A B C D E F G H I J K L M N O P Q R S T U V W X Z _

A

AbstractAmdServant - Class in ome.services.blitz.impl

throttled implementation base class which can be used by _ServiceInterfaceOperations implementors and injected into a tie servant.

AbstractAmdServant(ServiceInterface, BlitzExecutor) - Constructor for class ome.services.blitz.impl.AbstractAmdServant

AbstractBuffer - Class in ome.io.nio

AbstractClassIdsOptionsQuery - Class in ome.services.query

simple abstract class that provides a common Definitions containing: IdsQueryParameterDef, ome.services.query.OptionsQueryParameterDef, and ClassQueryParameterDef.

AbstractClassIdsOptionsQuery(Parameters) - Constructor for class ome.services.query.AbstractClassIdsOptionsQuery

AbstractFileSystemService - Class in ome.io.nio

AbstractFileSystemService(String) - Constructor for class ome.io.nio.AbstractFileSystemService

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

Base Redirector

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, SqlAction, String, String) - Constructor for class ome.services.blitz.repo.AbstractRepositoryI

AbstractRepositoryI(ObjectAdapter, Registry, Executor, SqlAction, String, FileMaker) - Constructor for class ome.services.blitz.repo.AbstractRepositoryI

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(Job) - Method in class ome.services.procs.ProcessorSkeleton

access(File) - Method in class omero.util.TempFileManager

Returns true if the current user can write to the give directory.

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..

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(String) - Method in class ome.services.blitz.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

acquisitionData() - Method in class omero.sys.ParametersI

Sets the acquisition data parameter to true.

action - Variable in class ome.services.messages.EventLogMessage

action - Variable in class ome.tools.hibernate.EventMethodInterceptor

activate(long) - Method in interface ome.api.IShare

Turns on the access control lists attached to the given share for the current session.

activate() - Method in interface ome.api.StatefulServiceInterface

Completely restore this service for active use from whatever passivation it has implemented.

activate() - Method in class ome.services.JobBean

Does almost nothing.

activate() - Method in class ome.services.RawFileBean

activate() - Method in class ome.services.RawPixelsBean

activate() - Method in class ome.services.RenderingBean

activate() - Method in class ome.services.SearchBean

activate(long) - Method in class ome.services.sharing.ShareBean

activate() - Method in class ome.services.ThumbnailBean

activate_async(AMD_StatefulServiceInterface_activate, Current) - Method in class ome.services.blitz.impl.AbstractAmdServant

activate_async(AMD_IShare_activate, long, Current) - Method in class ome.services.blitz.impl.ShareI

activate_async(AMD_StatefulServiceInterface_activate, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI

activate_async(AMD_StatefulServiceInterface_activate, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI

activateAndWait(Current) - Method in class ome.services.blitz.impl.ProcessorCallbackI

Generates a UUID-based Identity with the category of PROCESSORCALLBACK.value and then calls {@link #activateAndWait(Current, Ice.Identity).

activateAndWait(Current, Identity) - Method in class ome.services.blitz.impl.ProcessorCallbackI

Primary method which adds this instance to IceStorm, waits for a response from any active processor services, and finally unregister itself before returning the first processor instance which responded.

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

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

add(EventLog) - Method in class ome.services.eventlogs.EventBacklog

Adds the given EventLog instance to the end of a queue for later popping if no equivalent EventLog is present.

add(GraphStep, long[]) - Method in class ome.services.export.ExporterIndex

add(Document, String, String, LuceneOptions) - Method in class ome.services.fulltext.BridgeHelper

Helper method which takes the parameters from the #set(String, Object, Document, Store, org.apache.lucene.document.Field.Index, Float) method (possibly modified) as well as the parsed String value which should be added to the index, and adds two fields.

add() - Method in class ome.services.graphs.GraphState

add() - Method in interface ome.services.graphs.GraphStep.Callback

add(GraphEntry, long[][]) - Method in class ome.services.graphs.GraphTables

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

addAllDisabled(String...) - Method in class ome.security.basic.CurrentDetails

addApplicationListener(ApplicationListener) - Method in class ome.services.messages.GlobalMulticaster

addApplicationListenerBean(String) - Method in class ome.services.messages.GlobalMulticaster

addArray(int[][], int, int, int) - Method in class pojos.util.UploadMask

Adds a Mask Shape to the appropriate ROIClass, creating one if necessary.

addCallback(String, SessionCallback) - Method in class ome.services.sessions.SessionManagerImpl

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

addCleanup(RegisterServiceCleanupMessage) - Method in class ome.security.basic.CurrentDetails

Add a RegisterServiceCleanupMessage to the current thread for cleanup by the ServiceHandler on exit.

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

addCodomainMap_async(AMD_RenderingEngine_addCodomainMap, CodomainMapContext, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI

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

addDisabled(String) - Method in class ome.security.basic.CurrentDetails

addError(Throwable, File, String[], String) - Method in class ome.formats.importer.util.ErrorHandler

Add detailed error to error container array

addEventLog(Class<? extends IObject>, long) - Method in class ome.services.eventlogs.EventLogLoader

Adds an EventLog for the given Class and id to the backlog.

addFile(String) - Method in class ome.formats.importer.util.ErrorContainer

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 omero.sys.ParametersI

addId(RLong) - Method in class omero.sys.ParametersI

addIds(Collection<Long>) - Method in class omero.sys.ParametersI

addImage(Image) - Method in class ome.services.blitz.impl.OmeroMetadata

addImage(byte[], int, int, int) - Method in class pojos.util.UploadMask

Adds a Mask Shape to the appropriate ROIClass, creating one if necessary.

addImage_async(AMD_Exporter_addImage, long, Current) - Method in class ome.services.blitz.impl.ExporterI

adding - Variable in class ome.services.eventlogs.EventBacklog

Switch between the adding and the removing states.

additions() - Method in class ome.security.basic.EventListenersFactoryBean

addKeyword(String) - Method in class pojos.WorkflowData

Adds a new keyword to the workflow.

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 omero.sys.ParametersI

addLong(String, RLong) - Method in class omero.sys.ParametersI

addLongs(String, Collection<Long>) - Method in class omero.sys.ParametersI

addMasks(Map<Integer, MaskData>) - Method in class pojos.util.ROIComponent

Adds the Masks in the maskSet to the component.

addModelProcessor(ModelProcessor) - Method in class ome.formats.OMEROMetadataStoreClient

Adds a model processor to the end of the processing chain.

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

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

addOrReplace(RepoFile, Long) - Method in class ome.services.scripts.ScriptRepoHelper

addOrReplace(SqlAction, ServiceFactory, RepoFile, Long) - Method in class ome.services.scripts.ScriptRepoHelper

addProcessor(ProcessorPrx, Current) - Method in class ome.services.blitz.impl.SharedResourcesI

addProject(String, String) - Method in class ome.formats.OMEROMetadataStoreClient

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.

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

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

addSessionCallback(String, SessionCallback) - Method in class ome.services.sessions.state.SessionCache

addShapeData(ShapeData) - Method in class pojos.ROIData

Adds ShapeData object to ROIData.

addUser(long, Experimenter) - Method in interface ome.api.IShare

Adds experimenter to share

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

Adds experimenters to share

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

admin - Variable in class ome.services.delete.DeleteBean

admin - Variable in class ome.services.sharing.ShareBean

AdminAction - Interface in ome.security

action for passing to SecuritySystem.runAsAdmin(AdminAction).

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) - Constructor for class ome.logic.AdminImpl

advices - Variable in class ome.services.util.Executor.Impl

afterPropertiesSet() - Method in class ome.security.KeyAndTrustStoreConfiguration

afterTransactionBegin(Transaction) - Method in class ome.security.basic.OmeroInterceptor

afterTransactionCompletion(Transaction) - Method in class ome.security.basic.OmeroInterceptor

agent - Variable in class ome.formats.importer.ImportConfig

aggByQuery(String, String, String, Parameters) - Method in class ome.logic.QueryImpl

aggMapByQuery(String, String, String, String, Parameters) - Method in class ome.logic.QueryImpl

all(String[]) - Static method in class prefs

Calls Preferences.childrenNames() and returns the array.

AllEntitiesPseudoLogLoader<T extends ome.model.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 omero.sys.ParametersI

Removes the experimenter parameter from the map.

allGrps() - Method in class omero.sys.ParametersI

Removes the group parameter from the map.

allow(ObjectPrx) - Method in class ome.services.blitz.impl.ServiceFactoryI

ALLOW_LEADING_WILDCARD - Static variable in interface ome.api.Search

Default leading-wildcard setting

allowAdministration() - Method in class ome.services.blitz.Router

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(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(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(Class<? extends IObject>, Details, long) - Method in class ome.security.CompositeACLVoter

allowLoad(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_INDEX - Static variable in class ome.formats.model.ColorsFactory

Index of the red component of a color.

ALPHA_INDEX - Static variable in class omeis.providers.re.ColorsFactory

Index of the red component of a color.

ALPHA_TEXT - Static variable in class ome.formats.model.ChannelProcessor

Name of the blue component when it is a graphics image.

alphalessRendering - Variable in class omeis.providers.re.Optimizations

We can do alphaless rendering

alreadyRouted(Current) - Method in class ome.services.blitz.redirect.AbstractRedirector

alreadySeen(Object) - Method in class ome.tools.hibernate.UpdateFilter

analyzer - Variable in class ome.logic.QueryImpl

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

AnnotationData - Class in pojos

Holds a textual annotation of a given data object and a reference to the Experimenter that wrote it.

AnnotationData(Class<? extends Annotation>) - Constructor for class pojos.AnnotationData

Creates a new instance.

AnnotationData(A) - Constructor for class pojos.AnnotationData

Creates a new instance.

AnnotationGraphSpec - Class in ome.services.graphs

GraphSpec specialized for deleting annotations.

AnnotationGraphSpec(List<String>) - Constructor for class ome.services.graphs.AnnotationGraphSpec

Creates a new instance.

AnnotationGraphSpec(Map<String, String>, List<String>) - Constructor for class ome.services.graphs.AnnotationGraphSpec

Creates a new instance.

annotations - Variable in class ome.formats.importer.ImportConfig

ANNOTATIONS - Static variable in class pojos.ChannelData

Identifies the Channel#ANNOTATIONLINKS field.

ANNOTATIONS - Static variable in class pojos.DatasetData

Identifies the Dataset#ANNOTATIONLINKS field.

ANNOTATIONS - Static variable in class pojos.ImageData

Identifies the Image#ANNOTATIONLINKS field.

ANNOTATIONS - Static variable in class pojos.PlateData

Identifies the Plate#ANNOTATIONLINKS field.

AnnotationUtils - Class in ome.annotations

Checks metadata constraints on API calls.

AnnotationUtils() - Constructor for class ome.annotations.AnnotationUtils

AopContextInitializer - Class in ome.services.blitz.fire

AopContextInitializer(ServiceFactory, Principal, AtomicBoolean) - Constructor for class ome.services.blitz.fire.AopContextInitializer

ApiConsistencyCheck - Class in ome.services.blitz.util

Checks all servant definitions (see: ome/services/blitz-servantDefinitions.xml) to guarantee that the RMI and the Blitz APIs match.

ApiConsistencyCheck() - Constructor for class ome.services.blitz.util.ApiConsistencyCheck

ApiConstraintChecker - Class in ome.annotations

Checks metadata constraints on API calls.

ApiConstraintChecker() - Constructor for class ome.annotations.ApiConstraintChecker

append(String) - Method in class ome.tools.hibernate.QueryBuilder

Simple delegate method to allow appending arbitrary strings.

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

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.

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 - Static variable in class pojos.LightSourceData

Indicates that the light source is a arc.

archiveImage - Variable in class ome.formats.importer.ImportConfig

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(String...) - Static method in class prefs

Converts varargs to a String-array.

asAnnotation() - Method in class pojos.DataObject

Returns the hosted IObject as an Annotation.

asAwtShape() - Method in class omero.model.SmartEllipseI

asAwtShape() - Method in class omero.model.SmartLineI

asAwtShape() - Method in class omero.model.SmartMaskI

asAwtShape() - Method in class omero.model.SmartPathI

asAwtShape() - Method in class omero.model.SmartPointI

asAwtShape() - Method in class omero.model.SmartPolygonI

asAwtShape() - Method in class omero.model.SmartPolylineI

asAwtShape() - Method in class omero.model.SmartRectI

asAwtShape() - Method in interface omero.model.SmartShape

Converst the current SmartShape to a Shape.

asAwtShape() - Method in class omero.model.SmartTextI

ASCENDING_LETTER - Static variable in class pojos.PlateData

Indicates that the column or row is a letter starting from A.

ASCENDING_NUMBER - Static variable in class pojos.PlateData

Indicates that the column or row is a number starting from 1.

asChannel() - Method in class pojos.DataObject

Returns the hosted IObject as a Well.

asClassOrNull(String) - Method in class ome.services.fulltext.FullTextIndexer

asDataset() - Method in class pojos.DataObject

Returns the hosted IObject as a Dataset.

asExperimenter() - Method in class pojos.DataObject

Returns the hosted IObject as an Experimenter.

asGroup() - Method in class pojos.DataObject

Returns the hosted IObject as an Experimenter Group.

asIAnnotated() - Method in class pojos.DataObject

not null; may through class-cast exception

asImage() - Method in class pojos.DataObject

Returns the hosted IObject as an Image.

asIObject() - Method in class pojos.DataObject

not null; no exceptions.

asPixels() - Method in class pojos.DataObject

Returns the hosted IObject as a Pixels.

asPlate() - Method in class pojos.DataObject

Returns the hosted IObject as a Plate.

asPoints() - Method in class omero.model.SmartEllipseI

asPoints() - Method in class omero.model.SmartLineI

asPoints() - Method in class omero.model.SmartMaskI

asPoints() - Method in class omero.model.SmartPathI

asPoints() - Method in class omero.model.SmartPointI

asPoints() - Method in class omero.model.SmartPolygonI

asPoints() - Method in class omero.model.SmartPolylineI

asPoints() - Method in class omero.model.SmartRectI

asPoints() - Method in interface omero.model.SmartShape

Provides some, possibly lossy, bounding polygon of this SmartShape via points.

asPoints() - Method in class omero.model.SmartTextI

asPojo(IObject) - Static method in class pojos.DataObject

Converts the passed IObject into its corresponding Pojo object.

asPojos(Collection) - Static method in class pojos.DataObject

Converts the collection of IObjects into the corresponding DataObjects

asPojos(Map) - Static method in class pojos.DataObject

Converts the map of IObjects into the corresponding DataObjects

asProject() - Method in class pojos.DataObject

Returns the hosted IObject as a Project.

asProperties() - Method in class ome.system.Login

produces a copy of the internal fields as a Properties instance.

asProperties() - Method in class ome.system.Server

produces a copy of the internal fields as a Properties instance.

asroot - Variable in class ome.services.sessions.SessionManagerImpl

A private session for use only by this instance for running methods via Executor.

asScreen() - Method in class pojos.DataObject

Returns the hosted IObject as a Screen.

assemble(Serializable, Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType

assertManaged(IObject) - Method in class ome.logic.AdminImpl

assertNodes(Set<String>) - Method in class ome.services.blitz.fire.Ring

asWell() - Method in class pojos.DataObject

Returns the hosted IObject as a Well.

asWellSample() - Method in class pojos.DataObject

Returns the hosted IObject as a Well.

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

attachImageToDataset(Dataset, Image, Current) - Method in class ome.services.blitz.gateway.OmeroGateway

attachImageToDataset(Dataset, Image) - Method in interface ome.services.blitz.gateway.services.DataService

Attach an image to a dataset.

attachImageToDataset(Dataset, Image) - Method in class ome.services.blitz.gateway.services.impl.DataServiceImpl

AttributeNewUserGroupBean - Class in ome.security.auth

Handles the ":attribute:" specifier from etc/omero.properties.

AttributeNewUserGroupBean(String) - 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

available() - Method in class ome.services.pixeldata.PersistentEventLogLoader

availableCommands_async(AMD_IDelete_availableCommands, Current) - Method in class ome.services.blitz.impl.DeleteI

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 - 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 omerojava.util.ReadOnlyByteArray

The original array.

BaseGraphSpec - Class in ome.services.graphs

GraphSpec which takes the id of some id as the root of deletion.

BaseGraphSpec(String, String...) - Constructor for class ome.services.graphs.BaseGraphSpec

Simplified constructor, primarily used for testing.

BaseGraphSpec(List<String>) - Constructor for class ome.services.graphs.BaseGraphSpec

BaseGraphSpec.SubSpecIterator - Class in ome.services.graphs

Iterator which walks returns all GraphSpecs which are reachable from the given spec, depth first including the spec itself.

BaseGraphSpec.SubSpecIterator(GraphSpec) - Constructor for class ome.services.graphs.BaseGraphSpec.SubSpecIterator

basename() - Method in class ome.services.scripts.RepoFile

basic - Variable in class ome.security.SecuritySystemHolder

BasicACLVoter - Class in ome.security.basic

BasicACLVoter(CurrentDetails, SystemTypes, TokenHolder, SecurityFilter) - Constructor for class ome.security.basic.BasicACLVoter

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) - 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

batchSize - Variable in class ome.services.eventlogs.EventLogLoader

batchSize - Variable in class ome.services.search.SearchValues

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

beforeTransactionCompletion(Transaction) - Method in class ome.security.basic.OmeroInterceptor

BfPixelBuffer - Class in ome.io.bioformats

PixelBuffer implementation which uses Bio-Formats to read pixels data directly from original files.

BfPixelBuffer(String, IFormatReader) - Constructor for class ome.io.bioformats.BfPixelBuffer

We may want a constructor that takes the id of an imported file or that takes a File object?

BfPixelsStoreI - Class in ome.services.blitz.repo

BfPixelsStoreI(String, ImageReader) - Constructor for class ome.services.blitz.repo.BfPixelsStoreI

BfPixelsWrapper - Class in ome.io.bioformats

BfPixelsWrapper(String, IFormatReader) - Constructor for class ome.io.bioformats.BfPixelsWrapper

We may want a constructor that takes the id of an imported file or that takes a File object?

BfPyramidPixelBuffer - Class in ome.io.bioformats

PixelBuffer implementation which uses Bio-Formats to read pixels data directly from original files.

BfPyramidPixelBuffer(Pixels, String, boolean) - Constructor for class ome.io.bioformats.BfPyramidPixelBuffer

We may want a constructor that takes the id of an imported file or that takes a File object?

BfPyramidPixelBuffer(TileSizes, Pixels, String, boolean) - Constructor for class ome.io.bioformats.BfPyramidPixelBuffer

Full constructor taking a TileSizes implementation which defines how large the pyramid tiles will be.

bfReader - Variable in class ome.io.bioformats.BfPixelBuffer

BfRenderingEngineI - Class in ome.services.blitz.repo

BfRenderingEngineI() - Constructor for class ome.services.blitz.repo.BfRenderingEngineI

BinaryMaskQuantizer - Class in omeis.providers.re.quantum

Quantization process for binary masks.

BinaryMaskQuantizer(QuantumDef, PixelsType) - Constructor for class omeis.providers.re.quantum.BinaryMaskQuantizer

Creates a new strategy.

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.

BlitzConfiguration - Class in ome.services.blitz.util

Factory bean which creates an instance as well as the proper ObjectAdapter and adds initial, well-known servants.

BlitzConfiguration(Ring, SessionManager, SecuritySystem, Executor) - 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) - Constructor for class ome.services.blitz.util.BlitzConfiguration

Like #BlitzConfiguration(ome.services.sessions.SessionManager, SecuritySystem, Executor) but allows properties to be specified via an InitializationData instance.

BlitzConfiguration(Ring, SessionManager, SecuritySystem, Executor, Map<String, ObjectFactory>) - Constructor for class ome.services.blitz.util.BlitzConfiguration

Like #BlitzConfiguration(ome.services.sessions.SessionManager, SecuritySystem, Executor) but allows ObjectFactory instances to be specified via a Map.

BlitzConfiguration(InitializationData, Ring, SessionManager, SecuritySystem, Executor, Map<String, ObjectFactory>) - Constructor for class ome.services.blitz.util.BlitzConfiguration

Full constructor

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

BlobShareStore() - Constructor for class ome.services.sharing.BlobShareStore

block(long) - Method in class omero.grid.DeleteCallbackI

Should only be used if the default logic of the process methods is kept in place.

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_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

BooleanAnnotationData - Class in pojos

Boolean annotation.

BooleanAnnotationData() - Constructor for class pojos.BooleanAnnotationData

Creates a new instance.

BooleanAnnotationData(boolean) - Constructor for class pojos.BooleanAnnotationData

Creates a new instance.

BooleanAnnotationData(BooleanAnnotation) - Constructor for class pojos.BooleanAnnotationData

Creates a new instance.

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

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

BULK_ANNOTATIONS_NS - Static variable in class pojos.FileAnnotationData

The name space used to indicate that the FileAnnotation is a Bulk Annotations file.

byAnnotatedWith(Annotation...) - Method in interface ome.api.Search

Finds entities annotated with an Annotation similar to the example.

byAnnotatedWith(Annotation...) - Method in class ome.services.SearchBean

byAnnotatedWith_async(AMD_Search_byAnnotatedWith, List<Annotation>, Current) - Method in class ome.services.blitz.impl.SearchI

byFullText(String) - Method in interface ome.api.Search

Passes the query as is to the Lucene backend.

byFullText(String) - Method in class ome.services.SearchBean

byFullText_async(AMD_Search_byFullText, String, Current) - Method in class ome.services.blitz.impl.SearchI

byGroupForTags(String) - Method in interface ome.api.Search

Returns transient (without ID) TagAnnotation instances which represent all the tags in the given group.

byGroupForTags(String) - Method in class ome.services.SearchBean

byGroupForTags_async(AMD_Search_byGroupForTags, String, Current) - Method in class ome.services.blitz.impl.SearchI

byHqlQuery(String, Parameters) - Method in interface ome.api.Search

Delegates to IQuery.findAllByQuery(String, Parameters) method to take advantage of the Search.and(), Search.or(), and Search.not() methods, or queue-semantics.

byHqlQuery(String, Parameters) - Method in class ome.services.SearchBean

byHqlQuery_async(AMD_Search_byHqlQuery, String, Parameters, Current) - Method in class ome.services.blitz.impl.SearchI

bySimilarTerms(String...) - Method in interface ome.api.Search

Returns transient (without ID) TextAnnotation instances which represent terms which are similar to the give terms.

bySimilarTerms(String...) - Method in class ome.services.SearchBean

bySimilarTerms_async(AMD_Search_bySimilarTerms, List<String>, Current) - Method in class ome.services.blitz.impl.SearchI

bySomeMustNone(String[], String[], String[]) - Method in interface ome.api.Search

Builds a Lucene query and passes it to Search.byFullText(String).

bySomeMustNone(String[], String[], String[]) - Method in class ome.services.SearchBean

bySomeMustNone_async(AMD_Search_bySomeMustNone, List<String>, List<String>, List<String>, Current) - Method in class ome.services.blitz.impl.SearchI

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 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.

byteArrayToHexString(byte[]) - Static method in class ome.formats.OMEROMetadataStoreClient

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 omero.util.IceMapper

cache - Variable in class ome.services.sessions.SessionManagerImpl

CacheFactory - Class in ome.services.sessions.state

CacheFactory() - Constructor for class ome.services.sessions.state.CacheFactory

CacheListener - Class in ome.services.sessions.state

Basic CacheEventListener which does nothing.

CacheListener() - Constructor for class ome.services.sessions.state.CacheListener

calculate(Pixels) - Method in class ome.io.nio.SimpleBackOff

calculate() - Method in class ome.io.nio.SimpleBackOff

calculateBackOff(int) - Method in class ome.services.db.SelfCorrectingDataSource

calculateMessageDigest() - Method in interface ome.api.RawPixelsStore

calculateMessageDigest() - Method in class ome.io.bioformats.BfPixelBuffer

calculateMessageDigest() - Method in class ome.io.bioformats.BfPyramidPixelBuffer

calculateMessageDigest() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

calculateMessageDigest() - Method in interface ome.io.nio.PixelBuffer

Calculates a SHA-1 message digest for the entire pixel buffer.

calculateMessageDigest() - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

calculateMessageDigest() - Method in class ome.services.RawPixelsBean

calculateMessageDigest_async(AMD_RawPixelsStore_calculateMessageDigest, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI

calculateMessageDigest_async(AMD_RawPixelsStore_calculateMessageDigest, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI

calculateXYWidths(Pixels, int) - Method in class ome.services.ThumbnailCtx

Calculates the ratio of the two sides of a Pixel set and returns the X and Y widths based on the longest side maintaining aspect ratio.

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() - 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

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

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

cancel() - Method in class ome.formats.importer.ImportCandidates.SCANNING

Can be called to cancel the current action.

cancel - Variable in class ome.formats.importer.util.ErrorFilePart

cancel() - Method in class ome.formats.importer.util.FileUploader

cancel's upload

cancel(Current) - Method in class ome.services.blitz.impl.DeleteHandleI

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

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

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(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_async(AMD_IAdmin_canUpdate, IObject, Current) - Method in class ome.services.blitz.impl.AdminI

caseSensitive - Variable in class ome.services.search.SearchValues

cause(Throwable) - Static method in class ome.services.blitz.gateway.services.util.ServiceUtilities

cb - Variable in class ome.services.throttling.Task

cd - Variable in class ome.security.basic.BasicSecuritySystem

cd - Variable in class ome.security.basic.EventLogListener

ceId - Variable in class ome.system.SimpleEventContext

ceType - Variable in class ome.system.SimpleEventContext

cgId - Variable in class ome.system.SimpleEventContext

cgName - Variable in class ome.system.SimpleEventContext

chainedList - Variable in class ome.services.search.SearchAction

List of IObject instances which have currently been found.

chainedSearch(List<IObject>) - Method in class ome.services.search.SearchAction

Set the current list of found ids from previous searches, which should be chained in this search.

changeDistinguisedName(String, String) - Method in class ome.security.auth.PasswordProviders

changeExpiredCredentials(String, String, String) - Method in interface ome.api.IAdmin

Used after an ExpiredCredentialsException instance is thrown.

changeExpiredCredentials(String, String, String) - Method in class ome.logic.AdminImpl

changeExpiredCredentials_async(AMD_IAdmin_changeExpiredCredentials, String, String, String, Current) - Method in class ome.services.blitz.impl.AdminI

changeGroup(IObject, String) - Method in interface ome.api.IAdmin

call details.setGroup() on this instance.

changeGroup(IObject, String) - Method in class ome.logic.AdminImpl

changeGroup_async(AMD_IAdmin_changeGroup, IObject, String, Current) - Method in class ome.services.blitz.impl.AdminI

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.JdbcPasswordProvider

changePassword(String, String) - Method in interface ome.security.auth.PasswordProvider

Attempts to change the password for the given user.

changePassword(String, String) - Method in class ome.security.auth.PasswordProviders

changePassword_async(AMD_IAdmin_changePassword, RString, Current) - Method in class ome.services.blitz.impl.AdminI

changePasswordWithOldPassword(String, String) - Method in interface ome.api.IAdmin

change the password for the current user by passing the old password.

changePasswordWithOldPassword(String, String) - Method in class ome.logic.AdminImpl

changePasswordWithOldPassword_async(AMD_IAdmin_changePasswordWithOldPassword, RString, RString, Current) - Method in class ome.services.blitz.impl.AdminI

changePermissions(IObject, Permissions) - Method in interface ome.api.IAdmin

call defaults.setPermissions() on this instance.

changePermissions(IObject, Permissions) - Method in class ome.logic.AdminImpl

the implementation of this method is somewhat tricky in that Permissions changes must be allowed even when other updates are not.

changePermissions_async(AMD_IAdmin_changePermissions, IObject, Permissions, Current) - Method in class ome.services.blitz.impl.AdminI

ChangeSecurityContextEvent - Class in ome.services.sessions.events

InteralMessage published by the SessionManager when setSecurityContext() is called.

ChangeSecurityContextEvent(Object, String, IObject, IObject) - Constructor for class ome.services.sessions.events.ChangeSecurityContextEvent

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

ChannelAcquisitionData - Class in pojos

Object hosting the acquisition related to a logical channel.

ChannelAcquisitionData(LogicalChannel) - Constructor for class pojos.ChannelAcquisitionData

Creates a new instance.

ChannelData - Class in ome.formats.model

Represents all the metadata required to make accurate decisions about channel colour and name.

ChannelData() - Constructor for class ome.formats.model.ChannelData

ChannelData - Class in pojos

The data that makes up an OME Channel along with links to its logical channel.

ChannelData(int) - Constructor for class pojos.ChannelData

Creates a new instance.

ChannelData(int, Channel) - Constructor for class pojos.ChannelData

Creates a new instance.

CHANNELID_QUERY - Static variable in class ome.services.delete.DeleteBean

ChannelProcessor - Class in ome.formats.model

Processes the pixels sets of an IObjectContainerStore and ensures that LogicalChannel containers are present in the container cache, and populating channel name and colour where appropriate.

ChannelProcessor() - Constructor for class ome.formats.model.ChannelProcessor

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

checkAndRegister() - Method in class ome.services.JobBean

checkArgs(Object...) - Method in class ome.services.graphs.GraphEntry

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

checkedCast(ObjectPrx) - Static method in class ome.services.sharing.data.ObjPrxHelper

checkedCast(ObjectPrx, Map<String, String>) - Static method in class ome.services.sharing.data.ObjPrxHelper

checkedCast(ObjectPrx, String) - Static method in class ome.services.sharing.data.ObjPrxHelper

checkedCast(ObjectPrx, String, Map<String, String>) - Static method in class ome.services.sharing.data.ObjPrxHelper

checkedCast(ObjectPrx) - Static method in class ome.services.sharing.data.ShareDataPrxHelper

checkedCast(ObjectPrx, Map<String, String>) - Static method in class ome.services.sharing.data.ShareDataPrxHelper

checkedCast(ObjectPrx, String) - Static method in class ome.services.sharing.data.ShareDataPrxHelper

checkedCast(ObjectPrx, String, Map<String, String>) - Static method in class ome.services.sharing.data.ShareDataPrxHelper

checkedCast(ObjectPrx) - Static method in class ome.services.sharing.data.ShareItemPrxHelper

checkedCast(ObjectPrx, Map<String, String>) - Static method in class ome.services.sharing.data.ShareItemPrxHelper

checkedCast(ObjectPrx, String) - Static method in class ome.services.sharing.data.ShareItemPrxHelper

checkedCast(ObjectPrx, String, Map<String, String>) - Static method in class ome.services.sharing.data.ShareItemPrxHelper

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

checkImageDelete_async(AMD_IDelete_checkImageDelete, long, boolean, Current) - Method in class ome.services.blitz.impl.DeleteI

checkIndex(int) - Method in class ome.util.mem.ReadOnlyByteArray

Makes sure that i is in [0, length).

checkIndex(int) - Method in class omerojava.util.ReadOnlyByteArray

Makes sure that i is in [0, length).

checkManagedDetails(IObject, Details) - Method in class ome.security.basic.BasicSecuritySystem

checkManagedDetails(IObject, Details) - Method in class ome.security.basic.OmeroInterceptor

checkManagedDetails(IObject, Details) - Method in interface ome.security.SecuritySystem

checks that a non-privileged user has not attempted to edit the entity's security details.

checkManagedDetails(IObject, Details) - Method in class ome.security.SecuritySystemHolder

checkManagedDetails(IObject, Details) - Method in class ome.security.sharing.SharingSecuritySystem

checkMethod(Object, Method, Principal, boolean) - Method in class ome.security.basic.BasicMethodSecurity

See MethodSecurity#checkMethod(Object, Method, Principal)

checkMethod(Object, Method, Principal, boolean) - Method in interface ome.security.MethodSecurity

Throws a SecurityViolation exception if the given Principal does not have the proper permissions to execute the given method.

checkNonNull(List<Point>) - Static method in class omero.model.SmartShape.Util

Used from assert statements of the form: assert Util.checkNonNull(points) : "Null points in " + this; in all the implementations of SmartShape.asPoints().

checkParameters() - Method in class ome.services.query.Query

check the Parameters instance against the Definitions instance for this Query.

checkPassword(String, String, boolean) - Method in interface ome.api.local.LocalAdmin

Checks password for given user.

checkPassword(String, String, boolean) - Method in class ome.logic.AdminImpl

If ldap plugin turned, creates Ldap accounts and authentication by LDAP available.

checkPassword(String, String, boolean) - Method in class ome.security.auth.ConfigurablePasswordProvider

If ConfigurablePasswordProvider.ignoreUnknown is true, returns null, since the base class knows no users.

checkPassword(String, String, boolean) - Method in class ome.security.auth.FilePasswordProvider

checkPassword(String, String, boolean) - Method in class ome.security.auth.JdbcPasswordProvider

Retrieves password from the database and calls ConfigurablePasswordProvider.comparePasswords(String, String).

checkPassword(String, String, boolean) - Method in class ome.security.auth.LdapPasswordProvider

checkPassword(String, String, boolean) - Method in interface ome.security.auth.PasswordProvider

Authenticates the give user given the password token.

checkPassword(String, String, boolean) - Method in class ome.security.auth.PasswordProviders

checkPassword(String, String, boolean) - Method in class ome.security.auth.providers.LdapPasswordProvider431

checkPassword(String) - Method in class ome.services.blitz.fire.Ring

Currently only returns false since if the regular password check performed by SessionManager cannot find the session, then the cluster has no extra information.

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

calls BasicSecuritySystem.isReady() and if not throws an ApiUsageException.

checkState() - Method in class ome.services.procs.ProcessSkeleton

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

checkWriteOperationAllowed(Session) - Method in class ome.tools.spring.ManualFlushHibernateTemplate

choose() - Method in class ome.security.CompositeACLVoter

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

Does nothing since all redirects are chosen during Redirector.getProxyOrNull(Context, String, Glacier2.SessionControlPrx, Ice.Current)

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

cleanTempDir() - Method in class omero.util.TempFileManager

Deletes TempFileManager.dir

cleanThread() - Method in class ome.tools.hibernate.SessionHandler

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 TempFileManager.lock and deletes TempFileManager.dir.

cleanUserDir() - Method in class omero.util.TempFileManager

Attempts to delete all directories under self.userdir other than the one owned by this process.

clear() - Method in interface ome.api.local.LocalQuery

clear() - Method in class ome.formats.importer.ImportLibrary

clear() - Method in class ome.logic.QueryImpl

clear() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

reset all statistics

clearDisabled() - Method in class ome.security.basic.CurrentDetails

clearErrors(int) - Method in class ome.formats.importer.util.ErrorHandler

clearLogs() - Method in class ome.security.basic.BasicSecuritySystem

clearLogs() - Method in class ome.security.basic.CurrentDetails

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

clearToken(GraphHolder) - Method in class ome.security.basic.TokenHolder

client - Class in omero

Central client-side blitz entry point.

client() - Constructor for class omero.client

Calls client.client(Ice.InitializationData) with a new InitializationData

client(InitializationData) - Constructor for class omero.client

Creates an Communicator from a InitializationData instance.

client(String) - Constructor for class omero.client

Creates an Communicator pointing at the given server using the #DEFAULT_PORT.

client(String, int) - Constructor for class omero.client

Creates an Communicator pointing at the given server with the non-standard port.

client(String[]) - Constructor for class omero.client

Calls client.client(String[], Ice.InitializationData) with a new InitializationData

client(String[], InitializationData) - Constructor for class omero.client

Creates an Communicator from command-line arguments.

client(File...) - Constructor for class omero.client

Creates an Communicator from multiple files.

client(Map) - Constructor for class omero.client

Creates an Communicator from a Map instance.

