLink
 
proxy() - Method in class ome.model.annotations.PlaneInfoAnnotationLink
 
proxy() - Method in class ome.model.annotations.PlateAcquisitionAnnotationLink
 
proxy() - Method in class ome.model.annotations.PlateAnnotationLink
 
proxy() - Method in class ome.model.annotations.ProjectAnnotationLink
 
proxy() - Method in class ome.model.annotations.ReagentAnnotationLink
 
proxy() - Method in class ome.model.annotations.RoiAnnotationLink
 
proxy() - Method in class ome.model.annotations.ScreenAnnotationLink
 
proxy() - Method in class ome.model.annotations.SessionAnnotationLink
 
proxy() - Method in class ome.model.annotations.ShapeAnnotationLink
 
proxy() - Method in class ome.model.annotations.TagAnnotation
 
proxy() - Method in class ome.model.annotations.TermAnnotation
 
proxy() - Method in class ome.model.annotations.TimestampAnnotation
 
proxy() - Method in class ome.model.annotations.WellAnnotationLink
 
proxy() - Method in class ome.model.annotations.XmlAnnotation
 
proxy() - Method in class ome.model.containers.Dataset
 
proxy() - Method in class ome.model.containers.DatasetImageLink
 
proxy() - Method in class ome.model.containers.Project
 
proxy() - Method in class ome.model.containers.ProjectDatasetLink
 
proxy() - Method in class ome.model.core.Channel
 
proxy() - Method in class ome.model.core.Image
 
proxy() - Method in class ome.model.core.LogicalChannel
 
proxy() - Method in class ome.model.core.OriginalFile
 
proxy() - Method in class ome.model.core.Pixels
 
proxy() - Method in class ome.model.core.PixelsOriginalFileMap
 
proxy() - Method in class ome.model.core.PlaneInfo
 
proxy() - Method in class ome.model.display.ChannelBinding
 
proxy() - Method in class ome.model.display.ContrastStretchingContext
 
proxy() - Method in class ome.model.display.PlaneSlicingContext
 
proxy() - Method in class ome.model.display.QuantumDef
 
proxy() - Method in class ome.model.display.RenderingDef
 
proxy() - Method in class ome.model.display.ReverseIntensityContext
 
proxy() - Method in class ome.model.display.Thumbnail
 
proxy() - Method in class ome.model.enums.AcquisitionMode
 
proxy() - Method in class ome.model.enums.ArcType
 
proxy() - Method in class ome.model.enums.Binning
 
proxy() - Method in class ome.model.enums.ChecksumAlgorithm
 
proxy() - Method in class ome.model.enums.ContrastMethod
 
proxy() - Method in class ome.model.enums.Correction
 
proxy() - Method in class ome.model.enums.DetectorType
 
proxy() - Method in class ome.model.enums.DimensionOrder
 
proxy() - Method in class ome.model.enums.EventType
 
proxy() - Method in class ome.model.enums.ExperimentType
 
proxy() - Method in class ome.model.enums.Family
 
proxy() - Method in class ome.model.enums.FilamentType
 
proxy() - Method in class ome.model.enums.FilterType
 
proxy() - Method in class ome.model.enums.Format
 
proxy() - Method in class ome.model.enums.Illumination
 
proxy() - Method in class ome.model.enums.Immersion
 
proxy() - Method in class ome.model.enums.LaserMedium
 
proxy() - Method in class ome.model.enums.LaserType
 
proxy() - Method in class ome.model.enums.Medium
 
proxy() - Method in class ome.model.enums.MicrobeamManipulationType
 
proxy() - Method in class ome.model.enums.MicroscopeType
 
proxy() - Method in class ome.model.enums.PhotometricInterpretation
 
proxy() - Method in class ome.model.enums.PixelsType
 
proxy() - Method in class ome.model.enums.Pulse
 
proxy() - Method in class ome.model.enums.RenderingModel
 
proxy() - Method in class ome.model.experiment.Experiment
 
proxy() - Method in class ome.model.experiment.MicrobeamManipulation
 
proxy() - Method in class ome.model.fs.Fileset
 
proxy() - Method in class ome.model.fs.FilesetEntry
 
proxy() - Method in class ome.model.fs.FilesetJobLink
 
proxy() - Method in class ome.model.internal.Link
 
proxy() - Method in class ome.model.jobs.ImportJob
 
proxy() - Method in class ome.model.jobs.IndexingJob
 
proxy() - Method in class ome.model.jobs.IntegrityCheckJob
 
proxy() - Method in class ome.model.jobs.JobOriginalFileLink
 
proxy() - Method in class ome.model.jobs.JobStatus
 
proxy() - Method in class ome.model.jobs.MetadataImportJob
 
proxy() - Method in class ome.model.jobs.ParseJob
 
proxy() - Method in class ome.model.jobs.PixelDataJob
 
proxy() - Method in class ome.model.jobs.ScriptJob
 
proxy() - Method in class ome.model.jobs.ThumbnailGenerationJob
 
proxy() - Method in class ome.model.jobs.UploadJob
 
proxy() - Method in class ome.model.meta.DBPatch
 
proxy() - Method in class ome.model.meta.Event
 
proxy() - Method in class ome.model.meta.EventLog
 
proxy() - Method in class ome.model.meta.Experimenter
 
proxy() - Method in class ome.model.meta.ExperimenterGroup
 
proxy() - Method in class ome.model.meta.ExternalInfo
 
proxy() - Method in class ome.model.meta.GroupExperimenterMap
 
proxy() - Method in class ome.model.meta.Namespace
 
proxy() - Method in class ome.model.meta.Node
 
proxy() - Method in class ome.model.meta.Session
 
proxy() - Method in class ome.model.meta.Share
 
proxy() - Method in class ome.model.meta.ShareMember
 
proxy() - Method in class ome.model.roi.Ellipse
 
proxy() - Method in class ome.model.roi.Label
 
proxy() - Method in class ome.model.roi.Line
 
proxy() - Method in class ome.model.roi.Mask
 
proxy() - Method in class ome.model.roi.Path
 
proxy() - Method in class ome.model.roi.Point
 
proxy() - Method in class ome.model.roi.Polygon
 
proxy() - Method in class ome.model.roi.Polyline
 
proxy() - Method in class ome.model.roi.Rect
 
proxy() - Method in class ome.model.roi.Roi
 
proxy() - Method in class ome.model.screen.Plate
 
proxy() - Method in class ome.model.screen.PlateAcquisition
 
proxy() - Method in class ome.model.screen.Reagent
 
proxy() - Method in class ome.model.screen.Screen
 
proxy() - Method in class ome.model.screen.ScreenPlateLink
 
proxy() - Method in class ome.model.screen.Well
 
proxy() - Method in class ome.model.screen.WellReagentLink
 
proxy() - Method in class ome.model.screen.WellSample
 
proxy() - Method in class ome.model.stats.StatsInfo
 
proxy() - Method in class ome.services.blitz.impl.ServiceFactoryI
 
ProxyCleanupFilter - Class in ome.tools.hibernate
removes all proxies from a return graph to prevent ClassCastExceptions and Session Closed exceptions.
ProxyCleanupFilter() - Constructor for class ome.tools.hibernate.ProxyCleanupFilter
Passes null to ProxyCleanupFilter#ProxyCleanupFilter(CurrentDetails) such that all restricted objects will be unloaded.
ProxyCleanupFilter(ACLVoter, CurrentDetails) - Constructor for class ome.tools.hibernate.ProxyCleanupFilter
Constructor take a CurrentDetails object in order to check the security restrictions on certain objects.
ProxyCleanupFilter.Interceptor - Class in ome.tools.hibernate
wraps a filter for each invocation
ProxyCleanupFilter.Interceptor(ACLVoter, SessionHandler, CurrentDetails) - Constructor for class ome.tools.hibernate.ProxyCleanupFilter.Interceptor
 
proxyForSession(Redirector.Context, String) - Method in class ome.services.blitz.redirect.AbstractRedirector
 
proxyNames - Variable in class ome.services.util.Executor.Impl
 
ProxySafeFilter - Class in ome.tools.hibernate
extension to ContextFilter to check for uninitialized Hibernate proxies before stepping into an entity or collection.
ProxySafeFilter() - Constructor for class ome.tools.hibernate.ProxySafeFilter
 
PsqlStrings - Class in ome.util.actions
 
pt(double, double) - Method in class ome.services.roi.GeomTool
 
PUBLIC - Static variable in class ome.model.internal.Permissions
an immutable Permissions instance with all Rights granted.
PublicRepositoryI - Class in ome.services.blitz.repo
An implementation of the PublicRepository interface.
PublicRepositoryI(RepositoryDao, ChecksumProviderFactory, String, String) - Constructor for class ome.services.blitz.repo.PublicRepositoryI
 
PublicRepositoryI.AMD_submit - Class in ome.services.blitz.repo
 
PublicRepositoryI.AMD_submit() - Constructor for class ome.services.blitz.repo.PublicRepositoryI.AMD_submit
 
publish(EventLogMessage) - Method in class ome.services.chgrp.ChgrpStep
Deprecated.
 
publisher - Variable in class ome.services.fulltext.BridgeHelper
 
publisher - Variable in class ome.services.sessions.stats.CounterFactory
 
publisherOrNull(String) - Method in class ome.services.blitz.fire.TopicManager.Impl
 
publishEvent(ApplicationEvent) - Method in class ome.system.OmeroContext
 
publishMessage(InternalMessage) - Method in class ome.services.blitz.repo.PublicRepositoryI
 
publishMessage(InternalMessage) - Method in class ome.system.OmeroContext
Convenience method around OmeroContext.publishEvent(org.springframework.context.ApplicationEvent) which catches all MessageException and unwraps the contained Throwable instance and rethrows.
pulse - Variable in class ome.model.acquisition.Laser
 
PULSE - Static variable in class ome.model.acquisition.Laser
 
Pulse - Class in ome.model.enums
 
Pulse() - Constructor for class ome.model.enums.Pulse
 
Pulse(Long) - Constructor for class ome.model.enums.Pulse
 
Pulse(Long, boolean) - Constructor for class ome.model.enums.Pulse
Main constructor.
Pulse(String) - Constructor for class ome.model.enums.Pulse
 
Pulse.Details - Class in ome.model.enums
 
Pulse.Details() - Constructor for class ome.model.enums.Pulse.Details
 
Pulse.Details(Object[]) - Constructor for class ome.model.enums.Pulse.Details
 
pump - Variable in class ome.model.acquisition.Laser
 
PUMP - Static variable in class ome.model.acquisition.Laser
 
purgeNode(String) - Method in class ome.services.blitz.fire.Ring
 
push(GraphOpts, EventContext) - Method in class ome.services.graphs.GraphEntry
Deprecated.
 
push(GraphOpts.Op, boolean, EventContext) - Method in class ome.services.graphs.GraphOpts
Deprecated.
Adds the given operation to the current list if the user has permissions to do so.
push(GraphOpts) - Method in class ome.services.graphs.GraphStep
Deprecated.
 
push(Object) - Method in class ome.util.ContextFilter
 
put(File, Dataset) - Method in class ome.formats.importer.ImportFixture
 
put(String, String) - Method in class ome.security.auth.AttributeSet
 
put(String, Object[]) - Method in class ome.security.basic.EventListenersFactoryBean
replaces the key with the provided objects or an empty list if none provided
put(Callback) - Method in class ome.services.throttling.Queue
 
put(Identity, Object) - Method in class omero.util.ServantHolder
 
putAll(Map<File, Dataset>) - Method in class ome.formats.importer.ImportFixture
 
putAt(String, Object) - Method in class ome.model.acquisition.Arc
 
putAt(String, Object) - Method in class ome.model.acquisition.Detector
 
putAt(String, Object) - Method in class ome.model.acquisition.DetectorSettings
 
putAt(String, Object) - Method in class ome.model.acquisition.Dichroic
 
putAt(String, Object) - Method in class ome.model.acquisition.Filament
 
putAt(String, Object) - Method in class ome.model.acquisition.Filter
 
putAt(String, Object) - Method in class ome.model.acquisition.FilterSet
 
putAt(String, Object) - Method in class ome.model.acquisition.FilterSetEmissionFilterLink
 
putAt(String, Object) - Method in class ome.model.acquisition.FilterSetExcitationFilterLink
 
putAt(String, Object) - Method in class ome.model.acquisition.GenericExcitationSource
 
putAt(String, Object) - Method in class ome.model.acquisition.ImagingEnvironment
 
putAt(String, Object) - Method in class ome.model.acquisition.Instrument
 
putAt(String, Object) - Method in class ome.model.acquisition.Laser
 
putAt(String, Object) - Method in class ome.model.acquisition.LightEmittingDiode
 
putAt(String, Object) - Method in class ome.model.acquisition.LightPath
 
putAt(String, Object) - Method in class ome.model.acquisition.LightPathEmissionFilterLink
 
putAt(String, Object) - Method in class ome.model.acquisition.LightPathExcitationFilterLink
 
putAt(String, Object) - Method in class ome.model.acquisition.LightSettings
 
putAt(String, Object) - Method in class ome.model.acquisition.LightSource
 
putAt(String, Object) - Method in class ome.model.acquisition.Microscope
 
putAt(String, Object) - Method in class ome.model.acquisition.Objective
 
putAt(String, Object) - Method in class ome.model.acquisition.ObjectiveSettings
 
putAt(String, Object) - Method in class ome.model.acquisition.OTF
 
putAt(String, Object) - Method in class ome.model.acquisition.StageLabel
 
putAt(String, Object) - Method in class ome.model.acquisition.TransmittanceRange
 
putAt(String, Object) - Method in class ome.model.annotations.Annotation
 
putAt(String, Object) - Method in class ome.model.annotations.AnnotationAnnotationLink
 
putAt(String, Object) - Method in class ome.model.annotations.BasicAnnotation
 
putAt(String, Object) - Method in class ome.model.annotations.BooleanAnnotation
 
putAt(String, Object) - Method in class ome.model.annotations.ChannelAnnotationLink
 
putAt(String, Object) - Method in class ome.model.annotations.CommentAnnotation
 
putAt(String, Object) - Method in class ome.model.annotations.DatasetAnnotationLink
 
putAt(String, Object) - Method in class ome.model.annotations.DetectorAnnotationLink
 
putAt(String, Object) - Method in class ome.model.annotations.DichroicAnnotationLink
 
putAt(String, Object) - Method in class ome.model.annotations.DoubleAnnotation
 
putAt(String, Object) - Method in class ome.model.annotations.ExperimenterAnnotationLink
 
putAt(String, Object) - Method in class ome.model.annotations.ExperimenterGroupAnnotationLink
 
putAt(String, Object) - Method in class ome.model.annotations.FileAnnotation
 
putAt(String, Object) - Method in class ome.model.annotations.FilesetAnnotationLink
 
putAt(String, Object) - Method in class ome.model.annotations.FilterAnnotationLink
 
putAt(String, Object) - Method in class ome.model.annotations.ImageAnnotationLink
 
putAt(String, Object) - Method in class ome.model.annotations.InstrumentAnnotationLink
 
putAt(String, Object) - Method in class ome.model.annotations.LightPathAnnotationLink
 
putAt(String, Object) - Method in class ome.model.annotations.LightSourceAnnotationLink
 
putAt(String, Object) - Method in class ome.model.annotations.ListAnnotation
 
putAt(String, Object) - Method in class ome.model.annotations.LongAnnotation
 
putAt(String, Object) - Method in class ome.model.annotations.MapAnnotation
 
putAt(String, Object) - Method in class ome.model.annotations.NamespaceAnnotationLink
 
putAt(String, Object) - Method in class ome.model.annotations.NodeAnnotationLink
 
putAt(String, Object) - Method in class ome.model.annotations.NumericAnnotation
 
putAt(String, Object) - Method in class ome.model.annotations.ObjectiveAnnotationLink
 
putAt(String, Object) - Method in class ome.model.annotations.OriginalFileAnnotationLink
 
putAt(String, Object) - Method in class ome.model.annotations.PlaneInfoAnnotationLink
 
putAt(String, Object) - Method in class ome.model.annotations.PlateAcquisitionAnnotationLink
 
putAt(String, Object) - Method in class ome.model.annotations.PlateAnnotationLink
 
putAt(String, Object) - Method in class ome.model.annotations.ProjectAnnotationLink
 
putAt(String, Object) - Method in class ome.model.annotations.ReagentAnnotationLink
 
putAt(String, Object) - Method in class ome.model.annotations.RoiAnnotationLink
 
putAt(String, Object) - Method in class ome.model.annotations.ScreenAnnotationLink
 
putAt(String, Object) - Method in class ome.model.annotations.SessionAnnotationLink
 
putAt(String, Object) - Method in class ome.model.annotations.ShapeAnnotationLink
 
putAt(String, Object) - Method in class ome.model.annotations.TagAnnotation
 
putAt(String, Object) - Method in class ome.model.annotations.TermAnnotation
 
putAt(String, Object) - Method in class ome.model.annotations.TextAnnotation
 
putAt(String, Object) - Method in class ome.model.annotations.TimestampAnnotation
 
putAt(String, Object) - Method in class ome.model.annotations.TypeAnnotation
 
putAt(String, Object) - Method in class ome.model.annotations.WellAnnotationLink
 
putAt(String, Object) - Method in class ome.model.annotations.XmlAnnotation
 
putAt(String, Object) - Method in class ome.model.containers.Dataset
 
putAt(String, Object) - Method in class ome.model.containers.DatasetImageLink
 
putAt(String, Object) - Method in class ome.model.containers.Project
 
putAt(String, Object) - Method in class ome.model.containers.ProjectDatasetLink
 
putAt(String, Object) - Method in class ome.model.core.Channel
 
putAt(String, Object) - Method in class ome.model.core.Image
 
putAt(String, Object) - Method in class ome.model.core.LogicalChannel
 
putAt(String, Object) - Method in class ome.model.core.OriginalFile
 
putAt(String, Object) - Method in class ome.model.core.Pixels
 
putAt(String, Object) - Method in class ome.model.core.PixelsOriginalFileMap
 
putAt(String, Object) - Method in class ome.model.core.PlaneInfo
 
putAt(String, Object) - Method in class ome.model.display.ChannelBinding
 
putAt(String, Object) - Method in class ome.model.display.CodomainMapContext
 
putAt(String, Object) - Method in class ome.model.display.ContrastStretchingContext
 
putAt(String, Object) - Method in class ome.model.display.PlaneSlicingContext
 
putAt(String, Object) - Method in class ome.model.display.QuantumDef
 
putAt(String, Object) - Method in class ome.model.display.RenderingDef
 
putAt(String, Object) - Method in class ome.model.display.ReverseIntensityContext
 
putAt(String, Object) - Method in class ome.model.display.Thumbnail
 
putAt(String, Object) - Method in class ome.model.enums.AcquisitionMode
 
putAt(String, Object) - Method in class ome.model.enums.ArcType
 
putAt(String, Object) - Method in class ome.model.enums.Binning
 
putAt(String, Object) - Method in class ome.model.enums.ChecksumAlgorithm
 
putAt(String, Object) - Method in class ome.model.enums.ContrastMethod
 
putAt(String, Object) - Method in class ome.model.enums.Correction
 
putAt(String, Object) - Method in class ome.model.enums.DetectorType
 
putAt(String, Object) - Method in class ome.model.enums.DimensionOrder
 
putAt(String, Object) - Method in class ome.model.enums.EventType
 
putAt(String, Object) - Method in class ome.model.enums.ExperimentType
 
putAt(String, Object) - Method in class ome.model.enums.Family
 
putAt(String, Object) - Method in class ome.model.enums.FilamentType
 
putAt(String, Object) - Method in class ome.model.enums.FilterType
 
putAt(String, Object) - Method in class ome.model.enums.Format
 
putAt(String, Object) - Method in class ome.model.enums.Illumination
 
putAt(String, Object) - Method in class ome.model.enums.Immersion
 
putAt(String, Object) - Method in class ome.model.enums.LaserMedium
 
putAt(String, Object) - Method in class ome.model.enums.LaserType
 
putAt(String, Object) - Method in class ome.model.enums.Medium
 
putAt(String, Object) - Method in class ome.model.enums.MicrobeamManipulationType
 
putAt(String, Object) - Method in class ome.model.enums.MicroscopeType
 
putAt(String, Object) - Method in class ome.model.enums.PhotometricInterpretation
 
putAt(String, Object) - Method in class ome.model.enums.PixelsType
 
putAt(String, Object) - Method in class ome.model.enums.Pulse
 
putAt(String, Object) - Method in class ome.model.enums.RenderingModel
 
putAt(String, Object) - Method in class ome.model.experiment.Experiment
 
putAt(String, Object) - Method in class ome.model.experiment.MicrobeamManipulation
 
putAt(String, Object) - Method in class ome.model.fs.Fileset
 
putAt(String, Object) - Method in class ome.model.fs.FilesetEntry
 
putAt(String, Object) - Method in class ome.model.fs.FilesetJobLink
 
putAt(String, Object) - Method in class ome.model.internal.Details
 
putAt(String, Object) - Method in class ome.model.internal.Link
 
putAt(String, Object) - Method in interface ome.model.IObject
stores a value in this instance.
putAt(String, Object) - Method in class ome.model.jobs.ImportJob
 
putAt(String, Object) - Method in class ome.model.jobs.IndexingJob
 
putAt(String, Object) - Method in class ome.model.jobs.IntegrityCheckJob
 
putAt(String, Object) - Method in class ome.model.jobs.Job
 
putAt(String, Object) - Method in class ome.model.jobs.JobOriginalFileLink
 
putAt(String, Object) - Method in class ome.model.jobs.JobStatus
 
putAt(String, Object) - Method in class ome.model.jobs.MetadataImportJob
 
putAt(String, Object) - Method in class ome.model.jobs.ParseJob
 
putAt(String, Object) - Method in class ome.model.jobs.PixelDataJob
 
putAt(String, Object) - Method in class ome.model.jobs.ScriptJob
 
putAt(String, Object) - Method in class ome.model.jobs.ThumbnailGenerationJob
 
putAt(String, Object) - Method in class ome.model.jobs.UploadJob
 
putAt(String, Object) - Method in class ome.model.meta.DBPatch
 
putAt(String, Object) - Method in class ome.model.meta.Event
 
putAt(String, Object) - Method in class ome.model.meta.EventLog
 
putAt(String, Object) - Method in class ome.model.meta.Experimenter
 
putAt(String, Object) - Method in class ome.model.meta.ExperimenterGroup
 
putAt(String, Object) - Method in class ome.model.meta.ExternalInfo
 
putAt(String, Object) - Method in class ome.model.meta.GroupExperimenterMap
 
putAt(String, Object) - Method in class ome.model.meta.Namespace
 
putAt(String, Object) - Method in class ome.model.meta.Node
 
putAt(String, Object) - Method in class ome.model.meta.Session
 
putAt(String, Object) - Method in class ome.model.meta.Share
 
putAt(String, Object) - Method in class ome.model.meta.ShareMember
 
putAt(String, Object) - Method in class ome.model.roi.Ellipse
 
putAt(String, Object) - Method in class ome.model.roi.Label
 
putAt(String, Object) - Method in class ome.model.roi.Line
 
putAt(String, Object) - Method in class ome.model.roi.Mask
 
putAt(String, Object) - Method in class ome.model.roi.Path
 
putAt(String, Object) - Method in class ome.model.roi.Point
 
putAt(String, Object) - Method in class ome.model.roi.Polygon
 
putAt(String, Object) - Method in class ome.model.roi.Polyline
 
putAt(String, Object) - Method in class ome.model.roi.Rect
 
putAt(String, Object) - Method in class ome.model.roi.Roi
 
putAt(String, Object) - Method in class ome.model.roi.Shape
 
putAt(String, Object) - Method in class ome.model.screen.Plate
 
putAt(String, Object) - Method in class ome.model.screen.PlateAcquisition
 
putAt(String, Object) - Method in class ome.model.screen.Reagent
 
putAt(String, Object) - Method in class ome.model.screen.Screen
 
putAt(String, Object) - Method in class ome.model.screen.ScreenPlateLink
 
putAt(String, Object) - Method in class ome.model.screen.Well
 
putAt(String, Object) - Method in class ome.model.screen.WellReagentLink
 
putAt(String, Object) - Method in class ome.model.screen.WellSample
 
putAt(String, Object) - Method in class ome.model.stats.StatsInfo
 
putBytes(byte[]) - Method in class ome.util.checksum.AbstractChecksumProvider
 
putBytes(byte[], int, int) - Method in class ome.util.checksum.AbstractChecksumProvider
 
putBytes(ByteBuffer) - Method in class ome.util.checksum.AbstractChecksumProvider
 
putBytes(byte[]) - Method in interface ome.util.checksum.ChecksumProvider
Updates the internal checksum value with data from a byte array.
putBytes(byte[], int, int) - Method in interface ome.util.checksum.ChecksumProvider
Updates the internal checksum value with data from a chunk of a byte array.
putBytes(ByteBuffer) - Method in interface ome.util.checksum.ChecksumProvider
Updates the internal checksum value with data from a byte buffer.
putBytes(byte[]) - Method in class ome.util.checksum.FileSizeChecksumProviderImpl
 
putBytes(byte[], int, int) - Method in class ome.util.checksum.FileSizeChecksumProviderImpl
 
putBytes(ByteBuffer) - Method in class ome.util.checksum.FileSizeChecksumProviderImpl
 
putFile(String) - Method in class ome.util.checksum.AbstractChecksumProvider
 
putFile(String) - Method in interface ome.util.checksum.ChecksumProvider
Updates the internal checksum value with data from a file identified by a path.
putFile(String) - Method in class ome.util.checksum.FileSizeChecksumProviderImpl
 
putSession(String, SessionContext) - Method in class ome.services.sessions.state.SessionCache
Puts a session blindly into the context.
putStatus(MethodInvocation, SessionStatus) - Method in class ome.tools.hibernate.SessionHandler
 
PYR_LOCK_EXT - Static variable in class ome.io.bioformats.BfPyramidPixelBuffer
 
PYRAMID_SUFFIX - Static variable in class ome.io.nio.PixelsService
Suffix for an the image pyramid of a given pixels set.

Q

qaBaseURL - Variable in class ome.formats.importer.ImportConfig
 
qDef - Variable in class omeis.providers.re.quantum.QuantumStrategy
Reference to a quantumDef object.
quantization - Variable in class ome.model.display.RenderingDef
 
QUANTIZATION - Static variable in class ome.model.display.RenderingDef
 
Quantization_32_bit - Class in omeis.providers.re.quantum
Quantization process.
Quantization_32_bit(QuantumDef, Pixels) - Constructor for class omeis.providers.re.quantum.Quantization_32_bit
Creates a new strategy.
Quantization_8_16_bit - Class in omeis.providers.re.quantum
Quantization process.
Quantization_8_16_bit(QuantumDef, Pixels) - Constructor for class omeis.providers.re.quantum.Quantization_8_16_bit
Creates a new strategy.
Quantization_float - Class in omeis.providers.re.quantum
Quantization process.
Quantization_float(QuantumDef, Pixels) - Constructor for class omeis.providers.re.quantum.Quantization_float
Creates a new strategy.
QuantizationException - Exception in omeis.providers.re.quantum
This exception is thrown during the quantization process if something goes wrong.
QuantizationException() - Constructor for exception omeis.providers.re.quantum.QuantizationException
Creates a new exception.
QuantizationException(String) - Constructor for exception omeis.providers.re.quantum.QuantizationException
Constructs a new exception with the specified detail message.
QuantizationException(Throwable) - Constructor for exception omeis.providers.re.quantum.QuantizationException
Constructs a new exception with the specified cause.
QuantizationException(String, Throwable) - Constructor for exception omeis.providers.re.quantum.QuantizationException
Constructs a new exception with the specified detail message and cause.
quantize(double) - Method in class omeis.providers.re.quantum.BinaryMaskQuantizer
Implemented as specified in QuantumStrategy.
quantize(double) - Method in class omeis.providers.re.quantum.Quantization_32_bit
Implemented as specified in QuantumStrategy.
quantize(double) - Method in class omeis.providers.re.quantum.Quantization_8_16_bit
Implemented as specified in QuantumStrategy.
quantize(double) - Method in class omeis.providers.re.quantum.Quantization_float
Implemented as specified in QuantumStrategy.
quantize(double) - Method in class omeis.providers.re.quantum.QuantumStrategy
Maps a value from [windowStart, windowEnd] to a value in the codomain interval.
QuantumDef - Class in ome.model.display
These filter definitions are used by the security system to eliminate non-readable objects from queries.
QuantumDef() - Constructor for class ome.model.display.QuantumDef
 
QuantumDef(Long) - Constructor for class ome.model.display.QuantumDef
 
QuantumDef(Long, boolean) - Constructor for class ome.model.display.QuantumDef
Main constructor.
QuantumDef(Integer, Integer, Integer) - Constructor for class ome.model.display.QuantumDef
 
QuantumDef.Details - Class in ome.model.display
 
QuantumDef.Details() - Constructor for class ome.model.display.QuantumDef.Details
 
QuantumDef.Details(Object[]) - Constructor for class ome.model.display.QuantumDef.Details
 
QuantumFactory - Class in omeis.providers.re.quantum
Factory to create objects to carry out quantization for a given context.
QuantumFactory(List<Family>) - Constructor for class omeis.providers.re.quantum.QuantumFactory
Default constructor.
QuantumMap - Interface in omeis.providers.re.quantum
Provides methods to map value.
QuantumStrategy - Class in omeis.providers.re.quantum
Subclasses Work on explicit pixel types.
QuantumStrategy(QuantumDef, Pixels) - Constructor for class omeis.providers.re.quantum.QuantumStrategy
Creates a new instance.
query() - Method in class ome.services.eventlogs.AllEntitiesPseudoLogLoader
 
query() - Method in class ome.services.eventlogs.AllEventsLogLoader
 
query - Variable in class ome.services.eventlogs.EventLogLoader
Query string to be kept in sync with EventLogLoader.excludes.
query() - Method in class ome.services.eventlogs.EventLogLoader
 
query() - Method in class ome.services.eventlogs.EventLogQueue
 
query() - Method in class ome.services.eventlogs.PersistentEventLogLoader
 
query() - Method in class ome.services.pixeldata.PersistentEventLogLoader
Uses data from the PersistentEventLogLoader.dataPerUser "queue" to allow new requests to be processed even if one user adds a large number of PIXELDATA events.
Query<T> - Class in ome.services.query
base Query type to facilitate the creation of ORM queries.
Query(Definitions, Parameters) - Constructor for class ome.services.query.Query
main constructor used by subclasses.
query(Session) - Method in class ome.tools.hibernate.QueryBuilder
 
query - Variable in class omero.cmd.admin.UpdateSessionTimeoutRequestI
 
queryBackupIds(Session, int, GraphEntry, QueryBuilder) - Method in class ome.services.graphs.AbstractHierarchyGraphSpec
Deprecated.
 
queryBackupIds(Session, int, GraphEntry, QueryBuilder) - Method in class ome.services.graphs.BaseGraphSpec
Deprecated.
 
queryBackupIds(Session, int, GraphEntry, QueryBuilder) - Method in interface ome.services.graphs.GraphSpec
Deprecated.
If a given path is processed before its sub-path, this points to a one-to-one relationship.
QueryBuilder - Class in ome.tools.hibernate
Very thin wrapper around a StringBuilder to generate HQL queries.
QueryBuilder() - Constructor for class ome.tools.hibernate.QueryBuilder
 
QueryBuilder(boolean) - Constructor for class ome.tools.hibernate.QueryBuilder
Whether Session.createSQLQuery(String) should be used or not during QueryBuilder.__query(Session, boolean)
QueryBuilder(int) - Constructor for class ome.tools.hibernate.QueryBuilder
 
queryCacheHit(String, String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
queryCacheMiss(String, String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
queryCachePut(String, String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
QueryConstraints - Class in ome.services.delete
AdminAction which queries all datasets and annotations belonging to the given Image
QueryConstraints(LocalAdmin, LocalQuery, long, boolean) - Constructor for class ome.services.delete.QueryConstraints
 
QueryException - Exception in ome.services.query
something failed in looking up a query
QueryException(String) - Constructor for exception ome.services.query.QueryException
 
queryExecuted(String, int, long) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
queryFactory - Variable in class ome.logic.AbstractLevel1Service
 
queryFactory - Variable in class ome.logic.AbstractLevel2Service
 
QueryFactory - Class in ome.services.query
query locator which is configured by Spring.
QueryFactory(QuerySource...) - Constructor for class ome.services.query.QueryFactory
main constructor which takes a non-null array of query sources as its only argument.
QueryI - Class in ome.services.blitz.impl
Implementation of the IQuery service.
QueryI(IQuery, BlitzExecutor) - Constructor for class ome.services.blitz.impl.QueryI
 
QueryImpl - Class in ome.logic
Provides methods for directly querying object graphs.
QueryImpl() - Constructor for class ome.logic.QueryImpl
 
QueryNewUserGroupBean - Class in ome.security.auth
Handles the ":query:" specifier from etc/omero.properties.
QueryNewUserGroupBean(String) - Constructor for class ome.security.auth.QueryNewUserGroupBean
 
QueryParameter - Class in ome.parameters
arbitrary query parameter used by IQuery.
QueryParameter(String, Class, Object) - Constructor for class ome.parameters.QueryParameter
 
QueryParameterDef - Class in ome.services.query
definition of a slot into which a QueryParameter must fit.
QueryParameterDef(String, Class, boolean) - Constructor for class ome.services.query.QueryParameterDef
main constructor.
queryParameters() - Method in class ome.parameters.Parameters
copies all QueryParameters to an array.
queryService - Variable in class ome.services.eventlogs.EventLogLoader
 
QuerySource - Class in ome.services.query
contract for any source of queries.
QuerySource() - Constructor for class ome.services.query.QuerySource
 
queryString() - Method in class ome.tools.hibernate.QueryBuilder
Returns the current query as a String.
queryWithoutFilter(Session) - Method in class ome.tools.hibernate.QueryBuilder
 
Queue - Class in ome.services.throttling
Manages AMD-based method dispatches from blitz
Queue(OmeroContext) - Constructor for class ome.services.throttling.Queue
 
QUEUED - Static variable in interface ome.api.JobHandle
 

R

R_BAND - Static variable in class omeis.providers.re.RGBBuffer
Index of the red band in the image's data buffer.
random(int) - Method in class ome.services.roi.GeomTool
 
randomize(Random) - Method in class omero.model.SmartEllipseI
 
randomize(Random) - Method in class omero.model.SmartLineI
 
randomize(Random) - Method in class omero.model.SmartMaskI
 
randomize(Random) - Method in class omero.model.SmartPathI
 
randomize(Random) - Method in class omero.model.SmartPointI
 
randomize(Random) - Method in class omero.model.SmartPolygonI
 
randomize(Random) - Method in class omero.model.SmartPolylineI
 
randomize(Random) - Method in class omero.model.SmartRectI
 
randomize(Random) - Method in interface omero.model.SmartShape
Initializes this shape with completely random data.
randomize(Random) - Method in class omero.model.SmartTextI
 
rarray(RType...) - Static method in class omero.rtypes
 
rarray(Collection<RType>) - Static method in class omero.rtypes
 
Rat(long, long) - Static method in class ome.model.units.Conversion
Static helper for creating Conversion.Rat instances.
Rat(Conversion...) - Static method in class ome.model.units.Conversion
Static helper for creating Conversion.Rat instances.
RatingAnnotationData - Class in pojos
Annotation used to rate an object.
RatingAnnotationData() - Constructor for class pojos.RatingAnnotationData
Creates a new instance of value LEVEL_ZERO.
RatingAnnotationData(int) - Constructor for class pojos.RatingAnnotationData
Creates a new instance.
RatingAnnotationData(LongAnnotation) - Constructor for class pojos.RatingAnnotationData
Creates a new instance.
rawAccess(RawAccessRequest, Current) - Method in class ome.services.blitz.repo.AbstractRepositoryI
 
rawAccess() - Method in class ome.services.blitz.repo.RawAccessRequestI
 
RawAccessRequestI - Class in ome.services.blitz.repo
Command request for accessing a repository directly.
RawAccessRequestI(Registry) - Constructor for class ome.services.blitz.repo.RawAccessRequestI
 
RawFileBean - Class in ome.services
Raw file gateway which provides access to the OMERO file repository.
RawFileBean() - Constructor for class ome.services.RawFileBean
default constructor
RawFileBean(boolean) - Constructor for class ome.services.RawFileBean
overridden to allow Spring to set boolean
RawFileStore - Interface in ome.api
Raw file gateway which provides access to the OMERO file repository.
RawFileStoreI - Class in ome.services.blitz.impl
Implementation of the RawFileStore service.
RawFileStoreI(RawFileStore, BlitzExecutor) - Constructor for class ome.services.blitz.impl.RawFileStoreI
 
rawOption - Variable in class ome.services.graphs.AbstractHierarchyGraphSpec
Deprecated.
Original string contained in the options Map before parsing.
RawPixelsBean - Class in ome.services
Implementation of the RawPixelsStore stateful service.
RawPixelsBean() - Constructor for class ome.services.RawPixelsBean
default constructor
RawPixelsBean(boolean, String) - Constructor for class ome.services.RawPixelsBean
overridden to allow Spring to set boolean
RawPixelsStore - Interface in ome.api
Binary data provider.
RawPixelsStoreI - Class in ome.services.blitz.impl
Implementation of the RawPixelsStore service.
RawPixelsStoreI(RawPixelsStore, BlitzExecutor) - Constructor for class ome.services.blitz.impl.RawPixelsStoreI
 
rbool(boolean) - Static method in class omero.rtypes
 
rclass(String) - Static method in class omero.rtypes
 
RdfPrinter - Class in ome.util
walks an object graph producing RDF-like output.
RdfPrinter() - Constructor for class ome.util.RdfPrinter
 
rdouble(double) - Static method in class omero.rtypes
 
read(long, int) - Method in interface ome.api.RawFileStore
Delegates to FileBuffer
read(ByteBuffer) - Method in class ome.io.nio.FileBuffer
Delegates to FileChannel
read(ByteBuffer, long) - Method in class ome.io.nio.FileBuffer
Delegates to FileChannel
read(long, int) - Method in class ome.services.RawFileBean
 
read(String) - Method in class ome.services.scripts.ScriptRepoHelper
 
read_async(AMD_Exporter_read, long, int, Current) - Method in class ome.services.blitz.impl.ExporterI
 
read_async(AMD_RawFileStore_read, long, int, Current) - Method in class ome.services.blitz.impl.RawFileStoreI
 
read_async(AMD_RawFileStore_read, long, int, Current) - Method in class ome.services.blitz.repo.RepoRawFileStoreI
 
READ_ONLY - Static variable in class ome.model.internal.Permissions
an immutable Permissions instance with all Permissions.Right.WRITE rights turned off.
readBytes(int) - Method in class ome.services.sessions.stats.DelegatingStats
 
readBytes(int) - Method in class ome.services.sessions.stats.NullSessionStats
 
readBytes(int) - Method in interface ome.services.sessions.stats.SessionStats
 
readBytes(int) - Method in class ome.services.sessions.stats.SimpleSessionStats
 
reader - Variable in class ome.formats.importer.util.ErrorHandler.FILE_EXCEPTION
 
reader - Variable in class ome.formats.importer.util.ErrorHandler.INTERNAL_EXCEPTION
 
reader - Variable in class ome.io.bioformats.BfPixelBuffer
 
reader() - Method in class ome.io.bioformats.BfPixelBuffer
 
reader - Variable in class ome.io.bioformats.BfPyramidPixelBuffer
Bio-Formats implementation the delegate uses to read the backing TIFF.
readerClass - Static variable in class ome.services.util.DBEnumCheck
 
READERS_KEY - Static variable in class ome.formats.importer.ImportConfig
readersPath - Variable in class ome.formats.importer.ImportConfig
 
readOnly - Variable in class ome.security.basic.EventHandler
 
readOnly - Variable in class ome.services.sessions.SessionManagerImpl
 
READONLY_FLAG - Static variable in class pojos.ShapeData
Flag stating that the ROI is read only.
ReadOnlyByteArray - Class in ome.util.mem
A read-only slice of a given array.
ReadOnlyByteArray(byte[], int, int) - Constructor for class ome.util.mem.ReadOnlyByteArray
Creates a read-only slice of base.
ReadOnlyGroupSecurityViolation - Exception in ome.conditions
Extension of GroupSecurityViolation signalling that an admin or group owner has tried to make a modification in a private group OR that the member of a read-only group has tried to do the same.
ReadOnlyGroupSecurityViolation(String) - Constructor for exception ome.conditions.ReadOnlyGroupSecurityViolation
 
readOutRate - Variable in class ome.model.acquisition.DetectorSettings
 
READOUTRATE - Static variable in class ome.model.acquisition.DetectorSettings
 
Reagent - Class in ome.model.screen
These filter definitions are used by the security system to eliminate non-readable objects from queries.
Reagent() - Constructor for class ome.model.screen.Reagent
 
Reagent(Long) - Constructor for class ome.model.screen.Reagent
 
Reagent(Long, boolean) - Constructor for class ome.model.screen.Reagent
Main constructor.
Reagent(Screen) - Constructor for class ome.model.screen.Reagent
 
Reagent.Details - Class in ome.model.screen
 
Reagent.Details() - Constructor for class ome.model.screen.Reagent.Details
 
Reagent.Details(Object[]) - Constructor for class ome.model.screen.Reagent.Details
 
ReagentAnnotationLink - Class in ome.model.annotations
These filter definitions are used by the security system to eliminate non-readable objects from queries.
ReagentAnnotationLink() - Constructor for class ome.model.annotations.ReagentAnnotationLink
 
ReagentAnnotationLink(Long) - Constructor for class ome.model.annotations.ReagentAnnotationLink
 
ReagentAnnotationLink(Long, boolean) - Constructor for class ome.model.annotations.ReagentAnnotationLink
Main constructor.
ReagentAnnotationLink(IObject, IObject) - Constructor for class ome.model.annotations.ReagentAnnotationLink
 
ReagentAnnotationLink.Details - Class in ome.model.annotations
 
ReagentAnnotationLink.Details() - Constructor for class ome.model.annotations.ReagentAnnotationLink.Details
 
ReagentAnnotationLink.Details(Object[]) - Constructor for class ome.model.annotations.ReagentAnnotationLink.Details
 
reagentIdentifier - Variable in class ome.model.screen.Reagent
 
REAGENTIDENTIFIER - Static variable in class ome.model.screen.Reagent
 
reagentLinks - Variable in class ome.model.screen.Well
 
REAGENTLINKS - Static variable in class ome.model.screen.Well
 
REAGENTLINKSCOUNTPEROWNER - Static variable in class ome.model.screen.Well
 
reagents - Variable in class ome.model.screen.Screen
 
REAGENTS - Static variable in class ome.model.screen.Screen
 
reagentSetDescription - Variable in class ome.model.screen.Screen
 
REAGENTSETDESCRIPTION - Static variable in class ome.model.screen.Screen
 
reagentSetIdentifier - Variable in class ome.model.screen.Screen
 
REAGENTSETIDENTIFIER - Static variable in class ome.model.screen.Screen
 
reapSession(String) - Method in class ome.services.blitz.fire.SessionManagerI
Destroys all the ServiceFactoryI instances based on the given sessionId.
recompressSeries(TiffReader, int) - Method in class ome.io.bioformats.OmeroPixelsPyramidWriter
Re-compresses a source series, that is JPEG 2000 compressed, via its resolution level.
recreateCollection(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
Rect - Class in ome.model.roi
 
Rect() - Constructor for class ome.model.roi.Rect
 
Rect(Long) - Constructor for class ome.model.roi.Rect
 
Rect(Long, boolean) - Constructor for class ome.model.roi.Rect
Main constructor.
rect(double, double, double, double) - Method in class ome.services.roi.GeomTool
 
RectangleArea - Class in ome.util.math.geom2D
Represents a rectangle in the Euclidean space R2.
RectangleArea() - Constructor for class ome.util.math.geom2D.RectangleArea
Constructs a new RectangleAreaAdapter whose top-left corner is (0, 0) and whose width and height are both zero.
RectangleArea(int, int, int, int) - Constructor for class ome.util.math.geom2D.RectangleArea
Constructs a new RectangleAreaAdapter whose top-left corner is specified as (x, y) and whose width and height are specified by the arguments of the same name.
RectangleData - Class in pojos
Represents a rectangle in the Euclidean space R2.
RectangleData(Shape) - Constructor for class pojos.RectangleData
Creates a new instance.
RectangleData() - Constructor for class pojos.RectangleData
Creates a new instance with a default rectangle.
RectangleData(double, double, double, double) - Constructor for class pojos.RectangleData
Creates a new instance of the RectangleData.
red - Variable in class ome.model.core.Channel
 
RED - Static variable in class ome.model.core.Channel
 
red - Variable in class ome.model.display.ChannelBinding
 
RED - Static variable in class ome.model.display.ChannelBinding
 
red - Variable in class ome.model.screen.Well
 
RED - Static variable in class ome.model.screen.Well
 
RED_INDEX - Static variable in class ome.formats.model.ColorsFactory
Index of the red component of a color.
RED_INDEX - Static variable in class omeis.providers.re.ColorsFactory
Index of the red component of a color.
RED_TEXT - Static variable in class ome.formats.model.ChannelProcessor
Name of the red component when it is a graphics image.
Redirector - Interface in ome.services.blitz.redirect
Strategy interface for helping a Ring instance decide whether to redirect SessionPrx creation to another SessionManagerI instance.
Redirector.Context - Interface in ome.services.blitz.redirect
Interface implemented by Ring instances to allow passing in the context necessary for making strategy decisions.
ref - Variable in class ome.model.display.Thumbnail
 
REF - Static variable in class ome.model.display.Thumbnail
 
ReferenceProcessor - Class in ome.formats.model
Processes the references of an IObjectContainerStore and ensures that container references are consistent with the LSID stored in the IObjectContainer itself.
ReferenceProcessor() - Constructor for class ome.formats.model.ReferenceProcessor
 
reflectiveNewInstance(T) - Static method in class ome.util.ShallowCopy
 
refractiveIndex - Variable in class ome.model.acquisition.ObjectiveSettings
 
REFRACTIVEINDEX - Static variable in class ome.model.acquisition.ObjectiveSettings
 
refresh(T) - Method in interface ome.api.IQuery
refreshes an entire IObject graph, recursive loading all data for the managed instances in the graph from the database.
refresh(T) - Method in class ome.logic.QueryImpl
 
refresh(String, SessionContext) - Method in class ome.services.sessions.state.SessionCache
Used externally to refresh the SessionContext instance associated with the session uuid
refresh_async(AMD_IQuery_refresh, IObject, Current) - Method in class ome.services.blitz.impl.QueryI
 
refreshAll() - Method in class ome.system.OmeroContext
refreshes all the nested OmeroContexts within this instance.
refreshAllIfNecessary() - Method in class ome.system.OmeroContext
Calls #refreshAll() if {@link #isRunning()} throws an {@link IllegalStateException}.
refreshEventLogFromUpdatedAnnotations() - Method in class ome.util.SqlAction.Impl
 
refreshEventLogFromUpdatedAnnotations() - Method in interface ome.util.SqlAction
Convert the _updated_annotations table to REINDEX entries in the event log.
RegionDef - Class in omeis.providers.re.data
Identifies a rectangular region.
RegionDef() - Constructor for class omeis.providers.re.data.RegionDef
Creates a default instance.
RegionDef(int, int, int, int) - Constructor for class omeis.providers.re.data.RegionDef
Creates a rectangular region.
register(String, ObjectPrx, boolean) - Method in class ome.services.blitz.fire.TopicManager.Impl
 
register(String, ObjectPrx, boolean) - Method in interface ome.services.blitz.fire.TopicManager
Enforces no security constraints.
register(String, RString, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
Register an OriginalFile using its path
register(String, CheckedPath, String, Current) - Method in interface ome.services.blitz.repo.RepositoryDao
Register an OriginalFile object
register(String, CheckedPath, String, ServiceFactory, SqlAction) - Method in interface ome.services.blitz.repo.RepositoryDao
Like {@link #register(String, CheckedPath, String, Ice.Current) but does not create a new transaction.
register(String, CheckedPath, String, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
 
register(String, CheckedPath, String, ServiceFactory, SqlAction) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
Returned original file object is "live" within the Hibernate session.
register(Logger, Communicator, boolean) - Method in class omero.util.ObjectFactoryRegistry.ObjectFactory
 
registerAll(Ehcache, CacheEventListener...) - Method in class ome.services.sessions.state.CacheFactory
 
registerCallback(ProcessCallbackPrx, Current) - Method in class ome.services.blitz.impl.ScriptProcessI
 
registerCallback(RawFileStorePrx, int) - Method in class ome.services.blitz.repo.ManagedImportProcessI
 
registerCallback(ProcessCallback) - Method in interface ome.services.procs.Process
 
registerCallback(ProcessCallback) - Method in class ome.services.procs.ProcessSkeleton
 
registerPredicate(GraphPolicyRulePredicate) - Method in class ome.services.graphs.GraphPolicy
Use the given predicate in executing this graph policy.
registerPredicate(GraphPolicyRulePredicate) - Method in class omero.cmd.graphs.BaseGraphPolicyAdjuster
 
registerProxy(Current) - Method in class ome.services.blitz.repo.ManagedImportProcessI
Adds this instance to the current session so that clients can communicate with it.
registerServant(Identity, Object) - Method in class omero.cmd.SessionI
Registers the servant with the adapter (or throws an exception if one is already registered) as well as configures the servant in any post-Spring way necessary, based on the type of the servant.
RegisterServantMessage - Class in ome.services.blitz.util
InternalMessage raised when a servant should be registered for clean.
RegisterServantMessage(Object, Object, Current) - Constructor for class ome.services.blitz.util.RegisterServantMessage
 
RegisterServantMessage(Object, Object, String, Current) - Constructor for class ome.services.blitz.util.RegisterServantMessage
 
RegisterServiceCleanupMessage - Class in ome.services.messages
Published when some resource must be cleaned up after method execution.
RegisterServiceCleanupMessage(Object, Object) - Constructor for class ome.services.messages.RegisterServiceCleanupMessage
 
registerTrigger(String, Trigger) - Method in class ome.services.scheduler.SchedulerFactoryBean
Registers a JobDetailAwareTrigger.
Registry - Interface in ome.services.blitz.fire
Helper class which makes the RegistryPrx available within OmeroBlitz.
registry - Variable in class ome.services.blitz.fire.SessionManagerI
 
Registry.Impl - Class in ome.services.blitz.fire
 
Registry.Impl(Communicator) - Constructor for class ome.services.blitz.fire.Registry.Impl
 
reindex(T) - Method in class ome.services.fulltext.BridgeHelper
Publishes a ReindexMessage which will get processed asynchronously.
reindexAll(List<T>) - Method in class ome.services.fulltext.BridgeHelper
Publishes a ReindexMessage which will get processed asynchronously.
ReindexMessage<T extends IObject> - Class in ome.services.messages
Published when one or more IObject instances must be re-indexed.
ReindexMessage(Object, List<T>) - Constructor for class ome.services.messages.ReindexMessage
 
relatedTo - Variable in class ome.model.core.Pixels
 
RELATEDTO - Static variable in class ome.model.core.Pixels
 
relativeDN(String) - Method in class ome.security.auth.LdapConfig
Calculate the relative DN based on the current base.
release(String, int) - Method in class ome.services.graphs.GraphState
Deprecated.
 
release(String, int) - Method in interface ome.services.graphs.GraphStep.Callback
Deprecated.
 
release(GraphStep.Callback) - Method in class ome.services.graphs.GraphStep
Deprecated.
 
releaseDate - Static variable in class ome.formats.importer.Version
The data of the last release date.
releaseLock(String) - Method in class omero.util.ServantHolder
Releases the given lock if found, otherwise throws an InternalException
releaseSavepoint(String) - Method in class ome.util.actions.PostgresSqlAction
 
releaseSavepoint(String) - Method in interface ome.util.SqlAction
 
reload(String) - Method in interface ome.services.sessions.SessionManager
Similar to SessionManager.getEventContext(Principal) but uses the internal reload logic to get a fresh representation of the context.
reload(String) - Method in class ome.services.sessions.SessionManagerImpl
 
reload(SessionContext) - Method in class ome.services.sessions.SessionManagerImpl
Will be called in a synchronized block by SessionCache in order to allow for an update.
reload(String) - Method in class ome.services.sessions.state.SessionCache
Provides the reloading logic of the SessionCache for the SessionManagerImpl to use.
reload(SessionContext) - Method in interface ome.services.sessions.state.SessionCache.StaleCacheListener
Method called for every active session in the cache.
ReloadFilter - Class in ome.tools.hibernate
UpdateFilter subclass specialized for use with the Session.save(Object) (as opposed to Session.merge(Object)) method.
ReloadFilter(Session) - Constructor for class ome.tools.hibernate.ReloadFilter
 
ReloadingRefreshEventListener - Class in ome.tools.hibernate
responsible for responding to RefreshEvent. in particular in reloading the unloaded entities.
ReloadingRefreshEventListener() - Constructor for class ome.tools.hibernate.ReloadingRefreshEventListener
 
remove() - Method in interface ome.api.Search
Unsupported operation.
remove() - Method in class ome.services.eventlogs.EventBacklog
Removes and returns the next EventLog instance or null if none is present.
remove() - Method in class ome.services.eventlogs.EventLogLoader
 
remove() - Method in class ome.services.graphs.BaseGraphSpec.SubSpecIterator
Deprecated.
 
remove() - Method in class ome.services.SearchBean
 
remove(Serializable, SessionImplementor) - Method in class ome.util.CountCollectionPersister
 
remove() - Method in class ome.util.EmptyIterator
 
remove() - Method in class omeis.providers.re.codomain.CodomainChain
Removes all CodomainMapContexts except the identity and resets the interval.
remove(CodomainMapContext) - Method in class omeis.providers.re.codomain.CodomainChain
Removes a map context from the chain.
remove(Resources.Entry) - Method in class omero.util.Resources
 
remove(Identity) - Method in class omero.util.ServantHolder
 
remove_async(AMD_Search_remove, Current) - Method in class ome.services.blitz.impl.SearchI
 
remove_path(File) - Static method in class omero.util.TempFileManager
removeAllDisabled(String...) - Method in class ome.security.basic.CurrentDetails
 
removeAllListeners() - Method in class ome.services.messages.GlobalMulticaster
 
removeAnnotationAnnotationLink(AnnotationAnnotationLink) - Method in class ome.model.annotations.Annotation
removes a single element from this set and makes the inverse call on ome.model.annotations.AnnotationAnnotationLink
removeAnnotationAnnotationLink(AnnotationAnnotationLink, boolean) - Method in class ome.model.annotations.Annotation
removes the given AnnotationAnnotationLink from annotationLinks, allowing for recursion -- whether or not the removal will call unlinkAnnotation again if loaded.
removeAnnotationAnnotationLinkSet(Collection<AnnotationAnnotationLink>) - Method in class ome.model.annotations.Annotation
use like removeAnnotationAnnotationLink
removeApplicationListener(ApplicationListener) - Method in class ome.services.messages.GlobalMulticaster
 
removeApplicationListenerBean(String) - Method in class ome.services.messages.GlobalMulticaster
 
removeCallback(CmdCallbackPrx, Current) - Method in class omero.cmd.HandleI
 
removeChannel(Channel) - Method in class ome.model.core.LogicalChannel
removes a single element from this set and makes the inverse call on ome.model.core.Channel
removeChannel(Channel) - Method in class ome.model.core.Pixels
removes a single element from this set and makes the inverse call on ome.model.core.Channel
removeChannelAnnotationLink(ChannelAnnotationLink) - Method in class ome.model.core.Channel
removes a single element from this set and makes the inverse call on ome.model.annotations.ChannelAnnotationLink
removeChannelAnnotationLink(ChannelAnnotationLink, boolean) - Method in class ome.model.core.Channel
removes the given ChannelAnnotationLink from annotationLinks, allowing for recursion -- whether or not the removal will call unlinkChannel again if loaded.
removeChannelAnnotationLinkSet(Collection<ChannelAnnotationLink>) - Method in class ome.model.core.Channel
use like removeChannelAnnotationLink
removeChannelBinding(ChannelBinding) - Method in class ome.model.display.RenderingDef
removes a single element from this set and makes the inverse call on ome.model.display.ChannelBinding
removeChannelBindingSet(Collection<ChannelBinding>) - Method in class ome.model.display.RenderingDef
use like removeChannelBinding
removeChannelSet(Collection<Channel>) - Method in class ome.model.core.LogicalChannel
use like removeChannel
removeChannelSet(Collection<Channel>) - Method in class ome.model.core.Pixels
use like removeChannel
removeClientId(String) - Method in class omero.util.ServantHolder
 
removeCodomainMap(CodomainMapContext) - Method in class ome.services.RenderingBean
Implemented as specified by the RenderingEngine interface.
removeCodomainMap(CodomainMapContext) - Method in interface omeis.providers.re.RenderingEngine
Removes the specified context from the chain.
removeCodomainMap_async(AMD_RenderingEngine_removeCodomainMap, CodomainMapContext, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
removeCodomainMapContext(CodomainMapContext) - Method in class ome.model.display.RenderingDef
removes a single element from this set and makes the inverse call on ome.model.display.CodomainMapContext
removeCodomainMapContextSet(Collection<CodomainMapContext>) - Method in class ome.model.display.RenderingDef
use like removeCodomainMapContext
removeCollection(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
removeDatasetAnnotationLink(DatasetAnnotationLink) - Method in class ome.model.containers.Dataset
removes a single element from this set and makes the inverse call on ome.model.annotations.DatasetAnnotationLink
removeDatasetAnnotationLink(DatasetAnnotationLink, boolean) - Method in class ome.model.containers.Dataset
removes the given DatasetAnnotationLink from annotationLinks, allowing for recursion -- whether or not the removal will call unlinkDataset again if loaded.
removeDatasetAnnotationLinkSet(Collection<DatasetAnnotationLink>) - Method in class ome.model.containers.Dataset
use like removeDatasetAnnotationLink
removeDatasetImageLink(DatasetImageLink) - Method in class ome.model.containers.Dataset
removes a single element from this set and makes the inverse call on ome.model.containers.DatasetImageLink
removeDatasetImageLink(DatasetImageLink, boolean) - Method in class ome.model.containers.Dataset
removes the given DatasetImageLink from imageLinks, allowing for recursion -- whether or not the removal will call unlinkDataset again if loaded.
removeDatasetImageLink(DatasetImageLink) - Method in class ome.model.core.Image
removes a single element from this set and makes the inverse call on ome.model.containers.DatasetImageLink
removeDatasetImageLink(DatasetImageLink, boolean) - Method in class ome.model.core.Image
removes the given DatasetImageLink from datasetLinks, allowing for recursion -- whether or not the removal will call unlinkImage again if loaded.
removeDatasetImageLinkSet(Collection<DatasetImageLink>) - Method in class ome.model.containers.Dataset
use like removeDatasetImageLink
removeDatasetImageLinkSet(Collection<DatasetImageLink>) - Method in class ome.model.core.Image
use like removeDatasetImageLink
removeDetector(Detector) - Method in class ome.model.acquisition.Instrument
removes a single element from this set and makes the inverse call on ome.model.acquisition.Detector
removeDetectorAnnotationLink(DetectorAnnotationLink) - Method in class ome.model.acquisition.Detector
removes a single element from this set and makes the inverse call on ome.model.annotations.DetectorAnnotationLink
removeDetectorAnnotationLink(DetectorAnnotationLink, boolean) - Method in class ome.model.acquisition.Detector
removes the given DetectorAnnotationLink from annotationLinks, allowing for recursion -- whether or not the removal will call unlinkDetector again if loaded.
removeDetectorAnnotationLinkSet(Collection<DetectorAnnotationLink>) - Method in class ome.model.acquisition.Detector
use like removeDetectorAnnotationLink
removeDetectorSet(Collection<Detector>) - Method in class ome.model.acquisition.Instrument
use like removeDetector
removeDichroic(Dichroic) - Method in class ome.model.acquisition.Instrument
removes a single element from this set and makes the inverse call on ome.model.acquisition.Dichroic
removeDichroicAnnotationLink(DichroicAnnotationLink) - Method in class ome.model.acquisition.Dichroic
removes a single element from this set and makes the inverse call on ome.model.annotations.DichroicAnnotationLink
removeDichroicAnnotationLink(DichroicAnnotationLink, boolean) - Method in class ome.model.acquisition.Dichroic
removes the given DichroicAnnotationLink from annotationLinks, allowing for recursion -- whether or not the removal will call unlinkDichroic again if loaded.
removeDichroicAnnotationLinkSet(Collection<DichroicAnnotationLink>) - Method in class ome.model.acquisition.Dichroic
use like removeDichroicAnnotationLink
removeDichroicSet(Collection<Dichroic>) - Method in class ome.model.acquisition.Instrument
use like removeDichroic
removeDisabled(String) - Method in class ome.security.basic.CurrentDetails
 
RemovedSessionException - Exception in ome.conditions
Client attempted to access a Session which has either expired or been closed manually.
RemovedSessionException(String) - Constructor for exception ome.conditions.RemovedSessionException
 
removeEvent(Event) - Method in class ome.model.meta.Session
removes a single element from this set and makes the inverse call on ome.model.meta.Event
removeEventLog(EventLog) - Method in class ome.model.meta.Event
removes a single element from this set and makes the inverse call on ome.model.meta.EventLog
removeEventLogSet(Collection<EventLog>) - Method in class ome.model.meta.Event
use like removeEventLog
removeEventSet(Collection<Event>) - Method in class ome.model.meta.Session
use like removeEvent
removeExperimenterAnnotationLink(ExperimenterAnnotationLink) - Method in class ome.model.meta.Experimenter
removes a single element from this set and makes the inverse call on ome.model.annotations.ExperimenterAnnotationLink
removeExperimenterAnnotationLink(ExperimenterAnnotationLink, boolean) - Method in class ome.model.meta.Experimenter
removes the given ExperimenterAnnotationLink from annotationLinks, allowing for recursion -- whether or not the removal will call unlinkExperimenter again if loaded.
removeExperimenterAnnotationLinkSet(Collection<ExperimenterAnnotationLink>) - Method in class ome.model.meta.Experimenter
use like removeExperimenterAnnotationLink
removeExperimenterGroupAnnotationLink(ExperimenterGroupAnnotationLink) - Method in class ome.model.meta.ExperimenterGroup
removes a single element from this set and makes the inverse call on ome.model.annotations.ExperimenterGroupAnnotationLink
removeExperimenterGroupAnnotationLink(ExperimenterGroupAnnotationLink, boolean) - Method in class ome.model.meta.ExperimenterGroup
removes the given ExperimenterGroupAnnotationLink from annotationLinks, allowing for recursion -- whether or not the removal will call unlinkExperimenterGroup again if loaded.
removeExperimenterGroupAnnotationLinkSet(Collection<ExperimenterGroupAnnotationLink>) - Method in class ome.model.meta.ExperimenterGroup
use like removeExperimenterGroupAnnotationLink
removeFiles(List<Long>) - Method in class ome.io.nio.OriginalFilesService
Removes files from data repository based on a parameterized List of Long file ids
removeFilesetAnnotationLink(FilesetAnnotationLink) - Method in class ome.model.fs.Fileset
removes a single element from this set and makes the inverse call on ome.model.annotations.FilesetAnnotationLink
removeFilesetAnnotationLink(FilesetAnnotationLink, boolean) - Method in class ome.model.fs.Fileset
removes the given FilesetAnnotationLink from annotationLinks, allowing for recursion -- whether or not the removal will call unlinkFileset again if loaded.
removeFilesetAnnotationLinkSet(Collection<FilesetAnnotationLink>) - Method in class ome.model.fs.Fileset
use like removeFilesetAnnotationLink
removeFilesetEntry(FilesetEntry) - Method in class ome.model.core.OriginalFile
removes a single element from this set and makes the inverse call on ome.model.fs.FilesetEntry
removeFilesetEntry(FilesetEntry) - Method in class ome.model.fs.Fileset
removes a single element from this set and makes the inverse call on ome.model.fs.FilesetEntry
removeFilesetEntrySet(Collection<FilesetEntry>) - Method in class ome.model.core.OriginalFile
use like removeFilesetEntry
removeFilesetEntrySet(Collection<FilesetEntry>) - Method in class ome.model.fs.Fileset
use like removeFilesetEntry
removeFilesetJobLink(FilesetJobLink) - Method in class ome.model.fs.Fileset
removes a single element from this set and makes the inverse call on ome.model.fs.FilesetJobLink
removeFilesetJobLink(FilesetJobLink, boolean) - Method in class ome.model.fs.Fileset
removes the given FilesetJobLink from jobLinks, allowing for recursion -- whether or not the removal will call unlinkFileset again if loaded.
removeFilesetJobLinkSet(Collection<FilesetJobLink>) - Method in class ome.model.fs.Fileset
use like removeFilesetJobLink
removeFilter(Filter) - Method in class ome.model.acquisition.Instrument
removes a single element from this set and makes the inverse call on ome.model.acquisition.Filter
removeFilterAnnotationLink(FilterAnnotationLink) - Method in class ome.model.acquisition.Filter
removes a single element from this set and makes the inverse call on ome.model.annotations.FilterAnnotationLink
removeFilterAnnotationLink(FilterAnnotationLink, boolean) - Method in class ome.model.acquisition.Filter
removes the given FilterAnnotationLink from annotationLinks, allowing for recursion -- whether or not the removal will call unlinkFilter again if loaded.
removeFilterAnnotationLinkSet(Collection<FilterAnnotationLink>) - Method in class ome.model.acquisition.Filter
use like removeFilterAnnotationLink
removeFilterSet(Collection<Filter>) - Method in class ome.model.acquisition.Instrument
use like removeFilter
removeFilterSet(FilterSet) - Method in class ome.model.acquisition.Instrument
removes a single element from this set and makes the inverse call on ome.model.acquisition.FilterSet
removeFilterSetEmissionFilterLink(FilterSetEmissionFilterLink) - Method in class ome.model.acquisition.Filter
removes a single element from this set and makes the inverse call on ome.model.acquisition.FilterSetEmissionFilterLink
removeFilterSetEmissionFilterLink(FilterSetEmissionFilterLink, boolean) - Method in class ome.model.acquisition.Filter
removes the given FilterSetEmissionFilterLink from emissionFilterLink, allowing for recursion -- whether or not the removal will call unlinkFilter again if loaded.
removeFilterSetEmissionFilterLink(FilterSetEmissionFilterLink) - Method in class ome.model.acquisition.FilterSet
removes a single element from this set and makes the inverse call on ome.model.acquisition.FilterSetEmissionFilterLink
removeFilterSetEmissionFilterLink(FilterSetEmissionFilterLink, boolean) - Method in class ome.model.acquisition.FilterSet
removes the given FilterSetEmissionFilterLink from emissionFilterLink, allowing for recursion -- whether or not the removal will call unlinkFilterSet again if loaded.
removeFilterSetEmissionFilterLinkSet(Collection<FilterSetEmissionFilterLink>) - Method in class ome.model.acquisition.Filter
use like removeFilterSetEmissionFilterLink
removeFilterSetEmissionFilterLinkSet(Collection<FilterSetEmissionFilterLink>) - Method in class ome.model.acquisition.FilterSet
use like removeFilterSetEmissionFilterLink
removeFilterSetExcitationFilterLink(FilterSetExcitationFilterLink) - Method in class ome.model.acquisition.Filter
removes a single element from this set and makes the inverse call on ome.model.acquisition.FilterSetExcitationFilterLink
removeFilterSetExcitationFilterLink(FilterSetExcitationFilterLink, boolean) - Method in class ome.model.acquisition.Filter
removes the given FilterSetExcitationFilterLink from excitationFilterLink, allowing for recursion -- whether or not the removal will call unlinkFilter again if loaded.
removeFilterSetExcitationFilterLink(FilterSetExcitationFilterLink) - Method in class ome.model.acquisition.FilterSet
removes a single element from this set and makes the inverse call on ome.model.acquisition.FilterSetExcitationFilterLink
removeFilterSetExcitationFilterLink(FilterSetExcitationFilterLink, boolean) - Method in class ome.model.acquisition.FilterSet
removes the given FilterSetExcitationFilterLink from excitationFilterLink, allowing for recursion -- whether or not the removal will call unlinkFilterSet again if loaded.
removeFilterSetExcitationFilterLinkSet(Collection<FilterSetExcitationFilterLink>) - Method in class ome.model.acquisition.Filter
use like removeFilterSetExcitationFilterLink
removeFilterSetExcitationFilterLinkSet(Collection<FilterSetExcitationFilterLink>) - Method in class ome.model.acquisition.FilterSet
use like removeFilterSetExcitationFilterLink
removeFilterSetSet(Collection<FilterSet>) - Method in class ome.model.acquisition.Instrument
use like removeFilterSet
removeGroupExperimenterMap(GroupExperimenterMap) - Method in class ome.model.meta.Experimenter
removes a single element from this set and makes the inverse call on ome.model.meta.GroupExperimenterMap
removeGroupExperimenterMap(GroupExperimenterMap, boolean) - Method in class ome.model.meta.Experimenter
removes the given GroupExperimenterMap from groupExperimenterMap, allowing for recursion -- whether or not the removal will call unlinkExperimenter again if loaded.
removeGroupExperimenterMap(GroupExperimenterMap) - Method in class ome.model.meta.ExperimenterGroup
removes a single element from this set and makes the inverse call on ome.model.meta.GroupExperimenterMap
removeGroupExperimenterMap(GroupExperimenterMap, boolean) - Method in class ome.model.meta.ExperimenterGroup
removes the given GroupExperimenterMap from groupExperimenterMap, allowing for recursion -- whether or not the removal will call unlinkExperimenterGroup again if loaded.
removeGroupExperimenterMapSet(Collection<GroupExperimenterMap>) - Method in class ome.model.meta.Experimenter
use like removeGroupExperimenterMap
removeGroupExperimenterMapSet(Collection<GroupExperimenterMap>) - Method in class ome.model.meta.ExperimenterGroup
use like removeGroupExperimenterMap
removeGroupOwners(ExperimenterGroup, Experimenter...) - Method in interface ome.api.IAdmin
removes the given users from the owner list for this group.
removeGroupOwners(ExperimenterGroup, Experimenter...) - Method in class ome.logic.AdminImpl
 
removeGroupOwners_async(AMD_IAdmin_removeGroupOwners, ExperimenterGroup, List<Experimenter>, Current) - Method in class ome.services.blitz.impl.AdminI
 
removeGroups(Experimenter, ExperimenterGroup...) - Method in interface ome.api.IAdmin
Removes an experimenter from the given groups.
removeGroups(Experimenter, ExperimenterGroup...) - Method in class ome.logic.AdminImpl
 
removeGroups(Experimenter, ExperimenterGroup...) - Method in interface ome.security.auth.RoleProvider
 
removeGroups(Experimenter, ExperimenterGroup...) - Method in class ome.security.auth.SimpleRoleProvider
 
removeGroups_async(AMD_IAdmin_removeGroups, Experimenter, List<ExperimenterGroup>, Current) - Method in class ome.services.blitz.impl.AdminI
 
removeGuest(long, String) - Method in interface ome.api.IShare
Removes guest email address from share.
removeGuest(long, String) - Method in class ome.services.sharing.ShareBean
 
removeGuest_async(AMD_IShare_removeGuest, long, String, Current) - Method in class ome.services.blitz.impl.ShareI
 
removeGuests(long, String...) - Method in interface ome.api.IShare
Removes guest email addresses from the share.
removeGuests(long, String...) - Method in class ome.services.sharing.ShareBean
 
removeGuests_async(AMD_IShare_removeGuests, long, List<String>, Current) - Method in class ome.services.blitz.impl.ShareI
 
removeImage(Image) - Method in class ome.model.fs.Fileset
removes a single element from this set and makes the inverse call on ome.model.core.Image
removeImageAnnotationLink(ImageAnnotationLink) - Method in class ome.model.core.Image
removes a single element from this set and makes the inverse call on ome.model.annotations.ImageAnnotationLink
removeImageAnnotationLink(ImageAnnotationLink, boolean) - Method in class ome.model.core.Image
removes the given ImageAnnotationLink from annotationLinks, allowing for recursion -- whether or not the removal will call unlinkImage again if loaded.
removeImageAnnotationLinkSet(Collection<ImageAnnotationLink>) - Method in class ome.model.core.Image
use like removeImageAnnotationLink
removeImageSet(Collection<Image>) - Method in class ome.model.fs.Fileset
use like removeImage
removeInstrumentAnnotationLink(InstrumentAnnotationLink) - Method in class ome.model.acquisition.Instrument
removes a single element from this set and makes the inverse call on ome.model.annotations.InstrumentAnnotationLink
removeInstrumentAnnotationLink(InstrumentAnnotationLink, boolean) - Method in class ome.model.acquisition.Instrument
removes the given InstrumentAnnotationLink from annotationLinks, allowing for recursion -- whether or not the removal will call unlinkInstrument again if loaded.
removeInstrumentAnnotationLinkSet(Collection<InstrumentAnnotationLink>) - Method in class ome.model.acquisition.Instrument
use like removeInstrumentAnnotationLink
removeIObjectContainer(LSID) - Method in interface ome.formats.model.IObjectContainerStore
Removes an IObject container from within the OME-XML data model store.
removeIObjectContainer(LSID) - Method in class ome.formats.OMEROMetadataStoreClient
 
removeJobOriginalFileLink(JobOriginalFileLink) - Method in class ome.model.jobs.Job
removes a single element from this set and makes the inverse call on ome.model.jobs.JobOriginalFileLink
removeJobOriginalFileLink(JobOriginalFileLink, boolean) - Method in class ome.model.jobs.Job
removes the given JobOriginalFileLink from originalFileLinks, allowing for recursion -- whether or not the removal will call unlinkJob again if loaded.
removeJobOriginalFileLinkSet(Collection<JobOriginalFileLink>) - Method in class ome.model.jobs.Job
use like removeJobOriginalFileLink
removeLightPathAnnotationLink(LightPathAnnotationLink) - Method in class ome.model.acquisition.LightPath
removes a single element from this set and makes the inverse call on ome.model.annotations.LightPathAnnotationLink
removeLightPathAnnotationLink(LightPathAnnotationLink, boolean) - Method in class ome.model.acquisition.LightPath
removes the given LightPathAnnotationLink from annotationLinks, allowing for recursion -- whether or not the removal will call unlinkLightPath again if loaded.
removeLightPathAnnotationLinkSet(Collection<LightPathAnnotationLink>) - Method in class ome.model.acquisition.LightPath
use like removeLightPathAnnotationLink
removeLightPathEmissionFilterLink(LightPathEmissionFilterLink) - Method in class ome.model.acquisition.LightPath
removes a single element from this set and makes the inverse call on ome.model.acquisition.LightPathEmissionFilterLink
removeLightPathEmissionFilterLink(LightPathEmissionFilterLink, boolean) - Method in class ome.model.acquisition.LightPath
removes the given LightPathEmissionFilterLink from emissionFilterLink, allowing for recursion -- whether or not the removal will call unlinkLightPath again if loaded.
removeLightPathEmissionFilterLinkSet(Collection<LightPathEmissionFilterLink>) - Method in class ome.model.acquisition.LightPath
use like removeLightPathEmissionFilterLink
removeLightPathExcitationFilterLink(LightPathExcitationFilterLink) - Method in class ome.model.acquisition.LightPath
removes a single element from this set and makes the inverse call on ome.model.acquisition.LightPathExcitationFilterLink
removeLightPathExcitationFilterLink(LightPathExcitationFilterLink, boolean) - Method in class ome.model.acquisition.LightPath
removes the given LightPathExcitationFilterLink from excitationFilterLink, allowing for recursion -- whether or not the removal will call unlinkLightPath again if loaded.
removeLightPathExcitationFilterLinkSet(Collection<LightPathExcitationFilterLink>) - Method in class ome.model.acquisition.LightPath
use like removeLightPathExcitationFilterLink
removeLightSettings(LightSettings) - Method in class ome.model.experiment.MicrobeamManipulation
removes a single element from this set and makes the inverse call on ome.model.acquisition.LightSettings
removeLightSettingsSet(Collection<LightSettings>) - Method in class ome.model.experiment.MicrobeamManipulation
use like removeLightSettings
removeLightSource(LightSource) - Method in class ome.model.acquisition.Instrument
removes a single element from this set and makes the inverse call on ome.model.acquisition.LightSource
removeLightSourceAnnotationLink(LightSourceAnnotationLink) - Method in class ome.model.acquisition.LightSource
removes a single element from this set and makes the inverse call on ome.model.annotations.LightSourceAnnotationLink
removeLightSourceAnnotationLink(LightSourceAnnotationLink, boolean) - Method in class ome.model.acquisition.LightSource
removes the given LightSourceAnnotationLink from annotationLinks, allowing for recursion -- whether or not the removal will call unlinkLightSource again if loaded.
removeLightSourceAnnotationLinkSet(Collection<LightSourceAnnotationLink>) - Method in class ome.model.acquisition.LightSource
use like removeLightSourceAnnotationLink
removeLightSourceSet(Collection<LightSource>) - Method in class ome.model.acquisition.Instrument
use like removeLightSource
removeMicrobeamManipulation(MicrobeamManipulation) - Method in class ome.model.experiment.Experiment
removes a single element from this set and makes the inverse call on ome.model.experiment.MicrobeamManipulation
removeMicrobeamManipulationSet(Collection<MicrobeamManipulation>) - Method in class ome.model.experiment.Experiment
use like removeMicrobeamManipulation
removeMissingFilesFromDb(SqlAction, Session, List<OriginalFile>) - Method in class ome.services.scripts.ScriptRepoHelper
Given the current files on disk, #unregister(Long, Session) all files which have been removed from disk.
removeModelProcessor(ModelProcessor) - Method in class ome.formats.OMEROMetadataStoreClient
Removes a model processor from use.
removeNamespace(String) - Method in class pojos.ROIData
Removes the namespace from the ROI.
removeNamespaceAnnotationLink(NamespaceAnnotationLink) - Method in class ome.model.meta.Namespace
removes a single element from this set and makes the inverse call on ome.model.annotations.NamespaceAnnotationLink
removeNamespaceAnnotationLink(NamespaceAnnotationLink, boolean) - Method in class ome.model.meta.Namespace
removes the given NamespaceAnnotationLink from annotationLinks, allowing for recursion -- whether or not the removal will call unlinkNamespace again if loaded.
removeNamespaceAnnotationLinkSet(Collection<NamespaceAnnotationLink>) - Method in class ome.model.meta.Namespace
use like removeNamespaceAnnotationLink
removeNodeAnnotationLink(NodeAnnotationLink) - Method in class ome.model.meta.Node
removes a single element from this set and makes the inverse call on ome.model.annotations.NodeAnnotationLink
removeNodeAnnotationLink(NodeAnnotationLink, boolean) - Method in class ome.model.meta.Node
removes the given NodeAnnotationLink from annotationLinks, allowing for recursion -- whether or not the removal will call unlinkNode again if loaded.
removeNodeAnnotationLinkSet(Collection<NodeAnnotationLink>) - Method in class ome.model.meta.Node
use like removeNodeAnnotationLink
removeObject(long, T) - Method in interface ome.api.IShare
Removes existing item from the share.
removeObject(Identity) - Method in class ome.services.blitz.fire.Registry.Impl
 
