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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 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.
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
 
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
 
accept(File) - Method in class omero.gateway.util.TIFFFilter
Accepts or not the file with the declared file extensions.
accept(String) - Method in class omero.gateway.util.TIFFFilter
Accepts or not the file identified by its name.
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.Rectangle
 
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
 
acceptFilter(Filter) - Method in class ome.util.PermDetails
 
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
 
action - Variable in class ome.model.meta.EventLog
 
ACTION - Static variable in class ome.model.meta.EventLog
 
action - Variable in class ome.services.graphs.GraphPolicy.Details
the current plan for the object, may be mutated by GraphPolicy.review(Map, Details, Map, Set, boolean)
action - Variable in class ome.services.messages.EventLogMessage
 
action - Variable in class ome.tools.hibernate.EventMethodInterceptor
 
Action() - Constructor for class ome.tools.hibernate.EventMethodInterceptor.Action
 
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 ProcessorCallbackI.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 whether 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() - Constructor for class ome.formats.importer.ImportEvent.ADD
 
Add(Conversion...) - Static method in class ome.model.units.Conversion
Static helper for creating Conversion.Add instances.
Add(Conversion[]) - Constructor for class ome.model.units.Conversion.Add
 
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(Document, String, String, LuceneOptions) - Method in class ome.services.fulltext.BridgeHelper
Helper method which takes the parameters from the BridgeHelper.set(String, Object, Document, LuceneOptions) method (possibly modified) as well as the parsed String value which should be added to the index, and adds two fields.
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 omero.gateway.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
 
addElement(int, Object, Object) - Method in interface omero.gateway.cache.CacheService
Adds the specified element to the selected cache.
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.
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 omero.gateway.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.
addImagesToDataset(SecurityContext, Collection<ImageData>, DatasetData) - Method in class omero.gateway.facility.DataManagerFacility
Adds the ImageDatas to the given DatasetData
addImageToDataset(SecurityContext, ImageData, DatasetData) - Method in class omero.gateway.facility.DataManagerFacility
Adds the ImageData to the given DatasetData
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.
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 omero.gateway.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.
addPropertyChangeListener(PropertyChangeListener) - Method in class omero.gateway.facility.Facility
addPropertyChangeListener(PropertyChangeListener) - Method in class omero.gateway.Gateway
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 omero.gateway.model.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 class omero.cmd.graphs.DuplicateI
 
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
AdminFacility - Class in omero.gateway.facility
Facility for handling admin issues, e.g. creating users, groups, etc.
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
 
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_GROUPS_ID - Static variable in class omero.gateway.model.SearchParameters
The ID for searching across all groups
ALL_PROJECTIONS - Static variable in class ome.services.search.FullText
 
ALL_SCOPE - Static variable in class omero.gateway.model.SearchParameters
 
ALL_TYPES - Static variable in class omero.gateway.model.SearchParameters
 
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 alpha 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
 
AMD_submit() - Constructor for class ome.services.blitz.repo.PublicRepositoryI.AMD_submit
 
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
 
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
 
AnnotationData - Class in omero.gateway.model
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 omero.gateway.model.AnnotationData
Creates a new instance.
AnnotationData(A) - Constructor for class omero.gateway.model.AnnotationData
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
 
AnnotationListValue(String, ImportConfig, List<Annotation>) - Constructor for class ome.formats.importer.ImportConfig.AnnotationListValue
 
annotations - Variable in class ome.formats.importer.ImportConfig
 
ANNOTATIONS - Static variable in class omero.gateway.model.ChannelData
Identifies the Channel.ANNOTATIONLINKS field.
ANNOTATIONS - Static variable in class omero.gateway.model.DatasetData
Identifies the DatasetI.ANNOTATIONLINKS field.
ANNOTATIONS - Static variable in class omero.gateway.model.ImageData
Identifies the ImageI.ANNOTATIONLINKS field.
ANNOTATIONS - Static variable in class omero.gateway.model.PlateData
Identifies the PlateI.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 omero.gateway.model.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
 