CLIENT_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

clientId - Variable in class ome.services.blitz.impl.ServiceFactoryI

clientId(Current) - Static method in class ome.services.blitz.impl.ServiceFactoryI

Helpers method to extract the CLIENTUUID out of the given Ice.Current.

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

clone() - Method in class ome.services.sessions.state.CacheListener

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.AbstractAmdServant

close(Current) - Method in interface ome.services.blitz.impl.CloseableServant

close(Current) - Method in class ome.services.blitz.impl.DeleteHandleI

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() - Method in class ome.services.graphs.BaseGraphSpec

close() - Method in interface ome.services.graphs.GraphSpec

close() - Method in class ome.services.JobBean

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() - Method in class omero.grid.DeleteCallbackI

close(Current) - Method in class omero.grid.InteractiveProcessorI

close() - Method in class omero.grid.ProcessCallbackI

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.AbstractAmdServant

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

close_async(AMD_StatefulServiceInterface_close, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI

CloseableServant - Interface in ome.services.blitz.impl

Marker interface which distinguishes a servant which wants to have CloseableServant.close(Ice.Current) called on ServiceFactoryI.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.

closeOnDestroy(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI

closeService() - Method in class ome.services.blitz.gateway.services.GatewayFactory

closeService() - Method in interface ome.services.blitz.gateway.services.GatewayService

Close the service and all it's surrogate services.

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

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

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 omeis.providers.re.codomain

Each concrete subclass defines transformation parameters for a CodomainMap implementation.

CodomainMapContext() - Constructor for class omeis.providers.re.codomain.CodomainMapContext

collapse(boolean) - Method in class ome.services.graphs.GraphState

collapse(boolean) - Method in interface ome.services.graphs.GraphStep.Callback

collect(UnloadedCollector, Image) - Method in class ome.services.delete.DeleteBean

Walks the Image graph collecting unloaded instances of all entities for later delete.

collectionCast(Class<T>, List<IObject>) - Static method in class ome.services.blitz.gateway.services.util.ServiceUtilities

Helper method for the conversion of base types in containers(normally of type IObject) to a concrete type.

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

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

columnSets(GraphEntry, long[]) - Method in class ome.services.graphs.GraphTables

Returns all column sets where the first LENGTH - 1 members of "match" coincide with the values of the columns in the set.

COMBINED - Static variable in class ome.services.fulltext.BridgeHelper

Name of the Field which contains the union of all fields.

commands(Current) - Method in class ome.services.blitz.impl.DeleteHandleI

CommonsLoggingAdapter - Class in ome.services.blitz.util

A simple Adapter to have the ICE runtime log to our log file.

CommonsLoggingAdapter(Log) - Constructor for class ome.services.blitz.util.CommonsLoggingAdapter

COMPANION_FILE_NS - Static variable in class pojos.FileAnnotationData

The name space used to indicate that the FileAnnotation is a companion file.

companionFile - Variable in class ome.formats.importer.ImportConfig

compare(LSID, LSID) - Method in class ome.formats.OMEXMLModelComparator

compare(Dataset, Dataset) - Method in class ome.formats.SortDatasetsByName

compare(Project, Project) - Method in class ome.formats.SortProjectsByName

compare(Object, Object) - Method in class pojos.ROICoordinate

Implemented as specified by the Comparator I/F.

comparePasswords(String, String) - Method in class ome.security.auth.ConfigurablePasswordProvider

Compares the password provided by the user (unhashed) against the given trusted password.

comparePasswords(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.

COMPLEX_TYPE - Static variable in class pojos.PixelsData

Identifies the type used to store pixel values.

CompositeACLVoter - Class in ome.security

CompositeACLVoter(CurrentDetails, BasicACLVoter, SharingACLVoter) - Constructor for class ome.security.CompositeACLVoter

CompressImpl - Class in ome.logic

CompressImpl() - Constructor for class ome.logic.CompressImpl

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.

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.util.ErrorHandler

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

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.

configureDebug(Level) - Method in class ome.formats.importer.ImportConfig

Modifies the Log4j logging level of everything under the ome.format and loci package 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

configureLogging() - Static method in class ome.services.blitz.Entry

Most ome/omero classes use the Log and LogFactory classes for logging.

conn - Variable in class ome.services.sharing.FreezeShareStore

connect() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

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

ContainerI - Class in ome.services.blitz.impl

Implementation of the IContainer service.

ContainerI(IContainer, BlitzExecutor) - Constructor for class ome.services.blitz.impl.ContainerI

contains(Object) - Method in interface ome.api.local.LocalQuery

Tests if an object is currently contained in the session.

contains(Object) - Method in class ome.logic.QueryImpl

contains(long, Class<T>, long) - Method in class ome.services.sharing.ShareStore

contains(double, double) - Method in class ome.util.math.geom2D.EllipseArea

Required by the Shape I/F.

contains(double, double, double, double) - Method in class ome.util.math.geom2D.EllipseArea

Required by the Shape I/F.

contains(Point2D) - Method in class ome.util.math.geom2D.EllipseArea

Required by the Shape I/F.

contains(Rectangle2D) - Method in class ome.util.math.geom2D.EllipseArea

Required by the Shape I/F.

contains(double, double) - Method in class ome.util.math.geom2D.RectangleArea

Required by the Shape I/F.

contains(double, double, double, double) - Method in class ome.util.math.geom2D.RectangleArea

Required by the Shape I/F.

contains(Point2D) - Method in class ome.util.math.geom2D.RectangleArea

Required by the Shape I/F.

contains(Rectangle2D) - Method in class ome.util.math.geom2D.RectangleArea

Required by the Shape I/F.

contains(String) - Method in class pojos.WorkflowData

Returns true if the keyword exist in the workflow, false otherwise.

containsKey(Object) - Method in class ome.services.query.Definitions

contentLength - Variable in class ome.formats.importer.ImportEvent.FILE_UPLOAD_EVENT

context - Variable in class ome.logic.AdminImpl

context - Variable in class ome.services.blitz.fire.SessionManagerI

context - Variable in class ome.services.fulltext.FileParser

context - Variable in class ome.services.sessions.SessionManagerImpl

context - Variable in class ome.services.util.Executor.Impl

contOnError - Variable in class ome.formats.importer.ImportConfig

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 ome.services.blitz.impl.ServiceFactoryI

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

convertClientToServer(Pixels, double[][]) - Static method in class omerojava.util.GatewayUtils

convert the client data pixels to server byte array, also sets the data pixel size to the size of the pixels in the pixels Id param.

convertPojos(ContainerClass) - Static method in class ome.services.blitz.gateway.services.util.ServiceUtilities

Converts the specified POJO into the corresponding model.

ConvertToBlitzExceptionMessage - Class in ome.services.blitz.util

Internal event which gives third party services a chance to map their exceptions to a blitz exception.

ConvertToBlitzExceptionMessage(Object, Throwable) - Constructor for class ome.services.blitz.util.ConvertToBlitzExceptionMessage

convertXml(MetadataRetrieve) - Method in class ome.services.blitz.impl.ExporterI

Copiable - Interface in ome.util.mem

Requires an implementing class to provide deep copies of its instances.

CopiableArray - Class in ome.util.mem

This abstract class provides an implementation of the Copiable interface.

CopiableArray(int) - Constructor for class ome.util.mem.CopiableArray

Creates a new instance.

copy(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() - 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.

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

copyGroup(ExperimenterGroup) - Method in class ome.security.auth.SimpleRoleProvider

copyImage(long, int, int, int, int, List<Integer>, String, Current) - Method in class ome.services.blitz.gateway.OmeroGateway

copyImage(long, int, int, int, int, List<Integer>, String) - Method in interface ome.services.blitz.gateway.services.ImageService

Copy the image and pixels from image.

copyImage(long, int, int, int, int, List<Integer>, String) - Method in class ome.services.blitz.gateway.services.impl.ImageServiceImpl

copyList(List<T>) - Static method in class ome.services.search.SearchValues

copyObject(Filterable, ModelMapper) - Method in class omero.model.DetailsI

copyObject(Filterable, ModelMapper) - Method in class omero.model.PermissionsI

copyOfValues() - Method in class ome.services.search.SearchAction

copyPixels(long, List<Integer>, String, Current) - Method in class ome.services.blitz.gateway.OmeroGateway

copyPixels(long, int, int, int, int, List<Integer>, String) - Method in interface ome.services.blitz.gateway.services.ImageService

Copy the pixels set from pixels to a new set.

copyPixels(long, List<Integer>, String) - Method in interface ome.services.blitz.gateway.services.ImageService

Copy the pixels set from pixels to a new set.

copyPixels(long, int, int, int, int, List<Integer>, String) - Method in class ome.services.blitz.gateway.services.impl.ImageServiceImpl

copyPixels(long, List<Integer>, String) - Method in class ome.services.blitz.gateway.services.impl.ImageServiceImpl

copyPixelsXYTZ(long, int, int, int, int, List<Integer>, String, Current) - Method in class ome.services.blitz.gateway.OmeroGateway

copyTimestamp(Timestamp) - Static method in class ome.services.search.SearchValues

copyToken(IObject, IObject) - Method in class ome.security.basic.BasicSecuritySystem

See {@link TokenHolder#copyToken(IObject, IObject)

copyToken(IObject, IObject) - Method in class ome.security.basic.TokenHolder

copy a token from one IObject to another.

copyUser(Experimenter) - Method in class ome.security.auth.SimpleRoleProvider

copyValues(EntityPersister, Object, Object, SessionImplementor, Map) - Method in class ome.security.basic.MergeEventListener

copyValues(EntityPersister, Object, Object, SessionImplementor, Map, ForeignKeyDirection) - Method in class ome.security.basic.MergeEventListener

count - Variable in class ome.io.nio.SimpleBackOff

count() - Method in interface ome.services.sessions.SessionContext

Returns the SessionContext.Count instance held by this context.

count() - Method in class ome.services.sessions.SessionContextImpl

count - Variable in class ome.services.sessions.stats.LongCounter

countAnnotationsUsedNotOwned(Class, long) - Method in interface ome.api.IMetadata

Counts the number of annotation of a given type used by the specified user but not owned by the user.

countAnnotationsUsedNotOwned(Class, long) - Method in class ome.logic.MetadataImpl

Implemented as specified by the IMetadata I/F

countAnnotationsUsedNotOwned_async(AMD_IMetadata_countAnnotationsUsedNotOwned, String, long, Current) - Method in class ome.services.blitz.impl.MetadataI

countByPeriod_async(AMD_ITimeline_countByPeriod, List<String>, RTime, RTime, Parameters, Current) - Method in class ome.services.blitz.impl.TimelineI

countCachedContainers(Class<? extends IObject>, int...) - Method in interface ome.formats.model.IObjectContainerStore

Counts the number of containers the MetadataStore has of a given class and at a given index of the hierarchy if specified.

countCachedContainers(Class<? extends IObject>, int...) - Method in class ome.formats.OMEROMetadataStoreClient

countCachedReferences(Class<? extends IObject>, Class<? extends IObject>) - Method in interface ome.formats.model.IObjectContainerStore

Counts the number of references the MetadataStore has between objects of two classes.

countCachedReferences(Class<? extends IObject>, Class<? extends IObject>) - Method in class ome.formats.OMEROMetadataStoreClient

CounterFactory - Class in ome.services.sessions.stats

Factory for creating counter objects.

CounterFactory() - Constructor for class ome.services.sessions.stats.CounterFactory

countInDb() - Method in class ome.services.scripts.ScriptRepoHelper

countInDb(SqlAction) - Method in class ome.services.scripts.ScriptRepoHelper

countOnDisk() - Method in class ome.services.scripts.ScriptRepoHelper

Returns the number of files which match ScriptRepoHelper.SCRIPT_FILTER in ScriptRepoHelper.dir.

countSpecifiedAnnotations(Class, Set<String>, Set<String>, Parameters) - Method in interface ome.api.IMetadata

Counts the number of annotation of a given type.

countSpecifiedAnnotations(Class, Set<String>, Set<String>, Parameters) - Method in class ome.logic.MetadataImpl

Implemented as specified by the IMetadata I/F

countSpecifiedAnnotations_async(AMD_IMetadata_countSpecifiedAnnotations, String, List<String>, List<String>, Parameters, Current) - Method in class ome.services.blitz.impl.MetadataI

countTiles(Pixels) - Method in class ome.io.nio.SimpleBackOff

create(String, SessionControlPrx, Current) - Method in class ome.services.blitz.fire.SessionManagerI

create(String, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI

Create a file in the repository if one doesn't already exist.

create(int, List<GraphStep>, GraphSpec, GraphEntry, long[]) - Method in class ome.services.delete.DeleteStepFactory

create(int, List<GraphStep>, GraphSpec, GraphEntry, long[]) - Method in class ome.services.export.ExporterStepFactory

create(int, List<GraphStep>, GraphSpec, GraphEntry, long[]) - Method in interface ome.services.graphs.GraphStepFactory

create(String) - Method in class ome.services.roi.RoiTypes.ObjectFactory

create(String) - Method in class omero.rtypes.ObjectFactory

create(File) - Method in class omero.util.TempFileManager

If the given directory doesn't exist, creates it and returns true.

create_path() - Static method in class omero.util.TempFileManager

Calls TempFileManager.createPath(String, String, boolean) on TempFileManager.manager with defaults of "omero", ".tmp", and false.

create_path(String) - Static method in class omero.util.TempFileManager

Calls TempFileManager.createPath(String, String, boolean) on TempFileManager.manager with defaults of ".tmp", and false.

create_path(String, String) - Static method in class omero.util.TempFileManager

Calls TempFileManager.createPath(String, String, boolean) on TempFileManager.manager with ".tmp", and false arguments.

create_path(String, String, boolean) - Static method in class omero.util.TempFileManager

Calls TempFileManager.createPath(String, String, boolean) on TempFileManager.manager.

createAdapter() - Method in class ome.services.blitz.util.BlitzConfiguration

Creates an adapter with the name "BlitzAdapter", which must be properly configured via --Ice.Config or ICE_CONFIG or similar.

createAndPrepareMissingRenderingSettings(Set<Long>) - Method in class ome.services.ThumbnailCtx

Resets a given set of Pixels rendering settings to the default effectively creating any which do not exist.

createAndRegisterManager(SessionManager, SecuritySystem, Executor) - Method in class ome.services.blitz.util.BlitzConfiguration

createAndRegisterVerifier(SessionManager, Executor) - Method in class ome.services.blitz.util.BlitzConfiguration

createBfPixelBuffer(String, int) - Method in class ome.io.nio.PixelsService

Helper method to properly log any exceptions raised by Bio-Formats.

createBufferedImage() - Method in class ome.services.SVGRasterizer

Returns the image that represents the SVG document.

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

createClient(boolean) - Method in class omero.client

Creates a possibly insecure client instance and calls client.joinSession(String) using the current session id.

createCommunicator() - Method in class ome.services.blitz.util.BlitzConfiguration

createCommunicator(String, String[]) - Method in class ome.services.blitz.util.BlitzConfiguration

createData() - Method in class omero.util.RPSTileLoop

createData() - Method in class omero.util.TileLoop

Subclasses must provide a fresh instance of TileData.

createDataObject(T, Parameters) - Method in interface ome.api.IContainer

Creates the specified data object.

createDataObject(IObject, Parameters) - Method in class ome.logic.PojosImpl

Implemented as specified by the IContainer I/F

createDataObject_async(AMD_IContainer_createDataObject, IObject, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI

createDataObjects(IObject[], Parameters) - Method in interface ome.api.IContainer

convenience method to save network calls.

createDataObjects(IObject[], Parameters) - Method in class ome.logic.PojosImpl

Implemented as specified by the IContainer I/F

createDataObjects_async(AMD_IContainer_createDataObjects, List<IObject>, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI

createDetails() - Method in class ome.security.basic.CurrentDetails

Creates a Details object for the current security context.

createDirectories() - Method in class ome.services.util.ServerDirectoryCheck

createdOrModified(Class, Criteria) - Method in class ome.services.search.SearchAction

createdOrModified(Class, QueryBuilder, String) - Method in class ome.services.search.SearchAction

createdStart - Variable in class ome.services.search.SearchValues

createdStop - Variable in class ome.services.search.SearchValues

createEnumeration(T) - Method in interface ome.api.ITypes

createEnumeration(T) - Method in class ome.logic.TypesImpl

createEnumeration_async(AMD_ITypes_createEnumeration, IObject, Current) - Method in class ome.services.blitz.impl.TypesI

createException(MethodInvocation) - Method in class ome.tools.hibernate.EventMethodInterceptor.DisableAction

createExperimenter(Experimenter, ExperimenterGroup, ExperimenterGroup...) - Method in interface ome.api.IAdmin

create and return a new user in the given groups.

createExperimenter(Experimenter, ExperimenterGroup, ExperimenterGroup...) - Method in class ome.logic.AdminImpl

createExperimenter(Experimenter, ExperimenterGroup, ExperimenterGroup...) - Method in interface ome.security.auth.RoleProvider

createExperimenter(Experimenter, ExperimenterGroup, ExperimenterGroup...) - Method in class ome.security.auth.SimpleRoleProvider

createExperimenter_async(AMD_IAdmin_createExperimenter, Experimenter, ExperimenterGroup, List<ExperimenterGroup>, Current) - Method in class ome.services.blitz.impl.AdminI

createExperimenterWithPassword(Experimenter, String, ExperimenterGroup, ExperimenterGroup...) - Method in interface ome.api.IAdmin

create and return a new user in the given groups with password.

createExperimenterWithPassword(Experimenter, String, ExperimenterGroup, ExperimenterGroup...) - Method in class ome.logic.AdminImpl

createExperimenterWithPassword_async(AMD_IAdmin_createExperimenterWithPassword, Experimenter, RString, ExperimenterGroup, List<ExperimenterGroup>, Current) - Method in class ome.services.blitz.impl.AdminI

createExporter(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI

createFullTextThread(EventLogLoader) - Static method in class ome.services.fulltext.Main

createGateway(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI

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) - Method in class ome.security.auth.SimpleRoleProvider

createGroup(ExperimenterGroup) - Method in class ome.security.auth.SimpleRoleProvider

createGroup_async(AMD_IAdmin_createGroup, ExperimenterGroup, Current) - Method in class ome.services.blitz.impl.AdminI

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, int, int, List<Integer>, PixelsType, String, String, Current) - Method in class ome.services.blitz.gateway.OmeroGateway

createImage(int, int, int, int, List<Integer>, PixelsType, String, String) - Method in interface ome.services.blitz.gateway.services.ImageService

Create a new image of specified X,Y, Z, T and channels plus pixelsType with name and description

createImage(int, int, int, int, List<Integer>, PixelsType, String, String) - Method in class ome.services.blitz.gateway.services.impl.ImageServiceImpl

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

createInstance() - Method in class ome.security.basic.EventListenersFactoryBean

First, adds all default listeners.

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

createPath(String, String, boolean) - Method in class omero.util.TempFileManager

Uses File.createTempFile(String, String, File) to create temporary files and folders under TempFileManager.dir.

createPixelBuffer(Pixels) - Method in class ome.io.nio.PixelsService

Creates a PixelBuffer for a given pixels set.

createPlane(PlaneDef, int, Pixels, PixelBuffer) - Static method in class omeis.providers.re.data.PlaneFactory

Factory method to fetch plane data and create an object to access it.

createPrincipal() - Method in class ome.system.SessionInitializer

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.

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

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 ome.services.blitz.impl.ServiceFactoryI

Creates a proxy according to the ServantDefinition for the given name.

createSession(Principal, String) - Method in interface ome.api.ISession

Creates a new session and returns it to the user.

createSession(Principal, String) - Method in class ome.services.sessions.SessionBean

createSession() - Method in class omero.client

Calls client.createSession(String, String) with null values

createSession(String, String) - Method in class omero.client

Performs the actual logic of logging in, which is done via the #getRouter().

createSession_async(AMD_ISession_createSession, Principal, String, Current) - Method in class ome.services.blitz.impl.SessionI

createSessionContext(List<?>, SessionContext) - Method in class ome.services.sessions.SessionManagerImpl

Takes a snapshot as from #executeSessionContextLookup(ServiceFactory, Principal) and turns it into a SessionContext instance.

CreateSessionMessage - Class in ome.services.messages

Published after a successful session creation.

CreateSessionMessage(Object, String) - Constructor for class ome.services.messages.CreateSessionMessage

createSessionWithTimeout(Principal, long) - Method in interface ome.api.ISession

Allows an admin to create a Session for the give Principal

createSessionWithTimeout(Principal, long) - Method in class ome.services.sessions.SessionBean

createSessionWithTimeout_async(AMD_ISession_createSessionWithTimeout, Principal, long, Current) - Method in class ome.services.blitz.impl.SessionI

createSessionWithTimeouts(Principal, long, long) - Method in interface ome.api.ISession

Allows an admin to create a Session for the give Principal

createSessionWithTimeouts(Principal, long, long) - Method in class ome.services.sessions.SessionBean

createSessionWithTimeouts_async(AMD_ISession_createSessionWithTimeouts, Principal, long, long, Current) - Method in class ome.services.blitz.impl.SessionI

createShare(String, Timestamp, List<T>, List<Experimenter>, List<String>, boolean) - Method in interface ome.api.IShare

Creates share with all related: items, members, and guests.

createShare(Principal, boolean, long, String, String, long) - Method in interface ome.services.sessions.SessionManager

createShare(Principal, boolean, long, String, String, long) - Method in class ome.services.sessions.SessionManagerImpl

createShare(String, Timestamp, List<T>, List<Experimenter>, List<String>, boolean) - Method in class ome.services.sharing.ShareBean

createShare_async(AMD_IShare_createShare, String, RTime, List<IObject>, List<Experimenter>, List<String>, boolean, Current) - Method in class ome.services.blitz.impl.ShareI

createStats() - Method in class ome.services.sessions.stats.CounterFactory

createStore() - Method in class ome.formats.importer.ImportConfig

Create and return a new OMEROMetadataStoreClient

createSubpath(String) - Method in class ome.io.nio.AbstractFileSystemService

Makes sure that for a given path, it's subpath exists.

createSystemUser(Experimenter) - Method in interface ome.api.IAdmin

create and return a new system user.

createSystemUser(Experimenter) - Method in class ome.logic.AdminImpl

createSystemUser_async(AMD_IAdmin_createSystemUser, Experimenter, Current) - Method in class ome.services.blitz.impl.AdminI

createTempFile(String, String) - Static method in class omero.util.TempFileManager

Emulates File.createTempFile(String, String) by calling TempFileManager.create_path(String, String).

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

createUser(Experimenter, String) - Method in interface ome.api.IAdmin

create and return a new user.

createUser(Experimenter, String) - Method in class ome.logic.AdminImpl

createUser_async(AMD_IAdmin_createUser, Experimenter, String, Current) - Method in class ome.services.blitz.impl.AdminI

createUserDirectories(Set<String>) - Method in class ome.services.util.DropBoxDirectoryCheck

createUserFromLdap(String, String) - Method in class ome.logic.LdapImpl

Gets user from LDAP for checking him by requirements and setting his details on DB

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) - Method in interface ome.services.sessions.SessionManager

createWithAgent(Principal, String) - Method in interface ome.services.sessions.SessionManager

createWithAgent(Principal, String, String) - Method in class ome.services.sessions.SessionManagerImpl

createWithAgent(Principal, String) - Method in class ome.services.sessions.SessionManagerImpl

credentials - Variable in class ome.system.SessionInitializer

CRITICAL_USAGE - Static variable in class ome.logic.RepositoryInfoImpl

Percentage (100.0 - 0.0) of disk use which will cause an exception during RepositoryInfoImpl.sanityCheckRepository()

csId - Variable in class ome.system.SimpleEventContext

csName - Variable in class ome.system.SimpleEventContext

CSV - Static variable in class pojos.FileAnnotationData

Identifies the CSV file formats.

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.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

current - Variable in class ome.security.SecuritySystemHolder

current - Variable in class ome.services.throttling.Task

current_group - Static variable in class ome.tools.hibernate.SecurityFilter

current_user - Static variable in class ome.tools.hibernate.SecurityFilter

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 - Variable in class ome.tools.hibernate.ProxyCleanupFilter

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

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

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

D

data - Variable in class ome.services.roi.GeomTool

data - Variable in class ome.services.roi.PixelData

DatabaseIdentity - Class in ome.services.db

Represents the unique identity of this database, consisting of the omero.db.authority and omero.db.uuid properties.

DatabaseIdentity(String, SqlAction) - Constructor for class ome.services.db.DatabaseIdentity

DatabaseIdentity(String, String) - Constructor for class ome.services.db.DatabaseIdentity

DataObject - Class in pojos

Abstract superclass for objects that hold OMEDS data.

DataObject() - Constructor for class pojos.DataObject

dataPerUser - Variable in class ome.services.pixeldata.PersistentEventLogLoader

DataService - Interface in ome.services.blitz.gateway.services

DataServiceImpl - Class in ome.services.blitz.gateway.services.impl

DataServiceImpl(GatewayFactory) - Constructor for class ome.services.blitz.gateway.services.impl.DataServiceImpl

Instantiate the imageService with the serviceFactory.

DATASET_LINKS - Static variable in class pojos.ImageData

Identifies the Image#DATASETLINKS field.

DATASET_LINKS - Static variable in class pojos.ProjectData

Identifies the Project#DATASETLINKS field.

DatasetData - Class in pojos

The data that makes up an OME Dataset along with links to its contained Images and enclosing Project as well as the Experimenter that owns this Dataset.

DatasetData() - Constructor for class pojos.DatasetData

Creates a new instance.

DatasetData(Dataset) - Constructor for class pojos.DatasetData

Creates a new instance.

DataSink - Class in omerojava.util

Encapsulates access to the image raw data.

DATE(Connection, List<Date>) - Method in interface ome.tools.hibernate.ListAsSQLArrayUserType.ArrayFactory

DBEnumCheck - Class in ome.services.util

Hook run by the context to guarantee that various enumerations are up to date.

DBEnumCheck(Executor) - Constructor for class ome.services.util.DBEnumCheck

DBPatchCheck - Class in ome.services.util

Hook run by the context.

DBPatchCheck(Executor, LocalConfig) - Constructor for class ome.services.util.DBPatchCheck

dbPath(Shape) - Method in class ome.services.roi.GeomTool

dbVersion - Static variable in class ome.formats.importer.Version

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 - Static variable in class prefs

Activated by setting DBEUG=true in the environment.

debugAll - Variable in class ome.security.basic.EventListenersFactoryBean

DECILE - Static variable in class omeis.providers.re.quantum.QuantumStrategy

Determines the number of sub-intervals of the [globalMin, globalMax] interval.

decodeKey(byte[], Communicator) - Method in class ome.services.sharing.data.ShareItems

decodeKey(byte[], Communicator) - Method in class ome.services.sharing.data.ShareMap

decodeValue(byte[], Communicator) - Method in class ome.services.sharing.data.ShareItems

decodeValue(byte[], Communicator) - Method in class ome.services.sharing.data.ShareMap

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.tools.hibernate.ListAsSQLArrayUserType

def(String[]) - Static method in class prefs

Returns the current default if no argument is given, or sets the default to the given string (or "" if null) otherwise returing "Default set to: ... ".

DEFAULT - Static variable in class ome.services.graphs.GraphEntry

DEFAULT - Static variable in class pojos.GroupData

Identifies the default group.

DEFAULT - Static variable in class prefs

Key (and default value) of the property under prefs.ROOT which defines which "profile" (subnode} is in effect.

DEFAULT_ARRAYBUF_SIZE - Static variable in class ome.formats.importer.ImportLibrary

Default arraybuf size for planar data transfer. (1MB)

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 case sensitivity

DEFAULT_COMPRESSION_QUALITY - Static variable in class ome.services.ThumbnailBean

The default compression quality in fractional percent.

DEFAULT_FILL_COLOUR - Static variable in class pojos.ShapeSettingsData

The default fill color.

DEFAULT_FILL_COLOUR_ALPHA - Static variable in class pojos.ShapeSettingsData

The default fill color.

DEFAULT_FONT_FAMILY - Static variable in class pojos.ShapeSettingsData

The default font family.

DEFAULT_FONT_SIZE - Static variable in class pojos.ShapeSettingsData

The default font size.

DEFAULT_MERGED_BATCHES - Static variable in interface ome.api.Search

Default merged-batches

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 ome.system.Server

DEFAULT_RETURN_UNLOADED - Static variable in interface ome.api.Search

Default return-unloaded

DEFAULT_STROKE_COLOUR - Static variable in class pojos.ShapeSettingsData

The default stroke color.

DEFAULT_STROKE_WIDTH - Static variable in class pojos.ShapeSettingsData

The default stroke width.

DEFAULT_TIMEOUT - Static variable in class ome.system.UpgradeCheck

Default timeout is 10 seconds.

DEFAULT_USE_PROJECTIONS - Static variable in interface ome.api.Search

Default use-projections

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.

defaultTimeToIdle - Variable in class ome.services.sessions.SessionManagerImpl

defaultTimeToLive - Variable in class ome.services.sessions.SessionManagerImpl

DEFAULTWORKFLOW - Static variable in class pojos.WorkflowData

The default workflow, i.e. nothing .

define(Session, String, String, long, long, long, String, String) - Method in class ome.services.sessions.SessionManagerImpl

Definitions - Class in ome.services.query

container for QueryParameterDef instances.

Definitions(QueryParameterDef...) - Constructor for class ome.services.query.Definitions

defs - Variable in class ome.services.query.Query

container of QueryParameterDef instances.

DelegatingStats - Class in ome.services.sessions.stats

Delegates to a SessionStats which is acquired from DelegatingStats.stats().

DelegatingStats() - Constructor for class ome.services.sessions.stats.DelegatingStats

DelegatingStats(SessionStats[]) - Constructor for class ome.services.sessions.stats.DelegatingStats

delete(String, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI

delete(long) - Method in class ome.services.scripts.ScriptRepoHelper

delete(String) - Method in class ome.tools.hibernate.QueryBuilder

DeleteBean - Class in ome.services.delete

Strict implementation of the IDelete service interface which will use the SecuritySystem via SecuritySystem.runAsAdmin(AdminAction) to forcibly delete instances.

DeleteBean(LocalAdmin, SessionFactory) - Constructor for class ome.services.delete.DeleteBean

DeleteCallbackI - Class in omero.grid

Callback used for waiting until DeleteHandlePrx will return true on DeleteHandlePrx.finished().

DeleteCallbackI(client, DeleteHandlePrx) - Constructor for class omero.grid.DeleteCallbackI

deleteChannels(long) - Method in class ome.services.delete.DeleteBean

deleteComment(Annotation) - Method in interface ome.api.IShare

Deletes comment from the database.

deleteComment(Annotation) - Method in class ome.services.sharing.ShareBean

deleteComment_async(AMD_IShare_deleteComment, Annotation, Current) - Method in class ome.services.blitz.impl.ShareI

deleteCurrentId() - Method in class ome.services.eventlogs.PersistentEventLogLoader

deleteDataObject(IObject, Parameters) - Method in interface ome.api.IContainer

Deletes a data object.

deleteDataObject(IObject, Parameters) - Method in class ome.logic.PojosImpl

Implemented as specified by the IContainer I/F

deleteDataObject_async(AMD_IContainer_deleteDataObject, IObject, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI

deleteDataObjects(IObject[], Parameters) - Method in interface ome.api.IContainer

convenience method to save network calls.

deleteDataObjects(IObject[], Parameters) - Method in class ome.logic.PojosImpl

Implemented as specified by the IContainer I/F

deleteDataObjects_async(AMD_IContainer_deleteDataObjects, List<IObject>, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI

deleteEntity(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

deleteEnumeration(T) - Method in interface ome.api.ITypes

deletes enumeration value specified by object

deleteEnumeration(T) - Method in class ome.logic.TypesImpl

deleteEnumeration_async(AMD_ITypes_deleteEnumeration, IObject, Current) - Method in class ome.services.blitz.impl.TypesI

DeleteException - Exception in ome.services.delete

Exception which will be thrown by activities within DeleteSpec implementations.

DeleteException(String) - Constructor for exception ome.services.delete.DeleteException

deleteExperimenter(Experimenter) - Method in interface ome.api.IAdmin

removes a user by removing the password information for that user as well as all GroupExperimenterMap instances.

deleteExperimenter(Experimenter) - Method in class ome.logic.AdminImpl

deleteExperimenter_async(AMD_IAdmin_deleteExperimenter, Experimenter, Current) - Method in class ome.services.blitz.impl.AdminI

deleteGroup(ExperimenterGroup) - Method in interface ome.api.IAdmin

removes a group by first removing all users in the group, and then deleting the actual ExperimenterGroup instance.

deleteGroup(ExperimenterGroup) - Method in class ome.logic.AdminImpl

deleteGroup_async(AMD_IAdmin_deleteGroup, ExperimenterGroup, Current) - Method in class ome.services.blitz.impl.AdminI

DeleteHandleI - Class in ome.services.blitz.impl

Servant for the handle proxy from the IDelete service.

DeleteHandleI(ApplicationContext, Identity, ServiceFactoryI, AbstractFileSystemService, DeleteCommand[], int) - Constructor for class ome.services.blitz.impl.DeleteHandleI

Create and

DeleteI - Class in ome.services.blitz.impl

Implementation of the IDelete service.