removeObject(Identity) - Method in interface ome.services.blitz.fire.Registry
 
removeObject(long, T) - Method in class ome.services.sharing.ShareBean
 
removeObject_async(AMD_IShare_removeObject, long, IObject, Current) - Method in class ome.services.blitz.impl.ShareI
 
removeObjective(Objective) - Method in class ome.model.acquisition.Instrument
removes a single element from this set and makes the inverse call on ome.model.acquisition.Objective
removeObjectiveAnnotationLink(ObjectiveAnnotationLink) - Method in class ome.model.acquisition.Objective
removes a single element from this set and makes the inverse call on ome.model.annotations.ObjectiveAnnotationLink
removeObjectiveAnnotationLink(ObjectiveAnnotationLink, boolean) - Method in class ome.model.acquisition.Objective
removes the given ObjectiveAnnotationLink from annotationLinks, allowing for recursion -- whether or not the removal will call unlinkObjective again if loaded.
removeObjectiveAnnotationLinkSet(Collection<ObjectiveAnnotationLink>) - Method in class ome.model.acquisition.Objective
use like removeObjectiveAnnotationLink
removeObjectiveSet(Collection<Objective>) - Method in class ome.model.acquisition.Instrument
use like removeObjective
removeObjects(long, T...) - Method in interface ome.api.IShare
Remove existing items from the share.
removeObjects(long, T...) - Method in class ome.services.sharing.ShareBean
 
removeObjects_async(AMD_IShare_removeObjects, long, List<IObject>, Current) - Method in class ome.services.blitz.impl.ShareI
 
removeObjectSafely(Identity) - Method in class ome.services.blitz.fire.Registry.Impl
 
removeObjectSafely(Identity) - Method in interface ome.services.blitz.fire.Registry
 
removeOriginalFileAnnotationLink(OriginalFileAnnotationLink) - Method in class ome.model.core.OriginalFile
removes a single element from this set and makes the inverse call on ome.model.annotations.OriginalFileAnnotationLink
removeOriginalFileAnnotationLink(OriginalFileAnnotationLink, boolean) - Method in class ome.model.core.OriginalFile
removes the given OriginalFileAnnotationLink from annotationLinks, allowing for recursion -- whether or not the removal will call unlinkOriginalFile again if loaded.
removeOriginalFileAnnotationLinkSet(Collection<OriginalFileAnnotationLink>) - Method in class ome.model.core.OriginalFile
use like removeOriginalFileAnnotationLink
removeOTF(OTF) - Method in class ome.model.acquisition.Instrument
removes a single element from this set and makes the inverse call on ome.model.acquisition.OTF
removeOTFSet(Collection<OTF>) - Method in class ome.model.acquisition.Instrument
use like removeOTF
removeParams(Long) - Method in class ome.services.blitz.util.ParamsCache
Remove a cached JobParams instance.
removePassword(Long) - Method in class ome.util.actions.PostgresSqlAction
 
removePassword(Long) - Method in interface ome.util.SqlAction
 
removePath(File) - Method in class omero.util.TempFileManager
If the given file is under TempFileManager.dir, then it is deleted whether file or folder.
removePixels(List<Long>) - Method in class ome.io.nio.PixelsService
Removes files from data repository based on a parameterized List of Long pixels ids
removePixels(Pixels) - Method in class ome.model.core.Image
removes a single element from this set and makes the inverse call on ome.model.core.Pixels
removePixelsOriginalFileMap(PixelsOriginalFileMap) - Method in class ome.model.core.OriginalFile
removes a single element from this set and makes the inverse call on ome.model.core.PixelsOriginalFileMap
removePixelsOriginalFileMap(PixelsOriginalFileMap, boolean) - Method in class ome.model.core.OriginalFile
removes the given PixelsOriginalFileMap from pixelsFileMaps, allowing for recursion -- whether or not the removal will call unlinkOriginalFile again if loaded.
removePixelsOriginalFileMap(PixelsOriginalFileMap) - Method in class ome.model.core.Pixels
removes a single element from this set and makes the inverse call on ome.model.core.PixelsOriginalFileMap
removePixelsOriginalFileMap(PixelsOriginalFileMap, boolean) - Method in class ome.model.core.Pixels
removes the given PixelsOriginalFileMap from pixelsFileMaps, allowing for recursion -- whether or not the removal will call unlinkPixels again if loaded.
removePixelsOriginalFileMapSet(Collection<PixelsOriginalFileMap>) - Method in class ome.model.core.OriginalFile
use like removePixelsOriginalFileMap
removePixelsOriginalFileMapSet(Collection<PixelsOriginalFileMap>) - Method in class ome.model.core.Pixels
use like removePixelsOriginalFileMap
removePixelsSet(Collection<Pixels>) - Method in class ome.model.core.Image
use like removePixels
removePlaneInfo(PlaneInfo) - Method in class ome.model.core.Pixels
removes a single element from this set and makes the inverse call on ome.model.core.PlaneInfo
removePlaneInfoAnnotationLink(PlaneInfoAnnotationLink) - Method in class ome.model.core.PlaneInfo
removes a single element from this set and makes the inverse call on ome.model.annotations.PlaneInfoAnnotationLink
removePlaneInfoAnnotationLink(PlaneInfoAnnotationLink, boolean) - Method in class ome.model.core.PlaneInfo
removes the given PlaneInfoAnnotationLink from annotationLinks, allowing for recursion -- whether or not the removal will call unlinkPlaneInfo again if loaded.
removePlaneInfoAnnotationLinkSet(Collection<PlaneInfoAnnotationLink>) - Method in class ome.model.core.PlaneInfo
use like removePlaneInfoAnnotationLink
removePlaneInfoSet(Collection<PlaneInfo>) - Method in class ome.model.core.Pixels
use like removePlaneInfo
removePlateAcquisition(PlateAcquisition) - Method in class ome.model.screen.Plate
removes a single element from this set and makes the inverse call on ome.model.screen.PlateAcquisition
removePlateAcquisitionAnnotationLink(PlateAcquisitionAnnotationLink) - Method in class ome.model.screen.PlateAcquisition
removes a single element from this set and makes the inverse call on ome.model.annotations.PlateAcquisitionAnnotationLink
removePlateAcquisitionAnnotationLink(PlateAcquisitionAnnotationLink, boolean) - Method in class ome.model.screen.PlateAcquisition
removes the given PlateAcquisitionAnnotationLink from annotationLinks, allowing for recursion -- whether or not the removal will call unlinkPlateAcquisition again if loaded.
removePlateAcquisitionAnnotationLinkSet(Collection<PlateAcquisitionAnnotationLink>) - Method in class ome.model.screen.PlateAcquisition
use like removePlateAcquisitionAnnotationLink
removePlateAcquisitionSet(Collection<PlateAcquisition>) - Method in class ome.model.screen.Plate
use like removePlateAcquisition
removePlateAnnotationLink(PlateAnnotationLink) - Method in class ome.model.screen.Plate
removes a single element from this set and makes the inverse call on ome.model.annotations.PlateAnnotationLink
removePlateAnnotationLink(PlateAnnotationLink, boolean) - Method in class ome.model.screen.Plate
removes the given PlateAnnotationLink from annotationLinks, allowing for recursion -- whether or not the removal will call unlinkPlate again if loaded.
removePlateAnnotationLinkSet(Collection<PlateAnnotationLink>) - Method in class ome.model.screen.Plate
use like removePlateAnnotationLink
removeProcess(ProcessContainer.Process) - Method in class ome.services.blitz.repo.ProcessContainer
 
removeProcessor(ProcessorPrx, Current) - Method in class ome.services.blitz.impl.SharedResourcesI
 
removeProjectAnnotationLink(ProjectAnnotationLink) - Method in class ome.model.containers.Project
removes a single element from this set and makes the inverse call on ome.model.annotations.ProjectAnnotationLink
removeProjectAnnotationLink(ProjectAnnotationLink, boolean) - Method in class ome.model.containers.Project
removes the given ProjectAnnotationLink from annotationLinks, allowing for recursion -- whether or not the removal will call unlinkProject again if loaded.
removeProjectAnnotationLinkSet(Collection<ProjectAnnotationLink>) - Method in class ome.model.containers.Project
use like removeProjectAnnotationLink
removeProjectDatasetLink(ProjectDatasetLink) - Method in class ome.model.containers.Dataset
removes a single element from this set and makes the inverse call on ome.model.containers.ProjectDatasetLink
removeProjectDatasetLink(ProjectDatasetLink, boolean) - Method in class ome.model.containers.Dataset
removes the given ProjectDatasetLink from projectLinks, allowing for recursion -- whether or not the removal will call unlinkDataset again if loaded.
removeProjectDatasetLink(ProjectDatasetLink) - Method in class ome.model.containers.Project
removes a single element from this set and makes the inverse call on ome.model.containers.ProjectDatasetLink
removeProjectDatasetLink(ProjectDatasetLink, boolean) - Method in class ome.model.containers.Project
removes the given ProjectDatasetLink from datasetLinks, allowing for recursion -- whether or not the removal will call unlinkProject again if loaded.
removeProjectDatasetLinkSet(Collection<ProjectDatasetLink>) - Method in class ome.model.containers.Dataset
use like removeProjectDatasetLink
removeProjectDatasetLinkSet(Collection<ProjectDatasetLink>) - Method in class ome.model.containers.Project
use like removeProjectDatasetLink
removeReagent(Reagent) - Method in class ome.model.screen.Screen
removes a single element from this set and makes the inverse call on ome.model.screen.Reagent
removeReagentAnnotationLink(ReagentAnnotationLink) - Method in class ome.model.screen.Reagent
removes a single element from this set and makes the inverse call on ome.model.annotations.ReagentAnnotationLink
removeReagentAnnotationLink(ReagentAnnotationLink, boolean) - Method in class ome.model.screen.Reagent
removes the given ReagentAnnotationLink from annotationLinks, allowing for recursion -- whether or not the removal will call unlinkReagent again if loaded.
removeReagentAnnotationLinkSet(Collection<ReagentAnnotationLink>) - Method in class ome.model.screen.Reagent
use like removeReagentAnnotationLink
removeReagentSet(Collection<Reagent>) - Method in class ome.model.screen.Screen
use like removeReagent
removeRenderingDef(RenderingDef) - Method in class ome.model.core.Pixels
removes a single element from this set and makes the inverse call on ome.model.display.RenderingDef
removeRenderingDefSet(Collection<RenderingDef>) - Method in class ome.model.core.Pixels
use like removeRenderingDef
removeRoi(Roi) - Method in class ome.model.core.Image
removes a single element from this set and makes the inverse call on ome.model.roi.Roi
removeRoiAnnotationLink(RoiAnnotationLink) - Method in class ome.model.roi.Roi
removes a single element from this set and makes the inverse call on ome.model.annotations.RoiAnnotationLink
removeRoiAnnotationLink(RoiAnnotationLink, boolean) - Method in class ome.model.roi.Roi
removes the given RoiAnnotationLink from annotationLinks, allowing for recursion -- whether or not the removal will call unlinkRoi again if loaded.
removeRoiAnnotationLinkSet(Collection<RoiAnnotationLink>) - Method in class ome.model.roi.Roi
use like removeRoiAnnotationLink
removeRoiSet(Collection<Roi>) - Method in class ome.model.core.Image
use like removeRoi
removeScreenAnnotationLink(ScreenAnnotationLink) - Method in class ome.model.screen.Screen
removes a single element from this set and makes the inverse call on ome.model.annotations.ScreenAnnotationLink
removeScreenAnnotationLink(ScreenAnnotationLink, boolean) - Method in class ome.model.screen.Screen
removes the given ScreenAnnotationLink from annotationLinks, allowing for recursion -- whether or not the removal will call unlinkScreen again if loaded.
removeScreenAnnotationLinkSet(Collection<ScreenAnnotationLink>) - Method in class ome.model.screen.Screen
use like removeScreenAnnotationLink
removeScreenPlateLink(ScreenPlateLink) - Method in class ome.model.screen.Plate
removes a single element from this set and makes the inverse call on ome.model.screen.ScreenPlateLink
removeScreenPlateLink(ScreenPlateLink, boolean) - Method in class ome.model.screen.Plate
removes the given ScreenPlateLink from screenLinks, allowing for recursion -- whether or not the removal will call unlinkPlate again if loaded.
removeScreenPlateLink(ScreenPlateLink) - Method in class ome.model.screen.Screen
removes a single element from this set and makes the inverse call on ome.model.screen.ScreenPlateLink
removeScreenPlateLink(ScreenPlateLink, boolean) - Method in class ome.model.screen.Screen
removes the given ScreenPlateLink from plateLinks, allowing for recursion -- whether or not the removal will call unlinkScreen again if loaded.
removeScreenPlateLinkSet(Collection<ScreenPlateLink>) - Method in class ome.model.screen.Plate
use like removeScreenPlateLink
removeScreenPlateLinkSet(Collection<ScreenPlateLink>) - Method in class ome.model.screen.Screen
use like removeScreenPlateLink
removeSession(Session) - Method in class ome.model.meta.Node
removes a single element from this set and makes the inverse call on ome.model.meta.Session
removeSession(String) - Method in class ome.services.sessions.state.SessionCache
 
removeSessionAnnotationLink(SessionAnnotationLink) - Method in class ome.model.meta.Session
removes a single element from this set and makes the inverse call on ome.model.annotations.SessionAnnotationLink
removeSessionAnnotationLink(SessionAnnotationLink, boolean) - Method in class ome.model.meta.Session
removes the given SessionAnnotationLink from annotationLinks, allowing for recursion -- whether or not the removal will call unlinkSession again if loaded.
removeSessionAnnotationLinkSet(Collection<SessionAnnotationLink>) - Method in class ome.model.meta.Session
use like removeSessionAnnotationLink
removeSessionCallback(String, SessionCallback) - Method in class ome.services.sessions.state.SessionCache
 
removeSessionSet(Collection<Session>) - Method in class ome.model.meta.Node
use like removeSession
removeShape(Shape) - Method in class ome.model.roi.Roi
removes a single element from this set and makes the inverse call on ome.model.roi.Shape
removeShapeAnnotationLink(ShapeAnnotationLink) - Method in class ome.model.roi.Shape
removes a single element from this set and makes the inverse call on ome.model.annotations.ShapeAnnotationLink
removeShapeAnnotationLink(ShapeAnnotationLink, boolean) - Method in class ome.model.roi.Shape
removes the given ShapeAnnotationLink from annotationLinks, allowing for recursion -- whether or not the removal will call unlinkShape again if loaded.
removeShapeAnnotationLinkSet(Collection<ShapeAnnotationLink>) - Method in class ome.model.roi.Shape
use like removeShapeAnnotationLink
removeShapeData(ShapeData) - Method in class pojos.ROIData
Removes the ShapeData object from ROIData.
removeShapeSet(Collection<Shape>) - Method in class ome.model.roi.Roi
use like removeShape
removeStatus(MethodInvocation) - Method in class ome.tools.hibernate.SessionHandler
 
removeThumbnail(Thumbnail) - Method in class ome.model.core.Pixels
removes a single element from this set and makes the inverse call on ome.model.display.Thumbnail
removeThumbnails(List<Long>) - Method in class ome.io.nio.ThumbnailService
Removes files from data repository based on a parameterized List of Long thumbnail ids
removeThumbnailSet(Collection<Thumbnail>) - Method in class ome.model.core.Pixels
use like removeThumbnail
removeUnusedFiles() - Method in interface ome.api.IRepositoryInfo
Removes all files from the server that do not have an OriginalFile complement in the database, all the Pixels that do not have a complement in the database and all the Thumbnail's that do not have a complement in the database.
removeUnusedFiles() - Method in class ome.logic.RepositoryInfoImpl
 
removeUnusedFiles_async(AMD_IRepositoryInfo_removeUnusedFiles, Current) - Method in class ome.services.blitz.impl.RepositoryInfoI
 
removeUser(long, Experimenter) - Method in interface ome.api.IShare
Removes experimenter from share
removeUser(long, Experimenter) - Method in class ome.services.sharing.ShareBean
 
removeUser_async(AMD_IShare_removeUser, long, Experimenter, Current) - Method in class ome.services.blitz.impl.ShareI
 
removeUsers(long, List<Experimenter>) - Method in interface ome.api.IShare
Removes experimenters from share
removeUsers(long, List<Experimenter>) - Method in class ome.services.sharing.ShareBean
 
removeUsers_async(AMD_IShare_removeUsers, long, List<Experimenter>, Current) - Method in class ome.services.blitz.impl.ShareI
 
removeWell(Well) - Method in class ome.model.screen.Plate
removes a single element from this set and makes the inverse call on ome.model.screen.Well
removeWellAnnotationLink(WellAnnotationLink) - Method in class ome.model.screen.Well
removes a single element from this set and makes the inverse call on ome.model.annotations.WellAnnotationLink
removeWellAnnotationLink(WellAnnotationLink, boolean) - Method in class ome.model.screen.Well
removes the given WellAnnotationLink from annotationLinks, allowing for recursion -- whether or not the removal will call unlinkWell again if loaded.
removeWellAnnotationLinkSet(Collection<WellAnnotationLink>) - Method in class ome.model.screen.Well
use like removeWellAnnotationLink
removeWellReagentLink(WellReagentLink) - Method in class ome.model.screen.Reagent
removes a single element from this set and makes the inverse call on ome.model.screen.WellReagentLink
removeWellReagentLink(WellReagentLink, boolean) - Method in class ome.model.screen.Reagent
removes the given WellReagentLink from wellLinks, allowing for recursion -- whether or not the removal will call unlinkReagent again if loaded.
removeWellReagentLink(WellReagentLink) - Method in class ome.model.screen.Well
removes a single element from this set and makes the inverse call on ome.model.screen.WellReagentLink
removeWellReagentLink(WellReagentLink, boolean) - Method in class ome.model.screen.Well
removes the given WellReagentLink from reagentLinks, allowing for recursion -- whether or not the removal will call unlinkWell again if loaded.
removeWellReagentLinkSet(Collection<WellReagentLink>) - Method in class ome.model.screen.Reagent
use like removeWellReagentLink
removeWellReagentLinkSet(Collection<WellReagentLink>) - Method in class ome.model.screen.Well
use like removeWellReagentLink
removeWellSample(WellSample) - Method in class ome.model.core.Image
removes a single element from this set and makes the inverse call on ome.model.screen.WellSample
removeWellSample(WellSample) - Method in class ome.model.screen.PlateAcquisition
removes a single element from this set and makes the inverse call on ome.model.screen.WellSample
removeWellSample(WellSample) - Method in class ome.model.screen.Well
removes a single element from this set and makes the inverse call on ome.model.screen.WellSample
removeWellSampleSet(Collection<WellSample>) - Method in class ome.model.core.Image
use like removeWellSample
removeWellSampleSet(Collection<WellSample>) - Method in class ome.model.screen.PlateAcquisition
use like removeWellSample
removeWellSampleSet(Collection<WellSample>) - Method in class ome.model.screen.Well
use like removeWellSample
removeWellSet(Collection<Well>) - Method in class ome.model.screen.Plate
use like removeWell
removingOnly() - Method in class ome.services.eventlogs.EventBacklog
Check the current state of the EventBacklog.
render(PlaneDef) - Method in class ome.services.RenderingBean
Implemented as specified by the RenderingEngine interface.
render(PlaneDef) - Method in class omeis.providers.re.Renderer
Renders the data selected by pd according to the current rendering settings.
render(PlaneDef) - Method in interface omeis.providers.re.RenderingEngine
Renders the data selected by pd according to the current rendering settings.
render_async(AMD_RenderingEngine_render, PlaneDef, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
renderAsPackedInt(PlaneDef) - Method in class ome.services.RenderingBean
Implemented as specified by the RenderingEngine interface.
renderAsPackedInt(PlaneDef, PixelBuffer) - Method in class omeis.providers.re.Renderer
Renders the data selected by pd according to the current rendering settings.
renderAsPackedInt(PlaneDef) - Method in interface omeis.providers.re.RenderingEngine
Renders the data selected by pd according to the current rendering settings.
renderAsPackedInt_async(AMD_RenderingEngine_renderAsPackedInt, PlaneDef, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
renderCompressed(PlaneDef) - Method in class ome.services.RenderingBean
Implemented as specified by the RenderingEngine interface.
renderCompressed(PlaneDef) - Method in interface omeis.providers.re.RenderingEngine
Renders the data selected by pd according to the current rendering settings and compresses the resulting RGBA composite image.
renderCompressed_async(AMD_RenderingEngine_renderCompressed, PlaneDef, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
Renderer - Class in omeis.providers.re
Transforms raw image data into an RGB image that can be displayed on screen.
Renderer(QuantumFactory, List<RenderingModel>, Pixels, RenderingDef, PixelBuffer) - Constructor for class omeis.providers.re.Renderer
Creates a new instance to render the specified pixels set and get this new instance ready for rendering.
RENDERING_DEF_QUERY_PREFIX - Static variable in class ome.logic.PixelsImpl
Standard rendering definition HQL query prefix
RenderingBean - Class in ome.services
Provides the RenderingEngine service.
RenderingBean(PixelsService, LocalCompress, Executor, SecuritySystem) - Constructor for class ome.services.RenderingBean
Compression service Bean injector.
renderingDef - Variable in class ome.model.display.ChannelBinding
 
RENDERINGDEF - Static variable in class ome.model.display.ChannelBinding
 
renderingDef - Variable in class ome.model.display.CodomainMapContext
 
RENDERINGDEF - Static variable in class ome.model.display.CodomainMapContext
 
RenderingDef - Class in ome.model.display
These filter definitions are used by the security system to eliminate non-readable objects from queries.
RenderingDef() - Constructor for class ome.model.display.RenderingDef
 
RenderingDef(Long) - Constructor for class ome.model.display.RenderingDef
 
RenderingDef(Long, boolean) - Constructor for class ome.model.display.RenderingDef
Main constructor.
RenderingDef(Pixels, Integer, Integer, RenderingModel, QuantumDef) - Constructor for class ome.model.display.RenderingDef
 
RenderingDef.Details - Class in ome.model.display
 
RenderingDef.Details() - Constructor for class ome.model.display.RenderingDef.Details
 
RenderingDef.Details(Object[]) - Constructor for class ome.model.display.RenderingDef.Details
 
RenderingDefGraphSpec - Class in ome.services.graphs
Deprecated.
will be removed in OMERO 5.2, so use the new graphs implementation
RenderingDefGraphSpec(List<String>) - Constructor for class ome.services.graphs.RenderingDefGraphSpec
Deprecated.
Creates a new instance.
RenderingEngine - Interface in omeis.providers.re
Defines a service to render a given pixels set.
RenderingEngineI - Class in ome.services.blitz.impl
Implementation of the RenderingEngine service.
RenderingEngineI(RenderingEngine, BlitzExecutor) - Constructor for class ome.services.blitz.impl.RenderingEngineI
 
RenderingModel - Class in ome.model.enums
 
RenderingModel() - Constructor for class ome.model.enums.RenderingModel
 
RenderingModel(Long) - Constructor for class ome.model.enums.RenderingModel
 
RenderingModel(Long, boolean) - Constructor for class ome.model.enums.RenderingModel
Main constructor.
RenderingModel(String) - Constructor for class ome.model.enums.RenderingModel
 
RenderingModel.Details - Class in ome.model.enums
 
RenderingModel.Details() - Constructor for class ome.model.enums.RenderingModel.Details
 
RenderingModel.Details(Object[]) - Constructor for class ome.model.enums.RenderingModel.Details
 
RenderingSettingsI - Class in ome.services.blitz.impl
Implementation of the IRenderingSettings service.
RenderingSettingsI(IRenderingSettings, BlitzExecutor) - Constructor for class ome.services.blitz.impl.RenderingSettingsI
 
RenderingSettingsImpl - Class in ome.logic
Implementation of the IRenderingSettings I/F.
RenderingSettingsImpl() - Constructor for class ome.logic.RenderingSettingsImpl
 
RenderingStats - Class in omeis.providers.re
Exposes methods to time the various steps in the rendering process and provides a stats report.
RenderingStats(Renderer, PlaneDef) - Constructor for class omeis.providers.re.RenderingStats
Creates a new instance.
RenderingTask - Interface in omeis.providers.re
This interface represents a rendering operation task.
renderProjectedAsPackedInt(int, int, int, int, int) - Method in class ome.services.RenderingBean
Implemented as specified by the RenderingEngine interface.
renderProjectedAsPackedInt(int, int, int, int, int) - Method in interface omeis.providers.re.RenderingEngine
Performs a projection through selected optical sections of a particular timepoint with the currently active channels and renders the data for display.
renderProjectedAsPackedInt_async(AMD_RenderingEngine_renderProjectedAsPackedInt, ProjectionType, int, int, int, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
renderProjectedCompressed(int, int, int, int, int) - Method in class ome.services.RenderingBean
Implemented as specified by the RenderingEngine interface.
renderProjectedCompressed(int, int, int, int, int) - Method in interface omeis.providers.re.RenderingEngine
Performs a projection through selected optical sections of a particular timepoint with the currently active channels, renders the data for display and compresses the resulting RGBA composite image.
renderProjectedCompressed_async(AMD_RenderingEngine_renderProjectedCompressed, ProjectionType, int, int, int, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
ReorderedPixelData - Class in ome.io.nio
Represents a block of pixel data that needs to be re-ordered in accordance with a DeltaVision file.
ReorderedPixelData(String, ByteBuffer, int) - Constructor for class ome.io.nio.ReorderedPixelData
Default constructor.
repetitionRate - Variable in class ome.model.acquisition.Laser
 
REPETITIONRATE - Static variable in class ome.model.acquisition.Laser
 
replace(Object, Object, Object) - Method in class ome.model.units.GenericEnumType
 
replace(Object, Object, Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
 
repo - Variable in class ome.services.blitz.repo.RawAccessRequestI
 
repo - Variable in class ome.services.pixeldata.PersistentEventLogLoader
 
repo - Variable in class ome.util.SqlAction.DeleteLog
 
RepoFile - Class in ome.services.scripts
File type wrapper for paths which are intended for being stored in the database as a part of this repository.
RepoFile(File, String) - Constructor for class ome.services.scripts.RepoFile
Assumes that path is relative under root, and constructs a new File and calls RepoFile.RepoFile(File, File)
RepoFile(File, File) - Constructor for class ome.services.scripts.RepoFile
Both root and file are absolute paths to files.
repoFile(long) - Method in class ome.util.actions.PostgresSqlAction
 
repoFile(long) - Method in interface ome.util.SqlAction
 
RepoFile.FsFile - Class in ome.services.scripts
File type wrapper for actual OS files.
RepoRawFileStoreI - Class in ome.services.blitz.repo
An implementation of the RepoRawFileStore interface
RepoRawFileStoreI(BlitzExecutor, RawFileStore, Current) - Constructor for class ome.services.blitz.repo.RepoRawFileStoreI
 
reportForgottenPassword(String, String) - Method in interface ome.api.IAdmin
Deprecated. 
reportForgottenPassword(String, String) - Method in class ome.logic.AdminImpl
 
reportForgottenPassword_async(AMD_IAdmin_reportForgottenPassword, String, String, Current) - Method in class ome.services.blitz.impl.AdminI
 
reportingLoops - Variable in class ome.services.fulltext.FullTextIndexer
Frequency with which the percentage done should be calculated.
repoScriptCount(String, Set<String>) - Method in class ome.util.SqlAction.Impl
 
repoScriptCount(String, Set<String>) - Method in interface ome.util.SqlAction
 
repositories(Current) - Method in class ome.services.blitz.impl.SharedResourcesI
 
repositoryDao - Variable in class ome.services.blitz.repo.PublicRepositoryI
 
RepositoryDao - Interface in ome.services.blitz.repo
 
RepositoryDaoImpl - Class in ome.services.blitz.repo
DAO class for encapsulating operations related to resource access inside the repository.
RepositoryDaoImpl(Principal, Roles, Executor, Executor) - Constructor for class ome.services.blitz.repo.RepositoryDaoImpl
Primary constructor which takes all final fields.
RepositoryDaoImpl(Principal, Executor) - Constructor for class ome.services.blitz.repo.RepositoryDaoImpl
Previous constructor which should no longer be used.
RepositoryInfoI - Class in ome.services.blitz.impl
Implementation of the IRepositoryInfo service.
RepositoryInfoI(IRepositoryInfo, BlitzExecutor) - Constructor for class ome.services.blitz.impl.RepositoryInfoI
 
RepositoryInfoImpl - Class in ome.logic
Class implementation of the IRepositoryInfo service interface.
RepositoryInfoImpl() - Constructor for class ome.logic.RepositoryInfoImpl
 
RepositoryTask - Class in ome.tools
Class implementation of various mechanised tasks, database queries, file I/O, etc.
RepositoryTask(SqlAction) - Constructor for class ome.tools.RepositoryTask
Constructor
reps - Variable in class ome.services.fulltext.FullTextIndexer
 
reps - Variable in class ome.services.pixeldata.PixelDataHandler
 
requestFromUser() - Method in class ome.formats.importer.ImportConfig
if can't log in request needed information
requestHeartBeats() - Method in class ome.services.blitz.fire.SessionManagerI
Destroys all the ServiceFactoryI instances based on the given sessionId.
RequestObjectFactoryRegistry - Class in ome.services.blitz.impl.commands
Types which rely on the omero.model and omero.api objects rather than just the omero.cmd types.
RequestObjectFactoryRegistry() - Constructor for class ome.services.blitz.impl.commands.RequestObjectFactoryRegistry
 
RequestObjectFactoryRegistry - Class in ome.services.blitz.repo
Requests which are handled by the repository servants.
RequestObjectFactoryRegistry(Registry, TileSizes, RepositoryDao, Ring, PixelsService) - Constructor for class ome.services.blitz.repo.RequestObjectFactoryRegistry
 
RequestObjectFactoryRegistry - Class in omero.cmd
SPI type picked up from the Spring configuration and given a chance to register all its ObjectFactory instances with the Communicator.
RequestObjectFactoryRegistry(ExtendedMetadata, ACLVoter, Roles, PixelsService, ThumbnailService, MailUtil, PasswordUtil, SecuritySystem, PasswordProvider, GraphRequestFactory) - Constructor for class omero.cmd.RequestObjectFactoryRegistry
 
requests - Variable in class omero.cmd.graphs.Preprocessor
Deprecated.
 
requestToString(Request) - Method in class omero.cmd.graphs.Preprocessor
Deprecated.
Convert a single request to a pretty string.
REQUEUED - Static variable in interface ome.api.JobHandle
 
requiresCompanion(String) - Static method in class ome.services.util.DBEnumCheck
 
requiresPixelsPyramid() - Method in interface ome.api.RawPixelsStore
 
requiresPixelsPyramid(Pixels) - Method in class ome.io.nio.PixelsService
Returns true if a pyramid should be used for the given Pixels.
requiresPixelsPyramid() - Method in class ome.services.RawPixelsBean
 
requiresPixelsPyramid() - Method in class ome.services.RenderingBean
 
requiresPixelsPyramid() - Method in interface omeis.providers.re.RenderingEngine
 
requiresPixelsPyramid_async(AMD_PyramidService_requiresPixelsPyramid, Current) - Method in class ome.services.blitz.impl.AbstractPyramidServant
 
requiresPixelsPyramid_async(AMD_PyramidService_requiresPixelsPyramid, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
reset(String[]) - Static method in class ome.services.fulltext.Main
Can be used to reset the value that the PersistentEventLogLoader would read if started now.
resetDefaults(RenderingDef, Pixels) - Method in interface ome.api.IRenderingSettings
Resets the given rendering settings to those that are specified by the rendering engine intelligent pretty good image (PG) logic for the pixels set linked to that set of rendering settings.
resetDefaults() - Method in interface ome.api.Search
Resets all settings (non-query state) to the original default values, as if the instance had just be created.
resetDefaults() - Method in interface ome.api.ThumbnailStore
Resets the rendering definition for the active pixels set to its default settings.
resetDefaults(RenderingDef, Pixels) - Method in class ome.logic.RenderingSettingsImpl
Implemented as specified by the IRenderingSettings I/F
resetDefaults() - Method in class ome.services.SearchBean
 
resetDefaults() - Method in class ome.services.ThumbnailBean
 
resetDefaults_async(AMD_IRenderingSettings_resetDefaults, RenderingDef, Pixels, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
 
resetDefaults_async(AMD_Search_resetDefaults, Current) - Method in class ome.services.blitz.impl.SearchI
 
resetDefaults_async(AMD_ThumbnailStore_resetDefaults, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
 
resetDefaultsAndGenerateThumbnails(List<Long>, List<Long>) - Method in class ome.formats.OMEROMetadataStoreClient
Resets the defaults and generates thumbnails for a given set of Pixels IDs.
resetDefaultsByOwnerInSet(Class<T>, Set<Long>) - Method in interface ome.api.IRenderingSettings
Resets the rendering settings of a given group of containers based on the owner's (essentially a copy).
resetDefaultsByOwnerInSet(Class<T>, Set<Long>) - Method in class ome.logic.RenderingSettingsImpl
Implemented as specified by the IRenderingSettings I/F.
resetDefaultsByOwnerInSet_async(AMD_IRenderingSettings_resetDefaultsByOwnerInSet, String, List<Long>, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
 
resetDefaultSettings(boolean) - Method in class ome.services.RenderingBean
Implemented as specified by the RenderingEngine interface.
resetDefaultSettings(boolean) - Method in interface omeis.providers.re.RenderingEngine
Resets the default settings i.e. the default values internal to the Rendering engine.
resetDefaultSettings_async(AMD_RenderingEngine_resetDefaultSettings, boolean, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
resetDefaultsForPixels(long) - Method in interface ome.api.IRenderingSettings
Resets a Pixels' default rendering settings back to those that are specified by the rendering engine intelligent pretty good image (PG) logic.
resetDefaultsForPixels(long) - Method in class ome.logic.RenderingSettingsImpl
Implemented as specified by the IRenderingSettings I/F.
resetDefaultsForPixels_async(AMD_IRenderingSettings_resetDefaultsForPixels, long, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
 
resetDefaultsInDataset(long) - Method in interface ome.api.IRenderingSettings
Resets a dataset's rendering settings back to those that are specified by the rendering engine intelligent pretty good image (PG) logic.
resetDefaultsInDataset(long) - Method in class ome.logic.RenderingSettingsImpl
Implemented as specified by the IRenderingSettings I/F.
resetDefaultsInDataset_async(AMD_IRenderingSettings_resetDefaultsInDataset, long, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
 
resetDefaultsInImage(long) - Method in interface ome.api.IRenderingSettings
Resets an image's default rendering settings back to those that are specified by the rendering engine intelligent pretty good image (PG) logic.
resetDefaultsInImage(long) - Method in class ome.logic.RenderingSettingsImpl
Implemented as specified by the IRenderingSettings I/F.
resetDefaultsInImage_async(AMD_IRenderingSettings_resetDefaultsInImage, long, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
 
resetDefaultsInSet(Class<T>, Set<Long>) - Method in interface ome.api.IRenderingSettings
Resets a rendering settings back to one or many containers that are specified by the rendering engine intelligent pretty good image (PG) logic.
resetDefaultsInSet(Class<T>, Set<Long>) - Method in class ome.logic.RenderingSettingsImpl
Implemented as specified by the IRenderingSettings I/F.
resetDefaultsInSet_async(AMD_IRenderingSettings_resetDefaultsInSet, String, List<Long>, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
 
resetDefaultsNoSave(RenderingDef, Pixels) - Method in interface ome.api.IRenderingSettings
Resets the given rendering settings to those that are specified by the rendering engine intelligent pretty good image (PG) logic for the pixels set linked to that set of rendering settings.
resetDefaultsNoSave(RenderingDef, Pixels) - Method in class ome.logic.RenderingSettingsImpl
Implemented as specified by the IRenderingSettings I/F
resetDefaultsNoSave_async(AMD_IRenderingSettings_resetDefaultsNoSave, RenderingDef, Pixels, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
 
resetDetails(IObject, Object[], Object[], int, Details) - Method in class ome.security.basic.OmeroInterceptor
asks BasicSecuritySystem to create a new managed Details based on the previous state of this entity.
resetEnumerations(Class<T>) - Method in interface ome.api.ITypes
 
resetEnumerations(Class<T>) - Method in class ome.logic.TypesImpl
 
resetEnumerations_async(AMD_ITypes_resetEnumerations, String, Current) - Method in class ome.services.blitz.impl.TypesI
 
resetMinMaxInSet(Class<T>, Set<Long>) - Method in interface ome.api.IRenderingSettings
Resets a the channel windows for one or many containers back to their global minimum and global maximum for the channel.
resetMinMaxInSet(Class<T>, Set<Long>) - Method in class ome.logic.RenderingSettingsImpl
Implemented as specified by the IRenderingSettings I/F.
resetMinMaxInSet_async(AMD_IRenderingSettings_resetMinMaxInSet, String, List<Long>, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
 
ResetPasswordRequestI - Class in omero.cmd.admin
Callback interface allowing to reset password for the given user.
ResetPasswordRequestI(MailUtil, PasswordUtil, SecuritySystem, PasswordProvider) - Constructor for class omero.cmd.admin.ResetPasswordRequestI
 
resetReadFilter(Session) - Method in interface ome.api.local.LocalShare
 
resetReadFilter(Session) - Method in class ome.services.sharing.ShareBean
 
RESOLUTION_DESCRIPTIONS - Static variable in class ome.services.blitz.impl.AbstractPyramidServant
This is a fairly brittle mapping from the List> created by the PixelBuffers to the List which is remotely provided by Blitz.
resolveAlias(String) - Method in class ome.system.PreferenceContext
 
resolveConfigFile(String) - Method in class ome.services.blitz.util.BlitzConfiguration
Resolve the given config file to a concrete location, possibly throwing an exception if stored in a jar.
resolver - Variable in class ome.io.nio.PixelsService
Resolver of archived original file paths for pixels sets.
resource - Variable in class ome.services.messages.ParserOpenFileMessage
 
resource - Variable in class ome.services.messages.RegisterServiceCleanupMessage
 
ResourceError - Exception in ome.conditions
Represents a incorrectible/unforseeable event within the server that lead to a failure of a process.
ResourceError(String) - Constructor for exception ome.conditions.ResourceError
 
Resources - Class in omero.util
Container class for storing resources which should be cleaned up on close and periodically checked.
Resources() - Constructor for class omero.util.Resources
As Resources.Resources(int) but specifies a 60 second sleep period between task execution.
Resources(int) - Constructor for class omero.util.Resources
As Resources#Resources(int, ExecutorService) but uses a Executors.newSingleThreadExecutor().
Resources(int, ScheduledExecutorService) - Constructor for class omero.util.Resources
 
Resources.Entry - Interface in omero.util
Interface to be implemented by any object which wants to be managed by the Resources class.
response - Variable in class ome.services.throttling.Task
 
response(Object, OmeroContext) - Method in class ome.services.throttling.Task
Calls the response method
responseRunning(List<Long>, Current) - Method in class ome.services.blitz.impl.ProcessorCallbackI
Callback method which should not be called for this instance.
restartIfNeeded() - Method in class ome.services.scheduler.SchedulerFactoryBean
Similar to the SchedulerFactoryBean.isRunning() method, but properly handles the situation where the Scheduler has been completely shutdown and therefore must be replaced.
restrictions(IObject) - Method in interface ome.security.ACLVoter
Provide the active restrictions for this IObject.
restrictions(IObject) - Method in class ome.security.basic.BasicACLVoter
 
restrictions(IObject) - Method in class ome.security.CompositeACLVoter
 
restrictions(IObject) - Method in class ome.security.sharing.SharingACLVoter
 
RESUBMITTED - Static variable in interface ome.api.JobHandle
 
result - Variable in exception ome.model.units.BigResult
 
ResultHolder<U> - Class in ome.services.blitz.util
 
ResultHolder(long) - Constructor for class ome.services.blitz.util.ResultHolder
 
results() - Method in interface ome.api.Search
Returns up to batch size number of results along with the related query metadata.
results() - Method in class ome.services.SearchBean
 
results_async(AMD_Search_results, Current) - Method in class ome.services.blitz.impl.SearchI
 
retrieve(String) - Method in class ome.model.acquisition.Arc
 
retrieve(String) - Method in class ome.model.acquisition.Detector
 
retrieve(String) - Method in class ome.model.acquisition.DetectorSettings
 
retrieve(String) - Method in class ome.model.acquisition.Dichroic
 
retrieve(String) - Method in class ome.model.acquisition.Filament
 
retrieve(String) - Method in class ome.model.acquisition.Filter
 
retrieve(String) - Method in class ome.model.acquisition.FilterSet
 
retrieve(String) - Method in class ome.model.acquisition.FilterSetEmissionFilterLink
 
retrieve(String) - Method in class ome.model.acquisition.FilterSetExcitationFilterLink
 
retrieve(String) - Method in class ome.model.acquisition.GenericExcitationSource
 
retrieve(String) - Method in class ome.model.acquisition.ImagingEnvironment
 
retrieve(String) - Method in class ome.model.acquisition.Instrument
 
retrieve(String) - Method in class ome.model.acquisition.Laser
 
retrieve(String) - Method in class ome.model.acquisition.LightEmittingDiode
 
retrieve(String) - Method in class ome.model.acquisition.LightPath
 
retrieve(String) - Method in class ome.model.acquisition.LightPathEmissionFilterLink
 
retrieve(String) - Method in class ome.model.acquisition.LightPathExcitationFilterLink
 
retrieve(String) - Method in class ome.model.acquisition.LightSettings
 
retrieve(String) - Method in class ome.model.acquisition.LightSource
 
retrieve(String) - Method in class ome.model.acquisition.Microscope
 
retrieve(String) - Method in class ome.model.acquisition.Objective
 
retrieve(String) - Method in class ome.model.acquisition.ObjectiveSettings
 
retrieve(String) - Method in class ome.model.acquisition.OTF
 
retrieve(String) - Method in class ome.model.acquisition.StageLabel
 
retrieve(String) - Method in class ome.model.acquisition.TransmittanceRange
 
retrieve(String) - Method in class ome.model.annotations.Annotation
 
retrieve(String) - Method in class ome.model.annotations.AnnotationAnnotationLink
 
retrieve(String) - Method in class ome.model.annotations.BasicAnnotation
 
retrieve(String) - Method in class ome.model.annotations.BooleanAnnotation
 
retrieve(String) - Method in class ome.model.annotations.ChannelAnnotationLink
 
retrieve(String) - Method in class ome.model.annotations.CommentAnnotation
 
retrieve(String) - Method in class ome.model.annotations.DatasetAnnotationLink
 
retrieve(String) - Method in class ome.model.annotations.DetectorAnnotationLink
 
retrieve(String) - Method in class ome.model.annotations.DichroicAnnotationLink
 
retrieve(String) - Method in class ome.model.annotations.DoubleAnnotation
 
retrieve(String) - Method in class ome.model.annotations.ExperimenterAnnotationLink
 
retrieve(String) - Method in class ome.model.annotations.ExperimenterGroupAnnotationLink
 
retrieve(String) - Method in class ome.model.annotations.FileAnnotation
 
retrieve(String) - Method in class ome.model.annotations.FilesetAnnotationLink
 
retrieve(String) - Method in class ome.model.annotations.FilterAnnotationLink
 
retrieve(String) - Method in class ome.model.annotations.ImageAnnotationLink
 
retrieve(String) - Method in class ome.model.annotations.InstrumentAnnotationLink
 
retrieve(String) - Method in class ome.model.annotations.LightPathAnnotationLink
 
retrieve(String) - Method in class ome.model.annotations.LightSourceAnnotationLink
 
retrieve(String) - Method in class ome.model.annotations.ListAnnotation
 
retrieve(String) - Method in class ome.model.annotations.LongAnnotation
 
retrieve(String) - Method in class ome.model.annotations.MapAnnotation
 
retrieve(String) - Method in class ome.model.annotations.NamespaceAnnotationLink
 
retrieve(String) - Method in class ome.model.annotations.NodeAnnotationLink
 
retrieve(String) - Method in class ome.model.annotations.NumericAnnotation
 
retrieve(String) - Method in class ome.model.annotations.ObjectiveAnnotationLink
 
retrieve(String) - Method in class ome.model.annotations.OriginalFileAnnotationLink
 
retrieve(String) - Method in class ome.model.annotations.PlaneInfoAnnotationLink
 
retrieve(String) - Method in class ome.model.annotations.PlateAcquisitionAnnotationLink
 
retrieve(String) - Method in class ome.model.annotations.PlateAnnotationLink
 
retrieve(String) - Method in class ome.model.annotations.ProjectAnnotationLink
 
retrieve(String) - Method in class ome.model.annotations.ReagentAnnotationLink
 
retrieve(String) - Method in class ome.model.annotations.RoiAnnotationLink
 
retrieve(String) - Method in class ome.model.annotations.ScreenAnnotationLink
 
retrieve(String) - Method in class ome.model.annotations.SessionAnnotationLink
 
retrieve(String) - Method in class ome.model.annotations.ShapeAnnotationLink
 
retrieve(String) - Method in class ome.model.annotations.TagAnnotation
 
retrieve(String) - Method in class ome.model.annotations.TermAnnotation
 
retrieve(String) - Method in class ome.model.annotations.TextAnnotation
 
retrieve(String) - Method in class ome.model.annotations.TimestampAnnotation
 
retrieve(String) - Method in class ome.model.annotations.TypeAnnotation
 
retrieve(String) - Method in class ome.model.annotations.WellAnnotationLink
 
retrieve(String) - Method in class ome.model.annotations.XmlAnnotation
 
retrieve(String) - Method in class ome.model.containers.Dataset
 
retrieve(String) - Method in class ome.model.containers.DatasetImageLink
 
retrieve(String) - Method in class ome.model.containers.Project
 
retrieve(String) - Method in class ome.model.containers.ProjectDatasetLink
 
retrieve(String) - Method in class ome.model.core.Channel
 
retrieve(String) - Method in class ome.model.core.Image
 
retrieve(String) - Method in class ome.model.core.LogicalChannel
 
retrieve(String) - Method in class ome.model.core.OriginalFile
 
retrieve(String) - Method in class ome.model.core.Pixels
 
retrieve(String) - Method in class ome.model.core.PixelsOriginalFileMap
 
retrieve(String) - Method in class ome.model.core.PlaneInfo
 
retrieve(String) - Method in class ome.model.display.ChannelBinding
 
retrieve(String) - Method in class ome.model.display.CodomainMapContext
 
retrieve(String) - Method in class ome.model.display.ContrastStretchingContext
 
retrieve(String) - Method in class ome.model.display.PlaneSlicingContext
 
retrieve(String) - Method in class ome.model.display.QuantumDef
 
retrieve(String) - Method in class ome.model.display.RenderingDef
 
retrieve(String) - Method in class ome.model.display.ReverseIntensityContext
 
retrieve(String) - Method in class ome.model.display.Thumbnail
 
retrieve(String) - Method in class ome.model.enums.AcquisitionMode
 
retrieve(String) - Method in class ome.model.enums.ArcType
 
retrieve(String) - Method in class ome.model.enums.Binning
 
retrieve(String) - Method in class ome.model.enums.ChecksumAlgorithm
 
retrieve(String) - Method in class ome.model.enums.ContrastMethod
 
retrieve(String) - Method in class ome.model.enums.Correction
 
retrieve(String) - Method in class ome.model.enums.DetectorType
 
retrieve(String) - Method in class ome.model.enums.DimensionOrder
 
retrieve(String) - Method in class ome.model.enums.EventType
 
retrieve(String) - Method in class ome.model.enums.ExperimentType
 
retrieve(String) - Method in class ome.model.enums.Family
 
retrieve(String) - Method in class ome.model.enums.FilamentType
 
retrieve(String) - Method in class ome.model.enums.FilterType
 
retrieve(String) - Method in class ome.model.enums.Format
 
retrieve(String) - Method in class ome.model.enums.Illumination
 
retrieve(String) - Method in class ome.model.enums.Immersion
 
retrieve(String) - Method in class ome.model.enums.LaserMedium
 
retrieve(String) - Method in class ome.model.enums.LaserType
 
retrieve(String) - Method in class ome.model.enums.Medium
 
retrieve(String) - Method in class ome.model.enums.MicrobeamManipulationType
 
retrieve(String) - Method in class ome.model.enums.MicroscopeType
 
retrieve(String) - Method in class ome.model.enums.PhotometricInterpretation
 
retrieve(String) - Method in class ome.model.enums.PixelsType
 
retrieve(String) - Method in class ome.model.enums.Pulse
 
retrieve(String) - Method in class ome.model.enums.RenderingModel
 
retrieve(String) - Method in class ome.model.experiment.Experiment
 
retrieve(String) - Method in class ome.model.experiment.MicrobeamManipulation
 
retrieve(String) - Method in class ome.model.fs.Fileset
 
retrieve(String) - Method in class ome.model.fs.FilesetEntry
 
retrieve(String) - Method in class ome.model.fs.FilesetJobLink
 
retrieve(String) - Method in class ome.model.internal.Details
 
retrieve(String) - Method in class ome.model.internal.Link
 
retrieve(String) - Method in interface ome.model.IObject
retrieves a value from this instance.
retrieve(String) - Method in class ome.model.jobs.ImportJob
 
retrieve(String) - Method in class ome.model.jobs.IndexingJob
 
retrieve(String) - Method in class ome.model.jobs.IntegrityCheckJob
 
retrieve(String) - Method in class ome.model.jobs.Job
 
retrieve(String) - Method in class ome.model.jobs.JobOriginalFileLink
 
retrieve(String) - Method in class ome.model.jobs.JobStatus
 
retrieve(String) - Method in class ome.model.jobs.MetadataImportJob
 
retrieve(String) - Method in class ome.model.jobs.ParseJob
 
retrieve(String) - Method in class ome.model.jobs.PixelDataJob
 
retrieve(String) - Method in class ome.model.jobs.ScriptJob
 
retrieve(String) - Method in class ome.model.jobs.ThumbnailGenerationJob
 
retrieve(String) - Method in class ome.model.jobs.UploadJob
 
retrieve(String) - Method in class ome.model.meta.DBPatch
 
retrieve(String) - Method in class ome.model.meta.Event
 
retrieve(String) - Method in class ome.model.meta.EventLog
 
retrieve(String) - Method in class ome.model.meta.Experimenter
 
retrieve(String) - Method in class ome.model.meta.ExperimenterGroup
 
retrieve(String) - Method in class ome.model.meta.ExternalInfo
 
retrieve(String) - Method in class ome.model.meta.GroupExperimenterMap
 
retrieve(String) - Method in class ome.model.meta.Namespace
 
retrieve(String) - Method in class ome.model.meta.Node
 
retrieve(String) - Method in class ome.model.meta.Session
 
retrieve(String) - Method in class ome.model.meta.Share
 
retrieve(String) - Method in class ome.model.meta.ShareMember
 
retrieve(String) - Method in class ome.model.roi.Ellipse
 
retrieve(String) - Method in class ome.model.roi.Label
 
retrieve(String) - Method in class ome.model.roi.Line
 
retrieve(String) - Method in class ome.model.roi.Mask
 
retrieve(String) - Method in class ome.model.roi.Path
 
retrieve(String) - Method in class ome.model.roi.Point
 
retrieve(String) - Method in class ome.model.roi.Polygon
 
retrieve(String) - Method in class ome.model.roi.Polyline
 
retrieve(String) - Method in class ome.model.roi.Rect
 
retrieve(String) - Method in class ome.model.roi.Roi
 
retrieve(String) - Method in class ome.model.roi.Shape
 
retrieve(String) - Method in class ome.model.screen.Plate
 
retrieve(String) - Method in class ome.model.screen.PlateAcquisition
 
retrieve(String) - Method in class ome.model.screen.Reagent
 
retrieve(String) - Method in class ome.model.screen.Screen
 
retrieve(String) - Method in class ome.model.screen.ScreenPlateLink
 
retrieve(String) - Method in class ome.model.screen.Well
 
retrieve(String) - Method in class ome.model.screen.WellReagentLink
 
retrieve(String) - Method in class ome.model.screen.WellSample
 
retrieve(String) - Method in class ome.model.stats.StatsInfo
 
retrieveAllRndSettings(long, long) - Method in interface ome.api.IPixels
Retrieves all the rendering settings for a given pixels set and the passed user with the following objects pre-linked: renderingDef.quantization renderingDef.model renderingDef.waveRendering renderingDef.waveRendering.color renderingDef.waveRendering.family renderingDef.spatialDomainEnhancement
retrieveAllRndSettings(long, long) - Method in class ome.logic.PixelsImpl
Implemented as specified by the IPixels I/F.
retrieveAllRndSettings_async(AMD_IPixels_retrieveAllRndSettings, long, long, Current) - Method in class ome.services.blitz.impl.PixelsI
 
retrieveCollection(IObject, String, Parameters) - Method in interface ome.api.IContainer
Retrieves a collection with all members initialized ("loaded").
retrieveCollection(IObject, String, Parameters) - Method in class ome.logic.PojosImpl
Implemented as specified by the IContainer I/F
retrieveCollection_async(AMD_IContainer_retrieveCollection, IObject, String, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI
 
retrievePixDescription(long) - Method in interface ome.api.IPixels
Retrieves the pixels metadata with the following objects pre-linked: pixels.pixelsType pixels.pixelsDimensions pixels.channels pixels.channnels.statsInfo pixels.channnels.colorComponent pixels.channnels.logicalChannel pixels.channnels.logicalChannel.photometricInterpretation
retrievePixDescription(long) - Method in class ome.logic.PixelsImpl
 
retrievePixDescription_async(AMD_IPixels_retrievePixDescription, long, Current) - Method in class ome.services.blitz.impl.PixelsI
 
retrieveRndSettings(long) - Method in interface ome.api.IPixels
Retrieves the rendering settings for a given pixels set and the currently logged in user.
retrieveRndSettings(long) - Method in class ome.logic.PixelsImpl
Implemented as specified by the IPixels I/F.
retrieveRndSettings_async(AMD_IPixels_retrieveRndSettings, long, Current) - Method in class ome.services.blitz.impl.PixelsI
 
retrieveRndSettingsFor(long, long) - Method in interface ome.api.IPixels
Retrieves the rendering settings for a given pixels set and the passed user with the following objects pre-linked: renderingDef.quantization renderingDef.model renderingDef.waveRendering renderingDef.waveRendering.color renderingDef.waveRendering.family renderingDef.spatialDomainEnhancement
retrieveRndSettingsFor(long, long) - Method in class ome.logic.PixelsImpl
Implemented as specified by the IPixels I/F.
retrieveRndSettingsFor_async(AMD_IPixels_retrieveRndSettingsFor, long, long, Current) - Method in class ome.services.blitz.impl.PixelsI
 
returnedClass() - Method in class ome.model.units.GenericEnumType
 
returnedClass() - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
 
returnSeen(Object) - Method in class ome.tools.hibernate.UpdateFilter
 
returnUnloaded - Variable in class ome.services.search.SearchValues
 
reusedSession - Variable in class omero.cmd.SessionI
 
reverse - Variable in class ome.model.display.ReverseIntensityContext
 
REVERSE - Static variable in class ome.model.display.ReverseIntensityContext
 
reverse(ModelBased) - Method in interface ome.util.ReverseModelMapper
 
reverse(Collection) - Method in interface ome.util.ReverseModelMapper
 
reverse(Object) - Method in class omero.util.IceMapper
 
reverse(Collection) - Method in class omero.util.IceMapper
Copied from ModelMapper.findCollection(Collection) This could be unified in that a method findCollection(Collection, Map) was added with ModelMapper calling findCollection(source,model2target) and #reverseCollection(Collection) calling findCollection(source,target2model).
reverse(Collection, Class) - Method in class omero.util.IceMapper
Creates a collection assignable to the given type.
reverse(Map) - Method in class omero.util.IceMapper
 
reverse(ModelBased) - Method in class omero.util.IceMapper
Copied from ReverseModelMapper#map(ModelBased)
reverseArray(List, Class) - Method in class omero.util.IceMapper
Supports the separate case of reversing for arrays.
ReverseIntensityContext - Class in ome.model.display
 
ReverseIntensityContext() - Constructor for class ome.model.display.ReverseIntensityContext
 
ReverseIntensityContext(Long) - Constructor for class ome.model.display.ReverseIntensityContext
 
ReverseIntensityContext(Long, boolean) - Constructor for class ome.model.display.ReverseIntensityContext
Main constructor.
ReverseIntensityContext(Boolean) - Constructor for class ome.model.display.ReverseIntensityContext
 
ReverseIntensityContext - Class in omeis.providers.re.codomain
The empty context of the reverse intensity map.
ReverseIntensityContext() - Constructor for class omeis.providers.re.codomain.ReverseIntensityContext
 
ReverseModelMapper - Interface in ome.util
 
reverseNamedList(List<NamedValue>) - Static method in class omero.util.IceMapper
 
reverseStringStringMap(Map<String, RString>) - Static method in class omero.util.IceMapper
Reverse a String→String map's values from RStrings.
review(Map<String, Set<GraphPolicy.Details>>, GraphPolicy.Details, Map<String, Set<GraphPolicy.Details>>, Set<String>, boolean) - Method in class ome.services.graphs.GraphPolicy
The action to take about the link between the mapped objects.
review(Map<String, Set<GraphPolicy.Details>>, GraphPolicy.Details, Map<String, Set<GraphPolicy.Details>>, Set<String>, boolean) - Method in class omero.cmd.graphs.BaseGraphPolicyAdjuster
 
revision - Static variable in class ome.formats.importer.Version
The repository revision.
RevisionDate - Annotation Type in ome.annotations
annotation used for tracking source code changes.
revisionDate - Static variable in class ome.formats.importer.Version
The data of the last repository revision.
RevisionNumber - Annotation Type in ome.annotations
annotation used for tracking source code changes.
revoke(Permissions.Role, Permissions.Right...) - Method in class ome.model.internal.Permissions
turns off the rights for the given role.
revokeAll(Permissions) - Method in class ome.model.internal.Permissions
takes a permissions instance and ANDs it with the current instance.
rewriteHql(String, String, Object) - Method in class ome.util.actions.PostgresSqlAction
The temp_ids infrastructure was never properly put in place for the "psql" profile.
rewriteHql(String, String, Object) - Method in class ome.util.SqlAction.Impl
 
rewriteHql(String, String, Object) - Method in interface ome.util.SqlAction
Allows the specific database implementations a chance to modify queries.
rfloat(float) - Static method in class omero.rtypes
 
RGBAIntBuffer - Class in omeis.providers.re
Holds the data of an RGBA image.
RGBAIntBuffer(int, int) - Constructor for class omeis.providers.re.RGBAIntBuffer
Creates a new 4-band packed integer buffer.
RGBBuffer - Class in omeis.providers.re
Holds the data of an RGB image.
RGBBuffer() - Constructor for class omeis.providers.re.RGBBuffer
Simple constructor to avoid memory allocations.
RGBBuffer(int, int) - Constructor for class omeis.providers.re.RGBBuffer
Creates a new 3-band buffer.
RGBIntBuffer - Class in omeis.providers.re
Holds the data of an RGB image.
RGBIntBuffer(int, int) - Constructor for class omeis.providers.re.RGBIntBuffer
Creates a new 3-band packed integer buffer.
Ring - Class in ome.services.blitz.fire
Distributed ring of BlitzConfiguration objects which manages lookups of sessions and other resources from all the blitzes which take part in the cluster.
Ring(String, Executor) - Constructor for class ome.services.blitz.fire.Ring
 
Ring(String, Executor, Redirector) - Constructor for class ome.services.blitz.fire.Ring
 
ring - Variable in class ome.services.blitz.fire.SessionManagerI
 
rint(int) - Static method in class omero.rtypes
 
rinternal(Internal) - Static method in class omero.rtypes
 
rlist(RType...) - Static method in class omero.rtypes
 
rlist(Collection<RType>) - Static method in class omero.rtypes
 
rlong(long) - Static method in class omero.rtypes
 
rmap() - Static method in class omero.rtypes
 
rmap(Map<String, RType>) - Static method in class omero.rtypes
 
rmap(String, RType) - Static method in class omero.rtypes
 
robject(IObject) - Static method in class omero.rtypes
 
Roi - Class in ome.model.roi
These filter definitions are used by the security system to eliminate non-readable objects from queries.
Roi() - Constructor for class ome.model.roi.Roi
 
Roi(Long) - Constructor for class ome.model.roi.Roi
 
Roi(Long, boolean) - Constructor for class ome.model.roi.Roi
Main constructor.
roi - Variable in class ome.model.roi.Shape
 
ROI - Static variable in class ome.model.roi.Shape
 
Roi.Details - Class in ome.model.roi
 
Roi.Details() - Constructor for class ome.model.roi.Roi.Details
 
Roi.Details(Object[]) - Constructor for class ome.model.roi.Roi.Details
 
RoiAnnotationLink - Class in ome.model.annotations
These filter definitions are used by the security system to eliminate non-readable objects from queries.
RoiAnnotationLink() - Constructor for class ome.model.annotations.RoiAnnotationLink
 
RoiAnnotationLink(Long) - Constructor for class ome.model.annotations.RoiAnnotationLink
 
RoiAnnotationLink(Long, boolean) - Constructor for class ome.model.annotations.RoiAnnotationLink
Main constructor.
RoiAnnotationLink(IObject, IObject) - Constructor for class ome.model.annotations.RoiAnnotationLink
 
RoiAnnotationLink.Details - Class in ome.model.annotations
 
RoiAnnotationLink.Details() - Constructor for class ome.model.annotations.RoiAnnotationLink.Details
 
RoiAnnotationLink.Details(Object[]) - Constructor for class ome.model.annotations.RoiAnnotationLink.Details
 
roiByImageAndNs(long, String) - Method in class ome.util.actions.PostgresSqlAction
 
roiByImageAndNs(long, String) - Method in interface ome.util.SqlAction
 
ROIComponent - Class in pojos.util
Component hosting the ROI.
ROIComponent(long) - Constructor for class pojos.util.ROIComponent
Instantiate the ROIComponent.
ROICoordinate - Class in pojos
Defines a plane.
ROICoordinate() - Constructor for class pojos.ROICoordinate
Creates a default instance.
ROICoordinate(int, int) - Constructor for class pojos.ROICoordinate
Creates a new instance.
ROIData - Class in pojos
Converts the ROI object.
ROIData(Roi) - Constructor for class pojos.ROIData
Creates a new instance.
ROIData() - Constructor for class pojos.ROIData
Create a new instance of an ROIData object.
RoiI - Class in ome.services.blitz.impl
implementation of the IRoi service interface.
RoiI(BlitzExecutor, GeomTool, SqlAction) - Constructor for class ome.services.blitz.impl.RoiI
 
RoiI.RoiResultMapper - Class in ome.services.blitz.impl
 
RoiI.RoiResultMapper(RoiOptions) - Constructor for class ome.services.blitz.impl.RoiI.RoiResultMapper
 
RoiI.RoiResultMapReturnMapper - Class in ome.services.blitz.impl
 
RoiI.RoiResultMapReturnMapper(RoiOptions) - Constructor for class ome.services.blitz.impl.RoiI.RoiResultMapReturnMapper
 
RoiI.RoiResultReturnMapper - Class in ome.services.blitz.impl
 
RoiI.RoiResultReturnMapper(RoiOptions) - Constructor for class ome.services.blitz.impl.RoiI.RoiResultReturnMapper
 
rois - Variable in class ome.model.core.Image
 
ROIS - Static variable in class ome.model.core.Image
 
RoiTypes - Class in ome.services.roi
Intelligent server-side representations of the Roi and Shape types.
RoiTypes() - Constructor for class ome.services.roi.RoiTypes
 
RoiTypes.RoiTypesObjectFactoryRegistry - Class in ome.services.roi
 
RoiTypes.RoiTypesObjectFactoryRegistry() - Constructor for class ome.services.roi.RoiTypes.RoiTypesObjectFactoryRegistry
 
roleProvider - Variable in class ome.logic.AdminImpl
 
RoleProvider - Interface in ome.security.auth
Provides user and group creation, deletion, and modification for use by services.
roles - Variable in class ome.security.basic.AbstractSecurityFilter
 
roles - Variable in class ome.security.basic.BasicACLVoter
 
roles - Variable in class ome.security.basic.BasicSecuritySystem
 
roles - Variable in class ome.services.blitz.repo.RepositoryDaoImpl
 
roles - Variable in class ome.services.sessions.SessionManagerImpl
 
Roles - Class in ome.system
encapsulates the naming scheme for critical system groups and accounts.
Roles() - Constructor for class ome.system.Roles
default constructor which assigns hard-coded values to all roles
Roles(long, String, long, String, long, String, long, String, long, String) - Constructor for class ome.system.Roles
constructor which allows full specification of all roles
RolesAllowed - Annotation Type in ome.annotations
Security annotation which specifies a list of user roles which will be permitted to execute this method.
rollback(EventLog) - Method in class ome.services.eventlogs.EventLogLoader
 
rollback(String, int) - Method in class ome.services.graphs.GraphState
Deprecated.
 
rollback(String, int) - Method in interface ome.services.graphs.GraphStep.Callback
Deprecated.
 
rollback(GraphStep.Callback) - Method in class ome.services.graphs.GraphStep
Deprecated.
 
rollbackOnly() - Method in class ome.services.graphs.GraphStep
Deprecated.
 
rollbackSavepoint(String) - Method in class ome.util.actions.PostgresSqlAction
 
rollbackSavepoint(String) - Method in interface ome.util.SqlAction
 
RomioPixelBuffer - Class in ome.io.nio
Class implementation of the PixelBuffer interface for standard "proprietary" ROMIO/OMEIS data format.
RomioPixelBuffer(String, Pixels) - Constructor for class ome.io.nio.RomioPixelBuffer
Creates a new instance.
RomioPixelBuffer(String, Pixels, boolean) - Constructor for class ome.io.nio.RomioPixelBuffer
Creates a new instance, with manual setting of RomioPixelBuffer.permitModification.
root(Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
 
ROOT - Static variable in class prefs
"omero.prefs", the value of the root Preferences node used for all configuration work.
ROOT_DEFAULT - Static variable in class ome.io.nio.AbstractFileSystemService
 
RootException - Exception in ome.conditions
abstract superclass of all Omero exceptions.
RootException(String) - Constructor for exception ome.conditions.RootException
 
ROUTED_FROM - Static variable in class ome.services.blitz.redirect.AbstractRedirector
 
Router - Class in ome.services.blitz
Wrapper around a call to 'glacier2router' to permit Java control over the process.
Router() - Constructor for class ome.services.blitz.Router
 
row - Variable in class ome.model.screen.Well
 
ROW - Static variable in class ome.model.screen.Well
 
rowNamingConvention - Variable in class ome.model.screen.Plate
 
ROWNAMINGCONVENTION - Static variable in class ome.model.screen.Plate
 
rows - Variable in class ome.model.screen.Plate
 
ROWS - Static variable in class ome.model.screen.Plate
 
rps - Variable in class omero.util.RPSTileData
 
RPSTileData - Class in omero.util
Access strategy which can be implemented by diverse resources
RPSTileData(RPSTileLoop, RawPixelsStorePrx) - Constructor for class omero.util.RPSTileData
 
RPSTileLoop - Class in omero.util
Helper subclass of TileLoop which handles unloaded Pixels instances and manages the creation of the RPSTileData.
RPSTileLoop(ServiceFactoryPrx, Pixels) - Constructor for class omero.util.RPSTileLoop
 
rset(RType...) - Static method in class omero.rtypes
 
rset(Collection<RType>) - Static method in class omero.rtypes
 
rstring(String) - Static method in class omero.rtypes
 
RTF - Static variable in class pojos.FileAnnotationData
Identifies the RTF file formats.
rtime(long) - Static method in class omero.rtypes
 
rtime(Date) - Static method in class omero.rtypes
 
rtime_max() - Static method in class omero.rtypes
 
rtime_min() - Static method in class omero.rtypes
 
rtime_str(String) - Static method in class omero.rtypes
 
rtype(Object) - Static method in class omero.rtypes
Attempts to dispatch to the other omero.rtypes.* static methods to create a proper RType subclass by checking the type of the input.
RTYPEDICT - Static variable in class omero.util.IceMapper
 
RTypeMapper - Class in omero.util
Extension of IceMapper which guarantees that RCollection and RMap instances are properly created.
RTypeMapper(IceMapper.ReturnMapping) - Constructor for class omero.util.RTypeMapper
 
rtypes - Class in omero
Abstract class similar to Arrays or Collections which is responsible for creating RTypes from static factory methods.
rtypes() - Constructor for class omero.rtypes
 
rtypes.Conversion - Interface in omero
SPI-style interface which helps the omero server to properly convert omero.RType objects into Java-native objects for use in Hibernate.
rtypes.RTypeObjectFactoryRegistry - Class in omero
 
rtypes.RTypeObjectFactoryRegistry() - Constructor for class omero.rtypes.RTypeObjectFactoryRegistry
 
rules - Variable in class ome.services.blitz.repo.path.FilePathNamingValidator
 
rules - Variable in class ome.services.blitz.repo.path.MakePathComponentSafe
 
run() - Method in class ome.formats.importer.util.ClientKeepAlive
 
run(int, int, int, int, int, int, int, int) - Method in interface ome.io.nio.TileLoopIteration
Invoke a single loop iteration.
run() - Method in class ome.services.blitz.Status
 
run() - Method in class ome.services.blitz.util.CheckAllJobs
 
run() - Method in class ome.services.delete.files.FileDeleter
 
run() - Method in interface ome.services.procs.IProcessManager
Runs the processing phase as root.
run(OmeroContext) - Method in class ome.services.throttling.Adapter
 
run(OmeroContext) - Method in class ome.services.throttling.Callback
 
run(OmeroContext) - Method in class ome.services.throttling.Callback2
 
run() - Method in class ome.services.throttling.Slot
 
run(OmeroContext) - Method in class ome.services.throttling.Task
 
run() - Method in class ome.services.util.ExecutionThread
Initializes the Session for this Thread if necessary, then calls ExecutionThread.doRun().
run() - Method in class ome.services.util.ServerDirectoryCheck
Synchronizes the ${omero.data.dir}/Server directory by creating a directory for any user who does not have one.
run() - Method in class ome.system.UpgradeCheck
If the UpgradeCheck.url has been set to null or the empty string, then no upgrade check will be performed (silently).
run() - Method in class omero.cmd.HandleI
NB: only executes if HandleI.state is State#CREATED.
run(TileData, int, int, int, int, int, int, int, int) - Method in interface omero.util.TileLoopIteration
Invoke a single loop iteration.
runAsAdmin() - Method in interface ome.security.AdminAction
executes with special privilegs within the SecuritySystem.
runAsAdmin(AdminAction) - Method in class ome.security.basic.BasicSecuritySystem
runAsAdmin(ExperimenterGroup, AdminAction) - Method in class ome.security.basic.BasicSecuritySystem
merge event is disabled for BasicSecuritySystem.runAsAdmin(AdminAction) because passing detached (client-side) entities to this method is particularly dangerous.
runAsAdmin(ExperimenterGroup, AdminAction) - Method in interface ome.security.SecuritySystem
Allows actions to be performed with the EventContext.isCurrentUserAdmin() flag enabled but without changing the value of EventContext.getCurrentUserId(), so that ownerships are properly handled.
runAsAdmin(AdminAction) - Method in interface ome.security.SecuritySystem
runAsAdmin(AdminAction) - Method in class ome.security.SecuritySystemHolder
 
runAsAdmin(ExperimenterGroup, AdminAction) - Method in class ome.security.SecuritySystemHolder
 
runAsAdmin(ExperimenterGroup, AdminAction) - Method in class ome.security.sharing.SharingSecuritySystem
 
runAsAdmin(AdminAction) - Method in class ome.security.sharing.SharingSecuritySystem
 
runAsAdmin() - Method in class ome.services.delete.QueryConstraints
 
runnableCall(Current, Task) - Method in class ome.services.blitz.impl.AbstractAmdServant
 
runnableCall(Current, Task) - Method in interface ome.services.blitz.util.BlitzExecutor
 
runnableCall(Current, Task) - Method in class ome.services.throttling.InThreadThrottlingStrategy
 
runnableCall(Current, Task) - Method in class ome.services.throttling.SerialThrottlingStrategy
 
RUNNING - Static variable in interface ome.api.JobHandle
 
runningProcess(long) - Method in interface ome.services.procs.IProcessManager
Returns a running Process for the id or null.
runningProcess(long) - Method in class ome.services.procs.ProcessManager
 
runQuery(String[], GraphEntry, Query, Session) - Method in class ome.services.graphs.BaseGraphSpec
Deprecated.
 
runScript_async(AMD_IScript_runScript, long, Map<String, RType>, RInt, Current) - Method in class ome.services.blitz.impl.ScriptI
 
rx - Variable in class ome.model.roi.Ellipse
 
RX - Static variable in class ome.model.roi.Ellipse
 
rx - Variable in class ome.model.roi.Rect
 
RX - Static variable in class ome.model.roi.Rect
 
ry - Variable in class ome.model.roi.Ellipse
 
RY - Static variable in class ome.model.roi.Ellipse
 

S

safeCharacter - Variable in class ome.services.blitz.repo.path.FilePathRestrictions
 
safeCharacters - Variable in class ome.services.blitz.repo.path.FilePathRestrictions
 
safeLongToInteger(Long) - Static method in class ome.io.nio.RomioPixelBuffer
Converts a Long value to an Integer safely.
safeRunnableCall(Current, Object, boolean, Callable<R>) - Method in class ome.services.blitz.impl.AbstractAmdServant
 
safeRunnableCall(Current, Object, boolean, Callable<R>) - Method in interface ome.services.blitz.util.BlitzExecutor
 
safeRunnableCall(Current, Object, boolean, Callable<R>) - Method in class ome.services.throttling.InThreadThrottlingStrategy
 
safeRunnableCall(Current, Object, boolean, Callable<R>) - Method in class ome.services.throttling.SerialThrottlingStrategy
 
salt - Variable in class ome.security.auth.ConfigurablePasswordProvider
Whether or not salting based on the user ID should be attempted.
saltedPasswordDigest(Long, String) - Method in class ome.security.auth.PasswordUtil
Creates an MD5 hash of the given clear text and base64 encodes it.
sameRights(Permissions) - Method in class ome.model.internal.Permissions
returns true if two Permissions instances have all the same Permissions.Right / Permissions.Role pairs granted.
samplesPerPixel - Variable in class ome.model.core.LogicalChannel
 