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 omero.gateway.model.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
Converts the current SmartShape to a Shape.
asAwtShape() - Method in class omero.model.SmartTextI
 
asCastedDataObjects(List) - Static method in class omero.gateway.util.PojoMapper
Converts each element of the collection into its corresponding DataObject.
ASCENDING_LETTER - Static variable in class omero.gateway.model.PlateData
Indicates that the column or row is a letter starting from A.
ASCENDING_NUMBER - Static variable in class omero.gateway.model.PlateData
Indicates that the column or row is a number starting from 1.
asChannel() - Method in class omero.gateway.model.DataObject
Returns the hosted IObject as a Well.
asClassOrNull(String) - Method in class ome.services.fulltext.FullTextIndexer
 
asDataObject(IObject) - Static method in class omero.gateway.util.PojoMapper
Converts the specified IObject into its corresponding DataObject.
asDataObjectMap(Class<K>, Class<V>, String, List) - Static method in class omero.gateway.util.PojoMapper
Converts each element of the list to a pair (key, value) in the map.
asDataObjects(Collection) - Static method in class omero.gateway.util.PojoMapper
Converts each element of the collection into its corresponding DataObject.
asDataObjects(List) - Static method in class omero.gateway.util.PojoMapper
Converts each element of the collection into its corresponding DataObject.
asDataObjects(IObject[]) - Static method in class omero.gateway.util.PojoMapper
Converts each element of the array into its corresponding DataObject.
asDataObjects(Map) - Static method in class omero.gateway.util.PojoMapper
Converts each pair (key, value) of the map.
asDataObjectsAsList(Collection) - Static method in class omero.gateway.util.PojoMapper
Converts each element of the collection into its corresponding DataObject.
asDataset() - Method in class omero.gateway.model.DataObject
Returns the hosted IObject as a Dataset.
asExperimenter() - Method in class omero.gateway.model.DataObject
Returns the hosted IObject as an Experimenter.
asGroup() - Method in class omero.gateway.model.DataObject
Returns the hosted IObject as an Experimenter Group.
asIAnnotated() - Method in class omero.gateway.model.DataObject
not null; may through class-cast exception
asImage() - Method in class omero.gateway.model.DataObject
Returns the hosted IObject as an Image.
asIObject() - Method in class omero.gateway.model.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 omero.gateway.model.DataObject
Returns the hosted IObject as a Pixels.
asPlate() - Method in class omero.gateway.model.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 omero.gateway.model.DataObject
Converts the passed IObject into its corresponding Pojo object.
asPojos(Collection) - Static method in class omero.gateway.model.DataObject
Converts the collection of IObjects into the corresponding DataObjects
asPojos(Map) - Static method in class omero.gateway.model.DataObject
Converts the map of IObjects into the corresponding DataObjects
asProject() - Method in class omero.gateway.model.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 omero.gateway.model.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.
assertNoUnlinking() - Method in class ome.services.graphs.GraphTraversal
Assert that GraphTraversal.unlinkTargets(boolean) need not be called.
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 omero.gateway.model.DataObject
Returns the hosted IObject as a Well.
asWellSample() - Method in class omero.gateway.model.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
 
attachAnnotation(SecurityContext, T, DataObject) - Method in class omero.gateway.facility.DataManagerFacility
Create/attach an AnnotationData to a given DataObject
attachFile(SecurityContext, File, String, String, String, DataObject) - Method in class omero.gateway.facility.DataManagerFacility
Attaches a File to a DataObject
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 - Variable in class omero.util.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.
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 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
 
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
 
BEGIN_POST_PROCESS(int, ImportContainer, IObject, Long, int, ImportSize) - Constructor for class ome.formats.importer.ImportEvent.BEGIN_POST_PROCESS
 
BEGIN_SAVE_TO_DB(int, ImportContainer, IObject, Long, int, ImportSize) - Constructor for class ome.formats.importer.ImportEvent.BEGIN_SAVE_TO_DB
 
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
 
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 Communicator 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.BlitzConfiguration(Ring, ome.services.sessions.SessionManager, SecuritySystem, Executor, int) 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
 
BOOLEAN() - Constructor for class ome.tools.hibernate.ListAsSQLArrayUserType.BOOLEAN
 
BOOLEAN(List<Boolean>) - Constructor for class ome.tools.hibernate.SqlArray.BOOLEAN
 