DeleteI(IDelete, BlitzExecutor, ThreadPool, int, String) - Constructor for class ome.services.blitz.impl.DeleteI

deleteImage(long, boolean) - Method in interface ome.api.IDelete

Deletes an Image and all related (subordinate) metadata as defined below.

deleteImage(long, boolean) - Method in class ome.services.delete.DeleteBean

deleteImage_async(AMD_IDelete_deleteImage, long, boolean, Current) - Method in class ome.services.blitz.impl.DeleteI

deleteImages(Set<Long>, boolean) - Method in interface ome.api.IDelete

Deletes several Image instances within a single transaction via the IDelete.deleteImage(long, boolean) method.

deleteImages(Set<Long>, boolean) - Method in class ome.services.delete.DeleteBean

deleteImages_async(AMD_IDelete_deleteImages, List<Long>, boolean, Current) - Method in class ome.services.blitz.impl.DeleteI

deleteImagesByDataset(long, boolean) - Method in interface ome.api.IDelete

Deletes the user-visible Image instances of the given Dataset within a single transaction via the IDelete.deleteImage(long, boolean).

deleteImagesByDataset(long, boolean) - Method in class ome.services.delete.DeleteBean

deleteImagesByDataset_async(AMD_IDelete_deleteImagesByDataset, long, boolean, Current) - Method in class ome.services.blitz.impl.DeleteI

deleteObject(IObject) - Method in interface ome.api.IUpdate

Deletes a single entity.

deleteObject(IObject) - Method in class ome.logic.UpdateImpl

deleteObject(IObject, Current) - Method in class ome.services.blitz.gateway.OmeroGateway

deleteObject(IObject) - Method in interface ome.services.blitz.gateway.services.DataService

Delete the object.

deleteObject(IObject) - Method in class ome.services.blitz.gateway.services.impl.DataServiceImpl

deleteObject_async(AMD_IUpdate_deleteObject, IObject, Current) - Method in class ome.services.blitz.impl.UpdateI

deleteObserver(IObserver) - Method in class ome.formats.importer.ImportLibrary

deleteObserver(IObserver) - Method in interface ome.formats.importer.IObservable

Delete observer

deleteObserver(IObserver) - Method in class ome.formats.importer.util.ClientKeepAlive

deleteObserver(IObserver) - Method in class ome.formats.importer.util.ErrorHandler

deleteObserver(IObserver) - Method in class ome.formats.importer.util.FileUploader

deletePlate(long) - Method in interface ome.api.IDelete

Deletes all the images contained in a plate as if deleted by: deleteImage(id, true) so that all Dataset and Annotation links are broken, with WellSamples removed first.

deletePlate(long) - Method in class ome.services.delete.DeleteBean

deletePlate_async(AMD_IDelete_deletePlate, long, Current) - Method in class ome.services.blitz.impl.DeleteI

deleteScript_async(AMD_IScript_deleteScript, long, Current) - Method in class ome.services.blitz.impl.ScriptI

Delete the script with id from the server.

deleteSettings(long) - Method in interface ome.api.IDelete

Deletes all rendering settings for the given Pixel id.

deleteSettings(long) - Method in class ome.services.delete.DeleteBean

deleteSettings_async(AMD_IDelete_deleteSettings, long, Current) - Method in class ome.services.blitz.impl.DeleteI

DeleteStep - Class in ome.services.delete

Single action performed by DeleteState.

DeleteStep(OmeroContext, int, List<GraphStep>, GraphSpec, GraphEntry, long[]) - Constructor for class ome.services.delete.DeleteStep

DeleteStepFactory - Class in ome.services.delete

Single action performed by DeleteState.

DeleteStepFactory(OmeroContext) - Constructor for class ome.services.delete.DeleteStepFactory

DEPTH - Static variable in class ome.formats.importer.ImportCandidates

depth - Variable in class ome.formats.importer.ImportCandidates.SCANNING

DEPTH_1BIT - Static variable in class omeis.providers.re.quantum.QuantumFactory

Flag to select a 1-bit depth (=2^1-1) output interval.

DEPTH_2BIT - Static variable in class omeis.providers.re.quantum.QuantumFactory

Flag to select a 2-bit depth (=2^2-1) output interval.

DEPTH_3BIT - Static variable in class omeis.providers.re.quantum.QuantumFactory

Flag to select a 3-bit depth (=2^3-1) output interval.

DEPTH_4BIT - Static variable in class omeis.providers.re.quantum.QuantumFactory

Flag to select a 4-bit depth (=2^4-1) output interval.

DEPTH_5BIT - Static variable in class omeis.providers.re.quantum.QuantumFactory

Flag to select a 5-bit depth (=2^5-1) output interval.

DEPTH_6BIT - Static variable in class omeis.providers.re.quantum.QuantumFactory

Flag to select a 6-bit depth (=2^6-1) output interval.

DEPTH_7BIT - Static variable in class omeis.providers.re.quantum.QuantumFactory

Flag to select a 7-bit depth (=2^7-1) output interval.

DEPTH_8BIT - Static variable in class omeis.providers.re.quantum.QuantumFactory

Flag to select a 8-bit depth (=2^8-1) output interval.

DESCENDING_LETTER - Static variable in class pojos.PlateData

Indicates that the column or row is a letter starting from Z or P.

DESCENDING_NUMBER - Static variable in class pojos.PlateData

Indicates that the column or row is a letter starting from 26 or 16.

description() - Method in class ome.services.procs.ProcessManager.Work

description() - Method in class ome.services.search.SearchAction

Returns the SearchAction subclass as the description.

description - Variable in class ome.services.util.Executor.Descriptive

description() - Method in class ome.services.util.Executor.Descriptive

description() - Method in interface ome.services.util.Executor.SqlWork

Return a description of what this work will be doing for logging purposes.

description() - Method in interface ome.services.util.Executor.Work

Returns a description of what this work will be doing for logging purposes.

DESCRIPTION - Static variable in class pojos.DatasetData

Identifies the Dataset#DESCRIPTION field.

DESCRIPTION - Static variable in class pojos.GroupData

Identifies the ExperimenterGroup#DESCRIPTION field.

DESCRIPTION - Static variable in class pojos.ImageData

Identifies the Image#DESCRIPTION field.

DESCRIPTION - Static variable in class pojos.PlateData

Identifies the Plate#DESCRIPTION field.

DESCRIPTION - Static variable in class pojos.ProjectData

Identifies the Project#DESCRIPTION field.

DESCRIPTION - Static variable in class pojos.ScreenData

Identifies the Screen#DESCRIPTION field.

destroy() - Method in class ome.services.blitz.fire.Ring

destroy(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI

Destruction simply decrements the reference count for a session to allow reconnecting to it.

destroy() - Method in class ome.services.blitz.util.BlitzConfiguration

destroy() - Method in class ome.services.roi.RoiTypes.ObjectFactory

destroy() - Method in class ome.services.throttling.Queue

destroy() - Method in class ome.tools.spring.ShutdownSafeEhcacheManagerFactoryBean

destroy() - Method in class omero.rtypes.ObjectFactory

DestroySessionMessage - Class in ome.services.messages

Published before a session destruction.

DestroySessionMessage(Object, String) - Constructor for class ome.services.messages.DestroySessionMessage

detach(String) - Method in interface ome.services.sessions.SessionManager

Allows decrementing the reference count for a session without calling the actual SessionManager.close(String) logic.

detach(String) - Method in class ome.services.sessions.SessionManagerImpl

detachOnDestroy(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI

DetailsI - Class in omero.model

DetailsI() - Constructor for class omero.model.DetailsI

detailsIndex(String[]) - Static method in class ome.tools.hibernate.HibernateUtils

DetectorData - Class in pojos

Hosts a detector.

DetectorData(Detector) - Constructor for class pojos.DetectorData

Creates a new instance.

determineColor(Integer) - Static method in class ome.formats.model.ColorsFactory

Determines the color corresponding to the passed value.

DichroicData - Class in pojos

Hosts the dichroic.

DichroicData(Dichroic) - Constructor for class pojos.DichroicData

Creates a new instance.

diff(PlanePoint) - Method in class ome.util.math.geom2D.PlanePoint

Calculates the sum of this vector with the reciprocal of the specified argument.

DimensionsOutOfBoundsException - Exception in ome.io.nio

DimensionsOutOfBoundsException(String) - Constructor for exception ome.io.nio.DimensionsOutOfBoundsException

dimOrder - Variable in class ome.formats.importer.ImportSize

direction - Variable in class ome.util.math.geom2D.Line

The unit vector that, given the Line.origin point, identifies this line.

directionX1 - Variable in class ome.util.math.geom2D.Segment

The end point of the segment's first element.

directionX2 - Variable in class ome.util.math.geom2D.Segment

The end point of the segment's second element.

dirname() - Method in class ome.services.scripts.RepoFile

dirtyMetadata(long) - Method in class ome.services.ThumbnailCtx

Whether or not the thumbnail metadata for a given Pixels ID is dirty (the RenderingDef has been updated since the Thumbnail was).

disable(String...) - Method in class ome.security.basic.BasicSecuritySystem

disable(String...) - Method in interface ome.security.SecuritySystem

disables components of the backend for the current Thread.

disable(String...) - Method in class ome.security.SecuritySystemHolder

disable(String...) - Method in class ome.security.sharing.SharingSecuritySystem

disabled(MethodInvocation) - Method in class ome.tools.hibernate.EventMethodInterceptor.DisableAction

disableFilters(Session) - Method in class ome.services.query.Query

turns the filters off that are listed in Query.newlyEnabledFilters

disableReadFilter(Object) - Method in class ome.security.basic.BasicSecuritySystem

disable this filer.

disassemble(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType

discriminator(String) - Method in class ome.services.roi.GeomTool

Maps from multiple possible user-provided names of shapes (e.g.

dispatch(String[]) - Static method in class prefs

Uses the first string in the argument array to reflectively invoke another method with the same signature on prefs.

dispose() - Method in class ome.services.sessions.state.CacheListener

distance(PlanePoint) - Method in class ome.util.math.geom2D.PlanePoint

Calculates the distance between this point and the specified argument.

doAction(SecureAction, T...) - Method in class ome.security.basic.BasicSecuritySystem

It would be better to catch the SecureAction#updateObject(IObject) method in a try/finally block, but since flush can be so poorly controlled that's not possible. instead, we use the one time token which is removed this Object is checked for privileges.

doAction(SecureAction, T...) - Method in interface ome.security.SecuritySystem

doAction(SecureAction, T...) - Method in class ome.security.SecuritySystemHolder

doAction(SecureAction, T...) - Method in class ome.security.sharing.SharingSecuritySystem

doCheckPassword(String, String, Properties, boolean) - Method in class ome.security.auth.FilePasswordProvider

doClose() - Method in class ome.services.sharing.BlobShareStore

doClose() - Method in class ome.services.sharing.FreezeShareStore

doClose() - Method in class ome.services.sharing.ShareStore

doContains(long, Class<T>, long) - Method in class ome.services.sharing.BlobShareStore

doContains(long, Class<T>, long) - Method in class ome.services.sharing.FreezeShareStore

doContains(long, Class<T>, long) - Method in class ome.services.sharing.ShareStore

doDestroy() - Method in class ome.services.blitz.impl.ServiceFactoryI

Performs the actual cleanup operation on all the resources shared between this and other ServiceFactoryI instances in the same Session.

doFilter(String, Object) - Method in class ome.tools.hibernate.ProxyCleanupFilter

doFilter(String, Filterable) - Method in class ome.tools.hibernate.ProxySafeFilter

doFilter(String, Collection) - Method in class ome.tools.hibernate.ProxySafeFilter

doImport() - Method in class ome.formats.importer.ImportFixture

runs import by looping through all files and then calling: ImportLibrary.open(String) ImportLibrary#calculateImageCount(String) ImportLibrary#importMetadata() ImportLibrary#importData(long, String)

doImport() - Method in class ome.formats.importer.util.TinyImportFixture

doImport() - Method in class ome.formats.OMEROImportFixture

runs import by looping through all files and then calling: ImportLibrary.open(String) ImportLibrary#calculateImageCount(String) ImportLibrary#importMetadata() ImportLibrary#importData(long, String, ome.formats.testclient.ImportLibrary.Step)

doIndexing(FullTextSession) - Method in class ome.services.fulltext.FullTextIndexer

doInHibernate(Session) - Method in class ome.services.query.Query

template method defined by HibernateTemplate.

doInit() - Method in class ome.services.sharing.BlobShareStore

doInit() - Method in class ome.services.sharing.FreezeShareStore

doInit() - Method in class ome.services.sharing.ShareStore

doMore(int) - Method in class ome.services.fulltext.FullTextIndexer

Default implementation suggests doing more if fewer than FullTextIndexer.reps runs have been made and if there are still more than EventLogLoader.batchSize x 100 backlog entries.

doParse(File) - Method in class ome.services.fulltext.FileParser

Template method to parse a File into manageable chunks.

doParse(File) - Method in class ome.services.fulltext.PdfParser

doRun(SqlAction, Session) - Method in class ome.services.blitz.impl.DeleteHandleI

doRun() - Method in class ome.services.fulltext.FullTextThread

Passes the FullTextIndexer instance to Executor.Work#doWork(org.springframework.transaction.TransactionStatus, org.hibernate.Session, ome.system.ServiceFactory) between calls to DetailsFieldBridge.lock() and DetailsFieldBridge.unlock() in order to guarantee that no other FieldBridge can edit the property.

doRun() - Method in class ome.services.pixeldata.PixelDataThread

doRun() - Method in class ome.services.procs.ProcessManager

doRun() - Method in class ome.services.util.ExecutionThread

doSet(Share, ShareData, List<ShareItem>) - Method in class ome.services.sharing.BlobShareStore

doSet(Share, ShareData, List<ShareItem>) - Method in class ome.services.sharing.FreezeShareStore

doSet(Share, ShareData, List<ShareItem>) - Method in class ome.services.sharing.ShareStore

doStop() - Method in class omero.grid.InteractiveProcessorI

dot(PlanePoint) - Method in class ome.util.math.geom2D.PlanePoint

Calulates the dot product of this vector by the specified argument.

doThumbnails - Variable in class ome.formats.importer.ImportConfig

DOUBLE(Connection, List<Double>) - Method in interface ome.tools.hibernate.ListAsSQLArrayUserType.ArrayFactory

DOUBLE - Static variable in class omeis.providers.re.data.PlaneFactory

Identifies the type used to store pixel values.

DOUBLE - Static variable in class omerojava.util.PixelTypes

Identifies the type used to store pixel values.

DOUBLE_COMPLEX_TYPE - Static variable in class pojos.PixelsData

Identifies the type used to store pixel values.

DOUBLE_TYPE - Static variable in class omeis.providers.re.data.PlaneFactory

Identifies the DOUBLE data type used to store pixel values, as per OME spec.

DOUBLE_TYPE - Static variable in class pojos.PixelsData

Identifies the type used to store pixel values.

DoubleAnnotationData - Class in pojos

Wraps a double annotation.

DoubleAnnotationData(double) - Constructor for class pojos.DoubleAnnotationData

Creates a new instance.

DoubleAnnotationData() - Constructor for class pojos.DoubleAnnotationData

Creates a new instance.

DoubleAnnotationData(DoubleAnnotation) - Constructor for class pojos.DoubleAnnotationData

Creates a new instance.

DoubleConverter - Class in omerojava.util

Packs a sequence of bytes representing a big-endian double into a double value of appropriate integer type.

DoubleConverter() - Constructor for class omerojava.util.DoubleConverter

doUpdate() - Method in class ome.services.sessions.state.SessionCache

Will only ever be accessed by a single thread.

down(String, Current) - Method in class ome.services.blitz.fire.Ring

Called when any node goes down.

download(long, File) - Method in class omero.client

download(long, File, int) - Method in class omero.client

doWork(Session, ServiceFactory) - Method in class ome.services.fulltext.FullTextIndexer

Runs FullTextIndexer.doIndexing(FullTextSession) within a Lucene transaction.

doWork(Session, ServiceFactory) - Method in class ome.services.pixeldata.PixelDataHandler

Handles only single elements from the PersistentEventLogLoader in order to keep transactions short and safe.

doWork(Session, ServiceFactory) - Method in class ome.services.procs.ProcessManager.Work

doWork(Session, ServiceFactory) - Method in class ome.services.search.AnnotatedWith

doWork(Session, ServiceFactory) - Method in class ome.services.search.Complement

doWork(Session, ServiceFactory) - Method in class ome.services.search.FullText

doWork(Session, ServiceFactory) - Method in class ome.services.search.HqlQuery

doWork(Session, ServiceFactory) - Method in class ome.services.search.Intersection

doWork(Session, ServiceFactory) - Method in class ome.services.search.SimilarTerms

doWork(Session, ServiceFactory) - Method in class ome.services.search.TagsAndGroups

doWork(Session, ServiceFactory) - Method in class ome.services.search.Union

doWork(SqlAction) - Method in interface ome.services.util.Executor.SqlWork

doWork(Session, ServiceFactory) - Method in interface ome.services.util.Executor.Work

Work method.

drop(String[]) - Static method in class prefs

Drops the entire profile (subnode) via Preferences.removeNode().

DropBoxDirectoryCheck - Class in ome.services.util

Hook run by the context at startup to create a drop-box directory per user.

DropBoxDirectoryCheck(String, SqlAction) - Constructor for class ome.services.util.DropBoxDirectoryCheck

dsAllQuery - Static variable in class ome.services.delete.QueryConstraints

dsNotOwnQuery - Static variable in class ome.services.delete.QueryConstraints

DV_FORMAT - Static variable in class ome.io.nio.PixelsService

The DeltaVision file format enumeration value

E

ec - Variable in class ome.services.graphs.GraphStep

Information as to the current login.

EDITOR_EXPERIMENT_NS - Static variable in interface ome.api.IMetadata

The name space used to indicate that the FileAnnotation is an experiment.

EDITOR_EXPERIMENT_NS - Static variable in class pojos.FileAnnotationData

The name space used to indicate that the FileAnnotation is an experiment.

EDITOR_PROTOCOL_NS - Static variable in interface ome.api.IMetadata

The name space used to indicate that the FileAnnotation is a protocol.

EDITOR_PROTOCOL_NS - Static variable in class pojos.FileAnnotationData

The name space used to indicate that the FileAnnotation is a protocol.

editScript_async(AMD_IScript_editScript, OriginalFile, String, Current) - Method in class ome.services.blitz.impl.ScriptI

elementType - Variable in class ome.services.query.CollectionQueryParameterDef

ellipse(double, double, double, double) - Method in class ome.services.roi.GeomTool

ellipse(double, double, double, double, int, int) - Method in class ome.services.roi.GeomTool

EllipseArea - Class in ome.util.math.geom2D

Represents an ellipse in the Euclidean space R².

EllipseArea(float, float, float, float) - Constructor for class ome.util.math.geom2D.EllipseArea

Creates a new instance.

EllipseData - Class in pojos

Represents an ellipse in the Euclidean space R².

EllipseData(Shape) - Constructor for class pojos.EllipseData

Creates a new instance of Ellipse data from an existing shape.

EllipseData() - Constructor for class pojos.EllipseData

Creates a new instance of EllipseData.

EllipseData(double, double, double, double) - Constructor for class pojos.EllipseData

Creates a new instance of the EllipseData.

email - Variable in class ome.formats.importer.ImportConfig

EMAIL - Static variable in class pojos.ExperimenterData

Identifies the Experimenter#EMAIL field.

empty() - Method in class ome.formats.importer.ImportConfig.StrValue

empty() - Method in class ome.formats.importer.ImportConfig.Value

EMPTY - Static variable in class ome.services.fulltext.FileParser

Iterable which returns an empty Iterator.

emptyCleanups() - Method in class ome.security.basic.CurrentDetails

Returns the current cleanups and resets the Set.

enable(String...) - Method in class ome.security.basic.BasicSecuritySystem

enable(String...) - Method in interface ome.security.SecuritySystem

enables components of the backend for the current Thread.

enable(String...) - Method in class ome.security.SecuritySystemHolder

enable(String...) - Method in class ome.security.sharing.SharingSecuritySystem

enabled - Variable in class ome.services.sharing.data.ShareData

enableFilters(Session) - Method in class ome.services.query.PojosFindHierarchiesQueryDefinition

enableFilters(Session) - Method in class ome.services.query.PojosGetImagesByOptionsQueryDefinition

enableFilters(Session) - Method in class ome.services.query.PojosGetImagesQueryDefinition

enableFilters(Session) - Method in class ome.services.query.PojosGetUserImagesQueryDefinition

enableFilters(Session) - Method in class ome.services.query.PojosLoadHierarchyQueryDefinition

enableFilters(Session) - Method in class ome.services.query.Query

does nothing by default, but can be overriden by subclasses to enable particular filters.

enableKeepAlive(int) - Method in class omero.client

Resets the "omero.keep_alive" property on the current Communicator which is used on initialization to determine the time-period between checks.

enableReadFilter(Object) - Method in class ome.security.basic.BasicSecuritySystem

enables the read filter such that graph queries will have non-visible entities silently removed from the return value.

encodeKey(Object, Communicator) - Method in class ome.services.sharing.data.ShareItems

encodeKey(Object, Communicator) - Method in class ome.services.sharing.data.ShareMap

encodePassword(String) - Method in class ome.security.auth.ConfigurablePasswordProvider

Encodes the password as it would be encoded for a check by ConfigurablePasswordProvider.comparePasswords(String, String)

encodePassword(String) - Method in interface ome.security.auth.PasswordUtility

encodeValue(Object, Communicator) - Method in class ome.services.sharing.data.ShareItems

encodeValue(Object, Communicator) - Method in class ome.services.sharing.data.ShareMap

encryptedConnection - Variable in class ome.formats.importer.ImportConfig

endIO(int) - Method in class omeis.providers.re.RenderingStats

Notifies the end of pixels data retrieval for the specified wavelength (channel).

endMalloc() - Method in class omeis.providers.re.RenderingStats

Notifies the end of the allocation of an RGB memory buffers for the rendering process.

endRendering() - Method in class omeis.providers.re.RenderingStats

Notifies the end of the trasnformation of the raw pixels data.

endTime(RTime) - Method in class omero.sys.ParametersI

Sets the value of the end time parameter.

endTransaction(boolean) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

entityIds - Variable in class ome.services.messages.EventLogMessage

entityIsDetached(MergeEvent, Map) - Method in class ome.security.basic.MergeEventListener

entityIsTransient(MergeEvent, Map) - Method in class ome.security.basic.MergeEventListener

entityType - Variable in class ome.services.messages.EventLogMessage

entries - Variable in class ome.services.graphs.BaseGraphSpec

The paths which make up this delete specification.

entries() - Method in class ome.services.graphs.BaseGraphSpec

entries() - Method in interface ome.services.graphs.GraphSpec

Returns a copy of the list of GraphEntry instances contained in this GraphSpec

Entry - Class in ome.services.blitz

OMERO.blitz startup code.

Entry(String) - Constructor for class ome.services.blitz.Entry

Stores name of the OmeroContext which is to be used by this instance.

entry - Variable in class ome.services.graphs.GraphStep

GraphEntry instance which is active for this step.

entrySet() - Method in class ome.services.graphs.GraphState

entrySet() - Method in interface ome.services.graphs.GraphStep.Callback

EnumerationException - Exception in ome.formats.enums

EnumerationException(String, Class<? extends IObject>, String) - Constructor for exception ome.formats.enums.EnumerationException

EnumerationHandler - Interface in ome.formats.enums.handler

An enumeration handler whose purpose is to provide extra logic, such as regular expression matching, for the lookup of enumerations for a specific type.

EnumerationProvider - Interface in ome.formats.enums

An enumeration provider, whose job is to make OMERO enumerations available to a consumer based on a set of criteria.

EnumHandlerFactory - Class in ome.formats.enums.handler

Factory for all available enumeration handlers.

EnumHandlerFactory() - Constructor for class ome.formats.enums.handler.EnumHandlerFactory

env() - Method in class omero.client

Helper method to access session environment

ENV - Static variable in class prefs

Environment variable which can be set to override the current, active profile.

environment(String, String) - Method in class ome.services.sessions.SessionManagerImpl

envItems - Variable in class ome.services.sharing.FreezeShareStore

envLocation - Variable in class ome.services.sharing.FreezeShareStore

envMap - Variable in class ome.services.sharing.FreezeShareStore

envRoot - Variable in class ome.services.sharing.FreezeShareStore

EPSILON - Static variable in class ome.logic.RenderingSettingsImpl

The value used to compare double and float.

equals(Object) - Method in class ome.tools.FileSystem

Public equals implementation based on name only (very loose equals)

equals(Object, Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType

equals(Object) - Method in class ome.util.math.geom2D.Line

Overridden to reflect equality of abstract values (data object) as opposite to object identity.

equals(Object) - Method in class ome.util.math.geom2D.PlanePoint

Overridden to reflect equality of abstract values (data object) as opposite to object identity.

equals(double, double) - Method in class ome.util.math.geom2D.PlanePoint

Check to see if the point values are equal.

equals(double, double, double) - Method in class ome.util.math.geom2D.Segment

Performs an equality test based on a point on this line defined by k as in getPoint() and another given point.

equals(Object) - Method in class ome.util.math.geom2D.Segment

Overridden to reflect equality of abstract values (data object) as opposite to object identity.

equals(Object) - Method in class omeis.providers.re.codomain.CodomainMapContext

This method is overridden so that objects of the same class are considered the same.

equals(Object) - Method in class omeis.providers.re.data.PlaneDef

Overridden to reflect equality of abstract values (data object) as opposite to object identity.

equals(Object) - Method in class pojos.ROICoordinate

Overridden to control if the passed object equals the current one.

ERROR - Static variable in interface ome.api.JobHandle

error(String) - Method in class ome.services.blitz.util.CommonsLoggingAdapter

ErrorContainer - Class in ome.formats.importer.util

Container for errors

ErrorContainer() - Constructor for class ome.formats.importer.util.ErrorContainer

errorCount() - Method in class ome.formats.importer.util.ErrorHandler

ErrorFilePart - Class in ome.formats.importer.util

ErrorFilePart(String, File) - Constructor for class ome.formats.importer.util.ErrorFilePart

Calls parent 'FilePart' class

ErrorHandler - Class in ome.formats.importer.util

Top of the error handling hierarchy.

ErrorHandler(ImportConfig) - Constructor for class ome.formats.importer.util.ErrorHandler

Initialize

ErrorHandler.EXCEPTION_EVENT - Class in ome.formats.importer.util

ErrorHandler.EXCEPTION_EVENT(Exception) - Constructor for class ome.formats.importer.util.ErrorHandler.EXCEPTION_EVENT

ErrorHandler.FILE_EXCEPTION - Class in ome.formats.importer.util

ErrorHandler.FILE_EXCEPTIONs are thrown any time in the context of a particular file and otherwise unspecified exception takes place.

ErrorHandler.FILE_EXCEPTION(String, Exception, String[], String) - Constructor for class ome.formats.importer.util.ErrorHandler.FILE_EXCEPTION

ErrorHandler.INTERNAL_EXCEPTION - Class in ome.formats.importer.util

ErrorHandler.INTERNAL_EXCEPTION(String, Exception, String[], String) - Constructor for class ome.formats.importer.util.ErrorHandler.INTERNAL_EXCEPTION

ErrorHandler.MISSING_LIBRARY - Class in ome.formats.importer.util

A ErrorHandler.FILE_EXCEPTION caused specifically by some library (native or otherwise) not being installed locally.

ErrorHandler.MISSING_LIBRARY(String, MissingLibraryException, String[], String) - Constructor for class ome.formats.importer.util.ErrorHandler.MISSING_LIBRARY

ErrorHandler.UNKNOWN_FORMAT - Class in ome.formats.importer.util

Unlike FILE_EXECEPTION, UKNOWN_FORMAT does not have a reader since bio-formats is telling us that it does not know how to handle the given file.

ErrorHandler.UNKNOWN_FORMAT(String, Exception, Object) - Constructor for class ome.formats.importer.util.ErrorHandler.UNKNOWN_FORMAT

ErrorHandler.UNREADABLE_FILE - Class in ome.formats.importer.util

Similar to UKNOWN_FORMAT UNREADABLE_FILE specifies that the file which is being accessed is unreadable (does not exist or canRead is false), so if the user is specifically saying that the file should be imported, there may be some underlying issue.

ErrorHandler.UNREADABLE_FILE(String, Exception, Object) - Constructor for class ome.formats.importer.util.ErrorHandler.UNREADABLE_FILE

errorIfInvalid(QueryParameter) - Method in class ome.services.query.CollectionQueryParameterDef

errorIfInvalid(QueryParameter) - Method in class ome.services.query.QueryParameterDef

validation method called by Query.checkParameters().

errorIfInvalidState() - Method in class ome.services.JobBean

errorIfInvalidState() - Method in class ome.services.RenderingBean

errorIfInvalidState() - Method in class ome.services.ThumbnailBean

errorIfNullPixels() - Method in class ome.services.RenderingBean

Throws an ApiUsageException if the pixels are not set.

errorIfNullPixels() - Method in class ome.services.ThumbnailBean

errorIfNullPixelsAndRenderingDef() - Method in class ome.services.ThumbnailBean

errorIfNullRenderer() - Method in class ome.services.RenderingBean

Reloads the rendering engine if null and has been made passive or throws an ApiUsageException if the rendering engine is not set.

errorIfNullRenderingDef() - Method in class ome.services.RenderingBean

Throws an ApiUsageException if the rendering settings are not set.

errorIfNullRenderingDef() - Method in class ome.services.ThumbnailBean

errorOnViolation(Class, Method, Object[]) - Static method in class ome.annotations.ApiConstraintChecker

errors - Variable in class ome.formats.importer.util.ErrorHandler

errors(Current) - Method in class ome.services.blitz.impl.DeleteHandleI

evaluateLinkages(IObject) - Method in class ome.security.basic.OmeroInterceptor

Checks the details of the objects which the given object links to in order to guarantee that linkages are valid.

EventBacklog - Class in ome.services.eventlogs

Thread-safe java.util-like Container for storing EventLog instances for later parsing.

EventBacklog() - Constructor for class ome.services.eventlogs.EventBacklog

EventContext - Interface in ome.system

manages authenticated principals and other context for a given event.

EventHandler - Class in ome.security.basic

method interceptor responsible for login and creation of Events.

EventHandler(SqlAction, BasicSecuritySystem, SessionFactory, TransactionAttributeSource) - Constructor for class ome.security.basic.EventHandler

only public constructor, used for dependency injection.

EventHandler(SqlAction, BasicSecuritySystem, SessionFactory, TransactionAttributeSource, boolean) - Constructor for class ome.security.basic.EventHandler

EventListenersFactoryBean - Class in ome.security.basic

configuring all the possible event listeners within XML can be cumbersome.

EventListenersFactoryBean(CurrentDetails, TokenHolder, ACLVoter, OmeroInterceptor) - Constructor for class ome.security.basic.EventListenersFactoryBean

EventLogListener - Class in ome.security.basic

responsible for responding to all Hibernate Events.

EventLogListener(CurrentDetails) - Constructor for class ome.security.basic.EventLogListener

main constructor.

EventLogLoader - Class in ome.services.eventlogs

Data access object for the FullTextIndexer which provides an Iterator interface for EventLog instances to be properly indexed.

EventLogLoader() - Constructor for class ome.services.eventlogs.EventLogLoader

EventLogMessage - Class in ome.services.messages

Published when an event log should be saved at the end of a transaction.

EventLogMessage(Object, String, Class<? extends IObject>, List<Long>) - Constructor for class ome.services.messages.EventLogMessage

EventMethodInterceptor - Class in ome.tools.hibernate

filter which can be added to any event type in order to catch execution.

EventMethodInterceptor() - Constructor for class ome.tools.hibernate.EventMethodInterceptor

EventMethodInterceptor(EventMethodInterceptor.Action) - Constructor for class ome.tools.hibernate.EventMethodInterceptor

EventMethodInterceptor.Action - Class in ome.tools.hibernate

EventMethodInterceptor.Action() - Constructor for class ome.tools.hibernate.EventMethodInterceptor.Action

EventMethodInterceptor.DisableAction - Class in ome.tools.hibernate

EventMethodInterceptor.DisableAction() - Constructor for class ome.tools.hibernate.EventMethodInterceptor.DisableAction

evict(Object) - Method in interface ome.api.local.LocalQuery

Removes an object graph from the session.

evict(Object) - Method in class ome.logic.QueryImpl

ex - Variable in class ome.services.roi.GeomTool

exception - Variable in class ome.formats.importer.ImportEvent.FILE_UPLOAD_EVENT

exception - Variable in class ome.formats.importer.util.ErrorHandler.EXCEPTION_EVENT

exception - Variable in class ome.services.throttling.Task

exception(Throwable, OmeroContext) - Method in class ome.services.throttling.Task

excludes - Variable in class ome.services.eventlogs.EventLogLoader

Array of class types which will get excluded from indexing.

execute(HibernateCallback) - Method in interface ome.api.local.LocalQuery

Executes a HibernateCallback

execute(Query<T>) - Method in interface ome.api.local.LocalQuery

Executes a locally defined Query.

execute(String[]) - Method in class ome.formats.importer.ImportCandidates

Method called during ImportCandidates.ImportCandidates(OMEROWrapper, String[], IObserver) to operate on all the given paths.

execute(HibernateCallback) - Method in class ome.logic.QueryImpl

execute(Query<T>) - Method in class ome.logic.QueryImpl

execute(int) - Method in class ome.services.graphs.GraphState

execute(Principal, Executor.Work) - Method in interface ome.services.util.Executor

Executes a Executor.Work instance wrapped in two layers of AOP.

execute(Principal, Executor.Work) - Method in class ome.services.util.Executor.Impl

Executes a Executor.Work instance wrapped in two layers of AOP.

execute(RMap, Current) - Method in class omero.grid.InteractiveProcessorI

executePasswordCheck(String, String) - Method in interface ome.services.sessions.SessionManager

Executes a password check using the Executor framework.

executePasswordCheck(String, String) - Method in class ome.services.sessions.SessionManagerImpl

executePost() - Method in class ome.formats.importer.util.HtmlMessenger

Execute a post action and retrieve server reply This method executes the post created when this class is instantiated

executeSql(Executor.SqlWork) - Method in interface ome.services.util.Executor

Executes a Executor.SqlWork wrapped with a transaction.

executeSql(Executor.SqlWork) - Method in class ome.services.util.Executor.Impl

Executes a SqkWork in transaction.

ExecutionThread - Class in ome.services.util

Thread which can be started and will appropriately acquire a session, then use the Executor to complete its work.

ExecutionThread(SessionManager, Executor, Executor.Work, Principal) - Constructor for class ome.services.util.ExecutionThread

Main constructor.

executor - Variable in class ome.logic.UpdateImpl

executor - Variable in class ome.services.blitz.fire.SessionManagerI

executor - Variable in class ome.services.blitz.redirect.AbstractRedirector

executor - Variable in class ome.services.sessions.SessionManagerImpl

executor - Variable in class ome.services.sharing.ShareBean

executor - Variable in class ome.services.util.ExecutionThread

Executor - Interface in ome.services.util

Simple execution/work interface which can be used for internal tasks which need to have a full working implementation.

Executor.Descriptive - Class in ome.services.util

Executor.Descriptive(Object, String, Object...) - Constructor for class ome.services.util.Executor.Descriptive

Executor.Impl - Class in ome.services.util

Executor.Impl(CurrentDetails, SessionFactory, SqlAction, String[]) - Constructor for class ome.services.util.Executor.Impl

Executor.Impl(CurrentDetails, SessionFactory, SqlAction, String[], ExecutorService) - Constructor for class ome.services.util.Executor.Impl

Executor.SimpleSqlWork - Class in ome.services.util

Simple adapter which takes a String for Executor.Descriptive.description

Executor.SimpleSqlWork(Object, String, Object...) - Constructor for class ome.services.util.Executor.SimpleSqlWork

Executor.SimpleWork - Class in ome.services.util

Simple adapter which takes a String for Executor.Descriptive.description

Executor.SimpleWork(Object, String, Object...) - Constructor for class ome.services.util.Executor.SimpleWork

Executor.SqlWork - Interface in ome.services.util

Work SPI to perform actions related to stateless sessions.