SAMPLESPERPIXEL - Static variable in class ome.model.core.LogicalChannel
 
sanityCheckPixels(Pixels, Pixels) - Method in interface ome.api.IRenderingSettings
Checks if the specified sets of pixels are compatible.
sanityCheckPixels(Pixels, Pixels) - Method in class ome.logic.RenderingSettingsImpl
Implemented as specified by the IRenderingSettings I/F
sanityCheckPixels_async(AMD_IRenderingSettings_sanityCheckPixels, Pixels, Pixels, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
 
sanityCheckRepository() - Method in interface ome.api.IRepositoryInfo
Checks that image data repository has not exceeded 95% disk space use level.
sanityCheckRepository() - Method in class ome.logic.RepositoryInfoImpl
 
sanityCheckRepository_async(AMD_IRepositoryInfo_sanityCheckRepository, Current) - Method in class ome.services.blitz.impl.RepositoryInfoI
 
save() - Method in interface ome.api.RawFileStore
Saves the OriginalFile associated with the service if it has been modified.
save() - Method in interface ome.api.RawPixelsStore
 
save() - Method in class ome.formats.importer.transfers.TransferState
Calls RawFileStorePrx.save() and stores the resultant OriginalFile for future inspection along with the local checksum.
save() - Method in class ome.services.blitz.measurements.MeasurementStore
 
save() - Method in interface ome.services.blitz.measurements.OmeroMeasurementStore
 
save() - Method in class ome.services.RawFileBean
 
save() - Method in class ome.services.RawPixelsBean
 
save_async(AMD_RawFileStore_save, Current) - Method in class ome.services.blitz.impl.RawFileStoreI
 
save_async(AMD_RawPixelsStore_save, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
save_async(AMD_RawPixelsStore_save, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
SAVE_EVENT - Static variable in class ome.security.basic.SaveEventListener
 
saveAll() - Method in class ome.formats.importer.ImportConfig
 
saveAndReturnArray(IObject[]) - Method in interface ome.api.IUpdate
 
saveAndReturnArray(IObject[]) - Method in class ome.logic.UpdateImpl
 
saveAndReturnArray_async(AMD_IUpdate_saveAndReturnArray, List<IObject>, Current) - Method in class ome.services.blitz.impl.UpdateI
 
saveAndReturnIds(IObject[]) - Method in interface ome.api.IUpdate
Logic differs from other methods.
saveAndReturnIds(IObject[]) - Method in class ome.logic.UpdateImpl
 
saveAndReturnIds_async(AMD_IUpdate_saveAndReturnIds, List<IObject>, Current) - Method in class ome.services.blitz.impl.UpdateI
 
saveAndReturnObject(T) - Method in interface ome.api.IUpdate
 
saveAndReturnObject(IObject) - Method in class ome.logic.UpdateImpl
 
saveAndReturnObject_async(AMD_IUpdate_saveAndReturnObject, IObject, Current) - Method in class ome.services.blitz.impl.UpdateI
 
saveArray(IObject[]) - Method in interface ome.api.IUpdate
 
saveArray(IObject[]) - Method in class ome.logic.UpdateImpl
 
saveArray_async(AMD_IUpdate_saveArray, List<IObject>, Current) - Method in class ome.services.blitz.impl.UpdateI
 
saveAsNewSettings() - Method in class ome.services.RenderingBean
Implemented as specified by the RenderingEngine interface.
saveAsNewSettings() - Method in interface omeis.providers.re.RenderingEngine
Saves the current rendering settings in the database as a new RenderingDef and loads the object into the current RenderingEngine.
saveAsNewSettings_async(AMD_RenderingEngine_saveAsNewSettings, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
saveCollection(Collection<IObject>) - Method in interface ome.api.IUpdate
 
saveCollection(Collection) - Method in class ome.logic.UpdateImpl
 
saveCollection_async(AMD_IUpdate_saveCollection, List<IObject>, Current) - Method in class ome.services.blitz.impl.UpdateI
 
saveCurrentSettings() - Method in class ome.services.RenderingBean
Implemented as specified by the RenderingEngine interface.
saveCurrentSettings() - Method in interface omeis.providers.re.RenderingEngine
Saves the current rendering settings in the database.
saveCurrentSettings_async(AMD_RenderingEngine_saveCurrentSettings, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
savedDataset - Variable in class ome.formats.importer.ImportConfig
 
savedDirectory - Variable in class ome.formats.importer.ImportConfig
 
savedImagesNotInPlates - Variable in class ome.services.blitz.impl.MetadataStoreI
 
savedPlates - Variable in class ome.services.blitz.impl.MetadataStoreI
 
savedProject - Variable in class ome.formats.importer.ImportConfig
 
savedScreen - Variable in class ome.formats.importer.ImportConfig
 
SaveEventListener - Class in ome.security.basic
event listener which will only handle newly created (transient) objects in a given graph.
SaveEventListener(CurrentDetails, TokenHolder) - Constructor for class ome.security.basic.SaveEventListener
main constructor.
saveFileset(String, Fileset, ChecksumAlgorithm, List<CheckedPath>, Current) - Method in interface ome.services.blitz.repo.RepositoryDao
Fill the various fields of the Fileset and then save the entire instance into the database.
saveFileset(String, Fileset, ChecksumAlgorithm, List<CheckedPath>, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
 
saveGui() - Method in class ome.formats.importer.ImportConfig
Saves gui specific values for which it makes sense to have a preferences values.
SaveI - Class in ome.services.blitz.impl.commands
Permits saving a single IObject instance.
SaveI() - Constructor for class ome.services.blitz.impl.commands.SaveI
 
saveJob(T, Current) - Method in interface ome.services.blitz.repo.RepositoryDao
Create a job from an instance provided by either the client or the server.
saveJob(Job, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
 
saveObject(IObject) - Method in interface ome.api.IUpdate
 
saveObject(IObject) - Method in class ome.logic.UpdateImpl
 
saveObject(IObject, Current) - Method in interface ome.services.blitz.repo.RepositoryDao
Save the given model object.
saveObject(IObject, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
 
saveObject_async(AMD_IUpdate_saveObject, IObject, Current) - Method in class ome.services.blitz.impl.UpdateI
 
saveOmeroRoiToMetadataStore(List<Roi>, MetadataStore) - Static method in class loci.ome.io.OmeroReader
Converts omero.model.Roi to ome.xml.model.* and updates the MetadataStore
savepoint(String) - Method in class ome.services.graphs.GraphState
Deprecated.
 
savepoint(String) - Method in interface ome.services.graphs.GraphStep.Callback
Deprecated.
 
savepoint(GraphStep.Callback) - Method in class ome.services.graphs.GraphStep
Deprecated.
 
saveRndSettings(RenderingDef) - Method in interface ome.api.IPixels
Saves the specified rendering settings.
saveRndSettings(RenderingDef) - Method in class ome.logic.PixelsImpl
 
saveRndSettings_async(AMD_IPixels_saveRndSettings, RenderingDef, Current) - Method in class ome.services.blitz.impl.PixelsI
 
saveToDB(FilesetJobLink) - Method in class ome.formats.OMEROMetadataStore
Saves the current object graph to the database.
saveToDB(FilesetJobLink) - Method in class ome.formats.OMEROMetadataStoreClient
Updates the server side MetadataStore with a list of our objects and references and saves them into the database.
saveToDB_async(AMD_MetadataStore_saveToDB, FilesetJobLink, Current) - Method in class ome.services.blitz.impl.MetadataStoreI
 
scalar(double) - Method in class ome.util.math.geom2D.PlanePoint
Multiplies this vector by the specified scalar.
scale - Variable in class ome.model.meta.Node
 
SCALE - Static variable in class ome.model.meta.Node
 
scale(double) - Method in class ome.util.math.geom2D.EllipseArea
Implemented as specified by the PlaneArea I/F.
scale(double) - Method in interface ome.util.math.geom2D.PlaneArea
Resets the bounding Rectangle of the planeArea according to the specified scaling factor.
scale(double) - Method in class ome.util.math.geom2D.RectangleArea
Implemented as specified by the PlaneArea I/F.
scaleBufferedImage(BufferedImage, float, float) - Method in interface ome.api.IScale
Scales a buffered image using defined X and Y axis scale factors.
scaleBufferedImage(BufferedImage, float, float) - Method in class ome.logic.AWTScaleService
 
scaleBufferedImage(BufferedImage, float, float) - Method in class ome.logic.JavaImageScalingService
 
ScaleRedirector - Class in ome.services.blitz.redirect
Planned implementation (NYI): will use the "Node.scale" column to randomly choose a target.
ScaleRedirector(Executor) - Constructor for class ome.services.blitz.redirect.ScaleRedirector
 
scalingFactor - Variable in class ome.io.nio.SimpleBackOff
 
scheduledFor - Variable in class ome.model.jobs.Job
 
SCHEDULEDFOR - Static variable in class ome.model.jobs.Job
 
SchedulerFactoryBean - Class in ome.services.scheduler
Produces a SchedulerFactoryBean() - Constructor for class ome.services.scheduler.SchedulerFactoryBean
 
SCORE - Static variable in interface ome.api.Search
String constant used to look up the score value of Lucene queries returned by this interface.
screen - Variable in class ome.model.screen.Reagent
 
SCREEN - Static variable in class ome.model.screen.Reagent
 
Screen - Class in ome.model.screen
These filter definitions are used by the security system to eliminate non-readable objects from queries.
Screen() - Constructor for class ome.model.screen.Screen
 
Screen(Long) - Constructor for class ome.model.screen.Screen
 
Screen(Long, boolean) - Constructor for class ome.model.screen.Screen
Main constructor.
Screen(String) - Constructor for class ome.model.screen.Screen
 
Screen.Details - Class in ome.model.screen
 
Screen.Details() - Constructor for class ome.model.screen.Screen.Details
 
Screen.Details(Object[]) - Constructor for class ome.model.screen.Screen.Details
 
SCREEN_LINKS - Static variable in class pojos.PlateData
Identifies the Plate#SCREENLINKS field.
ScreenAnnotationLink - Class in ome.model.annotations
These filter definitions are used by the security system to eliminate non-readable objects from queries.
ScreenAnnotationLink() - Constructor for class ome.model.annotations.ScreenAnnotationLink
 
ScreenAnnotationLink(Long) - Constructor for class ome.model.annotations.ScreenAnnotationLink
 
ScreenAnnotationLink(Long, boolean) - Constructor for class ome.model.annotations.ScreenAnnotationLink
Main constructor.
ScreenAnnotationLink(IObject, IObject) - Constructor for class ome.model.annotations.ScreenAnnotationLink
 
ScreenAnnotationLink.Details - Class in ome.model.annotations
 
ScreenAnnotationLink.Details() - Constructor for class ome.model.annotations.ScreenAnnotationLink.Details
 
ScreenAnnotationLink.Details(Object[]) - Constructor for class ome.model.annotations.ScreenAnnotationLink.Details
 
ScreenData - Class in pojos
The data that makes up an OME Screen along with links to its contained Plates and the Experimenter that owns this Screen.
ScreenData() - Constructor for class pojos.ScreenData
Creates a new instance.
ScreenData(Screen) - Constructor for class pojos.ScreenData
Creates a new instance.
screenLinks - Variable in class ome.model.screen.Plate
 
SCREENLINKS - Static variable in class ome.model.screen.Plate
 
SCREENLINKSCOUNTPEROWNER - Static variable in class ome.model.screen.Plate
 
ScreenPlateLink - Class in ome.model.screen
These filter definitions are used by the security system to eliminate non-readable objects from queries.
ScreenPlateLink() - Constructor for class ome.model.screen.ScreenPlateLink
 
ScreenPlateLink(Long) - Constructor for class ome.model.screen.ScreenPlateLink
 
ScreenPlateLink(Long, boolean) - Constructor for class ome.model.screen.ScreenPlateLink
Main constructor.
ScreenPlateLink(IObject, IObject) - Constructor for class ome.model.screen.ScreenPlateLink
 
ScreenPlateLink.Details - Class in ome.model.screen
 
ScreenPlateLink.Details() - Constructor for class ome.model.screen.ScreenPlateLink.Details
 
ScreenPlateLink.Details(Object[]) - Constructor for class ome.model.screen.ScreenPlateLink.Details
 
script(ScriptJob) - Method in class ome.services.blitz.repo.ManagedImportRequestI
 
SCRIPT_REPO - Static variable in class ome.services.scripts.ScriptRepoHelper
Id used by all script repositories.
ScriptFileType - Class in ome.services.scripts
Definition of the script types that will be accepted by the server.
ScriptFileType(String, String) - Constructor for class ome.services.scripts.ScriptFileType
 
ScriptFileType(String, String, String, String) - Constructor for class ome.services.scripts.ScriptFileType
 
ScriptFinder - Class in ome.services.scripts
Looks up an official script based on path for internal use.
ScriptFinder(Roles, String, Executor, File) - Constructor for class ome.services.scripts.ScriptFinder
 
ScriptFinder(Roles, Principal, Executor, File) - Constructor for class ome.services.scripts.ScriptFinder
 
ScriptI - Class in ome.services.blitz.impl
implementation of the IScript service interface.
ScriptI(BlitzExecutor, ScriptRepoHelper, ChecksumProviderFactory, ParamsCache) - Constructor for class ome.services.blitz.impl.ScriptI
 
ScriptJob - Class in ome.model.jobs
 
ScriptJob() - Constructor for class ome.model.jobs.ScriptJob
 
ScriptJob(Long) - Constructor for class ome.model.jobs.ScriptJob
 
ScriptJob(Long, boolean) - Constructor for class ome.model.jobs.ScriptJob
Main constructor.
ScriptProcess - Class in ome.services.procs.scripts
 
ScriptProcess(Processor) - Constructor for class ome.services.procs.scripts.ScriptProcess
 
ScriptProcessI - Class in ome.services.blitz.impl
 
ScriptProcessI(ServiceFactoryI, Current, InteractiveProcessorPrx, _InteractiveProcessorOperations, ProcessPrx) - Constructor for class ome.services.blitz.impl.ScriptProcessI
 
ScriptProcessor - Class in ome.services.procs.scripts
 
ScriptProcessor() - Constructor for class ome.services.procs.scripts.ScriptProcessor
 
scriptRepo(long, Set<String>) - Method in class ome.util.SqlAction.Impl
 
scriptRepo(long, Set<String>) - Method in interface ome.util.SqlAction
Similar to SqlAction.fileRepo(long), but only returns values for files which are also scripts.
ScriptRepoHelper - Class in ome.services.scripts
Strategy used by the ScriptRepository for registering, loading, and saving files.
ScriptRepoHelper(Executor, String, Roles) - Constructor for class ome.services.scripts.ScriptRepoHelper
 
ScriptRepoHelper(File, Executor, Principal, Roles) - Constructor for class ome.services.scripts.ScriptRepoHelper
 
ScriptRepoHelper(String, File, Executor, Principal, Roles) - Constructor for class ome.services.scripts.ScriptRepoHelper
 
ScriptRepositoryI - Class in ome.services.blitz.repo
Repository which makes the included script files available to users.
ScriptRepositoryI(ObjectAdapter, Registry, Executor, Principal, ScriptRepoHelper, PublicRepositoryI) - Constructor for class ome.services.blitz.repo.ScriptRepositoryI
 
scripts - Variable in class ome.services.blitz.impl.ScriptI
 
Search - Interface in ome.api
Central search interface, allowing Web2.0 style queries.
SearchAction - Class in ome.services.search
Serializable action used by SearchBean to generate results lazily.
SearchAction(SearchValues) - Constructor for class ome.services.search.SearchAction
 
searchAll() - Method in interface ome.api.ILdap
Searches all Experimenter list on LDAP for attribute objectClass = person.
searchAll() - Method in class ome.logic.LdapImpl
 
searchAll_async(AMD_ILdap_searchAll, Current) - Method in class ome.services.blitz.impl.LdapI
 
SearchBean - Class in ome.services
Implements the Search interface.
SearchBean(Executor, Class<? extends Analyzer>) - Constructor for class ome.services.SearchBean
 
SearchBean() - Constructor for class ome.services.SearchBean
Empty constructor required by EJB and self configuration.
searchByAttribute(String, String, String) - Method in interface ome.api.ILdap
Searches all Experimenter in LDAP for specified attribute
searchByAttribute(String, String, String) - Method in class ome.logic.LdapImpl
 
searchByAttribute_async(AMD_ILdap_searchByAttribute, String, String, String, Current) - Method in class ome.services.blitz.impl.LdapI
 
searchByAttributes(String, String[], String[]) - Method in interface ome.api.ILdap
Searches all Experimenter in LDAP for specified attributes.
searchByAttributes(String, String[], String[]) - Method in class ome.logic.LdapImpl
 
searchByAttributes_async(AMD_ILdap_searchByAttributes, String, List<String>, List<String>, Current) - Method in class ome.services.blitz.impl.LdapI
 
searchByDN(String) - Method in interface ome.api.ILdap
Searches one Experimenter in LDAP for specified Distinguished Name - String
searchByDN(String) - Method in class ome.logic.LdapImpl
 
searchByDN_async(AMD_ILdap_searchByDN, String, Current) - Method in class ome.services.blitz.impl.LdapI
 
searchDnInGroups(String, String) - Method in interface ome.api.ILdap
Searches Distinguished Name - String in groups
searchDnInGroups(String, String) - Method in class ome.logic.LdapImpl
 
searchDnInGroups_async(AMD_ILdap_searchDnInGroups, String, String, Current) - Method in class ome.services.blitz.impl.LdapI
 
SearchI - Class in ome.services.blitz.impl
Implementation of the Search service.
SearchI(Search, BlitzExecutor) - Constructor for class ome.services.blitz.impl.SearchI
 
SearchValues - Class in ome.services.search
Values used by SearchBean to store user requests.
SearchValues() - Constructor for class ome.services.search.SearchValues
 
sec - Variable in class ome.logic.AbstractLevel2Service
 
sec - Variable in class ome.security.auth.SimpleRoleProvider
 
sec - Variable in class ome.services.AbstractStatefulBean
 
sec - Variable in class ome.services.procs.ProcessManager.Work
SecuritySystem in order to perform a secure save on the Job instance.
secondLevelCacheHit(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
secondLevelCacheMiss(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
secondLevelCachePut(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
seconds - Variable in exception ome.conditions.LockTimeout
Informational field on number of seconds that the lock was tried for.
secSys - Variable in class ome.security.basic.EventHandler
 
SecureAction - Interface in ome.security
action for passing to SecuritySystem#doAction(IObject, SecureAction).
SecureMerge - Class in ome.tools.hibernate
Helper originally from SimpleRoleProvider for merging admin objects.
SecureMerge(Session) - Constructor for class ome.tools.hibernate.SecureMerge
 
SecureMerge(Session, boolean) - Constructor for class ome.tools.hibernate.SecureMerge
 
security - Variable in class omero.cmd.admin.UpdateSessionTimeoutRequestI
 
securityFilter - Variable in class ome.security.basic.BasicACLVoter
 
SecurityFilter - Interface in ome.security
Base filter interface ...
SecurityFilterHolder - Class in ome.security
Security dispatcher holding each currently active SecurityFilter instance and allowing dispatching between them.
SecurityFilterHolder(CurrentDetails, OneGroupSecurityFilter, AllGroupsSecurityFilter) - Constructor for class ome.security.SecurityFilterHolder
 
SecuritySystem - Interface in ome.security
central security interface.
securitySystem - Variable in class ome.services.blitz.fire.SessionManagerI
 
SecuritySystemHolder - Class in ome.security
Security dispatcher holding each currently active SecuritySystem instance and allowing dispatching between them.
SecuritySystemHolder(BasicSecuritySystem, SharingSecuritySystem) - Constructor for class ome.security.SecuritySystemHolder
 
SecurityViolation - Exception in ome.conditions
User does not have permissions to perform given action.
SecurityViolation(String) - Constructor for exception ome.conditions.SecurityViolation
 
Segment - Class in ome.util.math.geom2D
A segment in the Euclidean space R2.
Segment(double, double, double, double) - Constructor for class ome.util.math.geom2D.Segment
Creates a new instance.
select(String...) - Method in class ome.tools.hibernate.QueryBuilder
 
selectCurrentEventLog(String) - Method in class ome.util.actions.PostgresSqlAction
 
selectCurrentEventLog(String) - Method in class ome.util.SqlAction.Impl
 
selectCurrentEventLog(String) - Method in interface ome.util.SqlAction
 
SelfConfigurableService - Interface in ome.system
 
selfConfigure() - Method in class ome.logic.AbstractLevel1Service
This method was previously called by the EJB container, but is no longer needed.
selfConfigure() - Method in class ome.logic.AbstractLevel2Service
This method was previously called by the EJB container, but is no longer needed.
selfConfigure(OmeroContext) - Method in class ome.logic.HardWiredInterceptor
Calls OmeroContext.applyBeanPropertyValues(Object, String) to have properties injected.
selfConfigure(SessionManager, ServiceFactory, SessionCache) - Static method in class ome.security.basic.BasicSecuritySystem
Simplified factory method which generates all the security primitives internally.
selfConfigure() - Method in class ome.services.AbstractStatefulBean
 
selfConfigure() - Method in interface ome.system.SelfConfigurableService
 
SelfCorrectingDataSource - Class in ome.services.db
DataSource delegate which wraps the
SelfCorrectingDataSource(DataSource, long) - Constructor for class ome.services.db.SelfCorrectingDataSource
 
SelfCorrectingDataSource(DataSource, long, int, long) - Constructor for class ome.services.db.SelfCorrectingDataSource
 
sendBlind(Set<String>, String) - Method in class ome.services.mail.MailSender
 
sendBlind(Set<String>, String, String) - Method in class ome.services.mail.MailSender
 
sendEmail(String, String, String, String, boolean, List<String>, List<String>) - Method in class ome.services.mail.MailUtil
Main method which takes typical email fields as arguments, to prepare and populate the given new MimeMessage instance and send.
sendEmail(String, String, String, boolean, List<String>, List<String>) - Method in class ome.services.mail.MailUtil
Overloaded method which takes typical email fields as arguments, to prepare and populate the given new MimeMessage instance and send.
sendEmail(Collection<EventLog>) - Method in class ome.services.mail.ObjectMailSender
 
SendEmailRequestI - Class in omero.cmd.mail
Callback interface allowing to send email using JavaMailSender, supporting MIME messages through preparation callbacks.
SendEmailRequestI(MailUtil) - Constructor for class omero.cmd.mail.SendEmailRequestI
 
sender - Variable in class ome.services.mail.MailUtil
 
sender - Variable in class ome.services.mail.ServerUpMailSender
 
sendErrors() - Method in class ome.formats.importer.util.ErrorHandler
Send existing errors in ErrorContainer array to server
sendFiles - Variable in class ome.formats.importer.ImportConfig
 
sendFiles - Variable in class ome.formats.importer.ImportEvent.DEBUG_SEND
 
sendFiles - Variable in class ome.formats.importer.util.ErrorHandler
 
sendLogFile - Variable in class ome.formats.importer.ImportConfig
 
sendLogs - Variable in class ome.formats.importer.ImportEvent.DEBUG_SEND
 
sendLogs - Variable in class ome.formats.importer.util.ErrorHandler
 
sendReport - Variable in class ome.formats.importer.ImportConfig
 
separatorChar - Static variable in class ome.services.blitz.repo.path.FsFile
the separator character for delimiting repository path components
serialNumber - Variable in class ome.model.acquisition.Detector
 
SERIALNUMBER - Static variable in class ome.model.acquisition.Detector
 
serialNumber - Variable in class ome.model.acquisition.Dichroic
 
SERIALNUMBER - Static variable in class ome.model.acquisition.Dichroic
 
serialNumber - Variable in class ome.model.acquisition.Filter
 
SERIALNUMBER - Static variable in class ome.model.acquisition.Filter
 
serialNumber - Variable in class ome.model.acquisition.FilterSet
 
SERIALNUMBER - Static variable in class ome.model.acquisition.FilterSet
 
serialNumber - Variable in class ome.model.acquisition.LightSource
 
SERIALNUMBER - Static variable in class ome.model.acquisition.LightSource
 
serialNumber - Variable in class ome.model.acquisition.Microscope
 
SERIALNUMBER - Static variable in class ome.model.acquisition.Microscope
 
serialNumber - Variable in class ome.model.acquisition.Objective
 
SERIALNUMBER - Static variable in class ome.model.acquisition.Objective
 
SerialThrottlingStrategy - Class in ome.services.throttling
Throttling implementation which only allows a single invocation to be run at any given time.
SerialThrottlingStrategy(OmeroContext) - Constructor for class ome.services.throttling.SerialThrottlingStrategy
 
series - Variable in class ome.formats.importer.ImportEvent.IMPORT_STEP
 
series - Variable in class ome.formats.importer.ImportEvent.PROGRESS_EVENT
 
series - Variable in class ome.model.core.Image
 
SERIES - Static variable in class ome.model.core.Image
 
seriesCount - Variable in class ome.formats.importer.ImportEvent.IMPORT_STEP
 
ServantHolder - Class in omero.util
Manager for all active servants in a single session.
ServantHolder(String) - Constructor for class omero.util.ServantHolder
 
ServantHolder(String, int) - Constructor for class omero.util.ServantHolder
 
servantsPerSession - Variable in class ome.services.blitz.fire.SessionManagerI
 
server - Variable in class loci.ome.io.OMECredentials
 
Server - Class in ome.system
Provides simplified handling of server properties when creating a ServiceFactory.
Server(String) - Constructor for class ome.system.Server
standard constructor which users Server.DEFAULT_PORT.
Server(String, int) - Constructor for class ome.system.Server
extended constructor.
SERVER_NAME_SEPARATOR - Static variable in class ome.formats.importer.ImportConfig
Delimiter used to encode multiple servers in one preferences value.
ServerDirectoryCheck - Class in ome.services.util
Hook run by the context at startup to create needed directories for the server.
ServerDirectoryCheck(String) - Constructor for class ome.services.util.ServerDirectoryCheck
 
ServerDownMailSender - Class in ome.services.mail
Send an email to all members of the system group when the server is shutting down.
ServerDownMailSender() - Constructor for class ome.services.mail.ServerDownMailSender
 
ServerFilePathTransformer - Class in ome.services.blitz.repo.path
Transform between repository FsFile path and server-local File.
ServerFilePathTransformer() - Constructor for class ome.services.blitz.repo.path.ServerFilePathTransformer
 
serverPaths - Variable in class ome.services.blitz.repo.PublicRepositoryI
 
ServerUpMailSender - Class in ome.services.mail
Announces to all members of the system group that the server has come up.
ServerUpMailSender(MailSender) - Constructor for class ome.services.mail.ServerUpMailSender
 
ServerVersionCheck - Class in ome.services.util
Hook run by the context.
ServerVersionCheck(String) - Constructor for class ome.services.util.ServerVersionCheck
 
service - Variable in class ome.services.blitz.impl.AbstractAmdServant
If there is no undering ome.* service, then this value can be null.
service - Variable in class ome.services.util.Executor.Impl
 
ServiceFactory - Class in ome.system
Entry point for all client calls.
ServiceFactory() - Constructor for class ome.system.ServiceFactory
default constructor which obtains the global static client context from OmeroContext.
ServiceFactory(Login) - Constructor for class ome.system.ServiceFactory
constructor which obtains a new (non-static) client context, passing in the Properties representation of the Login for configuration.
ServiceFactory(Server) - Constructor for class ome.system.ServiceFactory
constructor which obtains a new (non-static) client context, passing in the Properties representation of the Server for configuration.
ServiceFactory(Server, Login) - Constructor for class ome.system.ServiceFactory
constructor which obtains a new (non-static) client context, passing in the Properties representation of both the Server and the Login for configuration.
ServiceFactory(Properties) - Constructor for class ome.system.ServiceFactory
constructor which obtains a new client context, passing in the provided properties for configuration.
ServiceFactory(OmeroContext) - Constructor for class ome.system.ServiceFactory
constructor which uses the provided OmeroContext for all loookups.
ServiceFactory(String) - Constructor for class ome.system.ServiceFactory
constructor which finds the global static OmeroContext with the given name.
ServiceFactoryAware - Interface in ome.services.blitz.util
Servant which is aware of the ServiceFactoryI-instance which it belongs to and will have it injected on instantiation.
ServiceFactoryI - Class in ome.services.blitz.impl
Responsible for maintaining all servants for a single session.
ServiceFactoryI(Current, ServantHolder, SessionControlPrx, OmeroContext, SessionManager, Executor, Principal, List<HardWiredInterceptor>, TopicManager, Registry) - Constructor for class ome.services.blitz.impl.ServiceFactoryI
 
ServiceFactoryI(boolean, Current, ServantHolder, SessionControlPrx, OmeroContext, SessionManager, Executor, Principal, List<HardWiredInterceptor>, TopicManager, Registry, String) - Constructor for class ome.services.blitz.impl.ServiceFactoryI
 
ServiceHandler - Class in ome.services.util
 
ServiceHandler(CurrentDetails) - Constructor for class ome.services.util.ServiceHandler
 
ServiceHandler(CurrentDetails, long, long) - Constructor for class ome.services.util.ServiceHandler
 
ServiceInterface - Interface in ome.api
Marker interface representing an OMERO API Interface.
session - Variable in class ome.model.meta.Event
 
SESSION - Static variable in class ome.model.meta.Event
 
Session - Class in ome.model.meta
 
Session() - Constructor for class ome.model.meta.Session
 
Session(Long) - Constructor for class ome.model.meta.Session
 
Session(Long, boolean) - Constructor for class ome.model.meta.Session
Main constructor.
Session(Node, String, Experimenter, Long, Long, Timestamp, String) - Constructor for class ome.model.meta.Session
 
session - Variable in class ome.system.SessionInitializer
 
session - Variable in class omero.cmd.graphs.BaseGraphTraversalProcessor
 
session - Variable in class omero.model.DetailsI
 
session - Variable in class omero.util.RPSTileLoop
 
Session.Details - Class in ome.model.meta
 
Session.Details() - Constructor for class ome.model.meta.Session.Details
 
Session.Details(Object[]) - Constructor for class ome.model.meta.Session.Details
 
SessionAnnotationLink - Class in ome.model.annotations
These filter definitions are used by the security system to eliminate non-readable objects from queries.
SessionAnnotationLink() - Constructor for class ome.model.annotations.SessionAnnotationLink
 
SessionAnnotationLink(Long) - Constructor for class ome.model.annotations.SessionAnnotationLink
 
SessionAnnotationLink(Long, boolean) - Constructor for class ome.model.annotations.SessionAnnotationLink
Main constructor.
SessionAnnotationLink(IObject, IObject) - Constructor for class ome.model.annotations.SessionAnnotationLink
 
SessionAnnotationLink.Details - Class in ome.model.annotations
 
SessionAnnotationLink.Details() - Constructor for class ome.model.annotations.SessionAnnotationLink.Details
 
SessionAnnotationLink.Details(Object[]) - Constructor for class ome.model.annotations.SessionAnnotationLink.Details
 
SessionAware - Interface in omero.cmd
Servant which is aware of the SessionI-instance which it belongs to and will have it injected on instantiation.
SessionBean - Class in ome.services.sessions
Implementation of ISession.
SessionBean(SessionManager, Executor, CurrentDetails) - Constructor for class ome.services.sessions.SessionBean
 
SessionCache - Class in ome.services.sessions.state
Synchronized and lockable state for the SessionManager.
SessionCache() - Constructor for class ome.services.sessions.state.SessionCache
 
SessionCache.StaleCacheListener - Interface in ome.services.sessions.state
Observer pattern used to refresh sessions in doUpdate.
SessionCallback - Interface in ome.services.sessions
 
SessionCallback.SimpleCloseCallback - Class in ome.services.sessions
Assumes that only close() will be called.
SessionCallback.SimpleCloseCallback() - Constructor for class ome.services.sessions.SessionCallback.SimpleCloseCallback
 
sessionContext - Variable in exception ome.conditions.SessionTimeoutException
 
SessionContext - Interface in ome.services.sessions
Extends EventContext to hold a Session.
SessionContext.Count - Class in ome.services.sessions
Synchronized counter which can be passed between SessionContext instances as they are recreated.
SessionContext.Count(String) - Constructor for class ome.services.sessions.SessionContext.Count
 
SessionContextImpl - Class in ome.services.sessions
 
SessionContextImpl(Session, List<Long>, List<Long>, List<String>, SessionStats, SessionContext) - Constructor for class ome.services.sessions.SessionContextImpl
 
SessionContextImpl(Session, List<Long>, List<Long>, List<String>, SessionStats, Roles, SessionContext) - Constructor for class ome.services.sessions.SessionContextImpl
 
SessionException - Exception in ome.conditions
Base session related exception.
SessionException(String) - Constructor for exception ome.conditions.SessionException
 
sessionFactory - Variable in class ome.logic.AbstractLevel1Service
 
SessionFactory - Class in ome.tools.hibernate
Simple source of Thread-aware Session instances.
SessionFactory(SessionFactory, SqlAction) - Constructor for class ome.tools.hibernate.SessionFactory
 
SessionHandler - Class in ome.tools.hibernate
interceptor which delegates to HibernateInterceptor for stateless services but which keeps a WeakHashMap of sessions keyed by the stateful service reference.
SessionHandler(SessionFactory) - Constructor for class ome.tools.hibernate.SessionHandler
constructor taking a DataSource and a SessionFactory.
SessionI - Class in ome.services.blitz.impl
Implementation of the ISession service.
SessionI(ISession, BlitzExecutor) - Constructor for class ome.services.blitz.impl.SessionI
 
SessionI - Class in omero.cmd
 
SessionI(boolean, Current, ServantHolder, SessionControlPrx, OmeroContext, SessionManager, Executor, Principal, String) - Constructor for class omero.cmd.SessionI
 
sessionId(String) - Method in class ome.util.actions.PostgresSqlAction
 
sessionId(String) - Method in interface ome.util.SqlAction
 
sessionId(String, String) - Static method in class omero.cmd.SessionI
Definition of session ids: "session-/"
sessionId() - Method in class omero.cmd.SessionI
Returns the Identity for this instance as defined by SessionI.sessionId(String, String)
sessionInit() - Method in class ome.services.util.ExecutionThread
 
SessionInitializer - Class in ome.system
Manages the creation of a single Session created via the injected ISession service.
SessionInitializer() - Constructor for class ome.system.SessionInitializer
 
sessionKey - Variable in class ome.formats.importer.ImportConfig
 
sessionManager - Variable in class ome.logic.UpdateImpl
 
sessionManager - Variable in class ome.security.basic.BasicSecuritySystem
 
sessionManager - Variable in class ome.services.blitz.fire.SessionManagerI
 
SessionManager - Interface in ome.services.sessions
Responsible for holding onto Session instances for optimized login.
sessionManager - Variable in class ome.services.sharing.ShareBean
 
sessionManager - Variable in class omero.cmd.SessionI
 
SessionManager.CreationRequest - Class in ome.services.sessions
Extensible data object which can be passed to create* methods to stop the explosion of different methods.
SessionManager.CreationRequest() - Constructor for class ome.services.sessions.SessionManager.CreationRequest
 
SessionManagerI - Class in ome.services.blitz.fire
Central login logic for all OMERO.blitz clients.
SessionManagerI(Ring, ObjectAdapter, SecuritySystem, SessionManager, Executor, TopicManager, Registry, int) - Constructor for class ome.services.blitz.fire.SessionManagerI
 
SessionManagerImpl - Class in ome.services.sessions
Is for ISession a cache and will be kept there in sync?
SessionManagerImpl() - Constructor for class ome.services.sessions.SessionManagerImpl
 
sessions - Variable in class ome.model.meta.Node
 
SESSIONS - Static variable in class ome.model.meta.Node
 
sessions - Variable in class ome.system.SessionInitializer
 
SessionsCreatedCounter - Class in ome.services.sessions.stats
Counter for all the objects read in a session.
SessionsCreatedCounter(int) - Constructor for class ome.services.sessions.stats.SessionsCreatedCounter
 
SessionsCreatedStatsMessage - Class in ome.services.messages.stats
Published when some limit in user/group/session activity has been reached.
SessionsCreatedStatsMessage(Object, long) - Constructor for class ome.services.messages.stats.SessionsCreatedStatsMessage
 
SessionStats - Interface in ome.services.sessions.stats
Thread-safe counter for all
SessionTimeoutException - Exception in ome.conditions
The given session has expired and can no longer be used.
SessionTimeoutException(String, Object) - Constructor for exception ome.conditions.SessionTimeoutException
 
sessionToHolder - Variable in class ome.services.blitz.fire.SessionManagerI
An internal mapping to all ServiceFactoryI instances for a given session since there is no method on ObjectAdapter to retrieve all servants.
set(T) - Method in class ome.formats.importer.ImportConfig.Value
Sets the in-memory value, which will get persisted on ImportConfig.Value.store() when ImportConfig.saveAll() is called.
set(Permissions.Flag) - Method in class ome.model.internal.Permissions
turn a given Permissions.Flag on.
set(U) - Method in class ome.services.blitz.util.ResultHolder
 
set(String, Object, Document, LuceneOptions) - Method in class ome.services.fulltext.BridgeHelper
Method to be implemented by all bridges.
set(String, Object, Document, LuceneOptions) - Method in class ome.services.fulltext.bridges.ProjectWithImageNameBridge
If the "value" argument is a Project, this bridge gathers all images and adds them to the index with a slightly reduced boost value.
set(String, Object, Document, LuceneOptions) - Method in class ome.services.fulltext.bridges.TablesBridge
Primary entry point for all bridges.
set(String, Object, Document, LuceneOptions) - Method in class ome.services.fulltext.FullTextBridge
Default implementation of the #set(String, Object, Document, Store, org.apache.lucene.document.Field.Index, Float) method which calls #set_file(String, IObject, Document, Store, org.apache.lucene.document.Field.Index, Float) #set_annotations(String, Object, Document, Store, org.apache.lucene.document.Field.Index, Float), #set_details(String, Object, Document, Store, org.apache.lucene.document.Field.Index, Float), and finally #set_custom(String, Object, Document, Store, org.apache.lucene.document.Field.Index, Float).
set(Share, long, List<T>, List<Long>, List<String>, boolean) - Method in class ome.services.sharing.ShareStore
 
set(String, Object, Document, LuceneOptions) - Method in class ome.util.DetailsFieldBridge
 
set(int, byte) - Method in class ome.util.mem.ByteArray
Writes value into the element at the index position within this slice.
set(int, byte[]) - Method in class ome.util.mem.ByteArray
Copies the values in buf into this slice, starting from index.
set(int, int, InputStream) - Method in class ome.util.mem.ByteArray
Writes up to maxLength bytes from the supplied stream into this slice, starting from index.
set(Copiable, int) - Method in class ome.util.mem.CopiableArray
Replaces the element at the specified position with the specified Copiable.
set(int, int, boolean) - Method in class omero.model.PermissionsI
 
set(String[]) - Static method in class prefs
Takes an array of length 2, using args[0] as the key and args[1] as the value to be set.
set_annotations(String, IObject, Document, LuceneOptions) - Method in class ome.services.fulltext.FullTextBridge
Walks the various Annotation instances attached to the object argument and adds various levels to the index.
set_custom(String, IObject, Document, LuceneOptions) - Method in class ome.services.fulltext.FullTextBridge
Loops over each field bridge class and calls its FieldBridge#set(String, Object, Document, Store, org.apache.lucene.document.Field.Index, Float) method.
set_details(String, IObject, Document, LuceneOptions) - Method in class ome.services.fulltext.FullTextBridge
Parses all ownership and time-based details to the index for the given object.
set_file(String, IObject, Document, LuceneOptions) - Method in class ome.services.fulltext.FullTextBridge
Uses #parse(OriginalFile) to get a Reader for the given file which is then passed to #add(Document, String, Reader, Float) using the field name "file".
setAbsolutePath(String) - Method in class ome.formats.importer.util.ErrorContainer
set path for file
setAcquisitionDate(Timestamp) - Method in class ome.model.core.Image
 
setAction(String) - Method in class ome.model.meta.EventLog
 
setAction(String) - Method in class ome.services.mail.ObjectMailSender
 
setActive(long, boolean) - Method in interface ome.api.IShare
 
setActive(Boolean) - Method in class ome.model.display.ChannelBinding
 
setActive(Boolean) - Method in class ome.model.meta.Share
 
setActive(int, boolean) - Method in class ome.services.RenderingBean
Implemented as specified by the RenderingEngine interface.
setActive(long, boolean) - Method in class ome.services.sharing.ShareBean
 
setActive(int, boolean) - Method in class omeis.providers.re.Renderer
Makes a particular channel active or inactive.
setActive(int, boolean) - Method in interface omeis.providers.re.RenderingEngine
Maps the specified channel if true, unmaps the channel otherwise.
setActive_async(AMD_RenderingEngine_setActive, int, boolean, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
setActive_async(AMD_IShare_setActive, long, boolean, Current) - Method in class ome.services.blitz.impl.ShareI
 
setAdmin(boolean) - Method in class ome.security.basic.BasicEventContext
 
setAdminService(IAdmin) - Method in class ome.services.RawFileBean
 
setAgent(String) - Method in class omero.client
Sets the user agent string for this client.
setAirPressure(Pressure) - Method in class ome.model.acquisition.ImagingEnvironment
 
setAirPressure(Pressure) - Method in class pojos.ImageAcquisitionData
Sets the air pressure.
setAirPressure(double) - Method in class pojos.ImageAcquisitionData
setAliases(String[]) - Method in class ome.system.Preference
Setter injector
setAllowLeadingWildcard(boolean) - Method in interface ome.api.Search
Permits full-text queries with a leading query if true.
setAllowLeadingWildcard(boolean) - Method in class ome.services.SearchBean
 
setAllowLeadingWildcard_async(AMD_Search_setAllowLeadingWildcard, boolean, Current) - Method in class ome.services.blitz.impl.SearchI
 
setAllPixels(List<PixelsData>) - Method in class pojos.ImageData
Sets the set of pixels related to this image.
setAlpha(Integer) - Method in class ome.model.core.Channel
 
setAlpha(Integer) - Method in class ome.model.display.ChannelBinding
 
setAlpha(Integer) - Method in class ome.model.screen.Well
 
setAlpha(Integer) - Method in class pojos.WellData
Sets the alpha component of the color associated to the well.
setAlphalessRendering(boolean) - Method in class omeis.providers.re.Optimizations
Enable or disable the alphaless rendering optimization.
setAlternateStylesheet(String) - Method in class ome.services.SVGRasterizer
Sets the alternate stylesheet to use.
setAmplificationGain(Double) - Method in class ome.model.acquisition.Detector
 
setAnalyzer(Class<? extends Analyzer>) - Method in class ome.logic.QueryImpl
 
setAnalyzer(Class<? extends Analyzer>) - Method in class ome.services.SearchBean
Injector used by Spring.
setAnchor(String) - Method in class ome.model.roi.Label
 
setAnnotationLinks(Set<DetectorAnnotationLink>) - Method in class ome.model.acquisition.Detector
setter for annotationLinks should be avoided.
setAnnotationLinks(Set<DichroicAnnotationLink>) - Method in class ome.model.acquisition.Dichroic
setter for annotationLinks should be avoided.
setAnnotationLinks(Set<FilterAnnotationLink>) - Method in class ome.model.acquisition.Filter
setter for annotationLinks should be avoided.
setAnnotationLinks(Set<InstrumentAnnotationLink>) - Method in class ome.model.acquisition.Instrument
setter for annotationLinks should be avoided.
setAnnotationLinks(Set<LightPathAnnotationLink>) - Method in class ome.model.acquisition.LightPath
setter for annotationLinks should be avoided.
setAnnotationLinks(Set<LightSourceAnnotationLink>) - Method in class ome.model.acquisition.LightSource
setter for annotationLinks should be avoided.
setAnnotationLinks(Set<ObjectiveAnnotationLink>) - Method in class ome.model.acquisition.Objective
setter for annotationLinks should be avoided.
setAnnotationLinks(Set<AnnotationAnnotationLink>) - Method in class ome.model.annotations.Annotation
setter for annotationLinks should be avoided.
setAnnotationLinks(Set<DatasetAnnotationLink>) - Method in class ome.model.containers.Dataset
setter for annotationLinks should be avoided.
setAnnotationLinks(Set<ProjectAnnotationLink>) - Method in class ome.model.containers.Project
setter for annotationLinks should be avoided.
setAnnotationLinks(Set<ChannelAnnotationLink>) - Method in class ome.model.core.Channel
setter for annotationLinks should be avoided.
setAnnotationLinks(Set<ImageAnnotationLink>) - Method in class ome.model.core.Image
setter for annotationLinks should be avoided.
setAnnotationLinks(Set<OriginalFileAnnotationLink>) - Method in class ome.model.core.OriginalFile
setter for annotationLinks should be avoided.
setAnnotationLinks(Set<PlaneInfoAnnotationLink>) - Method in class ome.model.core.PlaneInfo
setter for annotationLinks should be avoided.
setAnnotationLinks(Set<FilesetAnnotationLink>) - Method in class ome.model.fs.Fileset
setter for annotationLinks should be avoided.
setAnnotationLinks(Set<ExperimenterAnnotationLink>) - Method in class ome.model.meta.Experimenter
setter for annotationLinks should be avoided.
setAnnotationLinks(Set<ExperimenterGroupAnnotationLink>) - Method in class ome.model.meta.ExperimenterGroup
setter for annotationLinks should be avoided.
setAnnotationLinks(Set<NamespaceAnnotationLink>) - Method in class ome.model.meta.Namespace
setter for annotationLinks should be avoided.
setAnnotationLinks(Set<NodeAnnotationLink>) - Method in class ome.model.meta.Node
setter for annotationLinks should be avoided.
setAnnotationLinks(Set<SessionAnnotationLink>) - Method in class ome.model.meta.Session
setter for annotationLinks should be avoided.
setAnnotationLinks(Set<RoiAnnotationLink>) - Method in class ome.model.roi.Roi
setter for annotationLinks should be avoided.
setAnnotationLinks(Set<ShapeAnnotationLink>) - Method in class ome.model.roi.Shape
setter for annotationLinks should be avoided.
setAnnotationLinks(Set<PlateAnnotationLink>) - Method in class ome.model.screen.Plate
setter for annotationLinks should be avoided.
setAnnotationLinks(Set<PlateAcquisitionAnnotationLink>) - Method in class ome.model.screen.PlateAcquisition
setter for annotationLinks should be avoided.
setAnnotationLinks(Set<ReagentAnnotationLink>) - Method in class ome.model.screen.Reagent
setter for annotationLinks should be avoided.
setAnnotationLinks(Set<ScreenAnnotationLink>) - Method in class ome.model.screen.Screen
setter for annotationLinks should be avoided.
setAnnotationLinks(Set<WellAnnotationLink>) - Method in class ome.model.screen.Well
setter for annotationLinks should be avoided.
setAnnotationLinksCountPerOwner(Map<Long, Long>) - Method in class ome.model.acquisition.Detector
 
setAnnotationLinksCountPerOwner(Map<Long, Long>) - Method in class ome.model.acquisition.Dichroic
 
setAnnotationLinksCountPerOwner(Map<Long, Long>) - Method in class ome.model.acquisition.Filter
 
setAnnotationLinksCountPerOwner(Map<Long, Long>) - Method in class ome.model.acquisition.Instrument
 
setAnnotationLinksCountPerOwner(Map<Long, Long>) - Method in class ome.model.acquisition.LightPath
 
setAnnotationLinksCountPerOwner(Map<Long, Long>) - Method in class ome.model.acquisition.LightSource
 
setAnnotationLinksCountPerOwner(Map<Long, Long>) - Method in class ome.model.acquisition.Objective
 
setAnnotationLinksCountPerOwner(Map<Long, Long>) - Method in class ome.model.annotations.Annotation
 
setAnnotationLinksCountPerOwner(Map<Long, Long>) - Method in class ome.model.containers.Dataset
 
setAnnotationLinksCountPerOwner(Map<Long, Long>) - Method in class ome.model.containers.Project
 
setAnnotationLinksCountPerOwner(Map<Long, Long>) - Method in class ome.model.core.Channel
 
setAnnotationLinksCountPerOwner(Map<Long, Long>) - Method in class ome.model.core.Image
 
setAnnotationLinksCountPerOwner(Map<Long, Long>) - Method in class ome.model.core.OriginalFile
 
setAnnotationLinksCountPerOwner(Map<Long, Long>) - Method in class ome.model.core.PlaneInfo
 
setAnnotationLinksCountPerOwner(Map<Long, Long>) - Method in class ome.model.fs.Fileset
 
setAnnotationLinksCountPerOwner(Map<Long, Long>) - Method in class ome.model.meta.Experimenter
 
setAnnotationLinksCountPerOwner(Map<Long, Long>) - Method in class ome.model.meta.ExperimenterGroup
 
setAnnotationLinksCountPerOwner(Map<Long, Long>) - Method in class ome.model.meta.Namespace
 
setAnnotationLinksCountPerOwner(Map<Long, Long>) - Method in class ome.model.meta.Node
 
setAnnotationLinksCountPerOwner(Map<Long, Long>) - Method in class ome.model.meta.Session
 
setAnnotationLinksCountPerOwner(Map<Long, Long>) - Method in class ome.model.roi.Roi
 
setAnnotationLinksCountPerOwner(Map<Long, Long>) - Method in class ome.model.roi.Shape
 
setAnnotationLinksCountPerOwner(Map<Long, Long>) - Method in class ome.model.screen.Plate
 
setAnnotationLinksCountPerOwner(Map<Long, Long>) - Method in class ome.model.screen.PlateAcquisition
 
setAnnotationLinksCountPerOwner(Map<Long, Long>) - Method in class ome.model.screen.Reagent
 
setAnnotationLinksCountPerOwner(Map<Long, Long>) - Method in class ome.model.screen.Screen
 
setAnnotationLinksCountPerOwner(Map<Long, Long>) - Method in class ome.model.screen.Well
 
setAnnotations(Set) - Method in class pojos.DatasetData
Sets the annotations related to this dataset.
setAnnotations(Set) - Method in class pojos.ImageData
Sets the image's annotations.
setApplicationContext(ApplicationContext) - Method in class ome.logic.AdminImpl
 
setApplicationContext(ApplicationContext) - Method in class ome.logic.LdapImpl
 
setApplicationContext(ApplicationContext) - Method in class ome.security.auth.ConfigurablePasswordProvider
 
setApplicationContext(ApplicationContext) - Method in class ome.security.basic.BasicSecuritySystem
 
setApplicationContext(ApplicationContext) - Method in class ome.security.basic.GroupChmodStrategy
 
setApplicationContext(ApplicationContext) - Method in class ome.services.blitz.fire.SessionManagerI
 
setApplicationContext(ApplicationContext) - Method in class ome.services.blitz.impl.AbstractAmdServant
Creates an IceMethodInvoker for this instance if AbstractAmdServant.service is non-null.
setApplicationContext(ApplicationContext) - Method in class ome.services.blitz.impl.commands.RequestObjectFactoryRegistry
 
setApplicationContext(ApplicationContext) - Method in class ome.services.blitz.repo.PublicRepositoryI
 
setApplicationContext(ApplicationContext) - Method in class ome.services.blitz.repo.RequestObjectFactoryRegistry
 
setApplicationContext(ApplicationContext) - Method in class ome.services.blitz.util.ParamsCache
 
setApplicationContext(ApplicationContext) - Method in class ome.services.delete.Deletion.Builder
Deprecated.
 
setApplicationContext(ApplicationContext) - Method in class ome.services.fulltext.FileParser
 
setApplicationContext(ApplicationContext) - Method in class ome.services.fulltext.FullTextIndexer
 
setApplicationContext(ApplicationContext) - Method in class ome.services.graphs.GraphSpecPostProcessor
Deprecated.
 
setApplicationContext(ApplicationContext) - Method in class ome.services.scheduler.SchedulerFactoryBean
 
setApplicationContext(ApplicationContext) - Method in class ome.services.sessions.SessionManagerImpl
 
setApplicationContext(ApplicationContext) - Method in class ome.services.sessions.state.CacheFactory
 
setApplicationContext(ApplicationContext) - Method in class ome.services.sessions.state.SessionCache
Context injector.
setApplicationContext(ApplicationContext) - Method in class ome.services.sharing.BlobShareStore
Because there is a cyclic dependency (SF->ACLVoter->BlobStore->SF), we have to lazy-load the session factory via the context.
setApplicationContext(ApplicationContext) - Method in class ome.services.throttling.AbstractThrottlingStrategy
 
setApplicationContext(ApplicationContext) - Method in class ome.services.util.Executor.Impl
 
setApplicationContext(ApplicationContext) - Method in class ome.tools.hibernate.SessionHandler
 
setApplicationContext(ApplicationContext) - Method in class ome.tools.spring.InternalServiceFactory
simple injector for the ApplicationContext
setApplicationContext(ApplicationContext) - Method in class ome.tools.spring.ManagedServiceFactory
simple injector for the ApplicationContext
setApplicationContext(ApplicationContext) - Method in class ome.tools.spring.OnContextRefreshedEventListener
 
setApplicationContext(ApplicationContext) - Method in class omero.cmd.RequestObjectFactoryRegistry
 
setApplicationEventPublisher(ApplicationEventPublisher) - Method in class ome.io.nio.PixelsService
 
setApplicationEventPublisher(ApplicationEventPublisher) - Method in class ome.services.fulltext.BridgeHelper
 
setApplicationEventPublisher(ApplicationEventPublisher) - Method in class ome.services.fulltext.bridges.TablesBridge
 
setApplicationEventPublisher(ApplicationEventPublisher) - Method in class ome.services.sessions.stats.CounterFactory
 
setApplicationEventPublisher(ApplicationEventPublisher) - Method in class ome.services.sessions.stats.LongCounter
 
setAppVersion(String) - Method in class ome.formats.importer.util.ErrorContainer
 
setArcAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setArchived(Boolean) - Method in class ome.model.core.Image
 
setArcID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setArcLotNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setArcManufacturer(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setArcModel(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setArcPower(Power, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setArcSerialNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setArcType(ArcType, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setArgument(Map<String, Boolean>, String) - Static method in class ome.formats.importer.cli.CommandLineImporter
Set a conflicting argument and return the usage if the key is already set
setAtime(Timestamp) - Method in class ome.model.core.OriginalFile
 
setAttenuation(Double) - Method in class ome.model.acquisition.LightSettings
 
setBackgroundColor(Paint) - Method in class ome.services.SVGRasterizer
Sets the Paint to use for the background of the image.
setBaseDirFile(File) - Method in class ome.services.blitz.repo.path.ServerFilePathTransformer
Set the repository root directory, to which FsFile instances are considered to be relative.
setBaselineShift(String) - Method in class ome.model.roi.Label
 
setBatchSize(int) - Method in interface ome.api.Search
Sets the maximum number of results that will be returned by one call to Search.results().
setBatchSize(int) - Method in class ome.services.eventlogs.EventLogLoader
Set the number of EventLog instances will be loaded in a single run.
setBatchSize(int) - Method in class ome.services.SearchBean
 
setBatchSize_async(AMD_Search_setBatchSize, int, Current) - Method in class ome.services.blitz.impl.SearchI
 
setBeanFactory(BeanFactory) - Method in class ome.services.messages.GlobalMulticaster
 
setBeanName(String) - Method in class ome.services.graphs.BaseGraphSpec
Deprecated.
 
setBeanName(String) - Method in class ome.system.Preference
Setter injector
setBeginsWith(Collection<String>) - Method in class ome.system.metrics.DefaultMetrics
 
setBinaryFileFileName(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setBinaryFileMIMEType(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setBinaryFileSize(NonNegativeLong, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setBinaryOnlyMetadataFile(String) - Method in class ome.formats.OMEROMetadataStoreClient
 
setBinaryOnlyUUID(String) - Method in class ome.formats.OMEROMetadataStoreClient
 
setBinning(Binning) - Method in class ome.model.acquisition.DetectorSettings
 
setBit(byte[], int, int) - Method in class pojos.MaskData
Sets the bit value in a byte array at position bit to be the value value.
setBitResolution(Integer) - Method in class ome.model.display.QuantumDef
 
setBitSize(Integer) - Method in class ome.model.enums.PixelsType
 
setBlue(Integer) - Method in class ome.model.core.Channel
 
setBlue(Integer) - Method in class ome.model.display.ChannelBinding
 
setBlue(Integer) - Method in class ome.model.screen.Well
 
setBlue(Integer) - Method in class pojos.WellData
Sets the blue component of the color associated to the well.
setBlueValue(int, int) - Method in class omeis.providers.re.RGBAIntBuffer
Sets the Blue value for a particular pixel index.
setBlueValue(int, int) - Method in class omeis.providers.re.RGBBuffer
Sets the Blue value for a particular pixel index.
setBlueValue(int, int) - Method in class omeis.providers.re.RGBIntBuffer
Sets the Blue value for a particular pixel index.
setBooleanAnnotationAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setBooleanAnnotationAnnotator(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setBooleanAnnotationDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setBooleanAnnotationID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setBooleanAnnotationNamespace(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setBooleanAnnotationValue(Boolean, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setBoolValue(Boolean) - Method in class ome.model.annotations.BooleanAnnotation
 
setBounds(int, int, int, int) - Method in class ome.util.math.geom2D.EllipseArea
Implemented as specified in the PlaneArea I/F.
setBounds(int, int, int, int) - Method in interface ome.util.math.geom2D.PlaneArea
Sets the bounding Rectangle of the planeArea to the specified x, y, width, and height.
setBounds(int, int, int, int) - Method in class ome.util.math.geom2D.RectangleArea
Implemented as specified by the PlaneArea I/F.
setByteOrder(ByteOrder) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
Sets the pixel byte order.
setBytes(byte[]) - Method in class ome.model.roi.Mask
 
setC(int) - Method in class pojos.ShapeData
Sets the channel.
setCacheEventListeners(CacheEventListener[]) - Method in class ome.services.sessions.state.CacheFactory
 
setCacheManager(CacheManager) - Method in class ome.services.sessions.state.SessionCache
Injection method, also performs the creation of SessionCache.sessions
setCalibratedMagnification(Double) - Method in class ome.model.acquisition.Objective
 
setCallback(ClientCallbackPrx, Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
setCallback(RepoRawFileStoreI.Callback) - Method in class ome.services.blitz.repo.RepoRawFileStoreI
 
setCallContext(Map<String, String>) - Method in class ome.security.basic.BasicEventContext
 
setCaseSentivice(boolean) - Method in interface ome.api.Search
Sets the case sensitivity on all queries where case-sensitivity is supported.
setCaseSentivice(boolean) - Method in class ome.services.SearchBean
 
setCaseSentivice_async(AMD_Search_setCaseSentivice, boolean, Current) - Method in class ome.services.blitz.impl.SearchI
 
setCdEnd(Integer) - Method in class ome.model.display.QuantumDef
 
setCdStart(Integer) - Method in class ome.model.display.QuantumDef
 
setChanges(String) - Method in class ome.services.graphs.GraphPolicyRule
 
setChannel(int, Channel) - Method in class ome.model.core.Pixels
Sets the ome.model.core.Channel at the given index.
setChannelAcquisitionMode(AcquisitionMode, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setChannelAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setChannelBinding(int, ChannelBinding) - Method in class ome.model.display.RenderingDef
Sets the ome.model.display.ChannelBinding at the given index.
setChannelColor(Color, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setChannelContrastMethod(ContrastMethod, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setChannelEmissionWavelength(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setChannelExcitationWavelength(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
(non-Javadoc)
setChannelFilterSetRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setChannelFluor(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setChannelGlobalMinMax(long, int, double, double) - Method in interface ome.api.IPixels
Sets the channel global (all 2D optical sections corresponding to a particular channel) minimum and maximum for a Pixels set.
setChannelGlobalMinMax(int, double, double, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setChannelGlobalMinMax(long, int, double, double) - Method in class ome.logic.PixelsImpl
 
setChannelGlobalMinMax_async(AMD_IPixels_setChannelGlobalMinMax, long, int, double, double, Current) - Method in class ome.services.blitz.impl.PixelsI
 
setChannelID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setChannelIlluminationType(IlluminationType, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setChannelLightSourceSettingsAttenuation(PercentFraction, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setChannelLightSourceSettingsID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setChannelLightSourceSettingsWavelength(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setChannelLookupTable(int, String) - Method in class ome.services.RenderingBean
 
setChannelLookupTable(int, String) - Method in interface omeis.providers.re.RenderingEngine
 
setChannelLookupTable_async(AMD_RenderingEngine_setChannelLookupTable, int, String, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
setChannelName(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setChannelNDFilter(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setChannelPinholeSize(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setChannelPockelCellSetting(Integer, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setChannels(Set<Channel>) - Method in class ome.model.core.LogicalChannel
setter for channels should be avoided.
setChannels(List<Channel>) - Method in class ome.model.core.Pixels
setter for channels should be avoided.
setChannelSamplesPerPixel(PositiveInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setChannelWindow(int, double, double) - Method in class ome.services.RenderingBean
Implemented as specified by the RenderingEngine interface.
setChannelWindow(int, double, double) - Method in class omeis.providers.re.Renderer
Sets the pixels intensity interval for the specified channel.
setChannelWindow(int, double, double) - Method in interface omeis.providers.re.RenderingEngine
Returns the pixels intensity interval.
setChannelWindow_async(AMD_RenderingEngine_setChannelWindow, int, double, double, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
setChecksumAlgorithm(String) - Method in class ome.formats.importer.ImportContainer
 
setChecksumAlgorithm(ChecksumAlgorithm, List<Long>, Current) - Method in class ome.services.blitz.repo.ManagedRepositoryI
 
setChecksumProviderFactory(ChecksumProviderFactory) - Method in class ome.services.RawFileBean
ChecksumProviderFactory Bean injector
setChild(IObject) - Method in class ome.model.acquisition.FilterSetEmissionFilterLink
 
setChild(IObject) - Method in class ome.model.acquisition.FilterSetExcitationFilterLink
 
setChild(IObject) - Method in class ome.model.acquisition.LightPathEmissionFilterLink
 
setChild(IObject) - Method in class ome.model.acquisition.LightPathExcitationFilterLink
 
setChild(IObject) - Method in class ome.model.annotations.AnnotationAnnotationLink
 
setChild(IObject) - Method in class ome.model.annotations.ChannelAnnotationLink
 
setChild(IObject) - Method in class ome.model.annotations.DatasetAnnotationLink
 
setChild(IObject) - Method in class ome.model.annotations.DetectorAnnotationLink
 
setChild(IObject) - Method in class ome.model.annotations.DichroicAnnotationLink
 
setChild(IObject) - Method in class ome.model.annotations.ExperimenterAnnotationLink
 
setChild(IObject) - Method in class ome.model.annotations.ExperimenterGroupAnnotationLink
 
setChild(IObject) - Method in class ome.model.annotations.FilesetAnnotationLink
 
setChild(IObject) - Method in class ome.model.annotations.FilterAnnotationLink
 
setChild(IObject) - Method in class ome.model.annotations.ImageAnnotationLink
 
setChild(IObject) - Method in class ome.model.annotations.InstrumentAnnotationLink
 
setChild(IObject) - Method in class ome.model.annotations.LightPathAnnotationLink
 
setChild(IObject) - Method in class ome.model.annotations.LightSourceAnnotationLink
 
setChild(IObject) - Method in class ome.model.annotations.NamespaceAnnotationLink
 
setChild(IObject) - Method in class ome.model.annotations.NodeAnnotationLink
 
setChild(IObject) - Method in class ome.model.annotations.ObjectiveAnnotationLink
 
setChild(IObject) - Method in class ome.model.annotations.OriginalFileAnnotationLink
 
setChild(IObject) - Method in class ome.model.annotations.PlaneInfoAnnotationLink
 
setChild(IObject) - Method in class ome.model.annotations.PlateAcquisitionAnnotationLink
 
setChild(IObject) - Method in class ome.model.annotations.PlateAnnotationLink
 
setChild(IObject) - Method in class ome.model.annotations.ProjectAnnotationLink
 
setChild(IObject) - Method in class ome.model.annotations.ReagentAnnotationLink
 
setChild(IObject) - Method in class ome.model.annotations.RoiAnnotationLink
 
setChild(IObject) - Method in class ome.model.annotations.ScreenAnnotationLink
 
setChild(IObject) - Method in class ome.model.annotations.SessionAnnotationLink
 
setChild(IObject) - Method in class ome.model.annotations.ShapeAnnotationLink
 
setChild(IObject) - Method in class ome.model.annotations.WellAnnotationLink
 
setChild(IObject) - Method in class ome.model.containers.DatasetImageLink
 
setChild(IObject) - Method in class ome.model.containers.ProjectDatasetLink
 
setChild(IObject) - Method in class ome.model.core.PixelsOriginalFileMap
 
setChild(IObject) - Method in class ome.model.fs.FilesetJobLink
 
setChild(IObject) - Method in interface ome.model.ILink
 
setChild(IObject) - Method in class ome.model.jobs.JobOriginalFileLink
 
setChild(IObject) - Method in class ome.model.meta.GroupExperimenterMap
 
setChild(IObject) - Method in class ome.model.meta.ShareMember
 
setChild(IObject) - Method in class ome.model.screen.ScreenPlateLink
 
setChild(IObject) - Method in class ome.model.screen.WellReagentLink
 
setClasses(Set<String>) - Method in class ome.services.eventlogs.AllEntitiesPseudoLogLoader
 
setClient(OMEROMetadataStoreClient) - Method in class ome.formats.importer.util.ClientKeepAlive
 
setClientEndpoints(String, int) - Method in class ome.services.blitz.Router
 
setClientObject(boolean) - Method in class pojos.ShapeData
Sets to true if the object one that has been created client side, false otherwise.
setClientPath(String) - Method in class ome.model.fs.FilesetEntry
 
setClientSide(boolean) - Method in class pojos.ROIData
Sets the flag indicating if the object is a client-side object or not.
setClosed(Timestamp) - Method in class ome.model.meta.Session
 
setCo2percent(Double) - Method in class ome.model.acquisition.ImagingEnvironment
 
setCo2Percent(double) - Method in class pojos.ImageAcquisitionData
Sets the co2 level.
setCodomain(int, int) - Method in class omeis.providers.re.codomain.CodomainMapContext
Sets the codomain interval.
setCodomainInterval(int, int) - Method in class ome.services.RenderingBean
Implemented as specified by the RenderingEngine interface.
setCodomainInterval(int, int) - Method in class omeis.providers.re.Renderer
Sets the codomain interval i.e. a sub-interval of [0, 255].
setCodomainInterval(int, int) - Method in interface omeis.providers.re.RenderingEngine
Sets the sub-interval of the device space i.e. a discrete sub-interval of [0, 255]
setCodomainInterval_async(AMD_RenderingEngine_setCodomainInterval, int, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
setCodomainMapContext(int, CodomainMapContext) - Method in class ome.model.display.RenderingDef
Sets the ome.model.display.CodomainMapContext at the given index.
setCoefficient(Double) - Method in class ome.model.display.ChannelBinding
 
setColumn(Integer) - Method in class ome.model.screen.Well
 
setColumnNamingConvention(String) - Method in class ome.model.screen.Plate
 
setColumns(Integer) - Method in class ome.model.screen.Plate
 
setComment(String) - Method in class ome.formats.importer.util.ErrorContainer
 
setCommentAnnotationAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setCommentAnnotationAnnotator(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setCommentAnnotationDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setCommentAnnotationID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setCommentAnnotationNamespace(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setCommentAnnotationValue(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setCommentType(String) - Method in class ome.formats.importer.util.ErrorContainer
 
setComponents(List<ImageData>) - Method in class pojos.MultiImageData
Sets the images composing the file.
setCompression(Double) - Method in class ome.model.display.RenderingDef
 
setCompressionLevel(float) - Method in interface ome.api.local.LocalCompress
Sets the current compression level for the service.
setCompressionLevel(float) - Method in class ome.logic.CompressImpl
 
setCompressionLevel(float) - Method in class ome.services.RenderingBean
Implemented as specified by the RenderingEngine interface.
setCompressionLevel(float) - Method in interface omeis.providers.re.RenderingEngine
Sets the current compression level for the service.
setCompressionLevel_async(AMD_RenderingEngine_setCompressionLevel, float, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
setCompressionService(LocalCompress) - Method in class ome.services.ThumbnailBean
Compression service Bean injector.
setCondition(String) - Method in class ome.services.graphs.GraphPolicy
Set a named condition,
setCondition(String) - Method in class omero.cmd.graphs.BaseGraphPolicyAdjuster
 
setConfig(List<NamedValue>) - Method in class ome.model.meta.ExperimenterGroup
 
setConfigValue(String, String) - Method in interface ome.api.IConfig
set a configuration value in the backend store.
setConfigValue(String, String) - Method in class ome.logic.ConfigImpl
setConfigValue_async(AMD_IConfig_setConfigValue, String, String, Current) - Method in class ome.services.blitz.impl.ConfigI
 
setConfigValueIfEquals(String, String, String) - Method in interface ome.api.IConfig
Calls IConfig.setConfigValue(String, String) if and only if the configuration property is currently equal to the test argument.
setConfigValueIfEquals(String, String, String) - Method in class ome.logic.ConfigImpl
setConfigValueIfEquals_async(AMD_IConfig_setConfigValueIfEquals, String, String, String, Current) - Method in class ome.services.blitz.impl.ConfigI
 
setConn(String) - Method in class ome.model.meta.Node
 
setConstant(Boolean) - Method in class ome.model.display.PlaneSlicingContext
 
setConstant(boolean) - Method in class omeis.providers.re.codomain.PlaneSlicingContext
Sets the type of mapping.
setContactSystem(boolean) - Method in class ome.services.mail.FailedLoginMailSender
 
setContactUser(boolean) - Method in class ome.services.mail.FailedLoginMailSender
 
setContainingEvent(Event) - Method in class ome.model.meta.Event
 
setContent(Object) - Method in class pojos.AnnotationData
Sets the annotation value.
setContent(Object) - Method in class pojos.BooleanAnnotationData
Sets the text annotation.
setContent(Object) - Method in class pojos.DoubleAnnotationData
Sets the text annotation.
setContent(Object) - Method in class pojos.FileAnnotationData
Sets the text annotation.
setContent(Object) - Method in class pojos.LongAnnotationData
Sets the text annotation.
setContent(Object) - Method in class pojos.MapAnnotationData
 
setContent(Object) - Method in class pojos.RatingAnnotationData
Sets the text annotation.
setContent(Object) - Method in class pojos.TagAnnotationData
Sets the text annotation.
setContent(Object) - Method in class pojos.TermAnnotationData
Sets the text annotation.
setContent(Object) - Method in class pojos.TextualAnnotationData
Sets the text annotation.
setContent(Object) - Method in class pojos.TimeAnnotationData
Sets the time annotation.
setContent(Object) - Method in class pojos.XMLAnnotationData
Sets the annotation.
setContext(IObject) - Method in class ome.model.internal.Details
set entity to which this Details belongs.
setContext(Map<String, String>) - Method in class ome.security.basic.CurrentDetails
 
setContext(CodomainMapContext) - Method in interface omeis.providers.re.codomain.CodomainMap
Sets the parameters used to write the equation of the specified codomain transformation.
setContexts(Object[]) - Method in class ome.model.internal.Details
 
setContrastMethod(ContrastMethod) - Method in class ome.model.core.LogicalChannel
 
setContrastMethod(ContrastMethod) - Method in class pojos.ChannelData
Sets the contrast method value.
setCoordinates(int, int, int, int) - Method in class omeis.providers.re.codomain.ContrastStretchingContext
Sets the coordinates of the points used to determine the equations of the lines.
setCorrection(Correction) - Method in class ome.model.acquisition.Objective
 
setCorrectionCollar(Double) - Method in class ome.model.acquisition.ObjectiveSettings
 
setCorrectionCollar(double) - Method in class pojos.ImageAcquisitionData
Sets the correction of the objective.
setCounterFactory(CounterFactory) - Method in class ome.services.sessions.SessionManagerImpl
 
setCreationEvent(Event) - Method in interface ome.model.IDetails
 
setCreationEvent(Event) - Method in class ome.model.internal.Details
 
setCreationEvent(Event, Current) - Method in class omero.model.DetailsI
 
setCredentials(String) - Method in class ome.system.SessionInitializer
 
setCriteria(Criteria) - Method in class ome.services.query.Query
provide this Query instance with a Criteria to be used for retrieving data.
setCtime(Timestamp) - Method in class ome.model.core.OriginalFile
 
setCurrentDetails(CurrentDetails) - Method in class ome.logic.ConfigImpl
PreferenceContext setter for dependency injection.
setCurrentEventLog(long, String) - Method in class ome.util.actions.PostgresSqlAction
 
setCurrentEventLog(long, String) - Method in class ome.util.SqlAction.Impl
 
setCurrentEventLog(long, String) - Method in interface ome.util.SqlAction
 
setCurrentGroup(long) - Method in class ome.formats.OMEROMetadataStoreClient
Changes the default group of the currently logged in user.
setCurrentId(long) - Method in class ome.services.eventlogs.PersistentEventLogLoader
 
setCurrentLogFile(String, String) - Method in class ome.formats.OMEROMetadataStoreClient
 
setCurrentPatch(Integer) - Method in class ome.model.meta.DBPatch
 
setCurrentVersion(String) - Method in class ome.model.meta.DBPatch
 
setCustomAnnotationList(List<Annotation>) - Method in class ome.formats.importer.ImportContainer
Sets the list of custom, user specified, annotations to link to all images represented by this container.
setCustomImageNaming(boolean) - Method in class ome.formats.importer.ImportConfig
 
setCustomImageNaming(boolean) - Method in class ome.formats.importer.util.IniFileLoader
 
setCutIn(Length) - Method in class ome.model.acquisition.TransmittanceRange
 
setCutInTolerance(Length) - Method in class ome.model.acquisition.TransmittanceRange
 
setCutOut(Length) - Method in class ome.model.acquisition.TransmittanceRange
 
setCutOutTolerance(Length) - Method in class ome.model.acquisition.TransmittanceRange
 
setCx(Double) - Method in class ome.model.roi.Ellipse
 
setCx(Double) - Method in class ome.model.roi.Point
 
setCy(Double) - Method in class ome.model.roi.Ellipse
 
setCy(Double) - Method in class ome.model.roi.Point
 
setD(String) - Method in class ome.model.roi.Path
 
setData(byte[]) - Method in class ome.model.meta.Share
 
setDatabaseIdentity(DatabaseIdentity) - Method in class ome.logic.ConfigImpl
 
setDatadir(String) - Method in class ome.logic.RepositoryInfoImpl
Bean injection setter for data repository directory
setDataObjects(Set<DataObject>) - Method in class pojos.TagAnnotationData
Sets the collection of data objects related to that tag.
setDatasetAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDatasetDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDatasetExperimenterGroupRef(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDatasetExperimenterRef(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDatasetID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDatasetImageRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDatasetLinks(Set<ProjectDatasetLink>) - Method in class ome.model.containers.Project
setter for datasetLinks should be avoided.
setDatasetLinks(Set<DatasetImageLink>) - Method in class ome.model.core.Image
setter for datasetLinks should be avoided.
setDatasetLinksCountPerOwner(Map<Long, Long>) - Method in class ome.model.containers.Project
 
setDatasetLinksCountPerOwner(Map<Long, Long>) - Method in class ome.model.core.Image
 
setDatasetName(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDatasets(Set) - Method in class pojos.ImageData
Sets the datasets containing the image.
setDatasets(Set<DatasetData>) - Method in class pojos.ProjectData
Sets the datasets contained in this project.
setDataValue(double) - Method in class pojos.DoubleAnnotationData
Sets the rating value.
setDataValue(long) - Method in class pojos.LongAnnotationData
Sets the rating value.
setDb(boolean) - Method in class ome.system.Preference
Setter injector
setDebug(boolean) - Method in class ome.tools.hibernate.EventMethodInterceptor
 
setDebugAll(boolean) - Method in class ome.security.basic.EventListenersFactoryBean
for setter injection
setDebugLevel(int) - Method in class ome.formats.importer.ImportConfig
 
setDebugLevel(int) - Method in class ome.formats.importer.util.IniFileLoader
Set debug level for application
setDecoration(String) - Method in class ome.model.roi.Label
 
setDefaultBody(String) - Method in class ome.services.mail.MailSender
 
setDefaultEventType(String) - Method in class ome.model.meta.Session
 
setDefaultGroup(Experimenter, ExperimenterGroup) - Method in interface ome.api.IAdmin
sets the default group for a given user.
setDefaultGroup(Experimenter, ExperimenterGroup) - Method in class ome.logic.AdminImpl
 
setDefaultGroup(Experimenter, ExperimenterGroup) - Method in interface ome.security.auth.RoleProvider
 
setDefaultGroup(Experimenter, ExperimenterGroup) - Method in class ome.security.auth.SimpleRoleProvider
 
setDefaultGroup_async(AMD_IAdmin_setDefaultGroup, Experimenter, ExperimenterGroup, Current) - Method in class ome.services.blitz.impl.AdminI
 
setDefaultPixels(PixelsData) - Method in class pojos.ImageData
Sets the default set of pixels.
setDefaultSample(Integer) - Method in class ome.model.screen.Plate
 
setDefaultSample(int) - Method in class pojos.PlateData
Sets the default sample.
setDefaultT(Integer) - Method in class ome.model.display.RenderingDef
 
setDefaultT(int) - Method in class ome.services.RenderingBean
Implemented as specified by the RenderingEngine interface.
setDefaultT(int) - Method in class omeis.providers.re.Renderer
Sets the default timepoint index.
setDefaultT(int) - Method in interface omeis.providers.re.RenderingEngine
Sets the default timepoint index.
setDefaultT_async(AMD_RenderingEngine_setDefaultT, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
setDefaultTimeToIdle(long) - Method in class ome.services.sessions.SessionManagerImpl
 
setDefaultTimeToLive(long) - Method in class ome.services.sessions.SessionManagerImpl
 
setDefaultZ(Integer) - Method in class ome.model.display.RenderingDef
 
setDefaultZ(int) - Method in class ome.services.RenderingBean
Implemented as specified by the RenderingEngine interface.
setDefaultZ(int) - Method in class omeis.providers.re.Renderer
Sets the index of the default focal section.
setDefaultZ(int) - Method in interface omeis.providers.re.RenderingEngine
Sets the index of the default focal section.
setDefaultZ_async(AMD_RenderingEngine_setDefaultZ, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
setDeltaT(Time) - Method in class ome.model.core.PlaneInfo
 
setDescription(long, String) - Method in interface ome.api.IShare
 
setDescription(String) - Method in class ome.model.annotations.Annotation
 
setDescription(String) - Method in class ome.model.containers.Dataset
 
setDescription(String) - Method in class ome.model.containers.Project
 
setDescription(String) - Method in class ome.model.core.Image
 
setDescription(String) - Method in class ome.model.experiment.Experiment
 
setDescription(String) - Method in class ome.model.experiment.MicrobeamManipulation
 
setDescription(String) - Method in class ome.model.jobs.ScriptJob
 
setDescription(String) - Method in class ome.model.meta.ExperimenterGroup
 
setDescription(String) - Method in class ome.model.meta.Namespace
 
setDescription(String) - Method in class ome.model.roi.Roi
 
setDescription(String) - Method in class ome.model.screen.Plate
 
setDescription(String) - Method in class ome.model.screen.PlateAcquisition
 
setDescription(String) - Method in class ome.model.screen.Reagent
 
setDescription(String) - Method in class ome.model.screen.Screen
 
setDescription(long, String) - Method in class ome.services.sharing.ShareBean
 
setDescription(String) - Method in class pojos.AnnotationData
Sets the description of the underlying Annotation instance.
setDescription(String) - Method in class pojos.DatasetData
Sets the description of the dataset.
setDescription(String) - Method in class pojos.FileAnnotationData
Sets the description of the annotation.
setDescription(String) - Method in class pojos.FileData
Sets the description.
setDescription(String) - Method in class pojos.GroupData
Sets the name of the group.
setDescription(String) - Method in class pojos.ImageData
Sets the description of the image.
setDescription(String) - Method in class pojos.PlateAcquisitionData
Sets the name of the acquisition.
setDescription(String) - Method in class pojos.PlateData
Sets the description of the plate.
setDescription(String) - Method in class pojos.ProjectData
Sets the description of the project.
setDescription(String) - Method in class pojos.ScreenData
Sets the description of the screen.
setDescription(String) - Method in class pojos.XMLAnnotationData
Sets the description of the annotation.
setDescription_async(AMD_IShare_setDescription, long, String, Current) - Method in class ome.services.blitz.impl.ShareI
 