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 omero.gateway.model
Boolean annotation.
BooleanAnnotationData() - Constructor for class omero.gateway.model.BooleanAnnotationData
Creates a new instance.
BooleanAnnotationData(boolean) - Constructor for class omero.gateway.model.BooleanAnnotationData
Creates a new instance.
BooleanAnnotationData(BooleanAnnotation) - Constructor for class omero.gateway.model.BooleanAnnotationData
Creates a new instance.
BoolValue(String, ImportConfig, boolean) - Constructor for class ome.formats.importer.ImportConfig.BoolValue
 
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
 
BrowseFacility - Class in omero.gateway.facility
A Facility for browsing the data hierarchy and retrieving ProjectData, DatasetData, etc.
BTF - Static variable in class omero.gateway.util.TIFFFilter
Possible file extension.
build() - Method in class ome.formats.importer.targets.TargetBuilder
 
build() - Method in class omero.gateway.util.Requests.DiskUsageBuilder
Assemble and return the finished object.
Builder(AbstractFileSystemService, ExtendedMetadata) - Constructor for class ome.services.delete.Deletion.Builder
 
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(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.Chmod2I
 
buildResponse(int, Object) - Method in class omero.cmd.graphs.ChmodFacadeI
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.Delete2I
 
buildResponse(int, Object) - Method in class omero.cmd.graphs.DeleteFacadeI
Deprecated.
 
buildResponse(int, Object) - Method in class omero.cmd.graphs.DiskUsageI
 
buildResponse(int, Object) - Method in class omero.cmd.graphs.DuplicateI
 
buildResponse(int, Object) - Method in class omero.cmd.graphs.LegalGraphTargetsI
 
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 omero.gateway.model.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
 
bySimilarTerms(String...) - Method in interface ome.api.Search
Returns transient (without ID) TextAnnotation instances which represent terms which are similar to the given 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.
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
 
CACHE_SIZE - Static variable in interface omero.gateway.cache.CacheService
The default size of a cache.
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
 
CacheService - Interface in omero.gateway.cache
Defines the caching service interface.
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() - Method in class omero.gateway.model.DataObject
Returns true if the object can be annotated false otherwise, depending on permissions level.
canAnnotate(Current) - Method in class omero.model.PermissionsI
 
CANCEL() - Constructor for exception ome.formats.importer.ImportCandidates.CANCEL
 
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(String) - Constructor for exception omero.cmd.HandleI.Cancel
 
cancel(ERR, Throwable, String, String...) - Method in class omero.cmd.Helper
cancel(ERR, Throwable, String, Map<String, String>) - Method in class omero.cmd.Helper
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() - Method in class omero.gateway.model.DataObject
Returns true if the object can be deleted by the user currently logged in, false otherwise, depending on permissions level.
canDelete(Current) - Method in class omero.model.PermissionsI
 
canEdit() - Method in class ome.services.blitz.repo.CheckedPath
 
canEdit() - Method in class omero.gateway.model.DataObject
Returns true if the object can be edited by the user currently logged in false otherwise, depending on permissions level.
canEdit(Current) - Method in class omero.model.PermissionsI
 
canLink() - Method in class omero.gateway.model.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.
canLink(Current) - Method in class omero.model.PermissionsI
 
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 ExpiredCredentialException 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
InternalMessage 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 PasswordUtil.changeUserPasswordById(Long, String, METHOD) 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_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 omero.gateway.model
Object hosting the acquisition related to a logical channel.
ChannelAcquisitionData(LogicalChannel) - Constructor for class omero.gateway.model.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
 
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
 
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 omero.gateway.model
The data that makes up an OME Channel along with links to its logical channel.
ChannelData(int) - Constructor for class omero.gateway.model.ChannelData
Creates a new instance.
ChannelData(int, Channel) - Constructor for class omero.gateway.model.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
 
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).
checkIndex(int) - Method in class omero.util.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
 
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 this was constructed with the ignoreUnknown argument set to 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 Policy.isRestricted(IObject) 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 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
 