Executor.Work - Interface in ome.services.util

Work SPI to perform actions within the server as if they were fully wrapped in our service logic.

executorWorkCall(Executor.Work) - Method in class ome.services.blitz.impl.AbstractAmdServant

exists() - Method in interface ome.api.RawFileStore

Checks to see if a raw file exists with the file ID that the service was initialized with.

exists(OriginalFile) - Method in class ome.io.nio.OriginalFilesService

Returns whether or not an OriginalFile exists on disk.

exists(long) - Method in class ome.services.blitz.gateway.services.impl.RawFileStoreServiceImpl

exists(long) - Method in interface ome.services.blitz.gateway.services.RawFileStoreService

Does the file exist in the RawFileStore.

exists() - Method in class ome.services.RawFileBean

exists_async(AMD_RawFileStore_exists, Current) - Method in class ome.services.blitz.impl.RawFileStoreI

exists_async(AMD_RawFileStore_exists, Current) - Method in class ome.services.blitz.repo.RepoRawFileStoreI

exit(String[]) - Static method in class prefs

Uses the length of the argument array as the exit code.

exp(RLong) - Method in class omero.sys.ParametersI

Sets the value of the experimenter parameter.

EXPERIMENTER_PHOTO_NS - Static variable in class pojos.FileAnnotationData

The name space used to identify the experimenter photo.

ExperimenterData - Class in pojos

The data that makes up an OME Experimenter along with information about the Group the Experimenter belongs in.

ExperimenterData() - Constructor for class pojos.ExperimenterData

Creates a new instance.

ExperimenterData(Experimenter) - Constructor for class pojos.ExperimenterData

Creates a new instance.

expirationAsLong(long, Timestamp) - Static method in class ome.services.sharing.ShareBean

Convert a expiration into a long which can be set on Session.setTimeToLive(Long).

ExpiredServantMessage - Class in ome.services.blitz.util

ApplicationEvent which gets raised on CacheEventListener.notifyElementExpired(net.sf.ehcache.Ehcache, net.sf.ehcache.Element)

ExpiredServantMessage(Object, String) - Constructor for class ome.services.blitz.util.ExpiredServantMessage

expires(Current) - Method in class omero.grid.InteractiveProcessorI

EXPONENTIAL - Static variable in class omeis.providers.re.quantum.QuantumFactory

Flag to select a exponential map for the quantization process.

ExponentialMap - Class in omeis.providers.re.quantum

This class implements the QuantumMap interface.

ExponentialMap() - Constructor for class omeis.providers.re.quantum.ExponentialMap

export(String[]) - Static method in class prefs

Exports all properties in the current profile to System.out, or if a single argument is given, that is take to be the name of a target ouput file.

ExporterI - Class in ome.services.blitz.impl

Implementation of the Exporter service.

ExporterI(BlitzExecutor, DatabaseIdentity, PixelsService) - Constructor for class ome.services.blitz.impl.ExporterI

ExporterIndex - Class in ome.services.export

State maintained for each element type in the ExporterStepFactory.

ExporterIndex(int) - Constructor for class ome.services.export.ExporterIndex

ExporterStep - Class in ome.services.export

Marker action used during export.

ExporterStep(int, List<GraphStep>, GraphSpec, GraphEntry, long[]) - Constructor for class ome.services.export.ExporterStep

ExporterStepFactory - Class in ome.services.export

Counter which can be passed into the GraphState constructor and later used during export.

ExporterStepFactory(Executor, Principal) - Constructor for class ome.services.export.ExporterStepFactory

ExtendedMetadata - Interface in ome.tools.hibernate

extension of the model metadata provided by SessionFactory.

ExtendedMetadata.Immutables - Class in ome.tools.hibernate

ExtendedMetadata.Impl - Class in ome.tools.hibernate

Sole implementatino of ExtendedMetadata.

ExtendedMetadata.Impl() - Constructor for class ome.tools.hibernate.ExtendedMetadata.Impl

ExtendedMetadata.Locks - Class in ome.tools.hibernate

inner class which wraps the information (index number, path, etc) related to what fields a particular object can lock.

F

factory - Variable in class ome.security.basic.EventHandler

factory - Variable in class ome.services.blitz.impl.RoiI

factory - Variable in class ome.services.blitz.impl.ScriptI

factory - Variable in class ome.services.blitz.impl.TimelineI

factory - Variable in class ome.services.roi.GeomTool

factory - Variable in class ome.services.sessions.SessionManagerImpl

factory - Variable in class ome.services.util.Executor.Impl

factory - Variable in class ome.tools.hibernate.ListAsSQLArrayUserType

FACTORY - Static variable in class ome.tools.hibernate.SqlArray

Factory - Static variable in class omero.model.DetailsI

Factory - Static variable in class omero.model.PermissionsI

FETCH - Static variable in class ome.services.query.Query

imported constant for ease of use

fetchAlso(String...) - Method in interface ome.api.Search

Adds a fetch clause for loading non-annotation fields of returned entities.

fetchAlso(Map<T, String>) - Method in class ome.services.SearchBean

fetchAlso(String...) - Method in class ome.services.SearchBean

fetchAlso_async(AMD_Search_fetchAlso, List<String>, Current) - Method in class ome.services.blitz.impl.SearchI

fetchAnnotations(Class...) - Method in interface ome.api.Search

Queries the database for all annotations of the given types for all returned instances.

fetchAnnotations - Variable in class ome.services.search.SearchValues

fetchAnnotations(Class...) - Method in class ome.services.SearchBean

fetchAnnotations_async(AMD_Search_fetchAnnotations, List<String>, Current) - Method in class ome.services.blitz.impl.SearchI

fetchChildren(Criteria, Class, int) - Static method in class ome.services.query.Hierarchy

fetchCollection(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

fetchEntity(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

fetches - Variable in class ome.services.search.SearchValues

fetchParents(Criteria, Class, int) - Static method in class ome.services.query.Hierarchy

FILAMENT - Static variable in class pojos.LightSourceData

Indicates that the light source is a filament.

file - Variable in class ome.formats.importer.ImportCandidates.SCANNING

file - Variable in class ome.security.auth.FilePasswordProvider

Flat file read on each invocation with name, value pairs in Java Properties notation.

file(long, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI

file() - Method in class ome.services.scripts.RepoFile

FileAnnotationData - Class in pojos

Annotation to upload files to the server.

FileAnnotationData(File) - Constructor for class pojos.FileAnnotationData

Creates a new instance.

FileAnnotationData(FileAnnotation) - Constructor for class pojos.FileAnnotationData

Creates a new instance.

FileBuffer - Class in ome.io.nio

Raw file buffer which provides I/O operations within the OMERO file repository.

FileData - Class in pojos

DataObject used to handle the file visible via FS.

FileData(OriginalFile) - Constructor for class pojos.FileData

Creates a new instance.

FileData(OriginalFile, boolean) - Constructor for class pojos.FileData

Creates a new instance.

FileData(OriginalFile, boolean, boolean) - Constructor for class pojos.FileData

Creates a new instance.

fileExists(String, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI

Return true if a file exists in the repository.

fileIndex - Variable in class ome.formats.importer.ImportEvent.FILE_UPLOAD_EVENT

FileMaker - Class in ome.services.blitz.repo

Utility class for creating and cleaning up a repository lock file.

FileMaker(String) - Constructor for class ome.services.blitz.repo.FileMaker

filename - Variable in class ome.formats.importer.ImportEvent.FILE_UPLOAD_EVENT

filename - Variable in class ome.formats.importer.ImportEvent.PROGRESS_EVENT

fileName - Variable in class ome.formats.importer.ImportSize

filename - Variable in class ome.formats.importer.util.ErrorHandler.FILE_EXCEPTION

filename - Variable in class ome.formats.importer.util.ErrorHandler.INTERNAL_EXCEPTION

filename - Variable in class ome.formats.importer.util.ErrorHandler.UNKNOWN_FORMAT

filename - Variable in class ome.formats.importer.util.ErrorHandler.UNREADABLE_FILE

FILENAME - Static variable in class ome.formats.importer.util.TinyImportFixture

Hard-coded filename of the image to be imported

FileParser - Class in ome.services.fulltext

Object which attempts to parse any file given to it.

FileParser() - Constructor for class ome.services.fulltext.FileParser

FilePasswordProvider - Class in ome.security.auth

Example password provider which uses the given file as password lookup.

FilePasswordProvider(PasswordUtil, File) - Constructor for class ome.security.auth.FilePasswordProvider

FilePasswordProvider(PasswordUtil, File, boolean) - Constructor for class ome.security.auth.FilePasswordProvider

filePath - Variable in class ome.io.bioformats.BfPixelBuffer

FilePathResolver - Interface in ome.io.nio

Resolver for file paths and related metadata.

files - Variable in class ome.services.fulltext.FullTextBridge

FILES_PATH - Static variable in class ome.io.nio.AbstractFileSystemService

filesService - Variable in class ome.services.blitz.impl.MetadataStoreI

filesToString(File...) - Static method in class omero.client

FileSystem - Class in ome.tools

Extends Sun Microsystems java.io.File for J2SE 5 only.

FileSystem(String) - Constructor for class ome.tools.FileSystem

pass-thru constructor

FileSystem(URI) - Constructor for class ome.tools.FileSystem

pass-thru constructor

FileSystem(String, String) - Constructor for class ome.tools.FileSystem

pass-thru constructor

FileSystem(File, String) - Constructor for class ome.tools.FileSystem

pass-thru constructor

fileTotal - Variable in class ome.formats.importer.ImportEvent.FILE_UPLOAD_EVENT

FileUploadCounter - Class in ome.formats.importer.util

FileUploadCounter(RequestEntity, FileUploadCounter.ProgressListener) - Constructor for class ome.formats.importer.util.FileUploadCounter

Initialize class

FileUploadCounter.OutputStreamCounter - Class in ome.formats.importer.util

FileUploadCounter.OutputStreamCounter(OutputStream, FileUploadCounter.ProgressListener) - Constructor for class ome.formats.importer.util.FileUploadCounter.OutputStreamCounter

counter in bytes

FileUploadCounter.ProgressListener - Interface in ome.formats.importer.util

FileUploader - Class in ome.formats.importer.util

FileUploader(HttpClient) - Constructor for class ome.formats.importer.util.FileUploader

Initialize upload with httpClient

fileUploadErrors - Variable in class ome.formats.importer.util.ErrorHandler

fillObject(ReverseModelMapper) - Method in class omero.model.DetailsI

fillObject(ReverseModelMapper) - Method in class omero.model.PermissionsI

fillRelationships(SessionFactoryImplementor, Map<String, String>) - Method in class ome.tools.hibernate.ExtendedMetadata.Locks

For each of the fields contained in this ExtendedMetadata.Locks object, parse out the type and the field name and store those as the key and value in the "value" argument.

fillReplacement(MergeEvent) - Method in class ome.security.basic.MergeEventListener

fillServerError(ServerError, Throwable) - Static method in class omero.util.IceMapper

filter(String, Filterable) - Method in class ome.tools.hibernate.ProxyCleanupFilter

filter(String, Collection) - Method in class ome.tools.hibernate.ProxyCleanupFilter

filter(String, Map) - Method in class ome.tools.hibernate.ProxyCleanupFilter

filter(String, Filter) - Method in class ome.tools.hibernate.QueryBuilder

filter(String, Filterable) - Method in class ome.tools.hibernate.ReloadFilter

filter(String, Object) - Method in class ome.tools.hibernate.UpdateFilter

overrides ContextFilter.filter(String, Object) to allow only certain types to enter the Hibernate system

filter(String, Filterable) - Method in class ome.tools.hibernate.UpdateFilter

overrides ContextFilter.filter(String, Filterable) to return previously merged or previously checked items.

filter(String, Collection) - Method in class ome.tools.hibernate.UpdateFilter

overrides ContextFilter.filter(String, Collection) to return previously checked collections.

filter(String, Map) - Method in class ome.tools.hibernate.UpdateFilter

Prevents CountPerOwner from being loaded unnecessarily.

filter(String, Filterable) - Method in class omero.util.IceMapper

FILTERABLE - Static variable in class omero.util.IceMapper

FILTERABLE_ARRAY - Static variable in class omero.util.IceMapper

FILTERABLE_COLLECTION - Static variable in class omero.util.IceMapper

FILTERABLE_PRIMITIVE_MAP - Static variable in class omero.util.IceMapper

FilterData - Class in pojos

Object hosting a filter.

FilterData(Filter) - Constructor for class pojos.FilterData

Creates a new instance.

filterName - Static variable in class ome.tools.hibernate.SecurityFilter

FilterSetData - Class in pojos

Object hosting a filterSet.

FilterSetData(FilterSet) - Constructor for class pojos.FilterSetData

Creates a new instance.

finalizePixelStore() - Method in class ome.formats.OMEROMetadataStoreClient

Closes the active raw pixels store.

find(Class<T>, long) - Method in interface ome.api.IQuery

lookup an entity by class and id.

find(Class, long) - Method in class ome.logic.QueryImpl

find(String) - Method in interface ome.services.sessions.SessionManager

find(String) - Method in class ome.services.sessions.SessionManagerImpl

find_async(AMD_IQuery_find, String, long, Current) - Method in class ome.services.blitz.impl.QueryI

findAll(Class<T>, Filter) - Method in interface ome.api.IQuery

lookup all entities that belong to this class and match filter.

findAll(Class<T>, Filter) - Method in class ome.logic.QueryImpl

findAll_async(AMD_IQuery_findAll, String, Filter, Current) - Method in class ome.services.blitz.impl.QueryI

findAllByExample(T, Filter) - Method in interface ome.api.IQuery

search based on provided example entity.

findAllByExample(T, Filter) - Method in class ome.logic.QueryImpl

findAllByExample_async(AMD_IQuery_findAllByExample, IObject, Filter, Current) - Method in class ome.services.blitz.impl.QueryI

findAllByFullText(Class<T>, String, Parameters) - Method in interface ome.api.IQuery

executes a full text search based on Lucene.

findAllByFullText(Class<T>, String, Parameters) - Method in class ome.logic.QueryImpl

findAllByFullText_async(AMD_IQuery_findAllByFullText, String, String, Parameters, Current) - Method in class ome.services.blitz.impl.QueryI

findAllByQuery(String, Parameters) - Method in interface ome.api.IQuery

executes the stored query with the given name.

findAllByQuery(String, Parameters) - Method in class ome.logic.QueryImpl

findAllByQuery(String, Current) - Method in class ome.services.blitz.gateway.OmeroGateway

findAllByQuery(String) - Method in interface ome.services.blitz.gateway.services.DataService

Run the query against the iQuery interface.

findAllByQuery(String) - Method in class ome.services.blitz.gateway.services.impl.DataServiceImpl

findAllByQuery_async(AMD_IQuery_findAllByQuery, String, Parameters, Current) - Method in class ome.services.blitz.impl.QueryI

findAllByString(Class<T>, String, String, boolean, Filter) - Method in interface ome.api.IQuery

search a given field matching against a String.

findAllByString(Class<T>, String, String, boolean, Filter) - Method in class ome.logic.QueryImpl

findAllByString_async(AMD_IQuery_findAllByString, String, String, String, boolean, Filter, Current) - Method in class ome.services.blitz.impl.QueryI

findByExample(T) - Method in interface ome.api.IQuery

search based on provided example entity.

findByExample(T) - Method in class ome.logic.QueryImpl

findByExample_async(AMD_IQuery_findByExample, IObject, Current) - Method in class ome.services.blitz.impl.QueryI

findById(long, boolean) - Method in class ome.services.sharing.data.ShareMap

findById(long) - Method in class ome.services.sharing.data.ShareMap

findByImage_async(AMD_IRoi_findByImage, long, RoiOptions, Current) - Method in class ome.services.blitz.impl.RoiI

findByOwner(long, boolean) - Method in class ome.services.sharing.data.ShareMap

findByOwner(long) - Method in class ome.services.sharing.data.ShareMap

findByPlane_async(AMD_IRoi_findByPlane, long, int, int, RoiOptions, Current) - Method in class ome.services.blitz.impl.RoiI

findByQuery(String, Parameters) - Method in interface ome.api.IQuery

executes the stored query with the given name.

findByQuery(String, Parameters) - Method in class ome.logic.QueryImpl

findByQuery(String, Current) - Method in class ome.services.blitz.gateway.OmeroGateway

findByQuery(String) - Method in interface ome.services.blitz.gateway.services.DataService

Run the query against the iQuery interface.

findByQuery(String) - Method in class ome.services.blitz.gateway.services.impl.DataServiceImpl

findByQuery_async(AMD_IQuery_findByQuery, String, Parameters, Current) - Method in class ome.services.blitz.impl.QueryI

findByRoi_async(AMD_IRoi_findByRoi, long, RoiOptions, Current) - Method in class ome.services.blitz.impl.RoiI

findByShare(long, boolean) - Method in class ome.services.sharing.data.ShareItems

findByShare(long) - Method in class ome.services.sharing.data.ShareItems

findByString(Class<T>, String, String) - Method in interface ome.api.IQuery

search a given field matching against a String.

findByString(Class<T>, String, String) - Method in class ome.logic.QueryImpl

findByString_async(AMD_IQuery_findByString, String, String, String, Current) - Method in class ome.services.blitz.impl.QueryI

findByType(String, boolean) - Method in class ome.services.sharing.data.ShareItems

findByType(String) - Method in class ome.services.sharing.data.ShareItems

findByUser(String) - Method in interface ome.services.sessions.SessionManager

findByUser(String) - Method in class ome.services.sessions.SessionManagerImpl

findByUserAndAgent(String, String...) - Method in interface ome.services.sessions.SessionManager

Returns a non-null, possibly empty list of session instances belonging to the given user and with one of the given agents.

findByUserAndAgent(String, String...) - Method in class ome.services.sessions.SessionManagerImpl

findCollection(Collection) - Method in class omero.util.IceMapper

Overrides the findCollection logic of ModelMapper, since all Collections should be Lists in Ice.

findCollectionTarget(Object) - Method in class omero.util.RTypeMapper

findContainerHierarchies(Class<T>, Set<Long>, Parameters) - Method in interface ome.api.IContainer

Retrieves hierarchy trees in various hierarchies that contain the specified Images.

findContainerHierarchies(Class, Set, Parameters) - Method in class ome.logic.PojosImpl

Implemented as speficied by the IContainer I/F

findContainerHierarchies_async(AMD_IContainer_findContainerHierarchies, String, List<Long>, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI

findDirty(Object, Serializable, Object[], Object[], String[], Type[]) - Method in class ome.security.basic.OmeroInterceptor

default logic

findDN(String) - Method in interface ome.api.ILdap

Searchs unique Distinguished Name - String in LDAP for Common Name equals username.

findDN(String) - Method in class ome.logic.LdapImpl

findDN_async(AMD_ILdap_findDN, String, Current) - Method in class ome.services.blitz.impl.LdapI

findEnumeration(HashMap<String, IObject>, String) - Method in interface ome.formats.enums.handler.EnumerationHandler

Attempt to find an enumeration from an existing set of enumeration values.

findExperimenter(String) - Method in interface ome.api.ILdap

Searchs Experimenter by unique Distinguished Name - String in LDAP for Common Name equals username.

findExperimenter(String) - Method in class ome.logic.LdapImpl

findExperimenter_async(AMD_ILdap_findExperimenter, String, Current) - Method in class ome.services.blitz.impl.LdapI

findInDb(String, boolean) - Method in class ome.services.scripts.ScriptRepoHelper

findInDb(RepoFile, boolean) - Method in class ome.services.scripts.ScriptRepoHelper

findInDb(SqlAction, RepoFile, boolean) - Method in class ome.services.scripts.ScriptRepoHelper

Looks to see if a path is contained in the repository.

findKeyTarget(Object) - Method in class omero.util.RTypeMapper

findMethodAnnotations(Class, Method) - Static method in class ome.annotations.AnnotationUtils

finds all parameter annotations for the given class including on all implemented interfaces.

findParameterAnnotations(Class, Method) - Static method in class ome.annotations.AnnotationUtils

finds all parameter annotations for the given class including on all implemented interfaces.

findPixelSets(int, Class, int, Map) - Method in interface ome.api.IResults

finding PixelSets.

findPixelSetsPrimitive(int, String, int, Map) - Method in interface ome.api.IResults

findProxy(Redirector.Context, String) - Method in class ome.services.blitz.redirect.AbstractRedirector

finish() - Method in interface ome.services.procs.Process

finish() - Method in class ome.services.procs.ProcessSkeleton

finishCancelled() - Method in class ome.formats.importer.util.ErrorHandler

Action to take when finish cancelled

finishComplete() - Method in class ome.formats.importer.util.ErrorHandler

Action to take when finish completed

FINISHED - Static variable in interface ome.api.JobHandle

finished(Current) - Method in class ome.services.blitz.impl.DeleteHandleI

finished(int) - Method in class omero.grid.DeleteCallbackI

Client method to be overwritten when block is returning a non-null.

finishWithErroredFiles() - Method in class ome.formats.importer.util.ErrorHandler

Action to take when finish completed but with some errors (For example, missing files)

FIRSTNAME - Static variable in class pojos.ExperimenterData

Identifies the Experimenter#FIRSTNAME field.

firstPlane() - Method in class pojos.ROIData

Return the first plane that the ROI starts on.

fixNulledOrFilteredCollections(IObject, IObject, EntityPersister, SessionImplementor) - Static method in class ome.tools.hibernate.HibernateUtils

loads collections which have been filtered or nulled by the user

FLIM - Static variable in class ome.services.util.NamespaceCheck

FLIM_NS - Static variable in class pojos.FileAnnotationData

Identifies the FLIM namespace.

flipState() - Method in class ome.services.eventlogs.EventBacklog

Flips the EventBacklog to the "adding" state if it is empty, otherwise to the "removing" state.

FLOAT(Connection, List<Float>) - Method in interface ome.tools.hibernate.ListAsSQLArrayUserType.ArrayFactory

FLOAT - Static variable in class omeis.providers.re.data.PlaneFactory

Identifies the type used to store pixel values.

FLOAT - Static variable in class omerojava.util.PixelTypes

Identifies the type used to store pixel values.

FLOAT_TYPE - Static variable in class omeis.providers.re.data.PlaneFactory

Identifies the FLOAT data type used to store pixel values, as per OME spec.

FLOAT_TYPE - Static variable in class pojos.PixelsData

Identifies the type used to store pixel values.

FloatConverter - Class in omerojava.util

Packs a sequence of bytes representing a big-endian float into a double value of appropriate integer type.

FloatConverter() - Constructor for class omerojava.util.FloatConverter

flush() - Method in interface ome.api.local.LocalUpdate

flush() - Method in class ome.logic.UpdateImpl

flush() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

flushPreferences() - Method in class ome.formats.importer.util.IniFileLoader

Flush preferences to disk

FONT_BOLD - Static variable in class pojos.ShapeSettingsData

Set if font bold.

FONT_BOLD_ITALIC - Static variable in class pojos.ShapeSettingsData

Set if font bold.

FONT_ITALIC - Static variable in class pojos.ShapeSettingsData

Set if font italic.

FONT_REGULAR - Static variable in class pojos.ShapeSettingsData

Set if font bold.

ForceTransactionAttributeSource - Class in ome.tools.spring

Requires that all method calls have some other form of attribute source by throwing an exception if accessed;

ForceTransactionAttributeSource() - Constructor for class ome.tools.spring.ForceTransactionAttributeSource

forEachTile(TileLoopIteration, PixelBuffer, int, int) - Static method in class ome.io.nio.Utils

Iterates over every tile in a given pixel buffer based on the over arching dimensions and a requested maximum tile width and height.

forEachTile(TileLoopIteration, int, int, int, int, int, int, int) - Static method in class ome.io.nio.Utils

Iterates over every tile in a given pixel buffer based on the over arching dimensions and a requested maximum tile width and height.

forEachTile(int, int, TileLoopIteration) - Method in class omero.util.RPSTileLoop

Iterates over every tile in a given pixel based on the over arching dimensions and a requested maximum tile width and height.

forEachTile(int, int, int, int, int, int, int, TileLoopIteration) - Method in class omero.util.TileLoop

Iterates over every tile in a given pixel based on the over arching dimensions and a requested maximum tile width and height.

free(String) - Method in class ome.tools.FileSystem

This method will return the free space in kilobytes TODO - resolve the slash mount

free() - Method in class ome.tools.hibernate.SqlArray

FreezeShareStore - Class in ome.services.sharing

Entry to the Ice code generated data/ directory.

FreezeShareStore(String, File) - Constructor for class ome.services.sharing.FreezeShareStore

from - Variable in class ome.services.blitz.util.ConvertToBlitzExceptionMessage

from(String, String) - Method in class ome.tools.hibernate.QueryBuilder

fromClass(Class) - Static method in class ome.services.blitz.measurements.Helper

Factory method to generate Helper instances from the Class of a given column.

fromLsid(String) - Static method in class ome.services.blitz.measurements.Helper

Factory method to generate Helper instances from the LSID of a given column.

fromObjectContainerStore(IObjectContainerStore, int, int) - Static method in class ome.formats.model.ChannelData

Retrieves channel data from an object container store.

fromPoints(String) - Method in class pojos.ShapeData

Parses out the type from the points string.

fromRType(RType) - Method in class omero.util.IceMapper

Uses the omero.rtypes hierarchy to properly convert any RType to its internal representation.

fromString(String) - Method in class ome.formats.importer.ImportConfig.AnnotationListValue

fromString(String) - Method in class ome.formats.importer.ImportConfig.BoolValue

fromString(String) - Method in class ome.formats.importer.ImportConfig.DoubleArrayValue

fromString(String) - Method in class ome.formats.importer.ImportConfig.FileValue

fromString(String) - Method in class ome.formats.importer.ImportConfig.IntValue

fromString(String) - Method in class ome.formats.importer.ImportConfig.LongValue

fromString(String) - Method in class ome.formats.importer.ImportConfig.StrValue

fromString(String) - Method in class ome.formats.importer.ImportConfig.Value

fullImport(File, String) - Method in class ome.formats.OMEROImportFixture

Provides one complete import cycle.

fullname() - Method in class ome.services.scripts.RepoFile

FullText - Class in ome.services.search

Search based on Lucene's Query class.

FullText(SearchValues, String, Class<? extends Analyzer>) - Constructor for class ome.services.search.FullText

FullTextAnalyzer - Class in ome.services.fulltext

Analyzer implementation based largely on SimpleAnalyzer, but with extensions for handling scientific and OS-type strings.

FullTextAnalyzer() - Constructor for class ome.services.fulltext.FullTextAnalyzer

fullTextBridge - Variable in class ome.logic.UpdateImpl

FullTextBridge - Class in ome.services.fulltext

Primary definition of what will be indexed via Hibernate Search.

FullTextBridge() - Constructor for class ome.services.fulltext.FullTextBridge

Since this constructor provides the instance with no way of parsing OriginalFile binaries, all files will be assumed to have blank content.

FullTextBridge(OriginalFilesService, Map<String, FileParser>) - Constructor for class ome.services.fulltext.FullTextBridge

Constructor which provides an empty set of custom bridges.

FullTextBridge(OriginalFilesService, Map<String, FileParser>, Class<FieldBridge>[]) - Constructor for class ome.services.fulltext.FullTextBridge

Main constructor.

FullTextIndexer - Class in ome.services.fulltext

Simple action which can be done in an asynchronous thread in order to index Hibernate entities.

FullTextIndexer(EventLogLoader) - Constructor for class ome.services.fulltext.FullTextIndexer

FullTextThread - Class in ome.services.fulltext

Library entry-point for indexing.

FullTextThread(SessionManager, Executor, FullTextIndexer, FullTextBridge) - Constructor for class ome.services.fulltext.FullTextThread

Uses default Principal for indexing

FullTextThread(SessionManager, Executor, FullTextIndexer, FullTextBridge, boolean) - Constructor for class ome.services.fulltext.FullTextThread

Uses default Principal for indexing

FullTextThread(SessionManager, Executor, FullTextIndexer, FullTextBridge, Principal) - Constructor for class ome.services.fulltext.FullTextThread

Main constructor.

FullTextThread(SessionManager, Executor, FullTextIndexer, FullTextBridge, Principal, boolean) - Constructor for class ome.services.fulltext.FullTextThread

Main constructor.

G

G_BAND - Static variable in class omeis.providers.re.RGBBuffer

Index of the green band in the image's data buffer.

GatewayFactory - Class in ome.services.blitz.gateway.services

GatewayFactory(ServiceFactoryPrx) - Constructor for class ome.services.blitz.gateway.services.GatewayFactory

Create services from the serviceFactory.

GatewayHeartbeat - Class in omerojava.util

GatewayHeartbeat(GatewayPrx) - Constructor for class omerojava.util.GatewayHeartbeat

Create an instance of the OmeroJava class and create the heartbeat thread.

GatewayService - Interface in ome.services.blitz.gateway.services

GatewayUtils - Class in omerojava.util

GatewayUtils() - Constructor for class omerojava.util.GatewayUtils

generateRandomPasswd() - Method in class ome.security.auth.PasswordUtil

generateRepoUuid() - Method in class ome.services.blitz.repo.AbstractRepositoryI

Called when this repository is creating a new OriginalFile repository object.

generateRepoUuid() - Method in class ome.services.blitz.repo.ScriptRepositoryI

generateTiff_async(AMD_Exporter_generateTiff, Current) - Method in class ome.services.blitz.impl.ExporterI

generateXml(MetadataRetrieve) - Method in class ome.services.blitz.impl.ExporterI

generateXml_async(AMD_Exporter_generateXml, Current) - Method in class ome.services.blitz.impl.ExporterI

Generate XML and return the length

geomTool - Variable in class ome.services.blitz.impl.RoiI

GeomTool - Class in ome.services.roi

Strategy for handling the conversion between shapes and database-specific geometries.