setDetach(boolean, Current) - Method in class omero.grid.InteractiveProcessorI
 
setDetails(Details) - Method in class ome.model.acquisition.Detector
setDetails(Details) - Method in class ome.model.acquisition.DetectorSettings
setDetails(Details) - Method in class ome.model.acquisition.Dichroic
setDetails(Details) - Method in class ome.model.acquisition.Filter
setDetails(Details) - Method in class ome.model.acquisition.FilterSet
setDetails(Details) - Method in class ome.model.acquisition.FilterSetEmissionFilterLink
setDetails(Details) - Method in class ome.model.acquisition.FilterSetExcitationFilterLink
setDetails(Details) - Method in class ome.model.acquisition.ImagingEnvironment
setDetails(Details) - Method in class ome.model.acquisition.Instrument
setDetails(Details) - Method in class ome.model.acquisition.LightPath
setDetails(Details) - Method in class ome.model.acquisition.LightPathEmissionFilterLink
setDetails(Details) - Method in class ome.model.acquisition.LightPathExcitationFilterLink
setDetails(Details) - Method in class ome.model.acquisition.LightSettings
setDetails(Details) - Method in class ome.model.acquisition.LightSource
setDetails(Details) - Method in class ome.model.acquisition.Microscope
setDetails(Details) - Method in class ome.model.acquisition.Objective
setDetails(Details) - Method in class ome.model.acquisition.ObjectiveSettings
setDetails(Details) - Method in class ome.model.acquisition.OTF
setDetails(Details) - Method in class ome.model.acquisition.StageLabel
setDetails(Details) - Method in class ome.model.acquisition.TransmittanceRange
setDetails(Details) - Method in class ome.model.annotations.Annotation
setDetails(Details) - Method in class ome.model.annotations.AnnotationAnnotationLink
setDetails(Details) - Method in class ome.model.annotations.ChannelAnnotationLink
setDetails(Details) - Method in class ome.model.annotations.DatasetAnnotationLink
setDetails(Details) - Method in class ome.model.annotations.DetectorAnnotationLink
setDetails(Details) - Method in class ome.model.annotations.DichroicAnnotationLink
setDetails(Details) - Method in class ome.model.annotations.ExperimenterAnnotationLink
setDetails(Details) - Method in class ome.model.annotations.ExperimenterGroupAnnotationLink
setDetails(Details) - Method in class ome.model.annotations.FilesetAnnotationLink
setDetails(Details) - Method in class ome.model.annotations.FilterAnnotationLink
setDetails(Details) - Method in class ome.model.annotations.ImageAnnotationLink
setDetails(Details) - Method in class ome.model.annotations.InstrumentAnnotationLink
setDetails(Details) - Method in class ome.model.annotations.LightPathAnnotationLink
setDetails(Details) - Method in class ome.model.annotations.LightSourceAnnotationLink
setDetails(Details) - Method in class ome.model.annotations.NamespaceAnnotationLink
setDetails(Details) - Method in class ome.model.annotations.NodeAnnotationLink
setDetails(Details) - Method in class ome.model.annotations.ObjectiveAnnotationLink
setDetails(Details) - Method in class ome.model.annotations.OriginalFileAnnotationLink
setDetails(Details) - Method in class ome.model.annotations.PlaneInfoAnnotationLink
setDetails(Details) - Method in class ome.model.annotations.PlateAcquisitionAnnotationLink
setDetails(Details) - Method in class ome.model.annotations.PlateAnnotationLink
setDetails(Details) - Method in class ome.model.annotations.ProjectAnnotationLink
setDetails(Details) - Method in class ome.model.annotations.ReagentAnnotationLink
setDetails(Details) - Method in class ome.model.annotations.RoiAnnotationLink
setDetails(Details) - Method in class ome.model.annotations.ScreenAnnotationLink
setDetails(Details) - Method in class ome.model.annotations.SessionAnnotationLink
setDetails(Details) - Method in class ome.model.annotations.ShapeAnnotationLink
setDetails(Details) - Method in class ome.model.annotations.WellAnnotationLink
setDetails(Details) - Method in class ome.model.containers.Dataset
setDetails(Details) - Method in class ome.model.containers.DatasetImageLink
setDetails(Details) - Method in class ome.model.containers.Project
setDetails(Details) - Method in class ome.model.containers.ProjectDatasetLink
setDetails(Details) - Method in class ome.model.core.Channel
setDetails(Details) - Method in class ome.model.core.Image
setDetails(Details) - Method in class ome.model.core.LogicalChannel
setDetails(Details) - Method in class ome.model.core.OriginalFile
setDetails(Details) - Method in class ome.model.core.Pixels
setDetails(Details) - Method in class ome.model.core.PixelsOriginalFileMap
setDetails(Details) - Method in class ome.model.core.PlaneInfo
setDetails(Details) - Method in class ome.model.display.ChannelBinding
setDetails(Details) - Method in class ome.model.display.CodomainMapContext
setDetails(Details) - Method in class ome.model.display.QuantumDef
setDetails(Details) - Method in class ome.model.display.RenderingDef
setDetails(Details) - Method in class ome.model.display.Thumbnail
setDetails(Details) - Method in class ome.model.enums.AcquisitionMode
setDetails(Details) - Method in class ome.model.enums.ArcType
setDetails(Details) - Method in class ome.model.enums.Binning
setDetails(Details) - Method in class ome.model.enums.ChecksumAlgorithm
setDetails(Details) - Method in class ome.model.enums.ContrastMethod
setDetails(Details) - Method in class ome.model.enums.Correction
setDetails(Details) - Method in class ome.model.enums.DetectorType
setDetails(Details) - Method in class ome.model.enums.DimensionOrder
setDetails(Details) - Method in class ome.model.enums.EventType
setDetails(Details) - Method in class ome.model.enums.ExperimentType
setDetails(Details) - Method in class ome.model.enums.Family
setDetails(Details) - Method in class ome.model.enums.FilamentType
setDetails(Details) - Method in class ome.model.enums.FilterType
setDetails(Details) - Method in class ome.model.enums.Format
setDetails(Details) - Method in class ome.model.enums.Illumination
setDetails(Details) - Method in class ome.model.enums.Immersion
setDetails(Details) - Method in class ome.model.enums.LaserMedium
setDetails(Details) - Method in class ome.model.enums.LaserType
setDetails(Details) - Method in class ome.model.enums.Medium
setDetails(Details) - Method in class ome.model.enums.MicrobeamManipulationType
setDetails(Details) - Method in class ome.model.enums.MicroscopeType
setDetails(Details) - Method in class ome.model.enums.PhotometricInterpretation
setDetails(Details) - Method in class ome.model.enums.PixelsType
setDetails(Details) - Method in class ome.model.enums.Pulse
setDetails(Details) - Method in class ome.model.enums.RenderingModel
setDetails(Details) - Method in class ome.model.experiment.Experiment
setDetails(Details) - Method in class ome.model.experiment.MicrobeamManipulation
setDetails(Details) - Method in class ome.model.fs.Fileset
setDetails(Details) - Method in class ome.model.fs.FilesetEntry
setDetails(Details) - Method in class ome.model.fs.FilesetJobLink
setDetails(Details) - Method in class ome.model.internal.Link
setDetails(Details) - Method in class ome.model.jobs.Job
setDetails(Details) - Method in class ome.model.jobs.JobOriginalFileLink
setDetails(Details) - Method in class ome.model.jobs.JobStatus
setDetails(Details) - Method in class ome.model.meta.DBPatch
setDetails(Details) - Method in class ome.model.meta.Event
setDetails(Details) - Method in class ome.model.meta.EventLog
setDetails(Details) - Method in class ome.model.meta.Experimenter
setDetails(Details) - Method in class ome.model.meta.ExperimenterGroup
setDetails(Details) - Method in class ome.model.meta.ExternalInfo
setDetails(Details) - Method in class ome.model.meta.GroupExperimenterMap
setDetails(Details) - Method in class ome.model.meta.Namespace
setDetails(Details) - Method in class ome.model.meta.Node
setDetails(Details) - Method in class ome.model.meta.Session
setDetails(Details) - Method in class ome.model.meta.ShareMember
setDetails(Details) - Method in class ome.model.roi.Roi
setDetails(Details) - Method in class ome.model.roi.Shape
setDetails(Details) - Method in class ome.model.screen.Plate
setDetails(Details) - Method in class ome.model.screen.PlateAcquisition
setDetails(Details) - Method in class ome.model.screen.Reagent
setDetails(Details) - Method in class ome.model.screen.Screen
setDetails(Details) - Method in class ome.model.screen.ScreenPlateLink
setDetails(Details) - Method in class ome.model.screen.Well
setDetails(Details) - Method in class ome.model.screen.WellReagentLink
setDetails(Details) - Method in class ome.model.screen.WellSample
setDetails(Details) - Method in class ome.model.stats.StatsInfo
setDetector(Detector) - Method in class ome.model.acquisition.DetectorSettings
 
setDetector(Set<Detector>) - Method in class ome.model.acquisition.Instrument
setter for detector should be avoided.
setDetectorAmplificationGain(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDetectorAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDetectorGain(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDetectorID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDetectorLotNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDetectorManufacturer(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDetectorModel(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDetectorOffset(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDetectorSerialNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDetectorSettingBinning(Binning) - Method in class pojos.ChannelAcquisitionData
Sets the detector's binning.
setDetectorSettingOffset(double) - Method in class pojos.ChannelAcquisitionData
Sets the detector's setting offset.
setDetectorSettings(DetectorSettings) - Method in class ome.model.core.LogicalChannel
 
setDetectorSettingsBinning(Binning, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDetectorSettingsGain(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDetectorSettingsGain(double) - Method in class pojos.ChannelAcquisitionData
Sets the detector setting's gain.
setDetectorSettingsID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDetectorSettingsIntegration(PositiveInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDetectorSettingsOffset(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDetectorSettingsReadOutRate(Frequency, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDetectorSettingsReadOutRate(Frequency) - Method in class pojos.ChannelAcquisitionData
Sets the detector setting's read out rate.
setDetectorSettingsReadOutRate(double) - Method in class pojos.ChannelAcquisitionData
setDetectorSettingsVoltage(ElectricPotential, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDetectorSettingsVoltage(ElectricPotential) - Method in class pojos.ChannelAcquisitionData
Sets the detector setting's voltage.
setDetectorSettingsVoltage(double) - Method in class pojos.ChannelAcquisitionData
setDetectorSettingsZoom(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDetectorType(DetectorType, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDetectorVoltage(ElectricPotential, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDetectorZoom(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDichroic(Dichroic) - Method in class ome.model.acquisition.FilterSet
 
setDichroic(Set<Dichroic>) - Method in class ome.model.acquisition.Instrument
setter for dichroic should be avoided.
setDichroic(Dichroic) - Method in class ome.model.acquisition.LightPath
 
setDichroicAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDichroicID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDichroicLotNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDichroicManufacturer(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDichroicModel(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDichroicSerialNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDimensionOrder(DimensionOrder) - Method in class ome.model.core.Pixels
 
setDirection(String) - Method in class ome.model.roi.Label
 
setDirty(boolean) - Method in class pojos.DataObject
Sets to true if the value has been modified, otherwise.
setDirty(boolean) - Method in class pojos.ShapeData
Sets to true if the figure been changed from the server side version, false otherwise.
setDisabledSubsystems(Set<String>) - Method in class ome.security.basic.BasicEventContext
 
setDisallow(boolean[], int, boolean) - Static method in class ome.model.internal.Permissions
 
setDisallowAnnotate(boolean) - Method in class ome.model.internal.Permissions
 
setDisallowDelete(boolean) - Method in class ome.model.internal.Permissions
 
setDisallowEdit(boolean) - Method in class ome.model.internal.Permissions
 
setDisallowLink(boolean) - Method in class ome.model.internal.Permissions
 
setDiskSpaceChecking(boolean) - Method in class ome.services.RawFileBean
setter disk overflow checking
setDiskSpaceChecking(boolean) - Method in class ome.services.RawPixelsBean
 
setDiskSpaceChecking(boolean) - Method in class ome.services.ThumbnailBean
 
setDisplay(Boolean) - Method in class ome.model.meta.Namespace
 
setDisplayName(String) - Method in class ome.model.meta.Namespace
 
setDN(Long, String) - Method in interface ome.api.ILdap
Deprecated.
As of release 5.1, relevant model objects have the "ldap" property added to their state.
setDN(Long, String) - Method in class ome.logic.LdapImpl
Deprecated.
setDN_async(AMD_ILdap_setDN, RLong, String, Current) - Method in class ome.services.blitz.impl.LdapI
 
setDoThumbnails(boolean) - Method in class ome.formats.importer.ImportContainer
Sets whether or not we are performing thumbnail creation upon import completion.
setDoubleAnnotationAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDoubleAnnotationAnnotator(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDoubleAnnotationDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDoubleAnnotationID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDoubleAnnotationNamespace(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDoubleAnnotationValue(Double, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDoubleValue(Double) - Method in class ome.model.annotations.DoubleAnnotation
 
setDown(Timestamp) - Method in class ome.model.meta.Node
 
setDryRun(boolean) - Method in class ome.services.fulltext.FullTextIndexer
 
setEllipseAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setEllipseFillColor(Color, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setEllipseFillRule(FillRule, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setEllipseFontFamily(FontFamily, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setEllipseFontSize(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setEllipseFontStyle(FontStyle, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setEllipseID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setEllipseLineCap(LineCap, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setEllipseLocked(Boolean, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setEllipseRadiusX(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setEllipseRadiusY(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setEllipseStrokeColor(Color, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setEllipseStrokeDashArray(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setEllipseStrokeWidth(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setEllipseText(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setEllipseTheC(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setEllipseTheT(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setEllipseTheZ(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setEllipseTransform(AffineTransform, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setEllipseVisible(Boolean, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setEllipseX(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setEllipseY(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setEmail(String) - Method in class ome.formats.importer.util.ErrorContainer
 
setEmail(String) - Method in class ome.model.meta.Experimenter
 
setEmail(String) - Method in class pojos.ExperimenterData
Sets the e-mail of the experimenter.
setEmissionFilterLink(Set<FilterSetEmissionFilterLink>) - Method in class ome.model.acquisition.Filter
setter for emissionFilterLink should be avoided.
setEmissionFilterLink(Set<FilterSetEmissionFilterLink>) - Method in class ome.model.acquisition.FilterSet
setter for emissionFilterLink should be avoided.
setEmissionFilterLink(Set<LightPathEmissionFilterLink>) - Method in class ome.model.acquisition.LightPath
setter for emissionFilterLink should be avoided.
setEmissionFilterLinkCountPerOwner(Map<Long, Long>) - Method in class ome.model.acquisition.Filter
 
setEmissionFilterLinkCountPerOwner(Map<Long, Long>) - Method in class ome.model.acquisition.FilterSet
 
setEmissionFilterLinkCountPerOwner(Map<Long, Long>) - Method in class ome.model.acquisition.LightPath
 
setEmissionWave(Length) - Method in class ome.model.core.LogicalChannel
 
setEmissionWavelength(Length) - Method in class pojos.ChannelData
Sets the emission wavelength.
setEmissionWavelength(double) - Method in class pojos.ChannelData
setEnabled(boolean) - Method in class ome.services.mail.MailSender
 
setEncrypted(boolean) - Method in class loci.ome.io.OmeroReader
 
setEncryptedConnection(boolean) - Method in class ome.formats.OMEROMetadataStoreClient
 
setEndTime(Timestamp) - Method in class ome.model.screen.PlateAcquisition
 
setEntityId(Long) - Method in class ome.model.meta.EventLog
 
setEntityId(Long) - Method in class ome.model.meta.ExternalInfo
 
setEntityType(String) - Method in class ome.model.meta.EventLog
 
setEntityType(String) - Method in class ome.model.meta.ExternalInfo
 
setEnumerationProvider(EnumerationProvider) - Method in class ome.formats.OMEROMetadataStoreClient
Sets the active enumeration provider.
setError(Throwable) - Method in class ome.formats.importer.util.ErrorContainer
 
setError(String) - Method in class ome.services.graphs.GraphPolicyRule
 
setEvent(Event) - Method in class ome.model.meta.EventLog
 
setEvent(Event) - Method in class ome.security.basic.BasicEventContext
 
setEventContext(EventContext) - Method in class ome.services.graphs.GraphStep
Deprecated.
 
setEvents(Set<Event>) - Method in class ome.model.meta.Session
setter for events should be avoided.
setExcitationFilterLink(Set<FilterSetExcitationFilterLink>) - Method in class ome.model.acquisition.Filter
setter for excitationFilterLink should be avoided.
setExcitationFilterLink(Set<FilterSetExcitationFilterLink>) - Method in class ome.model.acquisition.FilterSet
setter for excitationFilterLink should be avoided.
setExcitationFilterLink(List<LightPathExcitationFilterLink>) - Method in class ome.model.acquisition.LightPath
setter for excitationFilterLink should be avoided.
setExcitationFilterLinkCountPerOwner(Map<Long, Long>) - Method in class ome.model.acquisition.Filter
 
setExcitationFilterLinkCountPerOwner(Map<Long, Long>) - Method in class ome.model.acquisition.FilterSet
 
setExcitationFilterLinkCountPerOwner(Map<Long, Long>) - Method in class ome.model.acquisition.LightPath
 
setExcitationWave(Length) - Method in class ome.model.core.LogicalChannel
 
setExcitationWavelength(Length) - Method in class pojos.ChannelData
Sets the excitation wavelength.
setExcitationWavelength(double) - Method in class pojos.ChannelData
setExcludes(String[]) - Method in class ome.services.eventlogs.EventLogLoader
Spring injector
setExecutor(Executor) - Method in class ome.logic.UpdateImpl
 
setExecutor(Executor) - Method in class ome.services.mail.MailSender
 
setExecutor(Executor) - Method in class ome.services.SearchBean
Injector used by Spring, currently, since SelfConfigurableService.selfConfigure() requires it.
setExecutor(Executor) - Method in class ome.services.sessions.SessionManagerImpl
 
setExperiment(Experiment) - Method in class ome.model.core.Image
 
setExperiment(Experiment) - Method in class ome.model.experiment.MicrobeamManipulation
 
setExperimentDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setExperimenter(Experimenter) - Method in class ome.model.meta.Event
 
setExperimenterAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setExperimenterEmail(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setExperimenterFirstName(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setExperimenterGroup(ExperimenterGroup) - Method in class ome.model.meta.Event
 
setExperimenterGroupAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setExperimenterGroupDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setExperimenterGroupExperimenterRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setExperimenterGroupID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setExperimenterGroupLeader(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setExperimenterGroupName(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setExperimenterID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setExperimenterInstitution(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setExperimenterLastName(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setExperimenterMiddleName(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setExperimenters(Set<ExperimenterData>) - Method in class pojos.GroupData
Sets the experimenters contained in this group.
setExperimenterUserName(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setExperimentExperimenterRef(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setExperimentID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setExperimentType(ExperimentType, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setExpiration(long, Timestamp) - Method in interface ome.api.IShare
 
setExpiration(long, Timestamp) - Method in class ome.services.sharing.ShareBean
 
setExpiration_async(AMD_IShare_setExpiration, long, RTime, Current) - Method in class ome.services.blitz.impl.ShareI
 
setExposureTime(Time) - Method in class ome.model.core.PlaneInfo
 
setExtendedMetadata(ExtendedMetadata) - Method in class ome.logic.AbstractLevel2Service
 
setExtendedMetadata(ExtendedMetadata) - Method in class ome.services.graphs.AbstractHierarchyGraphSpec
Deprecated.
Performs sanity checks on the entries found in ExtendedMetadata.
setExtendedMetadata(ExtendedMetadata) - Method in class ome.services.graphs.BaseGraphSpec
Deprecated.
 
setExtent(double, double) - Method in class omeis.providers.re.quantum.QuantumStrategy
Sets the maximum range of the input window.
setExternalDescription(String) - Method in class ome.model.screen.Well
 
setExternalDescription(String) - Method in class pojos.WellData
Sets the external description of the well.
setExternalIdentifier(String) - Method in class ome.model.screen.Plate
 
setExternalIdentifier(String) - Method in class ome.model.screen.Well
 
setExternalIdentifier(String) - Method in class pojos.PlateData
Sets the external identifier.
setExternalInfo(ExternalInfo) - Method in class ome.model.internal.Details
 
setExternalInfo(ExternalInfo, Current) - Method in class omero.model.DetailsI
 
setExtra(String) - Method in class ome.formats.importer.util.ErrorContainer
 
setFamily(Family) - Method in class ome.model.display.ChannelBinding
 
setFastShutdown(boolean) - Method in class omero.client
Sets the client.fastShutdown flag.
setFieldBridge(FieldBridge) - Static method in class ome.util.DetailsFieldBridge
 
setFilamentAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFilamentID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFilamentLotNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFilamentManufacturer(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFilamentModel(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFilamentPower(Power, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFilamentSerialNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFilamentType(FilamentType, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFile(File) - Method in class ome.formats.OMEROImportFixture
 
setFile(OriginalFile) - Method in class ome.model.annotations.FileAnnotation
 
setFileAnnotationAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFileAnnotationAnnotator(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFileAnnotationDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFileAnnotationID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFileAnnotationNamespace(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFileId(long) - Method in interface ome.api.RawFileStore
This method manages the state of the service.
setFileId(long) - Method in class ome.services.RawFileBean
 
setFileId_async(AMD_RawFileStore_setFileId, long, Current) - Method in class ome.services.blitz.impl.RawFileStoreI
 
setFileId_async(AMD_RawFileStore_setFileId, long, Current) - Method in class ome.services.blitz.repo.RepoRawFileStoreI
 
setFileIdWithBuffer(long, FileBuffer) - Method in class ome.services.RawFileBean
 
setFilePathResolver(FilePathResolver) - Method in class ome.io.nio.PixelsService
 
setFileRepo(Collection<Long>, String) - Method in class ome.util.actions.PostgresSqlAction
 
setFileRepo(Collection<Long>, String) - Method in interface ome.util.SqlAction
 
setFiles(String[]) - Method in class ome.formats.importer.util.ErrorContainer
 
setFileService(OriginalFilesService) - Method in class ome.logic.RepositoryInfoImpl
Bean injection setter for ROMIO file service
setFileset(Fileset) - Method in class ome.model.core.Image
 
setFileset(Fileset) - Method in class ome.model.fs.FilesetEntry
 
setFilesetEntries(Set<FilesetEntry>) - Method in class ome.model.core.OriginalFile
setter for filesetEntries should be avoided.
setFilesetEntry(int, FilesetEntry) - Method in class ome.model.fs.Fileset
Sets the ome.model.fs.FilesetEntry at the given index.
setFilesetJobLink(int, FilesetJobLink) - Method in class ome.model.fs.Fileset
Sets the ome.model.fs.FilesetJobLink at the given index.
setFileType(String) - Method in class ome.formats.importer.util.ErrorContainer
 
setFill(Color) - Method in class pojos.ShapeSettingsData
Set the fill color.
setFillColor(Integer) - Method in class ome.model.roi.Shape
 
setFillRule(String) - Method in class ome.model.roi.Shape
 
setFillRule(String) - Method in class pojos.ShapeSettingsData
Set the fill rule.
setFilter(Set<Filter>) - Method in class ome.model.acquisition.Instrument
setter for filter should be avoided.
setFilter(Filter) - Method in class ome.parameters.Parameters
 
setFilterAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFilterFilterWheel(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFilterID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFilterLotNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFilterManufacturer(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFilterModel(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFilterSerialNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFilterSet(Set<FilterSet>) - Method in class ome.model.acquisition.Instrument
setter for filterSet should be avoided.
setFilterSet(FilterSet) - Method in class ome.model.acquisition.OTF
 
setFilterSet(FilterSet) - Method in class ome.model.core.LogicalChannel
 
setFilterSetDichroicRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFilterSetEmissionFilterRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFilterSetExcitationFilterRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFilterSetID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFilterSetLotNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFilterSetManufacturer(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFilterSetModel(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFilterSetSerialNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFilterType(FilterType, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFilterWheel(String) - Method in class ome.model.acquisition.Filter
 
setFinished(Timestamp) - Method in class ome.model.jobs.Job
 
setFinished(Timestamp) - Method in class ome.model.meta.DBPatch
 
setFirstName(String) - Method in class ome.model.meta.Experimenter
 
setFirstName(String) - Method in class pojos.ExperimenterData
Sets the first name of the experimenter.
setFluor(String) - Method in class ome.model.core.LogicalChannel
 
setFluor(String) - Method in class pojos.ChannelData
Sets the fluor.
setFontFamily(String) - Method in class ome.model.roi.Shape
 
setFontFamily(String) - Method in class pojos.ShapeSettingsData
Returns the stroke.
setFontSize(Length) - Method in class ome.model.roi.Shape
 
setFontSize(int) - Method in class pojos.ShapeSettingsData
Deprecated.
setFontSize(Length) - Method in class pojos.ShapeSettingsData
Set the size of the font.
setFontStretch(String) - Method in class ome.model.roi.Shape
 
setFontStyle(String) - Method in class ome.model.roi.Shape
 
setFontStyle(String) - Method in class pojos.ShapeSettingsData
Sets the style of the font.
setFontVariant(String) - Method in class ome.model.roi.Shape
 
setFontWeight(String) - Method in class ome.model.roi.Shape
 
setFormat(Format) - Method in class ome.model.core.Image
 
setFrequencyMultiplication(Integer) - Method in class ome.model.acquisition.Laser
 
setFullTextBridge(FullTextBridge) - Method in class ome.logic.UpdateImpl
 
setG(String) - Method in class ome.model.roi.Shape
 
setGain(Double) - Method in class ome.model.acquisition.Detector
 
setGain(Double) - Method in class ome.model.acquisition.DetectorSettings
 
setGenericExcitationSourceAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setGenericExcitationSourceID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setGenericExcitationSourceLotNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setGenericExcitationSourceManufacturer(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setGenericExcitationSourceMap(List<MapPair>, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setGenericExcitationSourceModel(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setGenericExcitationSourcePower(Power, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setGenericExcitationSourceSerialNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setGlobalMax(Double) - Method in class ome.model.stats.StatsInfo
 
setGlobalMin(Double) - Method in class ome.model.stats.StatsInfo
 
setGlyphOrientationVertical(Integer) - Method in class ome.model.roi.Label
 
setGraphiteAddress(String) - Method in class ome.system.metrics.DefaultMetrics
 
setGreen(Integer) - Method in class ome.model.core.Channel
 
setGreen(Integer) - Method in class ome.model.display.ChannelBinding
 
setGreen(Integer) - Method in class ome.model.screen.Well
 
setGreen(Integer) - Method in class pojos.WellData
Sets the green component of the color associated to the well.
setGreenValue(int, int) - Method in class omeis.providers.re.RGBAIntBuffer
Sets the Green value for a particular pixel index.
setGreenValue(int, int) - Method in class omeis.providers.re.RGBBuffer
Sets the Green value for a particular pixel index.
setGreenValue(int, int) - Method in class omeis.providers.re.RGBIntBuffer
Sets the Green value for a particular pixel index.
setGroup(Long) - Method in class ome.formats.OMEROMetadataStoreClient
Sets the id which will be used by OMEROMetadataStoreClient.initializeServices(boolean) to set the call context for all services.
setGroup(ExperimenterGroup) - Method in class ome.model.internal.Details
 
setGroup(ExperimenterGroup) - Method in class ome.model.meta.Share
 
setGroup(ExperimenterGroup, Permissions) - Method in class ome.security.basic.BasicEventContext
 
setGroup(long) - Method in class ome.services.chgrp.ChgrpStepFactory
Deprecated.
Set the group id which will be passed to all new ChgrpStep instances.
setGroup(long) - Method in class ome.services.chown.ChownStepFactory
Deprecated.
Set the group id which will be passed to all new ChownStep instances.
setGroup(ExperimenterGroup, Current) - Method in class omero.model.DetailsI
 
setGroupAnnotate(boolean, Current) - Method in class omero.model.PermissionsI
 
setGroupAnnotate(boolean) - Method in class pojos.PermissionData
Sets to true if the group has annotate access, false otherwise.
setGroupExperimenterMap(List<GroupExperimenterMap>) - Method in class ome.model.meta.Experimenter
setter for groupExperimenterMap should be avoided.
setGroupExperimenterMap(int, GroupExperimenterMap) - Method in class ome.model.meta.Experimenter
Sets the ome.model.meta.GroupExperimenterMap at the given index.
setGroupExperimenterMap(Set<GroupExperimenterMap>) - Method in class ome.model.meta.ExperimenterGroup
setter for groupExperimenterMap should be avoided.
setGroupID(Long) - Method in class loci.ome.io.OmeroReader
 
setGroupName(String) - Method in class loci.ome.io.OmeroReader
 
setGroupname(String) - Method in class ome.model.jobs.Job
 
setGroupOwner(ExperimenterGroup, Experimenter) - Method in interface ome.api.IAdmin
adds the user to the owner list for this group.
setGroupOwner(ExperimenterGroup, Experimenter) - Method in class ome.logic.AdminImpl
 
setGroupOwner(Experimenter, ExperimenterGroup, boolean) - Method in interface ome.security.auth.RoleProvider
 
setGroupOwner(Experimenter, ExperimenterGroup, boolean) - Method in class ome.security.auth.SimpleRoleProvider
 
setGroupOwner_async(AMD_IAdmin_setGroupOwner, ExperimenterGroup, Experimenter, Current) - Method in class ome.services.blitz.impl.AdminI
 
setGroupPermissions(Permissions) - Method in class ome.system.SimpleEventContext
 
setGroupRead(boolean, Current) - Method in class omero.model.PermissionsI
 
setGroupRead(boolean) - Method in class pojos.PermissionData
Sets to true if the group has read access, false otherwise.
setGroups(List<GroupData>) - Method in class pojos.ExperimenterData
Sets the groups the experimenter is a member of.
setGroupWrite(boolean, Current) - Method in class omero.model.PermissionsI
 
setGroupWrite(boolean) - Method in class pojos.PermissionData
Sets to true if the group has write access, false otherwise.
setHash(String) - Method in class ome.model.core.OriginalFile
 
setHasher(ChecksumAlgorithm) - Method in class ome.model.core.OriginalFile
 
setHeight(Double) - Method in class ome.model.roi.Mask
 
setHeight(Double) - Method in class ome.model.roi.Rect
 
setHeight(int) - Method in class omeis.providers.re.data.RegionDef
Sets the height of the region.
setHeight(double) - Method in class pojos.MaskData
Sets the height of an untransformed mask.
setHeight(double) - Method in class pojos.RectangleData
Sets the height of an untransformed rectangle.
setHolder(ServantHolder) - Method in class ome.services.blitz.impl.AbstractAmdServant
Sets the ServantHolder for the current session so that on #close_async(AMD_StatefulServiceInterface_close, Current) it will be possible to cleanup the resources.
setHumidity(Double) - Method in class ome.model.acquisition.ImagingEnvironment
 
setHumidity(double) - Method in class pojos.ImageAcquisitionData
Sets the humidity.
setIceCommunicator(Communicator) - Method in class omero.util.ObjectFactoryRegistry
 
setIContainer(IContainer) - Method in class ome.logic.MetadataImpl
IContainer bean injector.
setId(String) - Method in class ome.io.bioformats.OmeroPixelsPyramidReader
 
setId(String) - Method in class ome.io.bioformats.OmeroPixelsPyramidWriter
 
setId(Long) - Method in class ome.model.acquisition.Detector
 
setId(Long) - Method in class ome.model.acquisition.DetectorSettings
 
setId(Long) - Method in class ome.model.acquisition.Dichroic
 
setId(Long) - Method in class ome.model.acquisition.Filter
 
setId(Long) - Method in class ome.model.acquisition.FilterSet
 
setId(Long) - Method in class ome.model.acquisition.FilterSetEmissionFilterLink
 
setId(Long) - Method in class ome.model.acquisition.FilterSetExcitationFilterLink
 
setId(Long) - Method in class ome.model.acquisition.ImagingEnvironment
 
setId(Long) - Method in class ome.model.acquisition.Instrument
 
setId(Long) - Method in class ome.model.acquisition.LightPath
 
setId(Long) - Method in class ome.model.acquisition.LightPathEmissionFilterLink
 
setId(Long) - Method in class ome.model.acquisition.LightPathExcitationFilterLink
 
setId(Long) - Method in class ome.model.acquisition.LightSettings
 
setId(Long) - Method in class ome.model.acquisition.LightSource
 
setId(Long) - Method in class ome.model.acquisition.Microscope
 
setId(Long) - Method in class ome.model.acquisition.Objective
 
setId(Long) - Method in class ome.model.acquisition.ObjectiveSettings
 
setId(Long) - Method in class ome.model.acquisition.OTF
 
setId(Long) - Method in class ome.model.acquisition.StageLabel
 
setId(Long) - Method in class ome.model.acquisition.TransmittanceRange
 
setId(Long) - Method in class ome.model.annotations.Annotation
 
setId(Long) - Method in class ome.model.annotations.AnnotationAnnotationLink
 
setId(Long) - Method in class ome.model.annotations.ChannelAnnotationLink
 
setId(Long) - Method in class ome.model.annotations.DatasetAnnotationLink
 
setId(Long) - Method in class ome.model.annotations.DetectorAnnotationLink
 
setId(Long) - Method in class ome.model.annotations.DichroicAnnotationLink
 
setId(Long) - Method in class ome.model.annotations.ExperimenterAnnotationLink
 
setId(Long) - Method in class ome.model.annotations.ExperimenterGroupAnnotationLink
 
setId(Long) - Method in class ome.model.annotations.FilesetAnnotationLink
 
setId(Long) - Method in class ome.model.annotations.FilterAnnotationLink
 
setId(Long) - Method in class ome.model.annotations.ImageAnnotationLink
 
setId(Long) - Method in class ome.model.annotations.InstrumentAnnotationLink
 
setId(Long) - Method in class ome.model.annotations.LightPathAnnotationLink
 
setId(Long) - Method in class ome.model.annotations.LightSourceAnnotationLink
 
setId(Long) - Method in class ome.model.annotations.NamespaceAnnotationLink
 
setId(Long) - Method in class ome.model.annotations.NodeAnnotationLink
 
setId(Long) - Method in class ome.model.annotations.ObjectiveAnnotationLink
 
setId(Long) - Method in class ome.model.annotations.OriginalFileAnnotationLink
 
setId(Long) - Method in class ome.model.annotations.PlaneInfoAnnotationLink
 
setId(Long) - Method in class ome.model.annotations.PlateAcquisitionAnnotationLink
 
setId(Long) - Method in class ome.model.annotations.PlateAnnotationLink
 
setId(Long) - Method in class ome.model.annotations.ProjectAnnotationLink
 
setId(Long) - Method in class ome.model.annotations.ReagentAnnotationLink
 
setId(Long) - Method in class ome.model.annotations.RoiAnnotationLink
 
setId(Long) - Method in class ome.model.annotations.ScreenAnnotationLink
 
setId(Long) - Method in class ome.model.annotations.SessionAnnotationLink
 
setId(Long) - Method in class ome.model.annotations.ShapeAnnotationLink
 
setId(Long) - Method in class ome.model.annotations.WellAnnotationLink
 
setId(Long) - Method in class ome.model.containers.Dataset
 
setId(Long) - Method in class ome.model.containers.DatasetImageLink
 
setId(Long) - Method in class ome.model.containers.Project
 
setId(Long) - Method in class ome.model.containers.ProjectDatasetLink
 
setId(Long) - Method in class ome.model.core.Channel
 
setId(Long) - Method in class ome.model.core.Image
 
setId(Long) - Method in class ome.model.core.LogicalChannel
 
setId(Long) - Method in class ome.model.core.OriginalFile
 
setId(Long) - Method in class ome.model.core.Pixels
 
setId(Long) - Method in class ome.model.core.PixelsOriginalFileMap
 
setId(Long) - Method in class ome.model.core.PlaneInfo
 
setId(Long) - Method in class ome.model.display.ChannelBinding
 
setId(Long) - Method in class ome.model.display.CodomainMapContext
 
setId(Long) - Method in class ome.model.display.QuantumDef
 
setId(Long) - Method in class ome.model.display.RenderingDef
 
setId(Long) - Method in class ome.model.display.Thumbnail
 
setId(Long) - Method in class ome.model.enums.AcquisitionMode
 
setId(Long) - Method in class ome.model.enums.ArcType
 
setId(Long) - Method in class ome.model.enums.Binning
 
setId(Long) - Method in class ome.model.enums.ChecksumAlgorithm
 
setId(Long) - Method in class ome.model.enums.ContrastMethod
 
setId(Long) - Method in class ome.model.enums.Correction
 
setId(Long) - Method in class ome.model.enums.DetectorType
 
setId(Long) - Method in class ome.model.enums.DimensionOrder
 
setId(Long) - Method in class ome.model.enums.EventType
 
setId(Long) - Method in class ome.model.enums.ExperimentType
 
setId(Long) - Method in class ome.model.enums.Family
 
setId(Long) - Method in class ome.model.enums.FilamentType
 
setId(Long) - Method in class ome.model.enums.FilterType
 
setId(Long) - Method in class ome.model.enums.Format
 
setId(Long) - Method in class ome.model.enums.Illumination
 
setId(Long) - Method in class ome.model.enums.Immersion
 
setId(Long) - Method in class ome.model.enums.LaserMedium
 
setId(Long) - Method in class ome.model.enums.LaserType
 
setId(Long) - Method in class ome.model.enums.Medium
 
setId(Long) - Method in class ome.model.enums.MicrobeamManipulationType
 
setId(Long) - Method in class ome.model.enums.MicroscopeType
 
setId(Long) - Method in class ome.model.enums.PhotometricInterpretation
 
setId(Long) - Method in class ome.model.enums.PixelsType
 
setId(Long) - Method in class ome.model.enums.Pulse
 
setId(Long) - Method in class ome.model.enums.RenderingModel
 
setId(Long) - Method in class ome.model.experiment.Experiment
 
setId(Long) - Method in class ome.model.experiment.MicrobeamManipulation
 
setId(Long) - Method in class ome.model.fs.Fileset
 
setId(Long) - Method in class ome.model.fs.FilesetEntry
 
setId(Long) - Method in class ome.model.fs.FilesetJobLink
 
setId(Long) - Method in class ome.model.internal.Link
 
setId(Long) - Method in interface ome.model.IObject
usually unneeded.
setId(Long) - Method in class ome.model.jobs.Job
 
setId(Long) - Method in class ome.model.jobs.JobOriginalFileLink
 
setId(Long) - Method in class ome.model.jobs.JobStatus
 
setId(Long) - Method in class ome.model.meta.DBPatch
 
setId(Long) - Method in class ome.model.meta.Event
 
setId(Long) - Method in class ome.model.meta.EventLog
 
setId(Long) - Method in class ome.model.meta.Experimenter
 
setId(Long) - Method in class ome.model.meta.ExperimenterGroup
 
setId(Long) - Method in class ome.model.meta.ExternalInfo
 
setId(Long) - Method in class ome.model.meta.GroupExperimenterMap
 
setId(Long) - Method in class ome.model.meta.Namespace
 
setId(Long) - Method in class ome.model.meta.Node
 
setId(Long) - Method in class ome.model.meta.Session
 
setId(Long) - Method in class ome.model.meta.ShareMember
 
setId(Long) - Method in class ome.model.roi.Roi
 
setId(Long) - Method in class ome.model.roi.Shape
 
setId(Long) - Method in class ome.model.screen.Plate
 
setId(Long) - Method in class ome.model.screen.PlateAcquisition
 
setId(Long) - Method in class ome.model.screen.Reagent
 
setId(Long) - Method in class ome.model.screen.Screen
 
setId(Long) - Method in class ome.model.screen.ScreenPlateLink
 
setId(Long) - Method in class ome.model.screen.Well
 
setId(Long) - Method in class ome.model.screen.WellReagentLink
 
setId(Long) - Method in class ome.model.screen.WellSample
 
setId(Long) - Method in class ome.model.stats.StatsInfo
 
setId(Long) - Method in class ome.services.blitz.repo.CheckedPath
 
setId(long) - Method in class pojos.DataObject
Sets the database id.
setIdOnly() - Method in class ome.services.SearchBean
 
setIllumination(Illumination) - Method in class ome.model.core.LogicalChannel
 
setIllumination(Illumination) - Method in class pojos.ChannelData
Sets the illumination value.
setImage(Image) - Method in class ome.model.core.Pixels
 
setImage(Image) - Method in class ome.model.roi.Roi
 
setImage(Image) - Method in class ome.model.screen.WellSample
 
setImage(ImageData) - Method in class pojos.PixelsData
Sets the image linked to this pixels' set.
setImage(Image) - Method in class pojos.ROIData
Sets the imageId for the ROI.
setImage(ImageData) - Method in class pojos.WellSampleData
Sets the image linked to this well sample.
setImageAcquisitionDate(Timestamp, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setImageAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setImageDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setImageDescription(String) - Method in class ome.model.jobs.ImportJob
 
setImageExperimenterGroupRef(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setImageExperimenterRef(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setImageExperimentRef(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setImageHeight(float) - Method in class ome.services.SVGRasterizer
Sets the height of the image to rasterize.
setImageID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setImageInstrumentRef(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setImageLinks(Set<DatasetImageLink>) - Method in class ome.model.containers.Dataset
setter for imageLinks should be avoided.
setImageLinksCountPerOwner(Map<Long, Long>) - Method in class ome.model.containers.Dataset
 
setImageMicrobeamManipulationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setImageName(String, int) - Method in class ome.formats.ImageNameMetadataStore
 
setImageName(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setImageName(String) - Method in class ome.model.jobs.ImportJob
 
setImageROIRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setImageROIRef(String, int, int) - Method in class ome.formats.OverlayMetadataStore
 
setImages(Set<Image>) - Method in class ome.model.fs.Fileset
setter for images should be avoided.
setImages(Set<ImageData>) - Method in class pojos.DatasetData
Sets the images contained in this dataset.
setImageWidth(float) - Method in class ome.services.SVGRasterizer
Sets the width of the image to rasterize.
setImagingEnvironment(ImagingEnvironment) - Method in class ome.model.core.Image
 
setImagingEnvironmentAirPressure(Pressure, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setImagingEnvironmentCO2Percent(PercentFraction, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setImagingEnvironmentHumidity(PercentFraction, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setImagingEnvironmentMap(List<MapPair>, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setImagingEnvironmentTemperature(Temperature, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setImmersion(Immersion) - Method in class ome.model.acquisition.Objective
 
setIndex(int) - Method in class ome.formats.importer.util.ErrorContainer
Set index
setInProgressImageResource(Resource) - Method in class ome.services.ThumbnailBean
In-progress image resource Bean injector.
setInput(String, String, Object) - Method in interface ome.api.ISession
Places an entry in the given session's input environment.
setInput(String, String, Object) - Method in class ome.services.sessions.SessionBean
 
setInput(String, String, Object) - Method in interface ome.services.sessions.SessionManager
Places the argument in the input environment under the given key, possibly initializing the Map Throws an exception if there is no Session with the given identifier.
setInput(String, String, Object) - Method in class ome.services.sessions.SessionManagerImpl
 
setInput(String, RType) - Method in class omero.client
Sets an item in the "input" shared (session) memory under the given name.
setInput_async(AMD_ISession_setInput, String, String, RType, Current) - Method in class ome.services.blitz.impl.SessionI
 
setInputEnd(Double) - Method in class ome.model.display.ChannelBinding
 
setInputStart(Double) - Method in class ome.model.display.ChannelBinding
 
setInstanceProvider(InstanceProvider) - Method in class ome.formats.OMEROMetadataStoreClient
Sets the active instance provider.
setInstitution(String) - Method in class ome.model.meta.Experimenter
 
setInstitution(String) - Method in class pojos.ExperimenterData
Sets the institution where the experimenter works.
setInstrument(Instrument) - Method in class ome.model.acquisition.Detector
 
setInstrument(Instrument) - Method in class ome.model.acquisition.Dichroic
 
setInstrument(Instrument) - Method in class ome.model.acquisition.Filter
 
setInstrument(Instrument) - Method in class ome.model.acquisition.FilterSet
 
setInstrument(Instrument) - Method in class ome.model.acquisition.LightSource
 
setInstrument(Instrument) - Method in class ome.model.acquisition.Objective
 
setInstrument(Instrument) - Method in class ome.model.acquisition.OTF
 
setInstrument(Instrument) - Method in class ome.model.core.Image
 
setInstrumentAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setInstrumentID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setIntegration(Integer) - Method in class ome.model.acquisition.DetectorSettings
 
setInterval(int, int) - Method in class omeis.providers.re.codomain.CodomainChain
Sets the codomain interval.
setIoService(ThumbnailService) - Method in class ome.services.ThumbnailBean
I/O service (ThumbnailService) Bean injector.
setIP(String) - Method in class omero.client
Sets the user ip string for this client.
setIPixels(IPixels) - Method in class ome.services.projection.ProjectionBean
IPixels bean injector.
setIPixels(IPixels) - Method in class ome.services.ThumbnailBean
Pixels service Bean injector.
setIRepositoryInfo(IRepositoryInfo) - Method in class ome.services.RawFileBean
Disk Space Usage service Bean injector
setIRepositoryInfo(IRepositoryInfo) - Method in class ome.services.RawPixelsBean
Disk Space Usage service Bean injector
setIRepositoryInfo(IRepositoryInfo) - Method in class ome.services.ThumbnailBean
Disk Space Usage service Bean injector
setIris(Boolean) - Method in class ome.model.acquisition.Objective
 
setIsSPW(Boolean) - Method in class ome.formats.importer.ImportContainer
Set true if the import container is filled in with a Screen/Plate/Well image structure.
setItemCount(Long) - Method in class ome.model.meta.Share
 
setJavaClasspath(String) - Method in class ome.formats.importer.util.ErrorContainer
 
setJavaVersion(String) - Method in class ome.formats.importer.util.ErrorContainer
 
setJobLinks(List<FilesetJobLink>) - Method in class ome.model.fs.Fileset
setter for jobLinks should be avoided.
setJobLinksCountPerOwner(Map<Long, Long>) - Method in class ome.model.fs.Fileset
 
setKey(String) - Method in class ome.services.eventlogs.PersistentEventLogLoader
 
setKey(String) - Method in class ome.util.MapPut
 
setKeyStore(String) - Method in class ome.security.KeyAndTrustStoreConfiguration
 
setKeyStorePassword(String) - Method in class ome.security.KeyAndTrustStoreConfiguration
 
setKeywords(List<String>) - Method in class ome.model.meta.Namespace
 
setKeywords(List<String[]>) - Method in class ome.model.roi.Roi
 
setKeywords(String) - Method in class pojos.WorkflowData
Sets the keywords of the workflow.
setKeywords(List<String>) - Method in class pojos.WorkflowData
Sets the keywords of the workflow.
setLabelAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLabelFillColor(Color, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLabelFillRule(FillRule, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLabelFontFamily(FontFamily, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLabelFontSize(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLabelFontStyle(FontStyle, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLabelID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLabelLineCap(LineCap, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLabelLocked(Boolean, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLabelName(String) - Method in class pojos.ImageAcquisitionData
Sets the name of the stage label.
setLabelStrokeColor(Color, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLabelStrokeDashArray(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLabelStrokeWidth(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLabelText(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLabelTheC(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLabelTheT(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLabelTheZ(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLabelTransform(AffineTransform, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLabelVisible(Boolean, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLabelX(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLabelY(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLanguages(String) - Method in class ome.services.SVGRasterizer
Sets the preferred language to use.
setLaserAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLaserFrequencyMultiplication(PositiveInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLaserID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLaserLaserMedium(LaserMedium, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLaserLotNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLaserManufacturer(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLaserMedium(LaserMedium) - Method in class ome.model.acquisition.Laser
 
setLaserModel(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLaserPockelCell(Boolean, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLaserPower(Power, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLaserPulse(Pulse, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLaserPump(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLaserRepetitionRate(Frequency, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLaserSerialNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLaserTuneable(Boolean, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLaserType(LaserType, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLaserWavelength(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLastName(String) - Method in class ome.model.meta.Experimenter
 
setLastName(String) - Method in class pojos.ExperimenterData
Sets the last name of the experimenter.
setLdap(Boolean) - Method in class ome.model.meta.Experimenter
 
setLdap(Boolean) - Method in class ome.model.meta.ExperimenterGroup
 
setLeaderOfGroups(List<Long>) - Method in class ome.security.basic.BasicEventContext
 
setLegacyUtil(PasswordUtil) - Method in class ome.security.auth.ConfigurablePasswordProvider
 
setLensNA(Double) - Method in class ome.model.acquisition.Objective
 
setLightEmittingDiodeAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLightEmittingDiodeID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLightEmittingDiodeLotNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLightEmittingDiodeManufacturer(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLightEmittingDiodeModel(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLightEmittingDiodePower(Power, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLightEmittingDiodeSerialNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLightPath(LightPath) - Method in class ome.model.core.LogicalChannel
 
setLightPathAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLightPathDichroicRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLightPathEmissionFilterRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLightPathExcitationFilterLink(int, LightPathExcitationFilterLink) - Method in class ome.model.acquisition.LightPath
Sets the ome.model.acquisition.LightPathExcitationFilterLink at the given index.
setLightPathExcitationFilterRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLightSettingsAttenuation(double) - Method in class pojos.ChannelAcquisitionData
Sets the attenuation of the light settings.
setLightSettingsWavelength(Length) - Method in class pojos.ChannelAcquisitionData
Sets the wavelength of the light source.
setLightSettingsWavelength(double) - Method in class pojos.ChannelAcquisitionData
setLightSource(Set<LightSource>) - Method in class ome.model.acquisition.Instrument
setter for lightSource should be avoided.
setLightSource(LightSource) - Method in class ome.model.acquisition.LightSettings
 
setLightSource(LightSourceData) - Method in class pojos.ChannelAcquisitionData
Sets the light source associated to the settings.
setLightSourceSettings(LightSettings) - Method in class ome.model.core.LogicalChannel
 
setLightSourceSettings(Set<LightSettings>) - Method in class ome.model.experiment.MicrobeamManipulation
setter for lightSourceSettings should be avoided.
setLimits(int, int) - Method in class omeis.providers.re.codomain.PlaneSlicingContext
Set the limits.
setLineAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLineCap(int) - Method in class pojos.ShapeSettingsData
Sets the line cap.
setLineFillColor(Color, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLineFillRule(FillRule, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLineFontFamily(FontFamily, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLineFontSize(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLineFontStyle(FontStyle, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLineID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLineLineCap(LineCap, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLineLocked(Boolean, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLineMarkerEnd(Marker, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLineMarkerStart(Marker, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLineStrokeColor(Color, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLineStrokeDashArray(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLineStrokeWidth(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLineText(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLineTheC(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLineTheT(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLineTheZ(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLineTransform(AffineTransform, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLineVisible(Boolean, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLineX1(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLineX2(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLineY1(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLineY2(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setListAnnotationAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setListAnnotationAnnotator(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setListAnnotationDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setListAnnotationID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setListAnnotationNamespace(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLockCandidates(Set<IObject>) - Method in class ome.security.basic.BasicEventContext
 
setLocked(Boolean) - Method in class ome.model.roi.Shape
 
setLogicalChannel(LogicalChannel) - Method in class ome.model.core.Channel
 
setLogs(Set<EventLog>) - Method in class ome.model.meta.Event
setter for logs should be avoided.
setLogs(List<EventLog>) - Method in class ome.security.basic.BasicEventContext
 
setLongAnnotationAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLongAnnotationAnnotator(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLongAnnotationDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLongAnnotationID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLongAnnotationNamespace(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLongAnnotationValue(Long, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLongValue(Long) - Method in class ome.model.annotations.LongAnnotation
 
setLookupTable(String) - Method in class ome.model.core.Channel
 
setLookupTable(String) - Method in class ome.model.display.ChannelBinding
 
setLotNumber(String) - Method in class ome.model.acquisition.Detector
 
setLotNumber(String) - Method in class ome.model.acquisition.Dichroic
 
setLotNumber(String) - Method in class ome.model.acquisition.Filter
 
setLotNumber(String) - Method in class ome.model.acquisition.FilterSet
 
setLotNumber(String) - Method in class ome.model.acquisition.LightSource
 
setLotNumber(String) - Method in class ome.model.acquisition.Microscope
 
setLotNumber(String) - Method in class ome.model.acquisition.Objective
 
setLowerLimit(Integer) - Method in class ome.model.display.PlaneSlicingContext
 
setLowerLimit(int) - Method in class omeis.providers.re.codomain.PlaneSlicingContext
Sets the value (in [intervalStart, intervalEnd]) used to set the level of the bit-plane < bit-plane selected.
setLsid(String) - Method in class ome.model.meta.ExternalInfo
 
setMailUtil(MailUtil) - Method in class ome.services.mail.MailSender
 
setManufacturer(String) - Method in class ome.model.acquisition.Detector
 
setManufacturer(String) - Method in class ome.model.acquisition.Dichroic
 
setManufacturer(String) - Method in class ome.model.acquisition.Filter
 
setManufacturer(String) - Method in class ome.model.acquisition.FilterSet
 
setManufacturer(String) - Method in class ome.model.acquisition.LightSource
 
setManufacturer(String) - Method in class ome.model.acquisition.Microscope
 
setManufacturer(String) - Method in class ome.model.acquisition.Objective
 
setMap(List<NamedValue>) - Method in class ome.model.acquisition.GenericExcitationSource
 
setMap(List<NamedValue>) - Method in class ome.model.acquisition.ImagingEnvironment
 
setMap(Map<String, Object>) - Method in class ome.util.MapPut
 
setMap(QuantumMap) - Method in class omeis.providers.re.quantum.QuantumStrategy
Sets the quantum map.
setMapAnnotationAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMapAnnotationAnnotator(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMapAnnotationDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMapAnnotationID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMapAnnotationNamespace(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMapAnnotationValue(List<MapPair>, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMapping(Family, double, boolean) - Method in class omeis.providers.re.quantum.QuantumStrategy
Sets the selected family, the curve coefficient and the noise reduction flag.
setMapValue(List<NamedValue>) - Method in class ome.model.annotations.MapAnnotation
 
setMarkerEnd(String) - Method in class pojos.ShapeSettingsData
Returns the marker end.
setMarkerStart(String) - Method in class pojos.ShapeSettingsData
Returns the marker start.
setMask(byte[]) - Method in class pojos.MaskData
Sets the mask image.
setMask(BufferedImage) - Method in class pojos.MaskData
Sets the mask from the bufferedImage.
setMaskAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMaskBinData(byte[], int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMaskBinData(byte[], int, int) - Method in class ome.formats.OverlayMetadataStore
 
setMaskFillColor(Color, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMaskFillRule(FillRule, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMaskFontFamily(FontFamily, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMaskFontSize(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMaskFontStyle(FontStyle, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMaskHeight(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMaskHeight(Double, int, int) - Method in class ome.formats.OverlayMetadataStore
 
setMaskID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMaskLineCap(LineCap, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMaskLocked(Boolean, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMaskStrokeColor(Color, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMaskStrokeColor(Color, int, int) - Method in class ome.formats.OverlayMetadataStore
 
setMaskStrokeDashArray(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMaskStrokeWidth(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMaskText(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMaskTheC(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMaskTheT(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMaskTheZ(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMaskTransform(AffineTransform, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMaskVisible(Boolean, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMaskWidth(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMaskWidth(Double, int, int) - Method in class ome.formats.OverlayMetadataStore
 
setMaskX(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMaskX(Double, int, int) - Method in class ome.formats.OverlayMetadataStore
 
setMaskY(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMaskY(Double, int, int) - Method in class ome.formats.OverlayMetadataStore
 
setMatches(String) - Method in class ome.services.graphs.GraphPolicyRule
 
setMaxClauseCount(Integer) - Method in class ome.services.SearchBean
Injector used by Spring.
setMaxFileSize(Long) - Method in class ome.services.fulltext.FileParser
 
setMaximumFieldCount(Integer) - Method in class ome.model.screen.PlateAcquisition
 
setMedia(String) - Method in class ome.services.SVGRasterizer
Sets the media to rasterize.
setMedium(Medium) - Method in class ome.model.acquisition.ObjectiveSettings
 
setMedium(Medium) - Method in class pojos.ImageAcquisitionData
Sets the medium of the objective.
setMemberOfGroups(List<Long>) - Method in class ome.security.basic.BasicEventContext
 
setMergedBatches(boolean) - Method in interface ome.api.Search
Set whether or not results from two separate queries can be returned in the same call to Search.results().
setMergedBatches(boolean) - Method in class ome.services.SearchBean
 
setMergedBatches_async(AMD_Search_setMergedBatches, boolean, Current) - Method in class ome.services.blitz.impl.SearchI
 
setMessage(String) - Method in interface ome.api.JobHandle
Sets the job's message string, and returns the previous value.
setMessage(String) - Method in class ome.model.jobs.Job
 
setMessage(String) - Method in class ome.model.meta.DBPatch
 
setMessage(String) - Method in class ome.model.meta.Session
 
setMessage(String, Current) - Method in class ome.services.blitz.impl.ScriptProcessI
 
setMessage(String) - Method in class ome.services.JobBean
 
setMessage_async(AMD_JobHandle_setMessage, String, Current) - Method in class ome.services.blitz.impl.JobHandleI
 
setMetadataOptions(MetadataOptions) - Method in class ome.formats.importer.OMEROWrapper
 
setMethodHardLimit(int) - Method in class ome.services.sessions.stats.CounterFactory
 
setMethodology(String) - Method in class ome.model.core.Pixels
 
setMethodSecurity(MethodSecurity) - Method in class ome.security.basic.BasicSecurityWiring
Setter injection.
setMetrics(Metrics) - Method in class ome.io.nio.PixelsService
 
setMicrobeamManipulation(MicrobeamManipulation) - Method in class ome.model.acquisition.LightSettings
 
setMicrobeamManipulation(Set<MicrobeamManipulation>) - Method in class ome.model.experiment.Experiment
setter for microbeamManipulation should be avoided.
setMicrobeamManipulationDescription(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMicrobeamManipulationExperimenterRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMicrobeamManipulationID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMicrobeamManipulationLightSourceSettingsAttenuation(PercentFraction, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMicrobeamManipulationLightSourceSettingsID(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMicrobeamManipulationLightSourceSettingsWavelength(Length, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMicrobeamManipulationROIRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMicrobeamManipulationType(MicrobeamManipulationType, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMicroscope(Microscope) - Method in class ome.model.acquisition.Instrument
 
setMicroscopeLotNumber(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMicroscopeManufacturer(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMicroscopeModel(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMicroscopeSerialNumber(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMicroscopeType(MicroscopeType, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMiddleName(String) - Method in class ome.model.meta.Experimenter
 
setMiddleName(String) - Method in class pojos.ExperimenterData
Sets the middle name of the experimenter.
setMimetype(String) - Method in class ome.model.core.OriginalFile
 
setMimeType(String) - Method in class ome.model.display.Thumbnail
 
setMimetype(OriginalFile) - Method in class ome.services.scripts.ScriptFileType
Sets the mimetype on the given OriginalFile if the name field matches the wildcard pattern for this instance.
setMimetype(OriginalFile) - Method in class ome.services.scripts.ScriptRepoHelper
 
setMode(AcquisitionMode) - Method in class ome.model.core.LogicalChannel
 
setMode(AcquisitionMode) - Method in class pojos.ChannelData
Sets the acquisition mode value.
setModel(String) - Method in class ome.model.acquisition.Detector
 
setModel(String) - Method in class ome.model.acquisition.Dichroic
 
setModel(String) - Method in class ome.model.acquisition.Filter
 
setModel(String) - Method in class ome.model.acquisition.FilterSet
 
setModel(String) - Method in class ome.model.acquisition.LightSource
 
setModel(String) - Method in class ome.model.acquisition.Microscope
 
setModel(String) - Method in class ome.model.acquisition.Objective
 
setModel(RenderingModel) - Method in class ome.model.display.RenderingDef
 
setModel(RenderingModel) - Method in class ome.services.RenderingBean
Implemented as specified by the RenderingEngine interface.
setModel(RenderingModel) - Method in class omeis.providers.re.Renderer
Specifies the model that dictates how transformed raw data has to be mapped onto a color space.
setModel(RenderingModel) - Method in interface omeis.providers.re.RenderingEngine
Specifies the model that dictates how transformed raw data has to be mapped onto a color space.
setModel_async(AMD_RenderingEngine_setModel, RenderingModel, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
setModelProcessors(List<ModelProcessor>) - Method in class ome.formats.OMEROMetadataStoreClient
Sets the current set of model processors.
setMtime(Timestamp) - Method in class ome.model.core.OriginalFile
 
setMultivalued(Boolean) - Method in class ome.model.meta.Namespace
 
setMutable(boolean) - Method in class ome.system.Preference
Setter injector
setName(String) - Method in class ome.formats.OMEROImportFixture
 
setName(String) - Method in class ome.model.acquisition.StageLabel
 
setName(String) - Method in class ome.model.annotations.Annotation
 
setName(String) - Method in class ome.model.containers.Dataset
 
setName(String) - Method in class ome.model.containers.Project
 
setName(String) - Method in class ome.model.core.Image
 
setName(String) - Method in class ome.model.core.LogicalChannel
 
setName(String) - Method in class ome.model.core.OriginalFile
 
setName(String) - Method in class ome.model.display.RenderingDef
 
setName(String) - Method in class ome.model.internal.NamedValue
 
setName(String) - Method in class ome.model.meta.ExperimenterGroup
 
setName(String) - Method in class ome.model.meta.Namespace
 
setName(String) - Method in class ome.model.roi.Roi
 
setName(String) - Method in class ome.model.screen.Plate
 
setName(String) - Method in class ome.model.screen.PlateAcquisition
 
setName(String) - Method in class ome.model.screen.Reagent
 
setName(String) - Method in class ome.model.screen.Screen
 
setName(String) - Method in class pojos.ChannelData
Sets the name of the logical channel.
setName(String) - Method in class pojos.DatasetData
Sets the name of the dataset.
setName(String) - Method in class pojos.GroupData
Sets the name of the group.
setName(String) - Method in class pojos.ImageData
Sets the name of the image.
setName(String) - Method in class pojos.PlateAcquisitionData
Sets the name of the acquisition.
setName(String) - Method in class pojos.PlateData
Sets the name of the plate.
setName(String) - Method in class pojos.ProjectData
Sets the name of the project.
setName(String) - Method in class pojos.ScreenData
Sets the name of the screen.
setNameSpace(String) - Method in class pojos.AnnotationData
Sets the name space of the underlying Annotation instance.
setNamespace(String) - Method in class pojos.WorkflowData
Sets the namespace of the workflow.
setNamespaceKeywords(String, String[]) - Method in class pojos.ROIData
Sets the namespace and keywords.
setNamespaceMap(Map<String, List<String>>) - Method in class pojos.ROIData
Sets the namespaces and keywords of the ROI from the map.
setNamespaces(List<String>) - Method in class ome.model.roi.Roi
 
setNdFilter(Double) - Method in class ome.model.core.LogicalChannel
 
setNDFilter(double) - Method in class pojos.ChannelData
Sets the ND filter.
setNode(Node) - Method in class ome.model.meta.Session
 
setNoiseReduction(Boolean) - Method in class ome.model.display.ChannelBinding
 
setNominalMagnification(Double) - Method in class ome.model.acquisition.Objective
 
setNoStatsInfo(boolean) - Method in class ome.formats.importer.ImportContainer
Sets whether or not we disabling StatsInfo population.
setNs(String) - Method in class ome.model.annotations.Annotation
 
setNumOfDirectories(int) - Method in class ome.formats.importer.ImportConfig
 
setNumOfDirectories(int) - Method in class ome.formats.importer.util.IniFileLoader
 
setObject(Object) - Method in class ome.util.MapPut
 
setObjectClass(Class<IObject>) - Method in class ome.services.mail.ObjectMailSender
 
setObjective(Set<Objective>) - Method in class ome.model.acquisition.Instrument
setter for objective should be avoided.
setObjective(Objective) - Method in class ome.model.acquisition.ObjectiveSettings
 
setObjective(Objective) - Method in class ome.model.acquisition.OTF
 
setObjectiveAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setObjectiveCalibratedMagnification(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setObjectiveCorrection(Correction, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setObjectiveID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setObjectiveImmersion(Immersion, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setObjectiveIris(Boolean, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setObjectiveLensNA(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setObjectiveLotNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setObjectiveManufacturer(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setObjectiveModel(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setObjectiveNominalMagnification(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setObjectiveSerialNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setObjectiveSettings(ObjectiveSettings) - Method in class ome.model.core.Image
 
setObjectiveSettingsCorrectionCollar(Double, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setObjectiveSettingsID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setObjectiveSettingsMedium(Medium, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setObjectiveSettingsRefractiveIndex(Double, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setObjectiveWorkingDistance(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setObjectsReadHardLimit(int) - Method in class ome.services.sessions.stats.CounterFactory
 
setObjectsWrittenHardLimit(int) - Method in class ome.services.sessions.stats.CounterFactory
 
setOffset(int, long) - Method in class ome.services.blitz.repo.ManagedImportProcessI
 
setOffsetValue(Double) - Method in class ome.model.acquisition.Detector
 
setOffsetValue(Double) - Method in class ome.model.acquisition.DetectorSettings
 
setOmeName(String) - Method in class ome.model.meta.Experimenter
 
setOnAllUsers(boolean) - Method in class ome.services.mail.FailedLoginMailSender
 
setOnSpecificUsers(Set<String>) - Method in class ome.services.mail.FailedLoginMailSender
 
setOpticalAxisAveraged(Boolean) - Method in class ome.model.acquisition.OTF
 
setOptions(Options) - Method in class ome.parameters.Parameters
 
setOrder(ByteOrder) - Method in class ome.io.nio.ReorderedPixelData
Set the byte order of the backing buffer.
setOrder(ByteOrder) - Method in class ome.util.PixelData
Set the byte order of the backing buffer.
setOriginalFile(OriginalFile) - Method in class ome.model.fs.FilesetEntry
 
setOriginalFileLinks(Set<JobOriginalFileLink>) - Method in class ome.model.jobs.Job
setter for originalFileLinks should be avoided.
setOriginalFileLinksCountPerOwner(Map<Long, Long>) - Method in class ome.model.jobs.Job
 
setOriginalFilesService(OriginalFilesService) - Method in class ome.services.RawFileBean
I/O service (OriginalFilesService) Bean injector.
setOriginalSettingsForPixels(long) - Method in interface ome.api.IRenderingSettings
Resets an Pixels' default rendering settings back to channel global minimum and maximum.
setOriginalSettingsForPixels(long) - Method in class ome.logic.RenderingSettingsImpl
Implemented as specified by the IRenderingSettings I/F.
setOriginalSettingsForPixels_async(AMD_IRenderingSettings_setOriginalSettingsForPixels, long, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
 
setOriginalSettingsInDataset(long) - Method in interface ome.api.IRenderingSettings
Resets a dataset's rendering settings back to channel global minimum and maximum.
setOriginalSettingsInDataset(long) - Method in class ome.logic.RenderingSettingsImpl
Implemented as specified by the IRenderingSettings I/F.
setOriginalSettingsInDataset_async(AMD_IRenderingSettings_setOriginalSettingsInDataset, long, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
 
setOriginalSettingsInImage(long) - Method in interface ome.api.IRenderingSettings
Resets an image's default rendering settings back to channel global minimum and maximum.
setOriginalSettingsInImage(long) - Method in class ome.logic.RenderingSettingsImpl
Implemented as specified by the IRenderingSettings I/F.
setOriginalSettingsInImage_async(AMD_IRenderingSettings_setOriginalSettingsInImage, long, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
 
setOriginalSettingsInSet(Class<T>, Set<Long>) - Method in interface ome.api.IRenderingSettings
Resets a rendering settings back to channel global minimum and maximum for the specified containers.
setOriginalSettingsInSet(Class<T>, Set<Long>) - Method in class ome.logic.RenderingSettingsImpl
Implemented as specified by the IRenderingSettings I/F.
setOriginalSettingsInSet_async(AMD_IRenderingSettings_setOriginalSettingsInSet, String, List<Long>, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
 
setOSArch(String) - Method in class ome.formats.importer.util.ErrorContainer
 
setOSName(String) - Method in class ome.formats.importer.util.ErrorContainer
 
setOSVersion(String) - Method in class ome.formats.importer.util.ErrorContainer
 
setOtf(Set<OTF>) - Method in class ome.model.acquisition.Instrument
setter for otf should be avoided.
setOtf(OTF) - Method in class ome.model.core.LogicalChannel
 
setOutput(String, String, Object) - Method in interface ome.api.ISession
Places an entry in the given session's output environment.
setOutput(String, String, Object) - Method in class ome.services.sessions.SessionBean
 
setOutput(String, String, Object) - Method in interface ome.services.sessions.SessionManager
Places the argument in the output environment under the given key, possibly initializing the Map Throws an exception if there is no Session with the given identifier.
setOutput(String, String, Object) - Method in class ome.services.sessions.SessionManagerImpl
 
setOutput(String, RType) - Method in class omero.client
Sets an item in the "output" shared (session) memory under the given name.
setOutput_async(AMD_ISession_setOutput, String, String, RType, Current) - Method in class ome.services.blitz.impl.SessionI
 
setOverlays(Map<byte[], Integer>) - Method in class ome.services.RenderingBean
Deprecated.
As of release 5.1.0, replaced by PlaneDef.setShapeIds(List).
setOverlays(Map<byte[], Integer>) - Method in class omeis.providers.re.Renderer
Sets a map of overlays to be rendered.
setOverlays(Map<byte[], Integer>) - Method in interface omeis.providers.re.RenderingEngine
Informs the rendering engine that it should render a set of overlays on each rendered frame.
setOverlays_async(AMD_RenderingEngine_setOverlays, RLong, RLong, Map<Long, Integer>, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
setOwner(Experimenter) - Method in interface ome.model.IDetails
 
setOwner(Experimenter) - Method in class ome.model.internal.Details
 
setOwner(Boolean) - Method in class ome.model.meta.GroupExperimenterMap
 
setOwner(Experimenter) - Method in class ome.model.meta.Session
 
setOwner(Experimenter) - Method in class ome.security.basic.BasicEventContext
 
setOwner(Experimenter, Current) - Method in class omero.model.DetailsI
 
setParameterValues(Properties) - Method in class ome.model.units.GenericEnumType
 
setParameterValues(Properties) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
 
setParams(byte[]) - Method in class ome.model.jobs.ParseJob
 
setParent(IObject) - Method in class ome.model.acquisition.FilterSetEmissionFilterLink
 
setParent(IObject) - Method in class ome.model.acquisition.FilterSetExcitationFilterLink
 
setParent(IObject) - Method in class ome.model.acquisition.LightPathEmissionFilterLink
 
setParent(IObject) - Method in class ome.model.acquisition.LightPathExcitationFilterLink
 
setParent(IObject) - Method in class ome.model.annotations.AnnotationAnnotationLink
 
setParent(IObject) - Method in class ome.model.annotations.ChannelAnnotationLink
 
setParent(IObject) - Method in class ome.model.annotations.DatasetAnnotationLink
 
setParent(IObject) - Method in class ome.model.annotations.DetectorAnnotationLink
 
setParent(IObject) - Method in class ome.model.annotations.DichroicAnnotationLink
 
setParent(IObject) - Method in class ome.model.annotations.ExperimenterAnnotationLink
 
setParent(IObject) - Method in class ome.model.annotations.ExperimenterGroupAnnotationLink
 
setParent(IObject) - Method in class ome.model.annotations.FilesetAnnotationLink
 
setParent(IObject) - Method in class ome.model.annotations.FilterAnnotationLink
 
setParent(IObject) - Method in class ome.model.annotations.ImageAnnotationLink
 
setParent(IObject) - Method in class ome.model.annotations.InstrumentAnnotationLink
 
setParent(IObject) - Method in class ome.model.annotations.LightPathAnnotationLink
 
setParent(IObject) - Method in class ome.model.annotations.LightSourceAnnotationLink
 
setParent(IObject) - Method in class ome.model.annotations.NamespaceAnnotationLink
 
setParent(IObject) - Method in class ome.model.annotations.NodeAnnotationLink
 
setParent(IObject) - Method in class ome.model.annotations.ObjectiveAnnotationLink
 
setParent(IObject) - Method in class ome.model.annotations.OriginalFileAnnotationLink
 
setParent(IObject) - Method in class ome.model.annotations.PlaneInfoAnnotationLink
 
setParent(IObject) - Method in class ome.model.annotations.PlateAcquisitionAnnotationLink
 
setParent(IObject) - Method in class ome.model.annotations.PlateAnnotationLink
 
setParent(IObject) - Method in class ome.model.annotations.ProjectAnnotationLink
 
setParent(IObject) - Method in class ome.model.annotations.ReagentAnnotationLink
 
setParent(IObject) - Method in class ome.model.annotations.RoiAnnotationLink
 
setParent(IObject) - Method in class ome.model.annotations.ScreenAnnotationLink
 
setParent(IObject) - Method in class ome.model.annotations.SessionAnnotationLink
 
setParent(IObject) - Method in class ome.model.annotations.ShapeAnnotationLink
 
setParent(IObject) - Method in class ome.model.annotations.WellAnnotationLink
 
setParent(IObject) - Method in class ome.model.containers.DatasetImageLink
 
setParent(IObject) - Method in class ome.model.containers.ProjectDatasetLink
 
setParent(IObject) - Method in class ome.model.core.PixelsOriginalFileMap
 
setParent(IObject) - Method in class ome.model.fs.FilesetJobLink
 
setParent(IObject) - Method in interface ome.model.ILink
 
setParent(IObject) - Method in class ome.model.jobs.JobOriginalFileLink
 
setParent(IObject) - Method in class ome.model.meta.GroupExperimenterMap
 
setParent(IObject) - Method in class ome.model.meta.ShareMember
 
setParent(IObject) - Method in class ome.model.screen.ScreenPlateLink
 
setParent(IObject) - Method in class ome.model.screen.WellReagentLink
 
setParentFilePath(String, int) - Method in class pojos.ImageData
Sets the path to the file hosting the image.
setPartial(Boolean) - Method in class ome.model.core.Image
 
setPassword(String) - Method in class loci.ome.io.OmeroReader
 
setPath(String) - Method in class ome.model.acquisition.OTF
 
setPath(String) - Method in class ome.model.core.OriginalFile
 
setPathSanitizer(Function<String, String>) - Method in class ome.services.blitz.repo.path.ServerFilePathTransformer
Set the string transformer that is used to make file-path components safe across platforms.
setPathToFile(String) - Method in class pojos.ImageData
Sets the path to the file.
setPerm1(long) - Method in class ome.model.internal.Permissions
 
setPerm1(long, Current) - Method in class omero.model.PermissionsI
 
setPerm1(Long) - Method in class omero.model.PermissionsI
 
setPermissions(Permissions) - Method in interface ome.model.IDetails
 
setPermissions(Permissions) - Method in class ome.model.internal.Details
 
setPermissions(Permissions, Current) - Method in class omero.model.DetailsI
 
setPermissionsBit(String, long, int) - Method in class ome.util.SqlAction.Impl
 
setPermissionsBit(String, long, int) - Method in interface ome.util.SqlAction
Sets the given permissions bit to 1.
setPermissionsForGroup(Long, Permissions) - Method in class ome.security.basic.BasicEventContext
Called during BasicACLVoter.allowLoad(org.hibernate.Session, Class, ome.model.internal.Details, long) to track groups that will need resolving later.
setPermissionsVerifier(String, int) - Method in class ome.services.blitz.Router
 
setPhotometricInterpretation(PhotometricInterpretation) - Method in class ome.model.core.LogicalChannel
 
setPhysicalSizeX(Length) - Method in class ome.model.core.Pixels
 
setPhysicalSizeY(Length) - Method in class ome.model.core.Pixels
 
setPhysicalSizeZ(Length) - Method in class ome.model.core.Pixels
 
setPinHoleSize(Length) - Method in class ome.model.core.LogicalChannel
 
setPinholeSize(Length) - Method in class pojos.ChannelData
Sets the pinhole size.
setPinholeSize(double) - Method in class pojos.ChannelData
Deprecated.
setPixelDataService(PixelsService) - Method in class ome.services.ThumbnailBean
Pixels service Bean injector.
setPixels(Pixels) - Method in class ome.model.core.Channel
 
setPixels(List<Pixels>) - Method in class ome.model.core.Image
setter for pixels should be avoided.
setPixels(int, Pixels) - Method in class ome.model.core.Image
Sets the ome.model.core.Pixels at the given index.
setPixels(Pixels) - Method in class ome.model.core.PlaneInfo
 
setPixels(Pixels) - Method in class ome.model.display.RenderingDef
 
setPixels(Pixels) - Method in class ome.model.display.Thumbnail
 
setPixels(Pixels) - Method in class ome.model.roi.Mask
 
setPixels(Pixels) - Method in class omero.util.RPSTileLoop
Called by the TileData implementation to update the RPSTileLoop.pixels instance for re-use by the client.
setPixelsBigEndian(Boolean, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPixelsBinDataBigEndian(Boolean, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPixelsData(PixelsService) - Method in class ome.logic.RenderingSettingsImpl
Sets injector.
setPixelsData(PixelsService) - Method in class ome.services.RawPixelsBean
 
setPixelsDimensionOrder(DimensionOrder, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPixelsFile(long, String, String) - Method in class ome.formats.OMEROMetadataStoreClient
Sets the path, name and repo in the pixels table.
setPixelsFile_async(AMD_MetadataStore_setPixelsFile, long, String, String, Current) - Method in class ome.services.blitz.impl.MetadataStoreI
 
setPixelsFileMaps(Set<PixelsOriginalFileMap>) - Method in class ome.model.core.OriginalFile
setter for pixelsFileMaps should be avoided.
setPixelsFileMaps(Set<PixelsOriginalFileMap>) - Method in class ome.model.core.Pixels
setter for pixelsFileMaps should be avoided.
setPixelsFileMapsCountPerOwner(Map<Long, Long>) - Method in class ome.model.core.OriginalFile
 
setPixelsFileMapsCountPerOwner(Map<Long, Long>) - Method in class ome.model.core.Pixels
 
setPixelsId(long, boolean) - Method in interface ome.api.RawPixelsStore
Initializes the stateful service for a given Pixels set.
setPixelsId(long) - Method in interface ome.api.ThumbnailStore
This method manages the state of the service; it must be invoked before using any other methods.
setPixelsID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPixelsId(long, boolean) - Method in class ome.services.RawPixelsBean
 