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
 
chgrp(String, Long, long) - Static method in class omero.gateway.util.Requests
Deprecated.
use Requests.Chgrp2Builder from Requests.chgrp(), see this method for an example
chgrp(String, Long, ChildOption, long) - Static method in class omero.gateway.util.Requests
Deprecated.
use Requests.Chgrp2Builder from Requests.chgrp(), see this method for an example
chgrp(String, Long, List<ChildOption>, long) - Static method in class omero.gateway.util.Requests
Deprecated.
use Requests.Chgrp2Builder from Requests.chgrp(), see this method for an example
chgrp(String, Long, boolean, long) - Static method in class omero.gateway.util.Requests
Deprecated.
use Requests.Chgrp2Builder from Requests.chgrp(), see this method for an example
chgrp(String, Long, ChildOption, boolean, long) - Static method in class omero.gateway.util.Requests
Deprecated.
use Requests.Chgrp2Builder from Requests.chgrp(), see this method for an example
chgrp(String, Long, List<ChildOption>, boolean, long) - Static method in class omero.gateway.util.Requests
Deprecated.
use Requests.Chgrp2Builder from Requests.chgrp(), see this method for an example
chgrp(String, List<Long>, long) - Static method in class omero.gateway.util.Requests
Deprecated.
use Requests.Chgrp2Builder from Requests.chgrp(), see this method for an example
chgrp(String, List<Long>, ChildOption, long) - Static method in class omero.gateway.util.Requests
Deprecated.
use Requests.Chgrp2Builder from Requests.chgrp(), see this method for an example
chgrp(String, List<Long>, List<ChildOption>, long) - Static method in class omero.gateway.util.Requests
Deprecated.
use Requests.Chgrp2Builder from Requests.chgrp(), see this method for an example
chgrp(String, List<Long>, boolean, long) - Static method in class omero.gateway.util.Requests
Deprecated.
use Requests.Chgrp2Builder from Requests.chgrp(), see this method for an example
chgrp(String, List<Long>, ChildOption, boolean, long) - Static method in class omero.gateway.util.Requests
Deprecated.
use Requests.Chgrp2Builder from Requests.chgrp(), see this method for an example
chgrp(String, List<Long>, List<ChildOption>, boolean, long) - Static method in class omero.gateway.util.Requests
Deprecated.
use Requests.Chgrp2Builder from Requests.chgrp(), see this method for an example
chgrp(Map<String, List<Long>>, long) - Static method in class omero.gateway.util.Requests
Deprecated.
use Requests.Chgrp2Builder from Requests.chgrp(), see this method for an example
chgrp(Map<String, List<Long>>, ChildOption, long) - Static method in class omero.gateway.util.Requests
Deprecated.
use Requests.Chgrp2Builder from Requests.chgrp(), see this method for an example
chgrp(Map<String, List<Long>>, List<ChildOption>, long) - Static method in class omero.gateway.util.Requests
Deprecated.
use Requests.Chgrp2Builder from Requests.chgrp(), see this method for an example
chgrp(Map<String, List<Long>>, boolean, long) - Static method in class omero.gateway.util.Requests
Deprecated.
use Requests.Chgrp2Builder from Requests.chgrp(), see this method for an example
chgrp(Map<String, List<Long>>, ChildOption, boolean, long) - Static method in class omero.gateway.util.Requests
Deprecated.
use Requests.Chgrp2Builder from Requests.chgrp(), see this method for an example
chgrp(Map<String, List<Long>>, List<ChildOption>, boolean, long) - Static method in class omero.gateway.util.Requests
Deprecated.
use Requests.Chgrp2Builder from Requests.chgrp(), see this method for an example
chgrp() - Static method in class omero.gateway.util.Requests
 