GeomTool(PixelData, SqlAction, SessionFactory) - Constructor for class ome.services.roi.GeomTool

GeomTool(PixelData, SqlAction, SessionFactory, Executor, String) - Constructor for class ome.services.roi.GeomTool

get(Class<T>, long) - Method in interface ome.api.IQuery

lookup an entity by class and id.

get() - Method in class ome.formats.importer.ImportConfig.FileValue

get() - Method in class ome.formats.importer.ImportConfig.Value

Returns the generic type contained by this holder.

get(Class, long) - Method in class ome.logic.QueryImpl

get(String, DirContextAdapter) - Method in class ome.security.auth.PersonContextMapper

get() - Method in class ome.services.blitz.util.ResultHolder

get(Identity) - Method in class ome.services.blitz.util.ServantHolder

get(Session, Class, long) - Method in class ome.services.fulltext.FullTextIndexer

get(Object) - Method in class ome.services.query.Definitions

get(String) - Method in class ome.services.query.Query

get the QueryParameter for this name argument.

get(PixelBuffer, int, int, int, int, int) - Method in class ome.services.roi.PixelData

get() - Method in class ome.services.sessions.SessionContext.Count

Return the current number of references which this session is aware of.

get(long) - Method in class ome.services.sharing.BlobShareStore

get(long) - Method in class ome.services.sharing.FreezeShareStore

get(long) - Method in class ome.services.sharing.ShareStore

get(Future<T>) - Method in interface ome.services.util.Executor

Helper method to perform Future.get() and properly unwrap the exceptions.

get(Future<T>) - Method in class ome.services.util.Executor.Impl

get(int) - Method in class ome.util.mem.CopiableArray

Return the Copiable at the specified position.

get(int) - Method in class ome.util.mem.ReadOnlyByteArray

Reads the element at the index position within this slice.

get(int) - Method in class omerojava.util.ReadOnlyByteArray

Reads the element at the index position within this slice.

get(String[]) - Static method in class prefs

Returns either the given key=value pairs (or all if no argument is given).

get_async(AMD_IQuery_get, String, long, Current) - Method in class ome.services.blitz.impl.QueryI

getA0() - Method in class omeis.providers.re.codomain.ContrastStretchingContext

Returns the slope of the first line.

getA1() - Method in class omeis.providers.re.codomain.ContrastStretchingContext

Returns the slope of the second line.

getA2() - Method in class omeis.providers.re.codomain.ContrastStretchingContext

Returns the slope of the third line.

getAbsolutePath() - Method in class ome.formats.importer.util.ErrorContainer

get path for file

getAbsolutePath() - Method in class pojos.FileData

Returns the absolute path.

getAcquisitionData() - Method in class omero.sys.ParametersI

getAcquisitionDate() - Method in class pojos.ImageData

Returns the acquisition date.

getActiveConnections(long) - Method in interface ome.api.IShare

Gets actual active connections to share.

getActiveConnections(long) - Method in class ome.services.sharing.ShareBean

getActiveConnections_async(AMD_IShare_getActiveConnections, long, Current) - Method in class ome.services.blitz.impl.ShareI

getAdapter() - Method in class ome.services.blitz.impl.ServiceFactoryI

getAdapter() - Method in class omero.client

getAdminService() - Method in class ome.services.blitz.gateway.services.GatewayFactory

Return the admin service.

getAdminService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI

getAdminService() - Method in class ome.system.ServiceFactory

getAdminSession() - Method in interface ome.services.blitz.fire.Registry

Create a new AdminSessionPrx with the RegistryPrx.

getAdminSession() - Method in class ome.services.blitz.fire.Registry.Impl

getAgent(Current) - Method in class ome.services.blitz.fire.SessionManagerI

getAirPressure() - Method in class pojos.ImageAcquisitionData

Returns the air pressure in bar

getAll(String) - Method in class ome.security.auth.AttributeSet

getAllDatasets() - Method in interface ome.api.IAnalysis

getAllEnumerations(Class<T>) - Method in interface ome.api.IPixels

Retrieves the exhaustive list of enumerations for a given enumeration class.

getAllEnumerations(Class<T>) - Method in class ome.logic.PixelsImpl

getAllEnumerations_async(AMD_IPixels_getAllEnumerations, String, Current) - Method in class ome.services.blitz.impl.PixelsI

getAllForImage(long) - Method in interface ome.api.IAnalysis

getAllGuests(long) - Method in interface ome.api.IShare

Get the email addresses for all share guests.

getAllGuests(long) - Method in class ome.services.sharing.ShareBean

getAllGuests_async(AMD_IShare_getAllGuests, long, Current) - Method in class ome.services.blitz.impl.ShareI

getAllMembers(long) - Method in interface ome.api.IShare

Get all users who are a member of the share.

getAllMembers(long) - Method in class ome.services.sharing.ShareBean

getAllMembers_async(AMD_IShare_getAllMembers, long, Current) - Method in class ome.services.blitz.impl.ShareI

getAllPixels() - Method in class pojos.ImageData

Returns all the sets of pixels related to this image.

getAllUsers(long) - Method in interface ome.api.IShare

Get a single set containing the login names of the Experimenters as well email addresses for guests.

getAllUsers(long) - Method in class ome.services.sharing.ShareBean

getAllUsers_async(AMD_IShare_getAllUsers, long, Current) - Method in class ome.services.blitz.impl.ShareI

getAlpha() - Method in class pojos.WellData

Returns the alpha component of the color associated to the well, or -1.

getAmplificationGain() - Method in class pojos.DetectorData

Returns the amplification gain of the detector.

getAnalysisService() - Method in class ome.system.ServiceFactory

getAndLogException(Throwable) - Method in class ome.services.util.ServiceHandler

getAnnotatableTypes() - Method in interface ome.tools.hibernate.ExtendedMetadata

Returns all the classes which implement IAnnotated

getAnnotatableTypes() - Method in class ome.tools.hibernate.ExtendedMetadata.Impl

getAnnotations() - Method in class pojos.DatasetData

Returns the annotations related to this dataset.

getAnnotations() - Method in class pojos.ImageData

Returns the annotations

getAnnotationsCounts() - Method in class pojos.DatasetData

Returns the number of annotations linked to the object, key: id of the user, value: number of annotation.

getAnnotationsCounts() - Method in class pojos.ImageData

Returns the number of annotations linked to the object, key: id of the user, value: number of annotation.

getAnnotationsCounts() - Method in class pojos.PlateAcquisitionData

Returns the number of annotations linked to the object, key: id of the user, value: number of annotation.

getAnnotationsCounts() - Method in class pojos.PlateData

Returns the number of annotations linked to the object, key: id of the user, value: number of annotation.

getAnnotationsCounts() - Method in class pojos.ProjectData

Returns the number of annotations linked to the object, key: id of the user, value: number of annotation.

getAnnotationsCounts() - Method in class pojos.ScreenData

Returns the number of annotations linked to the object, key: id of the user, value: number of annotation.

getAnnotationsCounts() - Method in class pojos.WellData

Returns the number of annotations linked to the object, key: id of the user, value: number of annotation.

getAnnotationTypes() - Method in interface ome.api.ITypes

Returns a list of classes which implement IAnnotated.

getAnnotationTypes() - Method in class ome.logic.TypesImpl

getAnnotationTypes() - Method in interface ome.tools.hibernate.ExtendedMetadata

Returns all the classes which subclass Annotation

getAnnotationTypes() - Method in class ome.tools.hibernate.ExtendedMetadata.Impl

getAnnotationTypes_async(AMD_ITypes_getAnnotationTypes, Current) - Method in class ome.services.blitz.impl.TypesI

getAppTitle() - Method in class ome.formats.importer.ImportConfig

getAppTitle() - Method in class ome.formats.importer.util.IniFileLoader

getAppVersion() - Method in class ome.formats.importer.util.ErrorContainer

getArchive() - Method in class ome.formats.importer.ImportContainer

getArray() - Method in class ome.tools.hibernate.SqlArray

getArray(long, int) - Method in class ome.tools.hibernate.SqlArray

getArray(Map<String, Class<?>>) - Method in class ome.tools.hibernate.SqlArray

getArray(long, int, Map<String, Class<?>>) - Method in class ome.tools.hibernate.SqlArray

getAttachedFile() - Method in class pojos.FileAnnotationData

Returns the file to upload to the server.

getAttribute(Experimenter) - Method in class ome.security.auth.PersonContextMapper

getAttributeSet(Experimenter) - Method in class ome.security.auth.PersonContextMapper

getAuthoritativeContainerCache() - Method in interface ome.formats.model.IObjectContainerStore

Returns the current authoritative LSID container cache.

getAuthoritativeContainerCache() - Method in class ome.formats.OMEROMetadataStoreClient

getAuthority() - Method in class ome.services.db.DatabaseIdentity

getAvailableFamilies() - Method in class ome.services.RenderingBean

Implemented as specified by the RenderingEngine interface.

getAvailableFamilies() - Method in interface omeis.providers.re.RenderingEngine

Returns the list of mapping families supported by the Rendering engine.

getAvailableFamilies_async(AMD_RenderingEngine_getAvailableFamilies, Current) - Method in class ome.services.blitz.impl.RenderingEngineI

getAvailableFamilies_async(AMD_RenderingEngine_getAvailableFamilies, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI

getAvailableModels() - Method in class ome.services.RenderingBean

Implemented as specified by the RenderingEngine interface.

getAvailableModels() - Method in interface omeis.providers.re.RenderingEngine

Returns the list of color models supported by the Rendering engine.

getAvailableModels_async(AMD_RenderingEngine_getAvailableModels, Current) - Method in class ome.services.blitz.impl.RenderingEngineI

getAvailableModels_async(AMD_RenderingEngine_getAvailableModels, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI

getB0() - Method in class omeis.providers.re.codomain.ContrastStretchingContext

Returns the y-intercept of the first line.

getB1() - Method in class omeis.providers.re.codomain.ContrastStretchingContext

Returns the y-intercept of the second line.

getB2() - Method in class omeis.providers.re.codomain.ContrastStretchingContext

Returns the y-intercept of the third line.

getBaseType() - Method in class ome.tools.hibernate.SqlArray

getBaseTypeName() - Method in class ome.tools.hibernate.SqlArray

getBatchSize() - Method in interface ome.api.Search

Returns the current batch size.

getBatchSize() - Method in class ome.services.eventlogs.EventLogLoader

getBatchSize() - Method in class ome.services.SearchBean

getBatchSize_async(AMD_Search_getBatchSize, Current) - Method in class ome.services.blitz.impl.SearchI

getBeanHelper() - Method in class ome.logic.AbstractLevel1Service

getBeanHelper() - Method in class ome.logic.AbstractLevel2Service

getBeanHelper() - Method in class ome.services.AbstractStatefulBean

getBfImageCount() - Method in class ome.formats.importer.ImportContainer

getBfImageNames() - Method in class ome.formats.importer.ImportContainer

getBfPixels() - Method in class ome.formats.importer.ImportContainer

getBit(byte[], int) - Method in class pojos.MaskData

Sets the bit value in a byte array at position bit to be the value value.

getBitDepth(PixelsType) - Method in interface ome.api.IPixels

Bit depth for a given pixel type.

getBitDepth(PixelsType) - Method in class ome.logic.PixelsImpl

getBitDepth_async(AMD_IPixels_getBitDepth, PixelsType, Current) - Method in class ome.services.blitz.impl.PixelsI

getBlitzAdapter() - Method in class ome.services.blitz.util.BlitzConfiguration

getBlitzManager() - Method in class ome.services.blitz.util.BlitzConfiguration

getBlitzVerifier() - Method in class ome.services.blitz.util.BlitzConfiguration

getBlue() - Method in class pojos.WellData

Returns the blue component of the color associated to the well, or -1.

getBlueBand() - Method in class omeis.providers.re.RGBBuffer

Returns the data buffer for the blue band.

getBlueValue(int) - Method in class omeis.providers.re.RGBAIntBuffer

Retrieves the Blue value for a particular pixel index.

getBlueValue(int) - Method in class omeis.providers.re.RGBBuffer

Retrieves the Blue value for a particular pixel index.

getBlueValue(int) - Method in class omeis.providers.re.RGBIntBuffer

Retrieves the Blue value for a particular pixel index.

getBody() - Method in class ome.util.mem.Handle

Returns a reference to the Body object that is currently paired up with this handle.

getBooleanAnnotationCount() - Method in class ome.services.blitz.impl.OmeroMetadata

getBooleanAnnotationDescription(int) - Method in class ome.services.blitz.impl.OmeroMetadata

getBooleanAnnotationID(int) - Method in class ome.services.blitz.impl.OmeroMetadata

getBooleanAnnotationNamespace(int) - Method in class ome.services.blitz.impl.OmeroMetadata

getBooleanAnnotationValue(int) - Method in class ome.services.blitz.impl.OmeroMetadata

getBoost() - Method in class ome.services.fulltext.SimpleLuceneOptions

getBounds() - Method in class ome.util.math.geom2D.EllipseArea

Required by the Shape I/F.

getBounds() - Method in class ome.util.math.geom2D.RectangleArea

Required by the Shape I/F.

getBounds2D() - Method in class ome.util.math.geom2D.EllipseArea

Required by the Shape I/F.

getBounds2D() - Method in class ome.util.math.geom2D.RectangleArea

Required by the Shape I/F.

getBuffer(long) - Method in class ome.services.roi.PixelData

getBugTrackerURL() - Method in class ome.formats.importer.util.IniFileLoader

getByName(String, Current) - Method in class ome.services.blitz.impl.ServiceFactoryI

getByPeriod_async(AMD_ITimeline_getByPeriod, List<String>, RTime, RTime, Parameters, boolean, Current) - Method in class ome.services.blitz.impl.TimelineI

getByteOrder() - Method in class ome.io.bioformats.BfPyramidPixelBuffer

Returns the current pixel byte order.

getBytesPerPixels(String) - Static method in class omerojava.util.GatewayUtils

Returns the number of bytes per pixel depending on the pixel type.

getByteWidth() - Method in interface ome.api.RawPixelsStore

getByteWidth() - Method in class ome.io.bioformats.BfPixelBuffer

getByteWidth() - Method in class ome.io.bioformats.BfPixelsWrapper

getByteWidth() - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getByteWidth() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getByteWidth() - Method in interface ome.io.nio.PixelBuffer

Returns the byte width for the pixel buffer.

getByteWidth() - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getByteWidth(long) - Method in class ome.services.blitz.gateway.services.impl.RawPixelsStoreServiceImpl

getByteWidth(long) - Method in interface ome.services.blitz.gateway.services.RawPixelsStoreService

Get the bytewidth of the image

getByteWidth() - Method in class ome.services.RawPixelsBean

getByteWidth_async(AMD_RawPixelsStore_getByteWidth, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI

getByteWidth_async(AMD_RawPixelsStore_getByteWidth, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI

getC() - Method in class pojos.ShapeData

Returns the channel.

getCalibratedMagnification() - Method in class pojos.ObjectiveData

Returns the objective's calibrated magnification factor.

getCallbackObject(String, String) - Method in class ome.services.sessions.SessionManagerImpl

getCallGroup() - Method in class ome.security.basic.CurrentDetails

getChannel() - Method in class ome.formats.model.ChannelData

Returns the channel this channel data is for.

getChannel(int, int) - Method in class ome.formats.OMEROMetadataStoreClient

getChannelAcquisitionMode(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata

getChannelBindings() - Method in class omeis.providers.re.Renderer

Returns an array containing the channel bindings.

getChannelBindingsAsList() - Method in class omeis.providers.re.Renderer

Returns a list containing the channel bindings.

getChannelColor(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata

getChannelContrastMethod(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata

getChannelCount(int) - Method in class ome.services.blitz.impl.OmeroMetadata

getChannelCurveCoefficient(int) - Method in class ome.services.RenderingBean

Implemented as specified by the RenderingEngine interface.

getChannelCurveCoefficient(int) - Method in interface omeis.providers.re.RenderingEngine

Returns the coefficient identifying a map in the family.

getChannelCurveCoefficient_async(AMD_RenderingEngine_getChannelCurveCoefficient, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI

getChannelCurveCoefficient_async(AMD_RenderingEngine_getChannelCurveCoefficient, int, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI

getChannelEmissionWavelength(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata

getChannelExcitationWavelength(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata

getChannelFamily(int) - Method in class ome.services.RenderingBean

Implemented as specified by the RenderingEngine interface.

getChannelFamily(int) - Method in interface omeis.providers.re.RenderingEngine

Returns the family associated to the specified channel.

getChannelFamily_async(AMD_RenderingEngine_getChannelFamily, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI

getChannelFamily_async(AMD_RenderingEngine_getChannelFamily, int, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI

getChannelFluor(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata

getChannelID(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata

getChannelIlluminationType(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata

getChannelIndex() - Method in class ome.formats.model.ChannelData

Returns the index of the channel this channel data is for.

getChannelLabeling() - Method in class pojos.ChannelData

Returns the label of the channel.

getChannelName(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata

getChannelNDFilter(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata

getChannelNoiseReduction(int) - Method in class ome.services.RenderingBean

Implemented as specified by the RenderingEngine interface.

getChannelNoiseReduction(int) - Method in interface omeis.providers.re.RenderingEngine

Returns true if the noise reduction algorithm used to map the pixels intensity values is turned on, false if the algorithm is turned off.

getChannelNoiseReduction_async(AMD_RenderingEngine_getChannelNoiseReduction, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI

getChannelNoiseReduction_async(AMD_RenderingEngine_getChannelNoiseReduction, int, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI

getChannelPinholeSize(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata

getChannelPockelCellSetting(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata

getChannelSamplesPerPixel(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata

getChannelStats(int) - Method in class ome.services.RenderingBean

Implemented as specified by the RenderingEngine interface.

getChannelStats(int) - Method in interface omeis.providers.re.RenderingEngine

getChannelStats_async(AMD_RenderingEngine_getChannelStats, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI

getChannelStats_async(AMD_RenderingEngine_getChannelStats, int, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI

getChannelWindowEnd(Long, int) - Method in class ome.services.blitz.gateway.services.impl.RenderingServiceImpl

getChannelWindowEnd(Long, int) - Method in interface ome.services.blitz.gateway.services.RenderingService

Get the channel max.

getChannelWindowEnd(int) - Method in class ome.services.RenderingBean

Implemented as specified by the RenderingEngine interface.

getChannelWindowEnd(int) - Method in interface omeis.providers.re.RenderingEngine

Returns the upper bound of the pixels intensity interval.

getChannelWindowEnd_async(AMD_RenderingEngine_getChannelWindowEnd, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI

getChannelWindowEnd_async(AMD_RenderingEngine_getChannelWindowEnd, int, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI

getChannelWindowStart(Long, int) - Method in class ome.services.blitz.gateway.services.impl.RenderingServiceImpl

getChannelWindowStart(Long, int) - Method in interface ome.services.blitz.gateway.services.RenderingService

Get the channel min.

getChannelWindowStart(int) - Method in class ome.services.RenderingBean

Implemented as specified by the RenderingEngine interface.

getChannelWindowStart(int) - Method in interface omeis.providers.re.RenderingEngine

Returns the lower bound of the pixels intensity interval.

getChannelWindowStart_async(AMD_RenderingEngine_getChannelWindowStart, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI

getChannelWindowStart_async(AMD_RenderingEngine_getChannelWindowStart, int, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI

getChildTransformer(Class) - Static method in class ome.services.query.Hierarchy

getClass(String) - Method in class ome.services.graphs.GraphState

getClass(String) - Method in interface ome.services.graphs.GraphStep.Callback

getClasses() - Method in interface ome.tools.hibernate.ExtendedMetadata

getClasses() - Method in class ome.tools.hibernate.ExtendedMetadata.Impl

getClassName(Class) - Static method in class ome.tools.StringUtils

getClient() - Method in class ome.formats.importer.util.ClientKeepAlive

getClientContext() - Static method in class ome.system.OmeroContext

create (if necessary) and return the single default client OmeroContext.

getClientContext(Properties) - Static method in class ome.system.OmeroContext

initialize a new client OmeroContext (named OmeroContext.CLIENT_CONTEXT), using the OmeroContext.getContext(Properties, String) method.

getCloseStatementCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

getCo2Percent() - Method in class pojos.ImageAcquisitionData

Returns the Co2 level, this is a percent value in the interval [0, 1].

getCodomainChain() - Method in class omeis.providers.re.Renderer

Returns the object that defines the sequence of spatial transformations to be applied to quantized data.

getCol(int, int, int, int) - Method in interface ome.api.RawPixelsStore

getCol(Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer

getCol(Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPixelsWrapper

getCol(Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getCol(Integer, Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getCol(Integer, Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer

Retrieves a particular column from this pixel buffer.

getCol(Integer, Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getCol(int, int, int, int) - Method in class ome.services.RawPixelsBean

getCol_async(AMD_RawPixelsStore_getCol, int, int, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI

getCol_async(AMD_RawPixelsStore_getCol, int, int, int, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI

getColDirect(Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPixelBuffer

getColDirect(Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getColDirect(Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getColDirect(Integer, Integer, Integer, Integer, byte[]) - Method in interface ome.io.nio.PixelBuffer

Retrieves a particular column from this pixel buffer.

getColDirect(Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getCollectionCount(String, String, Set<Long>, Parameters) - Method in interface ome.api.IContainer

Counts the number of members in a collection for a given object.

getCollectionCount(String, String, Set, Parameters) - Method in class ome.logic.PojosImpl

Implemented as specified by the IContainer I/F

getCollectionCount_async(AMD_IContainer_getCollectionCount, String, String, List<Long>, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI

getCollectionFetchCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

getCollectionLoadCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

getCollectionRecreateCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

getCollectionRemoveCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

getCollectionRoleNames() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

Get the names of all collection roles

getCollectionStatistics(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

Get collection statistics per role

getCollectionUpdateCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

getColor(ChannelData) - Static method in class ome.formats.model.ColorsFactory

Determines the color usually associated to the specified wavelength or explicitly defined for a particular channel.

getColor(int, Channel) - Static method in class omeis.providers.re.ColorsFactory

Determines the color usually associated to the specified wavelength.

getColor(int, Channel, LogicalChannel) - Static method in class omeis.providers.re.ColorsFactory

Determines the color usually associated to the specified wavelength.

getColorArray(ChannelBinding) - Static method in class omeis.providers.re.Renderer

Returns an array whose ascending indices represent the color components Red, Green and Blue.

getColSize() - Method in class ome.io.bioformats.BfPixelBuffer

getColSize() - Method in class ome.io.bioformats.BfPixelsWrapper

getColSize() - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getColSize() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getColSize() - Method in interface ome.io.nio.PixelBuffer

Retrieves the in memory size of a column of pixels in this pixel buffer.

getColSize() - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getColumn() - Method in class pojos.WellData

Returns the column used to indicate the location of the well on the grid.

getColumnSequenceIndex() - Method in class pojos.PlateData

Returns the index indicating how to label a column.

getComment() - Method in class ome.formats.importer.util.ErrorContainer

getCommentAnnotationCount() - Method in class ome.services.blitz.impl.OmeroMetadata

getCommentAnnotationDescription(int) - Method in class ome.services.blitz.impl.OmeroMetadata

getCommentAnnotationID(int) - Method in class ome.services.blitz.impl.OmeroMetadata

getCommentAnnotationNamespace(int) - Method in class ome.services.blitz.impl.OmeroMetadata

getCommentAnnotationValue(int) - Method in class ome.services.blitz.impl.OmeroMetadata

getCommentCount(Set<Long>) - Method in interface ome.api.IShare

Returns a map from share id to comment count.

getCommentCount(Set<Long>) - Method in class ome.services.sharing.ShareBean

getCommentCount_async(AMD_IShare_getCommentCount, List<Long>, Current) - Method in class ome.services.blitz.impl.ShareI

getComments(long) - Method in interface ome.api.IShare

Looks up all comments which belong to the share.

getComments(long) - Method in class ome.services.sharing.ShareBean

getComments_async(AMD_IShare_getComments, long, Current) - Method in class ome.services.blitz.impl.ShareI

getCommentType() - Method in class ome.formats.importer.util.ErrorContainer

getCommunicator() - Method in class ome.services.blitz.fire.Ring

getCommunicator() - Method in interface ome.services.blitz.redirect.Redirector.Context

Active communicator for use by the Redirector instance.

getCommunicator() - Method in class ome.services.blitz.repo.AbstractRepositoryI

getCommunicator() - Method in class ome.services.blitz.repo.InternalRepositoryConfig

getCommunicator() - Method in class ome.services.blitz.util.BlitzConfiguration

getCommunicator() - Method in class omero.client

Returns the Communicator for this instance or throws an exception if null.

getComponents() - Method in class pojos.MultiImageData

Returns the collection of images composing the file.

getCompressionLevel() - Method in interface ome.api.local.LocalCompress

Returns the current compression level for the service.

getCompressionLevel() - Method in class ome.logic.CompressImpl

getCompressionLevel() - Method in class ome.services.RenderingBean

Implemented as specified by the RenderingEngine interface.

getCompressionLevel() - Method in interface omeis.providers.re.RenderingEngine

Returns the current compression level for the service.

getCompressionLevel_async(AMD_RenderingEngine_getCompressionLevel, Current) - Method in class ome.services.blitz.impl.RenderingEngineI

getCompressionLevel_async(AMD_RenderingEngine_getCompressionLevel, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI

getConfig() - Method in class ome.formats.importer.OMEROWrapper

getConfigService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI

getConfigService() - Method in class ome.system.ServiceFactory

getConfigValue(String) - Method in interface ome.api.IConfig

retrieve a configuration value from the backend store.

getConfigValue(String) - Method in class ome.formats.OMEROMetadataStoreClient

Retrieves a configuration value from the IConfig service.

getConfigValue(String) - Method in class ome.logic.ConfigImpl

see IConfig.getConfigValue(String)

getConfigValue_async(AMD_IConfig_getConfigValue, String, Current) - Method in class ome.services.blitz.impl.ConfigI

getConnectCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

getConnection() - Method in class ome.services.db.SelfCorrectingDataSource

getConnection(String, String) - Method in class ome.services.db.SelfCorrectingDataSource

getContainerCache() - Method in interface ome.formats.model.IObjectContainerStore

Returns the current container cache.

getContainerCache() - Method in class ome.formats.OMEROMetadataStoreClient

getContainers() - Method in class ome.formats.importer.ImportCandidates

getContainers() - Method in class ome.services.blitz.repo.ImportableFiles

getContainerService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI

getContainerService() - Method in class ome.system.ServiceFactory

getContainerTypes() - Method in class ome.logic.TypesImpl

getContent() - Method in class pojos.AnnotationData

Returns the content of the annotation.

getContent() - Method in class pojos.BooleanAnnotationData

Returns the textual content of the annotation.

getContent() - Method in class pojos.DoubleAnnotationData

Returns the value.

getContent() - Method in class pojos.FileAnnotationData

Returns the original file.

getContent() - Method in class pojos.LongAnnotationData

Returns the rating value.

getContent() - Method in class pojos.RatingAnnotationData

Returns the rating value.

getContent() - Method in class pojos.TagAnnotationData

Returns the textual content of the annotation.

getContent() - Method in class pojos.TermAnnotationData

Returns the textual content of the annotation.

getContent() - Method in class pojos.TextualAnnotationData

Returns the textual content of the annotation.

getContent() - Method in class pojos.TimeAnnotationData

Returns the timestamp of the annotation.

getContent() - Method in class pojos.XMLAnnotationData

Returns the content of the annotation.

getContentAsString() - Method in class pojos.AnnotationData

Returns the content of the annotation as a String, which is parsed on a Class-by-Class basis.

getContentAsString() - Method in class pojos.BooleanAnnotationData

Returns the textual content of the annotation.

getContentAsString() - Method in class pojos.DoubleAnnotationData

Returns the value as a string.

getContentAsString() - Method in class pojos.FileAnnotationData

Returns the absolute path to the file

getContentAsString() - Method in class pojos.LongAnnotationData

Returns the value as a string.

getContentAsString() - Method in class pojos.RatingAnnotationData

Returns the rating value as a string.

getContentAsString() - Method in class pojos.TagAnnotationData

Returns the textual content of the annotation.

getContentAsString() - Method in class pojos.TermAnnotationData

Returns the textual content of the annotation.

getContentAsString() - Method in class pojos.TextualAnnotationData

Returns the textual content of the annotation.

getContentAsString() - Method in class pojos.TimeAnnotationData

Returns the time as a string.

getContentAsString() - Method in class pojos.XMLAnnotationData

Returns the textual content of the annotation.

getContentLength() - Method in class ome.formats.importer.util.FileUploadCounter

getContentMap(long) - Method in interface ome.api.IShare

Returns the contents of the share keyed by type.

getContentMap(long) - Method in class ome.services.sharing.ShareBean

getContentMap_async(AMD_IShare_getContentMap, long, Current) - Method in class ome.services.blitz.impl.ShareI

getContents(long) - Method in interface ome.api.IShare

Looks up all items belong to the share.

getContents(long) - Method in class ome.services.sharing.ShareBean

getContents_async(AMD_IShare_getContents, long, Current) - Method in class ome.services.blitz.impl.ShareI

getContentSize(long) - Method in interface ome.api.IShare

Returns the number of items in the share.

getContentSize(long) - Method in class ome.services.sharing.ShareBean

getContentSize_async(AMD_IShare_getContentSize, long, Current) - Method in class ome.services.blitz.impl.ShareI

getContentSubList(long, int, int) - Method in interface ome.api.IShare

Returns a range of items from the share.

getContentSubList(long, int, int) - Method in class ome.services.sharing.ShareBean

getContentSubList_async(AMD_IShare_getContentSubList, long, int, int, Current) - Method in class ome.services.blitz.impl.ShareI

getContentType() - Method in class ome.formats.importer.util.FileUploadCounter

getContext() - Method in interface ome.services.util.Executor

Provides access to the context for Work-API consumers who need to publish events, etc.

getContext() - Method in class ome.services.util.Executor.Impl

getContext(Properties, String) - Static method in class ome.system.OmeroContext

initialize a new client OmeroContext using the Properties provided as values for property (e.g.

getContext() - Method in class ome.system.ServiceFactory

Deprecated.

getContrastMethod() - Method in class pojos.ChannelAcquisitionData

Returns the contrast method.

getContrastMethod() - Method in class pojos.ChannelData

Returns the contrast method.

getContrastMethodAsEnum() - Method in class pojos.ChannelData

Returns the contrast method enumeration value.

getCorrection() - Method in class pojos.ObjectiveData

Returns the correction value of the objective.

getCorrectionCollar() - Method in class pojos.ImageAcquisitionData

Returns the correction collar of the objective.

getCount() - Method in class ome.io.nio.SimpleBackOff

getCount(String) - Method in class ome.services.export.ExporterStepFactory

getCountQuery(String) - Method in interface ome.tools.hibernate.ExtendedMetadata

Returns the query for obtaining the number of collection items to a particular instance.

getCountQuery(String) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl

Returns the query for obtaining the number of collection items to a particular instance.

getCreated() - Method in class pojos.DataObject

Returns the creation time of the object.

getCreationEvent(Current) - Method in class omero.model.DetailsI

getCurrent() - Method in class ome.services.blitz.util.RegisterServantMessage

getCurrent() - Method in class ome.services.blitz.util.UnregisterServantMessage

getCurrentDetails() - Method in class ome.services.graphs.BaseGraphSpec

getCurrentDetails() - Method in interface ome.services.graphs.GraphSpec

getCurrentEventContext() - Method in interface ome.api.StatefulServiceInterface

Returns the current EventContext for this instance.

getCurrentEventContext() - Method in class ome.security.basic.CurrentDetails

Public view on the data contained here.

getCurrentEventContext() - Method in class ome.services.AbstractStatefulBean

getCurrentEventContext() - Method in class ome.services.RenderingBean

Implemented as specified by the RenderingEngine interface.

getCurrentEventContext() - Method in class ome.services.ThumbnailBean

getCurrentEventContext_async(AMD_StatefulServiceInterface_getCurrentEventContext, Current) - Method in class ome.services.blitz.impl.AbstractAmdServant

getCurrentEventContext_async(AMD_StatefulServiceInterface_getCurrentEventContext, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI

getCurrentEventContext_async(AMD_StatefulServiceInterface_getCurrentEventContext, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI

getCurrentEventId() - Method in class ome.services.sessions.SessionContextImpl

getCurrentEventId() - Method in interface ome.system.EventContext

getCurrentEventId() - Method in class ome.system.SimpleEventContext

getCurrentEventType() - Method in class ome.services.sessions.SessionContextImpl

getCurrentEventType() - Method in interface ome.system.EventContext

getCurrentEventType() - Method in class ome.system.SimpleEventContext

getCurrentGroupId() - Method in class ome.services.sessions.SessionContextImpl

getCurrentGroupId() - Method in interface ome.system.EventContext

getCurrentGroupId() - Method in class ome.system.SimpleEventContext

getCurrentGroupName() - Method in class ome.services.sessions.SessionContextImpl

getCurrentGroupName() - Method in interface ome.system.EventContext

getCurrentGroupName() - Method in class ome.system.SimpleEventContext

getCurrentGroupPermissions() - Method in class ome.services.sessions.SessionContextImpl

getCurrentGroupPermissions() - Method in interface ome.system.EventContext

getCurrentGroupPermissions() - Method in class ome.system.SimpleEventContext

getCurrentId() - Method in class ome.services.eventlogs.PersistentEventLogLoader

Get current EventLog id.

getCurrentSessionId() - Method in class ome.services.sessions.SessionContextImpl

getCurrentSessionId() - Method in interface ome.system.EventContext

getCurrentSessionId() - Method in class ome.system.SimpleEventContext

getCurrentSessionUuid() - Method in class ome.services.sessions.SessionContextImpl

getCurrentSessionUuid() - Method in interface ome.system.EventContext

getCurrentSessionUuid() - Method in class ome.system.SimpleEventContext

getCurrentShareId() - Method in class ome.services.sessions.SessionContextImpl

getCurrentShareId() - Method in interface ome.system.EventContext

getCurrentShareId() - Method in class ome.system.SimpleEventContext

getCurrentUmask() - Method in class ome.services.sessions.SessionContextImpl

getCurrentUmask() - Method in class ome.system.SimpleEventContext

getCurrentUserId() - Method in class ome.services.sessions.SessionContextImpl

getCurrentUserId() - Method in interface ome.system.EventContext

getCurrentUserId() - Method in class ome.system.SimpleEventContext

getCurrentUserName() - Method in class ome.services.sessions.SessionContextImpl

getCurrentUserName() - Method in interface ome.system.EventContext

getCurrentUserName() - Method in class ome.system.SimpleEventContext

getCurrentUserNames() - Method in class ome.services.util.DropBoxDirectoryCheck

getCurveCoefficient() - Method in class omeis.providers.re.quantum.QuantumStrategy

Returns the coefficient identifying a curve within a given family.

getCustomAnnotationList() - Method in class ome.formats.importer.ImportContainer

The list of custom, user specified, annotations to link to all images represented by this container.

getCustomImageDescription() - Method in class ome.formats.importer.ImportContainer

Retrieves the current custom image description string.

getCustomImageName() - Method in class ome.formats.importer.ImportContainer

Retrieves the current custom image name string.

getCustomImageNaming() - Method in class ome.formats.importer.ImportConfig

getCustomImageNaming() - Method in class ome.formats.importer.util.IniFileLoader

getCustomPlateDescription() - Method in class ome.formats.importer.ImportContainer

Retrieves the current custom plate description string.

getCustomPlateName() - Method in class ome.formats.importer.ImportContainer

Retrieves the current custom plate name string.

getCutIn() - Method in class pojos.FilterData

Returns the cut in value or null.

getCutInTolerance() - Method in class pojos.FilterData

Returns the cut in tolerance value or null.

getCutOut() - Method in class pojos.FilterData

Returns the cut out value or null.

getCutOutTolerance() - Method in class pojos.FilterData

Returns the cut out tolerance value or null.

getData() - Method in class ome.io.nio.ReorderedPixelData

Returns the backing buffer for the pixel data.

getData() - Method in class omeis.providers.re.data.Plane2D

Returns the pixel data that is used to back this Plane.

getDataAsArray(Connection, Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.BOOLEAN

getDataAsArray(Connection, Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.DATE

getDataAsArray(Connection, Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.DOUBLE

getDataAsArray(Connection, Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.ENUM

getDataAsArray(Connection, Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.FLOAT

getDataAsArray(Connection, Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType

getDataAsArray(Connection, Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.INTEGER

getDataAsArray(Connection, Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.STRING

getDataAsArray(Connection, Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.STRING2

getDatabaseTime() - Method in interface ome.api.IConfig

checks the database for it's time using a SELECT statement.

getDatabaseTime() - Method in class ome.logic.ConfigImpl

see IConfig.getDatabaseTime()

getDatabaseTime_async(AMD_IConfig_getDatabaseTime, Current) - Method in class ome.services.blitz.impl.ConfigI

getDatabaseUuid() - Method in interface ome.api.IConfig

Provides the UUID for this OMERO (database) instance.

getDatabaseUuid() - Method in class ome.logic.ConfigImpl

getDatabaseUuid_async(AMD_IConfig_getDatabaseUuid, Current) - Method in class ome.services.blitz.impl.ConfigI

getDatabaseVersion() - Method in interface ome.api.local.LocalConfig

Retrieves the newest database patch.

getDatabaseVersion() - Method in class ome.logic.ConfigImpl

getDataBuffer() - Method in class omeis.providers.re.RGBAIntBuffer

Retrieves the data buffer that contains the pixel values.

getDataBuffer() - Method in class omeis.providers.re.RGBIntBuffer

Retrieves the data buffer that contains the pixel values.

getDataFromArray(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.BOOLEAN

getDataFromArray(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.DATE

getDataFromArray(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.DOUBLE

getDataFromArray(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.ENUM

getDataFromArray(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.FLOAT

getDataFromArray(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType

getDataFromArray(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.INTEGER

getDataFromArray(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.STRING

getDataFromArray(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.STRING2

getDataObjects() - Method in class pojos.TagAnnotationData

Returns the collection of data objects related to this tag.

getDataService() - Method in class ome.services.blitz.gateway.services.GatewayFactory

getDataset() - Method in class ome.formats.importer.util.TinyImportFixture

provides access to the created Dataset instance.

getDataset(long, boolean, Current) - Method in class ome.services.blitz.gateway.OmeroGateway

getDatasets(Project) - Method in class ome.formats.OMEROMetadataStoreClient

getDatasets(List<Long>, boolean, Current) - Method in class ome.services.blitz.gateway.OmeroGateway

getDatasets(List<Long>, boolean) - Method in interface ome.services.blitz.gateway.services.DataService

Get the Datasets with id's passed as list in ids.

getDatasets(List<Long>, boolean) - Method in class ome.services.blitz.gateway.services.impl.DataServiceImpl

getDatasets() - Method in class pojos.ImageData

Returns the datasets containing this image.

getDatasets() - Method in class pojos.ProjectData

Returns the datasets contained in this project.

getDatasetsForProject(long) - Method in interface ome.api.IAnalysis

getDatasetsFromProject(Project) - Static method in class omerojava.util.GatewayUtils

Get the datasets from the project, the project must have the datasets loaded already.

getDatasetsWithoutProjects() - Method in class ome.formats.OMEROMetadataStoreClient

getDataValue() - Method in class pojos.DoubleAnnotationData

Returns the value.

getDataValue() - Method in class pojos.LongAnnotationData

Returns the value.

getDate(Class) - Static method in class ome.system.Version

Parses the given class for its RevisionDate annotation.

getDebugLevel() - Method in class ome.formats.importer.ImportConfig

getDebugLevel() - Method in class ome.formats.importer.util.IniFileLoader

Returns the level of debugging which should be set on ImportConfig Any value lower than null will not call configureDebug.

getDefaultContext() - Method in class ome.system.ServiceFactory

used when no context name is provided to the constructor.