setPixelsId(long) - Method in class ome.services.ThumbnailBean
 
setPixelsId_async(AMD_RawPixelsStore_setPixelsId, long, boolean, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
setPixelsId_async(AMD_ThumbnailStore_setPixelsId, long, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
 
setPixelsId_async(AMD_RawPixelsStore_setPixelsId, long, boolean, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
setPixelsInterleaved(Boolean, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPixelSizeX(double) - Method in class pojos.PixelsData
Deprecated.
setPixelSizeX(Length) - Method in class pojos.PixelsData
Sets the dimension of a pixel along the X-axis
setPixelSizeY(double) - Method in class pojos.PixelsData
Deprecated.
setPixelSizeY(Length) - Method in class pojos.PixelsData
Sets the dimension of a pixel along the Y-axis
setPixelSizeZ(double) - Method in class pojos.PixelsData
Deprecated.
setPixelSizeZ(Length) - Method in class pojos.PixelsData
Sets the dimension of a pixel along the Z-axis
setPixelsMetadata(IPixels) - Method in class ome.logic.RenderingSettingsImpl
Sets injector.
setPixelsMetadata(IPixels) - Method in class ome.services.RawPixelsBean
 
setPixelsNamePathRepo(long, String, String, String) - Method in class ome.util.actions.PostgresSqlAction
 
setPixelsNamePathRepo(long, String, String, String) - Method in interface ome.util.SqlAction
 
setPixelsPhysicalSizeX(Length, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPixelsPhysicalSizeY(Length, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPixelsPhysicalSizeZ(Length, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPixelsService(PixelsService) - Method in class ome.logic.RepositoryInfoImpl
Bean injection setter for ROMIO pixels service
setPixelsService(PixelsService) - Method in class ome.services.projection.ProjectionBean
PixelsService bean injector.
setPixelsSignificantBits(PositiveInteger, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPixelsSizeC(PositiveInteger, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPixelsSizeT(PositiveInteger, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPixelsSizeX(PositiveInteger, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPixelsSizeY(PositiveInteger, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPixelsSizeZ(PositiveInteger, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPixelsTimeIncrement(Time, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPixelsType(PixelType, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPixelsType(PixelsType) - Method in class ome.model.acquisition.OTF
 
setPixelsType(PixelsType) - Method in class ome.model.core.Pixels
 
setPixelToMMFactor(float) - Method in class ome.services.SVGRasterizer
Sets the unit conversion factor to the specified value.
setPixelValue(int, double) - Method in class ome.util.PixelData
Sets the pixel intensity value of the pixel at a given offset within the backing buffer.
setPixelValueDirect(int, double) - Method in class ome.util.PixelData
Sets the pixel intensity value of the pixel at a given offset within the backing buffer.
setPlane(byte[], int, int, int) - Method in interface ome.api.RawPixelsStore
 
setPlane(Long, byte[], int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
Writes a plane to the server.
setPlane(ByteBuffer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer
 
setPlane(byte[], Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer
 
setPlane(ByteBuffer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
 
setPlane(byte[], Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
 
setPlane(ByteBuffer, Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
 
setPlane(byte[], Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
 
setPlane(ByteBuffer, Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer
Sets a particular 2D image plane in this pixel buffer.
setPlane(byte[], Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer
Sets a particular 2D image plane in this pixel buffer.
setPlane(ByteBuffer, Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer
Implemented as specified by PixelBuffer I/F.
setPlane(byte[], Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer
Implemented as specified by PixelBuffer I/F.
setPlane(byte[], int, int, int) - Method in class ome.services.RawPixelsBean
 
setPlane_async(AMD_RawPixelsStore_setPlane, byte[], int, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
setPlane_async(AMD_RawPixelsStore_setPlane, byte[], int, int, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
setPlaneAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPlaneDeltaT(Time, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPlaneExposureTime(Time, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPlaneHashSHA1(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPlaneInfo(Set<PlaneInfo>) - Method in class ome.model.core.Pixels
setter for planeInfo should be avoided.
setPlanePositionX(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPlanePositionY(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPlanePositionZ(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPlanePrevious(Integer) - Method in class ome.model.display.PlaneSlicingContext
 
setPlanes(int, int) - Method in class omeis.providers.re.codomain.PlaneSlicingContext
Sets the value of the selected planes i.e. the previous plane and the selected one.
setPlaneSelected(Integer) - Method in class ome.model.display.PlaneSlicingContext
 
setPlaneTheC(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPlaneTheT(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPlaneTheZ(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPlate(Plate) - Method in class ome.model.screen.PlateAcquisition
 
setPlate(Plate) - Method in class ome.model.screen.Well
 
setPlateAcquisition(PlateAcquisition) - Method in class ome.model.screen.WellSample
 
setPlateAcquisition(Set<PlateAcquisitionData>) - Method in class pojos.PlateData
Sets the plate acquisition linked to the plate.
setPlateAcquisitionAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPlateAcquisitionDescription(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPlateAcquisitionEndTime(Timestamp, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPlateAcquisitionID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPlateAcquisitionMaximumFieldCount(PositiveInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPlateAcquisitionName(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPlateAcquisitions(Set<PlateAcquisition>) - Method in class ome.model.screen.Plate
setter for plateAcquisitions should be avoided.
setPlateAcquisitionStartTime(Timestamp, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPlateAcquisitionWellSampleRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPlateAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPlateColumnNamingConvention(NamingConvention, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPlateColumns(PositiveInteger, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPlateDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPlateExternalIdentifier(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPlateFieldIndex(NonNegativeInteger, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPlateID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPlateLinks(Set<ScreenPlateLink>) - Method in class ome.model.screen.Screen
setter for plateLinks should be avoided.
setPlateLinksCountPerOwner(Map<Long, Long>) - Method in class ome.model.screen.Screen
 
setPlateName(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPlateRowNamingConvention(NamingConvention, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPlateRows(PositiveInteger, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPlates(Set<PlateData>) - Method in class pojos.ScreenData
Sets the plates contained in this screen.
setPlateStatus(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPlateWellOriginX(Length, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPlateWellOriginY(Length, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPockelCell(Boolean) - Method in class ome.model.acquisition.Laser
 
setPockelCell(int) - Method in class pojos.ChannelData
Sets the pockel cell.
setPockelCellSetting(Integer) - Method in class ome.model.core.LogicalChannel
 
setPointAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPointFillColor(Color, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPointFillRule(FillRule, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPointFontFamily(FontFamily, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPointFontSize(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPointFontStyle(FontStyle, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPointID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPointLineCap(LineCap, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPointLocked(Boolean, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPoints(String) - Method in class ome.model.roi.Polygon
 
setPoints(String) - Method in class ome.model.roi.Polyline
 
setPoints(List<Point2D.Double>, List<Point2D.Double>, List<Point2D.Double>, List<Integer>) - Method in class pojos.PolygonData
Sets the points in the polygon.
setPoints(List<Point2D.Double>, List<Point2D.Double>, List<Point2D.Double>, List<Integer>) - Method in class pojos.PolylineData
Sets the points in the polyline.
setPointStrokeColor(Color, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPointStrokeDashArray(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPointStrokeWidth(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPointText(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPointTheC(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPointTheT(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPointTheZ(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPointTransform(AffineTransform, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPointVisible(Boolean, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPointX(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPointY(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolygonAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolygonFillColor(Color, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolygonFillRule(FillRule, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolygonFontFamily(FontFamily, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolygonFontSize(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolygonFontStyle(FontStyle, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolygonID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolygonLineCap(LineCap, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolygonLocked(Boolean, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolygonPoints(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolygonStrokeColor(Color, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolygonStrokeDashArray(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolygonStrokeWidth(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolygonText(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolygonTheC(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolygonTheT(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolygonTheZ(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolygonTransform(AffineTransform, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolygonVisible(Boolean, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolylineAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolylineFillColor(Color, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolylineFillRule(FillRule, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolylineFontFamily(FontFamily, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolylineFontSize(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolylineFontStyle(FontStyle, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolylineID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolylineLineCap(LineCap, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolylineLocked(Boolean, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolylineMarkerEnd(Marker, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolylineMarkerStart(Marker, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolylinePoints(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolylineStrokeColor(Color, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolylineStrokeDashArray(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolylineStrokeWidth(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolylineText(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolylineTheC(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolylineTheT(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolylineTheZ(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolylineTransform(AffineTransform, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolylineVisible(Boolean, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPort(int) - Method in class loci.ome.io.OmeroReader
 
setPositionX(Length) - Method in class ome.model.acquisition.StageLabel
 
setPositionX(Length) - Method in class ome.model.core.PlaneInfo
 
setPositionX(Length) - Method in class pojos.ImageAcquisitionData
Sets the x-position.
setPositionX(double) - Method in class pojos.ImageAcquisitionData
setPositionY(Length) - Method in class ome.model.acquisition.StageLabel
 
setPositionY(Length) - Method in class ome.model.core.PlaneInfo
 
setPositionY(Length) - Method in class pojos.ImageAcquisitionData
Sets the y-position.
setPositionY(double) - Method in class pojos.ImageAcquisitionData
setPositionZ(Length) - Method in class ome.model.acquisition.StageLabel
 
setPositionZ(Length) - Method in class ome.model.core.PlaneInfo
 
setPositionZ(Length) - Method in class pojos.ImageAcquisitionData
Sets the z-position.
setPositionZ(double) - Method in class pojos.ImageAcquisitionData
setPosX(Length) - Method in class ome.model.screen.WellSample
 
setPosY(Length) - Method in class ome.model.screen.WellSample
 
setPower(Power) - Method in class ome.model.acquisition.LightSource
 
setPreferenceContext(PreferenceContext) - Method in class ome.logic.ConfigImpl
PreferenceContext setter for dependency injection.
setPreferences(List<Preference>) - Method in class ome.system.PreferenceContext
 
setPrefs(boolean) - Method in class ome.system.Preference
 
setPreviousPatch(Integer) - Method in class ome.model.meta.DBPatch
 
setPreviousVersion(String) - Method in class ome.model.meta.DBPatch
 
setPrimaryChannel(Channel) - Method in class ome.model.core.Pixels
Swaps the first element of channels with the first instance of the given element.
setPrimaryChannelBinding(ChannelBinding) - Method in class ome.model.display.RenderingDef
Swaps the first element of waveRendering with the first instance of the given element.
setPrimaryCodomainMapContext(CodomainMapContext) - Method in class ome.model.display.RenderingDef
Swaps the first element of spatialDomainEnhancement with the first instance of the given element.
setPrimaryColorEnabled(boolean) - Method in class omeis.providers.re.Optimizations
Enable or disable the primary color optimization.
setPrimaryFilesetEntry(FilesetEntry) - Method in class ome.model.fs.Fileset
Swaps the first element of usedFiles with the first instance of the given element.
setPrimaryFilesetJobLink(FilesetJobLink) - Method in class ome.model.fs.Fileset
Swaps the first element of jobLinks with the first instance of the given element.
setPrimaryGroupExperimenterMap(GroupExperimenterMap) - Method in class ome.model.meta.Experimenter
Swaps the first element of groupExperimenterMap with the first instance of the given element.
setPrimaryLightPathExcitationFilterLink(LightPathExcitationFilterLink) - Method in class ome.model.acquisition.LightPath
Swaps the first element of excitationFilterLink with the first instance of the given element.
setPrimaryPixels(Pixels) - Method in class ome.model.core.Image
Swaps the first element of pixels with the first instance of the given element.
setPrimaryShape(Shape) - Method in class ome.model.roi.Roi
Swaps the first element of shapes with the first instance of the given element.
setPrimaryWellSample(WellSample) - Method in class ome.model.screen.Well
Swaps the first element of wellSamples with the first instance of the given element.
setPrincipal(Principal) - Method in class ome.system.SessionInitializer
 
setPrincipalHolder(PrincipalHolder) - Method in class ome.security.basic.BasicSecurityWiring
Setter injection.
setPrincipalHolder(PrincipalHolder) - Method in class ome.services.sessions.SessionManagerImpl
 
setProcessManager(IProcessManager) - Method in class ome.services.JobBean
Process Manager Bean injector.
setProjectAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setProjectDatasetRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setProjectDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setProjectExperimenterGroupRef(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setProjectExperimenterRef(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setProjectID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setProjectLinks(Set<ProjectDatasetLink>) - Method in class ome.model.containers.Dataset
setter for projectLinks should be avoided.
setProjectLinksCountPerOwner(Map<Long, Long>) - Method in class ome.model.containers.Dataset
 
setProjectName(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setProjects(Set<ProjectData>) - Method in class pojos.DatasetData
Sets the projects containing the dataset.
setProperty(String, String) - Method in class ome.system.PreferenceContext
With ticket:2214, preferences are no longer mutable.
setProtocolDescription(String) - Method in class ome.model.screen.Screen
 
setProtocolDescription(String) - Method in class pojos.ScreenData
Sets the description of the protocol.
setProtocolIdentifier(String) - Method in class ome.model.screen.Screen
 
setProtocolIdentifier(String) - Method in class pojos.ScreenData
Sets the identifier of the protocol.
setPulse(Pulse) - Method in class ome.model.acquisition.Laser
 
setPump(LightSource) - Method in class ome.model.acquisition.Laser
 
setQuality(float) - Method in class ome.services.SVGRasterizer
Sets the quality of the image to rasterize when rasterizing to a JPEG.
setQuantization(QuantumDef) - Method in class ome.model.display.RenderingDef
 
setQuantizationMap(int, Family, double, boolean) - Method in class ome.services.RenderingBean
Implemented as specified by the RenderingEngine interface.
setQuantizationMap(Family, double, boolean) - Method in class omeis.providers.re.quantum.QuantumStrategy
Sets the selected family, the curve coefficient and the noise reduction flag and rebuilds the look-up table.
setQuantizationMap(int, Family, double, boolean) - Method in class omeis.providers.re.Renderer
Sets the mapping strategy for the specified channel.
setQuantizationMap(int, Family, double, boolean) - Method in interface omeis.providers.re.RenderingEngine
Sets the quantization map, one per channel.
setQuantizationMap_async(AMD_RenderingEngine_setQuantizationMap, int, Family, double, boolean, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
setQuantumStrategy(int) - Method in class ome.services.RenderingBean
Implemented as specified by the RenderingEngine interface.
setQuantumStrategy(int) - Method in class omeis.providers.re.Renderer
Sets the bit resolution.
setQuantumStrategy(int) - Method in interface omeis.providers.re.RenderingEngine
Sets the quantization strategy.
setQuantumStrategy_async(AMD_RenderingEngine_setQuantumStrategy, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
setQuery(Query) - Method in class ome.services.query.Query
provide this Query instance with a Query to be used for retrieving data.
setQueryFactory(QueryFactory) - Method in class ome.logic.AbstractLevel1Service
 
setQueryFactory(QueryFactory) - Method in class ome.logic.AbstractLevel2Service
 
setQueryService(LocalQuery) - Method in class ome.logic.AbstractLevel2Service
 
setQueryService(LocalQuery) - Method in class ome.logic.UpdateImpl
 
setQueryService(LocalQuery) - Method in class ome.services.AbstractStatefulBean
Query service Bean injector.
setQueryService(IQuery) - Method in class ome.services.eventlogs.EventLogLoader
Spring injector
setQueryService(IQuery) - Method in class ome.services.mail.MailSender
 
setQueryService(IQuery) - Method in class ome.services.procs.ProcessorSkeleton
 
setQueryString(String) - Method in class ome.services.mail.ObjectMailSender
 
setRadiusX(double) - Method in class pojos.EllipseData
Sets the radius along the X-axis.
setRadiusY(double) - Method in class pojos.EllipseData
Sets the radius along the Y-axis.
setRating(int) - Method in class pojos.RatingAnnotationData
Sets the rating value.
setReader(String) - Method in class ome.formats.importer.ImportContainer
Sets the reader class name used for reading the contents of this import container.
setReader(IFormatReader) - Method in interface ome.formats.model.IObjectContainerStore
Sets the Bio-Formats reader that will be used to populate the container store.
setReader(IFormatReader) - Method in class ome.formats.OMEROMetadataStoreClient
 
setReaderType(String) - Method in class ome.formats.importer.util.ErrorContainer
set file format for import
setReadOnly(boolean) - Method in class ome.security.basic.BasicEventContext
 
setReadOnly(boolean) - Method in class ome.services.sessions.SessionManagerImpl
 
setReadOnly(boolean) - Method in class pojos.ShapeData
Sets to true if the object is a read-only object, false otherwise.
setReadOutRate(Frequency) - Method in class ome.model.acquisition.DetectorSettings
 
setReagentAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setReagentDescription(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setReagentID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setReagentIdentifier(String) - Method in class ome.model.screen.Reagent
 
setReagentLinks(Set<WellReagentLink>) - Method in class ome.model.screen.Well
setter for reagentLinks should be avoided.
setReagentLinksCountPerOwner(Map<Long, Long>) - Method in class ome.model.screen.Well
 
setReagentName(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setReagentReagentIdentifier(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setReagents(Set<Reagent>) - Method in class ome.model.screen.Screen
setter for reagents should be avoided.
setReagentSetDescripion(String) - Method in class pojos.ScreenData
Sets the identifier of the reagent.
setReagentSetDescription(String) - Method in class ome.model.screen.Screen
 
setReagentSetIdentifier(String) - Method in class ome.model.screen.Screen
 
setReagentSetIdentifier(String) - Method in class pojos.ScreenData
Sets the identifier of the reagent.
setRectangleAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setRectangleFillColor(Color, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setRectangleFillRule(FillRule, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setRectangleFontFamily(FontFamily, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setRectangleFontSize(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setRectangleFontStyle(FontStyle, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setRectangleHeight(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setRectangleID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setRectangleLineCap(LineCap, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setRectangleLocked(Boolean, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setRectangleStrokeColor(Color, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setRectangleStrokeDashArray(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setRectangleStrokeWidth(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setRectangleText(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setRectangleTheC(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setRectangleTheT(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setRectangleTheZ(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setRectangleTransform(AffineTransform, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setRectangleVisible(Boolean, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setRectangleWidth(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setRectangleX(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setRectangleY(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setRed(Integer) - Method in class ome.model.core.Channel
 
setRed(Integer) - Method in class ome.model.display.ChannelBinding
 
setRed(Integer) - Method in class ome.model.screen.Well
 
setRed(Integer) - Method in class pojos.WellData
Sets the red component of the color associated to the well.
setRedValue(int, int) - Method in class omeis.providers.re.RGBAIntBuffer
Sets the Red value for a particular pixel index.
setRedValue(int, int) - Method in class omeis.providers.re.RGBBuffer
Sets the Red value for a particular pixel index.
setRedValue(int, int) - Method in class omeis.providers.re.RGBIntBuffer
Sets the Red value for a particular pixel index.
setRef(String) - Method in class ome.model.display.Thumbnail
 
setReference(OriginalFile) - Method in class pojos.ImageData
Sets the reference to the file to register.
setReferenceStringCache(Map<String, String[]>) - Method in interface ome.formats.model.IObjectContainerStore
Sets the string based reference cache for this container store.
setReferenceStringCache(Map<String, String[]>) - Method in class ome.formats.OMEROMetadataStoreClient
 
setRefPlateId(long) - Method in class pojos.PlateAcquisitionData
Sets the id of the plate this plate acquisition is for.
setRefractiveIndex(Double) - Method in class ome.model.acquisition.ObjectiveSettings
 
setRefractiveIndex(double) - Method in class pojos.ImageAcquisitionData
Sets the refractive index of the objective.
setRegion(int, long, byte[]) - Method in interface ome.api.RawPixelsStore
 
setRegion(Integer, Long, byte[]) - Method in class ome.io.bioformats.BfPixelBuffer
 
setRegion(Integer, Long, ByteBuffer) - Method in class ome.io.bioformats.BfPixelBuffer
 
setRegion(Integer, Long, byte[]) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
 
setRegion(Integer, Long, ByteBuffer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
 
setRegion(Integer, Long, byte[]) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
 
setRegion(Integer, Long, ByteBuffer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
 
setRegion(Integer, Long, byte[]) - Method in interface ome.io.nio.PixelBuffer
Sets a region in this pixel buffer.
setRegion(Integer, Long, ByteBuffer) - Method in interface ome.io.nio.PixelBuffer
Sets a region in this pixel buffer.
setRegion(Integer, Long, byte[]) - Method in class ome.io.nio.RomioPixelBuffer
Implemented as specified by PixelBuffer I/F.
setRegion(Integer, Long, ByteBuffer) - Method in class ome.io.nio.RomioPixelBuffer
Implemented as specified by PixelBuffer I/F.
setRegion(int, long, byte[]) - Method in class ome.services.RawPixelsBean
 
setRegion(RegionDef) - Method in class omeis.providers.re.data.PlaneDef
Sets the region to render.
setRegion_async(AMD_RawPixelsStore_setRegion, int, long, byte[], Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
setRegion_async(AMD_RawPixelsStore_setRegion, int, long, byte[], Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
setRegisteredFile(OriginalFile) - Method in class pojos.FileData
Sets the registered file.
setRegisteredFile(Image) - Method in class pojos.ImageData
Sets the registered file.
setRegistry(Registry) - Method in class ome.services.blitz.fire.Ring
Sets the Registry for this instance.
setRelatedTo(Pixels) - Method in class ome.model.core.Pixels
 
setRenderingDef(RenderingDef) - Method in class ome.model.display.ChannelBinding
 
setRenderingDef(RenderingDef) - Method in class ome.model.display.CodomainMapContext
 
setRenderingDefId(long) - Method in interface ome.api.ThumbnailStore
This method manages the state of the service; it should be invoked directly after setPixelsId.
setRenderingDefId(long) - Method in class ome.services.ThumbnailBean
 
setRenderingDefId_async(AMD_ThumbnailStore_setRenderingDefId, long, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
 
setRenderShapes(boolean) - Method in class omeis.providers.re.data.PlaneDef
Sets whether or not to render the shapes (masks).
setRepetitionRate(Frequency) - Method in class ome.model.acquisition.Laser
 
setRepetitions(int) - Method in class ome.services.fulltext.FullTextIndexer
Spring injector.
setRepetitions(int) - Method in class ome.services.pixeldata.PixelDataHandler
Spring injector.
setReplacement(IObject) - Method in class ome.model.internal.GraphHolder
used mostly by IUpdate.
setReportingLoops(int) - Method in class ome.services.fulltext.FullTextIndexer
 
setRepositoryPath(String) - Method in class pojos.FileData
Sets the path to the parent.
setResolutionLevel(int) - Method in interface ome.api.RawPixelsStore
 
setResolutionLevel(int) - Method in class ome.io.bioformats.BfPixelBuffer
 
setResolutionLevel(int) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
 
setResolutionLevel(IFD) - Method in class ome.io.bioformats.OmeroPixelsPyramidReader
 
setResolutionLevel(int) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
 
setResolutionLevel(int) - Method in interface ome.io.nio.PixelBuffer
Sets the active resolution level.
setResolutionLevel(int) - Method in class ome.io.nio.RomioPixelBuffer
 
setResolutionLevel(int) - Method in class ome.services.RawPixelsBean
 
setResolutionLevel(int) - Method in class ome.services.RenderingBean
 
setResolutionLevel(int) - Method in class omeis.providers.re.Renderer
Sets the active resolution level.
setResolutionLevel(int) - Method in interface omeis.providers.re.RenderingEngine
 
setResolutionLevel_async(AMD_PyramidService_setResolutionLevel, int, Current) - Method in class ome.services.blitz.impl.AbstractPyramidServant
 
setResolutionLevel_async(AMD_PyramidService_setResolutionLevel, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
setResponseIfNull(Response) - Method in class omero.cmd.Helper
Set the response if there is not currently run, in which case true is returned.
setRetry() - Method in class ome.io.messages.MissingPyramidMessage
 
setReturnUnloaded(boolean) - Method in interface ome.api.Search
Determines if all results should be returned as unloaded objects.
setReturnUnloaded(boolean) - Method in class ome.services.SearchBean
 
setReturnUnloaded_async(AMD_Search_setReturnUnloaded, boolean, Current) - Method in class ome.services.blitz.impl.SearchI
 
setReverse(Boolean) - Method in class ome.model.display.ReverseIntensityContext
 
setRGBA(int, int, int, int, int) - Method in class ome.services.RenderingBean
Implemented as specified by the RenderingEngine interface.
setRGBA(int, int, int, int, int) - Method in class omeis.providers.re.Renderer
Sets the color associated to the specified channel.
setRGBA(int, int, int, int, int) - Method in interface omeis.providers.re.RenderingEngine
Sets the four components composing the color associated to the specified channel.
setRGBA_async(AMD_RenderingEngine_setRGBA, int, int, int, int, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
setRightsRightsHeld(String) - Method in class ome.formats.OMEROMetadataStoreClient
 
setRightsRightsHolder(String) - Method in class ome.formats.OMEROMetadataStoreClient
 
setRoi(Roi) - Method in class ome.model.roi.Shape
 
setROIAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setROICoordinate(ROICoordinate) - Method in class pojos.ShapeData
Sets the ROICoordinate for the ShapeData
setROIDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setROIID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setROIID(String, int) - Method in class ome.formats.OverlayMetadataStore
 
setROIName(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setROINamespace(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setRois(Set<Roi>) - Method in class ome.model.core.Image
setter for rois should be avoided.
setRoles(Roles) - Method in class ome.services.mail.MailSender
 
setRoles(Roles) - Method in class ome.services.sessions.SessionManagerImpl
 
setRoot(MetadataRoot) - Method in class ome.formats.OMEROMetadataStoreClient
 
setRow(byte[], int, int, int, int) - Method in interface ome.api.RawPixelsStore
 
setRow(ByteBuffer, Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer
 
setRow(ByteBuffer, Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
 
setRow(ByteBuffer, Integer, Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
 
setRow(ByteBuffer, Integer, Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer
Sets a particular row or scanline in this pixel buffer.
setRow(ByteBuffer, Integer, Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer
Implemented as specified by PixelBuffer I/F.
setRow(Integer) - Method in class ome.model.screen.Well
 
setRow(byte[], int, int, int, int) - Method in class ome.services.RawPixelsBean
 
setRow_async(AMD_RawPixelsStore_setRow, byte[], int, int, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
setRow_async(AMD_RawPixelsStore_setRow, byte[], int, int, int, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
setRowNamingConvention(String) - Method in class ome.model.screen.Plate
 
setRows(Integer) - Method in class ome.model.screen.Plate
 
setRx(Double) - Method in class ome.model.roi.Ellipse
 
setRx(Double) - Method in class ome.model.roi.Rect
 
setRy(Double) - Method in class ome.model.roi.Ellipse
 
setSamplesPerPixel(Integer) - Method in class ome.model.core.LogicalChannel
 
setScale(Integer) - Method in class ome.model.meta.Node
 
setScaleService(IScale) - Method in class ome.services.ThumbnailBean
Scale service Bean injector.
setScheduledFor(Timestamp) - Method in class ome.model.jobs.Job
 
setScreen(Screen) - Method in class ome.model.screen.Reagent
 
setScreenAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setScreenDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setScreenID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setScreenLinks(Set<ScreenPlateLink>) - Method in class ome.model.screen.Plate
setter for screenLinks should be avoided.
setScreenLinksCountPerOwner(Map<Long, Long>) - Method in class ome.model.screen.Plate
 
setScreenName(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setScreenPlateRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setScreenProtocolDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setScreenProtocolIdentifier(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setScreenReagentSetDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setScreenReagentSetIdentifier(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setScreens(Set<ScreenData>) - Method in class pojos.PlateData
Sets the screens containing the plate.
setScreenType(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setSecurityContext(IObject, Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
setSecurityContext(Principal, IObject) - Method in interface ome.services.sessions.SessionManager
Sets the context for the current session to the given value.
setSecurityContext(Principal, IObject) - Method in class ome.services.sessions.SessionManagerImpl
 
setSecurityPassword(String, Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
setSecuritySystem(SecuritySystem) - Method in class ome.logic.AbstractLevel2Service
 
setSecuritySystem(SecuritySystem) - Method in class ome.services.AbstractStatefulBean
 
setSecuritySystem(SecuritySystem) - Method in class ome.services.blitz.impl.TimelineI
 
setSelectedFile(File) - Method in class ome.formats.importer.util.ErrorContainer
 
setSerialNumber(String) - Method in class ome.model.acquisition.Detector
 
setSerialNumber(String) - Method in class ome.model.acquisition.Dichroic
 
setSerialNumber(String) - Method in class ome.model.acquisition.Filter
 
setSerialNumber(String) - Method in class ome.model.acquisition.FilterSet
 
setSerialNumber(String) - Method in class ome.model.acquisition.LightSource
 
setSerialNumber(String) - Method in class ome.model.acquisition.Microscope
 
setSerialNumber(String) - Method in class ome.model.acquisition.Objective
 
setSeries(int) - Method in class ome.io.bioformats.BfPixelBuffer
Sets the current series in the underlying Bio-Formats reader.
setSeries(Integer) - Method in class ome.model.core.Image
 
setServer(String) - Method in class loci.ome.io.OmeroReader
 
setServerEndpoints(String, int) - Method in class ome.services.blitz.Router
 
setServiceCleanups(Set<RegisterServiceCleanupMessage>) - Method in class ome.security.basic.BasicEventContext
 
setServiceFactory(ServiceFactoryI) - Method in class ome.services.blitz.impl.ExporterI
 
setServiceFactory(ServiceFactoryI) - Method in class ome.services.blitz.impl.MetadataStoreI
 
setServiceFactory(ServiceFactoryI) - Method in class ome.services.blitz.impl.RawFileStoreI
 
setServiceFactory(ServiceFactoryI) - Method in class ome.services.blitz.impl.RenderingEngineI
 
setServiceFactory(ServiceFactoryI) - Method in class ome.services.blitz.impl.RoiI
 
setServiceFactory(ServiceFactoryI) - Method in class ome.services.blitz.impl.ScriptI
 
setServiceFactory(ServiceFactoryI) - Method in class ome.services.blitz.impl.SharedResourcesI
 
setServiceFactory(ServiceFactoryI) - Method in class ome.services.blitz.impl.TimelineI
 
setServiceFactory(ServiceFactoryI) - Method in class ome.services.blitz.repo.ManagedImportProcessI
 
setServiceFactory(Identity, ServiceFactoryI) - Method in class ome.services.blitz.util.FindServiceFactoryMessage
Store the information.
setServiceFactory(Identity, ServiceFactoryI) - Method in class ome.services.blitz.util.RegisterServantMessage
 
setServiceFactory(ServiceFactoryI) - Method in interface ome.services.blitz.util.ServiceFactoryAware
 
setSession(Session) - Method in class ome.model.meta.Event
 
setSession(Session) - Method in class ome.system.ServiceFactory
 
setSession(Session) - Method in class ome.system.SessionInitializer
 
setSession(SessionI) - Method in class omero.cmd.HandleI
 
setSession(SessionI) - Method in interface omero.cmd.SessionAware
 
setSessionCache(SessionCache) - Method in class ome.services.sessions.SessionManagerImpl
 
setSessionFactory(SessionFactory) - Method in class ome.logic.AbstractLevel1Service
delegates to HibernateDaoSupport.
setSessionFactory(SessionFactory) - Method in class ome.logic.TypesImpl
injector for usage by the container.
setSessionFactory(SessionFactory) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
Initializes the metadata needed by this instance.
setSessionID(String) - Method in class loci.ome.io.OmeroReader
 
setSessionManager(SessionManager) - Method in class ome.logic.UpdateImpl
 
setSessionManager(SessionManager) - Method in class ome.security.basic.BasicMethodSecurity
 
setSessionManager(SessionManager) - Method in class ome.services.blitz.impl.TimelineI
 
setSessionManager(String, int) - Method in class ome.services.blitz.Router
 
setSessions(Set<Session>) - Method in class ome.model.meta.Node
setter for sessions should be avoided.
setSessionService(ISession) - Method in class ome.system.SessionInitializer
 
setSettings(Set<RenderingDef>) - Method in class ome.model.core.Pixels
setter for settings should be avoided.
setSettingsService(IRenderingSettings) - Method in class ome.services.ThumbnailBean
Rendering settings service Bean injector.
setSha1(String) - Method in class ome.model.core.Pixels
 
setShape(int, Shape) - Method in class ome.model.roi.Roi
Sets the ome.model.roi.Shape at the given index.
setShapeIds(List<Long>) - Method in class omeis.providers.re.data.PlaneDef
Sets whether or not to render the shapes (masks).
setShapes(List<Shape>) - Method in class ome.model.roi.Roi
setter for shapes should be avoided.
setShapeSettings(Shape) - Method in class pojos.ShapeData
Set the settings associated to the shape.
setShareId(Long) - Method in class ome.security.basic.BasicEventContext
 
setShareId(Long) - Method in interface ome.services.sessions.SessionContext
The Share id is the only mutable bit in the SessionContext.
setShareId(Long) - Method in class ome.services.sessions.SessionContextImpl
 
setSignificantBits(Integer) - Method in class ome.model.core.Pixels
 
setSize(Long) - Method in class ome.model.core.OriginalFile
 
setSizeC(Integer) - Method in class ome.model.core.Pixels
 
setSizeC(int) - Method in class pojos.PixelsData
Sets the number of channels.
setSizeT(Integer) - Method in class ome.model.core.Pixels
 
setSizeT(int) - Method in class pojos.PixelsData
Sets the number of time-points.
setSizeX(Integer) - Method in class ome.model.acquisition.OTF
 
setSizeX(Integer) - Method in class ome.model.core.Pixels
 
setSizeX(Integer) - Method in class ome.model.display.Thumbnail
 
setSizeX(int) - Method in class pojos.PixelsData
Sets the number of pixels along the X-axis.
setSizeY(Integer) - Method in class ome.model.acquisition.OTF
 
setSizeY(Integer) - Method in class ome.model.core.Pixels
 
setSizeY(Integer) - Method in class ome.model.display.Thumbnail
 
setSizeY(int) - Method in class pojos.PixelsData
Sets the number of pixels along the Y-axis.
setSizeZ(Integer) - Method in class ome.model.core.Pixels
 
setSizeZ(int) - Method in class pojos.PixelsData
Sets the number of pixels along the Z-axis.
setSlf4jMinutes(int) - Method in class ome.system.metrics.DefaultMetrics
 
setSource(OriginalFile) - Method in class ome.model.roi.Roi
 
setSpatialDomainEnhancement(List<CodomainMapContext>) - Method in class ome.model.display.RenderingDef
setter for spatialDomainEnhancement should be avoided.
setSqlAction(SqlAction) - Method in class ome.logic.ConfigImpl
SqlAction setter for dependency injection.
setSqlAction(SqlAction) - Method in class ome.logic.RepositoryInfoImpl
Bean injection setter for SQL operations
setSqlAction(SqlAction) - Method in class ome.services.eventlogs.PersistentEventLogLoader
 
setSqlAction(SqlAction) - Method in class ome.services.fulltext.FullTextIndexer
Since these instances are used repeatedly, we need to check for already set SqlAction
setSqlAction(SqlAction) - Method in class ome.services.pixeldata.PixelDataHandler
Since these instances are used repeatedly, we need to check for already set SqlAction
setSqlAction(SqlAction) - Method in class ome.services.RawPixelsBean
SQL action Bean injector
setSqlAction(SqlAction) - Method in class ome.services.sharing.BlobShareStore
 
setSqlAction(SqlAction) - Method in class ome.services.util.Executor.SimpleWork
 
setSqlAction(SqlAction) - Method in class ome.util.TableIdGenerator
 
setStack(byte[], int, int, int) - Method in interface ome.api.RawPixelsStore
 
setStack(ByteBuffer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer
 
setStack(byte[], Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer
 
setStack(ByteBuffer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
 
setStack(byte[], Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
 
setStack(ByteBuffer, Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
 
setStack(byte[], Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
 
setStack(ByteBuffer, Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer
Sets the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel buffer.
setStack(byte[], Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer
Sets the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel buffer.
setStack(ByteBuffer, Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer
Implemented as specified by PixelBuffer I/F.
setStack(byte[], Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer
Implemented as specified by PixelBuffer I/F.
setStack(byte[], int, int, int) - Method in class ome.services.RawPixelsBean
 
setStack_async(AMD_RawPixelsStore_setStack, byte[], int, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
setStack_async(AMD_RawPixelsStore_setStack, byte[], int, int, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
setStageLabel(StageLabel) - Method in class ome.model.core.Image
 
setStageLabelName(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setStageLabelX(Length, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setStageLabelY(Length, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setStageLabelZ(Length, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setStaleCacheListener(SessionCache.StaleCacheListener) - Method in class ome.services.sessions.state.SessionCache
 
setStarted(Timestamp) - Method in class ome.model.jobs.Job
 
setStarted(Timestamp) - Method in class ome.model.meta.Session
 
setStartTime(Timestamp) - Method in class ome.model.screen.PlateAcquisition
 
setStatisticsEnabled(boolean) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
Enable statistics logs (this is a dynamic parameter)
setStatsInfo(StatsInfo) - Method in class ome.model.core.Channel
 
setStatsInfo(Channel, StatsInfo) - Method in class ome.util.SqlAction.Impl
 
setStatsInfo(Channel, StatsInfo) - Method in interface ome.util.SqlAction
 
setStatus(String) - Method in interface ome.api.JobHandle
Updates the JobStatus for the current job.
setStatus(int) - Method in class ome.formats.importer.util.ErrorContainer
set the status for this error
setStatus(JobStatus) - Method in class ome.model.jobs.Job
 
setStatus(String) - Method in class ome.model.meta.Event
 
setStatus(String) - Method in class ome.model.screen.Plate
 
setStatus(String) - Method in class ome.model.screen.Well
 
setStatus(String) - Method in class ome.services.JobBean
 
setStatus(String) - Method in class pojos.PlateData
Sets the status.
setStatus(String) - Method in class pojos.WellData
Sets the status of the well.
setStatus_async(AMD_JobHandle_setStatus, String, Current) - Method in class ome.services.blitz.impl.JobHandleI
 
setStatusAndMessage(String, String) - Method in interface ome.api.JobHandle
Like JobHandle.setStatus(String) but also sets the message.
setStatusAndMessage(String, String) - Method in class ome.services.JobBean
 
setStatusAndMessage_async(AMD_JobHandle_setStatusAndMessage, String, RString, Current) - Method in class ome.services.blitz.impl.JobHandleI
 
setSteps(int) - Method in class omero.cmd.Helper
 
setStop(boolean) - Method in class ome.services.eventlogs.EventLogLoader
Called by controlling objects (a worker thread) in order to free up the thread.
setStride(int) - Method in class omeis.providers.re.data.PlaneDef
Returns the stride.
setStroke(Color) - Method in class pojos.ShapeSettingsData
Set the stroke color.
setStrokeColor(Integer) - Method in class ome.model.roi.Shape
 
setStrokeDashArray(String) - Method in class ome.model.roi.Shape
 
setStrokeDashArray(double[]) - Method in class pojos.ShapeSettingsData
Set the stroke dashes.
setStrokeDashOffset(Integer) - Method in class ome.model.roi.Shape
 
setStrokeLineCap(String) - Method in class ome.model.roi.Shape
 
setStrokeLineJoin(String) - Method in class ome.model.roi.Shape
 
setStrokeMiterLimit(Integer) - Method in class ome.model.roi.Shape
 
setStrokeWidth(Length) - Method in class ome.model.roi.Shape
 
setStrokeWidth(Double) - Method in class pojos.ShapeSettingsData
setStrokeWidth(Length) - Method in class pojos.ShapeSettingsData
Set the stroke width.
setSubjectPrefix(String) - Method in class ome.services.mail.MailSender
 
setSubmitted(Timestamp) - Method in class ome.model.jobs.Job
 
setT(int) - Method in class pojos.ShapeData
Sets the time-point.
setTagAnnotationAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setTagAnnotationAnnotator(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setTagAnnotationDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setTagAnnotationID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setTagAnnotationNamespace(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setTagAnnotationValue(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setTagDescription(String) - Method in class pojos.TagAnnotationData
Sets the description of the tag.
setTagDescriptions(List<TextualAnnotationData>) - Method in class pojos.TagAnnotationData
Sets the tag's descriptions.
setTagValue(String) - Method in class pojos.TagAnnotationData
Sets the value of the tag.
setTarget(IObject) - Method in class ome.formats.importer.ImportContainer
 
setTemperature(Temperature) - Method in class ome.model.acquisition.ImagingEnvironment
 
setTemperature(Temperature) - Method in class pojos.ImageAcquisitionData
Sets the temperature.
setTemperature(double) - Method in class pojos.ImageAcquisitionData
setTemplatePrefix(String) - Method in class ome.model.fs.Fileset
 
setTerm(String) - Method in class pojos.TermAnnotationData
Sets the term.
setTermAnnotationAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setTermAnnotationAnnotator(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setTermAnnotationDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setTermAnnotationID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setTermAnnotationNamespace(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setTermAnnotationValue(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setTermDescription(String) - Method in class pojos.TermAnnotationData
Sets the description of the tag.
setTermValue(String) - Method in class ome.model.annotations.TermAnnotation
 
setText(String) - Method in class pojos.EllipseData
Sets the text of the shape.
setText(String) - Method in class pojos.LineData
Sets the text of the shape.
setText(String) - Method in class pojos.MaskData
Sets the text of the shape.
setText(String) - Method in class pojos.PointData
Sets the text of the shape.
setText(String) - Method in class pojos.PolygonData
Sets the text of the shape.
setText(String) - Method in class pojos.PolylineData
Sets the text of the shape.
setText(String) - Method in class pojos.RectangleData
Sets the text of the shape.
setText(String) - Method in class pojos.TextData
Sets the text of the shape.
setText(String) - Method in class pojos.TextualAnnotationData
Sets the text.
setText(String) - Method in class pojos.XMLAnnotationData
Sets the text value.
setTextValue(String) - Method in class ome.model.annotations.TextAnnotation
 
setTextValue(String) - Method in class ome.model.roi.Ellipse
 
setTextValue(String) - Method in class ome.model.roi.Label
 
setTextValue(String) - Method in class ome.model.roi.Line
 
setTextValue(String) - Method in class ome.model.roi.Mask
 
setTextValue(String) - Method in class ome.model.roi.Path
 
setTextValue(String) - Method in class ome.model.roi.Point
 
setTextValue(String) - Method in class ome.model.roi.Polygon
 
setTextValue(String) - Method in class ome.model.roi.Polyline
 
setTextValue(String) - Method in class ome.model.roi.Rect
 
setTheC(Integer) - Method in class ome.model.core.PlaneInfo
 
setTheC(Integer) - Method in class ome.model.roi.Shape
 
setTheT(Integer) - Method in class ome.model.core.PlaneInfo
 
setTheT(Integer) - Method in class ome.model.roi.Shape
 
setTheZ(Integer) - Method in class ome.model.core.PlaneInfo
 
setTheZ(Integer) - Method in class ome.model.roi.Shape
 
setThumbnails(Set<Thumbnail>) - Method in class ome.model.core.Pixels
setter for thumbnails should be avoided.
setThumbnailService(ThumbnailService) - Method in class ome.logic.RepositoryInfoImpl
Bean injection setter for ROMIO thumbnail service
setTie(TieBase) - Method in class ome.services.blitz.impl.RawFileStoreI
 
setTie(TieBase) - Method in interface omero.util.TieAware
 
setTiffDataFirstC(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setTiffDataFirstT(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setTiffDataFirstZ(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setTiffDataIFD(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setTiffDataPlaneCount(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setTile(byte[], int, int, int, int, int, int, int) - Method in interface ome.api.RawPixelsStore
 
setTile(Long, byte[], int, int, int, int, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
Writes a tile of pixels to the server.
setTile(byte[], Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer
 
setTile(byte[], Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
 
setTile(byte[], Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
 
setTile(byte[], Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer
Sets a tile in this pixel buffer.
setTile(byte[], Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer
 
setTile(byte[], int, int, int, int, int, int, int) - Method in class ome.services.RawPixelsBean
 
setTile(byte[], int, int, int, int, int, int, int) - Method in class omero.util.RPSTileData
 
setTile(byte[], int, int, int, int, int, int, int) - Method in interface omero.util.TileData
 
setTile_async(AMD_RawPixelsStore_setTile, byte[], int, int, int, int, int, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
setTile_async(AMD_RawPixelsStore_setTile, byte[], int, int, int, int, int, int, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
setTime(Timestamp) - Method in class ome.model.meta.Event
 
setTimeIncrement(Time) - Method in class ome.model.core.Pixels
 
setTimeout(int) - Method in class ome.services.blitz.Router
 
setTimepoint(byte[], int) - Method in interface ome.api.RawPixelsStore
 
setTimepoint(ByteBuffer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer
 
setTimepoint(byte[], Integer) - Method in class ome.io.bioformats.BfPixelBuffer
 
setTimepoint(ByteBuffer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
 
setTimepoint(byte[], Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
 
setTimepoint(ByteBuffer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
 
setTimepoint(byte[], Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
 
setTimepoint(ByteBuffer, Integer) - Method in interface ome.io.nio.PixelBuffer
Sets the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel buffer.
setTimepoint(byte[], Integer) - Method in interface ome.io.nio.PixelBuffer
Sets the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel buffer.
setTimepoint(ByteBuffer, Integer) - Method in class ome.io.nio.RomioPixelBuffer
Implemented as specified by PixelBuffer I/F.
setTimepoint(byte[], Integer) - Method in class ome.io.nio.RomioPixelBuffer
Implemented as specified by PixelBuffer I/F.
setTimepoint(Timestamp) - Method in class ome.model.screen.WellSample
 
setTimepoint(byte[], int) - Method in class ome.services.RawPixelsBean
 
setTimepoint_async(AMD_RawPixelsStore_setTimepoint, byte[], int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
setTimepoint_async(AMD_RawPixelsStore_setTimepoint, byte[], int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
setTimestampAnnotationAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setTimestampAnnotationAnnotator(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setTimestampAnnotationDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setTimestampAnnotationID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setTimestampAnnotationNamespace(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setTimestampAnnotationValue(Timestamp, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setTimeToIdle(Long) - Method in class ome.model.meta.Session
 
setTimeToLive(Long) - Method in class ome.model.meta.Session
 
setTimeValue(Timestamp) - Method in class ome.model.annotations.TimestampAnnotation
 
settings - Variable in class ome.model.core.Pixels
 
SETTINGS - Static variable in class ome.model.core.Pixels
 
settings - Variable in class pojos.ShapeData
The representation of the shape.
SETTINGSID_QUERY - Static variable in class ome.services.delete.DeleteBean
 
setToken(String) - Method in class ome.formats.importer.util.ErrorContainer
 
setToken(Token, Token) - Method in class ome.model.internal.GraphHolder
set the Token for this GraphHolder but only if you posses the current Token.
setToken(GraphHolder) - Method in class ome.security.basic.TokenHolder
 
setTransform(String) - Method in class ome.model.roi.Shape
 
setTransform(String) - Method in class pojos.ShapeData
Sets the Affine transform of the shape.
setTransmittance(Double) - Method in class ome.model.acquisition.TransmittanceRange
 
setTransmittanceRange(TransmittanceRange) - Method in class ome.model.acquisition.Filter
 
setTransmittanceRangeCutIn(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setTransmittanceRangeCutInTolerance(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setTransmittanceRangeCutOut(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setTransmittanceRangeCutOutTolerance(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setTransmittanceRangeTransmittance(PercentFraction, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setTrustStore(String) - Method in class ome.security.KeyAndTrustStoreConfiguration
 
setTrustStorePassword(String) - Method in class ome.security.KeyAndTrustStoreConfiguration
 
setTuneable(Boolean) - Method in class ome.model.acquisition.Laser
 
setType(ArcType) - Method in class ome.model.acquisition.Arc
 
setType(DetectorType) - Method in class ome.model.acquisition.Detector
 
setType(FilamentType) - Method in class ome.model.acquisition.Filament
 
setType(FilterType) - Method in class ome.model.acquisition.Filter
 
setType(LaserType) - Method in class ome.model.acquisition.Laser
 
setType(MicroscopeType) - Method in class ome.model.acquisition.Microscope
 
setType(ExperimentType) - Method in class ome.model.experiment.Experiment
 
setType(MicrobeamManipulationType) - Method in class ome.model.experiment.MicrobeamManipulation
 
setType(String) - Method in class ome.model.jobs.Job
 
setType(EventType) - Method in class ome.model.meta.Event
 
setType(String) - Method in class ome.model.screen.Screen
 
setType(String) - Method in class ome.model.screen.Well
 
setTypes(ITypes) - Method in class ome.services.eventlogs.PersistentEventLogLoader
 
setTypesService(ITypes) - Method in class ome.services.JobBean
Types service Bean injector.
setTypesService(ITypes) - Method in class ome.services.procs.ProcessorSkeleton
 
setUIBounds(Rectangle) - Method in class ome.formats.importer.ImportConfig
 
setUIBounds(Rectangle) - Method in class ome.formats.importer.util.IniFileLoader
Set ui bounds for application
setUmask(Permissions) - Method in class ome.security.basic.BasicEventContext
 
setUnit(UnitsElectricPotential) - Method in class ome.model.units.ElectricPotential
 
setUnit(UnitsFrequency) - Method in class ome.model.units.Frequency
 
setUnit(UnitsLength) - Method in class ome.model.units.Length
 
setUnit(UnitsPower) - Method in class ome.model.units.Power
 
setUnit(UnitsPressure) - Method in class ome.model.units.Pressure
 
setUnit(UnitsTemperature) - Method in class ome.model.units.Temperature
 
setUnit(UnitsTime) - Method in class ome.model.units.Time
 
setUnit(UnitsElectricPotential, Current) - Method in class omero.model.ElectricPotentialI
 
setUnit(UnitsFrequency, Current) - Method in class omero.model.FrequencyI
 
setUnit(UnitsLength, Current) - Method in class omero.model.LengthI
 
setUnit(UnitsPower, Current) - Method in class omero.model.PowerI
 
setUnit(UnitsPressure, Current) - Method in class omero.model.PressureI
 
setUnit(UnitsTemperature, Current) - Method in class omero.model.TemperatureI
 
setUnit(UnitsTime, Current) - Method in class omero.model.TimeI
 
setUp() - Method in class ome.formats.importer.ImportFixture
checks for the necessary fields and initializes the ImportLibrary
setUp() - Method in class ome.formats.importer.util.TinyImportFixture
checks for the necessary fields and initializes the ImportLibrary
setUp() - Method in class ome.formats.OMEROImportFixture
checks for the necessary fields and initializes the ImportLibrary
setUp(Timestamp) - Method in class ome.model.meta.Node
 
setUpdateEvent(Event) - Method in class ome.model.internal.Details
 
setUpdateEvent(Event) - Method in class ome.model.meta.ExternalInfo.Details
setUpdateEvent(Event, Current) - Method in class omero.model.DetailsI
 
setUpdateInterval(long) - Method in class ome.services.sessions.state.SessionCache
Inject time in milliseconds between updates.
setUpdateService(LocalUpdate) - Method in class ome.logic.AbstractLevel2Service
 
setUpdateService(LocalUpdate) - Method in class ome.services.AbstractStatefulBean
 
setUpdateService(IUpdate) - Method in class ome.services.procs.ProcessorSkeleton
 
setUploadUrl(String) - Method in class ome.formats.importer.util.ErrorContainer
 
setUpperLimit(Integer) - Method in class ome.model.display.PlaneSlicingContext
 
setUpperLimit(int) - Method in class omeis.providers.re.codomain.PlaneSlicingContext
Sets the value (in [intervalStart, intervalEnd]) used to set the level of the bit-plane > bit-plane selected.
setUsedFiles(String[]) - Method in class ome.formats.importer.ImportContainer
Set the list of image file names that belong to this import container.
setUsedFiles(List<FilesetEntry>) - Method in class ome.model.fs.Fileset
setter for usedFiles should be avoided.
setUseProjections(boolean) - Method in interface ome.api.Search
Determines if Lucene queries should not hit the database.
setUseProjections(boolean) - Method in class ome.services.SearchBean
 
setUseProjections_async(AMD_Search_setUseProjections, boolean, Current) - Method in class ome.services.blitz.impl.SearchI
 
setUseQuaqua(boolean) - Method in class ome.formats.importer.ImportConfig
 
setUseQuaqua(boolean) - Method in class ome.formats.importer.util.IniFileLoader
 
setUserAgent(String) - Method in class ome.model.meta.Session
 
setUserAnnotate(boolean, Current) - Method in class omero.model.PermissionsI
 
setUserDisableHistory(boolean) - Method in class ome.formats.importer.ImportConfig
 
setUserDisableHistory(boolean) - Method in class ome.formats.importer.util.IniFileLoader
Set debug level for application
setUserFullPath(boolean) - Method in class ome.formats.importer.ImportConfig
 
setUserFullPath(boolean) - Method in class ome.formats.importer.util.IniFileLoader
 
setUserId(long) - Method in class ome.services.ThumbnailCtx
Sets the user ID to use for queries.
setUserIP(String) - Method in class ome.model.meta.Session
 
setUsername(String) - Method in class loci.ome.io.OmeroReader
 
setUsername(String) - Method in class ome.model.jobs.Job
 
setUserPassword(Long, String) - Method in class ome.util.SqlAction.Impl
 
setUserPassword(Long, String) - Method in interface ome.util.SqlAction
 
setUserPixels(Double[]) - Method in class ome.formats.importer.ImportContainer
 
setUserRead(boolean, Current) - Method in class omero.model.PermissionsI
 
setUserRead(boolean) - Method in class pojos.PermissionData
Sets to true if the user has read access, false otherwise.
setUserSpecifiedAnnotations(List<Annotation>) - Method in interface ome.formats.model.IObjectContainerStore
Sets the user specified image annotations.
setUserSpecifiedAnnotations(List<Annotation>) - Method in class ome.formats.OMEROMetadataStoreClient
 
setUserSpecifiedDescription(String) - Method in class ome.formats.importer.ImportContainer
Sets the custom image/plate description for import.
setUserSpecifiedDescription(String) - Method in interface ome.formats.model.IObjectContainerStore
Sets the user specified image/plate description.
setUserSpecifiedDescription(String) - Method in class ome.formats.OMEROMetadataStoreClient
 
setUserSpecifiedName(String) - Method in class ome.formats.importer.ImportContainer
Sets the custom image/plate name for import.
setUserSpecifiedName(String) - Method in interface ome.formats.model.IObjectContainerStore
Sets the user specified image/plate name.
setUserSpecifiedName(String) - Method in class ome.formats.OMEROMetadataStoreClient
 
setUserSpecifiedPhysicalPixelSizes(Double, Double, Double) - Method in interface ome.formats.model.IObjectContainerStore
Sets the user specified physical pixel sizes.
setUserSpecifiedPhysicalPixelSizes(Double, Double, Double) - Method in class ome.formats.OMEROMetadataStoreClient
 
setUserSpecifiedTarget(IObject) - Method in interface ome.formats.model.IObjectContainerStore
Sets the user specified linkage target (usually a Dataset for Images and a Screen for Plates).
setUserSpecifiedTarget(IObject) - Method in class ome.formats.OMEROMetadataStoreClient
 
setUserStyleSheetURI(String) - Method in class ome.services.SVGRasterizer
Sets the uri of the user stylesheet.
setUserWrite(boolean, Current) - Method in class omero.model.PermissionsI
 
setUserWrite(boolean) - Method in class pojos.PermissionData
Sets to true if the user has write access, false otherwise.
setUUID(String) - Method in class ome.formats.OMEROMetadataStoreClient
 
setUuid(String) - Method in class ome.model.meta.ExternalInfo
 
setUuid(String) - Method in class ome.model.meta.Node
 
setUuid(String) - Method in class ome.model.meta.Session
 
setUuid(String) - Method in class ome.services.sessions.SessionManagerImpl
 
setUUIDFileName(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setUUIDValue(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setValue(String) - Method in class ome.model.enums.AcquisitionMode
 
setValue(String) - Method in class ome.model.enums.ArcType
 
setValue(String) - Method in class ome.model.enums.Binning
 
setValue(String) - Method in class ome.model.enums.ChecksumAlgorithm
 
setValue(String) - Method in class ome.model.enums.ContrastMethod
 
setValue(String) - Method in class ome.model.enums.Correction
 
setValue(String) - Method in class ome.model.enums.DetectorType
 
setValue(String) - Method in class ome.model.enums.DimensionOrder
 
setValue(String) - Method in class ome.model.enums.EventType
 
setValue(String) - Method in class ome.model.enums.ExperimentType
 
setValue(String) - Method in class ome.model.enums.Family
 
setValue(String) - Method in class ome.model.enums.FilamentType
 
setValue(String) - Method in class ome.model.enums.FilterType
 
setValue(String) - Method in class ome.model.enums.Format
 
setValue(String) - Method in class ome.model.enums.Illumination
 
setValue(String) - Method in class ome.model.enums.Immersion
 
setValue(String) - Method in class ome.model.enums.LaserMedium
 
setValue(String) - Method in class ome.model.enums.LaserType
 
setValue(String) - Method in class ome.model.enums.Medium
 
setValue(String) - Method in class ome.model.enums.MicrobeamManipulationType
 
setValue(String) - Method in class ome.model.enums.MicroscopeType
 
setValue(String) - Method in class ome.model.enums.PhotometricInterpretation
 
setValue(String) - Method in class ome.model.enums.PixelsType
 
setValue(String) - Method in class ome.model.enums.Pulse
 
setValue(String) - Method in class ome.model.enums.RenderingModel
 
setValue(String) - Method in class ome.model.internal.NamedValue
 
setValue(String) - Method in class ome.model.jobs.JobStatus
 
setValue(double) - Method in class ome.model.units.ElectricPotential
 
setValue(double) - Method in class ome.model.units.Frequency
 
setValue(double) - Method in class ome.model.units.Length
 
setValue(double) - Method in class ome.model.units.Power
 
setValue(double) - Method in class ome.model.units.Pressure
 
setValue(double) - Method in class ome.model.units.Temperature
 
setValue(double) - Method in class ome.model.units.Time
 
setValue(double) - Method in interface ome.model.units.Unit
 
setValue(double, Current) - Method in class omero.model.ElectricPotentialI
 
setValue(double, Current) - Method in class omero.model.FrequencyI
 
setValue(double, Current) - Method in class omero.model.LengthI
 
setValue(double, Current) - Method in class omero.model.PowerI
 
setValue(double, Current) - Method in class omero.model.PressureI
 
setValue(double, Current) - Method in class omero.model.TemperatureI
 
setValue(double, Current) - Method in class omero.model.TimeI
 
setValue(boolean) - Method in class pojos.BooleanAnnotationData
Returns the text.
setValue(IObject) - Method in class pojos.DataObject
Sets the IObject.
setVectorEffect(String) - Method in class ome.model.roi.Shape
 
setVersion(Integer) - Method in class ome.model.acquisition.Detector
 
setVersion(Integer) - Method in class ome.model.acquisition.DetectorSettings
 
setVersion(Integer) - Method in class ome.model.acquisition.Dichroic
 
setVersion(Integer) - Method in class ome.model.acquisition.Filter
 
setVersion(Integer) - Method in class ome.model.acquisition.FilterSet
 
setVersion(Integer) - Method in class ome.model.acquisition.FilterSetEmissionFilterLink
 
setVersion(Integer) - Method in class ome.model.acquisition.FilterSetExcitationFilterLink
 
setVersion(Integer) - Method in class ome.model.acquisition.ImagingEnvironment
 
setVersion(Integer) - Method in class ome.model.acquisition.Instrument
 
setVersion(Integer) - Method in class ome.model.acquisition.LightPath
 
setVersion(Integer) - Method in class ome.model.acquisition.LightPathEmissionFilterLink
 
setVersion(Integer) - Method in class ome.model.acquisition.LightPathExcitationFilterLink
 
setVersion(Integer) - Method in class ome.model.acquisition.LightSettings
 
setVersion(Integer) - Method in class ome.model.acquisition.LightSource
 
setVersion(Integer) - Method in class ome.model.acquisition.Microscope
 
setVersion(Integer) - Method in class ome.model.acquisition.Objective
 
setVersion(Integer) - Method in class ome.model.acquisition.ObjectiveSettings
 
setVersion(Integer) - Method in class ome.model.acquisition.OTF
 
setVersion(Integer) - Method in class ome.model.acquisition.StageLabel
 
setVersion(Integer) - Method in class ome.model.acquisition.TransmittanceRange
 
setVersion(Integer) - Method in class ome.model.annotations.Annotation
 
setVersion(Integer) - Method in class ome.model.annotations.AnnotationAnnotationLink
 
setVersion(Integer) - Method in class ome.model.annotations.ChannelAnnotationLink
 
setVersion(Integer) - Method in class ome.model.annotations.DatasetAnnotationLink
 
setVersion(Integer) - Method in class ome.model.annotations.DetectorAnnotationLink
 
setVersion(Integer) - Method in class ome.model.annotations.DichroicAnnotationLink
 
setVersion(Integer) - Method in class ome.model.annotations.ExperimenterAnnotationLink
 
setVersion(Integer) - Method in class ome.model.annotations.ExperimenterGroupAnnotationLink
 
setVersion(Integer) - Method in class ome.model.annotations.FilesetAnnotationLink
 
setVersion(Integer) - Method in class ome.model.annotations.FilterAnnotationLink
 
setVersion(Integer) - Method in class ome.model.annotations.ImageAnnotationLink
 
setVersion(Integer) - Method in class ome.model.annotations.InstrumentAnnotationLink
 
setVersion(Integer) - Method in class ome.model.annotations.LightPathAnnotationLink
 
setVersion(Integer) - Method in class ome.model.annotations.LightSourceAnnotationLink
 
setVersion(Integer) - Method in class ome.model.annotations.NamespaceAnnotationLink
 
setVersion(Integer) - Method in class ome.model.annotations.NodeAnnotationLink
 
setVersion(Integer) - Method in class ome.model.annotations.ObjectiveAnnotationLink
 
setVersion(Integer) - Method in class ome.model.annotations.OriginalFileAnnotationLink
 
setVersion(Integer) - Method in class ome.model.annotations.PlaneInfoAnnotationLink
 
setVersion(Integer) - Method in class ome.model.annotations.PlateAcquisitionAnnotationLink
 
setVersion(Integer) - Method in class ome.model.annotations.PlateAnnotationLink
 
setVersion(Integer) - Method in class ome.model.annotations.ProjectAnnotationLink
 
setVersion(Integer) - Method in class ome.model.annotations.ReagentAnnotationLink
 
setVersion(Integer) - Method in class ome.model.annotations.RoiAnnotationLink
 
setVersion(Integer) - Method in class ome.model.annotations.ScreenAnnotationLink
 
setVersion(Integer) - Method in class ome.model.annotations.SessionAnnotationLink
 
setVersion(Integer) - Method in class ome.model.annotations.ShapeAnnotationLink
 
setVersion(Integer) - Method in class ome.model.annotations.WellAnnotationLink
 
setVersion(Integer) - Method in class ome.model.containers.Dataset
 
setVersion(Integer) - Method in class ome.model.containers.DatasetImageLink
 
setVersion(Integer) - Method in class ome.model.containers.Project
 
setVersion(Integer) - Method in class ome.model.containers.ProjectDatasetLink
 
setVersion(Integer) - Method in class ome.model.core.Channel
 
setVersion(Integer) - Method in class ome.model.core.Image
 
setVersion(Integer) - Method in class ome.model.core.LogicalChannel
 
setVersion(Integer) - Method in class ome.model.core.OriginalFile
 
setVersion(Integer) - Method in class ome.model.core.Pixels
 
setVersion(Integer) - Method in class ome.model.core.PixelsOriginalFileMap
 
setVersion(Integer) - Method in class ome.model.core.PlaneInfo
 
setVersion(Integer) - Method in class ome.model.display.ChannelBinding
 
setVersion(Integer) - Method in class ome.model.display.CodomainMapContext
 
setVersion(Integer) - Method in class ome.model.display.QuantumDef
 
setVersion(Integer) - Method in class ome.model.display.RenderingDef
 
setVersion(Integer) - Method in class ome.model.display.Thumbnail
 
setVersion(Integer) - Method in class ome.model.experiment.Experiment
 
setVersion(Integer) - Method in class ome.model.experiment.MicrobeamManipulation
 
setVersion(Integer) - Method in class ome.model.fs.Fileset
 
setVersion(Integer) - Method in class ome.model.fs.FilesetEntry
 
setVersion(Integer) - Method in class ome.model.fs.FilesetJobLink
 
setVersion(Integer) - Method in interface ome.model.IMutable
use with caution.
setVersion(Integer) - Method in class ome.model.internal.Link
 
setVersion(Integer) - Method in class ome.model.jobs.Job
 
setVersion(Integer) - Method in class ome.model.jobs.JobOriginalFileLink
 
setVersion(Integer) - Method in class ome.model.meta.Experimenter
 
setVersion(Integer) - Method in class ome.model.meta.ExperimenterGroup
 
setVersion(Integer) - Method in class ome.model.meta.GroupExperimenterMap
 
setVersion(Integer) - Method in class ome.model.meta.Namespace
 
setVersion(Integer) - Method in class ome.model.meta.Node
 
setVersion(Integer) - Method in class ome.model.meta.Session
 
setVersion(Integer) - Method in class ome.model.meta.ShareMember
 
setVersion(Integer) - Method in class ome.model.roi.Roi
 
setVersion(Integer) - Method in class ome.model.roi.Shape
 
setVersion(Integer) - Method in class ome.model.screen.Plate
 
setVersion(Integer) - Method in class ome.model.screen.PlateAcquisition
 
setVersion(Integer) - Method in class ome.model.screen.Reagent
 
setVersion(Integer) - Method in class ome.model.screen.Screen
 
setVersion(Integer) - Method in class ome.model.screen.ScreenPlateLink
 
setVersion(Integer) - Method in class ome.model.screen.Well
 
setVersion(Integer) - Method in class ome.model.screen.WellReagentLink
 
setVersion(Integer) - Method in class ome.model.screen.WellSample
 
setVersion(Integer) - Method in class ome.model.stats.StatsInfo
 
setVersion(int) - Method in class pojos.DataObject
Sets the version of the object if it is immutable.
setVersionInfo(List<NamedValue>) - Method in class ome.model.jobs.MetadataImportJob
 
setVersionInfo(List<NamedValue>) - Method in class ome.model.jobs.UploadJob
 
setVersionNumber(String) - Method in class ome.formats.importer.ImportConfig
 
setVisibility(Boolean) - Method in class ome.model.roi.Shape
 
setVisibility(Preference.Visibility) - Method in class ome.system.Preference
Setter injector
setVisible(boolean) - Method in class pojos.ShapeData
Sets to true if the shape is visible, false otherwise.
setVoltage(ElectricPotential) - Method in class ome.model.acquisition.Detector
 
setVoltage(ElectricPotential) - Method in class ome.model.acquisition.DetectorSettings
 
setWaveIncrement(Integer) - Method in class ome.model.core.Pixels
 
setWavelength(Length) - Method in class ome.model.acquisition.Laser
 
setWavelength(Length) - Method in class ome.model.acquisition.LightSettings
 
setWavelength(int) - Method in exception omeis.providers.re.quantum.QuantizationException
Sets the index of the wavelength that couldn't be rendered.
setWaveRendering(List<ChannelBinding>) - Method in class ome.model.display.RenderingDef
setter for waveRendering should be avoided.
setWaveStart(Integer) - Method in class ome.model.core.Pixels
 
setWell(Well) - Method in class ome.model.screen.WellSample
 
setWellAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setWellColor(Color, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setWellColumn(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setWellExternalDescription(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setWellExternalIdentifier(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setWellID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setWellLinks(Set<WellReagentLink>) - Method in class ome.model.screen.Reagent
setter for wellLinks should be avoided.
setWellLinksCountPerOwner(Map<Long, Long>) - Method in class ome.model.screen.Reagent
 
setWellOriginX(Length) - Method in class ome.model.screen.Plate
 
setWellOriginY(Length) - Method in class ome.model.screen.Plate
 
setWellReagentRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setWellRow(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setWells(Set<Well>) - Method in class ome.model.screen.Plate
setter for wells should be avoided.
setWellSample(Set<WellSample>) - Method in class ome.model.screen.PlateAcquisition
setter for wellSample should be avoided.
setWellSample(int, WellSample) - Method in class ome.model.screen.Well
Sets the ome.model.screen.WellSample at the given index.
setWellSampleID(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setWellSampleImageRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setWellSampleIndex(NonNegativeInteger, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setWellSamplePositionX(Length, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setWellSamplePositionY(Length, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setWellSamples(Set<WellSample>) - Method in class ome.model.core.Image
setter for wellSamples should be avoided.
setWellSamples(List<WellSample>) - Method in class ome.model.screen.Well
setter for wellSamples should be avoided.
setWellSamples(List<WellSampleData>) - Method in class pojos.WellData
Sets the well samples linked to the well.
setWellSampleTimepoint(Timestamp, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setWellType(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setWellType(String) - Method in class pojos.WellData
Sets a human readable identifier for the screening status e.g. empty, positive control, etc.
setWidth(Double) - Method in class ome.model.roi.Mask
 
setWidth(Double) - Method in class ome.model.roi.Rect
 
setWidth(int) - Method in class omeis.providers.re.data.RegionDef
Sets the width of the region.
setWidth(double) - Method in class pojos.MaskData
Sets the width of an untransformed mask.
setWidth(double) - Method in class pojos.RectangleData
Sets width of an untransformed rectangle.
setWindow(double, double) - Method in class omeis.providers.re.quantum.QuantumStrategy
Sets the input window interval.
setWorkingDistance(Length) - Method in class ome.model.acquisition.Objective
 
setWorldAnnotate(boolean, Current) - Method in class omero.model.PermissionsI
 
setWorldRead(boolean, Current) - Method in class omero.model.PermissionsI
 
setWorldRead(boolean) - Method in class pojos.PermissionData
Sets to true if the world has read access, false otherwise.
setWorldWrite(boolean, Current) - Method in class omero.model.PermissionsI
 
setWorldWrite(boolean) - Method in class pojos.PermissionData
Sets to true if the world has write access, false otherwise.
setWritingMode(String) - Method in class ome.model.roi.Label
 
setX(Double) - Method in class ome.model.roi.Label
 
setX(Double) - Method in class ome.model.roi.Mask
 
setX(Double) - Method in class ome.model.roi.Rect
 
setX(int) - Method in class omeis.providers.re.data.PlaneDef
Selects a plane in the set identified by this object.
setX(int) - Method in class omeis.providers.re.data.RegionDef
Sets the x-coordinate of the top-left corner.
setX(double) - Method in class pojos.EllipseData
Sets the x-coordinate of the center of the ellipse.
setX(double) - Method in class pojos.MaskData
Sets the x-coordinate top-left corner of an untransformed mask.
setX(double) - Method in class pojos.PointData
set the x-coordinate of the shape.
setX(double) - Method in class pojos.RectangleData
Sets the x-coordinate of the top-left corner of an untransformed rectangle.
setX(double) - Method in class pojos.TextData
Sets the x-coordinate of the text field.
setX1(Double) - Method in class ome.model.roi.Line
 
setX1(double) - Method in class pojos.LineData
Set the x-coordinate of the starting point of an untransformed line.
setX2(Double) - Method in class ome.model.roi.Line
 
setX2(double) - Method in class pojos.LineData
Set the x-coordinate of the end point of an untransformed line.
setXend(Integer) - Method in class ome.model.display.ContrastStretchingContext
 
setXEnd(int) - Method in class omeis.providers.re.codomain.ContrastStretchingContext
Sets the x-coodinate of the pEnd point.
setXMLAnnotationAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setXMLAnnotationAnnotator(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setXMLAnnotationDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setXMLAnnotationID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setXMLAnnotationNamespace(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setXMLAnnotationValue(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setXMLParserValidating(boolean) - Method in class ome.services.SVGRasterizer
Sets whether or not the XML parser used to parse SVG document should be validating or not, depending on the specified parameter.
setXstart(Integer) - Method in class ome.model.display.ContrastStretchingContext
 
setXStart(int) - Method in class omeis.providers.re.codomain.ContrastStretchingContext
Sets the x-coodinate of the pStart point.
setY(Double) - Method in class ome.model.roi.Label
 
setY(Double) - Method in class ome.model.roi.Mask
 
setY(Double) - Method in class ome.model.roi.Rect
 
setY(int) - Method in class omeis.providers.re.data.PlaneDef
Selects a plane in the set identified by this object.
setY(int) - Method in class omeis.providers.re.data.RegionDef
Sets the y-coordinate of the top-left corner.
setY(double) - Method in class pojos.EllipseData
Sets the y-coordinate of the center of the ellipse.
setY(double) - Method in class pojos.MaskData
Sets the y-coordinate top-left corner of an untransformed mask.
setY(double) - Method in class pojos.PointData
set the y-coordinate of the shape.
setY(double) - Method in class pojos.RectangleData
Sets the y-coordinate of the top-left corner of an untransformed rectangle.
setY(double) - Method in class pojos.TextData
Sets the y-coordinate of the text field.
setY1(Double) - Method in class ome.model.roi.Line
 
setY1(double) - Method in class pojos.LineData
Set the y-coordinate of the starting point of an untransformed line.
setY2(Double) - Method in class ome.model.roi.Line
 
setY2(double) - Method in class pojos.LineData
Set the y-coordinate of the end point of an untransformed line.
setYend(Integer) - Method in class ome.model.display.ContrastStretchingContext
 
setYEnd(int) - Method in class omeis.providers.re.codomain.ContrastStretchingContext
Sets the y-coodinate of the pEnd point.
setYstart(Integer) - Method in class ome.model.display.ContrastStretchingContext
 
setYStart(int) - Method in class omeis.providers.re.codomain.ContrastStretchingContext
Sets the y-coodinate of the pStart point.
setZ(int) - Method in class omeis.providers.re.data.PlaneDef
Selects a plane in the set identified by this object.
setZ(int) - Method in class pojos.ShapeData
Sets the z-section.
setZoom(Double) - Method in class ome.model.acquisition.Detector
 
setZoom(Double) - Method in class ome.model.acquisition.DetectorSettings
 
sf - Variable in class ome.logic.TypesImpl
 
sf - Variable in class ome.security.auth.SimpleRoleProvider
 
sf - Variable in class ome.security.basic.BasicSecuritySystem
 
sf - Variable in class ome.services.blitz.impl.MetadataStoreI
 
sf - Variable in class ome.services.blitz.util.FindServiceFactoryMessage
 
sf - Variable in class ome.services.delete.DeleteBean
 
sha1 - Variable in class ome.model.core.Pixels
 
SHA1 - Static variable in class ome.model.core.Pixels
 
sha1(File) - Method in class omero.client
Calculates the local sha1 for a file.
SHA1ChecksumProviderImpl - Class in ome.util.checksum
An implementation of the ChecksumProvider interface using SHA1 as the secure hash algorithm.
SHA1ChecksumProviderImpl() - Constructor for class ome.util.checksum.SHA1ChecksumProviderImpl
 
shallowCopy() - Method in class ome.model.internal.Details
 
shallowCopy(Details) - Method in class ome.model.internal.Details
Method which takes all the fields of the given Details instance and sets unloaded proxies of them into the current instance.
ShallowCopy - Class in ome.util
 
ShallowCopy() - Constructor for class ome.util.ShallowCopy
 
Shape - Class in ome.model.roi
These filter definitions are used by the security system to eliminate non-readable objects from queries.
Shape() - Constructor for class ome.model.roi.Shape
 
Shape(Long) - Constructor for class ome.model.roi.Shape
 
Shape(Long, boolean) - Constructor for class ome.model.roi.Shape
Main constructor.
Shape(Roi) - Constructor for class ome.model.roi.Shape
 
Shape.Details - Class in ome.model.roi
 
Shape.Details() - Constructor for class ome.model.roi.Shape.Details
 
Shape.Details(Object[]) - Constructor for class ome.model.roi.Shape.Details
 
Shape_FontSize - Static variable in class ome.formats.model.UnitsFactory
 
Shape_StrokeWidth - Static variable in class ome.formats.model.UnitsFactory
 
ShapeAnnotationLink - Class in ome.model.annotations
These filter definitions are used by the security system to eliminate non-readable objects from queries.
ShapeAnnotationLink() - Constructor for class ome.model.annotations.ShapeAnnotationLink
 
ShapeAnnotationLink(Long) - Constructor for class ome.model.annotations.ShapeAnnotationLink
 
ShapeAnnotationLink(Long, boolean) - Constructor for class ome.model.annotations.ShapeAnnotationLink
Main constructor.
ShapeAnnotationLink(IObject, IObject) - Constructor for class ome.model.annotations.ShapeAnnotationLink
 
ShapeAnnotationLink.Details - Class in ome.model.annotations
 
ShapeAnnotationLink.Details() - Constructor for class ome.model.annotations.ShapeAnnotationLink.Details
 
ShapeAnnotationLink.Details(Object[]) - Constructor for class ome.model.annotations.ShapeAnnotationLink.Details
 
ShapeData - Class in pojos
Hosts a shape.
ShapeData(Shape, boolean) - Constructor for class pojos.ShapeData
Creates a new instance.
ShapeData(Shape) - Constructor for class pojos.ShapeData
Creates a new instance.
ShapeProcessor - Class in ome.formats.model
Processes the shapes of a IObjectContainerStore and ensures that the ROI containers are present.
ShapeProcessor() - Constructor for class ome.formats.model.ShapeProcessor
 
shapes - Variable in class ome.model.roi.Roi
 
SHAPES - Static variable in class ome.model.roi.Roi
 
ShapeSettingsData - Class in pojos
Stores the settings related to a given shape.
Share - Class in ome.model.meta
 
Share() - Constructor for class ome.model.meta.Share
 
Share(Long) - Constructor for class ome.model.meta.Share
 
Share(Long, boolean) - Constructor for class ome.model.meta.Share
Main constructor.
Share(ExperimenterGroup, Long, Boolean, byte[]) - Constructor for class ome.model.meta.Share
 