Chgrp2Builder() - Constructor for class omero.gateway.util.Requests.Chgrp2Builder
Instantiate a new Chgrp2.
Chgrp2I - Class in omero.cmd.graphs
Request to move model objects to a different experiment group, replacing version 5.0's 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).
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.
chmod(String, Long, String) - Static method in class omero.gateway.util.Requests
Deprecated.
use Requests.Chmod2Builder from Requests.chmod(), see this method for an example
chmod(String, Long, ChildOption, String) - Static method in class omero.gateway.util.Requests
Deprecated.
use Requests.Chmod2Builder from Requests.chmod(), see this method for an example
chmod(String, Long, List<ChildOption>, String) - Static method in class omero.gateway.util.Requests
Deprecated.
use Requests.Chmod2Builder from Requests.chmod(), see this method for an example
chmod(String, Long, boolean, String) - Static method in class omero.gateway.util.Requests
Deprecated.
use Requests.Chmod2Builder from Requests.chmod(), see this method for an example
chmod(String, Long, ChildOption, boolean, String) - Static method in class omero.gateway.util.Requests
Deprecated.
use Requests.Chmod2Builder from Requests.chmod(), see this method for an example
chmod(String, Long, List<ChildOption>, boolean, String) - Static method in class omero.gateway.util.Requests
Deprecated.
use Requests.Chmod2Builder from Requests.chmod(), see this method for an example
chmod(String, List<Long>, String) - Static method in class omero.gateway.util.Requests
Deprecated.
use Requests.Chmod2Builder from Requests.chmod(), see this method for an example
chmod(String, List<Long>, ChildOption, String) - Static method in class omero.gateway.util.Requests
Deprecated.
use Requests.Chmod2Builder from Requests.chmod(), see this method for an example
chmod(String, List<Long>, List<ChildOption>, String) - Static method in class omero.gateway.util.Requests
Deprecated.
use Requests.Chmod2Builder from Requests.chmod(), see this method for an example
chmod(String, List<Long>, boolean, String) - Static method in class omero.gateway.util.Requests
Deprecated.
use Requests.Chmod2Builder from Requests.chmod(), see this method for an example
chmod(String, List<Long>, ChildOption, boolean, String) - Static method in class omero.gateway.util.Requests
Deprecated.
use Requests.Chmod2Builder from Requests.chmod(), see this method for an example
chmod(String, List<Long>, List<ChildOption>, boolean, String) - Static method in class omero.gateway.util.Requests
Deprecated.
use Requests.Chmod2Builder from Requests.chmod(), see this method for an example
chmod(Map<String, List<Long>>, String) - Static method in class omero.gateway.util.Requests
Deprecated.
use Requests.Chmod2Builder from Requests.chmod(), see this method for an example
chmod(Map<String, List<Long>>, ChildOption, String) - Static method in class omero.gateway.util.Requests
Deprecated.
use Requests.Chmod2Builder from Requests.chmod(), see this method for an example
chmod(Map<String, List<Long>>, List<ChildOption>, String) - Static method in class omero.gateway.util.Requests
Deprecated.
use Requests.Chmod2Builder from Requests.chmod(), see this method for an example
chmod(Map<String, List<Long>>, boolean, String) - Static method in class omero.gateway.util.Requests
Deprecated.
use Requests.Chmod2Builder from Requests.chmod(), see this method for an example
chmod(Map<String, List<Long>>, ChildOption, boolean, String) - Static method in class omero.gateway.util.Requests
Deprecated.
use Requests.Chmod2Builder from Requests.chmod(), see this method for an example
chmod(Map<String, List<Long>>, List<ChildOption>, boolean, String) - Static method in class omero.gateway.util.Requests
Deprecated.
use Requests.Chmod2Builder from Requests.chmod(), see this method for an example
chmod() - Static method in class omero.gateway.util.Requests
 