getDefaultContext() - Method in class ome.tools.spring.InternalServiceFactory

returns null to prevent the lookup of any context, but rather wait on injection as a ApplicationContextAware

getDefaultContext() - Method in class ome.tools.spring.ManagedServiceFactory

returns null to prevent the lookup of any context, but rather wait on injection as a ApplicationContextAware

getDefaultGroup(long) - Method in interface ome.api.IAdmin

retrieve the default group for the given user id.

getDefaultGroup(long) - Method in class ome.logic.AdminImpl

getDefaultGroup() - Method in class pojos.ExperimenterData

Returns the default Group for this Experimenter

getDefaultGroup_async(AMD_IAdmin_getDefaultGroup, long, Current) - Method in class ome.services.blitz.impl.AdminI

getDefaultGroupLevel() - Method in class ome.formats.OMEROMetadataStoreClient

Retrieve teh default groups permission 'level'.

getDefaultGroupName() - Method in class ome.formats.OMEROMetadataStoreClient

Retrieve the default group's name

getDefaultPixels() - Method in class pojos.ImageData

Returns the default set of pixels.

getDefaultSample() - Method in class pojos.PlateData

Returns the currently selected field or 0.

getDefaultScriptDir() - Static method in class ome.services.scripts.ScriptRepoHelper

Directory which will be used as the root of this repository if no directory is passed to a constructor.

getDefaultT(Long) - Method in class ome.services.blitz.gateway.services.impl.RenderingServiceImpl

getDefaultT(Long) - Method in interface ome.services.blitz.gateway.services.RenderingService

Get the default T point of the image

getDefaultT() - Method in class ome.services.RenderingBean

Implemented as specified by the RenderingEngine interface.

getDefaultT() - Method in interface omeis.providers.re.RenderingEngine

Returns the default timepoint index.

getDefaultT_async(AMD_RenderingEngine_getDefaultT, Current) - Method in class ome.services.blitz.impl.RenderingEngineI

getDefaultT_async(AMD_RenderingEngine_getDefaultT, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI

getDefaultZ(Long) - Method in class ome.services.blitz.gateway.services.impl.RenderingServiceImpl

getDefaultZ(Long) - Method in interface ome.services.blitz.gateway.services.RenderingService

Get the default Z section of the image

getDefaultZ() - Method in class ome.services.RenderingBean

Implemented as specified by the RenderingEngine interface.

getDefaultZ() - Method in interface omeis.providers.re.RenderingEngine

Returns the index of the default focal section.

getDefaultZ_async(AMD_RenderingEngine_getDefaultZ, Current) - Method in class ome.services.blitz.impl.RenderingEngineI

getDefaultZ_async(AMD_RenderingEngine_getDefaultZ, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI

getDeleteService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI

getDeleteService() - Method in class ome.system.ServiceFactory

getDescription(Current) - Method in class ome.services.blitz.repo.AbstractRepositoryI

getDescription(long) - Method in class ome.services.blitz.repo.AbstractRepositoryI

getDescription() - Method in class pojos.DatasetData

Returns the description of the dataset.

getDescription() - Method in class pojos.FileAnnotationData

Returns the description of the annotation.

getDescription() - Method in class pojos.FileData

Returns the description of the file.

getDescription() - Method in class pojos.GroupData

Returns the description of the group.

getDescription() - Method in class pojos.ImageData

Returns the description of the image.

getDescription() - Method in class pojos.PlateAcquisitionData

Returns the description of the plate acquisition.

getDescription() - Method in class pojos.PlateData

Returns the description of the plate.

getDescription() - Method in class pojos.ProjectData

Returns the description of the project.

getDescription() - Method in class pojos.ScreenData

Returns the description of the screen.

getDescription() - Method in class pojos.XMLAnnotationData

Returns the description of the annotation.

getDetails(Object[], String[]) - Static method in class ome.tools.hibernate.HibernateUtils

getDetails() - Method in class pojos.DataObject

Returns the details of the object.

getDetector(int, int) - Method in class ome.formats.OMEROMetadataStoreClient

getDetector() - Method in class pojos.ChannelAcquisitionData

Returns the detector used for that channel.

getDetectorBinningAsEnum() - Method in class pojos.ChannelAcquisitionData

Returns the binning enumeration value.

getDetectors() - Method in class pojos.InstrumentData

Returns the collection of detectors.

getDetectorSettingsBinning() - Method in class pojos.ChannelAcquisitionData

Returns the Binning factor.

getDetectorSettingsGain() - Method in class pojos.ChannelAcquisitionData

Returns the gain set on the detector.

getDetectorSettingsOffset() - Method in class pojos.ChannelAcquisitionData

Returns the offset set on the detector.

getDetectorSettingsReadOutRate() - Method in class pojos.ChannelAcquisitionData

Returns the Read out rate set on the detector.

getDetectorSettingsVoltage() - Method in class pojos.ChannelAcquisitionData

Returns the voltage set on the detector.

getDichroic() - Method in class pojos.FilterSetData

Returns the dichroic if any.

getDichroic() - Method in class pojos.LightPathData

Returns the dichroic if any.

getDichroics() - Method in class pojos.InstrumentData

Returns the collection of dichroics.

getDir() - Method in class ome.services.blitz.repo.FileMaker

getDirectProxy() - Method in class ome.services.blitz.fire.Ring

Returns the proxy information for the local SessionManager.

getDirectProxy() - Method in interface ome.services.blitz.redirect.Redirector.Context

String representation of the proxy to the local node which may be contacted to create new sessions.

getDirectProxy() - Method in class ome.services.blitz.util.BlitzConfiguration

Return a direct proxy to the session manager in this object adapter.

getDn(Experimenter) - Method in class ome.security.auth.PersonContextMapper

getDnById(Long) - Method in class ome.security.auth.PasswordUtil

getDoThumbnails() - Method in class ome.formats.importer.ImportContainer

Retrieves whether or not we are performing thumbnail creation upon import completion.

getDoubleAnnotationCount() - Method in class ome.services.blitz.impl.OmeroMetadata

getDoubleAnnotationDescription(int) - Method in class ome.services.blitz.impl.OmeroMetadata

getDoubleAnnotationID(int) - Method in class ome.services.blitz.impl.OmeroMetadata

getDoubleAnnotationNamespace(int) - Method in class ome.services.blitz.impl.OmeroMetadata

getDoubleAnnotationValue(int) - Method in class ome.services.blitz.impl.OmeroMetadata

getEmail() - Method in class ome.formats.importer.util.ErrorContainer

getEmail() - Method in class pojos.ExperimenterData

Returns the e-mail of the experimenter.

getEmissionFilters() - Method in class pojos.FilterSetData

Returns the collections of emission filters if any.

getEmissionFilters() - Method in class pojos.LightPathData

Returns the collections of emission filters if any.

getEmissionWavelength() - Method in class pojos.ChannelData

Returns the emission wavelength of the channel.

getEndTime() - Method in class omero.sys.ParametersI

Returns the value of the end time parameter.

getEndTime() - Method in class pojos.PlateAcquisitionData

Returns the time when the last image was collected.

getEntity(String, Serializable) - Method in class ome.security.basic.OmeroInterceptor

getEntityDeleteCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

getEntityFetchCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

getEntityInsertCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

getEntityLoadCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

getEntityName(Object) - Method in class ome.security.basic.OmeroInterceptor

getEntityNames() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

Get the names of all entities

getEntityStatistics(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

find entity statistics per name

getEntityUpdateCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

getEnumeration(Class<T>, String) - Method in interface ome.api.IPixels

Retrieves a particular enumeration for a given enumeration class.

getEnumeration(Class<T>, String) - Method in interface ome.api.ITypes

lookup an enumeration value.

getEnumeration(Class<T>, String, boolean) - Method in interface ome.formats.enums.EnumerationProvider

Retrieves an enumeration.

getEnumeration(Class<T>, String, boolean) - Method in class ome.formats.enums.IQueryEnumProvider

getEnumeration(Class<T>, String) - Method in class ome.logic.PixelsImpl

getEnumeration(Class<T>, String) - Method in class ome.logic.TypesImpl

getEnumeration_async(AMD_IPixels_getEnumeration, String, String, Current) - Method in class ome.services.blitz.impl.PixelsI

getEnumeration_async(AMD_ITypes_getEnumeration, String, String, Current) - Method in class ome.services.blitz.impl.TypesI

getEnumerationProvider() - Method in class ome.formats.OMEROMetadataStoreClient

Retrieves the active enumeration provider.

getEnumerations(Class<T>) - Method in interface ome.formats.enums.EnumerationProvider

Retrieves all enumerations of a specific type.

getEnumerations(Class<T>) - Method in class ome.formats.enums.IQueryEnumProvider

getEnumerationsWithEntries() - Method in interface ome.api.ITypes

Gets all metadata classes which are IEnum type with contained objects.

getEnumerationsWithEntries() - Method in class ome.logic.TypesImpl

getEnumerationsWithEntries_async(AMD_ITypes_getEnumerationsWithEntries, Current) - Method in class ome.services.blitz.impl.TypesI

getEnumerationTypes() - Method in interface ome.api.ITypes

Gets all metadata classes which are IEnum type.

getEnumerationTypes() - Method in class ome.logic.TypesImpl

getEnumerationTypes_async(AMD_ITypes_getEnumerationTypes, Current) - Method in class ome.services.blitz.impl.TypesI

getError() - Method in class ome.formats.importer.util.ErrorContainer

getEvent() - Method in class ome.security.basic.CurrentDetails

getEvent(Current) - Method in class ome.services.blitz.fire.SessionManagerI

getEvent() - Method in class ome.system.Login

simple getter for the event type passed into the constructor

getEventContext() - Method in interface ome.api.IAdmin

returns an implementation of EventContext loaded with the security for the current user and thread.

getEventContext() - Method in class ome.logic.AdminImpl

getEventContext(boolean) - Method in class ome.security.basic.BasicSecuritySystem

getEventContext() - Method in class ome.security.basic.BasicSecuritySystem

getEventContext() - Method in interface ome.security.SecuritySystem

Calls SecuritySystem.getEventContext(boolean) with a false as "refresh".

getEventContext(boolean) - Method in interface ome.security.SecuritySystem

If refresh is false, returns the current EventContext stored in the session.

getEventContext() - Method in class ome.security.SecuritySystemHolder

getEventContext(boolean) - Method in class ome.security.SecuritySystemHolder

getEventContext() - Method in class ome.security.sharing.SharingSecuritySystem

getEventContext(boolean) - Method in class ome.security.sharing.SharingSecuritySystem

getEventContext() - Method in class ome.services.blitz.impl.ServiceFactoryI

getEventContext(Principal) - Method in interface ome.services.sessions.SessionManager

Provides a partial EventContext for the current Session.

getEventContext(Principal) - Method in class ome.services.sessions.SessionManagerImpl

getEventContext_async(AMD_IAdmin_getEventContext, Current) - Method in class ome.services.blitz.impl.AdminI

getEventLogsByPeriod_async(AMD_ITimeline_getEventLogsByPeriod, RTime, RTime, Parameters, Current) - Method in class ome.services.blitz.impl.TimelineI

getEvents(long, Experimenter, Timestamp, Timestamp) - Method in interface ome.api.IShare

Gets events for share per experimenter for period of time.

getEvents(long, Experimenter, Timestamp, Timestamp) - Method in class ome.services.sharing.ShareBean

getEvents_async(AMD_IShare_getEvents, long, Experimenter, RTime, RTime, Current) - Method in class ome.services.blitz.impl.ShareI

getEventType() - Method in class ome.system.Principal

getException() - Method in exception ome.util.messages.MessageException

Get the exception which this instance wraps.

getExceptionThrown() - Method in class ome.system.UpgradeCheck

getExcitationFilters() - Method in class pojos.FilterSetData

Returns the collections of excitation filters if any.

getExcitationFilters() - Method in class pojos.LightPathData

Returns the collections of excitation filters if any.

getExcitationWavelength() - Method in class pojos.ChannelData

Returns the excitation wavelength of the channel.

getExclude(int) - Method in class ome.services.graphs.AnnotationGraphSpec

Returns the value from "...

getExecutor() - Method in class ome.services.blitz.impl.ServiceFactoryI

getExecutor() - Method in class ome.services.scheduler.ThreadPool

getExperimenter(long) - Method in interface ome.api.IAdmin

fetch an Experimenter and all related groups.

getExperimenter(long) - Method in class ome.logic.AdminImpl

getExperimenter() - Method in class omero.sys.ParametersI

Returns the value of the experimenter parameter.

getExperimenter_async(AMD_IAdmin_getExperimenter, long, Current) - Method in class ome.services.blitz.impl.AdminI

getExperimenterID() - Method in class ome.formats.importer.ImportLibrary

getExperimenterID() - Method in class ome.formats.OMEROMetadataStoreClient

getExperimenters() - Method in class pojos.GroupData

Returns the experimenters contained in this group.

getExtendedMetadata() - Method in class ome.logic.AbstractLevel2Service

getExternalDescription() - Method in class pojos.WellData

Returns the external description of the well.

getExternalIdentifier() - Method in class pojos.PlateData

Returns the external identifier of the plate.

getExternalInfo(Current) - Method in class omero.model.DetailsI

getExtra() - Method in class ome.formats.importer.util.ErrorContainer

getFailureClass() - Method in exception ome.formats.enums.EnumerationException

getFailureClass() - Method in exception ome.formats.model.ModelException

Returns the class that was used during a failed instantiation.

getFamily(String) - Method in class omeis.providers.re.quantum.QuantumFactory

Helper method to retrieve a Family enumeration from the database.

getFamily() - Method in class omeis.providers.re.quantum.QuantumStrategy

Returns the mapping family.

getFeedbackUrl() - Method in class ome.formats.importer.ImportConfig

getFilament(int, int) - Method in class ome.formats.OMEROMetadataStoreClient

getFile() - Method in class ome.formats.importer.ImportContainer

getFile(ServiceFactory) - Method in class ome.services.scripts.ScriptFinder

getFileBuffer(OriginalFile) - Method in class ome.io.nio.OriginalFilesService

Returns FileBuffer based on OriginalFile path

getFileFormat() - Method in class ome.formats.importer.util.ErrorContainer

get the file format for import

getFileFormat() - Method in class pojos.FileAnnotationData

Returns the format of the uploaded file.

getFileID() - Method in class pojos.FileAnnotationData

Returns the id of the file.

getFileIds() - Method in class ome.tools.RepositoryTask

This public method is used to return a list of file ids that require deletion from the disk repository.

getFileKind() - Method in class pojos.FileAnnotationData

Returns a user readable description of the file.

getFileName() - Method in class pojos.FileAnnotationData

Returns the name of the file.

getFilePath(OriginalFile, Current) - Method in class ome.services.blitz.repo.AbstractRepositoryI

getFilePath(OriginalFile, Current) - Method in class ome.services.blitz.repo.InternalRepositoryI

getFilePath(OriginalFile, Current) - Method in class ome.services.blitz.repo.LegacyRepositoryI

getFilePath(OriginalFile, Current) - Method in class ome.services.blitz.repo.ScriptRepositoryI

getFilePath(OriginalFile, Current) - Method in class ome.services.blitz.repo.TemporaryRepositoryI

getFilePath() - Method in class pojos.FileAnnotationData

Returns the absolute path to the file.

getFileRepo(OriginalFile) - Method in class ome.services.blitz.repo.AbstractRepositoryI

getFiles() - Method in class ome.formats.importer.util.ErrorContainer

getFileSize() - Method in class pojos.FileAnnotationData

Returns the size of the file.

getFilesPath(Long) - Method in class ome.io.nio.AbstractFileSystemService

Returns a numbered path relative to the root of this service, but is ignorant of FS and similar constructs.

getFileType() - Method in class ome.formats.importer.util.ErrorContainer

getFill() - Method in class pojos.ShapeSettingsData

Returns the fill color.

getFillRule() - Method in class pojos.ShapeSettingsData

Returns the fill rule.

getFilteredCompanionFiles() - Method in class ome.formats.OMEROMetadataStoreClient

Returns the current set of filtered companion files that the Bio-Formats image reader contains.

getFilteredSeriesCompanionFiles() - Method in class ome.formats.OMEROMetadataStoreClient

Returns the current set of filtered companion files that the Bio-Formats image reader contains for the current series.

getFilters() - Method in class pojos.InstrumentData

Returns the collection of filters.

getFilterSet() - Method in class ome.formats.model.ChannelData

Returns the filter set for the logical channel of this channel data.

getFilterSet(int, int) - Method in class ome.formats.OMEROMetadataStoreClient

getFilterSet() - Method in class pojos.ChannelAcquisitionData

Returns the filter set or null.

getFilterSet() - Method in class pojos.OTFData

Returns the associated filter set.

getFilterSetEmissionFilter() - Method in class ome.formats.model.ChannelData

Returns the filter set's emission filter for the logical channel of this channel data.

getFilterSetExcitationFilter() - Method in class ome.formats.model.ChannelData

Returns the filter set's excitation filter for the logical channel of this channel data.

getFilterSets() - Method in class pojos.InstrumentData

Returns the collection of filter sets.

getFilterWheel() - Method in class pojos.FilterData

Returns the wheel.

getFirst(String) - Method in class ome.security.auth.AttributeSet

getFirstName() - Method in class pojos.ExperimenterData

Returns the first name of the experimenter.

getFluor() - Method in class pojos.ChannelData

Returns the Fluorophore used.

getFlushCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

getFont() - Method in class pojos.ShapeSettingsData

Get the style of the font for Shape.

getFontFamily() - Method in class pojos.ShapeSettingsData

Returns the stroke.

getFontSize() - Method in class pojos.ShapeSettingsData

Returns the stroke.

getFontStyle() - Method in class pojos.ShapeSettingsData

Returns the font style.

getForceFileArchiveOn() - Method in class ome.formats.importer.ImportConfig

getForceFileArchiveOn() - Method in class ome.formats.importer.util.IniFileLoader

getFormat() - Method in class pojos.ImageData

Returns the format of the image.

getForumUrl() - Method in class ome.formats.importer.ImportConfig

getForumUrl() - Method in class ome.formats.importer.util.IniFileLoader

getFreeSpaceInKilobytes() - Method in interface ome.api.IRepositoryInfo

This method returns the free or available space on this file system including nested subdirectories.

getFreeSpaceInKilobytes() - Method in class ome.logic.RepositoryInfoImpl

getFreeSpaceInKilobytes_async(AMD_IRepositoryInfo_getFreeSpaceInKilobytes, Current) - Method in class ome.services.blitz.impl.RepositoryInfoI

getGain() - Method in class pojos.DetectorData

Returns the gain of the detector.

getGlobalMax() - Method in class omeis.providers.re.quantum.QuantumStrategy

Returns the maximum of all maxima.

getGlobalMax() - Method in class pojos.ChannelData

Returns the global maximum of the channel i.e. the maximum of all maxima.

getGlobalMin() - Method in class omeis.providers.re.quantum.QuantumStrategy

Returns the minimum of all minima.

getGlobalMin() - Method in class pojos.ChannelData

Returns the global minimum of the channel i.e. the minimum of all minima.

getGreen() - Method in class pojos.WellData

Returns the green component of the color associated to the well, or -1.

getGreenBand() - Method in class omeis.providers.re.RGBBuffer

Returns the data buffer for the green band.

getGreenValue(int) - Method in class omeis.providers.re.RGBAIntBuffer

Retrieves the Green value for a particular pixel index.

getGreenValue(int) - Method in class omeis.providers.re.RGBBuffer

Retrieves the Green value for a particular pixel index.

getGreenValue(int) - Method in class omeis.providers.re.RGBIntBuffer

Retrieves the Green value for a particular pixel index.

getGridQuery() - Method in interface ome.services.blitz.fire.Registry

Returns an active QueryPrx or null if none is available.

getGridQuery() - Method in class ome.services.blitz.fire.Registry.Impl

getGroup(long) - Method in interface ome.api.IAdmin

fetch an ExperimenterGroup and all contained users.

getGroup(long) - Method in class ome.logic.AdminImpl

getGroup() - Method in class ome.security.basic.CurrentDetails

getGroup(Current) - Method in class ome.services.blitz.fire.SessionManagerI

getGroup() - Method in class ome.system.Login

simple getter for the group name passed into the constructor

getGroup() - Method in class ome.system.Principal

getGroup(Current) - Method in class omero.model.DetailsI

getGroup() - Method in class omero.sys.ParametersI

Returns the value of the group parameter.

getGroup_async(AMD_IAdmin_getGroup, long, Current) - Method in class ome.services.blitz.impl.AdminI

getGroupAttribute(String) - Method in class ome.security.auth.LdapConfig

getGroupFilter() - Method in class ome.security.auth.LdapConfig

getGroups() - Method in class pojos.ExperimenterData

Returns the groups the experimenter is a member of.

getGuestGroupName() - Method in class ome.system.Roles

getHandler(Class<? extends IObject>) - Method in class ome.formats.enums.handler.EnumHandlerFactory

Returns an enumeration handler for a specific enumeration type.

getHandler(Class<? extends IObject>) - Method in class ome.formats.model.handler.ModelObjectHandlerFactory

Returns an enumeration handler for a specific enumeration type.

getHeight() - Method in class omeis.providers.re.data.RegionDef

Returns the height of the region.

getHeight() - Method in class pojos.MaskData

Returns the height of the mask.

getHeight() - Method in class pojos.RectangleData

Returns the height untransformed rectangle.

getHibernateClass(String) - Method in class ome.services.graphs.BaseGraphSpec

getHibernateClass(String) - Method in interface ome.services.graphs.GraphSpec

Return the Hibernate type (ome.model.*) for the given table.

getHibernateClass(String) - Method in interface ome.tools.hibernate.ExtendedMetadata

Given the name of a database table or alternatively the simple class name (non-fully qualified) of an IObject, this method returns the class which Hibernate will map that table to.

getHibernateClass(String) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl

getHomeUrl() - Method in class ome.formats.importer.ImportConfig

getHomeUrl() - Method in class ome.formats.importer.util.IniFileLoader

getHost() - Method in class ome.system.Server

simple getter for the server host passed into the constructor

getHttpClient() - Method in class ome.formats.importer.util.HtmlMessenger

getHumidity() - Method in class pojos.ImageAcquisitionData

Returns the humidity level, this is a value in the interval [0, 1]

getHypercube(List<Integer>, List<Integer>, List<Integer>) - Method in interface ome.api.RawPixelsStore

getHypercube(List<Integer>, List<Integer>, List<Integer>) - Method in class ome.io.bioformats.BfPixelBuffer

getHypercube(List<Integer>, List<Integer>, List<Integer>, byte[]) - Method in class ome.io.bioformats.BfPixelsWrapper

getHypercube(List<Integer>, List<Integer>, List<Integer>) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getHypercube(List<Integer>, List<Integer>, List<Integer>) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getHypercube(List<Integer>, List<Integer>, List<Integer>) - Method in interface ome.io.nio.PixelBuffer

Retrieves a hypercube from this pixel buffer.

getHypercube(List<Integer>, List<Integer>, List<Integer>) - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getHypercube(List<Integer>, List<Integer>, List<Integer>) - Method in class ome.services.RawPixelsBean

getHypercube_async(AMD_RawPixelsStore_getHypercube, List<Integer>, List<Integer>, List<Integer>, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI

getHypercube_async(AMD_RawPixelsStore_getHypercube, List<Integer>, List<Integer>, List<Integer>, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI

getHypercubeDirect(List<Integer>, List<Integer>, List<Integer>, byte[]) - Method in class ome.io.bioformats.BfPixelBuffer

getHypercubeDirect(List<Integer>, List<Integer>, List<Integer>, byte[]) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getHypercubeDirect(List<Integer>, List<Integer>, List<Integer>, byte[]) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getHypercubeDirect(List<Integer>, List<Integer>, List<Integer>, byte[]) - Method in interface ome.io.nio.PixelBuffer

Retrieves a hypercube from the given pixels directly.

getHypercubeDirect(List<Integer>, List<Integer>, List<Integer>, byte[]) - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getHypercubeSize(List<Integer>, List<Integer>, List<Integer>) - Method in class ome.io.bioformats.BfPixelBuffer

getHypercubeSize(List<Integer>, List<Integer>, List<Integer>) - Method in class ome.io.bioformats.BfPixelsWrapper

getHypercubeSize(List<Integer>, List<Integer>, List<Integer>) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getHypercubeSize(List<Integer>, List<Integer>, List<Integer>) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getHypercubeSize(List<Integer>, List<Integer>, List<Integer>) - Method in interface ome.io.nio.PixelBuffer

Retrieves a the size of a hypercube from this pixel buffer.

getHypercubeSize(List<Integer>, List<Integer>, List<Integer>) - Method in class ome.io.nio.RomioPixelBuffer

getIContainer() - Method in class ome.services.blitz.gateway.services.GatewayFactory

Return the IContainer service.

getId() - Method in class ome.io.bioformats.BfPixelBuffer

getId() - Method in class ome.io.bioformats.BfPixelsWrapper

getId() - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getId() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getId() - Method in interface ome.io.nio.PixelBuffer

Delegates to Pixels.getId().

getId() - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getId() - Method in class ome.services.graphs.GraphEntry

getId() - Method in class pojos.DataObject

Returns the database id of the IObject or -1 if null

getIdByOrder(int) - Method in class ome.services.export.ExporterIndex

Returns the id of an object based on the order in which it was added.

getIdentity(String) - Method in class ome.services.blitz.impl.ServiceFactoryI

Constructs an Identity from the name of this ServiceFactoryI and from the given String which for stateless services are defined by the instance fields #adminKey, #configKey, etc. and for stateful services are UUIDs.

getIds() - Method in class ome.services.sessions.state.SessionCache

Since all methods which use SessionCache.getIds() will subsequently check for the existing session, we do not block here.

getIllumination() - Method in class pojos.ChannelAcquisitionData

Returns the illumination.

getIllumination() - Method in class pojos.ChannelData

Returns the illumination.

getIlluminationAsEnum() - Method in class pojos.ChannelData

Returns the illumination enumeration value.

getImage(long, Current) - Method in class ome.services.blitz.gateway.OmeroGateway

getImage(long) - Method in interface ome.services.blitz.gateway.services.ImageService

Get the image information for an image.

getImage(long) - Method in class ome.services.blitz.gateway.services.impl.ImageServiceImpl

getImage(int) - Method in class ome.services.blitz.impl.OmeroMetadata

getImage() - Method in class pojos.PixelsData

Returns the image linked to this pixels' set.

getImage() - Method in class pojos.ROIData

Returns the image for the ROI.

getImage() - Method in class pojos.WellSampleData

Returns the image related to that sample if any.

getImageAcquiredDate(int) - Method in class ome.services.blitz.impl.OmeroMetadata

getImageAndCount(Image[], long, UnloadedCollector) - Method in class ome.services.delete.DeleteBean

Uses the locally defined query to load an Image and calls DeleteBean.collect(UnloadedCollector, Image) in order to define a list of what will be deleted.

getImageAnnotationRef(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata

getImageAnnotationRefCount(int) - Method in class ome.services.blitz.impl.OmeroMetadata

getImageByName(String, Current) - Method in class ome.services.blitz.gateway.OmeroGateway

getImageByName(String) - Method in interface ome.services.blitz.gateway.services.DataService

Get the list of images with name containing imageName.

getImageByName(String) - Method in class ome.services.blitz.gateway.services.impl.DataServiceImpl

getImageCount() - Method in class ome.services.blitz.impl.OmeroMetadata

getImageDescription(int) - Method in class ome.services.blitz.impl.OmeroMetadata

getImageFromDatasetByName(long, String, Current) - Method in class ome.services.blitz.gateway.OmeroGateway

getImageFromDatasetByName(Long, String) - Method in interface ome.services.blitz.gateway.services.DataService

Get the images from the dataset with name, this can use wild cards.

getImageFromDatasetByName(Long, String) - Method in class ome.services.blitz.gateway.services.impl.DataServiceImpl

getImageID(int) - Method in class ome.services.blitz.impl.OmeroMetadata

getImageName(int) - Method in class ome.services.blitz.impl.OmeroMetadata

getImageNames() - Method in class ome.formats.ImageNameMetadataStore

Retrieves the current map of Image names held.

getImageObjectiveSettings(int) - Method in class ome.formats.OMEROMetadataStoreClient

getImageReader() - Method in class ome.formats.importer.OMEROWrapper

Return the base image reader

getImages(Class<T>, Set<Long>, Parameters) - Method in interface ome.api.IContainer

Retrieve a user's (or all users') images within any given container.

getImages(Class, Set, Parameters) - Method in class ome.logic.PojosImpl

Implemented as specified by the IContainer I/F

getImages(ContainerClass, List<Long>, Current) - Method in class ome.services.blitz.gateway.OmeroGateway

getImages(ContainerClass, List<Long>) - Method in interface ome.services.blitz.gateway.services.DataService

Retrieves the images contained in containers specified by the node type.

getImages(ContainerClass, List<Long>) - Method in class ome.services.blitz.gateway.services.impl.DataServiceImpl

getImages() - Method in class pojos.DatasetData

Returns a set of images contained in the dataset.

getImages_async(AMD_IContainer_getImages, String, List<Long>, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI

getImagesByOptions(Parameters) - Method in interface ome.api.IContainer

Retrieve images by options.

getImagesByOptions(Parameters) - Method in class ome.logic.PojosImpl

Implemented as specified by the IContainer I/F

getImagesByOptions_async(AMD_IContainer_getImagesByOptions, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI

getImageService() - Method in class ome.services.blitz.gateway.services.GatewayFactory

getImagesForDataset(long) - Method in interface ome.api.IAnalysis

getImagesFromDataset(Dataset) - Static method in class omerojava.util.GatewayUtils

Get the images from the Dataset, the Dataset must be loaded in the project beforehand.

getImagesFromProject(Project) - Static method in class omerojava.util.GatewayUtils

Get the images from the Project, the images must be loaded in the project beforehand.

getImageSize(PlaneDef) - Method in class omeis.providers.re.Renderer

Returns the size, in bytes, of the RGBBuffer that would be rendered from the plane selected by pd.

getImagingEnvironment(int) - Method in class ome.formats.OMEROMetadataStoreClient

getImagingEnvironmentId() - Method in class pojos.ImageAcquisitionData

Returns the id of the StageLabel or -1 if not already linked to the image.

getImmersion() - Method in class pojos.ObjectiveData

Returns the immersion value of the objective.

getImmutableFields() - Method in class ome.tools.hibernate.ExtendedMetadata.Immutables

getImmutableFields(Class<? extends IObject>) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl

getImplicitContext() - Method in class omero.client

Returns the ImplicitContext which defines what properties will be sent on every method invocation.

getImportTypes() - Method in class ome.logic.TypesImpl

getIndex() - Method in class ome.formats.importer.util.ErrorContainer

get the index for this error container

getIndex() - Method in class ome.services.fulltext.SimpleLuceneOptions

getIndex() - Method in class pojos.ChannelData

Returns the channel's index.

getIndex() - Method in class pojos.ImageData

Returns the index of the image within the multi-images file.

getIniVersionNumber() - Method in class ome.formats.importer.ImportConfig

getInput(String, String) - Method in interface ome.api.ISession

Retrieves an entry from the given session's input environment.

getInput(String, String) - Method in class ome.services.sessions.SessionBean

getInput(String, String) - Method in interface ome.services.sessions.SessionManager

Returns the input environment Object stored under the given key or null if none present.

getInput(String, String) - Method in class ome.services.sessions.SessionManagerImpl

getInput(String) - Method in class omero.client

Retrieves an item from the "input" shared (session) memory.

getInput_async(AMD_ISession_getInput, String, String, Current) - Method in class ome.services.blitz.impl.SessionI

getInputEnd() - Method in class omeis.providers.re.metadata.StatsFactory

Returns the input end.

getInputKeys(String) - Method in interface ome.api.ISession

Retrieves all keys in the sesson's input environment.

getInputKeys(String) - Method in class ome.services.sessions.SessionBean

getInputKeys() - Method in class omero.client

Returns a list of keys for all items in the "input" shared (session) memory

getInputKeys_async(AMD_ISession_getInputKeys, String, Current) - Method in class ome.services.blitz.impl.SessionI

getInputs(String) - Method in interface ome.api.ISession

Retrieves all inputs from the given session's input environment.

getInputs(String) - Method in class ome.services.sessions.SessionBean

getInputs_async(AMD_ISession_getInputs, String, Current) - Method in class ome.services.blitz.impl.SessionI

getInputStart() - Method in class omeis.providers.re.metadata.StatsFactory

Returns the input start.

getInserted() - Method in class pojos.ImageData

Returns the insertion time of the image.

getInstance(Class<T>) - Method in class ome.formats.model.BlitzInstanceProvider

getInstance(Class<T>) - Method in interface ome.formats.model.InstanceProvider

Retrieves an instance.

getInstance(String) - Static method in class ome.system.OmeroContext

create (if necessary) and return the single default OmeroContext named by the beanFactoryName parameter.

getInstanceProvider() - Method in class ome.formats.importer.ImportLibrary

getInstanceProvider() - Method in class ome.formats.OMEROMetadataStoreClient

Retrieves the active enumeration provider.

getInstitution() - Method in class pojos.ExperimenterData

Returns the institution where the experimenter works.

getInstrumentId() - Method in class pojos.ImageData

Returns the id of the instrument if any.

getInternalServiceFactory(String, String, int, int, String) - Method in interface ome.services.blitz.fire.Registry

Try to return a ServiceFactory from the grid.

getInternalServiceFactory(String, String, int, int, String) - Method in class ome.services.blitz.fire.Registry.Impl

getInternalValue(String) - Method in interface ome.api.local.LocalConfig

Provides a configuration value, ignoring the visibility of the given value.

getInternalValue(String) - Method in class ome.logic.ConfigImpl

getIntervalEnd() - Method in class omeis.providers.re.codomain.CodomainChain

Returns the upper bound of the codomain interval.

getIntervalStart() - Method in class omeis.providers.re.codomain.CodomainChain

Returns the lower bound of the codomain interval.

getIObjectContainer(Class<? extends IObject>, LinkedHashMap<Index, Integer>) - Method in interface ome.formats.model.IObjectContainerStore

Retrieves an IObject container for a given class and location within the OME-XML data model.

getIObjectContainer(Class<? extends IObject>, LinkedHashMap<Index, Integer>) - Method in class ome.formats.OMEROMetadataStoreClient

getIObjectContainers(Class<? extends IObject>) - Method in interface ome.formats.model.IObjectContainerStore

Retrieves all IObject containers of a given class.

getIObjectContainers(Class<? extends IObject>) - Method in class ome.formats.OMEROMetadataStoreClient

getIPixels() - Method in class ome.services.blitz.gateway.services.GatewayFactory

Get the iPixels Service.

getIQuery() - Method in class ome.formats.OMEROMetadataStoreClient

getIQuery() - Method in class ome.services.blitz.gateway.services.GatewayFactory

Get the IQuery Service.