ShareBean - Class in ome.services.sharing
Note: SessionManager should not be used to obtain the Share data since it may not be completely in sync. i.e.
ShareBean(LocalAdmin, SessionManager, ShareStore, Executor, MailUtil) - Constructor for class ome.services.sharing.ShareBean
 
sharedResources(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
SharedResourcesI - Class in ome.services.blitz.impl
Implementation of the SharedResources interface.
SharedResourcesI(BlitzExecutor, TopicManager, Registry, ScriptRepoHelper, ParamsCache) - Constructor for class ome.services.blitz.impl.SharedResourcesI
 
SharedResourcesI(BlitzExecutor, TopicManager, Registry, ScriptRepoHelper, ParamsCache, long) - Constructor for class ome.services.blitz.impl.SharedResourcesI
 
SharedResourcesI(BlitzExecutor, TopicManager, Registry, ScriptRepoHelper, ParamsCache, long, long) - Constructor for class ome.services.blitz.impl.SharedResourcesI
 
ShareI - Class in ome.services.blitz.impl
Implementation of the IShare service.
ShareI(IShare, BlitzExecutor) - Constructor for class ome.services.blitz.impl.ShareI
 
shareId - Variable in class ome.system.SimpleEventContext
 
ShareMember - Class in ome.model.meta
 
ShareMember() - Constructor for class ome.model.meta.ShareMember
 
ShareMember(Long) - Constructor for class ome.model.meta.ShareMember
 
ShareMember(Long, boolean) - Constructor for class ome.model.meta.ShareMember
Main constructor.
ShareMember(IObject, IObject) - Constructor for class ome.model.meta.ShareMember
 
ShareMember.Details - Class in ome.model.meta
 
ShareMember.Details() - Constructor for class ome.model.meta.ShareMember.Details
 
ShareMember.Details(Object[]) - Constructor for class ome.model.meta.ShareMember.Details
 
ShareRestrictionTransactionAttributeSource - Class in ome.services.sharing
Prevents methods from setting the transaction to readOnly = false when a share is activated.
ShareRestrictionTransactionAttributeSource(CurrentDetails, SessionCache) - Constructor for class ome.services.sharing.ShareRestrictionTransactionAttributeSource
 
ShareStore - Class in ome.services.sharing
Entry to the Ice code generated data/ directory.
ShareStore() - Constructor for class ome.services.sharing.ShareStore
 
sharesToSessions(List<ShareData>) - Method in class ome.services.sharing.ShareBean
 
shareToSession(ShareData) - Method in class ome.services.sharing.ShareBean
 
sharing - Variable in class ome.security.SecuritySystemHolder
 
SharingACLVoter - Class in ome.security.sharing
 
SharingACLVoter(CurrentDetails, SystemTypes, ShareStore, TokenHolder) - Constructor for class ome.security.sharing.SharingACLVoter
 
SharingSecuritySystem - Class in ome.security.sharing
central security interface.
SharingSecuritySystem(BasicSecuritySystem) - Constructor for class ome.security.sharing.SharingSecuritySystem
 
SHORT - Static variable in class ome.util.PixelData
Identifies the type used to store pixel values.
SHORT - Static variable in class omeis.providers.re.data.PlaneFactory
Identifies the type used to store pixel values.
shortName - Variable in class ome.formats.importer.ImportEvent.COUNT_EVENT
 
shouldBeOmitted(String) - Static method in class ome.services.util.DBEnumCheck
 
shutdown(boolean) - Method in class ome.services.blitz.Entry
Calls OmeroContext.closeAll() to recursively close all OMERO.blitz resources in the reverse order that they were created.
shutdown(Current) - Method in class ome.services.blitz.impl.ScriptProcessI
 
shutdown() - Method in class ome.services.blitz.repo.ManagedImportProcessI
 
shutdown() - Method in interface ome.services.blitz.repo.ProcessContainer.Process
 
shutdownAll() - Method in class ome.services.blitz.repo.ProcessContainer
Called on shutdown of the server.
ShutdownMessage - Class in ome.util.messages
Published when the server is shutting down.
ShutdownMessage(Object) - Constructor for class ome.util.messages.ShutdownMessage
 
ShutdownSafeEhcacheManagerFactoryBean - Class in ome.tools.spring
Workaround for the Spring/EHCache shutdown sequence.
ShutdownSafeEhcacheManagerFactoryBean() - Constructor for class ome.tools.spring.ShutdownSafeEhcacheManagerFactoryBean
 
SiftingWhileRejectingDefaultAppender - Class in ome.util.logback
 
SiftingWhileRejectingDefaultAppender() - Constructor for class ome.util.logback.SiftingWhileRejectingDefaultAppender
 
signal - Variable in class ome.util.messages.UserSignalMessage
 
signed - Variable in class omeis.providers.re.data.Plane2D
The sign of the type
significantBits - Variable in class ome.model.core.Pixels
 
SIGNIFICANTBITS - Static variable in class ome.model.core.Pixels
 
SimilarTerms - Class in ome.services.search
Search to find similar terms to some given terms.
SimilarTerms(SearchValues, String...) - Constructor for class ome.services.search.SimilarTerms
 
SimpleBackOff - Class in ome.io.nio
Basic BackOff implementation which attempts several writes of the default block size on startup, and uses that as a scaling factor for all subsequent calculations.
SimpleBackOff() - Constructor for class ome.io.nio.SimpleBackOff
 
SimpleBackOff(TileSizes) - Constructor for class ome.io.nio.SimpleBackOff
 
simpleDelete(Map<String, String>, Executor, Principal, long) - Method in class ome.services.scripts.ScriptRepoHelper
Unlike ScriptRepoHelper.delete(long) this method simply performs the DB delete on the given original file id.
SimpleEventContext - Class in ome.system
simple, non-thread-safe, serializable EventContext
SimpleEventContext() - Constructor for class ome.system.SimpleEventContext
Constructor for subclasses
SimpleEventContext(EventContext) - Constructor for class ome.system.SimpleEventContext
copy constructor.
SimpleLuceneOptions - Class in ome.services.fulltext
Implementation of LuceneOptions which takes an existing instance and possible overrides for each of the values.
SimpleLuceneOptions(LuceneOptions, Float) - Constructor for class ome.services.fulltext.SimpleLuceneOptions
 
SimpleLuceneOptions(LuceneOptions, Field.Store) - Constructor for class ome.services.fulltext.SimpleLuceneOptions
 
SimpleLuceneOptions(LuceneOptions, Field.Index, Field.Store) - Constructor for class ome.services.fulltext.SimpleLuceneOptions
 
SimpleLuceneOptions(LuceneOptions, Float, Field.Index, Field.Store) - Constructor for class ome.services.fulltext.SimpleLuceneOptions
 
SimpleRoleProvider - Class in ome.security.auth
Implements RoleProvider.
SimpleRoleProvider(SecuritySystem, SessionFactory) - Constructor for class ome.security.auth.SimpleRoleProvider
 
SimpleRoleProvider(SecuritySystem, SessionFactory, AtomicBoolean) - Constructor for class ome.security.auth.SimpleRoleProvider
 
SimpleSessionStats - Class in ome.services.sessions.stats
 
SimpleSessionStats(ObjectsReadCounter, ObjectsWrittenCounter, MethodCounter) - Constructor for class ome.services.sessions.stats.SimpleSessionStats
 
singleBitOn(Permissions.Role, Permissions.Right) - Static method in class ome.model.internal.Permissions
returns a long with only a single 1 defined by role/right
singleBitOut(Permissions.Role, Permissions.Right) - Static method in class ome.model.internal.Permissions
returns a long with only a single 0 defined by role/right
singleFile(File, ImportConfig) - Method in class ome.formats.importer.ImportCandidates
Return an import container for a single file
size() - Method in interface ome.api.RawFileStore
Returns the size of the file on disk (not as stored in the database since that value will only be updated on RawFileStore.save().
size() - Method in class ome.formats.importer.ImportCandidates
 
size - Variable in class ome.formats.importer.ImportEvent.PROGRESS_EVENT
 
size() - Method in class ome.io.nio.FileBuffer
 
size - Variable in class ome.model.core.OriginalFile
 
SIZE - Static variable in class ome.model.core.OriginalFile
 
size(String) - Method in class ome.security.auth.AttributeSet
 
size() - Method in class ome.security.basic.CurrentDetails
 
size() - Method in interface ome.security.basic.PrincipalHolder
Get the number of active principal contexts.
size() - Method in class ome.services.blitz.repo.CheckedPath
Return the size of this file on the underlying filesystem.
size() - Method in class ome.services.export.ExporterIndex
Deprecated.
 
size() - Method in class ome.services.graphs.GraphState
Deprecated.
 
size() - Method in interface ome.services.graphs.GraphStep.Callback
Deprecated.
 
size() - Method in class ome.services.graphs.GraphSteps
Deprecated.
 
size() - Method in class ome.services.query.Definitions
 
size() - Method in class ome.services.RawFileBean
 
size() - Method in class ome.services.scheduler.ThreadPool
 
size() - Method in class ome.system.metrics.DefaultSnapshot
 
size() - Method in interface ome.system.metrics.Snapshot
 
size() - Method in class ome.tools.hibernate.ExtendedMetadata.Locks
the total number of fields for this entity.
size() - Method in class ome.util.PixelData
Returns the pixel count of this block of pixel data.
size() - Method in class omero.util.Resources
 
size_async(AMD_RawFileStore_size, Current) - Method in class ome.services.blitz.impl.RawFileStoreI
 
sizeC - Variable in class ome.formats.importer.ImportSize
 
sizeC - Variable in class ome.model.core.Pixels
 
SIZEC - Static variable in class ome.model.core.Pixels
 
sizeC - Variable in class ome.services.formats.OmeroReader
 
sizeImages() - Method in class ome.services.blitz.impl.OmeroMetadata
 
sizeOfAnnotationLinks() - Method in class ome.model.acquisition.Detector
returns the size of annotationLinks.
sizeOfAnnotationLinks() - Method in class ome.model.acquisition.Dichroic
returns the size of annotationLinks.
sizeOfAnnotationLinks() - Method in class ome.model.acquisition.Filter
returns the size of annotationLinks.
sizeOfAnnotationLinks() - Method in class ome.model.acquisition.Instrument
returns the size of annotationLinks.
sizeOfAnnotationLinks() - Method in class ome.model.acquisition.LightPath
returns the size of annotationLinks.
sizeOfAnnotationLinks() - Method in class ome.model.acquisition.LightSource
returns the size of annotationLinks.
sizeOfAnnotationLinks() - Method in class ome.model.acquisition.Objective
returns the size of annotationLinks.
sizeOfAnnotationLinks() - Method in class ome.model.annotations.Annotation
returns the size of annotationLinks.
sizeOfAnnotationLinks() - Method in class ome.model.containers.Dataset
returns the size of annotationLinks.
sizeOfAnnotationLinks() - Method in class ome.model.containers.Project
returns the size of annotationLinks.
sizeOfAnnotationLinks() - Method in class ome.model.core.Channel
returns the size of annotationLinks.
sizeOfAnnotationLinks() - Method in class ome.model.core.Image
returns the size of annotationLinks.
sizeOfAnnotationLinks() - Method in class ome.model.core.OriginalFile
returns the size of annotationLinks.
sizeOfAnnotationLinks() - Method in class ome.model.core.PlaneInfo
returns the size of annotationLinks.
sizeOfAnnotationLinks() - Method in class ome.model.fs.Fileset
returns the size of annotationLinks.
sizeOfAnnotationLinks() - Method in interface ome.model.IAnnotated
 
sizeOfAnnotationLinks() - Method in class ome.model.meta.Experimenter
returns the size of annotationLinks.
sizeOfAnnotationLinks() - Method in class ome.model.meta.ExperimenterGroup
returns the size of annotationLinks.
sizeOfAnnotationLinks() - Method in class ome.model.meta.Namespace
returns the size of annotationLinks.
sizeOfAnnotationLinks() - Method in class ome.model.meta.Node
returns the size of annotationLinks.
sizeOfAnnotationLinks() - Method in class ome.model.meta.Session
returns the size of annotationLinks.
sizeOfAnnotationLinks() - Method in class ome.model.roi.Roi
returns the size of annotationLinks.
sizeOfAnnotationLinks() - Method in class ome.model.roi.Shape
returns the size of annotationLinks.
sizeOfAnnotationLinks() - Method in class ome.model.screen.Plate
returns the size of annotationLinks.
sizeOfAnnotationLinks() - Method in class ome.model.screen.PlateAcquisition
returns the size of annotationLinks.
sizeOfAnnotationLinks() - Method in class ome.model.screen.Reagent
returns the size of annotationLinks.
sizeOfAnnotationLinks() - Method in class ome.model.screen.Screen
returns the size of annotationLinks.
sizeOfAnnotationLinks() - Method in class ome.model.screen.Well
returns the size of annotationLinks.
sizeOfChannels() - Method in class ome.model.core.LogicalChannel
returns the size of channels.
sizeOfChannels() - Method in class ome.model.core.Pixels
returns the size of channels.
sizeOfDatasetLinks() - Method in class ome.model.containers.Project
returns the size of datasetLinks.
sizeOfDatasetLinks() - Method in class ome.model.core.Image
returns the size of datasetLinks.
sizeOfDetector() - Method in class ome.model.acquisition.Instrument
returns the size of detector.
sizeOfDichroic() - Method in class ome.model.acquisition.Instrument
returns the size of dichroic.
sizeOfEmissionFilterLink() - Method in class ome.model.acquisition.Filter
returns the size of emissionFilterLink.
sizeOfEmissionFilterLink() - Method in class ome.model.acquisition.FilterSet
returns the size of emissionFilterLink.
sizeOfEmissionFilterLink() - Method in class ome.model.acquisition.LightPath
returns the size of emissionFilterLink.
sizeOfEvents() - Method in class ome.model.meta.Session
returns the size of events.
sizeOfExcitationFilterLink() - Method in class ome.model.acquisition.Filter
returns the size of excitationFilterLink.
sizeOfExcitationFilterLink() - Method in class ome.model.acquisition.FilterSet
returns the size of excitationFilterLink.
sizeOfExcitationFilterLink() - Method in class ome.model.acquisition.LightPath
returns the size of excitationFilterLink.
sizeOfFilesetEntries() - Method in class ome.model.core.OriginalFile
returns the size of filesetEntries.
sizeOfFilter() - Method in class ome.model.acquisition.Instrument
returns the size of filter.
sizeOfFilterSet() - Method in class ome.model.acquisition.Instrument
returns the size of filterSet.
sizeOfGroupExperimenterMap() - Method in class ome.model.meta.Experimenter
returns the size of groupExperimenterMap.
sizeOfGroupExperimenterMap() - Method in class ome.model.meta.ExperimenterGroup
returns the size of groupExperimenterMap.
sizeOfImageLinks() - Method in class ome.model.containers.Dataset
returns the size of imageLinks.
sizeOfImages() - Method in class ome.model.fs.Fileset
returns the size of images.
sizeOfJobLinks() - Method in class ome.model.fs.Fileset
returns the size of jobLinks.
sizeOfLightSource() - Method in class ome.model.acquisition.Instrument
returns the size of lightSource.
sizeOfLightSourceSettings() - Method in class ome.model.experiment.MicrobeamManipulation
returns the size of lightSourceSettings.
sizeOfLogs() - Method in class ome.model.meta.Event
returns the size of logs.
sizeOfMicrobeamManipulation() - Method in class ome.model.experiment.Experiment
returns the size of microbeamManipulation.
sizeOfObjective() - Method in class ome.model.acquisition.Instrument
returns the size of objective.
sizeOfOriginalFileLinks() - Method in class ome.model.jobs.Job
returns the size of originalFileLinks.
sizeOfOtf() - Method in class ome.model.acquisition.Instrument
returns the size of otf.
sizeOfPixels() - Method in class ome.model.core.Image
returns the size of pixels.
sizeOfPixelsFileMaps() - Method in class ome.model.core.OriginalFile
returns the size of pixelsFileMaps.
sizeOfPixelsFileMaps() - Method in class ome.model.core.Pixels
returns the size of pixelsFileMaps.
sizeOfPlaneInfo() - Method in class ome.model.core.Pixels
returns the size of planeInfo.
sizeOfPlateAcquisitions() - Method in class ome.model.screen.Plate
returns the size of plateAcquisitions.
sizeOfPlateLinks() - Method in class ome.model.screen.Screen
returns the size of plateLinks.
sizeOfProjectLinks() - Method in class ome.model.containers.Dataset
returns the size of projectLinks.
sizeOfReagentLinks() - Method in class ome.model.screen.Well
returns the size of reagentLinks.
sizeOfReagents() - Method in class ome.model.screen.Screen
returns the size of reagents.
sizeOfRois() - Method in class ome.model.core.Image
returns the size of rois.
sizeOfScreenLinks() - Method in class ome.model.screen.Plate
returns the size of screenLinks.
sizeOfSessions() - Method in class ome.model.meta.Node
returns the size of sessions.
sizeOfSettings() - Method in class ome.model.core.Pixels
returns the size of settings.
sizeOfShapes() - Method in class ome.model.roi.Roi
returns the size of shapes.
sizeOfSpatialDomainEnhancement() - Method in class ome.model.display.RenderingDef
returns the size of spatialDomainEnhancement.
sizeOfThumbnails() - Method in class ome.model.core.Pixels
returns the size of thumbnails.
sizeOfUsedFiles() - Method in class ome.model.fs.Fileset
returns the size of usedFiles.
sizeOfWaveRendering() - Method in class ome.model.display.RenderingDef
returns the size of waveRendering.
sizeOfWellLinks() - Method in class ome.model.screen.Reagent
returns the size of wellLinks.
sizeOfWells() - Method in class ome.model.screen.Plate
returns the size of wells.
sizeOfWellSample() - Method in class ome.model.screen.PlateAcquisition
returns the size of wellSample.
sizeOfWellSamples() - Method in class ome.model.core.Image
returns the size of wellSamples.
sizeOfWellSamples() - Method in class ome.model.screen.Well
returns the size of wellSamples.
sizes - Variable in class ome.io.nio.PixelsService
TileSizes implementation for default values
sizes - Variable in class ome.io.nio.SimpleBackOff
 
sizeT - Variable in class ome.formats.importer.ImportSize
 
sizeT - Variable in class ome.model.core.Pixels
 
SIZET - Static variable in class ome.model.core.Pixels
 
sizeT - Variable in class ome.services.formats.OmeroReader
 
sizeX - Variable in class ome.formats.importer.ImportSize
 
sizeX - Variable in class ome.model.acquisition.OTF
 
SIZEX - Static variable in class ome.model.acquisition.OTF
 
sizeX - Variable in class ome.model.core.Pixels
 
SIZEX - Static variable in class ome.model.core.Pixels
 
sizeX - Variable in class ome.model.display.Thumbnail
 
SIZEX - Static variable in class ome.model.display.Thumbnail
 
sizeX - Variable in class ome.services.formats.OmeroReader
 
sizeX - Variable in class omeis.providers.re.data.Plane2D
Number of pixels along the X-axis.
sizeY - Variable in class ome.formats.importer.ImportSize
 
sizeY - Variable in class ome.model.acquisition.OTF
 
SIZEY - Static variable in class ome.model.acquisition.OTF
 
sizeY - Variable in class ome.model.core.Pixels
 
SIZEY - Static variable in class ome.model.core.Pixels
 
sizeY - Variable in class ome.model.display.Thumbnail
 
SIZEY - Static variable in class ome.model.display.Thumbnail
 
sizeY - Variable in class ome.services.formats.OmeroReader
 
sizeY - Variable in class omeis.providers.re.data.Plane2D
Number of pixels along the Y-axis.
sizeZ - Variable in class ome.formats.importer.ImportSize
 
sizeZ - Variable in class ome.model.core.Pixels
 
SIZEZ - Static variable in class ome.model.core.Pixels
 
sizeZ - Variable in class ome.services.formats.OmeroReader
 
skip() - Method in class ome.services.graphs.GraphEntry
Deprecated.
A KEEP setting is a way of putting a KEEP suggestion to vote.
skipFrom() - Method in class ome.tools.hibernate.QueryBuilder
 
SkipHeadI - Class in omero.cmd.graphs
The skip-head request performs the wrapped request twice: once in dry run mode to discover from which model objects to start, and then actually starting from those objects.
SkipHeadI(GraphPathBean, GraphRequestFactory) - Constructor for class omero.cmd.graphs.SkipHeadI
Construct a new skip-head request; called from GraphRequestFactory.getRequest(Class).
SkipHeadPolicy - Class in omero.cmd.graphs
Adjust graph traversal policy to prevent descent into inclusions beyond certain types.
SkipHeadPolicy() - Constructor for class omero.cmd.graphs.SkipHeadPolicy
 
skipWhere() - Method in class ome.tools.hibernate.QueryBuilder
 
sleepFor(long) - Static method in class ome.services.util.SleepTimer
Sleep for the given number of milliseconds.
SleepTimer - Class in ome.services.util
Provides a timer for having a thread sleep that prematurely awakens when the server is to shut down, so the sleeping does not keep the server running.
SleepTimer() - Constructor for class ome.services.util.SleepTimer
 
slice - Variable in class omeis.providers.re.data.Plane2D
The slice we're working with
Slot - Class in ome.services.throttling
Worker which consumes from the Queue.
Slot(Queue) - Constructor for class ome.services.throttling.Slot
 
sm - Variable in class ome.services.blitz.impl.TimelineI
 
SmartEllipseI - Class in omero.model
 
SmartEllipseI() - Constructor for class omero.model.SmartEllipseI
 
SmartLineI - Class in omero.model
 
SmartLineI() - Constructor for class omero.model.SmartLineI
 
SmartMaskI - Class in omero.model
 
SmartMaskI() - Constructor for class omero.model.SmartMaskI
 
SmartPathI - Class in omero.model
 
SmartPathI() - Constructor for class omero.model.SmartPathI
 
SmartPointI - Class in omero.model
 
SmartPointI() - Constructor for class omero.model.SmartPointI
 
SmartPolygonI - Class in omero.model
 
SmartPolygonI() - Constructor for class omero.model.SmartPolygonI
 
SmartPolylineI - Class in omero.model
 
SmartPolylineI() - Constructor for class omero.model.SmartPolylineI
 
SmartRectI - Class in omero.model
 
SmartRectI() - Constructor for class omero.model.SmartRectI
 
SmartShape - Interface in omero.model
Orthogonal interface hierarchy of types for working with the Shape hierarchy.
SmartShape.PointCallback - Interface in omero.model
Callback interface passed every point which is within the area of this shape.
SmartShape.Util - Class in omero.model
Utility class used as a mixin by all of the SmartShape implementations.
SmartShape.Util() - Constructor for class omero.model.SmartShape.Util
 
SmartTextI - Class in omero.model
THIS CLASS IS CURRENTLY BROKEN.
SmartTextI() - Constructor for class omero.model.SmartTextI
 
SmtpAuthenticator - Class in ome.security
 
SmtpAuthenticator(String, String) - Constructor for class ome.security.SmtpAuthenticator
 
Snapshot - Interface in ome.system.metrics
Thin wrapper around Snapshot
SomeMustNone - Class in ome.services.search
FullText subclass which parses 3 arrays of strings into into a single Lucene query.
SomeMustNone(SearchValues, String[], String[], String[], Class<? extends Analyzer>) - Constructor for class ome.services.search.SomeMustNone
 
SortDatasetsByName - Class in ome.formats
 
SortDatasetsByName() - Constructor for class ome.formats.SortDatasetsByName
 
sortOriginalFileIds(Session, Collection<Long>) - Static method in class ome.services.graphs.ModelObjectSequencer
Sort a list of original file IDs such that files precede containing directories.
SortProjectsByName - Class in ome.formats
 
SortProjectsByName() - Constructor for class ome.formats.SortProjectsByName
 
source - Variable in class ome.formats.importer.util.ErrorHandler.UNKNOWN_FORMAT
 
source - Variable in class ome.formats.importer.util.ErrorHandler.UNREADABLE_FILE
 
source - Variable in class ome.model.roi.Roi
 
SOURCE - Static variable in class ome.model.roi.Roi
 
sources - Variable in class ome.services.query.QueryFactory
sources available for lookups.
spatialDomainEnhancement - Variable in class ome.model.display.RenderingDef
 
SPATIALDOMAINENHANCEMENT - Static variable in class ome.model.display.RenderingDef
 
spec - Variable in class ome.services.graphs.GraphStep
Deprecated.
GraphSpec instance which is active for this step.
specs - Variable in class ome.services.delete.Deletion.Builder
Deprecated.
 
sql - Variable in class ome.logic.AdminImpl
 
sql - Variable in class ome.security.basic.EventHandler
 
sql - Variable in class ome.services.blitz.impl.MetadataStoreI
 
sql - Variable in class ome.services.blitz.impl.RoiI
 
sql - Variable in class ome.services.eventlogs.PersistentEventLogLoader
 
sql - Variable in class ome.services.OmeroFilePathResolver
SQL action instance for this class.
sql - Variable in class ome.services.roi.GeomTool
 
sqlAction - Variable in class ome.services.sharing.BlobShareStore
 
sqlAction - Variable in class ome.services.util.Executor.Impl
 
SqlAction - Interface in ome.util
Single wrapper for all JDBC activities.
SqlAction.DeleteLog - Class in ome.util
Record-class which matches _fs_deletelog.
SqlAction.DeleteLog() - Constructor for class ome.util.SqlAction.DeleteLog
 
SqlAction.IdRowMapper - Class in ome.util
 
SqlAction.IdRowMapper() - Constructor for class ome.util.SqlAction.IdRowMapper
 
SqlAction.Impl - Class in ome.util
Base implementation which can be used
SqlAction.Impl() - Constructor for class ome.util.SqlAction.Impl
 
SqlAction.LoggingSqlAction - Class in ome.util
 
SqlAction.LoggingSqlAction() - Constructor for class ome.util.SqlAction.LoggingSqlAction
 
SqlAction.StringRowMapper - Class in ome.util
 
SqlAction.StringRowMapper() - Constructor for class ome.util.SqlAction.StringRowMapper
 
SqlArray<T> - Class in ome.tools.hibernate
Hibernate type to store a java array using SQL ARRAY.
SqlArray(List<T>, int) - Constructor for class ome.tools.hibernate.SqlArray
 
SqlArray(List<T>, int, String) - Constructor for class ome.tools.hibernate.SqlArray
 
SqlArray.BOOLEAN - Class in ome.tools.hibernate
 
SqlArray.BOOLEAN(List<Boolean>) - Constructor for class ome.tools.hibernate.SqlArray.BOOLEAN
 
SqlArray.DATE - Class in ome.tools.hibernate
 
SqlArray.DATE(List<Date>) - Constructor for class ome.tools.hibernate.SqlArray.DATE
 
SqlArray.DOUBLE - Class in ome.tools.hibernate
 
SqlArray.DOUBLE(List<Double>) - Constructor for class ome.tools.hibernate.SqlArray.DOUBLE
 
SqlArray.FLOAT - Class in ome.tools.hibernate
 
SqlArray.FLOAT(List<Float>) - Constructor for class ome.tools.hibernate.SqlArray.FLOAT
 
SqlArray.INTEGER - Class in ome.tools.hibernate
 
SqlArray.INTEGER(List<Integer>) - Constructor for class ome.tools.hibernate.SqlArray.INTEGER
 
SqlArray.STRING - Class in ome.tools.hibernate
 
SqlArray.STRING(List<String>) - Constructor for class ome.tools.hibernate.SqlArray.STRING
 
SqlArray.STRING2 - Class in ome.tools.hibernate
 
SqlArray.STRING2(List<String[]>) - Constructor for class ome.tools.hibernate.SqlArray.STRING2
 
sqlTypes() - Method in class ome.model.units.GenericEnumType
 
sqlTypes() - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
 
srcFiles - Variable in class ome.formats.importer.ImportEvent.FILESET_UPLOAD_END
 
ss - Variable in class ome.services.blitz.impl.TimelineI
 
stack - Variable in class ome.services.graphs.GraphStep
Deprecated.
Stack of other GraphStep instances which show where this step is in the entire graph.
stackAsString(Throwable) - Static method in class ome.util.ModelMapper
 
stackTraceAsString(Throwable) - Method in class ome.services.blitz.repo.PublicRepositoryI
 
StageLabel - Class in ome.model.acquisition
These filter definitions are used by the security system to eliminate non-readable objects from queries.
StageLabel() - Constructor for class ome.model.acquisition.StageLabel
 
StageLabel(Long) - Constructor for class ome.model.acquisition.StageLabel
 
StageLabel(Long, boolean) - Constructor for class ome.model.acquisition.StageLabel
Main constructor.
StageLabel(String) - Constructor for class ome.model.acquisition.StageLabel
 
stageLabel - Variable in class ome.model.core.Image
 
STAGELABEL - Static variable in class ome.model.core.Image
 
StageLabel.Details - Class in ome.model.acquisition
 
StageLabel.Details() - Constructor for class ome.model.acquisition.StageLabel.Details
 
StageLabel.Details(Object[]) - Constructor for class ome.model.acquisition.StageLabel.Details
 
StageLabel_X - Static variable in class ome.formats.model.UnitsFactory
 
StageLabel_Y - Static variable in class ome.formats.model.UnitsFactory
 
StageLabel_Z - Static variable in class ome.formats.model.UnitsFactory
 
standalone(String[]) - Static method in class ome.services.fulltext.Main
Starts up and simply waits until told by the grid to disconnect.
start() - Method in class ome.formats.importer.cli.CommandLineImporter
 
start(TransferState) - Method in class ome.formats.importer.transfers.AbstractFileTransfer
Minimal start method which logs the file, calls TransferState.start(), and loads the RawFileStorePrx which any implementation will need.
start() - Method in class ome.formats.importer.transfers.TransferState
 
start() - Method in class ome.formats.importer.util.ProportionalTimeEstimatorImpl
 
start() - Method in interface ome.formats.importer.util.TimeEstimator
Starts the time counting.
start() - Method in class ome.services.blitz.Entry
Obtains the named OmeroContext, creating it if necessary, and then delegates to Communicator.waitForShutdown() until either it is externally shutdown, or until a signal is caught.
start() - Method in class ome.services.blitz.Router
 
start(EventContext, SqlAction, Session, String, long, Map<String, String>) - Method in class ome.services.delete.Deletion
Deprecated.
Returns the number of steps that are available.
start() - Method in class ome.services.fulltext.FullTextThread
Called by Spring on creation.
start(GraphStep.Callback) - Method in class ome.services.graphs.GraphStep
Deprecated.
 
start() - Method in class ome.services.mail.SubethaSMTP
 
start() - Method in class ome.services.pixeldata.PixelDataThread
Called by Spring on creation.
start() - Method in class ome.services.util.DBPatchCheck
 
start() - Method in class ome.services.util.ServerVersionCheck
Prints simple banner with OMERO version.
started - Variable in class ome.model.jobs.Job
 
STARTED - Static variable in class ome.model.jobs.Job
 
started - Variable in class ome.model.meta.Session
 
STARTED - Static variable in class ome.model.meta.Session
 
startIO(int) - Method in class omeis.providers.re.RenderingStats
Notifies the start of pixels data retrieval for the specified wavelength (channel).
startMalloc() - Method in class omeis.providers.re.RenderingStats
Notifies the start of the allocation of an RGB memory buffer for the rendering process.
startProcess(ServiceFactory, long) - Method in class ome.services.procs.ProcessManager.Work
 
startRendering() - Method in class omeis.providers.re.RenderingStats
Notifies the start of the trasnformation of the raw pixels data.
startTime - Variable in class ome.model.screen.PlateAcquisition
 
STARTTIME - Static variable in class ome.model.screen.PlateAcquisition
 
startTime - Variable in class ome.parameters.Filter
 
startTime(Timestamp) - Method in class ome.parameters.Parameters
 
startTime(RTime) - Method in class omero.sys.ParametersI
Sets the value of the start time parameter.
statefulExecutor - Variable in class ome.services.blitz.repo.RepositoryDaoImpl
 
StatefulServiceInterface - Interface in ome.api
OMERO API Interface with stateful semantics.
stats() - Method in interface ome.services.sessions.SessionContext
Return a SessionStats implementation for this session.
stats() - Method in class ome.services.sessions.SessionContextImpl
 
stats() - Method in class ome.services.sessions.stats.CurrentSessionStats
 
stats() - Method in class ome.services.sessions.stats.DelegatingStats
Intended to be overwritten by subclasses.
stats() - Method in class ome.services.sessions.stats.PerSessionStats
 
stats() - Method in class ome.services.sessions.stats.PerThreadStats
 
StatsFactory - Class in omeis.providers.re.metadata
Computes two types of statistics: The PixelsStats and the location stats.
StatsFactory() - Constructor for class omeis.providers.re.metadata.StatsFactory
 
statsInfo - Variable in class ome.model.core.Channel
 
STATSINFO - Static variable in class ome.model.core.Channel
 
StatsInfo - Class in ome.model.stats
These filter definitions are used by the security system to eliminate non-readable objects from queries.
StatsInfo() - Constructor for class ome.model.stats.StatsInfo
 
StatsInfo(Long) - Constructor for class ome.model.stats.StatsInfo
 
StatsInfo(Long, boolean) - Constructor for class ome.model.stats.StatsInfo
Main constructor.
StatsInfo(Double, Double) - Constructor for class ome.model.stats.StatsInfo
 
StatsInfo.Details - Class in ome.model.stats
 
StatsInfo.Details() - Constructor for class ome.model.stats.StatsInfo.Details
 
StatsInfo.Details(Object[]) - Constructor for class ome.model.stats.StatsInfo.Details
 
status - Variable in class ome.model.jobs.Job
 
STATUS - Static variable in class ome.model.jobs.Job
 
status - Variable in class ome.model.meta.Event
 
STATUS - Static variable in class ome.model.meta.Event
 
status - Variable in class ome.model.screen.Plate
 
STATUS - Static variable in class ome.model.screen.Plate
 
status - Variable in class ome.model.screen.Well
 
STATUS - Static variable in class ome.model.screen.Well
 
status() - Method in class ome.services.blitz.Entry
 
Status - Class in ome.services.blitz
Status check for OMERO.blitz.
Status(String[]) - Constructor for class ome.services.blitz.Status
 
STDIN - Static variable in class prefs
Storing the standard in as a Properties instance as early as possible to prevent lost data.
step - Variable in class ome.formats.importer.ImportEvent.IMPORT_STEP
 
step(int, int, Current) - Method in class ome.formats.importer.ImportLibrary.ImportCallback
 
step(int) - Method in class ome.services.blitz.impl.commands.SaveI
 
step(int) - Method in class ome.services.blitz.repo.ManagedImportRequestI
 
step(int) - Method in class ome.services.blitz.repo.RawAccessRequestI
 
step(int) - Method in class omero.cmd.admin.CurrentSessionsRequestI
 
step(int) - Method in class omero.cmd.admin.ResetPasswordRequestI
 
step(int) - Method in class omero.cmd.admin.UpdateSessionTimeoutRequestI
 
step(int) - Method in class omero.cmd.basic.DoAllI
 
step(int) - Method in class omero.cmd.basic.ListRequestsI
 
step(int) - Method in class omero.cmd.basic.TimingI
 
step(int, int, Current) - Method in class omero.cmd.CmdCallbackI
Called periodically by the server to signal that processing is moving forward.
step(int) - Method in class omero.cmd.fs.ManageImageBinariesI
 
step(int) - Method in class omero.cmd.fs.OriginalMetadataRequestI
 
step(int) - Method in class omero.cmd.fs.UsedFilesRequestI
 
step(int) - Method in class omero.cmd.graphs.Chgrp2I
 
step(int) - Method in class omero.cmd.graphs.ChgrpFacadeI
Deprecated.
 
step(int) - Method in class omero.cmd.graphs.ChgrpI
Deprecated.
 
step(int) - Method in class omero.cmd.graphs.Chmod2I
 
step(int) - Method in class omero.cmd.graphs.ChmodFacadeI
Deprecated.
 
step(int) - Method in class omero.cmd.graphs.ChmodI
Deprecated.
 
step(int) - Method in class omero.cmd.graphs.Chown2I
 
step(int) - Method in class omero.cmd.graphs.ChownFacadeI
Deprecated.
 
step(int) - Method in class omero.cmd.graphs.ChownI
Deprecated.
 
step(int) - Method in class omero.cmd.graphs.Delete2I
 
step(int) - Method in class omero.cmd.graphs.DeleteFacadeI
Deprecated.
 
step(int) - Method in class omero.cmd.graphs.DeleteI
Deprecated.
 
step(int) - Method in class omero.cmd.graphs.DiskUsageI
 
step(int) - Method in class omero.cmd.graphs.GraphSpecListI
Deprecated.
 
step(int) - Method in class omero.cmd.graphs.SkipHeadI
 
step(int) - Method in interface omero.cmd.IRequest
Single uncancellable action which will be performed by this IRequest.
step(int) - Method in class omero.cmd.mail.SendEmailRequestI
 
steps(SqlAction, Session, ServiceFactory) - Method in class omero.cmd.HandleI
 
stop() - Method in class ome.formats.importer.transfers.TransferState
 
stop(long) - Method in class ome.formats.importer.transfers.TransferState
 
stop() - Method in class ome.formats.importer.util.ProportionalTimeEstimatorImpl
 
stop(long) - Method in class ome.formats.importer.util.ProportionalTimeEstimatorImpl
 
stop() - Method in interface ome.formats.importer.util.TimeEstimator
Stops the time counting and updates the internal time counter.
stop(long) - Method in interface ome.formats.importer.util.TimeEstimator
Stops the time counting and updates the internal updates the internal time counter and counter of total number of transmitted bytes.
stop() - Method in class ome.services.delete.Deletion
Deprecated.
 
stop() - Method in class ome.services.fulltext.FullTextThread
Called by Spring on destruction.
stop() - Method in class ome.services.mail.SubethaSMTP
 
stop() - Method in class ome.services.pixeldata.PixelDataThread
Called by Spring on destruction.
stop() - Method in class ome.services.util.ServerVersionCheck
Prints simple banner with "Stopping OMERO"
stop() - Method in class ome.system.metrics.DefaultTimer.Context
 
stop() - Method in interface ome.system.metrics.Timer.Context
 
stop() - Method in class omeis.providers.re.RenderingStats
Notifies this object that the rendering process has finished.
stop(Current) - Method in class omero.grid.InteractiveProcessorI
Cancels the current process, nulls the value, and returns immediately if detach is false.
store() - Method in class ome.formats.importer.ImportConfig.PassValue
 
store() - Method in class ome.formats.importer.ImportConfig.Value
Stores the current value back to some medium.
store - Variable in class ome.formats.OMEROImportFixture
 
store - Variable in class ome.security.basic.BasicSecuritySystem
 
store - Variable in class ome.services.blitz.impl.MetadataStoreI
 
store - Variable in class ome.services.sharing.ShareBean
 
store(Object, Object) - Method in class omero.util.IceMapper
 
storeShareData(long, ShareData) - Method in class ome.services.sharing.ShareBean
 
STRING - Static variable in class ome.services.query.StringQuery
parameter name for the definition of the HQL string.
STRING(Connection, List<String>) - Method in interface ome.tools.hibernate.ListAsSQLArrayUserType.ArrayFactory
 
STRING2(Connection, List<String[]>) - Method in interface ome.tools.hibernate.ListAsSQLArrayUserType.ArrayFactory
 
STRING_TO_RSTRING - Static variable in class omero.util.IceMapper
 
stringFromSvnString(String) - Static method in class ome.system.Version
Parses the given String to remove the leading "$", keyword name, and colons.
stringLongToEntity(String, long) - Method in class ome.services.query.HierarchyNavigatorWrap
Convert the given type string and database ID to the model object.
StringQuery - Class in ome.services.query
simple HQL query.
StringQuery(Parameters) - Constructor for class ome.services.query.StringQuery
Default constructor, used primarily for testing.
StringQuery(SqlAction, Parameters) - Constructor for class ome.services.query.StringQuery
 
StringQuerySource - Class in ome.services.query
interprets the query id as an HQL query.
StringQuerySource() - Constructor for class ome.services.query.StringQuerySource
Default constructor, used primarily for testing.
StringQuerySource(SqlAction) - Constructor for class ome.services.query.StringQuerySource
 
stringToType(String) - Method in class ome.services.query.HierarchyNavigatorWrap
Convert the given type string to the object type.
strokeColor - Variable in class ome.model.roi.Shape
 
STROKECOLOR - Static variable in class ome.model.roi.Shape
 
strokeDashArray - Variable in class ome.model.roi.Shape
 
STROKEDASHARRAY - Static variable in class ome.model.roi.Shape
 
strokeDashOffset - Variable in class ome.model.roi.Shape
 
STROKEDASHOFFSET - Static variable in class ome.model.roi.Shape
 
strokeLineCap - Variable in class ome.model.roi.Shape
 
STROKELINECAP - Static variable in class ome.model.roi.Shape
 
strokeLineJoin - Variable in class ome.model.roi.Shape
 
STROKELINEJOIN - Static variable in class ome.model.roi.Shape
 
strokeMiterLimit - Variable in class ome.model.roi.Shape
 
STROKEMITERLIMIT - Static variable in class ome.model.roi.Shape
 
strokeWidth - Variable in class ome.model.roi.Shape
 
STROKEWIDTH - Static variable in class ome.model.roi.Shape
 
subcancel(HandleI.Cancel, DoAllI.X) - Method in class omero.cmd.basic.DoAllI
 
SubethaSMTP - Class in ome.services.mail
Simple server bean which can be started on Spring context creation and shutdown when the application is editing.
SubethaSMTP(MessageHandlerFactory) - Constructor for class ome.services.mail.SubethaSMTP
 
SubethaSMTP(MessageHandlerFactory, int) - Constructor for class ome.services.mail.SubethaSMTP
 
subhelper(Request, Status) - Method in class omero.cmd.Helper
Run IRequest.init(Helper) on a sub-command by creating a new Helper instance.
subject - Variable in class ome.services.graphs.GraphPolicy.Details
the unloaded instance
submit(Job) - Method in interface ome.api.JobHandle
Submits a Job and returns its database id.
submit(Job) - Method in class ome.services.JobBean
 
submit(Callable<T>) - Method in class ome.services.util.Executor.Impl
 
submit(Map<String, String>, Callable<T>) - Method in class ome.services.util.Executor.Impl
 
submit(Executor.Priority, Callable<T>) - Method in class ome.services.util.Executor.Impl
 
submit(Executor.Priority, Map<String, String>, Callable<T>) - Method in class ome.services.util.Executor.Impl
 
submit(Callable<T>) - Method in interface ome.services.util.Executor
Call Executor.submit(Map, Callable) with a null callContext.
submit(Map<String, String>, Callable<T>) - Method in interface ome.services.util.Executor
Simple submission method which can be used in conjunction with a call to Executor.execute(Principal, Work) to overcome the no-multiple-login rule.
submit(Executor.Priority, Callable<T>) - Method in interface ome.services.util.Executor
Simple submission method with a Executor.Priority.
submit(Executor.Priority, Map<String, String>, Callable<T>) - Method in interface ome.services.util.Executor
Like Executor.submit(Map, Callable) but provide info to which priority queue should be used.
submit_async(AMD_JobHandle_submit, Job, Current) - Method in class ome.services.blitz.impl.JobHandleI
 
submit_async(AMD_Session_submit, Request, Current) - Method in class omero.cmd.SessionI
 
submitRequest(ServiceFactoryI, Request, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
 
SUBMITTED - Static variable in interface ome.api.JobHandle
 
submitted - Variable in class ome.model.jobs.Job
 
SUBMITTED - Static variable in class ome.model.jobs.Job
 
subscribe(String, ObjectPrx, Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
subselect(QueryBuilder) - Method in class ome.tools.hibernate.QueryBuilder
Appends the string representation of the QueryBuilder argument inside of parentheses.
subtypeEquals(int, int, String) - Method in class ome.tools.hibernate.ExtendedMetadata.Locks
returns true is the indexed subtype returns the same class type as the klass argument.
subtypeName(int, int) - Method in class ome.tools.hibernate.ExtendedMetadata.Locks
retrieves the full Hibernate path for this component field.
succeeded(GraphStep) - Method in class ome.services.graphs.GraphSteps
Deprecated.
 
success(SqlAction.DeleteLog) - Method in class ome.services.messages.DeleteLogMessage
 
success - Variable in class ome.services.messages.LoginAttemptMessage
 
sudo(Current, String) - Method in class ome.services.blitz.repo.PublicRepositoryI
Provide a Current like the given one, except with the request context session UUID replaced.
suggestChecksumAlgorithm(List<ChecksumAlgorithm>, Current) - Method in class ome.services.blitz.repo.ManagedRepositoryI
 
suggestExclusion(ServiceFactoryPrx, ImportContainer) - Method in interface ome.formats.importer.exclusions.FileExclusion
Given the current session attempt to discover if the given container should be skipped, i.e.
suggestExclusion(ServiceFactoryPrx, ImportContainer) - Method in class ome.formats.importer.exclusions.FilenameExclusion
 
suggestImportPaths(FsFile, FsFile, List<FsFile>, Class<? extends FormatReader>, ChecksumAlgorithm, Current) - Method in class ome.services.blitz.repo.ManagedRepositoryI
Take a relative path that the user would like to see in his or her upload area, and provide an import location instance whose paths correspond to existing directories corresponding to the sanitized file paths.
sum(PlanePoint) - Method in class ome.util.math.geom2D.PlanePoint
Calculates the sum of this vector with the specified argument.
SUM_INTENSITY - Static variable in interface ome.api.IProjection
Sum intensity projection
superspec - Variable in class ome.services.graphs.BaseGraphSpec
Deprecated.
Path of the superspec.
SVGRasterizer - Class in ome.services
This class provides a simple and method based API for converting a SVG document fragment to a BufferedImage.
SVGRasterizer(String) - Constructor for class ome.services.SVGRasterizer
Constructs a new SVGRasterizer.
SVGRasterizer(URL) - Constructor for class ome.services.SVGRasterizer
Constructs a new SVGRasterizer.
SVGRasterizer(InputStream) - Constructor for class ome.services.SVGRasterizer
Constructs a new SVGRasterizer converter.
SVGRasterizer(Reader) - Constructor for class ome.services.SVGRasterizer
Constructs a new SVGRasterizer converter.
SVGRasterizer.Rasterizer - Class in ome.services
An image transcoder that stores the resulting image.
SVGRasterizer.Rasterizer() - Constructor for class ome.services.SVGRasterizer.Rasterizer
 
SVN_DATE_FORMAT - Static variable in class ome.system.Version
Date format used by Subversions "Date" keyword.
swapIfRequired(byte[]) - Method in class ome.io.bioformats.BfPixelsWrapper
cgb - stolen from ImportLibrary - slightly modified Examines a byte array to see if it needs to be byte swapped and modifies the byte array directly.
Sym(String) - Static method in class ome.model.units.Conversion
Static helper for creating Conversion.Sym instances.
symbol - Variable in enum ome.model.enums.UnitsElectricPotential
 
symbol - Variable in enum ome.model.enums.UnitsFrequency
 
symbol - Variable in enum ome.model.enums.UnitsLength
 
symbol - Variable in enum ome.model.enums.UnitsPower
 
symbol - Variable in enum ome.model.enums.UnitsPressure
 
symbol - Variable in enum ome.model.enums.UnitsTemperature
 
symbol - Variable in enum ome.model.enums.UnitsTime
 
SymlinkFileTransfer - Class in ome.formats.importer.transfers
Local-only file transfer mechanism which makes use of soft-linking.
SymlinkFileTransfer() - Constructor for class ome.formats.importer.transfers.SymlinkFileTransfer
 
synchronizeJobs() - Method in class ome.services.blitz.util.CheckAllJobs
 
synchronizeJobs(List<Long>) - Method in class ome.util.actions.PostgresSqlAction
 
synchronizeJobs(List<Long>) - Method in interface ome.util.SqlAction
 
synchronizeLdapUser(String) - Method in class ome.logic.LdapImpl
 
synchronizeLoginCache() - Method in interface ome.api.IAdmin
uses JMX to refresh the login cache if supported.
synchronizeLoginCache() - Method in class ome.logic.AdminImpl
 
synchronizeLoginCache_async(AMD_IAdmin_synchronizeLoginCache, Current) - Method in class ome.services.blitz.impl.AdminI
 
sys(String[]) - Static method in class prefs
Replaces the user Preferences instance with the system Preferences and continues dispatching.
SYSTEM - Static variable in class pojos.GroupData
Identifies the System group.
systemService - Variable in class ome.services.util.Executor.Impl
 
SystemTypes - Class in ome.security
Defines what IObject classes are considered "system" types.
SystemTypes() - Constructor for class ome.security.SystemTypes
 
SystemTypes(Roles) - Constructor for class ome.security.SystemTypes
 
sysTypes - Variable in class ome.security.basic.BasicACLVoter
 
sysTypes - Variable in class ome.security.basic.BasicSecuritySystem
 

T

t - Variable in exception ome.util.messages.MessageException
 
table - Variable in class ome.services.graphs.GraphStep
Deprecated.
Parsed table name used for the SQL/HQL statements.
TableIdGenerator - Class in ome.util
OMERO-specific id generation strategy.
TableIdGenerator() - Constructor for class ome.util.TableIdGenerator
 
TablesBridge - Class in ome.services.fulltext.bridges
Bridge for parsing OMERO.tables attached to container types.
TablesBridge() - Constructor for class ome.services.fulltext.bridges.TablesBridge
 
TagAnnotation - Class in ome.model.annotations
 
TagAnnotation() - Constructor for class ome.model.annotations.TagAnnotation
 
TagAnnotation(Long) - Constructor for class ome.model.annotations.TagAnnotation
 
TagAnnotation(Long, boolean) - Constructor for class ome.model.annotations.TagAnnotation
Main constructor.
TagAnnotationData - Class in pojos
A tag annotation can either be related to an image or a tag but not to both at the same time.
TagAnnotationData(String, boolean) - Constructor for class pojos.TagAnnotationData
Creates a new instance.
TagAnnotationData(String) - Constructor for class pojos.TagAnnotationData
Creates a new instance.
TagAnnotationData(String, String) - Constructor for class pojos.TagAnnotationData
Creates a new instance.
TagAnnotationData(String, String, boolean) - Constructor for class pojos.TagAnnotationData
Creates a new instance.
TagAnnotationData(TagAnnotation) - Constructor for class pojos.TagAnnotationData
Creates a new instance.
TagAnnotationData(TagAnnotation, List<CommentAnnotation>) - Constructor for class pojos.TagAnnotationData
Creates a new instance.
TagsAndGroups - Class in ome.services.search
Query template used by SearchBean to store user requests.
TagsAndGroups(SearchValues, String, boolean) - Constructor for class ome.services.search.TagsAndGroups
 
take() - Method in class ome.services.throttling.Queue
 
takeover() - Method in class ome.services.blitz.repo.AbstractRepositoryI
Method called in a background thread which may end up waiting indefinitely on the repository lock file ("${omero.data.dir}/.omero/repository/${omero.db.uuid}/repo_uuid").
target - Variable in class ome.formats.importer.ImportEvent.PROGRESS_EVENT
 
target2model - Variable in class omero.util.IceMapper
 
targetClass - Variable in class ome.formats.importer.ImportConfig
 
targetId - Variable in class ome.formats.importer.ImportConfig
 
targetId - Variable in class omero.cmd.graphs.Preprocessor.GraphModifyTarget
Deprecated.
 
TargetProcessor - Class in ome.formats.model
Processes the IObjectContainerStore and populates references for the linkage target object of choice.
TargetProcessor() - Constructor for class ome.formats.model.TargetProcessor
 
targetType - Variable in class omero.cmd.graphs.Preprocessor.GraphModifyTarget
Deprecated.
 
targetTypeHierarchy - Static variable in class omero.cmd.graphs.Preprocessor
Deprecated.
the target type hierarchy, an ordered list descending from higher to lower
Task - Class in ome.services.throttling
Simple base task which contains logic for routing calls reflectively to ice_response and ice_exception of any AMD callback.
Task(Object, Current, boolean) - Constructor for class ome.services.throttling.Task
 
tearDown() - Method in class ome.formats.importer.ImportFixture
sets ImportLibrary, OMEROMetadataStoreClient, and file array to null.
tearDown() - Method in class ome.formats.importer.util.TinyImportFixture
 
tearDown() - Method in class ome.formats.OMEROImportFixture
sets ImportLibrary, OMEROMetadataStore, and file array to null.
temperature - Variable in class ome.model.acquisition.ImagingEnvironment
 
TEMPERATURE - Static variable in class ome.model.acquisition.ImagingEnvironment
 
Temperature - Class in ome.model.units
class storing both a Temperature and a unit for that Temperature (e.g. m, in, ly, etc.) encapsulated in a UnitsTemperature instance.
Temperature() - Constructor for class ome.model.units.Temperature
Deprecated.
Temperature(double, String) - Constructor for class ome.model.units.Temperature
 
Temperature(double, UnitsTemperature) - Constructor for class ome.model.units.Temperature
 
Temperature(double, Unit<Temperature>) - Constructor for class ome.model.units.Temperature
 
Temperature(Temperature) - Constructor for class ome.model.units.Temperature
 
TemperatureI - Class in omero.model
Blitz wrapper around the Temperature class.
TemperatureI() - Constructor for class omero.model.TemperatureI
 
TemperatureI(double, UnitsTemperature) - Constructor for class omero.model.TemperatureI
 
TemperatureI(double, Unit<Temperature>) - Constructor for class omero.model.TemperatureI
 
TemperatureI(Temperature, Unit<Temperature>) - Constructor for class omero.model.TemperatureI
Copy constructor that converts the given Temperature based on the given ome-xml enum
TemperatureI(double, UnitsTemperature) - Constructor for class omero.model.TemperatureI
Copy constructor that converts the given Temperature based on the given ome.model enum
TemperatureI(Temperature, String) - Constructor for class omero.model.TemperatureI
Copy constructor that converts the given Temperature based on the given enum string.
TemperatureI(Temperature, UnitsTemperature) - Constructor for class omero.model.TemperatureI
Copy constructor that converts between units if possible.
TemperatureI(Temperature) - Constructor for class omero.model.TemperatureI
Convert a Bio-Formats Length to an OMERO Length.
TempFileManager - Class in omero.util
Creates temporary files and folders and makes a best effort to remove them on exit (or sooner).
TempFileManager() - Constructor for class omero.util.TempFileManager
Default constructor, passes "omero" to TempFileManager.TempFileManager(String)
TempFileManager(String) - Constructor for class omero.util.TempFileManager
Initializes a TempFileManager instance with a userDir containing the given prefix value.
templateMessage - Variable in class ome.logic.AdminImpl
 
templatePrefix - Variable in class ome.model.fs.Fileset
 
TEMPLATEPREFIX - Static variable in class ome.model.fs.Fileset
 
templateRoot - Variable in class ome.services.blitz.repo.ManagedRepositoryI
 
TemporaryRepositoryI - Class in ome.services.blitz.repo
Simple repository service to make the ${java.io.tmpdir} available at runtime.
TemporaryRepositoryI(ObjectAdapter, Registry, Executor, Principal, PublicRepositoryI) - Constructor for class ome.services.blitz.repo.TemporaryRepositoryI
 
TermAnnotation - Class in ome.model.annotations
 
TermAnnotation() - Constructor for class ome.model.annotations.TermAnnotation
 
TermAnnotation(Long) - Constructor for class ome.model.annotations.TermAnnotation
 
TermAnnotation(Long, boolean) - Constructor for class ome.model.annotations.TermAnnotation
Main constructor.
TermAnnotationData - Class in pojos
Defines a Term Annotation.
TermAnnotationData(String) - Constructor for class pojos.TermAnnotationData
Creates a new instance.
TermAnnotationData(TermAnnotation) - Constructor for class pojos.TermAnnotationData
Creates a new instance.
termValue - Variable in class ome.model.annotations.TermAnnotation
 
TERMVALUE - Static variable in class ome.model.annotations.TermAnnotation
 
test(String[]) - Static method in class prefs
Simple test framework, callable from the command line via "java prefs test"
TEXT - Static variable in class pojos.FileAnnotationData
Identifies the Text file formats.
TextAnnotation - Class in ome.model.annotations
 
TextAnnotation() - Constructor for class ome.model.annotations.TextAnnotation
 
TextAnnotation(Long) - Constructor for class ome.model.annotations.TextAnnotation
 
TextAnnotation(Long, boolean) - Constructor for class ome.model.annotations.TextAnnotation
Main constructor.
TextData - Class in pojos
Represents a Text in the Euclidean space R2.
TextData(Shape) - Constructor for class pojos.TextData
Creates a new instance of Text data from an existing shape.
TextData() - Constructor for class pojos.TextData
Creates a new instance of TextData, creating a new TextI Object.
TextData(String, double, double) - Constructor for class pojos.TextData
Creates a new instance of the TextData, sets the centre and major, minor axes.
TextualAnnotationData - Class in pojos
Basic textual annotation used to add comments to a given object.
TextualAnnotationData() - Constructor for class pojos.TextualAnnotationData
Creates a new instance.
TextualAnnotationData(String) - Constructor for class pojos.TextualAnnotationData
Creates a new instance.
TextualAnnotationData(CommentAnnotation) - Constructor for class pojos.TextualAnnotationData
Creates a new instance.
textValue - Variable in class ome.model.annotations.TextAnnotation
 
TEXTVALUE - Static variable in class ome.model.annotations.TextAnnotation
 
textValue - Variable in class ome.model.roi.Ellipse
 
TEXTVALUE - Static variable in class ome.model.roi.Ellipse
 
textValue - Variable in class ome.model.roi.Label
 
TEXTVALUE - Static variable in class ome.model.roi.Label
 
textValue - Variable in class ome.model.roi.Line
 
TEXTVALUE - Static variable in class ome.model.roi.Line
 
textValue - Variable in class ome.model.roi.Mask
 
TEXTVALUE - Static variable in class ome.model.roi.Mask
 
textValue - Variable in class ome.model.roi.Path
 
TEXTVALUE - Static variable in class ome.model.roi.Path
 
textValue - Variable in class ome.model.roi.Point
 
TEXTVALUE - Static variable in class ome.model.roi.Point
 
textValue - Variable in class ome.model.roi.Polygon
 
TEXTVALUE - Static variable in class ome.model.roi.Polygon
 
textValue - Variable in class ome.model.roi.Polyline
 
TEXTVALUE - Static variable in class ome.model.roi.Polyline
 
textValue - Variable in class ome.model.roi.Rect
 
TEXTVALUE - Static variable in class ome.model.roi.Rect
 
theC - Variable in class ome.model.core.PlaneInfo
 
THEC - Static variable in class ome.model.core.PlaneInfo
 
theC - Variable in class ome.model.roi.Shape
 
THEC - Static variable in class ome.model.roi.Shape
 
theT - Variable in class ome.model.core.PlaneInfo
 
THET - Static variable in class ome.model.core.PlaneInfo
 
theT - Variable in class ome.model.roi.Shape
 
THET - Static variable in class ome.model.roi.Shape
 
theZ - Variable in class ome.model.core.PlaneInfo
 
THEZ - Static variable in class ome.model.core.PlaneInfo
 
theZ - Variable in class ome.model.roi.Shape
 
THEZ - Static variable in class ome.model.roi.Shape
 
ThreadPool - Class in ome.services.scheduler
Produces a ThreadPool(int, int, long) - Constructor for class ome.services.scheduler.ThreadPool
 
threadSafe - Variable in class ome.util.messages.InternalMessage
 
ThrottlingStrategy - Interface in ome.services.throttling
Strategy interface for controlling the execution of blitz methods.
throwable - Variable in class ome.services.eventlogs.EventLogFailure
 
throwCreationViolation(IObject) - Method in interface ome.security.ACLVoter
throws a SecurityViolation based on the given IObject and the context of the current user.
throwCreationViolation(IObject) - Method in class ome.security.basic.BasicACLVoter
 
throwCreationViolation(IObject) - Method in class ome.security.CompositeACLVoter
 
throwCreationViolation(IObject) - Method in class ome.security.sharing.SharingACLVoter
 
throwDeleteViolation(IObject) - Method in interface ome.security.ACLVoter
throws a SecurityViolation based on the given IObject and the context of the current user.
throwDeleteViolation(IObject) - Method in class ome.security.basic.BasicACLVoter
 
throwDeleteViolation(IObject) - Method in class ome.security.CompositeACLVoter
 
throwDeleteViolation(IObject) - Method in class ome.security.sharing.SharingACLVoter
 
throwDisabled(String) - Method in class ome.security.sharing.SharingACLVoter
 
throwIfAlreadySet(Object, Object) - Method in class ome.services.util.BeanHelper
 
throwIfCancelled() - Method in class ome.services.sessions.events.ChangeSecurityContextEvent
 
throwIfInitialized(Object) - Method in class ome.services.blitz.util.BlitzConfiguration
If this configuration is finished and BlitzConfiguration.communicator is not-null, throw a IllegalStateException
throwLoadViolation(IObject) - Method in interface ome.security.ACLVoter
throws a SecurityViolation based on the given IObject and the context of the current user.
throwLoadViolation(IObject) - Method in class ome.security.basic.BasicACLVoter
 
throwLoadViolation(IObject) - Method in class ome.security.CompositeACLVoter
 
throwLoadViolation(IObject) - Method in class ome.security.sharing.SharingACLVoter
 
throwMissingPyramidException(String, Pixels) - Method in interface ome.io.nio.BackOff
 
throwMissingPyramidException(String, Pixels) - Method in class ome.io.nio.SimpleBackOff
 
throwNullCollectionException(String) - Method in class ome.model.acquisition.Arc
 
throwNullCollectionException(String) - Method in class ome.model.acquisition.Detector
 
throwNullCollectionException(String) - Method in class ome.model.acquisition.DetectorSettings
 
throwNullCollectionException(String) - Method in class ome.model.acquisition.Dichroic
 
throwNullCollectionException(String) - Method in class ome.model.acquisition.Filament
 
throwNullCollectionException(String) - Method in class ome.model.acquisition.Filter
 
throwNullCollectionException(String) - Method in class ome.model.acquisition.FilterSet
 
throwNullCollectionException(String) - Method in class ome.model.acquisition.FilterSetEmissionFilterLink
 
throwNullCollectionException(String) - Method in class ome.model.acquisition.FilterSetExcitationFilterLink
 
throwNullCollectionException(String) - Method in class ome.model.acquisition.GenericExcitationSource
 
throwNullCollectionException(String) - Method in class ome.model.acquisition.ImagingEnvironment
 
throwNullCollectionException(String) - Method in class ome.model.acquisition.Instrument
 
throwNullCollectionException(String) - Method in class ome.model.acquisition.Laser
 
throwNullCollectionException(String) - Method in class ome.model.acquisition.LightEmittingDiode
 
throwNullCollectionException(String) - Method in class ome.model.acquisition.LightPath
 
throwNullCollectionException(String) - Method in class ome.model.acquisition.LightPathEmissionFilterLink
 
throwNullCollectionException(String) - Method in class ome.model.acquisition.LightPathExcitationFilterLink
 
throwNullCollectionException(String) - Method in class ome.model.acquisition.LightSettings
 
throwNullCollectionException(String) - Method in class ome.model.acquisition.LightSource
 
throwNullCollectionException(String) - Method in class ome.model.acquisition.Microscope
 
throwNullCollectionException(String) - Method in class ome.model.acquisition.Objective
 
throwNullCollectionException(String) - Method in class ome.model.acquisition.ObjectiveSettings
 
throwNullCollectionException(String) - Method in class ome.model.acquisition.OTF
 
throwNullCollectionException(String) - Method in class ome.model.acquisition.StageLabel
 
throwNullCollectionException(String) - Method in class ome.model.acquisition.TransmittanceRange
 
throwNullCollectionException(String) - Method in class ome.model.annotations.Annotation
 
throwNullCollectionException(String) - Method in class ome.model.annotations.AnnotationAnnotationLink
 
throwNullCollectionException(String) - Method in class ome.model.annotations.BasicAnnotation
 
throwNullCollectionException(String) - Method in class ome.model.annotations.BooleanAnnotation
 
throwNullCollectionException(String) - Method in class ome.model.annotations.ChannelAnnotationLink
 
throwNullCollectionException(String) - Method in class ome.model.annotations.CommentAnnotation
 
throwNullCollectionException(String) - Method in class ome.model.annotations.DatasetAnnotationLink
 
throwNullCollectionException(String) - Method in class ome.model.annotations.DetectorAnnotationLink
 
throwNullCollectionException(String) - Method in class ome.model.annotations.DichroicAnnotationLink
 
throwNullCollectionException(String) - Method in class ome.model.annotations.DoubleAnnotation
 
throwNullCollectionException(String) - Method in class ome.model.annotations.ExperimenterAnnotationLink
 
throwNullCollectionException(String) - Method in class ome.model.annotations.ExperimenterGroupAnnotationLink
 
throwNullCollectionException(String) - Method in class ome.model.annotations.FileAnnotation
 
throwNullCollectionException(String) - Method in class ome.model.annotations.FilesetAnnotationLink
 
throwNullCollectionException(String) - Method in class ome.model.annotations.FilterAnnotationLink
 
throwNullCollectionException(String) - Method in class ome.model.annotations.ImageAnnotationLink
 
throwNullCollectionException(String) - Method in class ome.model.annotations.InstrumentAnnotationLink
 
throwNullCollectionException(String) - Method in class ome.model.annotations.LightPathAnnotationLink
 
throwNullCollectionException(String) - Method in class ome.model.annotations.LightSourceAnnotationLink
 
throwNullCollectionException(String) - Method in class ome.model.annotations.ListAnnotation
 
throwNullCollectionException(String) - Method in class ome.model.annotations.LongAnnotation
 
throwNullCollectionException(String) - Method in class ome.model.annotations.MapAnnotation
 
throwNullCollectionException(String) - Method in class ome.model.annotations.NamespaceAnnotationLink
 
throwNullCollectionException(String) - Method in class ome.model.annotations.NodeAnnotationLink
 
throwNullCollectionException(String) - Method in class ome.model.annotations.NumericAnnotation
 
throwNullCollectionException(String) - Method in class ome.model.annotations.ObjectiveAnnotationLink
 
throwNullCollectionException(String) - Method in class ome.model.annotations.OriginalFileAnnotationLink
 
throwNullCollectionException(String) - Method in class ome.model.annotations.PlaneInfoAnnotationLink
 
throwNullCollectionException(String) - Method in class ome.model.annotations.PlateAcquisitionAnnotationLink
 
throwNullCollectionException(String) - Method in class ome.model.annotations.PlateAnnotationLink
 
throwNullCollectionException(String) - Method in class ome.model.annotations.ProjectAnnotationLink
 
throwNullCollectionException(String) - Method in class ome.model.annotations.ReagentAnnotationLink
 
throwNullCollectionException(String) - Method in class ome.model.annotations.RoiAnnotationLink
 
throwNullCollectionException(String) - Method in class ome.model.annotations.ScreenAnnotationLink
 
throwNullCollectionException(String) - Method in class ome.model.annotations.SessionAnnotationLink
 
throwNullCollectionException(String) - Method in class ome.model.annotations.ShapeAnnotationLink
 
throwNullCollectionException(String) - Method in class ome.model.annotations.TagAnnotation
 
throwNullCollectionException(String) - Method in class ome.model.annotations.TermAnnotation
 
throwNullCollectionException(String) - Method in class ome.model.annotations.TextAnnotation
 
throwNullCollectionException(String) - Method in class ome.model.annotations.TimestampAnnotation
 
throwNullCollectionException(String) - Method in class ome.model.annotations.TypeAnnotation
 
throwNullCollectionException(String) - Method in class ome.model.annotations.WellAnnotationLink
 
throwNullCollectionException(String) - Method in class ome.model.annotations.XmlAnnotation
 
throwNullCollectionException(String) - Method in class ome.model.containers.Dataset
 
throwNullCollectionException(String) - Method in class ome.model.containers.DatasetImageLink
 
throwNullCollectionException(String) - Method in class ome.model.containers.Project
 
throwNullCollectionException(String) - Method in class ome.model.containers.ProjectDatasetLink
 
throwNullCollectionException(String) - Method in class ome.model.core.Channel
 
throwNullCollectionException(String) - Method in class ome.model.core.Image
 
throwNullCollectionException(String) - Method in class ome.model.core.LogicalChannel
 
throwNullCollectionException(String) - Method in class ome.model.core.OriginalFile
 
throwNullCollectionException(String) - Method in class ome.model.core.Pixels
 
throwNullCollectionException(String) - Method in class ome.model.core.PixelsOriginalFileMap
 
throwNullCollectionException(String) - Method in class ome.model.core.PlaneInfo
 
throwNullCollectionException(String) - Method in class ome.model.display.ChannelBinding
 
throwNullCollectionException(String) - Method in class ome.model.display.CodomainMapContext
 
throwNullCollectionException(String) - Method in class ome.model.display.ContrastStretchingContext
 
throwNullCollectionException(String) - Method in class ome.model.display.PlaneSlicingContext
 
throwNullCollectionException(String) - Method in class ome.model.display.QuantumDef
 
throwNullCollectionException(String) - Method in class ome.model.display.RenderingDef
 
throwNullCollectionException(String) - Method in class ome.model.display.ReverseIntensityContext
 
throwNullCollectionException(String) - Method in class ome.model.display.Thumbnail
 
throwNullCollectionException(String) - Method in class ome.model.enums.AcquisitionMode
 
throwNullCollectionException(String) - Method in class ome.model.enums.ArcType
 
throwNullCollectionException(String) - Method in class ome.model.enums.Binning
 
throwNullCollectionException(String) - Method in class ome.model.enums.ChecksumAlgorithm
 
throwNullCollectionException(String) - Method in class ome.model.enums.ContrastMethod
 
throwNullCollectionException(String) - Method in class ome.model.enums.Correction
 
throwNullCollectionException(String) - Method in class ome.model.enums.DetectorType
 
throwNullCollectionException(String) - Method in class ome.model.enums.DimensionOrder
 
throwNullCollectionException(String) - Method in class ome.model.enums.EventType
 
throwNullCollectionException(String) - Method in class ome.model.enums.ExperimentType
 
throwNullCollectionException(String) - Method in class ome.model.enums.Family
 
throwNullCollectionException(String) - Method in class ome.model.enums.FilamentType
 
throwNullCollectionException(String) - Method in class ome.model.enums.FilterType
 
throwNullCollectionException(String) - Method in class ome.model.enums.Format
 
throwNullCollectionException(String) - Method in class ome.model.enums.Illumination
 
throwNullCollectionException(String) - Method in class ome.model.enums.Immersion
 
throwNullCollectionException(String) - Method in class ome.model.enums.LaserMedium
 
throwNullCollectionException(String) - Method in class ome.model.enums.LaserType
 
throwNullCollectionException(String) - Method in class ome.model.enums.Medium
 
throwNullCollectionException(String) - Method in class ome.model.enums.MicrobeamManipulationType
 
throwNullCollectionException(String) - Method in class ome.model.enums.MicroscopeType
 
throwNullCollectionException(String) - Method in class ome.model.enums.PhotometricInterpretation
 
throwNullCollectionException(String) - Method in class ome.model.enums.PixelsType
 
throwNullCollectionException(String) - Method in class ome.model.enums.Pulse
 
throwNullCollectionException(String) - Method in class ome.model.enums.RenderingModel
 
throwNullCollectionException(String) - Method in class ome.model.experiment.Experiment
 
throwNullCollectionException(String) - Method in class ome.model.experiment.MicrobeamManipulation
 
throwNullCollectionException(String) - Method in class ome.model.fs.Fileset
 
throwNullCollectionException(String) - Method in class ome.model.fs.FilesetEntry
 
throwNullCollectionException(String) - Method in class ome.model.fs.FilesetJobLink
 
throwNullCollectionException(String) - Method in class ome.model.internal.Link
 
throwNullCollectionException(String) - Method in class ome.model.jobs.ImportJob
 
throwNullCollectionException(String) - Method in class ome.model.jobs.IndexingJob
 
throwNullCollectionException(String) - Method in class ome.model.jobs.IntegrityCheckJob
 
throwNullCollectionException(String) - Method in class ome.model.jobs.Job
 
throwNullCollectionException(String) - Method in class ome.model.jobs.JobOriginalFileLink
 
throwNullCollectionException(String) - Method in class ome.model.jobs.JobStatus
 
throwNullCollectionException(String) - Method in class ome.model.jobs.MetadataImportJob
 
throwNullCollectionException(String) - Method in class ome.model.jobs.ParseJob
 
throwNullCollectionException(String) - Method in class ome.model.jobs.PixelDataJob
 
throwNullCollectionException(String) - Method in class ome.model.jobs.ScriptJob
 
throwNullCollectionException(String) - Method in class ome.model.jobs.ThumbnailGenerationJob
 
throwNullCollectionException(String) - Method in class ome.model.jobs.UploadJob
 
throwNullCollectionException(String) - Method in class ome.model.meta.DBPatch
 
throwNullCollectionException(String) - Method in class ome.model.meta.Event
 
throwNullCollectionException(String) - Method in class ome.model.meta.EventLog
 
throwNullCollectionException(String) - Method in class ome.model.meta.Experimenter
 
throwNullCollectionException(String) - Method in class ome.model.meta.ExperimenterGroup
 
throwNullCollectionException(String) - Method in class ome.model.meta.ExternalInfo
 
throwNullCollectionException(String) - Method in class ome.model.meta.GroupExperimenterMap
 
throwNullCollectionException(String) - Method in class ome.model.meta.Namespace
 
throwNullCollectionException(String) - Method in class ome.model.meta.Node
 
throwNullCollectionException(String) - Method in class ome.model.meta.Session
 
throwNullCollectionException(String) - Method in class ome.model.meta.Share
 
throwNullCollectionException(String) - Method in class ome.model.meta.ShareMember
 
throwNullCollectionException(String) - Method in class ome.model.roi.Ellipse
 
throwNullCollectionException(String) - Method in class ome.model.roi.Label
 
throwNullCollectionException(String) - Method in class ome.model.roi.Line
 
throwNullCollectionException(String) - Method in class ome.model.roi.Mask
 
throwNullCollectionException(String) - Method in class ome.model.roi.Path
 
throwNullCollectionException(String) - Method in class ome.model.roi.Point
 
throwNullCollectionException(String) - Method in class ome.model.roi.Polygon
 
throwNullCollectionException(String) - Method in class ome.model.roi.Polyline
 
throwNullCollectionException(String) - Method in class ome.model.roi.Rect
 
throwNullCollectionException(String) - Method in class ome.model.roi.Roi
 
throwNullCollectionException(String) - Method in class ome.model.roi.Shape
 
throwNullCollectionException(String) - Method in class ome.model.screen.Plate
 
throwNullCollectionException(String) - Method in class ome.model.screen.PlateAcquisition
 
throwNullCollectionException(String) - Method in class ome.model.screen.Reagent
 
throwNullCollectionException(String) - Method in class ome.model.screen.Screen
 
throwNullCollectionException(String) - Method in class ome.model.screen.ScreenPlateLink
 
throwNullCollectionException(String) - Method in class ome.model.screen.Well
 
throwNullCollectionException(String) - Method in class ome.model.screen.WellReagentLink
 
throwNullCollectionException(String) - Method in class ome.model.screen.WellSample
 
throwNullCollectionException(String) - Method in class ome.model.stats.StatsInfo
 
throwOnNullData(long, ShareData) - Method in class ome.services.sharing.ShareBean
 
throwUpdateViolation(IObject) - Method in interface ome.security.ACLVoter
throws a SecurityViolation based on the given IObject and the context of the current user.
throwUpdateViolation(IObject) - Method in class ome.security.basic.BasicACLVoter
 
throwUpdateViolation(IObject) - Method in class ome.security.CompositeACLVoter
 
throwUpdateViolation(IObject) - Method in class ome.security.sharing.SharingACLVoter
 
Thumbnail - Class in ome.model.display
These filter definitions are used by the security system to eliminate non-readable objects from queries.
Thumbnail() - Constructor for class ome.model.display.Thumbnail
 
Thumbnail(Long) - Constructor for class ome.model.display.Thumbnail
 
Thumbnail(Long, boolean) - Constructor for class ome.model.display.Thumbnail
Main constructor.
Thumbnail(Pixels, String, Integer, Integer) - Constructor for class ome.model.display.Thumbnail
 
Thumbnail.Details - Class in ome.model.display
 
Thumbnail.Details() - Constructor for class ome.model.display.Thumbnail.Details
 
Thumbnail.Details(Object[]) - Constructor for class ome.model.display.Thumbnail.Details
 
ThumbnailBean - Class in ome.services
Provides methods for directly querying object graphs.
ThumbnailBean() - Constructor for class ome.services.ThumbnailBean
default constructor
ThumbnailBean(boolean) - Constructor for class ome.services.ThumbnailBean
overridden to allow Spring to set boolean
ThumbnailCtx - Class in ome.services
 
ThumbnailCtx(IQuery, IUpdate, IPixels, IRenderingSettings, ThumbnailService, SecuritySystem, long) - Constructor for class ome.services.ThumbnailCtx
Default constructor.
ThumbnailCtx.NoThumbnail - Exception in ome.services
Marker exception which is thrown by all methods which wish to tell their callers that for whatever reason the desired Thumbnail is not available, in which case the caller can use a *Direct method instead.
ThumbnailCtx.NoThumbnail(String) - Constructor for exception ome.services.ThumbnailCtx.NoThumbnail
 
thumbnailExists(Integer, Integer) - Method in interface ome.api.ThumbnailStore
Checks if a thumbnail of a particular size exists for a pixels set.
thumbnailExists(Integer, Integer) - Method in class ome.services.ThumbnailBean
 
thumbnailExists_async(AMD_ThumbnailStore_thumbnailExists, RInt, RInt, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
 
ThumbnailFileDeletions - Class in ome.services.delete.files
Helper class which sorts through a number of file-based deletions before processing them.
ThumbnailFileDeletions(AbstractFileSystemService, Set<Long>) - Constructor for class ome.services.delete.files.ThumbnailFileDeletions
 
ThumbnailGenerationJob - Class in ome.model.jobs
 
ThumbnailGenerationJob() - Constructor for class ome.model.jobs.ThumbnailGenerationJob
 
ThumbnailGenerationJob(Long) - Constructor for class ome.model.jobs.ThumbnailGenerationJob
 