Chmod2Builder() - Constructor for class omero.gateway.util.Requests.Chmod2Builder
Instantiate a new Chmod2.
Chmod2I - Class in omero.cmd.graphs
Request to change the permissions on model objects, replacing version 5.0's 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).
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
chown(String, Long, long) - Static method in class omero.gateway.util.Requests
Deprecated.
use Requests.Chown2Builder from Requests.chown(), see this method for an example
chown(String, Long, ChildOption, long) - Static method in class omero.gateway.util.Requests
Deprecated.
use Requests.Chown2Builder from Requests.chown(), see this method for an example
chown(String, Long, List<ChildOption>, long) - Static method in class omero.gateway.util.Requests
Deprecated.
use Requests.Chown2Builder from Requests.chown(), see this method for an example
chown(String, Long, boolean, long) - Static method in class omero.gateway.util.Requests
Deprecated.
use Requests.Chown2Builder from Requests.chown(), see this method for an example
chown(String, Long, ChildOption, boolean, long) - Static method in class omero.gateway.util.Requests
Deprecated.
use Requests.Chown2Builder from Requests.chown(), see this method for an example
chown(String, Long, List<ChildOption>, boolean, long) - Static method in class omero.gateway.util.Requests
Deprecated.
use Requests.Chown2Builder from Requests.chown(), see this method for an example
chown(String, List<Long>, long) - Static method in class omero.gateway.util.Requests
Deprecated.
use Requests.Chown2Builder from Requests.chown(), see this method for an example
chown(String, List<Long>, ChildOption, long) - Static method in class omero.gateway.util.Requests
Deprecated.
use Requests.Chown2Builder from Requests.chown(), see this method for an example
chown(String, List<Long>, List<ChildOption>, long) - Static method in class omero.gateway.util.Requests
Deprecated.
use Requests.Chown2Builder from Requests.chown(), see this method for an example
chown(String, List<Long>, boolean, long) - Static method in class omero.gateway.util.Requests
Deprecated.
use Requests.Chown2Builder from Requests.chown(), see this method for an example
chown(String, List<Long>, ChildOption, boolean, long) - Static method in class omero.gateway.util.Requests
Deprecated.
use Requests.Chown2Builder from Requests.chown(), see this method for an example
chown(String, List<Long>, List<ChildOption>, boolean, long) - Static method in class omero.gateway.util.Requests
Deprecated.
use Requests.Chown2Builder from Requests.chown(), see this method for an example
chown(Map<String, List<Long>>, long) - Static method in class omero.gateway.util.Requests
Deprecated.
use Requests.Chown2Builder from Requests.chown(), see this method for an example
chown(Map<String, List<Long>>, ChildOption, long) - Static method in class omero.gateway.util.Requests
Deprecated.
use Requests.Chown2Builder from Requests.chown(), see this method for an example
chown(Map<String, List<Long>>, List<ChildOption>, long) - Static method in class omero.gateway.util.Requests
Deprecated.
use Requests.Chown2Builder from Requests.chown(), see this method for an example
chown(Map<String, List<Long>>, boolean, long) - Static method in class omero.gateway.util.Requests
Deprecated.
use Requests.Chown2Builder from Requests.chown(), see this method for an example
chown(Map<String, List<Long>>, ChildOption, boolean, long) - Static method in class omero.gateway.util.Requests
Deprecated.
use Requests.Chown2Builder from Requests.chown(), see this method for an example
chown(Map<String, List<Long>>, List<ChildOption>, boolean, long) - Static method in class omero.gateway.util.Requests
Deprecated.
use Requests.Chown2Builder from Requests.chown(), see this method for an example
chown() - Static method in class omero.gateway.util.Requests
 
Chown2Builder() - Constructor for class omero.gateway.util.Requests.Chown2Builder
Instantiate a new Chown2.
Chown2I - Class in omero.cmd.graphs
Request to give model objects to a different experimenter, replacing version 5.0's 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).
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
Deletes the top-level temporary directory.
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
Releases the lock and deletes the top-level temporary directory.
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() - Static method in class omero.gateway.facility.Facility
Clears the Facility object cache
clear() - Method in class omero.gateway.model.SearchResultCollection
 
clear() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
reset all statistics
clearAllCaches() - Method in interface omero.gateway.cache.CacheService
Clears all the caches.
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.
clearCache(int) - Method in interface omero.gateway.cache.CacheService
Clears the specified cache.
clearCache() - Method in class omero.gateway.rnd.DataSink
Erases the cache.
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 Server.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
 
ClientPathExclusion - Class in ome.formats.importer.exclusions
Voter which checks the original filepath from the client (FilesetEntry.getClientPath()) for existence.
ClientPathExclusion() - Constructor for class ome.formats.importer.exclusions.ClientPathExclusion
 
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).
closeConnector(SecurityContext) - Method in class omero.gateway.Gateway
Close a connector for a certain SecurityContext
closed - Variable in class ome.model.meta.Session
 
CLOSED - Static variable in class ome.model.meta.Session
 
closeImport(SecurityContext, String) - Method in class omero.gateway.Gateway
Close Import for a certain user
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
 
CloseOnNoSessionContext() - Constructor for class ome.security.basic.BasicSecurityWiring.CloseOnNoSessionContext
 
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
 
closeService(SecurityContext, StatefulServiceInterfacePrx) - Method in class omero.gateway.Gateway
Close a service
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 uploader 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(CmdCallbackI) - 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
 
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.
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
 
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 omero.gateway.model.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 omero.gateway.model.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 omero.gateway.model.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(LoginCredentials) - Method in class omero.gateway.Gateway
Connect to the server
connect() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
CONNECTION - Static variable in exception omero.gateway.exception.RenderingServiceException
Indicates that the error occurred due to a connection failure.
ConnectionStatus - Enum in omero.gateway.exception
The various connections status.
consolidate() - Method in class omero.gateway.model.SearchResultCollection
Removes results which DataObjects are not set
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(Object) - Method in class omero.gateway.model.SearchResultCollection
 