getIScript() - Method in class ome.services.blitz.gateway.services.GatewayFactory

Return the IScript service.

getIsSPW() - Method in class ome.formats.importer.ImportContainer

getIterator() - Method in class pojos.ROIData

Returns the iterator of the collection of the map.

getITypes() - Method in class ome.services.blitz.gateway.services.GatewayFactory

Get the types service.

getIUpdate() - Method in class ome.services.blitz.gateway.services.GatewayFactory

Get the iUpdate Service.

getJavaClasspath() - Method in class ome.formats.importer.util.ErrorContainer

getJavaVersion() - Method in class ome.formats.importer.util.ErrorContainer

getJob() - Method in interface ome.api.JobHandle

getJob(Current) - Method in class ome.services.blitz.impl.ScriptProcessI

getJob() - Method in class ome.services.JobBean

getJob(Current) - Method in class omero.grid.InteractiveProcessorI

getJob_async(AMD_JobHandle_getJob, Current) - Method in class ome.services.blitz.impl.JobHandleI

getKeepAlive() - Method in class ome.formats.OMEROMetadataStoreClient

Returns clientKeepAlive created in store

getKeywords() - Method in class pojos.WorkflowData

Returns the keywords of this workflow.

getKeywordsAsList() - Method in class pojos.WorkflowData

Returns the keywords of this workflow as a list.

getKind() - Method in class pojos.LightSourceData

Returns the kind of light source.

getLabel() - Method in class pojos.PlateAcquisitionData

Returns the label associated to the plate acquisition.

getLabelName() - Method in class pojos.ImageAcquisitionData

Returns the name of the stage label.

getLaser(int, int) - Method in class ome.formats.OMEROMetadataStoreClient

getLaserFrequencyMultiplication() - Method in class pojos.LightSourceData

Returns the frequency multiplication of the laser.

getLaserMedium() - Method in class pojos.LightSourceData

Returns the laser's medium.

getLaserPockelCell() - Method in class pojos.LightSourceData

Returns the pockel cell flag of the laser.

getLaserPulse() - Method in class pojos.LightSourceData

Returns the pulse of the laser.

getLaserPump() - Method in class pojos.LightSourceData

Returns the pump.

getLaserRepetitionRate() - Method in class pojos.LightSourceData

Returns the repetition rate (Hz) if the laser is repetitive.

getLaserTuneable() - Method in class pojos.LightSourceData

Returns the value of the tuneable field or null if no value set.

getLaserWavelength() - Method in class pojos.LightSourceData

Returns the laser's wavelength.

getLast() - Method in class ome.security.basic.CurrentDetails

getLast() - Method in interface ome.security.basic.PrincipalHolder

Get the last, i.e. currently active, principal.

getLastModified() - Method in class pojos.AnnotationData

Returns the time when the annotation was last modified.

getLastName() - Method in class pojos.ExperimenterData

Returns the last name of the experimenter.

getLastUpdated() - Method in class ome.services.sessions.state.SessionCache

getLdapService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI

getLdapService() - Method in class ome.system.ServiceFactory

getLeaderOfGroupIds(Experimenter) - Method in interface ome.api.IAdmin

Finds the ids for all groups for which the given Experimenter is owner/leader.

getLeaderOfGroupIds(Experimenter) - Method in class ome.logic.AdminImpl

getLeaderOfGroupIds_async(AMD_IAdmin_getLeaderOfGroupIds, Experimenter, Current) - Method in class ome.services.blitz.impl.AdminI

getLeaderOfGroupsList() - Method in class ome.services.sessions.SessionContextImpl

getLeaderOfGroupsList() - Method in interface ome.system.EventContext

getLeaderOfGroupsList() - Method in class ome.system.SimpleEventContext

getLeaders() - Method in class pojos.GroupData

Returns the experimenters contained in this group.

getLeaves() - Method in class omero.sys.ParametersI

getLensNA() - Method in class pojos.ObjectiveData

Returns the objective's LensNA.

getLightEmittingDiode(int, int) - Method in class ome.formats.OMEROMetadataStoreClient

getLightPath() - Method in class pojos.ChannelAcquisitionData

Returns the light path or null.

getLightPathEmissionFilters() - Method in class ome.formats.model.ChannelData

Returns the collection of emission filters in the light path.

getLightPathExcitationFilters() - Method in class ome.formats.model.ChannelData

Returns the collection of excitation filters in the light path.

getLightSource() - Method in class ome.formats.model.ChannelData

Returns the light source for the light source settings of this channel data.

getLightSource() - Method in class pojos.ChannelAcquisitionData

Returns the source of light.

getLightSourceModel() - Method in class pojos.LightSourceData

Returns the model of the light source.

getLightSources() - Method in class pojos.InstrumentData

Returns the collection of light sources.

getLightSourceSettings() - Method in class ome.formats.model.ChannelData

Returns the light source settings for the logical channel of this channel data.

getLigthSettingsAttenuation() - Method in class pojos.ChannelAcquisitionData

Returns the attenuation of the light source, percent value between 0 and 1.

getLigthSettingsWavelength() - Method in class pojos.ChannelAcquisitionData

Returns the wavelength of the light source.

getLimit() - Method in class omero.sys.ParametersI

Returns the value of the limit parameter.

getLine(int, int) - Method in class ome.formats.OMEROMetadataStoreClient

getLine() - Method in class ome.services.blitz.repo.FileMaker

getLineCap() - Method in class pojos.ShapeSettingsData

Returns the shape of the end of the line..

getListAnnotation(int) - Method in class ome.formats.OMEROMetadataStoreClient

getLocationStats() - Method in class omeis.providers.re.metadata.StatsFactory

Returns the statistics.

getLockCandidates(IObject) - Method in interface ome.tools.hibernate.ExtendedMetadata

walks the IObject argument non-recursively and gathers all IObject instances which will be linkd to by the creation or updating of the argument.

getLockCandidates(IObject) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl

walks the IObject argument non-recursively and gathers all IObject instances which will be linkd to by the creation or updating of the argument.

getLockCandidates(IObject) - Method in class ome.tools.hibernate.ExtendedMetadata.Locks

getLockChecks(Class<? extends IObject>) - Method in interface ome.tools.hibernate.ExtendedMetadata

returns all class/field name pairs which may possibly link to an object of type klass.

getLockChecks(Class<? extends IObject>) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl

returns all class/field name pairs which may possibly link to an object of type klass.

getLockingIds(IObject) - Method in interface ome.api.local.LocalAdmin

Returns a map from Class (as string) to a count for all entities which point to the given IObject.

getLockingIds(IObject) - Method in class ome.logic.AdminImpl

getLockingIds(IObject, Long) - Method in class ome.logic.AdminImpl

getLogFile() - Method in class ome.formats.importer.ImportConfig

getLogFile() - Method in class ome.formats.importer.util.IniFileLoader

getLogger() - Method in class ome.services.util.BeanHelper

getLogicalChannel() - Method in class ome.formats.model.ChannelData

Returns the logical channel for this channel data.

getLogs() - Method in class ome.security.basic.BasicSecuritySystem

getLogs() - Method in class ome.security.basic.CurrentDetails

getLogString(SelfConfigurableService) - Method in class ome.services.util.BeanHelper

getLongAnnotation(int) - Method in class ome.formats.OMEROMetadataStoreClient

getLongAnnotationCount() - Method in class ome.services.blitz.impl.OmeroMetadata

getLongAnnotationDescription(int) - Method in class ome.services.blitz.impl.OmeroMetadata

getLongAnnotationID(int) - Method in class ome.services.blitz.impl.OmeroMetadata

getLongAnnotationNamespace(int) - Method in class ome.services.blitz.impl.OmeroMetadata

getLongAnnotationValue(int) - Method in class ome.services.blitz.impl.OmeroMetadata

getLotNumber() - Method in class pojos.DetectorData

Returns the lot number of the detector.

getLotNumber() - Method in class pojos.DichroicData

Returns the lot number.

getLotNumber() - Method in class pojos.FilterData

Returns the lot number.

getLotNumber() - Method in class pojos.FilterSetData

Returns the lot number.

getLotNumber() - Method in class pojos.LightSourceData

Returns the lot of number the light source.

getLotNumber() - Method in class pojos.ObjectiveData

Returns the lot number of the detector.

getLowerLimit() - Method in class omeis.providers.re.codomain.PlaneSlicingContext

Returns the constant level for bit-planes < planeSelected w.r.t the higher-order bits.

getManagedServerContext() - Static method in class ome.system.OmeroContext

create (if necessary) and return the single default managed OmeroContext.

getManagerList(boolean) - Method in class ome.services.blitz.fire.Ring

getManagerList(boolean) - Method in interface ome.services.blitz.redirect.Redirector.Context

Return all known managers in the current cluster context, possibly filtering out the inactive ones.

getManufacturer() - Method in class pojos.DetectorData

Returns the manufacturer of the detector.

getManufacturer() - Method in class pojos.DichroicData

Returns the manufacturer.

getManufacturer() - Method in class pojos.FilterData

Returns the manufacturer.

getManufacturer() - Method in class pojos.FilterSetData

Returns the manufacturer.

getManufacturer() - Method in class pojos.LightSourceData

Returns the manufacturer of the light source.

getManufacturer() - Method in class pojos.ObjectiveData

Returns the manufacturer of the detector.

getMarkerEnd() - Method in class pojos.ShapeSettingsData

Returns the marker end.

getMarkerStart() - Method in class pojos.ShapeSettingsData

Returns the marker start.

getMask(int, int) - Method in class ome.formats.OMEROMetadataStoreClient

getMask() - Method in class pojos.MaskData

Returns the mask as a byte array.

getMaskAsBinaryArray() - Method in class pojos.MaskData

Returns the mask image.

getMaskAsBufferedImage() - Method in class pojos.MaskData

Returns the mask image.

getMaskPoints() - Method in class pojos.PolygonData

Returns the points in the polygon.

getMaskPoints() - Method in class pojos.PolylineData

Returns the points in the Polyline.

getMatcher(String) - Method in class ome.services.graphs.GraphEntry

getMaximumFieldCount() - Method in class pojos.PlateAcquisitionData

Returns the maximum number of fields in any well.

getMaxPlaneHeight() - Method in class ome.io.nio.ConfiguredTileSizes

getMaxPlaneHeight() - Method in interface ome.io.nio.TileSizes

getMaxPlaneWidth() - Method in class ome.io.nio.ConfiguredTileSizes

getMaxPlaneWidth() - Method in interface ome.io.nio.TileSizes

getMeasuredRois_async(AMD_IRoi_getMeasuredRois, long, long, RoiOptions, Current) - Method in class ome.services.blitz.impl.RoiI

getMeasuredRoisMap_async(AMD_IRoi_getMeasuredRoisMap, long, List<Long>, RoiOptions, Current) - Method in class ome.services.blitz.impl.RoiI

getMedium() - Method in class pojos.ImageAcquisitionData

Returns the medium of the objective.

getMediumAsEnum() - Method in class pojos.ImageAcquisitionData

Returns the medium enumeration value.

getMemberCount(Set<Long>) - Method in interface ome.api.IShare

Returns a map from share id to the count of total members (including the owner).

getMemberCount(Set<Long>) - Method in class ome.services.sharing.ShareBean

getMemberCount_async(AMD_IShare_getMemberCount, List<Long>, Current) - Method in class ome.services.blitz.impl.ShareI

getMemberOfGroupIds(Experimenter) - Method in interface ome.api.IAdmin

Finds the ids for all groups for which the given Experimenter is a member.

getMemberOfGroupIds(Experimenter) - Method in class ome.logic.AdminImpl

getMemberOfGroupIds_async(AMD_IAdmin_getMemberOfGroupIds, Experimenter, Current) - Method in class ome.services.blitz.impl.AdminI

getMemberOfGroupsList() - Method in class ome.services.sessions.SessionContextImpl

getMemberOfGroupsList() - Method in interface ome.system.EventContext

getMemberOfGroupsList() - Method in class ome.system.SimpleEventContext

getMemberShares(boolean) - Method in interface ome.api.IShare

Gets all shares where current Experimenter is a member.

getMemberShares(boolean) - Method in class ome.services.sharing.ShareBean

getMemberShares_async(AMD_IShare_getMemberShares, boolean, Current) - Method in class ome.services.blitz.impl.ShareI

getMemberSharesFor(Experimenter, boolean) - Method in interface ome.api.IShare

Gets all shares where given Experimenter is a member.

getMemberSharesFor(Experimenter, boolean) - Method in class ome.services.sharing.ShareBean

getMemberSharesFor_async(AMD_IShare_getMemberSharesFor, Experimenter, boolean, Current) - Method in class ome.services.blitz.impl.ShareI

getMessage() - Method in exception ome.io.nio.PixelBufferException

getMessageDigest() - Method in class ome.io.bioformats.BfPixelsWrapper

getMetadata(long) - Method in class ome.services.ThumbnailCtx

Retrieves the Thumbnail object for a given Pixels ID.

getMetadata() - Method in class omeis.providers.re.Renderer

Returns the Pixels set the rendering engine is for.

getMetadataOnly() - Method in class ome.formats.importer.ImportContainer

Retrieves the metadata only flag.

getMetadataOptions() - Method in class ome.formats.importer.OMEROWrapper

getMetadataService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI

getMetadataService() - Method in class ome.system.ServiceFactory

getMethod(String) - Method in class ome.services.blitz.util.IceMethodInvoker

For testing the cached method.

getMethodCount() - Method in class ome.services.messages.stats.MethodStatsMessage

getMicrobeamManipulation(int, int) - Method in class ome.formats.OMEROMetadataStoreClient

getMicrobeamManipulationLightSourceSettings(int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

getMicroscopeLotNumber() - Method in class pojos.InstrumentData

Returns the lot number of the microscope.

getMicroscopeManufacturer() - Method in class pojos.InstrumentData

Returns the model of the microscope.

getMicroscopeModel() - Method in class pojos.InstrumentData

Returns the model of the microscope.

getMicroscopeSerialNumber() - Method in class pojos.InstrumentData

Returns the serial number of the microscope.

getMicroscopeType() - Method in class pojos.InstrumentData

Returns the type of microscope.

getMiddleName() - Method in class pojos.ExperimenterData

Returns the middle name of the experimenter.

getMode() - Method in class pojos.ChannelAcquisitionData

Returns the mode.

getMode() - Method in class pojos.ChannelData

Returns the mode.

getModeAsEnum() - Method in class pojos.ChannelData

Returns the acquisition enumeration value.

getModel() - Method in class ome.services.RenderingBean

Implemented as specified by the RenderingEngine interface.

getModel() - Method in interface omeis.providers.re.RenderingEngine

Returns the model that dictates how transformed raw data has to be mapped onto a color space.

getModel() - Method in class pojos.DetectorData

Returns the manufacturer of the detector.

getModel() - Method in class pojos.DichroicData

Returns the model.

getModel() - Method in class pojos.FilterData

Returns the model.

getModel() - Method in class pojos.FilterSetData

Returns the model.

getModel() - Method in class pojos.ObjectiveData

Returns the model of the objective.

getModel_async(AMD_RenderingEngine_getModel, Current) - Method in class ome.services.blitz.impl.RenderingEngineI

getModel_async(AMD_RenderingEngine_getModel, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI

getModelProcessors() - Method in class ome.formats.OMEROMetadataStoreClient

Retrieves the current list of model processors the metadata store is using.

getMostRecentAnnotationLinks_async(AMD_ITimeline_getMostRecentAnnotationLinks, List<String>, List<String>, List<String>, Parameters, Current) - Method in class ome.services.blitz.impl.TimelineI

getMostRecentObjects_async(AMD_ITimeline_getMostRecentObjects, List<String>, Parameters, boolean, Current) - Method in class ome.services.blitz.impl.TimelineI

getMostRecentShareCommentLinks_async(AMD_ITimeline_getMostRecentShareCommentLinks, Parameters, Current) - Method in class ome.services.blitz.impl.TimelineI

getMyOpenAgentSessions(String) - Method in interface ome.api.ISession

Like ISession.getMyOpenSessions() but returns only those sessions with the given agent string.

getMyOpenAgentSessions(String) - Method in class ome.services.sessions.SessionBean

getMyOpenAgentSessions_async(AMD_ISession_getMyOpenAgentSessions, String, Current) - Method in class ome.services.blitz.impl.SessionI

getMyOpenClientSessions() - Method in interface ome.api.ISession

Like ISession.getMyOpenSessions() but returns only those sessions started by official OMERO clients.

getMyOpenClientSessions() - Method in class ome.services.sessions.SessionBean

getMyOpenClientSessions_async(AMD_ISession_getMyOpenClientSessions, Current) - Method in class ome.services.blitz.impl.SessionI

getMyOpenSessions() - Method in interface ome.api.ISession

Returns a list of open sessions for the current user.

getMyOpenSessions() - Method in class ome.services.sessions.SessionBean

getMyOpenSessions_async(AMD_ISession_getMyOpenSessions, Current) - Method in class ome.services.blitz.impl.SessionI

getMyUserPhotos() - Method in interface ome.api.IAdmin

Retrieve the OriginalFile objectd attached to this user as specified by {@link #uploadMyUserPhoto(String, String, byte[]).

getMyUserPhotos() - Method in class ome.logic.AdminImpl

getMyUserPhotos_async(AMD_IAdmin_getMyUserPhotos, Current) - Method in class ome.services.blitz.impl.AdminI

getName() - Method in class ome.logic.HardWiredInterceptor

Can be implemented by all subclasses, so that they can configure themselves in HardWiredInterceptor.selfConfigure(OmeroContext).

getName() - Method in class ome.security.basic.BasicSecurityWiring

Lookup name.

getName() - Method in class ome.services.graphs.BaseGraphSpec

getName() - Method in class ome.services.graphs.GraphEntry

getName(Matcher) - Method in class ome.services.graphs.GraphEntry

getName() - Method in interface ome.services.graphs.GraphSpec

The name of this specification.

getName() - Method in class ome.services.roi.PopulateRoiJob

getName() - Method in class ome.services.scripts.ScriptFinder

Subclasses should override to return the name of the file under scripts/ which should be uploaded.

getName() - Method in interface ome.services.sessions.SessionCallback

getName() - Method in class ome.services.sessions.SessionCallback.SimpleCloseCallback

getName() - Method in class ome.system.Login

simple getter for the user name passed into the constructor

getName() - Method in class ome.system.Preference

getName() - Method in class ome.system.Principal

getName() - Method in class pojos.ChannelData

Returns the name of the channel.

getName() - Method in class pojos.DatasetData

Returns the name of the dataset.

getName() - Method in class pojos.FileData

Returns the name of the file.

getName() - Method in class pojos.GroupData

Returns the name of the group.

getName() - Method in class pojos.ImageData

Returns the name of the image.

getName() - Method in class pojos.PlateAcquisitionData

Returns the name of the plate acquisition.

getName() - Method in class pojos.PlateData

Returns the name of the plate.

getName() - Method in class pojos.ProjectData

Returns the name of the project.

getName() - Method in class pojos.ScreenData

Returns the name of the screen.

getNameSpace() - Method in class pojos.AnnotationData

Retrieves the nameSpace of the underlying Annotation instance.

getNameSpace() - Method in class pojos.TermAnnotationData

Returns the namespace of the term.

getNameSpace() - Method in class pojos.WorkflowData

Returns the namespace of this workflow.

getNamespaceKeywords(String) - Method in class pojos.ROIData

Returns the keywords of the namespace on the ROI.

getNamespaceKeywords() - Method in class pojos.ROIData

Returns the keywords of the ROI.

getNamespaces() - Method in class pojos.ROIData

Returns the namespace of the ROI.

getNDFilter() - Method in class pojos.ChannelData

Returns the ND filter wavelength of the channel.

getNewUserGroup() - Method in class ome.security.auth.LdapConfig

getNodeUuid(Current) - Method in class ome.services.blitz.fire.Ring

getNoiseReduction() - Method in class omeis.providers.re.quantum.QuantumStrategy

Returns true if the noise reduction algorithm is turned on, false if turned off.

getNominalMagnification() - Method in class pojos.ObjectiveData

Returns the objective's nominal magnification factor.

getNumOfDirectories() - Method in class ome.formats.importer.ImportConfig

getNumOfDirectories() - Method in class ome.formats.importer.util.IniFileLoader

getObject(String, int) - Method in class ome.services.export.ExporterStepFactory

getObject() - Method in interface ome.services.sessions.SessionCallback

getObject() - Method in class ome.services.sessions.SessionCallback.SimpleCloseCallback

getObject() - Method in class ome.services.sessions.state.CacheFactory

getObjectAdapter() - Method in class ome.services.blitz.repo.AbstractRepositoryI

getObjectAdapter() - Method in class ome.services.blitz.repo.InternalRepositoryConfig

getObjectByLSID(LSID) - Method in class ome.formats.OMEROMetadataStore

Retrieves an object from the internal object graph by LSID.

getObjective(int, int) - Method in class ome.formats.OMEROMetadataStoreClient

getObjective() - Method in class pojos.ImageAcquisitionData

Returns the objective used to capture the image.

getObjective() - Method in class pojos.OTFData

Returns the associated objective.

getObjectives() - Method in class pojos.InstrumentData

Returns the collection of objectives.

getObjectiveSettingsId() - Method in class pojos.ImageAcquisitionData

Returns the id of the Objective settings or -1 if not already linked to the image.

getObjectsRead() - Method in class ome.services.messages.stats.ObjectsReadStatsMessage

getObjectsWritten() - Method in class ome.services.messages.stats.ObjectsWrittenStatsMessage

getObjectType() - Method in class ome.security.basic.EventListenersFactoryBean

this FactoryBean produces a Map instance for use in LocalSessionFactoryBean.setEventListeners(Map)

getOffset() - Method in class omero.sys.ParametersI

Returns the value of the offset parameter.

getOffset() - Method in class pojos.DetectorData

Returns the offset of the detector.

getOp(Matcher) - Method in class ome.services.graphs.GraphEntry

getOptimisticFailureCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

getOptimizations() - Method in class omeis.providers.re.Renderer

Returns the optimizations that the renderer currently has enabled.

getOrCreateParams(long, Current) - Method in class omero.grid.ParamsHelper

Get the script params for the file.

getOrder() - Method in class ome.io.nio.ReorderedPixelData

Returns the byte order of the backing buffer.

getOriginalEnumerations() - Method in interface ome.api.ITypes

Gets all original values.

getOriginalEnumerations() - Method in class ome.logic.TypesImpl

getOriginalEnumerations_async(AMD_ITypes_getOriginalEnumerations, Current) - Method in class ome.services.blitz.impl.TypesI

getOriginalFilePath(AbstractFileSystemService, Pixels) - Method in interface ome.io.nio.FilePathResolver

Retrieves the original file path for a given set of pixels.

getOriginalFilePath(Pixels) - Method in class ome.io.nio.PixelsService

Retrieves the original file path for a given set of pixels.

getOriginalFilePath(AbstractFileSystemService, Pixels) - Method in class ome.services.OmeroFilePathResolver

getOriginalGlobalMax() - Method in class omeis.providers.re.quantum.QuantumStrategy

Returns the original maximum of all minima.

getOriginalGlobalMin() - Method in class omeis.providers.re.quantum.QuantumStrategy

Returns the original minimum of all minima.

getOriginalMimetype() - Method in class pojos.FileAnnotationData

Returns the format of the original file.

getOrphan() - Method in class omero.sys.ParametersI

getOSArch() - Method in class ome.formats.importer.util.ErrorContainer

getOSName() - Method in class ome.formats.importer.util.ErrorContainer

getOSVersion() - Method in class ome.formats.importer.util.ErrorContainer

getOTF(int, int) - Method in class ome.formats.OMEROMetadataStoreClient

getOTF() - Method in class pojos.ChannelAcquisitionData

Returns the OTF used for that channel.

getOTF() - Method in class pojos.InstrumentData

Returns the collection of OTFs.

getOutput(String, String) - Method in interface ome.api.ISession

Retrieves an entry from the session's output environment.

getOutput(String, String) - Method in class ome.services.sessions.SessionBean

getOutput(String, String) - Method in interface ome.services.sessions.SessionManager

Returns the output environment Object stored under the given key or null if none present.

getOutput(String, String) - Method in class ome.services.sessions.SessionManagerImpl

getOutput(String) - Method in class omero.client

Retrieves an item from the "output" shared (session) memory.

getOutput_async(AMD_ISession_getOutput, String, String, Current) - Method in class ome.services.blitz.impl.SessionI

getOutputKeys(String) - Method in interface ome.api.ISession

Retrieves all keys in the sesson's output environment.

getOutputKeys(String) - Method in class ome.services.sessions.SessionBean

getOutputKeys() - Method in class omero.client

Returns a list of keys for all items in the "output" shared (session) memory

getOutputKeys_async(AMD_ISession_getOutputKeys, String, Current) - Method in class ome.services.blitz.impl.SessionI

getOutputs(String) - Method in interface ome.api.ISession

Retrieves all outputs from the given session's input environment.

getOutputs(String) - Method in class ome.services.sessions.SessionBean

getOutputs_async(AMD_ISession_getOutputs, String, Current) - Method in class ome.services.blitz.impl.SessionI

getOverlays() - Method in class omeis.providers.re.Renderer

Returns the current set of overlays to be rendered.

getOwner() - Method in class ome.security.basic.CurrentDetails

getOwner(Current) - Method in class omero.model.DetailsI

getOwner() - Method in class pojos.DataObject

Returns the owner of the object.

getOwnShares(boolean) - Method in interface ome.api.IShare

Gets all owned shares for the current Experimenter

getOwnShares(boolean) - Method in class ome.services.sharing.ShareBean

getOwnShares_async(AMD_IShare_getOwnShares, boolean, Current) - Method in class ome.services.blitz.impl.ShareI

getParams_async(AMD_IScript_getParams, long, Current) - Method in class ome.services.blitz.impl.ScriptI

Get the Parameters of the script.

getParentFilePath() - Method in class pojos.ImageData

Returns the path to the file hosting the image.

getParentTransformer(Class) - Static method in class ome.services.query.Hierarchy

getPassword() - Method in class ome.system.Login

simple getter for the password passed into the constructor

getPasswordAuthentication() - Method in class ome.security.SmtpAuthenticator

getPastConnections(long) - Method in interface ome.api.IShare

Gets previous connections to share.

getPastConnections(long) - Method in class ome.services.sharing.ShareBean

getPastConnections_async(AMD_IShare_getPastConnections, long, Current) - Method in class ome.services.blitz.impl.ShareI

getPatcher() - Method in class ome.services.sharing.data.ObjHolder

getPatcher() - Method in class ome.services.sharing.data.ShareDataHolder

getPatcher() - Method in class ome.services.sharing.data.ShareItemHolder

getPath() - Method in class ome.io.bioformats.BfPixelBuffer

getPath() - Method in class ome.io.bioformats.BfPixelsWrapper

getPath() - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getPath() - Method in class ome.io.nio.AbstractBuffer

getPath() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getPath() - Method in interface ome.io.nio.PixelBuffer

Retrieves the full path to this pixel buffer on disk

getPath(Matcher) - Method in class ome.services.graphs.GraphEntry

getPath() - Method in class pojos.FileData

Returns the (relative) path of the file.

getPath() - Method in class pojos.OTFData

Returns the path.

getPathIterator(AffineTransform) - Method in class ome.util.math.geom2D.EllipseArea

Required by the Shape I/F.

getPathIterator(AffineTransform, double) - Method in class ome.util.math.geom2D.EllipseArea

Required by the Shape I/F.

getPathIterator(AffineTransform) - Method in class ome.util.math.geom2D.RectangleArea

Required by the Shape I/F.

getPathIterator(AffineTransform, double) - Method in class ome.util.math.geom2D.RectangleArea

Required by the Shape I/F.

getPaths() - Method in class ome.formats.importer.ImportCandidates

getPathToFile() - Method in class pojos.ImageData

Returns the path to the file.

getPerm1(Current) - Method in class omero.model.PermissionsI

getPermissions(Current) - Method in class omero.model.DetailsI

getPermissions() - Method in class pojos.DataObject

Returns the permission of the object.

getPinholeSize() - Method in class pojos.ChannelData

Returns the pin hole size of the channel.

getPixelBuffer(Pixels) - Method in class ome.io.nio.PixelsService

Deprecated. In the future callers should use the more descriptive PixelsService.getPixelBuffer(Pixels, boolean).

getPixelBuffer(Pixels, boolean) - Method in class ome.io.nio.PixelsService

Returns a pixel buffer for a given set of pixels.

getPixelIds() - Method in class ome.tools.RepositoryTask

This public method is used to return a list of pixel ids that require deletion from the disk repository.

getPixels() - Method in class ome.formats.importer.util.TinyImportFixture

getPixels() - Method in class ome.formats.OMEROImportFixture

Accessor for the created pixels.

getPixels(long, Current) - Method in class ome.services.blitz.gateway.OmeroGateway

getPixels(long) - Method in interface ome.services.blitz.gateway.services.ImageService

Get the pixels information for an image.

getPixels(long) - Method in class ome.services.blitz.gateway.services.impl.ImageServiceImpl

getPixels(Long) - Method in class ome.services.blitz.gateway.services.impl.RenderingServiceImpl

getPixels(Long) - Method in interface ome.services.blitz.gateway.services.RenderingService

Get the pixels of the Rendering engine.

getPixels() - Method in class ome.services.RenderingBean

Implemented as specified by the RenderingEngine interface.

getPixels(long) - Method in class ome.services.ThumbnailCtx

Retrieves the Pixels object for a given Pixels ID.

getPixels() - Method in class omeis.providers.re.Renderer

Returns the object that allows to access the pixels raw data.

getPixels() - Method in interface omeis.providers.re.RenderingEngine

Returns the Pixels set the Rendering engine is for.

getPixels() - Method in class omero.util.RPSTileLoop

After saving the binary data, the update event of the Pixels instance will be updated and therefore need to be reloaded.

getPixels_async(AMD_RenderingEngine_getPixels, Current) - Method in class ome.services.blitz.impl.RenderingEngineI

getPixels_async(AMD_RenderingEngine_getPixels, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI

getPixelsArrayAsByte() - Method in class omerojava.util.Plane1D

Return the pixels array of the mapped data.

getPixelsArrayAsByte(boolean) - Method in class omerojava.util.Plane2D

Return the pixels array of the mapped data.

getPixelsArrayAsDouble() - Method in class omerojava.util.Plane1D

Return the pixels array of the mapped data.

getPixelsArrayAsDouble(boolean) - Method in class omerojava.util.Plane2D

Return the pixels array of the mapped data.

getPixelsArrayAsInt() - Method in class omerojava.util.Plane1D

Return the pixels array of the mapped data.

getPixelsArrayAsInt(boolean) - Method in class omerojava.util.Plane2D

Return the pixels array of the mapped data.

getPixelsArrayAsLong() - Method in class omerojava.util.Plane1D

Return the pixels array of the mapped data.

getPixelsArrayAsLong(boolean) - Method in class omerojava.util.Plane2D

Return the pixels array of the mapped data.

getPixelsArrayAsShort() - Method in class omerojava.util.Plane1D

Return the pixels array of the mapped data.

getPixelsArrayAsShort(boolean) - Method in class omerojava.util.Plane2D

Return the pixels array of the mapped data.

getPixelsBinDataBigEndian(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata

getPixelsDimensionOrder(int) - Method in class ome.services.blitz.impl.OmeroMetadata

getPixelsFromDataset(Dataset) - Static method in class omerojava.util.GatewayUtils

Get the pixels from the Dataset, the pixels must be loaded in the Dataset beforehand.

getPixelsFromImage(long, Current) - Method in class ome.services.blitz.gateway.OmeroGateway

getPixelsFromImage(long) - Method in interface ome.services.blitz.gateway.services.DataService

Get the pixels associated with the image.

getPixelsFromImage(long) - Method in class ome.services.blitz.gateway.services.impl.DataServiceImpl

getPixelsFromImageList(List<Image>) - Static method in class omerojava.util.GatewayUtils

Get the pixels from the list of images, these images must have the pixels loaded beforehand.

getPixelsFromProject(Project) - Static method in class omerojava.util.GatewayUtils

Get the pixels from the Project, the pixels must be loaded in the project beforehand.

getPixelsId() - Method in interface ome.api.RawPixelsStore

Returns the current Pixels set identifier.

getPixelsID(int) - Method in class ome.services.blitz.impl.OmeroMetadata

getPixelsId() - Method in class ome.services.RawPixelsBean

getPixelsId_async(AMD_RawPixelsStore_getPixelsId, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI

getPixelsId_async(AMD_RawPixelsStore_getPixelsId, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI

getPixelsImageMap(List<Image>) - Static method in class omerojava.util.GatewayUtils

create a map of pixelsId to pixels from the images in the image list.

getPixelSizeX() - Method in class pojos.PixelsData

Returns the dimension of a pixel along the X-axis, dimension is in microns.

getPixelSizeY() - Method in class pojos.PixelsData

Returns the dimension of a pixel along the Y-axis, dimension is in microns.

getPixelSizeZ() - Method in class pojos.PixelsData

Returns the dimension of a pixel along the Z-axis, dimension is in microns.

getPixelsParams(Pixels) - Method in interface ome.io.nio.FilePathResolver

Retrieves the pixels set's stored parameters.

getPixelsParams(Pixels) - Method in class ome.services.OmeroFilePathResolver

getPixelsPath(Long) - Method in class ome.io.nio.AbstractFileSystemService

Returns a numbered path relative to the root of this service, but is ignorant of FS and similar constructs.

getPixelsPhysicalSizeX(int) - Method in class ome.services.blitz.impl.OmeroMetadata

getPixelsPhysicalSizeY(int) - Method in class ome.services.blitz.impl.OmeroMetadata

getPixelsPhysicalSizeZ(int) - Method in class ome.services.blitz.impl.OmeroMetadata

getPixelsService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI

getPixelsService() - Method in class ome.system.ServiceFactory

getPixelsSizeC(int) - Method in class ome.services.blitz.impl.OmeroMetadata

getPixelsSizeT(int) - Method in class ome.services.blitz.impl.OmeroMetadata

getPixelsSizeX(int) - Method in class ome.services.blitz.impl.OmeroMetadata

getPixelsSizeY(int) - Method in class ome.services.blitz.impl.OmeroMetadata

getPixelsSizeZ(int) - Method in class ome.services.blitz.impl.OmeroMetadata

getPixelsTimeIncrement(int) - Method in class ome.services.blitz.impl.OmeroMetadata

getPixelsType() - Method in class ome.io.bioformats.BfPixelsWrapper

cgb - created from the methods below?

getPixelsType(int) - Method in class ome.services.blitz.impl.OmeroMetadata

getPixelsType() - Method in class omeis.providers.re.Renderer

Returns the pixels type.

getPixelsType() - Method in class pojos.OTFData

Returns the pixels type.

getPixelsTypeLowerBound(int) - Method in class ome.services.RenderingBean

Implemented as specified by the RenderingEngine interface.