ThumbnailGenerationJob(Long, boolean) - Constructor for class ome.model.jobs.ThumbnailGenerationJob
Main constructor.
thumbnails - Variable in class ome.model.core.Pixels
 
THUMBNAILS - Static variable in class ome.model.core.Pixels
 
THUMBNAILS_PATH - Static variable in class ome.io.nio.AbstractFileSystemService
 
ThumbnailService - Class in ome.io.nio
 
ThumbnailService(String) - Constructor for class ome.io.nio.ThumbnailService
Constructor
ThumbnailStore - Interface in ome.api
Provides methods for dealing with thumbnails.
ThumbnailStoreI - Class in ome.services.blitz.impl
Implementation of the ThumbnailStore service.
ThumbnailStoreI(ThumbnailStore, BlitzExecutor) - Constructor for class ome.services.blitz.impl.ThumbnailStoreI
 
tie() - Method in class ome.services.blitz.repo.ManagedRepositoryI
 
tie() - Method in class ome.services.blitz.repo.PublicRepositoryI
Wrap the current instance with an TieBase so that it can be turned into a proxy.
TieAware - Interface in omero.util
Servant which is aware of the TieBase-instance which it belongs to and will have it injected on instantiation.
TileData - Interface in omero.util
Access strategy which can be implemented by diverse resources
TileLoop - Class in omero.util
 
TileLoop() - Constructor for class omero.util.TileLoop
 
TileLoopIteration - Interface in ome.io.nio
A single iteration of a tile for each loop.
TileLoopIteration - Interface in omero.util
A single iteration of a tile for each loop.
TileSizes - Interface in ome.io.nio
Strategy interface which is used by PixelsService to specify the default tile sizes as well as when tiling is necessary.
time - Variable in class ome.model.meta.Event
 
TIME - Static variable in class ome.model.meta.Event
 
Time - Class in ome.model.units
class storing both a Time and a unit for that Time (e.g. m, in, ly, etc.) encapsulated in a UnitsTime instance.
Time() - Constructor for class ome.model.units.Time
Deprecated.
Time(double, String) - Constructor for class ome.model.units.Time
 
Time(double, UnitsTime) - Constructor for class ome.model.units.Time
 
Time(double, Unit<Time>) - Constructor for class ome.model.units.Time
 
Time(Time) - Constructor for class ome.model.units.Time
 
time() - Method in class ome.system.metrics.DefaultTimer
 
time() - Method in interface ome.system.metrics.Timer
 
TimeAnnotationData - Class in pojos
Basic time annotation.
TimeAnnotationData() - Constructor for class pojos.TimeAnnotationData
Creates a default instance.
TimeAnnotationData(TimestampAnnotation) - Constructor for class pojos.TimeAnnotationData
Creates a new instance.
TimeEstimator - Interface in ome.formats.importer.util
Estimates the time left (ETA) during image resource upload to the server.
TimeI - Class in omero.model
Blitz wrapper around the Time class.
TimeI() - Constructor for class omero.model.TimeI
 
TimeI(double, UnitsTime) - Constructor for class omero.model.TimeI
 
TimeI(double, Unit<Time>) - Constructor for class omero.model.TimeI
 
TimeI(Time, Unit<Time>) - Constructor for class omero.model.TimeI
Copy constructor that converts the given Time based on the given ome-xml enum
TimeI(double, UnitsTime) - Constructor for class omero.model.TimeI
Copy constructor that converts the given Time based on the given ome.model enum
TimeI(Time, String) - Constructor for class omero.model.TimeI
Copy constructor that converts the given Time based on the given enum string.
TimeI(Time, UnitsTime) - Constructor for class omero.model.TimeI
Copy constructor that converts between units if possible.
TimeI(Time) - Constructor for class omero.model.TimeI
Convert a Bio-Formats Length to an OMERO Length.
timeIncrement - Variable in class ome.model.core.Pixels
 
TIMEINCREMENT - Static variable in class ome.model.core.Pixels
 
timeLeft - Variable in class ome.formats.importer.ImportEvent.FILE_UPLOAD_BYTES
 
TimelineI - Class in ome.services.blitz.impl
implementation of the ITimeline service interface.
TimelineI(BlitzExecutor) - Constructor for class ome.services.blitz.impl.TimelineI
 
timeOfEvent(Event) - Method in class pojos.DataObject
 
timepoint - Variable in class ome.model.screen.WellSample
 
TIMEPOINT - Static variable in class ome.model.screen.WellSample
 
timer(Object, String) - Method in class ome.system.metrics.DefaultMetrics
 
timer(Object, String) - Method in interface ome.system.metrics.Metrics
 
timer(Object, String) - Method in class ome.system.metrics.NullMetrics
 
Timer - Interface in ome.system.metrics
Thin wrapper around Timer
Timer.Context - Interface in ome.system.metrics
 
TimestampAnnotation - Class in ome.model.annotations
 
TimestampAnnotation() - Constructor for class ome.model.annotations.TimestampAnnotation
 
TimestampAnnotation(Long) - Constructor for class ome.model.annotations.TimestampAnnotation
 
TimestampAnnotation(Long, boolean) - Constructor for class ome.model.annotations.TimestampAnnotation
Main constructor.
timeToIdle - Variable in class ome.model.meta.Session
 
TIMETOIDLE - Static variable in class ome.model.meta.Session
 
timeToIdle - Variable in class ome.services.sessions.SessionManager.CreationRequest
 
timeToLive - Variable in class ome.model.meta.Session
 
TIMETOLIVE - Static variable in class ome.model.meta.Session
 
timeToLive - Variable in class ome.services.sessions.SessionManager.CreationRequest
 
timeValue - Variable in class ome.model.annotations.TimestampAnnotation
 
TIMEVALUE - Static variable in class ome.model.annotations.TimestampAnnotation
 
TimingI - Class in omero.cmd.basic
Diagnostic tool for testing call overhead.
TimingI() - Constructor for class omero.cmd.basic.TimingI
 
TinyImportFixture - Class in ome.formats.importer.util
test fixture which uses a hard-coded file ("tinyTest.d3d.dv") from the classpath, and adds them to a new UUID-named dataset.
TinyImportFixture(ServiceFactory) - Constructor for class ome.formats.importer.util.TinyImportFixture
 
tmpdir() - Method in class omero.util.TempFileManager
Returns a platform-specific user-writable temporary directory.
to - Variable in class ome.services.blitz.util.ConvertToBlitzExceptionMessage
 
TO - Static variable in class ome.services.mail.MapAnnotationSubethaListener
 
todbvalue(Object) - Method in enum ome.model.units.UNITS
Map from the CODE-based enums which are used in Java, Ice, etc.
toFile(File) - Method in class ome.services.blitz.repo.path.FsFile
Convert this instance to a File relative to the given File.
toJavaType(RInt) - Method in class ome.services.blitz.impl.MetadataStoreI
Transforms an OMERO RType into the corresponding Java type.
toJavaType(RLong) - Method in class ome.services.blitz.impl.MetadataStoreI
Transforms an OMERO RType into the corresponding Java type.
toJavaType(RBool) - Method in class ome.services.blitz.impl.MetadataStoreI
Transforms an OMERO RType into the corresponding Java type.
toJavaType(RFloat) - Method in class ome.services.blitz.impl.MetadataStoreI
Transforms an OMERO RType into the corresponding Java type.
toJavaType(RDouble) - Method in class ome.services.blitz.impl.MetadataStoreI
Transforms an OMERO RType into the corresponding Java type.
toJavaType(RString) - Method in class ome.services.blitz.impl.MetadataStoreI
Transforms an OMERO RType into the corresponding Java type.
Token - Class in ome.model.internal
authorization token to allow/revoke certain privileges.
Token() - Constructor for class ome.model.internal.Token
 
token - Variable in class omero.cmd.SessionI
Token in the form of a UUID for securing method invocations.
tokenHolder - Variable in class ome.security.basic.BasicACLVoter
 
tokenHolder - Variable in class ome.security.basic.BasicSecuritySystem
 
TokenHolder - Class in ome.security.basic
Manages a special token (a unique object) which can be inserted into IObject instances for special almost-administrative handling.
TokenHolder() - Constructor for class ome.security.basic.TokenHolder
 
tokenMatches(Token) - Method in class ome.model.internal.GraphHolder
check the Token for the IObject represented by this GraphHolder.
tokenStream(String, Reader) - Method in class ome.services.fulltext.FullTextAnalyzer
Returns a LowercaseAlphaNumericTokenizer
toLog() - Method in class ome.formats.importer.ImportCandidates.SCANNING
 
toLog() - Method in class ome.formats.importer.ImportEvent.FILE_UPLOAD_BYTES
 
toLog() - Method in class ome.formats.importer.ImportEvent.IMPORT_DONE
 
toLog() - Method in class ome.formats.importer.ImportEvent.IMPORT_STARTED
 
toLog() - Method in class ome.formats.importer.ImportEvent.IMPORT_STEP
 
toLog() - Method in class ome.formats.importer.ImportEvent.LOADED_IMAGE
 
toLog() - Method in class ome.formats.importer.ImportEvent.LOADING_IMAGE
 
toLog() - Method in class ome.formats.importer.ImportEvent.POST_UPLOAD_EVENT
 
toLog() - Method in class ome.formats.importer.ImportEvent.PROGRESS_EVENT
 
toLog() - Method in class ome.formats.importer.ImportEvent
 
toLog() - Method in class ome.formats.importer.util.ErrorHandler.FILE_EXCEPTION
 
toLog() - Method in class ome.formats.importer.util.ErrorHandler.INTERNAL_EXCEPTION
 
toLog() - Method in class ome.formats.importer.util.ErrorHandler.UNKNOWN_FORMAT
 
toLog() - Method in class ome.formats.importer.util.ErrorHandler.UNREADABLE_FILE
 
toNumber(double) - Static method in class pojos.ShapeData
Returns a double array as a number attribute value.
toPermissions(Object) - Static method in class ome.util.Utils
Returns a Permissions instance from its internal representation.
topicManager - Variable in class ome.services.blitz.fire.SessionManagerI
 
TopicManager - Interface in ome.services.blitz.fire
Local dispatcher to TopicManager
TopicManager.Impl - Class in ome.services.blitz.fire
 
TopicManager.Impl(Communicator) - Constructor for class ome.services.blitz.fire.TopicManager.Impl
 
TopicManager.TopicMessage - Class in ome.services.blitz.fire
 
TopicManager.TopicMessage(Object, String, ObjectPrxHelperBase, String, Object...) - Constructor for class ome.services.blitz.fire.TopicManager.TopicMessage
 
topicOrNull(String) - Method in class ome.services.blitz.fire.TopicManager.Impl
 
toPoints(Point2D.Double[]) - Static method in class pojos.ShapeData
Returns a Point2D.Double array as a Points attribute value. as specified in http://www.w3.org/TR/SVGMobile12/shapes.html#PointsBNF
toRType(Integer) - Method in class ome.formats.OMEROMetadataStoreClient
Transforms a Java type into the corresponding OMERO RType.
toRType(NonNegativeInteger) - Method in class ome.formats.OMEROMetadataStoreClient
Transforms a Java type into the corresponding OMERO RType.
toRType(NonNegativeLong) - Method in class ome.formats.OMEROMetadataStoreClient
Transforms a Java type into the corresponding OMERO RType.
toRType(PositiveFloat) - Method in class ome.formats.OMEROMetadataStoreClient
Transforms a Java type into the corresponding OMERO RType.
toRType(PercentFraction) - Method in class ome.formats.OMEROMetadataStoreClient
Transforms a Java type into the corresponding OMERO RType.
toRType(Long) - Method in class ome.formats.OMEROMetadataStoreClient
Transforms a Java type into the corresponding OMERO RType.
toRType(String) - Method in class ome.formats.OMEROMetadataStoreClient
Transforms a Java type into the corresponding OMERO RType.
toRType(Boolean) - Method in class ome.formats.OMEROMetadataStoreClient
Transforms a Java type into the corresponding OMERO RType.
toRType(Double) - Method in class ome.formats.OMEROMetadataStoreClient
Transforms a Java type into the corresponding OMERO RType.
toRType(Float) - Method in class ome.formats.OMEROMetadataStoreClient
Transforms a Java type into the corresponding OMERO RType.
toRType(Timestamp) - Method in class ome.formats.OMEROMetadataStoreClient
Transforms a Java type into the corresponding OMERO RType.
toRType(NamingConvention) - Method in class ome.formats.OMEROMetadataStoreClient
Transforms a Java type into the corresponding OMERO RType.
toRType(AffineTransform) - Method in class ome.formats.OMEROMetadataStoreClient
Transforms a Java type into the corresponding OMERO RType.
toRType(Color) - Method in class ome.formats.OMEROMetadataStoreClient
Transforms a Java type into the corresponding OMERO RType.
toRType(Object) - Method in class omero.util.IceMapper
 
toString() - Method in exception ome.formats.enums.EnumerationException
 
toString() - Method in class ome.formats.importer.ImportConfig.Value
 
toString() - Method in enum ome.formats.Index
 
toString() - Method in exception ome.formats.model.ModelException
 
toString() - Method in class ome.io.nio.AbstractBuffer
 
toString() - Method in class ome.io.nio.ConfiguredTileSizes
 
toString() - Method in class ome.io.nio.SimpleBackOff
 
toString() - Method in class ome.model.acquisition.Arc
 
toString() - Method in class ome.model.acquisition.Detector
 
toString() - Method in class ome.model.acquisition.DetectorSettings
 
toString() - Method in class ome.model.acquisition.Dichroic
 
toString() - Method in class ome.model.acquisition.Filament
 
toString() - Method in class ome.model.acquisition.Filter
 
toString() - Method in class ome.model.acquisition.FilterSet
 
toString() - Method in class ome.model.acquisition.FilterSetEmissionFilterLink
 
toString() - Method in class ome.model.acquisition.FilterSetExcitationFilterLink
 
toString() - Method in class ome.model.acquisition.GenericExcitationSource
 
toString() - Method in class ome.model.acquisition.ImagingEnvironment
 
toString() - Method in class ome.model.acquisition.Instrument
 
toString() - Method in class ome.model.acquisition.Laser
 
toString() - Method in class ome.model.acquisition.LightEmittingDiode
 
toString() - Method in class ome.model.acquisition.LightPath
 
toString() - Method in class ome.model.acquisition.LightPathEmissionFilterLink
 
toString() - Method in class ome.model.acquisition.LightPathExcitationFilterLink
 
toString() - Method in class ome.model.acquisition.LightSettings
 
toString() - Method in class ome.model.acquisition.LightSource
 
toString() - Method in class ome.model.acquisition.Microscope
 
toString() - Method in class ome.model.acquisition.Objective
 
toString() - Method in class ome.model.acquisition.ObjectiveSettings
 
toString() - Method in class ome.model.acquisition.OTF
 
toString() - Method in class ome.model.acquisition.StageLabel
 
toString() - Method in class ome.model.acquisition.TransmittanceRange
 
toString() - Method in class ome.model.annotations.Annotation
 
toString() - Method in class ome.model.annotations.AnnotationAnnotationLink
 
toString() - Method in class ome.model.annotations.BasicAnnotation
 
toString() - Method in class ome.model.annotations.BooleanAnnotation
 
toString() - Method in class ome.model.annotations.ChannelAnnotationLink
 
toString() - Method in class ome.model.annotations.CommentAnnotation
 
toString() - Method in class ome.model.annotations.DatasetAnnotationLink
 
toString() - Method in class ome.model.annotations.DetectorAnnotationLink
 
toString() - Method in class ome.model.annotations.DichroicAnnotationLink
 
toString() - Method in class ome.model.annotations.DoubleAnnotation
 
toString() - Method in class ome.model.annotations.ExperimenterAnnotationLink
 
toString() - Method in class ome.model.annotations.ExperimenterGroupAnnotationLink
 
toString() - Method in class ome.model.annotations.FileAnnotation
 
toString() - Method in class ome.model.annotations.FilesetAnnotationLink
 
toString() - Method in class ome.model.annotations.FilterAnnotationLink
 
toString() - Method in class ome.model.annotations.ImageAnnotationLink
 
toString() - Method in class ome.model.annotations.InstrumentAnnotationLink
 
toString() - Method in class ome.model.annotations.LightPathAnnotationLink
 
toString() - Method in class ome.model.annotations.LightSourceAnnotationLink
 
toString() - Method in class ome.model.annotations.ListAnnotation
 
toString() - Method in class ome.model.annotations.LongAnnotation
 
toString() - Method in class ome.model.annotations.MapAnnotation
 
toString() - Method in class ome.model.annotations.NamespaceAnnotationLink
 
toString() - Method in class ome.model.annotations.NodeAnnotationLink
 
toString() - Method in class ome.model.annotations.NumericAnnotation
 
toString() - Method in class ome.model.annotations.ObjectiveAnnotationLink
 
toString() - Method in class ome.model.annotations.OriginalFileAnnotationLink
 
toString() - Method in class ome.model.annotations.PlaneInfoAnnotationLink
 
toString() - Method in class ome.model.annotations.PlateAcquisitionAnnotationLink
 
toString() - Method in class ome.model.annotations.PlateAnnotationLink
 
toString() - Method in class ome.model.annotations.ProjectAnnotationLink
 
toString() - Method in class ome.model.annotations.ReagentAnnotationLink
 
toString() - Method in class ome.model.annotations.RoiAnnotationLink
 
toString() - Method in class ome.model.annotations.ScreenAnnotationLink
 
toString() - Method in class ome.model.annotations.SessionAnnotationLink
 
toString() - Method in class ome.model.annotations.ShapeAnnotationLink
 
toString() - Method in class ome.model.annotations.TagAnnotation
 
toString() - Method in class ome.model.annotations.TermAnnotation
 
toString() - Method in class ome.model.annotations.TextAnnotation
 
toString() - Method in class ome.model.annotations.TimestampAnnotation
 
toString() - Method in class ome.model.annotations.TypeAnnotation
 
toString() - Method in class ome.model.annotations.WellAnnotationLink
 
toString() - Method in class ome.model.annotations.XmlAnnotation
 
toString() - Method in class ome.model.containers.Dataset
 
toString() - Method in class ome.model.containers.DatasetImageLink
 
toString() - Method in class ome.model.containers.Project
 
toString() - Method in class ome.model.containers.ProjectDatasetLink
 
toString() - Method in class ome.model.core.Channel
 
toString() - Method in class ome.model.core.Image
 
toString() - Method in class ome.model.core.LogicalChannel
 
toString() - Method in class ome.model.core.OriginalFile
 
toString() - Method in class ome.model.core.Pixels
 
toString() - Method in class ome.model.core.PixelsOriginalFileMap
 
toString() - Method in class ome.model.core.PlaneInfo
 
toString() - Method in class ome.model.display.ChannelBinding
 
toString() - Method in class ome.model.display.CodomainMapContext
 
toString() - Method in class ome.model.display.ContrastStretchingContext
 
toString() - Method in class ome.model.display.PlaneSlicingContext
 
toString() - Method in class ome.model.display.QuantumDef
 
toString() - Method in class ome.model.display.RenderingDef
 
toString() - Method in class ome.model.display.ReverseIntensityContext
 
toString() - Method in class ome.model.display.Thumbnail
 
toString() - Method in class ome.model.enums.AcquisitionMode
 
toString() - Method in class ome.model.enums.ArcType
 
toString() - Method in class ome.model.enums.Binning
 
toString() - Method in class ome.model.enums.ChecksumAlgorithm
 
toString() - Method in class ome.model.enums.ContrastMethod
 
toString() - Method in class ome.model.enums.Correction
 
toString() - Method in class ome.model.enums.DetectorType
 
toString() - Method in class ome.model.enums.DimensionOrder
 
toString() - Method in class ome.model.enums.EventType
 
toString() - Method in class ome.model.enums.ExperimentType
 
toString() - Method in class ome.model.enums.Family
 
toString() - Method in class ome.model.enums.FilamentType
 
toString() - Method in class ome.model.enums.FilterType
 
toString() - Method in class ome.model.enums.Format
 
toString() - Method in class ome.model.enums.Illumination
 
toString() - Method in class ome.model.enums.Immersion
 
toString() - Method in class ome.model.enums.LaserMedium
 
toString() - Method in class ome.model.enums.LaserType
 
toString() - Method in class ome.model.enums.Medium
 
toString() - Method in class ome.model.enums.MicrobeamManipulationType
 
toString() - Method in class ome.model.enums.MicroscopeType
 
toString() - Method in class ome.model.enums.PhotometricInterpretation
 
toString() - Method in class ome.model.enums.PixelsType
 
toString() - Method in class ome.model.enums.Pulse
 
toString() - Method in class ome.model.enums.RenderingModel
 
toString() - Method in class ome.model.experiment.Experiment
 
toString() - Method in class ome.model.experiment.MicrobeamManipulation
 
toString() - Method in class ome.model.fs.Fileset
 
toString() - Method in class ome.model.fs.FilesetEntry
 
toString() - Method in class ome.model.fs.FilesetJobLink
 
toString() - Method in class ome.model.internal.Details
simple view of the Details.
toString(StringBuilder) - Method in class ome.model.internal.Details
 
toString() - Method in class ome.model.internal.Link
 
toString() - Method in class ome.model.internal.NamedValue
 
toString() - Method in class ome.model.internal.Permissions
produces a String representation of the Permissions similar to those on a Unix filesystem.
toString() - Method in class ome.model.jobs.ImportJob
 
toString() - Method in class ome.model.jobs.IndexingJob
 
toString() - Method in class ome.model.jobs.IntegrityCheckJob
 
toString() - Method in class ome.model.jobs.Job
 
toString() - Method in class ome.model.jobs.JobOriginalFileLink
 
toString() - Method in class ome.model.jobs.JobStatus
 
toString() - Method in class ome.model.jobs.MetadataImportJob
 
toString() - Method in class ome.model.jobs.ParseJob
 
toString() - Method in class ome.model.jobs.PixelDataJob
 
toString() - Method in class ome.model.jobs.ScriptJob
 
toString() - Method in class ome.model.jobs.ThumbnailGenerationJob
 
toString() - Method in class ome.model.jobs.UploadJob
 
toString() - Method in class ome.model.meta.DBPatch
 
toString() - Method in class ome.model.meta.Event
 
toString() - Method in class ome.model.meta.EventLog
 
toString() - Method in class ome.model.meta.Experimenter
 
toString() - Method in class ome.model.meta.ExperimenterGroup
 
toString() - Method in class ome.model.meta.ExternalInfo
 
toString() - Method in class ome.model.meta.GroupExperimenterMap
 
toString() - Method in class ome.model.meta.Namespace
 
toString() - Method in class ome.model.meta.Node
 
toString() - Method in class ome.model.meta.Session
 
toString() - Method in class ome.model.meta.Share
 
toString() - Method in class ome.model.meta.ShareMember
 
toString() - Method in class ome.model.roi.Ellipse
 
toString() - Method in class ome.model.roi.Label
 
toString() - Method in class ome.model.roi.Line
 
toString() - Method in class ome.model.roi.Mask
 
toString() - Method in class ome.model.roi.Path
 
toString() - Method in class ome.model.roi.Point
 
toString() - Method in class ome.model.roi.Polygon
 
toString() - Method in class ome.model.roi.Polyline
 
toString() - Method in class ome.model.roi.Rect
 
toString() - Method in class ome.model.roi.Roi
 
toString() - Method in class ome.model.roi.Shape
 
toString() - Method in class ome.model.screen.Plate
 
toString() - Method in class ome.model.screen.PlateAcquisition
 
toString() - Method in class ome.model.screen.Reagent
 
toString() - Method in class ome.model.screen.Screen
 
toString() - Method in class ome.model.screen.ScreenPlateLink
 
toString() - Method in class ome.model.screen.Well
 
toString() - Method in class ome.model.screen.WellReagentLink
 
toString() - Method in class ome.model.screen.WellSample
 
toString() - Method in class ome.model.stats.StatsInfo
 
toString() - Method in class ome.model.units.ElectricPotential
 
toString() - Method in class ome.model.units.Frequency
 
toString() - Method in class ome.model.units.Length
 
toString() - Method in class ome.model.units.Power
 
toString() - Method in class ome.model.units.Pressure
 
toString() - Method in class ome.model.units.Temperature
 
toString() - Method in class ome.model.units.Time
 
toString() - Method in class ome.parameters.Filter
 
toString() - Method in class ome.parameters.Options
 
toString() - Method in class ome.parameters.Parameters
 
toString() - Method in class ome.parameters.QueryParameter
 
toString() - Method in class ome.security.basic.BasicEventContext
 
toString() - Method in class ome.services.blitz.repo.CheckedPath
 
toString() - Method in class ome.services.blitz.repo.path.FsFile
Provides repository path with components separated by FsFile.separatorChar.
toString() - Method in class ome.services.graphs.BaseGraphSpec
Deprecated.
 
toString() - Method in class ome.services.graphs.GraphEntry
Deprecated.
 
toString() - Method in exception ome.services.graphs.GraphException
 
toString() - Method in class ome.services.graphs.GraphPolicyRule
 
toString() - Method in class ome.services.graphs.GraphState
Deprecated.
 
toString() - Method in class ome.services.graphs.GraphTables
Deprecated.
 
toString() - Method in class ome.services.scripts.RepoFile.FsFile
 
toString() - Method in class ome.services.scripts.RepoFile
 
toString() - Method in class ome.services.throttling.Task
 
toString() - Method in class ome.system.Principal
returns only the name of the instance because that is the expected behavior of Principal implementations
toString() - Method in class ome.tools.FileSystem
Public toString implementation
toString() - Method in class ome.tools.hibernate.QueryBuilder
 
toString() - Method in class ome.tools.hibernate.SqlArray
 
toString() - Method in class ome.tools.spring.InternalServiceFactory
 
toString() - Method in class ome.util.LSID
 
toString() - Method in class ome.util.SqlAction.DeleteLog
 
toString() - Method in class omeis.providers.re.codomain.CodomainChain
Overrides the toString method.
toString() - Method in class omeis.providers.re.data.PlaneDef
Overrides generic toString method to provide a specific string representation of this object.
toString() - Method in class omeis.providers.re.data.RegionDef
Overridden to return the region as a string.
toString() - Method in class omero.cmd.graphs.Preprocessor.GraphModifyTarget
Deprecated.
 
toString() - Method in class omero.cmd.SessionI
 
toString() - Method in class omero.model.ElectricPotentialI
 
toString() - Method in class omero.model.FrequencyI
 
toString() - Method in class omero.model.LengthI
 
toString() - Method in class omero.model.PermissionsI
produces a String representation of the PermissionsI similar to those on a Unix filesystem.
toString() - Method in class omero.model.PowerI
 
toString() - Method in class omero.model.PressureI
 
toString() - Method in class omero.model.TemperatureI
 
toString() - Method in class omero.model.TimeI
 
toString() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
toString() - Method in class pojos.DataObject
Overridden to return the name of the class and the object id.
toString() - Method in class pojos.ROICoordinate
Returns the string of the coordinates.
total - Variable in class ome.formats.importer.ImportEvent.COUNT_EVENT
 
total - Variable in class ome.formats.importer.ImportEvent.PROGRESS_EVENT
 
total() - Method in class ome.tools.hibernate.ExtendedMetadata.Locks
as opposed to ExtendedMetadata.Locks.size(), the returns the actual number of fields that will need to be checked.
TOTAL_PHYSICAL_MEMORY - Static variable in class ome.services.util.JvmSettingsCheck
TotalPhysicalMemorySize value from the OperatingSystem JMX bean at startup.
TOTAL_SIZE - Static variable in class ome.services.search.FullText
 
totalErrors - Variable in class ome.formats.importer.util.ErrorHandler
 
totalFiles - Variable in class ome.formats.importer.ImportCandidates.SCANNING
 
totalSharedItems() - Method in class ome.services.sharing.BlobShareStore
 
totalSharedItems() - Method in class ome.services.sharing.ShareStore
 
totalShares() - Method in class ome.services.sharing.BlobShareStore
 
totalShares() - Method in class ome.services.sharing.ShareStore
 
transfer - Variable in class ome.formats.importer.cli.CommandLineImporter
FileTransfer mechanism to be used for uploading
transfer(TransferState) - Method in class ome.formats.importer.transfers.AbstractExecFileTransfer
"Transfer" files by soft-linking them into place.
transfer(TransferState) - Method in interface ome.formats.importer.transfers.FileTransfer
Transfers a file and returns the appropriate checksum string for the source file.
transfer(TransferState) - Method in class ome.formats.importer.transfers.UploadFileTransfer
 
TransferState - Class in ome.formats.importer.transfers
Non-thread-safe argument holder for FileTransfer implementations.
TransferState(File, int, int, ImportProcessPrx, ImportLibrary, TimeEstimator, ChecksumProvider, byte[]) - Constructor for class ome.formats.importer.transfers.TransferState
State of the current file transfer.
transform - Variable in class ome.model.roi.Shape
 
TRANSFORM - Static variable in class ome.model.roi.Shape
 
transform(Function<String, String>) - Method in class ome.services.blitz.repo.path.FsFile
Transform each path component with the given transformer.
transform(int) - Method in class omeis.providers.re.codomain.CodomainChain
Applies the transformation.
transform(int) - Method in interface omeis.providers.re.codomain.CodomainMap
Performs the transformation.
transform(int, double) - Method in class omeis.providers.re.quantum.ExponentialMap
Implemented as specified in QuantumMap.
transform(double, double) - Method in class omeis.providers.re.quantum.ExponentialMap
Implemented as specified in QuantumMap.
transform(float, double) - Method in class omeis.providers.re.quantum.ExponentialMap
Implemented as specified in QuantumMap.
transform(int, double) - Method in class omeis.providers.re.quantum.LogarithmicMap
Implemented as specified in QuantumMap.
transform(double, double) - Method in class omeis.providers.re.quantum.LogarithmicMap
Implemented as specified in QuantumMap.
transform(float, double) - Method in class omeis.providers.re.quantum.LogarithmicMap
Implemented as specified in QuantumMap.
transform(int, double) - Method in class omeis.providers.re.quantum.PolynomialMap
Implemented as specified in QuantumMap.
transform(double, double) - Method in class omeis.providers.re.quantum.PolynomialMap
Implemented as specified in QuantumMap.
transform(float, double) - Method in class omeis.providers.re.quantum.PolynomialMap
Implemented as specified in QuantumMap.
transform(int, double) - Method in interface omeis.providers.re.quantum.QuantumMap
Maps the specified value.
transform(double, double) - Method in interface omeis.providers.re.quantum.QuantumMap
Maps the specified value.
transform(float, double) - Method in interface omeis.providers.re.quantum.QuantumMap
Maps the specified value.
transform(Predicate<Request>, Preprocessor.GraphModifyTarget, Set<Preprocessor.GraphModifyTarget>, Set<Preprocessor.GraphModifyTarget>) - Method in class omero.cmd.graphs.Preprocessor
Deprecated.
Transform the list of requests.
transformationMap - Variable in class ome.services.blitz.repo.path.FilePathRestrictions
 
transformationMatrix - Variable in class ome.services.blitz.repo.path.FilePathRestrictions
 
translateException(Throwable) - Method in class ome.services.util.BeanHelper
 
transmittance - Variable in class ome.model.acquisition.TransmittanceRange
 
TRANSMITTANCE - Static variable in class ome.model.acquisition.TransmittanceRange
 
transmittanceRange - Variable in class ome.model.acquisition.Filter
 
TRANSMITTANCERANGE - Static variable in class ome.model.acquisition.Filter
 
TransmittanceRange - Class in ome.model.acquisition
These filter definitions are used by the security system to eliminate non-readable objects from queries.
TransmittanceRange() - Constructor for class ome.model.acquisition.TransmittanceRange
 
TransmittanceRange(Long) - Constructor for class ome.model.acquisition.TransmittanceRange
 
TransmittanceRange(Long, boolean) - Constructor for class ome.model.acquisition.TransmittanceRange
Main constructor.
TransmittanceRange.Details - Class in ome.model.acquisition
 
TransmittanceRange.Details() - Constructor for class ome.model.acquisition.TransmittanceRange.Details
 
TransmittanceRange.Details(Object[]) - Constructor for class ome.model.acquisition.TransmittanceRange.Details
 
TransmittanceRange_CutIn - Static variable in class ome.formats.model.UnitsFactory
 
TransmittanceRange_CutInTolerance - Static variable in class ome.formats.model.UnitsFactory
 
TransmittanceRange_CutOut - Static variable in class ome.formats.model.UnitsFactory
 
TransmittanceRange_CutOutTolerance - Static variable in class ome.formats.model.UnitsFactory
 
treeList(String, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
 
treeList(String, CheckedPath, Current) - Method in interface ome.services.blitz.repo.RepositoryDao
 
treeList(String, CheckedPath, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
 
trimPaths(FsFile, List<FsFile>, Class<? extends FormatReader>) - Method in class ome.services.blitz.repo.ManagedRepositoryI
Trim off the start of long client-side paths.
trueClass(Class<T>) - Static method in class ome.util.Utils
finds the "true" class identified by a given Class object.
trueInstance(Class<T>) - Static method in class ome.util.Utils
instantiates an object using the trueClass.
truncate(long) - Method in interface ome.api.RawFileStore
Limits the size of a file to the given length.
truncate(long) - Method in class ome.io.nio.FileBuffer
 
truncate(long) - Method in class ome.services.RawFileBean
 
truncate_async(AMD_RawFileStore_truncate, long, Current) - Method in class ome.services.blitz.impl.RawFileStoreI
 
truncateIfSmaller(long) - Method in class ome.io.nio.FileBuffer
Only truncate if the size of the file is less than the size argument.
TryAgain - Exception in ome.conditions
Background processing necessary to process the request.
TryAgain(String, long) - Constructor for exception ome.conditions.TryAgain
 
tryLock() - Static method in class ome.util.DetailsFieldBridge
 
tSize - Variable in class ome.formats.importer.ImportSize
 
tuneable - Variable in class ome.model.acquisition.Laser
 
TUNEABLE - Static variable in class ome.model.acquisition.Laser
 
txSource - Variable in class ome.security.basic.EventHandler
 
type - Variable in class ome.model.acquisition.Arc
 
TYPE - Static variable in class ome.model.acquisition.Arc
 
type - Variable in class ome.model.acquisition.Detector
 
TYPE - Static variable in class ome.model.acquisition.Detector
 
type - Variable in class ome.model.acquisition.Filament
 
TYPE - Static variable in class ome.model.acquisition.Filament
 
type - Variable in class ome.model.acquisition.Filter
 
TYPE - Static variable in class ome.model.acquisition.Filter
 
type - Variable in class ome.model.acquisition.Laser
 
TYPE - Static variable in class ome.model.acquisition.Laser
 
type - Variable in class ome.model.acquisition.Microscope
 
TYPE - Static variable in class ome.model.acquisition.Microscope
 
type - Variable in class ome.model.experiment.Experiment
 
TYPE - Static variable in class ome.model.experiment.Experiment
 
type - Variable in class ome.model.experiment.MicrobeamManipulation
 
TYPE - Static variable in class ome.model.experiment.MicrobeamManipulation
 
type - Variable in class ome.model.jobs.Job
 
TYPE - Static variable in class ome.model.jobs.Job
 
type - Variable in class ome.model.meta.Event
 
TYPE - Static variable in class ome.model.meta.Event
 
type - Variable in class ome.model.screen.Screen
 
TYPE - Static variable in class ome.model.screen.Screen
 
type - Variable in class ome.model.screen.Well
 
TYPE - Static variable in class ome.model.screen.Well
 
type - Variable in class ome.parameters.QueryParameter
 
type - Variable in class ome.services.query.QueryParameterDef
type of this parameter.
type - Variable in class ome.system.Principal
 
type() - Method in interface omero.rtypes.Conversion
Specifies the type that can be expected from the rtypes.Conversion.convert(IceMapper) method.
TypeAnnotation - Class in ome.model.annotations
 
TypeAnnotation() - Constructor for class ome.model.annotations.TypeAnnotation
 
TypeAnnotation(Long) - Constructor for class ome.model.annotations.TypeAnnotation
 
TypeAnnotation(Long, boolean) - Constructor for class ome.model.annotations.TypeAnnotation
Main constructor.
types - Variable in class ome.security.policy.BasePolicy
 
types - Variable in class ome.services.eventlogs.PersistentEventLogLoader
 
types - Variable in class ome.services.graphs.AbstractHierarchyGraphSpec
Deprecated.
Type of each sub-step.
TypesI - Class in ome.services.blitz.impl
Implementation of the ITypes service.
TypesI(ITypes, BlitzExecutor) - Constructor for class ome.services.blitz.impl.TypesI
 
TypesImpl - Class in ome.logic
implementation of the ITypes service interface.
TypesImpl() - Constructor for class ome.logic.TypesImpl
 
typeToString(T) - Method in class ome.services.query.HierarchyNavigatorWrap
Convert the given object type to the type strings expected by HierarchyNavigator.

U

UINT16 - Static variable in class omeis.providers.re.data.PlaneFactory
Identifies the UINT16 data type used to store pixel values, as per OME spec.
UINT16_TYPE - Static variable in class pojos.PixelsData
Identifies the type used to store pixel values.
UINT32 - Static variable in class omeis.providers.re.data.PlaneFactory
Identifies the UINT32 data type used to store pixel values, as per OME spec.
UINT32_TYPE - Static variable in class pojos.PixelsData
Identifies the type used to store pixel values.
UINT8 - Static variable in class omeis.providers.re.data.PlaneFactory
Identifies the UINT8 data type used to store pixel values, as per OME spec.
UINT8_TYPE - Static variable in class pojos.PixelsData
Identifies the type used to store pixel values.
umask - Variable in class ome.system.SimpleEventContext
 
Union - Class in ome.services.search
Union SearchAction which combines two other search actions into one logical unit, e.g.
Union(SearchValues, SearchAction, SearchAction) - Constructor for class ome.services.search.Union
 
unique() - Method in class ome.parameters.Filter
state that this Filter should only return a single value if possible.
unique() - Method in class ome.parameters.Parameters
 
unique() - Method in class omero.sys.ParametersI
 
unique_alias(String) - Method in class ome.tools.hibernate.QueryBuilder
Obtain a unique alias to be used in the SQL.
UNIT - Static variable in class ome.model.units.ElectricPotential
 
UNIT - Static variable in class ome.model.units.Frequency
 
UNIT - Static variable in class ome.model.units.Length
 
UNIT - Static variable in class ome.model.units.Power
 
UNIT - Static variable in class ome.model.units.Pressure
 
UNIT - Static variable in class ome.model.units.Temperature
 
UNIT - Static variable in class ome.model.units.Time
 
Unit - Interface in ome.model.units
marker interface for all of ome.model.unit types.
UnitEnum - Interface in ome.model.units
marker interface for all of ome.model.unit enums.
UNITS - Enum in ome.model.units
 
UnitsElectricPotential - Enum in ome.model.enums
 
UnitsFactory - Class in ome.formats.model
Utility class to generate and convert unit objects.
UnitsFactory() - Constructor for class ome.formats.model.UnitsFactory
 
UnitsFrequency - Enum in ome.model.enums
 
UnitsLength - Enum in ome.model.enums
 
UnitsPower - Enum in ome.model.enums
 
UnitsPressure - Enum in ome.model.enums
 
UnitsTemperature - Enum in ome.model.enums
 
UnitsTime - Enum in ome.model.enums
 
UNKNOWN - Static variable in class pojos.FileAnnotationData
Indicates that the format is not recognized.
unlink(ILink[], Parameters) - Method in interface ome.api.IContainer
Removes links between OmeroDataObjects e.g Project-Dataset, Dataset-Image Note that the objects themselves aren't deleted, only the Link objects.
unlink(ILink[], Parameters) - Method in class ome.logic.PojosImpl
Implemented as specified by the IContainer I/F
unlink_async(AMD_IContainer_unlink, List<IObject>, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI
 
unlinkAnnotation(Annotation) - Method in class ome.model.acquisition.Detector
unlinks all ome.model.annotations.Annotation instances from this instance.
unlinkAnnotation(Annotation) - Method in class ome.model.acquisition.Dichroic
unlinks all ome.model.annotations.Annotation instances from this instance.
unlinkAnnotation(Annotation) - Method in class ome.model.acquisition.Filter
unlinks all ome.model.annotations.Annotation instances from this instance.
unlinkAnnotation(Annotation) - Method in class ome.model.acquisition.Instrument
unlinks all ome.model.annotations.Annotation instances from this instance.
unlinkAnnotation(Annotation) - Method in class ome.model.acquisition.LightPath
unlinks all ome.model.annotations.Annotation instances from this instance.
unlinkAnnotation(Annotation) - Method in class ome.model.acquisition.LightSource
unlinks all ome.model.annotations.Annotation instances from this instance.
unlinkAnnotation(Annotation) - Method in class ome.model.acquisition.Objective
unlinks all ome.model.annotations.Annotation instances from this instance.
unlinkAnnotation(Annotation) - Method in class ome.model.annotations.Annotation
unlinks all ome.model.annotations.Annotation instances from this instance.
unlinkAnnotation(Annotation) - Method in class ome.model.containers.Dataset
unlinks all ome.model.annotations.Annotation instances from this instance.
unlinkAnnotation(Annotation) - Method in class ome.model.containers.Project
unlinks all ome.model.annotations.Annotation instances from this instance.
unlinkAnnotation(Annotation) - Method in class ome.model.core.Channel
unlinks all ome.model.annotations.Annotation instances from this instance.
unlinkAnnotation(Annotation) - Method in class ome.model.core.Image
unlinks all ome.model.annotations.Annotation instances from this instance.
unlinkAnnotation(Annotation) - Method in class ome.model.core.OriginalFile
unlinks all ome.model.annotations.Annotation instances from this instance.
unlinkAnnotation(Annotation) - Method in class ome.model.core.PlaneInfo
unlinks all ome.model.annotations.Annotation instances from this instance.
unlinkAnnotation(Annotation) - Method in class ome.model.fs.Fileset
unlinks all ome.model.annotations.Annotation instances from this instance.
unlinkAnnotation(Annotation) - Method in interface ome.model.IAnnotated
 
unlinkAnnotation(Annotation) - Method in class ome.model.meta.Experimenter
unlinks all ome.model.annotations.Annotation instances from this instance.
unlinkAnnotation(Annotation) - Method in class ome.model.meta.ExperimenterGroup
unlinks all ome.model.annotations.Annotation instances from this instance.
unlinkAnnotation(Annotation) - Method in class ome.model.meta.Namespace
unlinks all ome.model.annotations.Annotation instances from this instance.
unlinkAnnotation(Annotation) - Method in class ome.model.meta.Node
unlinks all ome.model.annotations.Annotation instances from this instance.
unlinkAnnotation(Annotation) - Method in class ome.model.meta.Session
unlinks all ome.model.annotations.Annotation instances from this instance.
unlinkAnnotation(Annotation) - Method in class ome.model.roi.Roi
unlinks all ome.model.annotations.Annotation instances from this instance.
unlinkAnnotation(Annotation) - Method in class ome.model.roi.Shape
unlinks all ome.model.annotations.Annotation instances from this instance.
unlinkAnnotation(Annotation) - Method in class ome.model.screen.Plate
unlinks all ome.model.annotations.Annotation instances from this instance.
unlinkAnnotation(Annotation) - Method in class ome.model.screen.PlateAcquisition
unlinks all ome.model.annotations.Annotation instances from this instance.
unlinkAnnotation(Annotation) - Method in class ome.model.screen.Reagent
unlinks all ome.model.annotations.Annotation instances from this instance.
unlinkAnnotation(Annotation) - Method in class ome.model.screen.Screen
unlinks all ome.model.annotations.Annotation instances from this instance.
unlinkAnnotation(Annotation) - Method in class ome.model.screen.Well
unlinks all ome.model.annotations.Annotation instances from this instance.
unlinkDataset(Dataset) - Method in class ome.model.containers.Project
unlinks all ome.model.containers.Dataset instances from this instance.
unlinkDataset(Dataset) - Method in class ome.model.core.Image
unlinks all ome.model.containers.Dataset instances from this instance.
unlinkEmissionFilter(FilterSet) - Method in class ome.model.acquisition.Filter
unlinks all ome.model.acquisition.FilterSet instances from this instance.
unlinkEmissionFilter(Filter) - Method in class ome.model.acquisition.FilterSet
unlinks all ome.model.acquisition.Filter instances from this instance.
unlinkEmissionFilter(Filter) - Method in class ome.model.acquisition.LightPath
unlinks all ome.model.acquisition.Filter instances from this instance.
unlinkExcitationFilter(FilterSet) - Method in class ome.model.acquisition.Filter
unlinks all ome.model.acquisition.FilterSet instances from this instance.
unlinkExcitationFilter(Filter) - Method in class ome.model.acquisition.FilterSet
unlinks all ome.model.acquisition.Filter instances from this instance.
unlinkExcitationFilter(Filter) - Method in class ome.model.acquisition.LightPath
unlinks all ome.model.acquisition.Filter instances from this instance.
unlinkExperimenter(Experimenter) - Method in class ome.model.meta.ExperimenterGroup
unlinks all ome.model.meta.Experimenter instances from this instance.
unlinkExperimenterGroup(ExperimenterGroup) - Method in class ome.model.meta.Experimenter
unlinks all ome.model.meta.ExperimenterGroup instances from this instance.
unlinkImage(Image) - Method in class ome.model.containers.Dataset
unlinks all ome.model.core.Image instances from this instance.
unlinkJob(Job) - Method in class ome.model.fs.Fileset
unlinks all ome.model.jobs.Job instances from this instance.
unlinkOriginalFile(OriginalFile) - Method in class ome.model.core.Pixels
unlinks all ome.model.core.OriginalFile instances from this instance.
unlinkOriginalFile(OriginalFile) - Method in class ome.model.jobs.Job
unlinks all ome.model.core.OriginalFile instances from this instance.
unlinkPixels(Pixels) - Method in class ome.model.core.OriginalFile
unlinks all ome.model.core.Pixels instances from this instance.
unlinkPlate(Plate) - Method in class ome.model.screen.Screen
unlinks all ome.model.screen.Plate instances from this instance.
unlinkProject(Project) - Method in class ome.model.containers.Dataset
unlinks all ome.model.containers.Project instances from this instance.
unlinkReagent(Reagent) - Method in class ome.model.screen.Well
unlinks all ome.model.screen.Reagent instances from this instance.
unlinkScreen(Screen) - Method in class ome.model.screen.Plate
unlinks all ome.model.screen.Screen instances from this instance.
unlinkTargets(boolean) - Method in class ome.services.graphs.GraphTraversal
Prepare to remove links between the targeted model objects and the remainder of the model object graph.
unlinkWell(Well) - Method in class ome.model.screen.Reagent
unlinks all ome.model.screen.Well instances from this instance.
unload() - Method in class ome.model.acquisition.Arc
 
unload() - Method in class ome.model.acquisition.Detector
 
unload() - Method in class ome.model.acquisition.DetectorSettings
 
unload() - Method in class ome.model.acquisition.Dichroic
 
unload() - Method in class ome.model.acquisition.Filament
 
unload() - Method in class ome.model.acquisition.Filter
 
unload() - Method in class ome.model.acquisition.FilterSet
 
unload() - Method in class ome.model.acquisition.FilterSetEmissionFilterLink
 
unload() - Method in class ome.model.acquisition.FilterSetExcitationFilterLink
 
unload() - Method in class ome.model.acquisition.GenericExcitationSource
 
unload() - Method in class ome.model.acquisition.ImagingEnvironment
 
unload() - Method in class ome.model.acquisition.Instrument
 
unload() - Method in class ome.model.acquisition.Laser
 
unload() - Method in class ome.model.acquisition.LightEmittingDiode
 
unload() - Method in class ome.model.acquisition.LightPath
 
unload() - Method in class ome.model.acquisition.LightPathEmissionFilterLink
 
unload() - Method in class ome.model.acquisition.LightPathExcitationFilterLink
 
unload() - Method in class ome.model.acquisition.LightSettings
 
unload() - Method in class ome.model.acquisition.LightSource
 
unload() - Method in class ome.model.acquisition.Microscope
 
unload() - Method in class ome.model.acquisition.Objective
 
unload() - Method in class ome.model.acquisition.ObjectiveSettings
 
unload() - Method in class ome.model.acquisition.OTF
 
unload() - Method in class ome.model.acquisition.StageLabel
 
unload() - Method in class ome.model.acquisition.TransmittanceRange
 
unload() - Method in class ome.model.annotations.Annotation
 
unload() - Method in class ome.model.annotations.AnnotationAnnotationLink
 
unload() - Method in class ome.model.annotations.BasicAnnotation
 
unload() - Method in class ome.model.annotations.BooleanAnnotation
 
unload() - Method in class ome.model.annotations.ChannelAnnotationLink
 
unload() - Method in class ome.model.annotations.CommentAnnotation
 
unload() - Method in class ome.model.annotations.DatasetAnnotationLink
 
unload() - Method in class ome.model.annotations.DetectorAnnotationLink
 
unload() - Method in class ome.model.annotations.DichroicAnnotationLink
 
unload() - Method in class ome.model.annotations.DoubleAnnotation
 
unload() - Method in class ome.model.annotations.ExperimenterAnnotationLink
 
unload() - Method in class ome.model.annotations.ExperimenterGroupAnnotationLink
 
unload() - Method in class ome.model.annotations.FileAnnotation
 
unload() - Method in class ome.model.annotations.FilesetAnnotationLink
 
unload() - Method in class ome.model.annotations.FilterAnnotationLink
 
unload() - Method in class ome.model.annotations.ImageAnnotationLink
 
unload() - Method in class ome.model.annotations.InstrumentAnnotationLink
 
unload() - Method in class ome.model.annotations.LightPathAnnotationLink
 
unload() - Method in class ome.model.annotations.LightSourceAnnotationLink
 
unload() - Method in class ome.model.annotations.ListAnnotation
 
unload() - Method in class ome.model.annotations.LongAnnotation
 
unload() - Method in class ome.model.annotations.MapAnnotation
 
unload() - Method in class ome.model.annotations.NamespaceAnnotationLink
 
unload() - Method in class ome.model.annotations.NodeAnnotationLink
 
unload() - Method in class ome.model.annotations.NumericAnnotation
 
unload() - Method in class ome.model.annotations.ObjectiveAnnotationLink
 
unload() - Method in class ome.model.annotations.OriginalFileAnnotationLink
 
unload() - Method in class ome.model.annotations.PlaneInfoAnnotationLink
 
unload() - Method in class ome.model.annotations.PlateAcquisitionAnnotationLink
 
unload() - Method in class ome.model.annotations.PlateAnnotationLink
 
unload() - Method in class ome.model.annotations.ProjectAnnotationLink
 
unload() - Method in class ome.model.annotations.ReagentAnnotationLink
 
unload() - Method in class ome.model.annotations.RoiAnnotationLink
 
unload() - Method in class ome.model.annotations.ScreenAnnotationLink
 
unload() - Method in class ome.model.annotations.SessionAnnotationLink
 
unload() - Method in class ome.model.annotations.ShapeAnnotationLink
 
unload() - Method in class ome.model.annotations.TagAnnotation
 
unload() - Method in class ome.model.annotations.TermAnnotation
 
unload() - Method in class ome.model.annotations.TextAnnotation
 
unload() - Method in class ome.model.annotations.TimestampAnnotation
 
unload() - Method in class ome.model.annotations.TypeAnnotation
 
unload() - Method in class ome.model.annotations.WellAnnotationLink
 
unload() - Method in class ome.model.annotations.XmlAnnotation
 
unload() - Method in class ome.model.containers.Dataset
 
unload() - Method in class ome.model.containers.DatasetImageLink
 
unload() - Method in class ome.model.containers.Project
 
unload() - Method in class ome.model.containers.ProjectDatasetLink
 
unload() - Method in class ome.model.core.Channel
 
unload() - Method in class ome.model.core.Image
 
unload() - Method in class ome.model.core.LogicalChannel
 
unload() - Method in class ome.model.core.OriginalFile
 
unload() - Method in class ome.model.core.Pixels
 
unload() - Method in class ome.model.core.PixelsOriginalFileMap
 
unload() - Method in class ome.model.core.PlaneInfo
 
unload() - Method in class ome.model.display.ChannelBinding
 
unload() - Method in class ome.model.display.CodomainMapContext
 
unload() - Method in class ome.model.display.ContrastStretchingContext
 
unload() - Method in class ome.model.display.PlaneSlicingContext
 
unload() - Method in class ome.model.display.QuantumDef
 
unload() - Method in class ome.model.display.RenderingDef
 
unload() - Method in class ome.model.display.ReverseIntensityContext
 
unload() - Method in class ome.model.display.Thumbnail
 
unload() - Method in class ome.model.enums.AcquisitionMode
 
unload() - Method in class ome.model.enums.ArcType
 
unload() - Method in class ome.model.enums.Binning
 
unload() - Method in class ome.model.enums.ChecksumAlgorithm
 
unload() - Method in class ome.model.enums.ContrastMethod
 
unload() - Method in class ome.model.enums.Correction
 
unload() - Method in class ome.model.enums.DetectorType
 
unload() - Method in class ome.model.enums.DimensionOrder
 
unload() - Method in class ome.model.enums.EventType
 
unload() - Method in class ome.model.enums.ExperimentType
 
unload() - Method in class ome.model.enums.Family
 
unload() - Method in class ome.model.enums.FilamentType
 
unload() - Method in class ome.model.enums.FilterType
 
unload() - Method in class ome.model.enums.Format
 
unload() - Method in class ome.model.enums.Illumination
 
unload() - Method in class ome.model.enums.Immersion
 
unload() - Method in class ome.model.enums.LaserMedium
 
unload() - Method in class ome.model.enums.LaserType
 
unload() - Method in class ome.model.enums.Medium
 
unload() - Method in class ome.model.enums.MicrobeamManipulationType
 
unload() - Method in class ome.model.enums.MicroscopeType
 
unload() - Method in class ome.model.enums.PhotometricInterpretation
 
unload() - Method in class ome.model.enums.PixelsType
 
unload() - Method in class ome.model.enums.Pulse
 
unload() - Method in class ome.model.enums.RenderingModel
 
unload() - Method in class ome.model.experiment.Experiment
 
unload() - Method in class ome.model.experiment.MicrobeamManipulation
 
unload() - Method in class ome.model.fs.Fileset
 
unload() - Method in class ome.model.fs.FilesetEntry
 
unload() - Method in class ome.model.fs.FilesetJobLink
 
unload() - Method in class ome.model.internal.Link
 
unload() - Method in interface ome.model.IObject
set the loaded field to false, and set all non-ID fields to null.
unload() - Method in class ome.model.jobs.ImportJob
 
unload() - Method in class ome.model.jobs.IndexingJob
 
unload() - Method in class ome.model.jobs.IntegrityCheckJob
 
unload() - Method in class ome.model.jobs.Job
 
unload() - Method in class ome.model.jobs.JobOriginalFileLink
 
unload() - Method in class ome.model.jobs.JobStatus
 
unload() - Method in class ome.model.jobs.MetadataImportJob
 
unload() - Method in class ome.model.jobs.ParseJob
 
unload() - Method in class ome.model.jobs.PixelDataJob
 
unload() - Method in class ome.model.jobs.ScriptJob
 
unload() - Method in class ome.model.jobs.ThumbnailGenerationJob
 
unload() - Method in class ome.model.jobs.UploadJob
 
unload() - Method in class ome.model.meta.DBPatch
 
unload() - Method in class ome.model.meta.Event
 
unload() - Method in class ome.model.meta.EventLog
 
unload() - Method in class ome.model.meta.Experimenter
 
unload() - Method in class ome.model.meta.ExperimenterGroup
 
unload() - Method in class ome.model.meta.ExternalInfo
 
unload() - Method in class ome.model.meta.GroupExperimenterMap
 
unload() - Method in class ome.model.meta.Namespace
 
unload() - Method in class ome.model.meta.Node
 
unload() - Method in class ome.model.meta.Session
 
unload() - Method in class ome.model.meta.Share
 
unload() - Method in class ome.model.meta.ShareMember
 
unload() - Method in class ome.model.roi.Ellipse
 
unload() - Method in class ome.model.roi.Label
 
unload() - Method in class ome.model.roi.Line
 
unload() - Method in class ome.model.roi.Mask
 
unload() - Method in class ome.model.roi.Path
 
unload() - Method in class ome.model.roi.Point
 
unload() - Method in class ome.model.roi.Polygon
 
unload() - Method in class ome.model.roi.Polyline
 
unload() - Method in class ome.model.roi.Rect
 
unload() - Method in class ome.model.roi.Roi
 
unload() - Method in class ome.model.roi.Shape
 
unload() - Method in class ome.model.screen.Plate
 
unload() - Method in class ome.model.screen.PlateAcquisition
 
unload() - Method in class ome.model.screen.Reagent
 
unload() - Method in class ome.model.screen.Screen
 
unload() - Method in class ome.model.screen.ScreenPlateLink
 
unload() - Method in class ome.model.screen.Well
 
unload() - Method in class ome.model.screen.WellReagentLink
 
unload() - Method in class ome.model.screen.WellSample
 
unload() - Method in class ome.model.stats.StatsInfo
 
unload(Current) - Method in class omero.model.DetailsI
 
unload(Current) - Method in class omero.model.PermissionsI
 
UnloadedCollectionException - Exception in omero
 
UnloadedCollectionException(String) - Constructor for exception omero.UnloadedCollectionException
 
UnloadedEntityException - Exception in omero
 
UnloadedEntityException(String) - Constructor for exception omero.UnloadedEntityException
 
unloadedObjectCache - Variable in class ome.tools.hibernate.ProxyCleanupFilter
 
unloadReplacedObjects() - Method in class ome.tools.hibernate.UpdateFilter
provides an external hook to unload all files which have already been merged.
unlock() - Static method in class ome.util.DetailsFieldBridge
 
UNMAPPED - Static variable in class omero.util.IceMapper
Specifies a return type which should not be parsed.
unmodifiableAnnotationLinks() - Method in class ome.model.acquisition.Detector
Returns an unmodifiable collection-view
unmodifiableAnnotationLinks() - Method in class ome.model.acquisition.Dichroic
Returns an unmodifiable collection-view
unmodifiableAnnotationLinks() - Method in class ome.model.acquisition.Filter
Returns an unmodifiable collection-view
unmodifiableAnnotationLinks() - Method in class ome.model.acquisition.Instrument
Returns an unmodifiable collection-view
unmodifiableAnnotationLinks() - Method in class ome.model.acquisition.LightPath
Returns an unmodifiable collection-view
unmodifiableAnnotationLinks() - Method in class ome.model.acquisition.LightSource
Returns an unmodifiable collection-view
unmodifiableAnnotationLinks() - Method in class ome.model.acquisition.Objective
Returns an unmodifiable collection-view
unmodifiableAnnotationLinks() - Method in class ome.model.annotations.Annotation
Returns an unmodifiable collection-view
unmodifiableAnnotationLinks() - Method in class ome.model.containers.Dataset
Returns an unmodifiable collection-view
unmodifiableAnnotationLinks() - Method in class ome.model.containers.Project
Returns an unmodifiable collection-view
unmodifiableAnnotationLinks() - Method in class ome.model.core.Channel
Returns an unmodifiable collection-view
unmodifiableAnnotationLinks() - Method in class ome.model.core.Image
Returns an unmodifiable collection-view
unmodifiableAnnotationLinks() - Method in class ome.model.core.OriginalFile
Returns an unmodifiable collection-view
unmodifiableAnnotationLinks() - Method in class ome.model.core.PlaneInfo
Returns an unmodifiable collection-view
unmodifiableAnnotationLinks() - Method in class ome.model.fs.Fileset
Returns an unmodifiable collection-view
unmodifiableAnnotationLinks() - Method in interface ome.model.IAnnotated
 
unmodifiableAnnotationLinks() - Method in class ome.model.meta.Experimenter
Returns an unmodifiable collection-view
unmodifiableAnnotationLinks() - Method in class ome.model.meta.ExperimenterGroup
Returns an unmodifiable collection-view
unmodifiableAnnotationLinks() - Method in class ome.model.meta.Namespace
Returns an unmodifiable collection-view
unmodifiableAnnotationLinks() - Method in class ome.model.meta.Node
Returns an unmodifiable collection-view
unmodifiableAnnotationLinks() - Method in class ome.model.meta.Session
Returns an unmodifiable collection-view
unmodifiableAnnotationLinks() - Method in class ome.model.roi.Roi
Returns an unmodifiable collection-view
unmodifiableAnnotationLinks() - Method in class ome.model.roi.Shape
Returns an unmodifiable collection-view
unmodifiableAnnotationLinks() - Method in class ome.model.screen.Plate
Returns an unmodifiable collection-view
unmodifiableAnnotationLinks() - Method in class ome.model.screen.PlateAcquisition
Returns an unmodifiable collection-view
unmodifiableAnnotationLinks() - Method in class ome.model.screen.Reagent
Returns an unmodifiable collection-view
unmodifiableAnnotationLinks() - Method in class ome.model.screen.Screen
Returns an unmodifiable collection-view
unmodifiableAnnotationLinks() - Method in class ome.model.screen.Well
Returns an unmodifiable collection-view
unmodifiableChannels() - Method in class ome.model.core.LogicalChannel
Returns an unmodifiable collection-view
unmodifiableChannels() - Method in class ome.model.core.Pixels
Returns an unmodifiable collection-view
unmodifiableDatasetLinks() - Method in class ome.model.containers.Project
Returns an unmodifiable collection-view
unmodifiableDatasetLinks() - Method in class ome.model.core.Image
Returns an unmodifiable collection-view
unmodifiableDetector() - Method in class ome.model.acquisition.Instrument
Returns an unmodifiable collection-view
unmodifiableDichroic() - Method in class ome.model.acquisition.Instrument
Returns an unmodifiable collection-view
unmodifiableEmissionFilterLink() - Method in class ome.model.acquisition.Filter
Returns an unmodifiable collection-view
unmodifiableEmissionFilterLink() - Method in class ome.model.acquisition.FilterSet
Returns an unmodifiable collection-view
unmodifiableEmissionFilterLink() - Method in class ome.model.acquisition.LightPath
Returns an unmodifiable collection-view
unmodifiableEvents() - Method in class ome.model.meta.Session
Returns an unmodifiable collection-view
unmodifiableExcitationFilterLink() - Method in class ome.model.acquisition.Filter
Returns an unmodifiable collection-view
unmodifiableExcitationFilterLink() - Method in class ome.model.acquisition.FilterSet
Returns an unmodifiable collection-view
unmodifiableExcitationFilterLink() - Method in class ome.model.acquisition.LightPath
Returns an unmodifiable collection-view
unmodifiableFilesetEntries() - Method in class ome.model.core.OriginalFile
Returns an unmodifiable collection-view
unmodifiableFilter() - Method in class ome.model.acquisition.Instrument
Returns an unmodifiable collection-view
unmodifiableFilterSet() - Method in class ome.model.acquisition.Instrument
Returns an unmodifiable collection-view
unmodifiableGroupExperimenterMap() - Method in class ome.model.meta.Experimenter
Returns an unmodifiable collection-view
unmodifiableGroupExperimenterMap() - Method in class ome.model.meta.ExperimenterGroup
Returns an unmodifiable collection-view
unmodifiableImageLinks() - Method in class ome.model.containers.Dataset
Returns an unmodifiable collection-view
unmodifiableImages() - Method in class ome.model.fs.Fileset
Returns an unmodifiable collection-view
unmodifiableJobLinks() - Method in class ome.model.fs.Fileset
Returns an unmodifiable collection-view
unmodifiableLightSource() - Method in class ome.model.acquisition.Instrument
Returns an unmodifiable collection-view
unmodifiableLightSourceSettings() - Method in class ome.model.experiment.MicrobeamManipulation
Returns an unmodifiable collection-view
unmodifiableLogs() - Method in class ome.model.meta.Event
Returns an unmodifiable collection-view
unmodifiableMicrobeamManipulation() - Method in class ome.model.experiment.Experiment
Returns an unmodifiable collection-view
unmodifiableObjective() - Method in class ome.model.acquisition.Instrument
Returns an unmodifiable collection-view
unmodifiableOriginalFileLinks() - Method in class ome.model.jobs.Job
Returns an unmodifiable collection-view
unmodifiableOtf() - Method in class ome.model.acquisition.Instrument
Returns an unmodifiable collection-view
unmodifiablePixels() - Method in class ome.model.core.Image
Returns an unmodifiable collection-view
unmodifiablePixelsFileMaps() - Method in class ome.model.core.OriginalFile
Returns an unmodifiable collection-view
unmodifiablePixelsFileMaps() - Method in class ome.model.core.Pixels
Returns an unmodifiable collection-view
unmodifiablePlaneInfo() - Method in class ome.model.core.Pixels
Returns an unmodifiable collection-view
unmodifiablePlateAcquisitions() - Method in class ome.model.screen.Plate
Returns an unmodifiable collection-view
unmodifiablePlateLinks() - Method in class ome.model.screen.Screen
Returns an unmodifiable collection-view
unmodifiableProjectLinks() - Method in class ome.model.containers.Dataset
Returns an unmodifiable collection-view
unmodifiableReagentLinks() - Method in class ome.model.screen.Well
Returns an unmodifiable collection-view
unmodifiableReagents() - Method in class ome.model.screen.Screen
Returns an unmodifiable collection-view
unmodifiableRois() - Method in class ome.model.core.Image
Returns an unmodifiable collection-view
unmodifiableScreenLinks() - Method in class ome.model.screen.Plate
Returns an unmodifiable collection-view
unmodifiableSessions() - Method in class ome.model.meta.Node
Returns an unmodifiable collection-view
unmodifiableSettings() - Method in class ome.model.core.Pixels
Returns an unmodifiable collection-view
unmodifiableShapes() - Method in class ome.model.roi.Roi
Returns an unmodifiable collection-view
unmodifiableSpatialDomainEnhancement() - Method in class ome.model.display.RenderingDef
Returns an unmodifiable collection-view
unmodifiableThumbnails() - Method in class ome.model.core.Pixels
Returns an unmodifiable collection-view
unmodifiableUsedFiles() - Method in class ome.model.fs.Fileset
Returns an unmodifiable collection-view
unmodifiableWaveRendering() - Method in class ome.model.display.RenderingDef
Returns an unmodifiable collection-view
unmodifiableWellLinks() - Method in class ome.model.screen.Reagent
Returns an unmodifiable collection-view
unmodifiableWells() - Method in class ome.model.screen.Plate
Returns an unmodifiable collection-view
unmodifiableWellSample() - Method in class ome.model.screen.PlateAcquisition
Returns an unmodifiable collection-view
unmodifiableWellSamples() - Method in class ome.model.core.Image
Returns an unmodifiable collection-view
unmodifiableWellSamples() - Method in class ome.model.screen.Well
Returns an unmodifiable collection-view
unordered() - Method in interface ome.api.Search
Removes the current stack of order statements.
unordered() - Method in class ome.services.SearchBean
 
unordered_async(AMD_Search_unordered, Current) - Method in class ome.services.blitz.impl.SearchI
 
unregister(String, ObjectPrx) - Method in class ome.services.blitz.fire.TopicManager.Impl
 
unregister(String, ObjectPrx) - Method in interface ome.services.blitz.fire.TopicManager
 
unregister(Long, SqlAction) - Method in class ome.services.scripts.ScriptRepoHelper
Unregisters a given file from the script repository by setting its Repo uuid to null.
unregisterCallback(ProcessCallbackPrx, Current) - Method in class ome.services.blitz.impl.ScriptProcessI
 
unregisterCallback(ProcessCallback) - Method in interface ome.services.procs.Process
 
unregisterCallback(ProcessCallback) - Method in class ome.services.procs.ProcessSkeleton
 
unregisterServant(Identity) - Method in class omero.cmd.SessionI
unregisterServant(Identity, ObjectAdapter, ServantHolder) - Static method in class omero.cmd.SessionI
Reverts all the additions made by #registerServant(ServantInterface, Ice.Current, Ice.Identity) Now called by SessionManagerI in response to an UnregisterServantMessage
UnregisterServantMessage - Class in ome.services.blitz.util
InternalMessage raised when a servant should be removed from the adapter.
UnregisterServantMessage(Object, Current, ServantHolder) - Constructor for class ome.services.blitz.util.UnregisterServantMessage
 
unsafeNames - Variable in class ome.services.blitz.repo.path.FilePathRestrictions
 
unsafePrefixes - Variable in class ome.services.blitz.repo.path.FilePathRestrictions
 
unsafeSuffixes - Variable in class ome.services.blitz.repo.path.FilePathRestrictions
 
unSet(Permissions.Flag) - Method in class ome.model.internal.Permissions
turn a given Permissions.Flag off.
unsetGroupOwner(ExperimenterGroup, Experimenter) - Method in interface ome.api.IAdmin
removes the user from the owner list for this group.
unsetGroupOwner(ExperimenterGroup, Experimenter) - Method in class ome.logic.AdminImpl
 
unsetGroupOwner_async(AMD_IAdmin_unsetGroupOwner, ExperimenterGroup, Experimenter, Current) - Method in class ome.services.blitz.impl.AdminI
 
unwrap(RType) - Static method in class omero.rtypes
Descends into data structures unwrapping all RType objects as it goes.
unwrap(RType, Map<RType, Object>) - Static method in class omero.rtypes
Descends into data structures wrapping all elements as it goes.
unwrapCollection(Collection<RType>, Collection<Object>, Map<RType, Object>) - Static method in class omero.rtypes
 
unwrapRawFileBean(RawFileStore) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
Loads
up - Variable in class ome.model.meta.Node
 
UP - Static variable in class ome.model.meta.Node
 
update(IObservable, ImportEvent) - Method in class ome.formats.importer.cli.LoggingImportMonitor
 
update(IObservable, ImportEvent) - Method in interface ome.formats.importer.IObserver
Update observable on event
update(IObservable, ImportEvent) - Method in class ome.formats.importer.util.ErrorHandler
 
update(RepoFile, Long, Map<String, String>) - Method in class ome.services.scripts.ScriptRepoHelper
 
update(Session) - Method in interface ome.services.sessions.SessionManager
See ISession#updateSession(Session) for the logic that's implemented here.
update(Session, boolean) - Method in interface ome.services.sessions.SessionManager
Same as SessionManager.update(Session) but some security checks can be overridden.
update(Session) - Method in class ome.services.sessions.SessionManagerImpl
 
update(Session, boolean) - Method in class ome.services.sessions.SessionManagerImpl
 
update(Share, ShareData) - Method in class ome.services.sharing.ShareStore
 
update(int) - Method in class ome.system.metrics.DefaultHistogram
 
update(int) - Method in interface ome.system.metrics.Histogram
 
update(String) - Method in class ome.tools.hibernate.QueryBuilder
 
update(CodomainMapContext) - Method in class omeis.providers.re.codomain.CodomainChain
Updates a map context in the chain.
update - Variable in class omero.cmd.admin.UpdateSessionTimeoutRequestI
 
UPDATE_EVENT - Static variable in class ome.security.basic.UpdateEventListener
 
updateCodomainMap(CodomainMapContext) - Method in class ome.services.RenderingBean
Implemented as specified by the RenderingEngine interface.
updateCodomainMap(CodomainMapContext) - Method in interface omeis.providers.re.RenderingEngine
Updates the specified context.
updateCodomainMap_async(AMD_RenderingEngine_updateCodomainMap, CodomainMapContext, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
updateCollection(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
updateConfiguration(String, String) - Method in class ome.util.actions.PostgresSqlAction
 
updateConfiguration(String, String) - Method in interface ome.util.SqlAction
 
updated - Variable in class omero.cmd.admin.UpdateSessionTimeoutRequestI
 
updateDataObject(T, Parameters) - Method in interface ome.api.IContainer
Updates a data object.
updateDataObject(IObject, Parameters) - Method in class ome.logic.PojosImpl
Implemented as specified by the IContainer I/F
updateDataObject_async(AMD_IContainer_updateDataObject, IObject, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI
 
updateDataObjects(IObject[], Parameters) - Method in interface ome.api.IContainer
convenience method to save network calls.
updateDataObjects(IObject[], Parameters) - Method in class ome.logic.PojosImpl
Implemented as specified by the IContainer I/F
updateDataObjects_async(AMD_IContainer_updateDataObjects, List<IObject>, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI
 
updatedObjects(int) - Method in class ome.services.sessions.stats.DelegatingStats
 
updatedObjects(int) - Method in class ome.services.sessions.stats.NullSessionStats
 
updatedObjects(int) - Method in interface ome.services.sessions.stats.SessionStats
 
updatedObjects(int) - Method in class ome.services.sessions.stats.SimpleSessionStats
 
updateEntity(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
updateEnumeration(T) - Method in interface ome.api.ITypes
updates enumeration value specified by object
updateEnumeration(T) - Method in class ome.logic.TypesImpl
 
updateEnumeration_async(AMD_ITypes_updateEnumeration, IObject, Current) - Method in class ome.services.blitz.impl.TypesI
 
updateEnumerations(List<T>) - Method in interface ome.api.ITypes
updates enumeration value specified by object
updateEnumerations(List<T>) - Method in class ome.logic.TypesImpl
 
updateEnumerations_async(AMD_ITypes_updateEnumerations, List<IObject>, Current) - Method in class ome.services.blitz.impl.TypesI
 
UPDATEEVENT - Static variable in class ome.model.internal.Details
 
updateEvent(UserGroupUpdateEvent) - Method in class ome.services.sessions.state.SessionCache
Marks a new update request in State#lastUpdateRequest.
UpdateEventListener - Class in ome.security.basic
responsible for setting the updat event on all events shortly before being saved.
UpdateEventListener(CurrentDetails) - Constructor for class ome.security.basic.UpdateEventListener
main constructor. controls access to individual db rows..
updateExperimenter(Experimenter) - Method in interface ome.api.IAdmin
Updates an experimenter if admin or owner of group.
updateExperimenter(Experimenter) - Method in class ome.logic.AdminImpl
 
updateExperimenter_async(AMD_IAdmin_updateExperimenter, Experimenter, Current) - Method in class ome.services.blitz.impl.AdminI
 
updateExperimenterWithPassword(Experimenter, String) - Method in interface ome.api.IAdmin
Updates an experimenter if admin or owner of group.
updateExperimenterWithPassword(Experimenter, String) - Method in class ome.logic.AdminImpl
 
updateExperimenterWithPassword_async(AMD_IAdmin_updateExperimenterWithPassword, Experimenter, RString, Current) - Method in class ome.services.blitz.impl.AdminI
 
updateField(Session, String, RLong, boolean) - Method in class omero.cmd.admin.UpdateSessionTimeoutRequestI
 
updateFileSize(OriginalFile, long) - Method in class ome.formats.OMEROMetadataStoreClient
 
UpdateFilter - Class in ome.tools.hibernate
responsible for correlating entity identities during multiple calls to merge.
UpdateFilter() - Constructor for class ome.tools.hibernate.UpdateFilter
 
updateFlexReaderServerMaps() - Method in class ome.formats.importer.util.IniFileLoader
Updates the Flex reader server maps from the configuration file.
updateGroup(ExperimenterGroup) - Method in interface ome.api.IAdmin
Updates an experimenter group if admin or owner of group.
updateGroup(ExperimenterGroup) - Method in class ome.logic.AdminImpl
 
updateGroup_async(AMD_IAdmin_updateGroup, ExperimenterGroup, Current) - Method in class ome.services.blitz.impl.AdminI
 
UpdateI - Class in ome.services.blitz.impl
Implementation of the IUpdate service.
UpdateI(IUpdate, BlitzExecutor) - Constructor for class ome.services.blitz.impl.UpdateI
 
UpdateImpl - Class in ome.logic
implementation of the IUpdate service interface
UpdateImpl() - Constructor for class ome.logic.UpdateImpl
 
updateJob(Job, String, String, Current) - Method in interface ome.services.blitz.repo.RepositoryDao
Set both the message and the status of the given job.
updateJob(Job, String, String, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
 
updateMinMax(int, byte[], int) - Method in class ome.formats.importer.OMEROWrapper
 
updateObject(String, IObject, Map<String, Integer>) - Method in class ome.formats.OMEROMetadataStore
Updates a given model object in our object graph.
updateObject(T...) - Method in interface ome.security.SecureAction
executes with special privilegs within the SecuritySystem.
updateObject(T...) - Method in class ome.tools.hibernate.SecureMerge
 
updateObjects_async(AMD_MetadataStore_updateObjects, IObjectContainer[], Current) - Method in class ome.services.blitz.impl.MetadataStoreI
 
updateOrInsertConfigValue(String, String) - Method in class ome.util.SqlAction.Impl
 
updateOrInsertConfigValue(String, String) - Method in interface ome.util.SqlAction
 
updatePixels(List<Pixels>) - Method in class ome.formats.OMEROMetadataStoreClient
Updates a list of Pixels.
updateQuantumManager() - Method in class omeis.providers.re.Renderer
Updates the QuantumManager and configures it according to the current quantum definition.
updateReadFilter(Session) - Method in class ome.security.basic.BasicSecuritySystem
 
updateReferences(Map<String, String[]>) - Method in class ome.formats.OMEROMetadataStore
Updates our object graph references.
updateReferences_async(AMD_MetadataStore_updateReferences, Map<String, String[]>, Current) - Method in class ome.services.blitz.impl.MetadataStoreI
 
updateRows(PersistentCollection, Serializable, SessionImplementor) - Method in class ome.util.CountCollectionPersister
 
updateSelf(Experimenter) - Method in interface ome.api.IAdmin
Allows a user to update his/her own information.
updateSelf(Experimenter) - Method in class ome.logic.AdminImpl
 
updateSelf_async(AMD_IAdmin_updateSelf, Experimenter, Current) - Method in class ome.services.blitz.impl.AdminI
 
updateSession(Session) - Method in class ome.services.sessions.SessionBean
 
updateSession() - Method in class omero.cmd.admin.UpdateSessionTimeoutRequestI
 
UpdateSessionTimeoutRequestI - Class in omero.cmd.admin
 
UpdateSessionTimeoutRequestI(CurrentDetails, SessionManager, SecuritySystem) - Constructor for class omero.cmd.admin.UpdateSessionTimeoutRequestI
 