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(Timer.Context) - Constructor for class ome.system.metrics.DefaultTimer.Context
 
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.Push - Class in ome.services.messages
Published when an internal service would like to modify the current EventContext.
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
 
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.Int - Class in ome.model.units
Simply is a representation of a possibly large integer.
Conversion.Mul - Class in ome.model.units
Multiplies all Conversion instances via BigDecimal.multiply(BigDecimal).
Conversion.Pow - Class in ome.model.units
Exponentiates two Conversion instances via BigDecimal.pow(int).
Conversion.Rat - Class in ome.model.units
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.
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
 
convertRTypeToJava(RType) - Static method in class omero.gateway.util.ModelMapper
Converts the passed OMERO type into its corresponding Java type.
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
 
convertTypeForSearch(Class) - Static method in class omero.gateway.util.PojoMapper
Converts the specified type to its corresponding type for search.
convertTypeForSearchByQuery(Class) - Static method in class omero.gateway.util.PojoMapper
Converts the specified type to its corresponding type for search by HQL query
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 interface omero.cmd.graphs.IGraphModifyRequest
Deprecated.
Produce a clone of this object.
copy() - Method in class omero.gateway.SecurityContext
Returns a copy of the security context.
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(Duplicate) - Method in class omero.cmd.graphs.DuplicateI
 
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
 
copyMultimapForResponse(SetMultimap<String, Long>) - Static method in class omero.cmd.graphs.GraphUtil
Copy a multimap to a new map.
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
 
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
 
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(String) - Constructor for class ome.services.sessions.SessionContext.Count
 
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
 
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
 
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(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) with defaults of "omero", ".tmp", and false.
create_path(String) - Static method in class omero.util.TempFileManager
Calls TempFileManager.createPath(String, String, boolean) with defaults of ".tmp", and false.
create_path(String, String) - Static method in class omero.util.TempFileManager
Calls TempFileManager.createPath(String, String, boolean) with ".tmp", and false arguments.
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
 
createAnnotation(AnnotationData) - Static method in class omero.gateway.util.ModelMapper
Creates a new annotation IObject.
createAnnotationAndLink(IObject, AnnotationData) - Static method in class omero.gateway.util.ModelMapper
Creates a new annotation IObject.
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
 
createCache() - Method in interface omero.gateway.cache.CacheService
Creates a default cache.
createCache(int, int) - Method in interface omero.gateway.cache.CacheService
Creates a cache of a given type.
createCache(int) - Method in interface omero.gateway.cache.CacheService
Creates a cache of a given type.
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
 
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
 
createDataObjects_async(AMD_IContainer_createDataObjects, List<IObject>, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI
 
createDataset(SecurityContext, DatasetData, ProjectData) - Method in class omero.gateway.facility.DataManagerFacility
Creates the DatasetData on the server and attaches it to the ProjectData (if not null) (if the project doesn't exist on the server yet, it will be created, too)
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(SecurityContext, ExperimenterData, String, String, List<GroupData>, boolean, boolean) - Method in class omero.gateway.facility.AdminFacility
Creates an experimenter and returns it.
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(SecurityContext, GroupData, ExperimenterData, int) - Method in class omero.gateway.facility.AdminFacility
Creates a group and returns it.
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
 
createIObject(DataObject) - Static method in class omero.gateway.util.ModelMapper
Converts the specified DataObject into its corresponding IObject.
createIObject(DataObject, DataObject) - Static method in class omero.gateway.util.ModelMapper
Converts the specified DataObject into its corresponding IObject.
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 the top-level temporary directory.
createPixelBuffer(Pixels) - Method in class ome.io.nio.PixelsService
Creates a PixelBuffer for a given pixels set.
createPixelsStore(SecurityContext) - Method in class omero.gateway.Gateway
Create a RawPixelsStorePrx
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.
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 servant definition 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 client.getRouter(Ice.Communicator).
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
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
 
createTableResult(TablePrx, String, long) - Static method in class omero.gateway.util.PyTablesUtils
Transforms the passed table data for a given image.
createTableResult(TablePrx, long[]) - Static method in class omero.gateway.util.PyTablesUtils
Transforms a set of rows for the passed table.
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
 
createThumbnailStore(SecurityContext) - Method in class omero.gateway.Gateway
Create a ThumbnailStorePrx
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
 