UpdateSessionTimeoutRequestI.Factory - Class in omero.cmd.admin
 
UpdateSessionTimeoutRequestI.Factory(CurrentDetails, SessionManager, SecuritySystem) - Constructor for class omero.cmd.admin.UpdateSessionTimeoutRequestI.Factory
 
updateUsedFilesTotalSize() - Method in class ome.formats.importer.ImportContainer
 
UpgradeCheck - Class in ome.system
Contacts a given URL which should be an OME server which will return either an empty String or a URL which points to a needed upgrade.
UpgradeCheck(String, String, String) - Constructor for class ome.system.UpgradeCheck
UpgradeCheck(String, String, String, int) - Constructor for class ome.system.UpgradeCheck
Main constructor.
upload(File) - Method in class omero.client
 
upload(File, OriginalFile) - Method in class omero.client
 
upload(File, OriginalFile, Integer) - Method in class omero.client
Utility method to upload a file to the server
uploadBytes(long) - Method in class ome.formats.importer.transfers.TransferState
Raise the ImportEvent.FILE_UPLOAD_BYTES event to all observers.
uploadComplete(long) - Method in class ome.formats.importer.transfers.TransferState
Raise the ImportEvent.FILE_UPLOAD_COMPLETE event to all observers.
uploadedBytes - Variable in class ome.formats.importer.ImportEvent.FILE_UPLOAD_EVENT
 
uploadFile(ImportProcessPrx, String[], int, TimeEstimator) - Method in class ome.formats.importer.ImportLibrary
 
uploadFile(ImportProcessPrx, String[], int, ChecksumProviderFactory, TimeEstimator, byte[]) - Method in class ome.formats.importer.ImportLibrary
 
uploadFile(ErrorContainer) - Method in class ome.formats.importer.util.ErrorHandler
Upload a single ErrorContainer.
uploadFiles(String, int, ErrorContainer) - Method in class ome.formats.importer.util.FileUploader
Upload files from error container to url
uploadFileset(Fileset, ImportSettings, Current) - Method in class ome.services.blitz.repo.ManagedRepositoryI
Return a template based directory path.
uploadFilesToRepository(String[], ImportProcessPrx) - Method in class ome.formats.importer.ImportLibrary
Upload files to the managed repository.
UploadFileTransfer - Class in ome.formats.importer.transfers
Traditional file transfer mechanism which uploads files using the API.
UploadFileTransfer() - Constructor for class ome.formats.importer.transfers.UploadFileTransfer
 
UploadJob - Class in ome.model.jobs
 
UploadJob() - Constructor for class ome.model.jobs.UploadJob
 
UploadJob(Long) - Constructor for class ome.model.jobs.UploadJob
 
UploadJob(Long, boolean) - Constructor for class ome.model.jobs.UploadJob
Main constructor.
UploadMask - Class in pojos.util
Uploaded for masks.
UploadMask(long) - Constructor for class pojos.util.UploadMask
Creates a new instance.
uploadMask_async(AMD_IRoi_uploadMask, long, int, int, byte[], Current) - Method in class ome.services.blitz.impl.RoiI
 
uploadMyUserPhoto(String, String, byte[]) - Method in interface ome.api.IAdmin
Uploads a photo for the user which will be displayed on his/her profile.
uploadMyUserPhoto(String, String, byte[]) - Method in class ome.logic.AdminImpl
 
uploadMyUserPhoto_async(AMD_IAdmin_uploadMyUserPhoto, String, String, byte[], Current) - Method in class ome.services.blitz.impl.AdminI
 
uploadOfficialScript_async(AMD_IScript_uploadOfficialScript, String, String, Current) - Method in class ome.services.blitz.impl.ScriptI
 
UploadRmFileTransfer - Class in ome.formats.importer.transfers
Version of the default UploadFileTransfer which deletes all files in a transfer set if the upload is successful.
UploadRmFileTransfer() - Constructor for class ome.formats.importer.transfers.UploadRmFileTransfer
 
uploadScript_async(AMD_IScript_uploadScript, String, String, Current) - Method in class ome.services.blitz.impl.ScriptI
Upload script to the server.
uploadStarted() - Method in class ome.formats.importer.transfers.TransferState
Raise the ImportEvent.FILE_UPLOAD_STARTED event to all observers.
upperLimit - Variable in class ome.model.display.PlaneSlicingContext
 
UPPERLIMIT - Static variable in class ome.model.display.PlaneSlicingContext
 
usage() - Static method in class ome.formats.importer.cli.CommandLineImporter
Prints usage to STDERR and exits with return code 1.
usage() - Static method in class ome.services.fulltext.Main
 
usage(String[]) - Static method in class prefs
Returns a usage string array.
useCustomImageNaming - Variable in class ome.formats.importer.ImportConfig
 
usedFiles - Variable in class ome.formats.importer.util.ErrorHandler.FILE_EXCEPTION
 
usedFiles - Variable in class ome.formats.importer.util.ErrorHandler.INTERNAL_EXCEPTION
 
usedFiles - Variable in class ome.model.fs.Fileset
 
USEDFILES - Static variable in class ome.model.fs.Fileset
 
UsedFilesRequestI - Class in omero.cmd.fs
Lists the IDs of the original files associated with an image.
UsedFilesRequestI(PixelsService) - Constructor for class omero.cmd.fs.UsedFilesRequestI
Construct a new used files request.
useFirstAcceptable() - Method in class ome.services.blitz.repo.path.MakeNextDirectory
Use the first acceptable path (that with the lowest index for MakeNextDirectory.getPathFor(long)) and return the corresponding subdirectories.
useFullPath - Variable in class ome.formats.importer.ImportConfig
 
usePath(List<String>) - Method in class ome.services.blitz.repo.path.MakeNextDirectory
Actually use the path.
useProjections - Variable in class ome.services.search.SearchValues
 
user - Variable in class ome.services.messages.LoginAttemptMessage
 
USER - Static variable in class pojos.GroupData
Identifies the User group.
USER_IMMUTABLE - Static variable in class ome.model.internal.Permissions
R______ : user and only the user can only read
USER_PRIVATE - Static variable in class ome.model.internal.Permissions
RW____ : user and only user can read and write
USER_WRITEABLE - Static variable in class ome.model.internal.Permissions
RWR_R_ : all can read, user can write
userAgent - Variable in class ome.model.meta.Session
 
USERAGENT - Static variable in class ome.model.meta.Session
 
userGroups(String) - Method in class ome.security.auth.PasswordUtil
 
UserGroupUpdateEvent - Class in ome.services.sessions.events
InteralMessage published by the SecuritySystem when an Experimenter, ExperimenterGroup, or GroupExperimenterMap is inserted or updated.
UserGroupUpdateEvent(Object) - Constructor for class ome.services.sessions.events.UserGroupUpdateEvent
 
userId(String) - Method in class ome.security.auth.PasswordUtil
Get the user's ID
userIP - Variable in class ome.model.meta.Session
 
USERIP - Static variable in class ome.model.meta.Session
 
username - Variable in class loci.ome.io.OMECredentials
 
username - Variable in class ome.formats.importer.ImportConfig
 
username - Variable in class ome.model.jobs.Job
 
USERNAME - Static variable in class ome.model.jobs.Job
 
userName(long) - Method in class ome.security.auth.PasswordUtil
Get the user's name
username() - Method in class omero.util.TempFileManager
Returns the current OS-user's name.
usernameFilter(String) - Method in class ome.security.auth.LdapConfig
 
userPixels - Variable in class ome.formats.importer.ImportConfig
 
userProxy(String) - Method in interface ome.api.local.LocalAdmin
returns a possibly uninitialized proxy for the given user name.
userProxy(Long) - Method in interface ome.api.local.LocalAdmin
returns a possibly uninitialized proxy for the given user id.
userProxy(Long) - Method in class ome.logic.AdminImpl
 
userProxy(String) - Method in class ome.logic.AdminImpl
 
UserSignalMessage - Class in ome.util.messages
Published if the Posix USR1 or USR2 signal is received.
UserSignalMessage(Object, int) - Constructor for class ome.util.messages.UserSignalMessage
 
userSpecifiedDescription - Variable in class ome.formats.importer.ImportConfig
 
userSpecifiedName - Variable in class ome.formats.importer.ImportConfig
 
util - Variable in class ome.security.auth.ConfigurablePasswordProvider
 
Utils - Class in ome.io.nio
General utility methods for working with ROMIO classes.
Utils() - Constructor for class ome.io.nio.Utils
 
Utils - Class in ome.util
various tools needed throughout Omero.
Utils() - Constructor for class ome.util.Utils
 
uuid - Variable in class ome.model.meta.ExternalInfo
 
UUID - Static variable in class ome.model.meta.ExternalInfo
 
uuid - Variable in class ome.model.meta.Node
 
UUID - Static variable in class ome.model.meta.Node
 
uuid - Variable in class ome.model.meta.Session
 
UUID - Static variable in class ome.model.meta.Session
 
uuid - Variable in class ome.services.blitz.fire.Ring
UUID for this cluster node.
uuid() - Method in class ome.services.blitz.fire.Ring
 
uuid() - Method in interface ome.services.blitz.redirect.Redirector.Context
The UUID for the local node which will be used as the redirect lookup string for this Redirector.Context.
uuid - Variable in class ome.services.roi.GeomTool
 

V

valid(String) - Method in class ome.services.db.DatabaseIdentity
 
VALID() - Static method in class ome.util.Validation
 
valid(Pixels) - Static method in class ome.util.Validator
 
Validate - Annotation Type in ome.annotations
annotation used for determining the types of a Set
validate() - Method in class ome.model.acquisition.Arc
 
validate() - Method in class ome.model.acquisition.Detector
 
validate() - Method in class ome.model.acquisition.DetectorSettings
 
validate() - Method in class ome.model.acquisition.Dichroic
 
validate() - Method in class ome.model.acquisition.Filament
 
validate() - Method in class ome.model.acquisition.Filter
 
validate() - Method in class ome.model.acquisition.FilterSet
 
validate() - Method in class ome.model.acquisition.FilterSetEmissionFilterLink
 
validate() - Method in class ome.model.acquisition.FilterSetExcitationFilterLink
 
validate() - Method in class ome.model.acquisition.GenericExcitationSource
 
validate() - Method in class ome.model.acquisition.ImagingEnvironment
 
validate() - Method in class ome.model.acquisition.Instrument
 
validate() - Method in class ome.model.acquisition.Laser
 
validate() - Method in class ome.model.acquisition.LightEmittingDiode
 
validate() - Method in class ome.model.acquisition.LightPath
 
validate() - Method in class ome.model.acquisition.LightPathEmissionFilterLink
 
validate() - Method in class ome.model.acquisition.LightPathExcitationFilterLink
 
validate() - Method in class ome.model.acquisition.LightSettings
 
validate() - Method in class ome.model.acquisition.LightSource
 
validate() - Method in class ome.model.acquisition.Microscope
 
validate() - Method in class ome.model.acquisition.Objective
 
validate() - Method in class ome.model.acquisition.ObjectiveSettings
 
validate() - Method in class ome.model.acquisition.OTF
 
validate() - Method in class ome.model.acquisition.StageLabel
 
validate() - Method in class ome.model.acquisition.TransmittanceRange
 
validate() - Method in class ome.model.annotations.Annotation
 
validate() - Method in class ome.model.annotations.AnnotationAnnotationLink
 
validate() - Method in class ome.model.annotations.BasicAnnotation
 
validate() - Method in class ome.model.annotations.BooleanAnnotation
 
validate() - Method in class ome.model.annotations.ChannelAnnotationLink
 
validate() - Method in class ome.model.annotations.CommentAnnotation
 
validate() - Method in class ome.model.annotations.DatasetAnnotationLink
 
validate() - Method in class ome.model.annotations.DetectorAnnotationLink
 
validate() - Method in class ome.model.annotations.DichroicAnnotationLink
 
validate() - Method in class ome.model.annotations.DoubleAnnotation
 
validate() - Method in class ome.model.annotations.ExperimenterAnnotationLink
 
validate() - Method in class ome.model.annotations.ExperimenterGroupAnnotationLink
 
validate() - Method in class ome.model.annotations.FileAnnotation
 
validate() - Method in class ome.model.annotations.FilesetAnnotationLink
 
validate() - Method in class ome.model.annotations.FilterAnnotationLink
 
validate() - Method in class ome.model.annotations.ImageAnnotationLink
 
validate() - Method in class ome.model.annotations.InstrumentAnnotationLink
 
validate() - Method in class ome.model.annotations.LightPathAnnotationLink
 
validate() - Method in class ome.model.annotations.LightSourceAnnotationLink
 
validate() - Method in class ome.model.annotations.ListAnnotation
 
validate() - Method in class ome.model.annotations.LongAnnotation
 
validate() - Method in class ome.model.annotations.MapAnnotation
 
validate() - Method in class ome.model.annotations.NamespaceAnnotationLink
 
validate() - Method in class ome.model.annotations.NodeAnnotationLink
 
validate() - Method in class ome.model.annotations.NumericAnnotation
 
validate() - Method in class ome.model.annotations.ObjectiveAnnotationLink
 
validate() - Method in class ome.model.annotations.OriginalFileAnnotationLink
 
validate() - Method in class ome.model.annotations.PlaneInfoAnnotationLink
 
validate() - Method in class ome.model.annotations.PlateAcquisitionAnnotationLink
 
validate() - Method in class ome.model.annotations.PlateAnnotationLink
 
validate() - Method in class ome.model.annotations.ProjectAnnotationLink
 
validate() - Method in class ome.model.annotations.ReagentAnnotationLink
 
validate() - Method in class ome.model.annotations.RoiAnnotationLink
 
validate() - Method in class ome.model.annotations.ScreenAnnotationLink
 
validate() - Method in class ome.model.annotations.SessionAnnotationLink
 
validate() - Method in class ome.model.annotations.ShapeAnnotationLink
 
validate() - Method in class ome.model.annotations.TagAnnotation
 
validate() - Method in class ome.model.annotations.TermAnnotation
 
validate() - Method in class ome.model.annotations.TextAnnotation
 
validate() - Method in class ome.model.annotations.TimestampAnnotation
 
validate() - Method in class ome.model.annotations.TypeAnnotation
 
validate() - Method in class ome.model.annotations.WellAnnotationLink
 
validate() - Method in class ome.model.annotations.XmlAnnotation
 
validate() - Method in class ome.model.containers.Dataset
 
validate() - Method in class ome.model.containers.DatasetImageLink
 
validate() - Method in class ome.model.containers.Project
 
validate() - Method in class ome.model.containers.ProjectDatasetLink
 
validate() - Method in class ome.model.core.Channel
 
validate() - Method in class ome.model.core.Image
 
validate() - Method in class ome.model.core.LogicalChannel
 
validate() - Method in class ome.model.core.OriginalFile
 
validate() - Method in class ome.model.core.Pixels
 
validate() - Method in class ome.model.core.PixelsOriginalFileMap
 
validate() - Method in class ome.model.core.PlaneInfo
 
validate() - Method in class ome.model.display.ChannelBinding
 
validate() - Method in class ome.model.display.CodomainMapContext
 
validate() - Method in class ome.model.display.ContrastStretchingContext
 
validate() - Method in class ome.model.display.PlaneSlicingContext
 
validate() - Method in class ome.model.display.QuantumDef
 
validate() - Method in class ome.model.display.RenderingDef
 
validate() - Method in class ome.model.display.ReverseIntensityContext
 
validate() - Method in class ome.model.display.Thumbnail
 
validate() - Method in class ome.model.enums.AcquisitionMode
 
validate() - Method in class ome.model.enums.ArcType
 
validate() - Method in class ome.model.enums.Binning
 
validate() - Method in class ome.model.enums.ChecksumAlgorithm
 
validate() - Method in class ome.model.enums.ContrastMethod
 
validate() - Method in class ome.model.enums.Correction
 
validate() - Method in class ome.model.enums.DetectorType
 
validate() - Method in class ome.model.enums.DimensionOrder
 
validate() - Method in class ome.model.enums.EventType
 
validate() - Method in class ome.model.enums.ExperimentType
 
validate() - Method in class ome.model.enums.Family
 
validate() - Method in class ome.model.enums.FilamentType
 
validate() - Method in class ome.model.enums.FilterType
 
validate() - Method in class ome.model.enums.Format
 
validate() - Method in class ome.model.enums.Illumination
 
validate() - Method in class ome.model.enums.Immersion
 
validate() - Method in class ome.model.enums.LaserMedium
 
validate() - Method in class ome.model.enums.LaserType
 
validate() - Method in class ome.model.enums.Medium
 
validate() - Method in class ome.model.enums.MicrobeamManipulationType
 
validate() - Method in class ome.model.enums.MicroscopeType
 
validate() - Method in class ome.model.enums.PhotometricInterpretation
 
validate() - Method in class ome.model.enums.PixelsType
 
validate() - Method in class ome.model.enums.Pulse
 
validate() - Method in class ome.model.enums.RenderingModel
 
validate() - Method in class ome.model.experiment.Experiment
 
validate() - Method in class ome.model.experiment.MicrobeamManipulation
 
validate() - Method in class ome.model.fs.Fileset
 
validate() - Method in class ome.model.fs.FilesetEntry
 
validate() - Method in class ome.model.fs.FilesetJobLink
 
validate() - Method in class ome.model.internal.Link
 
validate() - Method in interface ome.model.IObject
calls the class-specific validator for this instance and returns the Validation object.
validate() - Method in class ome.model.jobs.ImportJob
 
validate() - Method in class ome.model.jobs.IndexingJob
 
validate() - Method in class ome.model.jobs.IntegrityCheckJob
 
validate() - Method in class ome.model.jobs.Job
 
validate() - Method in class ome.model.jobs.JobOriginalFileLink
 
validate() - Method in class ome.model.jobs.JobStatus
 
validate() - Method in class ome.model.jobs.MetadataImportJob
 
validate() - Method in class ome.model.jobs.ParseJob
 
validate() - Method in class ome.model.jobs.PixelDataJob
 
validate() - Method in class ome.model.jobs.ScriptJob
 
validate() - Method in class ome.model.jobs.ThumbnailGenerationJob
 
validate() - Method in class ome.model.jobs.UploadJob
 
validate() - Method in class ome.model.meta.DBPatch
 
validate() - Method in class ome.model.meta.Event
 
validate() - Method in class ome.model.meta.EventLog
 
validate() - Method in class ome.model.meta.Experimenter
 
validate() - Method in class ome.model.meta.ExperimenterGroup
 
validate() - Method in class ome.model.meta.ExternalInfo
 
validate() - Method in class ome.model.meta.GroupExperimenterMap
 
validate() - Method in class ome.model.meta.Namespace
 
validate() - Method in class ome.model.meta.Node
 
validate() - Method in class ome.model.meta.Session
 
validate() - Method in class ome.model.meta.Share
 
validate() - Method in class ome.model.meta.ShareMember
 
validate() - Method in class ome.model.roi.Ellipse
 
validate() - Method in class ome.model.roi.Label
 
validate() - Method in class ome.model.roi.Line
 
validate() - Method in class ome.model.roi.Mask
 
validate() - Method in class ome.model.roi.Path
 
validate() - Method in class ome.model.roi.Point
 
validate() - Method in class ome.model.roi.Polygon
 
validate() - Method in class ome.model.roi.Polyline
 
validate() - Method in class ome.model.roi.Rect
 
validate() - Method in class ome.model.roi.Roi
 
validate() - Method in class ome.model.roi.Shape
 
validate() - Method in class ome.model.screen.Plate
 
validate() - Method in class ome.model.screen.PlateAcquisition
 
validate() - Method in class ome.model.screen.Reagent
 
validate() - Method in class ome.model.screen.Screen
 
validate() - Method in class ome.model.screen.ScreenPlateLink
 
validate() - Method in class ome.model.screen.Well
 
validate() - Method in class ome.model.screen.WellReagentLink
 
validate() - Method in class ome.model.screen.WellSample
 
validate() - Method in class ome.model.stats.StatsInfo
 
validate(GraphState, Session, SqlAction, GraphOpts) - Method in class ome.services.chgrp.ChgrpStep
Deprecated.
 
validate(Session, GraphOpts) - Method in class ome.services.chown.ChownStep
Deprecated.
 
validate(int) - Method in class ome.services.graphs.GraphState
Deprecated.
 
validate(GraphState, Session, SqlAction, GraphOpts) - Method in class ome.services.graphs.GraphStep
Deprecated.
Action performed at the end of the transaction to give all rows the chance to invalidate other actions.
validate(IObject) - Static method in class ome.util.Validator
 
validate(Channel) - Static method in class ome.util.Validator
 
validate(ImagingEnvironment) - Static method in class ome.util.Validator
 
validated(GraphStep) - Method in class ome.services.graphs.GraphSteps
Deprecated.
 
validateEmail(String) - Method in class ome.services.mail.MailUtil
Helper Validate that this address conforms to the syntax rules of RFC 822.
validateFilePathNaming(FsFile) - Method in class ome.services.blitz.repo.path.FilePathNamingValidator
Validate the given FS file.
validateFilePathNaming(String) - Method in class ome.services.blitz.repo.path.FilePathNamingValidator
Validate the given file path.
validatePassword(String, String) - Method in class ome.logic.LdapImpl
Validates password for base.
validateScript_async(AMD_IScript_validateScript, Job, List<IObject>, Current) - Method in class ome.services.blitz.impl.ScriptI
 
validation() - Method in class ome.services.graphs.GraphState
Deprecated.
Prepares the next phase (GraphState.validate(int)) by returning how many validation steps should be performed.
validation() - Method in class ome.services.graphs.GraphStep
Deprecated.
 
Validation - Class in ome.util
collector for Model-validation status.
Validation() - Constructor for class ome.util.Validation
 
ValidationException - Exception in ome.conditions
More specific ApiUsageException, in that the specification of your data as outlined in the OME specification is incorrect.
ValidationException(String) - Constructor for exception ome.conditions.ValidationException
 
Validator - Class in ome.util
tests of model objects for validity.
Validator() - Constructor for class ome.util.Validator
 
value - Variable in class ome.model.enums.AcquisitionMode
 
VALUE - Static variable in class ome.model.enums.AcquisitionMode
 
value - Variable in class ome.model.enums.ArcType
 
VALUE - Static variable in class ome.model.enums.ArcType
 
value - Variable in class ome.model.enums.Binning
 
VALUE - Static variable in class ome.model.enums.Binning
 
value - Variable in class ome.model.enums.ChecksumAlgorithm
 
VALUE - Static variable in class ome.model.enums.ChecksumAlgorithm
 
value - Variable in class ome.model.enums.ContrastMethod
 
VALUE - Static variable in class ome.model.enums.ContrastMethod
 
value - Variable in class ome.model.enums.Correction
 
VALUE - Static variable in class ome.model.enums.Correction
 
value - Variable in class ome.model.enums.DetectorType
 
VALUE - Static variable in class ome.model.enums.DetectorType
 
value - Variable in class ome.model.enums.DimensionOrder
 
VALUE - Static variable in class ome.model.enums.DimensionOrder
 
value - Variable in class ome.model.enums.EventType
 
VALUE - Static variable in class ome.model.enums.EventType
 
value - Variable in class ome.model.enums.ExperimentType
 
VALUE - Static variable in class ome.model.enums.ExperimentType
 
value - Variable in class ome.model.enums.Family
 
VALUE - Static variable in class ome.model.enums.Family
 
value - Variable in class ome.model.enums.FilamentType
 
VALUE - Static variable in class ome.model.enums.FilamentType
 
value - Variable in class ome.model.enums.FilterType
 
VALUE - Static variable in class ome.model.enums.FilterType
 
value - Variable in class ome.model.enums.Format
 
VALUE - Static variable in class ome.model.enums.Format
 
value - Variable in class ome.model.enums.Illumination
 
VALUE - Static variable in class ome.model.enums.Illumination
 
value - Variable in class ome.model.enums.Immersion
 
VALUE - Static variable in class ome.model.enums.Immersion
 
value - Variable in class ome.model.enums.LaserMedium
 
VALUE - Static variable in class ome.model.enums.LaserMedium
 
value - Variable in class ome.model.enums.LaserType
 
VALUE - Static variable in class ome.model.enums.LaserType
 
value - Variable in class ome.model.enums.Medium
 
VALUE - Static variable in class ome.model.enums.Medium
 
value - Variable in class ome.model.enums.MicrobeamManipulationType
 
VALUE - Static variable in class ome.model.enums.MicrobeamManipulationType
 
value - Variable in class ome.model.enums.MicroscopeType
 
VALUE - Static variable in class ome.model.enums.MicroscopeType
 
value - Variable in class ome.model.enums.PhotometricInterpretation
 
VALUE - Static variable in class ome.model.enums.PhotometricInterpretation
 
value - Variable in class ome.model.enums.PixelsType
 
VALUE - Static variable in class ome.model.enums.PixelsType
 
value - Variable in class ome.model.enums.Pulse
 
VALUE - Static variable in class ome.model.enums.Pulse
 
value - Variable in class ome.model.enums.RenderingModel
 
VALUE - Static variable in class ome.model.enums.RenderingModel
 
value - Variable in class ome.model.jobs.JobStatus
 
VALUE - Static variable in class ome.model.jobs.JobStatus
 
VALUE - Static variable in class ome.model.units.ElectricPotential
 
VALUE - Static variable in class ome.model.units.Frequency
 
VALUE - Static variable in class ome.model.units.Length
 
VALUE - Static variable in class ome.model.units.Power
 
VALUE - Static variable in class ome.model.units.Pressure
 
VALUE - Static variable in class ome.model.units.Temperature
 
VALUE - Static variable in class ome.model.units.Time
 
value - Variable in class ome.parameters.QueryParameter
 
value(String) - Method in class ome.services.query.Query
get the Object value for this name argument.
valueMapper - Variable in class omeis.providers.re.quantum.QuantumStrategy
Reference to the value mapper.
valueOf(String) - Static method in enum ome.formats.importer.exclusions.AbstractFileExclusion.Exclusion
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ome.formats.importer.ImportConfig.VersionInfo
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ome.formats.importer.transfers.AbstractFileTransfer.Transfers
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ome.formats.Index
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ome.model.enums.UnitsElectricPotential
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ome.model.enums.UnitsFrequency
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ome.model.enums.UnitsLength
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ome.model.enums.UnitsPower
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ome.model.enums.UnitsPressure
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ome.model.enums.UnitsTemperature
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ome.model.enums.UnitsTime
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ome.model.internal.Permissions.Flag
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ome.model.internal.Permissions.Right
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ome.model.internal.Permissions.Role
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ome.model.units.UNITS
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ome.security.auth.PasswordUtil.METHOD
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ome.services.blitz.repo.path.FilePathRestrictionInstance
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ome.services.graphs.GraphOpts.Op
Deprecated.
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ome.services.graphs.GraphPolicy.Ability
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ome.services.graphs.GraphPolicy.Action
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ome.services.graphs.GraphPolicy.Orphan
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ome.services.util.Executor.Priority
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ome.system.Preference.Visibility
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ome.util.checksum.ChecksumType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum omero.cmd.graphs.Preprocessor.TargetType
Deprecated.
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum omero.grid.ProcessCallbackI.Action
Returns the enum constant of this type with the specified name.
values() - Static method in enum ome.formats.importer.exclusions.AbstractFileExclusion.Exclusion
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Method in class ome.formats.importer.ImportConfig
 
values() - Static method in enum ome.formats.importer.ImportConfig.VersionInfo
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ome.formats.importer.transfers.AbstractFileTransfer.Transfers
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ome.formats.Index
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ome.model.enums.UnitsElectricPotential
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ome.model.enums.UnitsFrequency
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ome.model.enums.UnitsLength
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ome.model.enums.UnitsPower
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ome.model.enums.UnitsPressure
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ome.model.enums.UnitsTemperature
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ome.model.enums.UnitsTime
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ome.model.internal.Permissions.Flag
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ome.model.internal.Permissions.Right
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ome.model.internal.Permissions.Role
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ome.model.units.UNITS
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ome.security.auth.PasswordUtil.METHOD
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ome.services.blitz.repo.path.FilePathRestrictionInstance
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ome.services.graphs.GraphOpts.Op
Deprecated.
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ome.services.graphs.GraphPolicy.Ability
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ome.services.graphs.GraphPolicy.Action
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ome.services.graphs.GraphPolicy.Orphan
Returns an array containing the constants of this enum type, in the order they are declared.
values - Variable in class ome.services.search.SearchAction
 
values() - Static method in enum ome.services.util.Executor.Priority
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ome.system.Preference.Visibility
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ome.util.checksum.ChecksumType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum omero.cmd.graphs.Preprocessor.TargetType
Deprecated.
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum omero.grid.ProcessCallbackI.Action
Returns an array containing the constants of this enum type, in the order they are declared.
vec(PlanePoint) - Method in class ome.util.math.geom2D.PlanePoint
Calculates the vector associated to this point and the specified argument.
vec(double, double) - Method in class ome.util.math.geom2D.PlanePoint
Calculates the vector associated to this point and the specified argument.
vectorEffect - Variable in class ome.model.roi.Shape
 
VECTOREFFECT - Static variable in class ome.model.roi.Shape
 
verbose - Variable in class ome.tools.hibernate.EventMethodInterceptor
 
verifyChecksums(List<Long>, Current) - Method in class ome.services.blitz.repo.ManagedRepositoryI
 
verifyUpload(List<String>, Current) - Method in class ome.services.blitz.repo.ManagedImportProcessI
 
Version - Class in ome.formats.importer
 
Version() - Constructor for class ome.formats.importer.Version
 
VERSION - Static variable in class ome.model.acquisition.Detector
 
version - Variable in class ome.model.acquisition.Detector
 
VERSION - Static variable in class ome.model.acquisition.DetectorSettings
 
version - Variable in class ome.model.acquisition.DetectorSettings
 
VERSION - Static variable in class ome.model.acquisition.Dichroic
 
version - Variable in class ome.model.acquisition.Dichroic
 
VERSION - Static variable in class ome.model.acquisition.Filter
 
version - Variable in class ome.model.acquisition.Filter
 
VERSION - Static variable in class ome.model.acquisition.FilterSet
 
version - Variable in class ome.model.acquisition.FilterSet
 
VERSION - Static variable in class ome.model.acquisition.FilterSetEmissionFilterLink
 
version - Variable in class ome.model.acquisition.FilterSetEmissionFilterLink
 
VERSION - Static variable in class ome.model.acquisition.FilterSetExcitationFilterLink
 
version - Variable in class ome.model.acquisition.FilterSetExcitationFilterLink
 
VERSION - Static variable in class ome.model.acquisition.ImagingEnvironment
 
version - Variable in class ome.model.acquisition.ImagingEnvironment
 
VERSION - Static variable in class ome.model.acquisition.Instrument
 
version - Variable in class ome.model.acquisition.Instrument
 
VERSION - Static variable in class ome.model.acquisition.LightPath
 
version - Variable in class ome.model.acquisition.LightPath
 
VERSION - Static variable in class ome.model.acquisition.LightPathEmissionFilterLink
 
version - Variable in class ome.model.acquisition.LightPathEmissionFilterLink
 
VERSION - Static variable in class ome.model.acquisition.LightPathExcitationFilterLink
 
version - Variable in class ome.model.acquisition.LightPathExcitationFilterLink
 
VERSION - Static variable in class ome.model.acquisition.LightSettings
 
version - Variable in class ome.model.acquisition.LightSettings
 
VERSION - Static variable in class ome.model.acquisition.LightSource
 
version - Variable in class ome.model.acquisition.LightSource
 
VERSION - Static variable in class ome.model.acquisition.Microscope
 
version - Variable in class ome.model.acquisition.Microscope
 
VERSION - Static variable in class ome.model.acquisition.Objective
 
version - Variable in class ome.model.acquisition.Objective
 
VERSION - Static variable in class ome.model.acquisition.ObjectiveSettings
 
version - Variable in class ome.model.acquisition.ObjectiveSettings
 
VERSION - Static variable in class ome.model.acquisition.OTF
 
version - Variable in class ome.model.acquisition.OTF
 
VERSION - Static variable in class ome.model.acquisition.StageLabel
 
version - Variable in class ome.model.acquisition.StageLabel
 
VERSION - Static variable in class ome.model.acquisition.TransmittanceRange
 
version - Variable in class ome.model.acquisition.TransmittanceRange
 
VERSION - Static variable in class ome.model.annotations.Annotation
 
version - Variable in class ome.model.annotations.Annotation
 
VERSION - Static variable in class ome.model.annotations.AnnotationAnnotationLink
 
version - Variable in class ome.model.annotations.AnnotationAnnotationLink
 
VERSION - Static variable in class ome.model.annotations.ChannelAnnotationLink
 
version - Variable in class ome.model.annotations.ChannelAnnotationLink
 
VERSION - Static variable in class ome.model.annotations.DatasetAnnotationLink
 
version - Variable in class ome.model.annotations.DatasetAnnotationLink
 
VERSION - Static variable in class ome.model.annotations.DetectorAnnotationLink
 
version - Variable in class ome.model.annotations.DetectorAnnotationLink
 
VERSION - Static variable in class ome.model.annotations.DichroicAnnotationLink
 
version - Variable in class ome.model.annotations.DichroicAnnotationLink
 
VERSION - Static variable in class ome.model.annotations.ExperimenterAnnotationLink
 
version - Variable in class ome.model.annotations.ExperimenterAnnotationLink
 
VERSION - Static variable in class ome.model.annotations.ExperimenterGroupAnnotationLink
 
version - Variable in class ome.model.annotations.ExperimenterGroupAnnotationLink
 
VERSION - Static variable in class ome.model.annotations.FilesetAnnotationLink
 
version - Variable in class ome.model.annotations.FilesetAnnotationLink
 
VERSION - Static variable in class ome.model.annotations.FilterAnnotationLink
 
version - Variable in class ome.model.annotations.FilterAnnotationLink
 
VERSION - Static variable in class ome.model.annotations.ImageAnnotationLink
 
version - Variable in class ome.model.annotations.ImageAnnotationLink
 
VERSION - Static variable in class ome.model.annotations.InstrumentAnnotationLink
 
version - Variable in class ome.model.annotations.InstrumentAnnotationLink
 
VERSION - Static variable in class ome.model.annotations.LightPathAnnotationLink
 
version - Variable in class ome.model.annotations.LightPathAnnotationLink
 
VERSION - Static variable in class ome.model.annotations.LightSourceAnnotationLink
 
version - Variable in class ome.model.annotations.LightSourceAnnotationLink
 
VERSION - Static variable in class ome.model.annotations.NamespaceAnnotationLink
 
version - Variable in class ome.model.annotations.NamespaceAnnotationLink
 
VERSION - Static variable in class ome.model.annotations.NodeAnnotationLink
 
version - Variable in class ome.model.annotations.NodeAnnotationLink
 
VERSION - Static variable in class ome.model.annotations.ObjectiveAnnotationLink
 
version - Variable in class ome.model.annotations.ObjectiveAnnotationLink
 
VERSION - Static variable in class ome.model.annotations.OriginalFileAnnotationLink
 
version - Variable in class ome.model.annotations.OriginalFileAnnotationLink
 
VERSION - Static variable in class ome.model.annotations.PlaneInfoAnnotationLink
 
version - Variable in class ome.model.annotations.PlaneInfoAnnotationLink
 
VERSION - Static variable in class ome.model.annotations.PlateAcquisitionAnnotationLink
 
version - Variable in class ome.model.annotations.PlateAcquisitionAnnotationLink
 
VERSION - Static variable in class ome.model.annotations.PlateAnnotationLink
 
version - Variable in class ome.model.annotations.PlateAnnotationLink
 
VERSION - Static variable in class ome.model.annotations.ProjectAnnotationLink
 
version - Variable in class ome.model.annotations.ProjectAnnotationLink
 
VERSION - Static variable in class ome.model.annotations.ReagentAnnotationLink
 
version - Variable in class ome.model.annotations.ReagentAnnotationLink
 
VERSION - Static variable in class ome.model.annotations.RoiAnnotationLink
 
version - Variable in class ome.model.annotations.RoiAnnotationLink
 
VERSION - Static variable in class ome.model.annotations.ScreenAnnotationLink
 
version - Variable in class ome.model.annotations.ScreenAnnotationLink
 
VERSION - Static variable in class ome.model.annotations.SessionAnnotationLink
 
version - Variable in class ome.model.annotations.SessionAnnotationLink
 
VERSION - Static variable in class ome.model.annotations.ShapeAnnotationLink
 
version - Variable in class ome.model.annotations.ShapeAnnotationLink
 
VERSION - Static variable in class ome.model.annotations.WellAnnotationLink
 
version - Variable in class ome.model.annotations.WellAnnotationLink
 
VERSION - Static variable in class ome.model.containers.Dataset
 
version - Variable in class ome.model.containers.Dataset
 
VERSION - Static variable in class ome.model.containers.DatasetImageLink
 
version - Variable in class ome.model.containers.DatasetImageLink
 
VERSION - Static variable in class ome.model.containers.Project
 
version - Variable in class ome.model.containers.Project
 
VERSION - Static variable in class ome.model.containers.ProjectDatasetLink
 
version - Variable in class ome.model.containers.ProjectDatasetLink
 
VERSION - Static variable in class ome.model.core.Channel
 
version - Variable in class ome.model.core.Channel
 
VERSION - Static variable in class ome.model.core.Image
 
version - Variable in class ome.model.core.Image
 
VERSION - Static variable in class ome.model.core.LogicalChannel
 
version - Variable in class ome.model.core.LogicalChannel
 
VERSION - Static variable in class ome.model.core.OriginalFile
 
version - Variable in class ome.model.core.OriginalFile
 
VERSION - Static variable in class ome.model.core.Pixels
 
version - Variable in class ome.model.core.Pixels
 
VERSION - Static variable in class ome.model.core.PixelsOriginalFileMap
 
version - Variable in class ome.model.core.PixelsOriginalFileMap
 
VERSION - Static variable in class ome.model.core.PlaneInfo
 
version - Variable in class ome.model.core.PlaneInfo
 
VERSION - Static variable in class ome.model.display.ChannelBinding
 
version - Variable in class ome.model.display.ChannelBinding
 
VERSION - Static variable in class ome.model.display.CodomainMapContext
 
version - Variable in class ome.model.display.CodomainMapContext
 
VERSION - Static variable in class ome.model.display.QuantumDef
 
version - Variable in class ome.model.display.QuantumDef
 
VERSION - Static variable in class ome.model.display.RenderingDef
 
version - Variable in class ome.model.display.RenderingDef
 
VERSION - Static variable in class ome.model.display.Thumbnail
 
version - Variable in class ome.model.display.Thumbnail
 
VERSION - Static variable in class ome.model.experiment.Experiment
 
version - Variable in class ome.model.experiment.Experiment
 
VERSION - Static variable in class ome.model.experiment.MicrobeamManipulation
 
version - Variable in class ome.model.experiment.MicrobeamManipulation
 
VERSION - Static variable in class ome.model.fs.Fileset
 
version - Variable in class ome.model.fs.Fileset
 
VERSION - Static variable in class ome.model.fs.FilesetEntry
 
version - Variable in class ome.model.fs.FilesetEntry
 
VERSION - Static variable in class ome.model.fs.FilesetJobLink
 
version - Variable in class ome.model.fs.FilesetJobLink
 
VERSION - Static variable in class ome.model.internal.Link
 
version - Variable in class ome.model.internal.Link
 
VERSION - Static variable in class ome.model.jobs.Job
 
version - Variable in class ome.model.jobs.Job
 
VERSION - Static variable in class ome.model.jobs.JobOriginalFileLink
 
version - Variable in class ome.model.jobs.JobOriginalFileLink
 
VERSION - Static variable in class ome.model.meta.Experimenter
 
version - Variable in class ome.model.meta.Experimenter
 
VERSION - Static variable in class ome.model.meta.ExperimenterGroup
 
version - Variable in class ome.model.meta.ExperimenterGroup
 
VERSION - Static variable in class ome.model.meta.GroupExperimenterMap
 
version - Variable in class ome.model.meta.GroupExperimenterMap
 
VERSION - Static variable in class ome.model.meta.Namespace
 
version - Variable in class ome.model.meta.Namespace
 
VERSION - Static variable in class ome.model.meta.Node
 
version - Variable in class ome.model.meta.Node
 
VERSION - Static variable in class ome.model.meta.Session
 
version - Variable in class ome.model.meta.Session
 
VERSION - Static variable in class ome.model.meta.ShareMember
 
version - Variable in class ome.model.meta.ShareMember
 
VERSION - Static variable in class ome.model.roi.Roi
 
version - Variable in class ome.model.roi.Roi
 
VERSION - Static variable in class ome.model.roi.Shape
 
version - Variable in class ome.model.roi.Shape
 
VERSION - Static variable in class ome.model.screen.Plate
 
version - Variable in class ome.model.screen.Plate
 
VERSION - Static variable in class ome.model.screen.PlateAcquisition
 
version - Variable in class ome.model.screen.PlateAcquisition
 
VERSION - Static variable in class ome.model.screen.Reagent
 
version - Variable in class ome.model.screen.Reagent
 
VERSION - Static variable in class ome.model.screen.Screen
 
version - Variable in class ome.model.screen.Screen
 
VERSION - Static variable in class ome.model.screen.ScreenPlateLink
 
version - Variable in class ome.model.screen.ScreenPlateLink
 
VERSION - Static variable in class ome.model.screen.Well
 
version - Variable in class ome.model.screen.Well
 
VERSION - Static variable in class ome.model.screen.WellReagentLink
 
version - Variable in class ome.model.screen.WellReagentLink
 
VERSION - Static variable in class ome.model.screen.WellSample
 
version - Variable in class ome.model.screen.WellSample
 
VERSION - Static variable in class ome.model.stats.StatsInfo
 
version - Variable in class ome.model.stats.StatsInfo
 
Version - Class in ome.system
static utililty for checking Omero classes for revision number and date.
Version() - Constructor for class ome.system.Version
 
VERSION_REGEX - Static variable in interface ome.api.IConfig
Defines how the omero.version Preference will be parsed into the form: Major.minor.patch for IConfig.getVersion()
versionInfo - Variable in class ome.model.jobs.MetadataImportJob
 
VERSIONINFO - Static variable in class ome.model.jobs.MetadataImportJob
 
versionInfo - Variable in class ome.model.jobs.UploadJob
 
VERSIONINFO - Static variable in class ome.model.jobs.UploadJob
 
versionNote - Static variable in class ome.formats.importer.Version
 
visibility - Variable in class ome.model.roi.Shape
 
VISIBILITY - Static variable in class ome.model.roi.Shape
 
VOID - Static variable in class omero.util.IceMapper
 
voltage - Variable in class ome.model.acquisition.Detector
 
VOLTAGE - Static variable in class ome.model.acquisition.Detector
 
voltage - Variable in class ome.model.acquisition.DetectorSettings
 
VOLTAGE - Static variable in class ome.model.acquisition.DetectorSettings
 

W

waitCompleted(ImportConfig) - Static method in class ome.formats.importer.cli.CommandLineImporter
Look for all ImportProcessPrx in the current session and close them if they return a non-null Response (i.e. they are done).
waitForLock - Variable in class ome.services.fulltext.FullTextThread
 
WAITING - Static variable in interface ome.api.JobHandle
 
waitOnFinishedDone() - Method in class omero.cmd.CmdCallbackI
 
waitOnInitialization() - Method in class omero.cmd.CmdCallbackI
Subclasses which must perform their own initialization before CmdCallbackI.onFinished(Response, Status, Current) is called should call {@link #waitOnInitialization() before accessing any initialized state.
walk() - Method in class ome.services.graphs.BaseGraphSpec
Deprecated.
 
walk(String[], GraphEntry, QueryBuilder) - Method in class ome.services.graphs.BaseGraphSpec
Deprecated.
Walks the parts given adding a new relationship between each.
walk() - Method in interface ome.services.graphs.GraphSpec
Deprecated.
Returns an iterator over all subspecs and their subspecs, depth-first.
warmUpFactor - Variable in class ome.io.nio.SimpleBackOff
 
warn(String, Object...) - Method in class omero.cmd.Helper
 
wasCancelled() - Method in class ome.formats.importer.ImportCandidates
 
wasSource(EventLogLoader) - Method in class ome.services.eventlogs.EventLogFailure
 
waveIncrement - Variable in class ome.model.core.Pixels
 
WAVEINCREMENT - Static variable in class ome.model.core.Pixels
 
wavelength - Variable in class ome.model.acquisition.Laser
 
WAVELENGTH - Static variable in class ome.model.acquisition.Laser
 
wavelength - Variable in class ome.model.acquisition.LightSettings
 
WAVELENGTH - Static variable in class ome.model.acquisition.LightSettings
 
waveRendering - Variable in class ome.model.display.RenderingDef
 
WAVERENDERING - Static variable in class ome.model.display.RenderingDef
 
waveStart - Variable in class ome.model.core.Pixels
 
WAVESTART - Static variable in class ome.model.core.Pixels
 
Well - Class in ome.model.screen
These filter definitions are used by the security system to eliminate non-readable objects from queries.
Well() - Constructor for class ome.model.screen.Well
 
Well(Long) - Constructor for class ome.model.screen.Well
 
Well(Long, boolean) - Constructor for class ome.model.screen.Well
Main constructor.
Well(Plate) - Constructor for class ome.model.screen.Well
 
well - Variable in class ome.model.screen.WellSample
 
WELL - Static variable in class ome.model.screen.WellSample
 
Well.Details - Class in ome.model.screen
 
Well.Details() - Constructor for class ome.model.screen.Well.Details
 
Well.Details(Object[]) - Constructor for class ome.model.screen.Well.Details
 
WellAnnotationLink - Class in ome.model.annotations
These filter definitions are used by the security system to eliminate non-readable objects from queries.
WellAnnotationLink() - Constructor for class ome.model.annotations.WellAnnotationLink
 
WellAnnotationLink(Long) - Constructor for class ome.model.annotations.WellAnnotationLink
 
WellAnnotationLink(Long, boolean) - Constructor for class ome.model.annotations.WellAnnotationLink
Main constructor.
WellAnnotationLink(IObject, IObject) - Constructor for class ome.model.annotations.WellAnnotationLink
 
WellAnnotationLink.Details - Class in ome.model.annotations
 
WellAnnotationLink.Details() - Constructor for class ome.model.annotations.WellAnnotationLink.Details
 
WellAnnotationLink.Details(Object[]) - Constructor for class ome.model.annotations.WellAnnotationLink.Details
 
WellData - Class in pojos
The data that makes up an OME Well and the Experimenter that owns this Well.
WellData() - Constructor for class pojos.WellData
Creates a new instance.
WellData(Well) - Constructor for class pojos.WellData
Creates a new instance.
wellLinks - Variable in class ome.model.screen.Reagent
 
WELLLINKS - Static variable in class ome.model.screen.Reagent
 
WELLLINKSCOUNTPEROWNER - Static variable in class ome.model.screen.Reagent
 
wellOriginX - Variable in class ome.model.screen.Plate
 
WELLORIGINX - Static variable in class ome.model.screen.Plate
 
wellOriginY - Variable in class ome.model.screen.Plate
 
WELLORIGINY - Static variable in class ome.model.screen.Plate
 
WellProcessor - Class in ome.formats.model
Processes the Wells of an IObjectContainerStore and ensures that the Plate has been populated and that it is validated and that if any PlateAcquisition objects are in the hierarchy that they have a name.
WellProcessor() - Constructor for class ome.formats.model.WellProcessor
 
WellReagentLink - Class in ome.model.screen
These filter definitions are used by the security system to eliminate non-readable objects from queries.
WellReagentLink() - Constructor for class ome.model.screen.WellReagentLink
 
WellReagentLink(Long) - Constructor for class ome.model.screen.WellReagentLink
 
WellReagentLink(Long, boolean) - Constructor for class ome.model.screen.WellReagentLink
Main constructor.
WellReagentLink(IObject, IObject) - Constructor for class ome.model.screen.WellReagentLink
 
WellReagentLink.Details - Class in ome.model.screen
 
WellReagentLink.Details() - Constructor for class ome.model.screen.WellReagentLink.Details
 
WellReagentLink.Details(Object[]) - Constructor for class ome.model.screen.WellReagentLink.Details
 
wells - Variable in class ome.model.screen.Plate
 
WELLS - Static variable in class ome.model.screen.Plate
 
WELLS - Static variable in class pojos.PlateData
Identifies the Plate#WELLS field.
wellSample - Variable in class ome.model.screen.PlateAcquisition
 
WELLSAMPLE - Static variable in class ome.model.screen.PlateAcquisition
 
WellSample - Class in ome.model.screen
These filter definitions are used by the security system to eliminate non-readable objects from queries.
WellSample() - Constructor for class ome.model.screen.WellSample
 
WellSample(Long) - Constructor for class ome.model.screen.WellSample
 
WellSample(Long, boolean) - Constructor for class ome.model.screen.WellSample
Main constructor.
WellSample(Well, Image) - Constructor for class ome.model.screen.WellSample
 
WellSample.Details - Class in ome.model.screen
 
WellSample.Details() - Constructor for class ome.model.screen.WellSample.Details
 
WellSample.Details(Object[]) - Constructor for class ome.model.screen.WellSample.Details
 
WellSample_PositionX - Static variable in class ome.formats.model.UnitsFactory
 
WellSample_PositionY - Static variable in class ome.formats.model.UnitsFactory
 
WellSampleData - Class in pojos
The data that makes up an OME WellSample along with links to its images and the Experimenter that owns this WellSample.
WellSampleData() - Constructor for class pojos.WellSampleData
Creates a new instance.
WellSampleData(WellSample) - Constructor for class pojos.WellSampleData
Creates a new instance.
wellSamples - Variable in class ome.model.core.Image
 
WELLSAMPLES - Static variable in class ome.model.core.Image
 
wellSamples - Variable in class ome.model.screen.Well
 
WELLSAMPLES - Static variable in class ome.model.screen.Well
 
where() - Method in class ome.tools.hibernate.QueryBuilder
Marks the end of all fetches by adding a "where" clause to the string.
whereClause() - Method in class ome.tools.hibernate.QueryBuilder
Similar to how skipFrom and skipWhere were previously used, this sets the current builder to QueryBuilder.where but without prefacing the "where " string.
width - Variable in class ome.model.roi.Mask
 
WIDTH - Static variable in class ome.model.roi.Mask
 
width - Variable in class ome.model.roi.Rect
 
WIDTH - Static variable in class ome.model.roi.Rect
 
willBeTriedAgain(GraphStep) - Method in class ome.services.graphs.GraphSteps
Deprecated.
 
work - Variable in class ome.services.util.ExecutionThread
 
WorkflowData - Class in pojos
The data that makes up an OME worflow object.
WorkflowData(Namespace) - Constructor for class pojos.WorkflowData
Creates a new instance.
WorkflowData(String, List<String>) - Constructor for class pojos.WorkflowData
Creates a new instance.
WorkflowData(String, String) - Constructor for class pojos.WorkflowData
Creates a new instance.
WorkflowData() - Constructor for class pojos.WorkflowData
Creates a new instance.
workingDistance - Variable in class ome.model.acquisition.Objective
 
WORKINGDISTANCE - Static variable in class ome.model.acquisition.Objective
 
WORLD_IMMUTABLE - Static variable in class ome.model.internal.Permissions
R_R_R_ : all can only read
WORLD_WRITEABLE - Static variable in class ome.model.internal.Permissions
RWRWRW : everyone can read and write
wrap(String, IObject) - Method in class ome.services.eventlogs.AllEntitiesPseudoLogLoader
 
wrap(Iterator<Reader>) - Method in class ome.services.fulltext.FileParser
Wraps an Iterator with an Iterable instance.
wrap(Reader) - Method in class ome.services.fulltext.FileParser
 
wrap(Hashtable<String, Object>) - Method in class omero.cmd.fs.OriginalMetadataRequestI
Use IceMapper to convert from Object instances in the given Hashtable to RType instances.
wrap(Object) - Static method in class omero.rtypes
Descends into data structures wrapping all elements as it goes.
wrap(Object, Map<Object, RType>) - Static method in class omero.rtypes
Descends into data structures wrapping all elements as it goes.
WrappableRequest<X> - Interface in omero.cmd.graphs
Requests that can be wrapped by a SkipHeadI request.
wrapSecurityViolation(SecurityViolation) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
 
write(byte[], long, int) - Method in interface ome.api.RawFileStore
Delegates to FileBuffer
write(ByteBuffer, long) - Method in class ome.io.nio.FileBuffer
Delegates to FileChannel
write(ByteBuffer) - Method in class ome.io.nio.FileBuffer
Delegates to FileChannel
write(byte[], long, int) - Method in class ome.services.RawFileBean
 
write(String, String) - Method in class ome.services.scripts.ScriptRepoHelper
 
write(RepoFile, String) - Method in class ome.services.scripts.ScriptRepoHelper
 
write_async(AMD_RawFileStore_write, byte[], long, int, Current) - Method in class ome.services.blitz.impl.RawFileStoreI
 
write_async(AMD_RawFileStore_write, byte[], long, int, Current) - Method in class ome.services.blitz.repo.RepoRawFileStoreI
 
writeImage(BufferedImage, TranscoderOutput) - Method in class ome.services.SVGRasterizer.Rasterizer
 
writeLine(String) - Method in class ome.services.blitz.repo.FileMaker
 
writer - Variable in class ome.io.bioformats.BfPyramidPixelBuffer
Bio-Formats implementation used to write to the backing TIFF.
WriteStrategy - Interface in ome.security
Responsible for determining which users can modify which objects in which contexts.
writingMode - Variable in class ome.model.roi.Label
 
WRITINGMODE - Static variable in class ome.model.roi.Label
 
writtenBytes(int) - Method in class ome.services.sessions.stats.DelegatingStats
 
writtenBytes(int) - Method in class ome.services.sessions.stats.NullSessionStats
 
writtenBytes(int) - Method in interface ome.services.sessions.stats.SessionStats
 
writtenBytes(int) - Method in class ome.services.sessions.stats.SimpleSessionStats
 
wSize - Variable in class ome.formats.importer.ImportSize
 

X

x - Variable in class ome.model.roi.Label
 
X - Static variable in class ome.model.roi.Label
 
x - Variable in class ome.model.roi.Mask
 
X - Static variable in class ome.model.roi.Mask
 
x - Variable in class ome.model.roi.Rect
 
X - Static variable in class ome.model.roi.Rect
 
x1 - Variable in class ome.model.roi.Line
 
X1 - Static variable in class ome.model.roi.Line
 
x1 - Variable in class ome.util.math.geom2D.PlanePoint
The first element.
x2 - Variable in class ome.model.roi.Line
 
X2 - Static variable in class ome.model.roi.Line
 
x2 - Variable in class ome.util.math.geom2D.PlanePoint
The second element.
xend - Variable in class ome.model.display.ContrastStretchingContext
 
XEND - Static variable in class ome.model.display.ContrastStretchingContext
 
XML - Static variable in class pojos.FileAnnotationData
Identifies the XML file formats.
XmlAnnotation - Class in ome.model.annotations
 
XmlAnnotation() - Constructor for class ome.model.annotations.XmlAnnotation
 
XmlAnnotation(Long) - Constructor for class ome.model.annotations.XmlAnnotation
 
XmlAnnotation(Long, boolean) - Constructor for class ome.model.annotations.XmlAnnotation
Main constructor.
XMLAnnotationData - Class in pojos
Defines an XML Annotation.
XMLAnnotationData() - Constructor for class pojos.XMLAnnotationData
Creates a new instance.
XMLAnnotationData(String) - Constructor for class pojos.XMLAnnotationData
Creates a new instance.
XMLAnnotationData(XmlAnnotation) - Constructor for class pojos.XMLAnnotationData
Creates a new instance.
xmlElectricPotentialEnumToOMERO(Unit<ElectricPotential>) - Static method in class ome.formats.model.UnitsFactory
 
xmlElectricPotentialEnumToOMERO(String) - Static method in class ome.formats.model.UnitsFactory
 
xmlFrequencyEnumToOMERO(Unit<Frequency>) - Static method in class ome.formats.model.UnitsFactory
 
xmlFrequencyEnumToOMERO(String) - Static method in class ome.formats.model.UnitsFactory
 
xmlLengthEnumToOMERO(Unit<Length>) - Static method in class ome.formats.model.UnitsFactory
 
xmlLengthEnumToOMERO(String) - Static method in class ome.formats.model.UnitsFactory
 
xmlPowerEnumToOMERO(Unit<Power>) - Static method in class ome.formats.model.UnitsFactory
 
xmlPowerEnumToOMERO(String) - Static method in class ome.formats.model.UnitsFactory
 
xmlPressureEnumToOMERO(Unit<Pressure>) - Static method in class ome.formats.model.UnitsFactory
 
xmlPressureEnumToOMERO(String) - Static method in class ome.formats.model.UnitsFactory
 
xmlTemperatureEnumToOMERO(Unit<Temperature>) - Static method in class ome.formats.model.UnitsFactory
 
xmlTemperatureEnumToOMERO(String) - Static method in class ome.formats.model.UnitsFactory
 
xmlTimeEnumToOMERO(Unit<Time>) - Static method in class ome.formats.model.UnitsFactory
 
xmlTimeEnumToOMERO(String) - Static method in class ome.formats.model.UnitsFactory
 
xstart - Variable in class ome.model.display.ContrastStretchingContext
 
XSTART - Static variable in class ome.model.display.ContrastStretchingContext
 
XY - Static variable in class omeis.providers.re.data.PlaneDef
Flag to identify an XY-plane.
XZ - Static variable in class omeis.providers.re.data.PlaneDef
Flag to identify an XZ-plane.

Y

y - Variable in class ome.model.roi.Label
 
Y - Static variable in class ome.model.roi.Label
 
y - Variable in class ome.model.roi.Mask
 
Y - Static variable in class ome.model.roi.Mask
 
y - Variable in class ome.model.roi.Rect
 
Y - Static variable in class ome.model.roi.Rect
 
y1 - Variable in class ome.model.roi.Line
 
Y1 - Static variable in class ome.model.roi.Line
 
y2 - Variable in class ome.model.roi.Line
 
Y2 - Static variable in class ome.model.roi.Line
 
yend - Variable in class ome.model.display.ContrastStretchingContext
 
YEND - Static variable in class ome.model.display.ContrastStretchingContext
 
ystart - Variable in class ome.model.display.ContrastStretchingContext
 
YSTART - Static variable in class ome.model.display.ContrastStretchingContext
 

Z

zero() - Method in class omeis.providers.re.RGBAIntBuffer
 
zero() - Method in class omeis.providers.re.RGBBuffer
Zeros out (sets every pixel offset to zero) each band.
zero() - Method in class omeis.providers.re.RGBIntBuffer
 
ZIP_EXTENSION - Static variable in class ome.formats.importer.util.FileUploader
The extension used for the zip.
zoom - Variable in class ome.model.acquisition.Detector
 
ZOOM - Static variable in class ome.model.acquisition.Detector
 
zoom - Variable in class ome.model.acquisition.DetectorSettings
 
ZOOM - Static variable in class ome.model.acquisition.DetectorSettings
 
zSize - Variable in class ome.formats.importer.ImportSize
 
ZY - Static variable in class omeis.providers.re.data.PlaneDef
Flag to identify an YZ-plane.

_

__del__() - Method in class omero.client
Calls closeSession() and ignores any exceptions.
__dont_use_me_factory - Variable in class ome.services.sharing.BlobShareStore
Used indirectly to obtain sessions for querying and updating the store during normal operation.
__redirect(long, _RawFileStoreTie, Current) - Method in class ome.services.blitz.impl.RawFileStoreI
 
_addGraph(ShareData, ShareBean.Graph) - Method in class ome.services.sharing.ShareBean
 
_cache - Variable in class ome.util.ContextFilter
 
_context - Variable in class ome.model.internal.Details
 
_context - Variable in class ome.util.ContextFilter
 
_creation - Variable in class ome.model.internal.Details
 
_dynamicFields - Variable in class ome.model.acquisition.Detector
 
_dynamicFields - Variable in class ome.model.acquisition.DetectorSettings
 
_dynamicFields - Variable in class ome.model.acquisition.Dichroic
 
_dynamicFields - Variable in class ome.model.acquisition.Filter
 
_dynamicFields - Variable in class ome.model.acquisition.FilterSet
 
_dynamicFields - Variable in class ome.model.acquisition.FilterSetEmissionFilterLink
 
_dynamicFields - Variable in class ome.model.acquisition.FilterSetExcitationFilterLink
 
_dynamicFields - Variable in class ome.model.acquisition.ImagingEnvironment
 
_dynamicFields - Variable in class ome.model.acquisition.Instrument
 
_dynamicFields - Variable in class ome.model.acquisition.LightPath
 
_dynamicFields - Variable in class ome.model.acquisition.LightPathEmissionFilterLink
 
_dynamicFields - Variable in class ome.model.acquisition.LightPathExcitationFilterLink
 
_dynamicFields - Variable in class ome.model.acquisition.LightSettings
 
_dynamicFields - Variable in class ome.model.acquisition.LightSource
 
_dynamicFields - Variable in class ome.model.acquisition.Microscope
 
_dynamicFields - Variable in class ome.model.acquisition.Objective
 
_dynamicFields - Variable in class ome.model.acquisition.ObjectiveSettings
 
_dynamicFields - Variable in class ome.model.acquisition.OTF
 
_dynamicFields - Variable in class ome.model.acquisition.StageLabel
 
_dynamicFields - Variable in class ome.model.acquisition.TransmittanceRange
 
_dynamicFields - Variable in class ome.model.annotations.Annotation
 
_dynamicFields - Variable in class ome.model.annotations.AnnotationAnnotationLink
 
_dynamicFields - Variable in class ome.model.annotations.ChannelAnnotationLink
 
_dynamicFields - Variable in class ome.model.annotations.DatasetAnnotationLink
 
_dynamicFields - Variable in class ome.model.annotations.DetectorAnnotationLink
 
_dynamicFields - Variable in class ome.model.annotations.DichroicAnnotationLink
 
_dynamicFields - Variable in class ome.model.annotations.ExperimenterAnnotationLink
 
_dynamicFields - Variable in class ome.model.annotations.ExperimenterGroupAnnotationLink
 
_dynamicFields - Variable in class ome.model.annotations.FilesetAnnotationLink
 
_dynamicFields - Variable in class ome.model.annotations.FilterAnnotationLink
 
_dynamicFields - Variable in class ome.model.annotations.ImageAnnotationLink
 
_dynamicFields - Variable in class ome.model.annotations.InstrumentAnnotationLink
 
_dynamicFields - Variable in class ome.model.annotations.LightPathAnnotationLink
 
_dynamicFields - Variable in class ome.model.annotations.LightSourceAnnotationLink
 
_dynamicFields - Variable in class ome.model.annotations.NamespaceAnnotationLink
 
_dynamicFields - Variable in class ome.model.annotations.NodeAnnotationLink
 
_dynamicFields - Variable in class ome.model.annotations.ObjectiveAnnotationLink
 
_dynamicFields - Variable in class ome.model.annotations.OriginalFileAnnotationLink
 
_dynamicFields - Variable in class ome.model.annotations.PlaneInfoAnnotationLink
 
_dynamicFields - Variable in class ome.model.annotations.PlateAcquisitionAnnotationLink
 
_dynamicFields - Variable in class ome.model.annotations.PlateAnnotationLink
 
_dynamicFields - Variable in class ome.model.annotations.ProjectAnnotationLink
 
_dynamicFields - Variable in class ome.model.annotations.ReagentAnnotationLink
 
_dynamicFields - Variable in class ome.model.annotations.RoiAnnotationLink
 
_dynamicFields - Variable in class ome.model.annotations.ScreenAnnotationLink
 
_dynamicFields - Variable in class ome.model.annotations.SessionAnnotationLink
 
_dynamicFields - Variable in class ome.model.annotations.ShapeAnnotationLink
 
_dynamicFields - Variable in class ome.model.annotations.WellAnnotationLink
 
_dynamicFields - Variable in class ome.model.containers.Dataset
 
_dynamicFields - Variable in class ome.model.containers.DatasetImageLink
 
_dynamicFields - Variable in class ome.model.containers.Project
 
_dynamicFields - Variable in class ome.model.containers.ProjectDatasetLink
 
_dynamicFields - Variable in class ome.model.core.Channel
 
_dynamicFields - Variable in class ome.model.core.Image
 
_dynamicFields - Variable in class ome.model.core.LogicalChannel
 
_dynamicFields - Variable in class ome.model.core.OriginalFile
 
_dynamicFields - Variable in class ome.model.core.Pixels
 
_dynamicFields - Variable in class ome.model.core.PixelsOriginalFileMap
 
_dynamicFields - Variable in class ome.model.core.PlaneInfo
 
_dynamicFields - Variable in class ome.model.display.ChannelBinding
 
_dynamicFields - Variable in class ome.model.display.CodomainMapContext
 
_dynamicFields - Variable in class ome.model.display.QuantumDef
 
_dynamicFields - Variable in class ome.model.display.RenderingDef
 
_dynamicFields - Variable in class ome.model.display.Thumbnail
 
_dynamicFields - Variable in class ome.model.enums.AcquisitionMode
 
_dynamicFields - Variable in class ome.model.enums.ArcType
 
_dynamicFields - Variable in class ome.model.enums.Binning
 
_dynamicFields - Variable in class ome.model.enums.ChecksumAlgorithm
 
_dynamicFields - Variable in class ome.model.enums.ContrastMethod
 
_dynamicFields - Variable in class ome.model.enums.Correction
 
_dynamicFields - Variable in class ome.model.enums.DetectorType
 
_dynamicFields - Variable in class ome.model.enums.DimensionOrder
 
_dynamicFields - Variable in class ome.model.enums.EventType
 
_dynamicFields - Variable in class ome.model.enums.ExperimentType
 
_dynamicFields - Variable in class ome.model.enums.Family
 
_dynamicFields - Variable in class ome.model.enums.FilamentType
 
_dynamicFields - Variable in class ome.model.enums.FilterType
 
_dynamicFields - Variable in class ome.model.enums.Format
 
_dynamicFields - Variable in class ome.model.enums.Illumination
 
_dynamicFields - Variable in class ome.model.enums.Immersion
 
_dynamicFields - Variable in class ome.model.enums.LaserMedium
 
_dynamicFields - Variable in class ome.model.enums.LaserType
 
_dynamicFields - Variable in class ome.model.enums.Medium
 
_dynamicFields - Variable in class ome.model.enums.MicrobeamManipulationType
 
_dynamicFields - Variable in class ome.model.enums.MicroscopeType
 
_dynamicFields - Variable in class ome.model.enums.PhotometricInterpretation
 
_dynamicFields - Variable in class ome.model.enums.PixelsType
 
_dynamicFields - Variable in class ome.model.enums.Pulse
 
_dynamicFields - Variable in class ome.model.enums.RenderingModel
 
_dynamicFields - Variable in class ome.model.experiment.Experiment
 
_dynamicFields - Variable in class ome.model.experiment.MicrobeamManipulation
 
_dynamicFields - Variable in class ome.model.fs.Fileset
 
_dynamicFields - Variable in class ome.model.fs.FilesetEntry
 
_dynamicFields - Variable in class ome.model.fs.FilesetJobLink
 
_dynamicFields - Variable in class ome.model.internal.Details
 
_dynamicFields - Variable in class ome.model.internal.Link
 
_dynamicFields - Variable in class ome.model.jobs.Job
 
_dynamicFields - Variable in class ome.model.jobs.JobOriginalFileLink
 
_dynamicFields - Variable in class ome.model.jobs.JobStatus
 
_dynamicFields - Variable in class ome.model.meta.DBPatch
 
_dynamicFields - Variable in class ome.model.meta.Event
 
_dynamicFields - Variable in class ome.model.meta.EventLog
 
_dynamicFields - Variable in class ome.model.meta.Experimenter
 
_dynamicFields - Variable in class ome.model.meta.ExperimenterGroup
 
_dynamicFields - Variable in class ome.model.meta.ExternalInfo
 
_dynamicFields - Variable in class ome.model.meta.GroupExperimenterMap
 
_dynamicFields - Variable in class ome.model.meta.Namespace
 
_dynamicFields - Variable in class ome.model.meta.Node
 
_dynamicFields - Variable in class ome.model.meta.Session
 
_dynamicFields - Variable in class ome.model.meta.ShareMember
 
_dynamicFields - Variable in class ome.model.roi.Roi
 
_dynamicFields - Variable in class ome.model.roi.Shape
 
_dynamicFields - Variable in class ome.model.screen.Plate
 
_dynamicFields - Variable in class ome.model.screen.PlateAcquisition
 
_dynamicFields - Variable in class ome.model.screen.Reagent
 
_dynamicFields - Variable in class ome.model.screen.Screen
 
_dynamicFields - Variable in class ome.model.screen.ScreenPlateLink
 
_dynamicFields - Variable in class ome.model.screen.Well
 
_dynamicFields - Variable in class ome.model.screen.WellReagentLink
 
_dynamicFields - Variable in class ome.model.screen.WellSample
 
_dynamicFields - Variable in class ome.model.stats.StatsInfo
 
_externalInfo - Variable in class ome.model.internal.Details
 
_filteredCollections - Variable in class ome.model.internal.Details
 
_getPixelBuffer(Pixels, boolean) - Method in class ome.io.nio.PixelsService
 
_group - Variable in class ome.model.internal.Details
 
_jdbc() - Method in class ome.util.actions.PostgresSqlAction
 
_jdbc() - Method in class ome.util.SqlAction.Impl
 
_loaded - Variable in class ome.model.acquisition.Detector
 
_loaded - Variable in class ome.model.acquisition.DetectorSettings
 
_loaded - Variable in class ome.model.acquisition.Dichroic
 
_loaded - Variable in class ome.model.acquisition.Filter
 
_loaded - Variable in class ome.model.acquisition.FilterSet
 
_loaded - Variable in class ome.model.acquisition.FilterSetEmissionFilterLink
 
_loaded - Variable in class ome.model.acquisition.FilterSetExcitationFilterLink
 
_loaded - Variable in class ome.model.acquisition.ImagingEnvironment
 
_loaded - Variable in class ome.model.acquisition.Instrument
 
_loaded - Variable in class ome.model.acquisition.LightPath
 
_loaded - Variable in class ome.model.acquisition.LightPathEmissionFilterLink
 
_loaded - Variable in class ome.model.acquisition.LightPathExcitationFilterLink
 
_loaded - Variable in class ome.model.acquisition.LightSettings
 
_loaded - Variable in class ome.model.acquisition.LightSource
 
_loaded - Variable in class ome.model.acquisition.Microscope
 
_loaded - Variable in class ome.model.acquisition.Objective
 
_loaded - Variable in class ome.model.acquisition.ObjectiveSettings
 
_loaded - Variable in class ome.model.acquisition.OTF
 
_loaded - Variable in class ome.model.acquisition.StageLabel
 
_loaded - Variable in class ome.model.acquisition.TransmittanceRange
 
_loaded - Variable in class ome.model.annotations.Annotation
 
_loaded - Variable in class ome.model.annotations.AnnotationAnnotationLink
 
_loaded - Variable in class ome.model.annotations.ChannelAnnotationLink
 
_loaded - Variable in class ome.model.annotations.DatasetAnnotationLink
 
_loaded - Variable in class ome.model.annotations.DetectorAnnotationLink
 
_loaded - Variable in class ome.model.annotations.DichroicAnnotationLink
 
_loaded - Variable in class ome.model.annotations.ExperimenterAnnotationLink
 
_loaded - Variable in class ome.model.annotations.ExperimenterGroupAnnotationLink
 
_loaded - Variable in class ome.model.annotations.FilesetAnnotationLink
 
_loaded - Variable in class ome.model.annotations.FilterAnnotationLink
 
_loaded - Variable in class ome.model.annotations.ImageAnnotationLink
 
_loaded - Variable in class ome.model.annotations.InstrumentAnnotationLink
 
_loaded - Variable in class ome.model.annotations.LightPathAnnotationLink
 
_loaded - Variable in class ome.model.annotations.LightSourceAnnotationLink
 
_loaded - Variable in class ome.model.annotations.NamespaceAnnotationLink
 
_loaded - Variable in class ome.model.annotations.NodeAnnotationLink
 
_loaded - Variable in class ome.model.annotations.ObjectiveAnnotationLink
 
_loaded - Variable in class ome.model.annotations.OriginalFileAnnotationLink
 
_loaded - Variable in class ome.model.annotations.PlaneInfoAnnotationLink
 
_loaded - Variable in class ome.model.annotations.PlateAcquisitionAnnotationLink
 
_loaded - Variable in class ome.model.annotations.PlateAnnotationLink
 
_loaded - Variable in class ome.model.annotations.ProjectAnnotationLink
 
_loaded - Variable in class ome.model.annotations.ReagentAnnotationLink
 
_loaded - Variable in class ome.model.annotations.RoiAnnotationLink
 
_loaded - Variable in class ome.model.annotations.ScreenAnnotationLink
 
_loaded - Variable in class ome.model.annotations.SessionAnnotationLink
 
_loaded - Variable in class ome.model.annotations.ShapeAnnotationLink
 
_loaded - Variable in class ome.model.annotations.WellAnnotationLink
 
_loaded - Variable in class ome.model.containers.Dataset
 
_loaded - Variable in class ome.model.containers.DatasetImageLink
 
_loaded - Variable in class ome.model.containers.Project
 
_loaded - Variable in class ome.model.containers.ProjectDatasetLink
 
_loaded - Variable in class ome.model.core.Channel
 
_loaded - Variable in class ome.model.core.Image
 
_loaded - Variable in class ome.model.core.LogicalChannel
 
_loaded - Variable in class ome.model.core.OriginalFile
 
_loaded - Variable in class ome.model.core.Pixels
 
_loaded - Variable in class ome.model.core.PixelsOriginalFileMap
 
_loaded - Variable in class ome.model.core.PlaneInfo
 
_loaded - Variable in class ome.model.display.ChannelBinding
 
_loaded - Variable in class ome.model.display.CodomainMapContext
 
_loaded - Variable in class ome.model.display.QuantumDef
 
_loaded - Variable in class ome.model.display.RenderingDef
 
_loaded - Variable in class ome.model.display.Thumbnail
 
_loaded - Variable in class ome.model.enums.AcquisitionMode
 
_loaded - Variable in class ome.model.enums.ArcType
 
_loaded - Variable in class ome.model.enums.Binning
 
_loaded - Variable in class ome.model.enums.ChecksumAlgorithm
 
_loaded - Variable in class ome.model.enums.ContrastMethod
 
_loaded - Variable in class ome.model.enums.Correction
 
_loaded - Variable in class ome.model.enums.DetectorType
 
_loaded - Variable in class ome.model.enums.DimensionOrder
 
_loaded - Variable in class ome.model.enums.EventType
 
_loaded - Variable in class ome.model.enums.ExperimentType
 
_loaded - Variable in class ome.model.enums.Family
 
_loaded - Variable in class ome.model.enums.FilamentType
 
_loaded - Variable in class ome.model.enums.FilterType
 
_loaded - Variable in class ome.model.enums.Format
 
_loaded - Variable in class ome.model.enums.Illumination
 
_loaded - Variable in class ome.model.enums.Immersion
 
_loaded - Variable in class ome.model.enums.LaserMedium
 
_loaded - Variable in class ome.model.enums.LaserType
 
_loaded - Variable in class ome.model.enums.Medium
 
_loaded - Variable in class ome.model.enums.MicrobeamManipulationType
 
_loaded - Variable in class ome.model.enums.MicroscopeType
 
_loaded - Variable in class ome.model.enums.PhotometricInterpretation
 
_loaded - Variable in class ome.model.enums.PixelsType
 
_loaded - Variable in class ome.model.enums.Pulse
 
_loaded - Variable in class ome.model.enums.RenderingModel
 
_loaded - Variable in class ome.model.experiment.Experiment
 
_loaded - Variable in class ome.model.experiment.MicrobeamManipulation
 
_loaded - Variable in class ome.model.fs.Fileset
 
_loaded - Variable in class ome.model.fs.FilesetEntry
 
_loaded - Variable in class ome.model.fs.FilesetJobLink
 
_loaded - Variable in class ome.model.internal.Link
 
_loaded - Variable in class ome.model.jobs.Job
 
_loaded - Variable in class ome.model.jobs.JobOriginalFileLink
 
_loaded - Variable in class ome.model.jobs.JobStatus
 
_loaded - Variable in class ome.model.meta.DBPatch
 
_loaded - Variable in class ome.model.meta.Event
 
_loaded - Variable in class ome.model.meta.EventLog
 
_loaded - Variable in class ome.model.meta.Experimenter
 
_loaded - Variable in class ome.model.meta.ExperimenterGroup
 
_loaded - Variable in class ome.model.meta.ExternalInfo
 
_loaded - Variable in class ome.model.meta.GroupExperimenterMap
 
_loaded - Variable in class ome.model.meta.Namespace
 
_loaded - Variable in class ome.model.meta.Node
 
_loaded - Variable in class ome.model.meta.Session
 
_loaded - Variable in class ome.model.meta.ShareMember
 
_loaded - Variable in class ome.model.roi.Roi
 
_loaded - Variable in class ome.model.roi.Shape
 
_loaded - Variable in class ome.model.screen.Plate
 
_loaded - Variable in class ome.model.screen.PlateAcquisition
 
_loaded - Variable in class ome.model.screen.Reagent
 
_loaded - Variable in class ome.model.screen.Screen
 
_loaded - Variable in class ome.model.screen.ScreenPlateLink
 
_loaded - Variable in class ome.model.screen.Well
 
_loaded - Variable in class ome.model.screen.WellReagentLink
 
_loaded - Variable in class ome.model.screen.WellSample
 
_loaded - Variable in class ome.model.stats.StatsInfo
 
_lookup(String) - Method in class ome.util.actions.PostgresSqlAction
 
_lookup(String) - Method in class ome.util.SqlAction.Impl
 
_owner - Variable in class ome.model.internal.Details
 
_perms - Variable in class ome.model.internal.Details
 
_update - Variable in class ome.model.internal.Details
 
_wait(Current) - Method in class ome.services.blitz.impl.ScriptProcessI
 
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OmeroJava Api

Version: 5.1.4-ice35-b55

Copyright © 2015 The University of Dundee & Open Microscopy Environment. All Rights Reserved.