CreationRequest() - Constructor for class ome.services.sessions.SessionManager.CreationRequest
 
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 omero.gateway.model.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
 
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
 
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.
DATA_STORED(int, ImportContainer, IObject, Long, int, ImportSize) - Constructor for class ome.formats.importer.ImportEvent.DATA_STORED
 
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
 
DataManagerFacility - Class in omero.gateway.facility
A Facility for saving, deleting and updating data objects
DataObject - Class in omero.gateway.model
Abstract superclass for objects that hold OMEDS data.
DataObject() - Constructor for class omero.gateway.model.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_LINKS - Static variable in class omero.gateway.model.ImageData
Identifies the ImageI.DATASETLINKS field.
DATASET_LINKS - Static variable in class omero.gateway.model.ProjectData
Identifies the ProjectI.DATASETLINKS field.
DATASET_STORED(int, ImportContainer, IObject, Long, int, ImportSize, Integer, Integer) - Constructor for class ome.formats.importer.ImportEvent.DATASET_STORED
 
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
 
DatasetData - Class in omero.gateway.model
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 omero.gateway.model.DatasetData
Creates a new instance.
DatasetData(Dataset) - Constructor for class omero.gateway.model.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
 
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
 
DataSink - Class in omero.gateway.rnd
Encapsulates access to the image raw data.
DataSourceException - Exception in omero.gateway.exception
Reports an error occurred while trying to pull out data from the pixels data repository.
DataSourceException() - Constructor for exception omero.gateway.exception.DataSourceException
Creates a new exception.
DataSourceException(String) - Constructor for exception omero.gateway.exception.DataSourceException
Constructs a new exception with the specified detail message.
DataSourceException(Throwable) - Constructor for exception omero.gateway.exception.DataSourceException
Constructs a new exception with the specified cause.
DataSourceException(String, Throwable) - Constructor for exception omero.gateway.exception.DataSourceException
Constructs a new exception with the specified detail message and cause.
DATE(Connection, List<Date>) - Method in interface ome.tools.hibernate.ListAsSQLArrayUserType.ArrayFactory
 
DATE() - Constructor for class ome.tools.hibernate.ListAsSQLArrayUserType.DATE
 
DATE(List<Date>) - Constructor for class ome.tools.hibernate.SqlArray.DATE
 
DATE_ACQUISITION - Static variable in class ome.util.search.LuceneQueryBuilder
 
DATE_ACQUISITION - Static variable in class omero.gateway.model.SearchParameters
Indicates that the date has to be interpreted as acquisition date
DATE_IMPORT - Static variable in class ome.util.search.LuceneQueryBuilder
 
DATE_IMPORT - Static variable in class omero.gateway.model.SearchParameters
Indicates that the date has to be interpreted as import date
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
 
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(Object, String) - Method in interface omero.log.Logger
Logs a debug message.
debug(Object, LogMessage) - Method in interface omero.log.Logger
Logs a debug message.
debug(Object, String) - Method in class omero.log.NullLogger
 
debug(Object, LogMessage) - Method in class omero.log.NullLogger
 
debug(Object, String) - Method in class omero.log.SimpleLogger
 
debug(Object, LogMessage) - Method in class omero.log.SimpleLogger
 
DEBUG - Static variable in class prefs
Activated by setting DBEUG=true in the environment.
DEBUG_SEND(boolean, boolean) - Constructor for class ome.formats.importer.ImportEvent.DEBUG_SEND
 
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 interface omero.gateway.cache.CacheService
Indicates to create a default cache.
DEFAULT - Static variable in class omero.gateway.model.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 omero.gateway.model.ShapeSettingsData
The default fill color.
DEFAULT_FILL_COLOUR_ALPHA - Static variable in class omero.gateway.model.ShapeSettingsData
The default fill color.
DEFAULT_FONT_FAMILY - Static variable in class omero.gateway.model.ShapeSettingsData
The default font family.
DEFAULT_FONT_SIZE - Static variable in class omero.gateway.model.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 omero.gateway.model.ShapeSettingsData
The default stroke color.
DEFAULT_STROKE_WIDTH - Static variable in class omero.gateway.model.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