getPixelsTypeLowerBound(int) - Method in class omeis.providers.re.Renderer

Returns the minimum value for that channels depending on the pixels type and the original range (globalmax, globalmin)

getPixelsTypeLowerBound(int) - Method in interface omeis.providers.re.RenderingEngine

Returns the minimum value for that channels depending on the pixels type and the original range (globalmax, globalmin)

getPixelsTypeLowerBound_async(AMD_RenderingEngine_getPixelsTypeLowerBound, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI

getPixelsTypeLowerBound_async(AMD_RenderingEngine_getPixelsTypeLowerBound, int, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI

getPixelsTypeMax() - Method in class omeis.providers.re.quantum.QuantumStrategy

Returns the upper bound of the pixels range or 0 if the value couldn't be set.

getPixelsTypeMin() - Method in class omeis.providers.re.quantum.QuantumStrategy

Returns the lower bound of the pixels range or 0 if the value couldn't be set.

getPixelsTypeUpperBound(int) - Method in class ome.services.RenderingBean

Implemented as specified by the RenderingEngine interface.

getPixelsTypeUpperBound(int) - Method in class omeis.providers.re.Renderer

Returns the maximum value for that channels depending on the pixels type and the original range (globalmax, globalmin)

getPixelsTypeUpperBound(int) - Method in interface omeis.providers.re.RenderingEngine

Returns the maximum value for that channels depending on the pixels type and the original range (globalmax, globalmin)

getPixelsTypeUpperBound_async(AMD_RenderingEngine_getPixelsTypeUpperBound, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI

getPixelsTypeUpperBound_async(AMD_RenderingEngine_getPixelsTypeUpperBound, int, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI

getPixelType(String, Current) - Method in class ome.services.blitz.gateway.OmeroGateway

getPixelType(String) - Method in interface ome.services.blitz.gateway.services.DataService

Get the pixelsType with type.

getPixelType(String) - Method in class ome.services.blitz.gateway.services.impl.DataServiceImpl

getPixelType() - Method in class pojos.PixelsData

Returns the pixels type.

getPixelTypes(Current) - Method in class ome.services.blitz.gateway.OmeroGateway

getPixelTypes() - Method in interface ome.services.blitz.gateway.services.DataService

Get the PixelTypes available in the system.

getPixelTypes() - Method in class ome.services.blitz.gateway.services.impl.DataServiceImpl

getPixelValue(int, int) - Method in class omeis.providers.re.data.Plane2D

Returns the pixel intensity value of the pixel at (x1, x2).

getPixelValue(int) - Method in class omeis.providers.re.data.Plane2D

Returns the pixel intensity value of the pixel at a given offset within the backing buffer.

getPixelValueDirect(int) - Method in class ome.io.nio.ReorderedPixelData

Returns the pixel intensity value of the pixel at a given offset within the backing buffer.

getPlane(int, int, int) - Method in interface ome.api.RawPixelsStore

getPlane(Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer

getPlane(Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPixelsWrapper

getPlane(Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getPlane(Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getPlane(Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer

Retrieves a particular 2D image plane from this pixel buffer.

getPlane(Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getPlane(long, int, int, int, Current) - Method in class ome.services.blitz.gateway.OmeroGateway

Get the raw plane for the pixels pixelsId, this returns a 2d array representing the plane, it returns doubles but will not lose data.

getPlane(long, int, int, int) - Method in class ome.services.blitz.gateway.services.impl.RawPixelsStoreServiceImpl

getPlane(long, int, int, int) - Method in interface ome.services.blitz.gateway.services.RawPixelsStoreService

get bytes to the plane c, t, z

getPlane(int, int, int) - Method in class ome.services.RawPixelsBean

getPlane(int, int, int) - Method in class omerojava.util.DataSink

Extracts a 2D plane from the pixels set this object is working for.

getPlane1D(Pixels, byte[]) - Static method in class omerojava.util.GatewayUtils

Extracts a 1D plane from the pixels set this object is working for.

getPlane2D(Pixels, byte[]) - Static method in class omerojava.util.GatewayUtils

Extracts a 2D plane from the pixels set this object is working for.

getPlane_async(AMD_RawPixelsStore_getPlane, int, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI

getPlane_async(AMD_RawPixelsStore_getPlane, int, int, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI

getPlaneCount(int) - Method in class ome.services.blitz.impl.OmeroMetadata

getPlaneCount() - Method in class pojos.ROIData

Returns the number of planes occupied by the ROI.

getPlaneDeltaT(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata

getPlaneDimsAsString(PlaneDef) - Method in class omeis.providers.re.Renderer

Returns a string with the dimensions of the specified plane.

getPlaneDirect(Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPixelBuffer

getPlaneDirect(Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getPlaneDirect(Integer, Integer, Integer, byte[]) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getPlaneDirect(Integer, Integer, Integer, byte[]) - Method in interface ome.io.nio.PixelBuffer

Retrieves a particular 2D image plane from this pixel buffer.

getPlaneDirect(Integer, Integer, Integer, byte[]) - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getPlaneExposureTime(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata

getPlaneOffset(int, int, int) - Method in interface ome.api.RawPixelsStore

getPlaneOffset(Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer

getPlaneOffset(Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelsWrapper

getPlaneOffset(Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getPlaneOffset(Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getPlaneOffset(Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer

Retrieves the offset for a particular 2D image plane in this pixel buffer.

getPlaneOffset(Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getPlaneOffset(int, int, int) - Method in class ome.services.RawPixelsBean

getPlaneOffset_async(AMD_RawPixelsStore_getPlaneOffset, int, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI

getPlaneOffset_async(AMD_RawPixelsStore_getPlaneOffset, int, int, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI

getPlanePositionX(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata

getPlanePositionY(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata

getPlanePositionZ(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata

getPlanePrevious() - Method in class omeis.providers.re.codomain.PlaneSlicingContext

Returns the value corresponding to the index of the bit-plane ranged just before the one selected.

getPlaneRegion(int, int, int, int, int) - Method in interface ome.api.RawPixelsStore

getPlaneRegion(Integer, Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer

getPlaneRegion(Integer, Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPixelsWrapper

getPlaneRegion(Integer, Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getPlaneRegion(Integer, Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getPlaneRegion(Integer, Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer

Retrieves a particular region of a 2D image plane from this pixel buffer.

getPlaneRegion(Integer, Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getPlaneRegion(int, int, int, int, int) - Method in class ome.services.RawPixelsBean

getPlaneRegion_async(AMD_RawPixelsStore_getPlaneRegion, int, int, int, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI

getPlaneRegion_async(AMD_RawPixelsStore_getPlaneRegion, int, int, int, int, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI

getPlaneRegionDirect(Integer, Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPixelBuffer

getPlaneRegionDirect(Integer, Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getPlaneRegionDirect(Integer, Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getPlaneRegionDirect(Integer, Integer, Integer, Integer, Integer, byte[]) - Method in interface ome.io.nio.PixelBuffer

Retrieves a region from a given plane directly.

getPlaneRegionDirect(Integer, Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getPlaneSelected() - Method in class omeis.providers.re.codomain.PlaneSlicingContext

Returns the value corresponding to the index of the selected bit-plane.

getPlaneSize() - Method in interface ome.api.RawPixelsStore

delegates to PixelBuffer

getPlaneSize() - Method in class ome.io.bioformats.BfPixelBuffer

getPlaneSize() - Method in class ome.io.bioformats.BfPixelsWrapper

getPlaneSize() - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getPlaneSize() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getPlaneSize() - Method in interface ome.io.nio.PixelBuffer

Retrieves the in memory size of a 2D image plane in this pixel buffer.

getPlaneSize() - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getPlaneSize(long) - Method in class ome.services.blitz.gateway.services.impl.RawPixelsStoreServiceImpl

getPlaneSize(long) - Method in interface ome.services.blitz.gateway.services.RawPixelsStoreService

Get the plane size of the current image.

getPlaneSize() - Method in class ome.services.RawPixelsBean

getPlaneSize_async(AMD_RawPixelsStore_getPlaneSize, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI

getPlaneSize_async(AMD_RawPixelsStore_getPlaneSize, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI

getPlaneTheC(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata

getPlaneTheT(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata

getPlaneTheZ(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata

getPlate() - Method in class pojos.WellData

Returns the plate containing this Well.

getPlateAcquisitions() - Method in class pojos.PlateData

Returns the plate acquisitions related to this plate.

getPlates() - Method in class pojos.ScreenData

Returns the plates contained in this screen.

getPlateType() - Method in class pojos.PlateData

Returns the type of plate e.g.

getPockelCell() - Method in class pojos.ChannelData

Returns the Pockels cell settings.

getPoint(double) - Method in class ome.util.math.geom2D.Line

Returns the point of this line defined by k.

getPoint(double) - Method in class ome.util.math.geom2D.Segment

Returns the point of this line defined by k.

getPoints(long, Session) - Method in class ome.services.roi.GeomTool

getPoints() - Method in class ome.util.math.geom2D.EllipseArea

Implemented as specified by the PlaneArea I/F.

getPoints() - Method in interface ome.util.math.geom2D.PlaneArea

Returns an array of PlanePoint contained in the PlaneArea.

getPoints() - Method in class ome.util.math.geom2D.RectangleArea

Implemented as specified by the PlaneArea I/F.

getPoints() - Method in class pojos.PolygonData

Returns the points in the polygon.

getPoints() - Method in class pojos.PolylineData

Returns the points in the Polyline.

getPoints1() - Method in class pojos.PolygonData

Returns the points in the polygon.

getPoints1() - Method in class pojos.PolylineData

Returns the points in the Polyline.

getPoints2() - Method in class pojos.PolygonData

Returns the points in the polygon.

getPoints2() - Method in class pojos.PolylineData

Returns the points in the Polyline.

getPoints_async(AMD_IRoi_getPoints, long, Current) - Method in class ome.services.blitz.impl.RoiI

getPojoTypes() - Method in class ome.logic.TypesImpl

getPort() - Method in class ome.system.Server

simple getter for the port passed into the constructor or the default port if none.

getPositionX() - Method in class pojos.ImageAcquisitionData

Returns the x-coordinate in the frame microscope.

getPositionX() - Method in class pojos.WellSampleData

Returns the position X.

getPositionY() - Method in class pojos.ImageAcquisitionData

Returns the y-coordinate in the frame microscope.

getPositionY() - Method in class pojos.WellSampleData

Returns the position Y.

getPositionZ() - Method in class pojos.ImageAcquisitionData

Returns the z-coordinate in the frame microscope.

getPower() - Method in class pojos.LightSourceData

Returns the power of the light source.

getPrefix() - Method in class ome.system.ServiceFactory

used by ServiceFactory.getServiceByClass(Class) to find the correct service proxy in the ServiceFactory.ctx

getPrefix() - Method in class ome.tools.spring.InternalServiceFactory

getPrefix() - Method in class ome.tools.spring.ManagedServiceFactory

getPrepareStatementCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

getPrincipal(MethodInvocation) - Method in class ome.logic.HardWiredInterceptor

getPrincipal() - Method in class ome.services.blitz.impl.ServiceFactoryI

getPrincipal() - Method in class ome.services.util.ExecutionThread

getProcessedIds(String) - Method in class ome.services.graphs.GraphState

Get the set of ids which were actually processed.

getProject(long) - Method in class ome.formats.OMEROMetadataStoreClient

getProjectID() - Method in class ome.formats.importer.ImportContainer

getProjectionService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI

getProjectionService() - Method in class ome.system.ServiceFactory

getProjects() - Method in class ome.formats.OMEROMetadataStoreClient

getProjects(List<Long>, boolean, Current) - Method in class ome.services.blitz.gateway.OmeroGateway

getProjects(List<Long>, boolean) - Method in interface ome.services.blitz.gateway.services.DataService

Get the projects in the users.

getProjects(List<Long>, boolean) - Method in class ome.services.blitz.gateway.services.impl.DataServiceImpl

getProjects() - Method in class pojos.DatasetData

Returns a set of projects containing the dataset.

getProjectsForDataset(long) - Method in interface ome.api.IAnalysis

getProjectsForUser(long) - Method in interface ome.api.IAnalysis

getProperties() - Method in class ome.security.auth.FilePasswordProvider

getProperties() - Method in class omero.client

Returns the active properties for this instance.

getProperty(String) - Method in class ome.system.OmeroContext

getProperty(String) - Method in class ome.system.PreferenceContext

Lookup method for getting access to the merged properties for this instance.

getProperty(String) - Method in class omero.client

Returns the property value for this key or the empty string if none.

getPropertyMap() - Method in class omero.client

Returns all properties which are prefixed with "omero." or "Ice."

getPropertyMap(Properties) - Method in class omero.client

Returns all properties which are prefixed with "omero." or "Ice."

getProtocolDescription() - Method in class pojos.ScreenData

Returns the description of the protocol.

getProtocolIdentifier() - Method in class pojos.ScreenData

Returns the identifier of the protocol.

getProxiedObject(T) - Static method in class ome.services.fulltext.BridgeHelper

Simpler wrapper to handle superclass proxy objects (e.g.

getProxy() - Method in class ome.services.blitz.impl.ScriptProcessI

getProxy(Current) - Method in class ome.services.blitz.repo.AbstractRepositoryI

getProxy() - Method in class ome.services.blitz.util.RegisterServantMessage

getProxyOrNull(String, SessionControlPrx, Current) - Method in class ome.services.blitz.fire.Ring

Delegates to the Ring.redirector strategy configured for this instance.

getProxyOrNull(Redirector.Context, String, SessionControlPrx, Current) - Method in class ome.services.blitz.redirect.AbstractRedirector

Returns null early if the Current has already once been routed by a Redirector implementation, returns an existing session if it can be found, or returns a null.

getProxyOrNull(Redirector.Context, String, SessionControlPrx, Current) - Method in class ome.services.blitz.redirect.ConfigRedirector

Create or retrieve and returns a SessionPrx which the current method takes control of.

getProxyOrNull(Redirector.Context, String, SessionControlPrx, Current) - Method in class ome.services.blitz.redirect.NullRedirector

Always returns null

getProxyOrNull(Redirector.Context, String, SessionControlPrx, Current) - Method in interface ome.services.blitz.redirect.Redirector

Create or retrieve and returns a SessionPrx which the current method takes control of.

getProxyOrNull(Redirector.Context, String, SessionControlPrx, Current) - Method in class ome.services.blitz.redirect.ScaleRedirector

getQuantumDef() - Method in class ome.services.RenderingBean

Implemented as specified by the RenderingEngine interface.

getQuantumDef() - Method in interface omeis.providers.re.RenderingEngine

Returns the quantization object.

getQuantumDef_async(AMD_RenderingEngine_getQuantumDef, Current) - Method in class ome.services.blitz.impl.RenderingEngineI

getQuantumDef_async(AMD_RenderingEngine_getQuantumDef, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI

getQuantumManager() - Method in class omeis.providers.re.Renderer

Returns the object that manages and allows to retrieve the objects that are used to quantize wavelength data.

getQueries() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

Get all executed query strings

getQueryCacheHitCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

getQueryCacheMissCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

getQueryCachePutCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

getQueryExecutionCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

getQueryExecutionMaxTime() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

getQueryExecutionMaxTimeQueryString() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

getQueryFactory() - Method in class ome.logic.AbstractLevel1Service

getQueryFactory() - Method in class ome.logic.AbstractLevel2Service

getQueryService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI

getQueryService() - Method in class ome.system.ServiceFactory

getQueryStatistics(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

Query statistics from query string (HQL or SQL)

getRadiusX() - Method in class pojos.EllipseData

Returns the radius along the X-axis.

getRadiusY() - Method in class pojos.EllipseData

Returns the radius along the Y-axis.

getRating() - Method in class pojos.RatingAnnotationData

Returns the rating value.

getRawFileStoreService() - Method in class ome.services.blitz.gateway.services.GatewayFactory

Return the raw file store service.

getRawPixelsStoreService() - Method in class ome.services.blitz.gateway.services.GatewayFactory

Return the raw pixels store service.

getRawPlane(long, int, int, int) - Method in interface ome.services.blitz.gateway.services.ImageService

Get the raw plane from the server with id pixelsId, and channels, c, timepoint t, and z-section z.

getRawPlane(long, int, int, int) - Method in class ome.services.blitz.gateway.services.impl.ImageServiceImpl

getReader() - Method in class ome.formats.importer.ImportContainer

getReader() - Method in interface ome.formats.model.IObjectContainerStore

Returns the current Bio-Formats reader that has been used to populate the container store.

getReader() - Method in class ome.formats.OMEROMetadataStoreClient

getReaderNames() - Static method in class ome.services.util.DBEnumCheck

getReaderType(String) - Method in class ome.formats.importer.ImportCandidates

Retrieve reader type for file specified in path

getReagentsCounts() - Method in class pojos.WellData

Returns the number of reagents linked to the object, key: id of the user, value: number of annotation.

getReagentSetDescripion() - Method in class pojos.ScreenData

Returns the description of the reagent set.

getReagentSetIdentifier() - Method in class pojos.ScreenData

Returns the identifier of the Reagent set.

getRed() - Method in class pojos.WellData

Returns the red component of the color associated to the well, or -1.

getRedBand() - Method in class omeis.providers.re.RGBBuffer

Returns the data buffer for the red band.

getRedirect(Redirector.Context) - Method in class ome.services.blitz.redirect.AbstractRedirector

Returns the current redirect, to which all calls to #getProxyOrNull(String, Glacier2.SessionControlPrx, Ice.Current) will be pointed.

getRedValue(int) - Method in class omeis.providers.re.RGBAIntBuffer

Retrieves the Red value for a particular pixel index.

getRedValue(int) - Method in class omeis.providers.re.RGBBuffer

Retrieves the Red value for a particular pixel index.

getRedValue(int) - Method in class omeis.providers.re.RGBIntBuffer

Retrieves the Red value for a particular pixel index.

getReference() - Method in class pojos.ImageData

Returns the reference to the file to register.

getReferenceCache() - Method in interface ome.formats.model.IObjectContainerStore

Returns the current reference cache.

getReferenceCache() - Method in class ome.formats.OMEROMetadataStoreClient

getReferenceCount(String) - Method in interface ome.api.ISession

Retrieves the current reference count for the given uuid.

getReferenceCount(String) - Method in class ome.services.sessions.SessionBean

getReferenceCount(String) - Method in interface ome.services.sessions.SessionManager

Return the number of client which are presumed to be attached to this session or throw an exception if there's no such session.

getReferenceCount(String) - Method in class ome.services.sessions.SessionManagerImpl

getReferenceCount_async(AMD_ISession_getReferenceCount, String, Current) - Method in class ome.services.blitz.impl.SessionI

getReferenceStringCache() - Method in interface ome.formats.model.IObjectContainerStore

Returns the current string based reference cache.

getReferenceStringCache() - Method in class ome.formats.OMEROMetadataStoreClient

getRefPlateId() - Method in class pojos.PlateAcquisitionData

Returns the id of the plate of reference.

getRefractiveIndex() - Method in class pojos.ImageAcquisitionData

Returns the refractive index of the objective.

getRegion(int, long) - Method in interface ome.api.RawPixelsStore

getRegion(Integer, Long) - Method in class ome.io.bioformats.BfPixelBuffer

getRegion(Integer, Long, byte[]) - Method in class ome.io.bioformats.BfPixelsWrapper

getRegion(Integer, Long) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getRegion(Integer, Long) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getRegion(Integer, Long) - Method in interface ome.io.nio.PixelBuffer

Retrieves a region from this pixel buffer.

getRegion(Integer, Long) - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getRegion(int, long) - Method in class ome.services.RawPixelsBean

getRegion() - Method in class omeis.providers.re.data.PlaneDef

Returns the region to render.

getRegion_async(AMD_RawPixelsStore_getRegion, int, long, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI

getRegion_async(AMD_RawPixelsStore_getRegion, int, long, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI

getRegionDirect(Integer, Long, byte[]) - Method in class ome.io.bioformats.BfPixelBuffer

getRegionDirect(Integer, Long, byte[]) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getRegionDirect(Integer, Long, byte[]) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getRegionDirect(Integer, Long, byte[]) - Method in interface ome.io.nio.PixelBuffer

Retrieves a region from this pixel buffer directly.

getRegionDirect(Integer, Long, byte[]) - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getRegistry() - Method in class ome.services.blitz.repo.InternalRepositoryConfig

getRegistry() - Method in class ome.services.blitz.util.BlitzConfiguration

getRelationship(String, String) - Method in interface ome.tools.hibernate.ExtendedMetadata

Walks both the #locksHolder and the #lockedByHolder data for "from" argument to see if there is any direct relationship to the "to" argument.

getRelationship(String, String) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl

Walks both the ExtendedMetadata.Impl.locksHolder and the ExtendedMetadata.Impl.lockedByHolder data for "from" argument to see if there is any direct relationship to th "to" argument.

getRenderedImage(long, int, int, Current) - Method in class ome.services.blitz.gateway.OmeroGateway

getRenderedImage(long, int, int) - Method in interface ome.services.blitz.gateway.services.ImageService

Render image as Buffered image.

getRenderedImage(long, int, int) - Method in class ome.services.blitz.gateway.services.impl.ImageServiceImpl

getRenderedImage(long, int, int) - Method in class ome.services.blitz.gateway.services.impl.RenderingServiceImpl

getRenderedImage(long, int, int) - Method in interface ome.services.blitz.gateway.services.RenderingService

Render image as Buffered image.

getRenderedImageMatrix(long, int, int, Current) - Method in class ome.services.blitz.gateway.OmeroGateway

getRenderedImageMatrix(long, int, int) - Method in interface ome.services.blitz.gateway.services.ImageService

Render image as 3d matrix.

getRenderedImageMatrix(long, int, int) - Method in class ome.services.blitz.gateway.services.impl.ImageServiceImpl

getRenderedImageMatrix(long, int, int) - Method in class ome.services.blitz.gateway.services.impl.RenderingServiceImpl

getRenderedImageMatrix(long, int, int) - Method in interface ome.services.blitz.gateway.services.RenderingService

Render image as 3d matrix.

getRenderingDef() - Method in class omeis.providers.re.Renderer

Returns the settings that define the transformation context.

getRenderingDefId() - Method in interface ome.api.ThumbnailStore

Return the id of the RenderingDef loaded in this instance.

getRenderingDefId() - Method in class ome.services.RenderingBean

getRenderingDefId() - Method in class ome.services.ThumbnailBean

getRenderingDefId() - Method in interface omeis.providers.re.RenderingEngine

Returns the id of the RederingDef loaded by either RenderingEngine.lookupRenderingDef(long) or RenderingEngine.loadRenderingDef(long).

getRenderingDefId_async(AMD_RenderingEngine_getRenderingDefId, Current) - Method in class ome.services.blitz.impl.RenderingEngineI

getRenderingDefId_async(AMD_ThumbnailStore_getRenderingDefId, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI

getRenderingDefId_async(AMD_RenderingEngine_getRenderingDefId, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI

getRenderingService() - Method in class ome.services.blitz.gateway.services.GatewayFactory

Return the rendering service.

getRenderingSettings(long) - Method in interface ome.api.IRenderingSettings

Returns the default rendering settings for a given pixels for the current user.

getRenderingSettings(long) - Method in class ome.logic.RenderingSettingsImpl

Implemented as specified by the IRenderingSettings I/F

getRenderingSettings_async(AMD_IRenderingSettings_getRenderingSettings, long, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI

getRenderingSettingsService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI

getRenderingSettingsService() - Method in class ome.system.ServiceFactory

getReorderedPixelOffset(int, int, int) - Static method in class ome.io.nio.ReorderedPixelData

Returns the re-ordered pixel offset.

getRepositoryInfoService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI

getRepositoryInfoService() - Method in class ome.system.ServiceFactory

getRepositorySpace() - Method in class ome.formats.OMEROMetadataStoreClient

getRepoUuid() - Method in class ome.services.blitz.repo.AbstractRepositoryI

getResolutionLevel() - Method in interface ome.api.RawPixelsStore

getResolutionLevel() - Method in class ome.io.bioformats.BfPixelBuffer

getResolutionLevel() - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getResolutionLevel() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getResolutionLevel() - Method in interface ome.io.nio.PixelBuffer

Retrieves the active resolution level.

getResolutionLevel() - Method in class ome.io.nio.RomioPixelBuffer

getResolutionLevel() - Method in class ome.services.RawPixelsBean

getResolutionLevel() - Method in class ome.services.RenderingBean

getResolutionLevel() - Method in class omeis.providers.re.Renderer

Retrieves the active resolution level.

getResolutionLevel() - Method in interface omeis.providers.re.RenderingEngine

getResolutionLevel_async(AMD_PyramidService_getResolutionLevel, Current) - Method in class ome.services.blitz.impl.AbstractPyramidServant

getResolutionLevel_async(AMD_PyramidService_getResolutionLevel, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI

getResolutionLevel_async(AMD_PyramidService_getResolutionLevel, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI

getResolutionLevels() - Method in interface ome.api.RawPixelsStore

getResolutionLevels() - Method in class ome.io.bioformats.BfPixelBuffer

getResolutionLevels() - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getResolutionLevels() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getResolutionLevels() - Method in interface ome.io.nio.PixelBuffer

Retrieves the number of resolution levels that the backing pixels pyramid contains.

getResolutionLevels() - Method in class ome.io.nio.RomioPixelBuffer

getResolutionLevels() - Method in class ome.services.RawPixelsBean

getResolutionLevels() - Method in class ome.services.RenderingBean

getResolutionLevels() - Method in class omeis.providers.re.Renderer

Retrieves the number of resolution levels that the backing pixels pyramid contains.

getResolutionLevels() - Method in interface omeis.providers.re.RenderingEngine

getResolutionLevels_async(AMD_PyramidService_getResolutionLevels, Current) - Method in class ome.services.blitz.impl.AbstractPyramidServant

getResolutionLevels_async(AMD_PyramidService_getResolutionLevels, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI

getResolutionLevels_async(AMD_PyramidService_getResolutionLevels, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI

getResults(int, Current) - Method in class ome.services.blitz.impl.ScriptProcessI

getResults() - Method in class ome.services.delete.QueryConstraints

getResults(ProcessPrx, Current) - Method in class omero.grid.InteractiveProcessorI

getResultSet() - Method in class ome.tools.hibernate.SqlArray

getResultSet(Map<String, Class<?>>) - Method in class ome.tools.hibernate.SqlArray

getResultSet(long, int) - Method in class ome.tools.hibernate.SqlArray

getResultSet(long, int, Map<String, Class<?>>) - Method in class ome.tools.hibernate.SqlArray

getResultsString(Object, IdentityHashMap<Object, String>) - Method in class ome.services.util.ServiceHandler

public for testing purposes.

getResultTypes() - Method in class ome.logic.TypesImpl

getRevision(Class) - Static method in class ome.system.Version

Parses the given class for its RevisionNumber annotation.

getRGBA(int) - Method in class ome.services.RenderingBean

Implemented as specified by the RenderingEngine interface.

getRGBA(int) - Method in interface omeis.providers.re.RenderingEngine

Returns a 4D-array representing the color associated to the specified channel.

getRGBA_async(AMD_RenderingEngine_getRGBA, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI

getRGBA_async(AMD_RenderingEngine_getRGBA, int, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI

getRing() - Method in class ome.services.blitz.util.BlitzConfiguration

getROI() - Method in class pojos.util.ROIComponent

Returns all the ROI in the component as a list.

getROI() - Method in class pojos.util.UploadMask

Returns the ROIs created from uploading the images.

getROICoordinate() - Method in class pojos.ShapeData

Returns the ROICoordinate for the ShapeData.

getRoiIds() - Method in class ome.services.blitz.measurements.MeasurementStore

getRoiIds() - Method in interface ome.services.blitz.measurements.OmeroMeasurementStore

Returns the ids of all Roi instances created during the save method.

getRoiMeasurements_async(AMD_IRoi_getRoiMeasurements, long, RoiOptions, Current) - Method in class ome.services.blitz.impl.RoiI

getRoiService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI

getRoiStats_async(AMD_IRoi_getRoiStats, long, Current) - Method in class ome.services.blitz.impl.RoiI

getRoot() - Method in class ome.formats.OMEROMetadataStoreClient

getRoot() - Method in class ome.services.blitz.impl.OmeroMetadata

getRootId() - Method in class ome.system.Roles

getRootName() - Method in class ome.system.Roles

getRouter(Communicator) - Static method in class omero.client

Acquires the default router, and throws an exception if it is not of type {Glacier2.RouterPrx}.

getRow(int, int, int, int) - Method in interface ome.api.RawPixelsStore

getRow(Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer

getRow(Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPixelsWrapper

getRow(Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getRow(Integer, Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getRow(Integer, Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer

Retrieves a particular row or scanline from this pixel buffer.

getRow(Integer, Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getRow(int, int, int, int) - Method in class ome.services.RawPixelsBean

getRow() - Method in class pojos.WellData

Returns the row used to indicate the location of the well on the grid.

getRow_async(AMD_RawPixelsStore_getRow, int, int, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI

getRow_async(AMD_RawPixelsStore_getRow, int, int, int, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI

getRowDirect(Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPixelBuffer

getRowDirect(Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getRowDirect(Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getRowDirect(Integer, Integer, Integer, Integer, byte[]) - Method in interface ome.io.nio.PixelBuffer

Retrieves a particular row or scanline from this pixel buffer.

getRowDirect(Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getRowOffset(int, int, int, int) - Method in interface ome.api.RawPixelsStore

getRowOffset(Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer

getRowOffset(Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelsWrapper

getRowOffset(Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getRowOffset(Integer, Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getRowOffset(Integer, Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer

Retrieves the offset for a particular row or scanline in this pixel buffer.

getRowOffset(Integer, Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getRowOffset(int, int, int, int) - Method in class ome.services.RawPixelsBean

getRowOffset_async(AMD_RawPixelsStore_getRowOffset, int, int, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI

getRowOffset_async(AMD_RawPixelsStore_getRowOffset, int, int, int, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI

getRowSequenceIndex() - Method in class pojos.PlateData

Returns the index indicating how to label a row.

getRowSize() - Method in interface ome.api.RawPixelsStore

getRowSize() - Method in class ome.io.bioformats.BfPixelBuffer

getRowSize() - Method in class ome.io.bioformats.BfPixelsWrapper

getRowSize() - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getRowSize() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getRowSize() - Method in interface ome.io.nio.PixelBuffer

Retrieves the in memory size of a row or scanline of pixels in this pixel buffer.

getRowSize() - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getRowSize(long) - Method in class ome.services.blitz.gateway.services.impl.RawPixelsStoreServiceImpl

getRowSize(long) - Method in interface ome.services.blitz.gateway.services.RawPixelsStoreService

Get the plane size of the current image.

getRowSize() - Method in class ome.services.RawPixelsBean

getRowSize_async(AMD_RawPixelsStore_getRowSize, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI

getRowSize_async(AMD_RawPixelsStore_getRowSize, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI

getScalingFactor() - Method in class ome.io.nio.SimpleBackOff

getScreens() - Method in class ome.formats.OMEROMetadataStoreClient

getScreens() - Method in class pojos.PlateData

Returns a set of screens containing the plate.

getScriptDir() - Method in class ome.services.scripts.ScriptRepoHelper

Returns the actual root of this repository.

getScriptID_async(AMD_IScript_getScriptID, String, Current) - Method in class ome.services.blitz.impl.ScriptI

Get the id of the official script with given path.

getScriptRepository(Current) - Method in class ome.services.blitz.impl.SharedResourcesI

getScripts_async(AMD_IScript_getScripts, Current) - Method in class ome.services.blitz.impl.ScriptI

Get Scripts will return all the scripts by id and name available on the server.

getScriptService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI

getScriptText_async(AMD_IScript_getScriptText, long, Current) - Method in class ome.services.blitz.impl.ScriptI

Return the script with the name to the user.

getScriptWithDetails_async(AMD_IScript_getScriptWithDetails, long, Current) - Method in class ome.services.blitz.impl.ScriptI

Return the script with the name to the user.

getSecondLevelCacheHitCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

getSecondLevelCacheMissCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

getSecondLevelCachePutCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

getSecondLevelCacheRegionNames() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

Get all second-level cache region names

getSecondLevelCacheStatistics(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

Second level cache statistics per region

getSecurityContexts(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI

getSecurityRoles() - Method in interface ome.api.IAdmin

returns the active Roles in use by the server.

getSecurityRoles() - Method in class ome.logic.AdminImpl

getSecurityRoles() - Method in class ome.security.basic.BasicSecuritySystem

getSecurityRoles() - Method in interface ome.security.SecuritySystem

getSecurityRoles() - Method in class ome.security.SecuritySystemHolder

getSecurityRoles() - Method in class ome.security.sharing.SharingSecuritySystem

getSecurityRoles_async(AMD_IAdmin_getSecurityRoles, Current) - Method in class ome.services.blitz.impl.AdminI

getSecuritySystem() - Method in class ome.logic.AbstractLevel2Service

getSelectedFile() - Method in class ome.formats.importer.util.ErrorContainer

getSerialNumber() - Method in class pojos.DetectorData

Returns the serial number of the detector.

getSerialNumber() - Method in class pojos.DichroicData

Returns the serial number.

getSerialNumber() - Method in class pojos.FilterData

Returns the serial number.

getSerialNumber() - Method in class pojos.FilterSetData

Returns the serial number.

getSerialNumber() - Method in class pojos.LightSourceData

Returns the serial number of the light source.

getSerialNumber() - Method in class pojos.ObjectiveData

Returns the serial number of the objective.

getSeries() - Method in class ome.io.bioformats.BfPixelBuffer

Retrieves the current series of the underlying Bio-Formats reader.

getSeries(Pixels) - Method in class ome.io.nio.PixelsService

Retrieves the series for a given set of pixels.

getServant(Identity) - Method in class ome.services.blitz.impl.ServiceFactoryI

getServant() - Method in class ome.services.blitz.util.RegisterServantMessage

getServantList() - Method in class ome.services.blitz.util.ServantHolder

getServerFileMimetype() - Method in class pojos.FileAnnotationData

Returns the file format as defined by the specification, corresponding to the file extension.

getServerList() - Method in class ome.formats.importer.ImportConfig

getServerPort() - Method in class ome.formats.importer.util.IniFileLoader

getServerTime() - Method in interface ome.api.IConfig

checks the current server for it's time.

getServerTime() - Method in class ome.logic.ConfigImpl

see IConfig.getServerTime()

getServerTime_async(AMD_IConfig_getServerTime, Current) - Method in class ome.services.blitz.impl.ConfigI

getServiceByClass(Class<T>) - Method in class ome.system.ServiceFactory

looks up services based on the current prefix and the class name of the service type.

getServiceFactory() - Method in class ome.formats.OMEROMetadataStoreClient

Returns the currently active service factory.

getServiceFactory(MethodInvocation) - Method in class ome.logic.HardWiredInterceptor

getServiceFactory(String, String) - Method in class ome.services.blitz.fire.SessionManagerI

getServiceFactory(Identity) - Method in class ome.services.blitz.fire.SessionManagerI

getServiceFactory() - Method in class omero.client

Deprecated.

getServiceFactoryIdentity(Current) - Method in class ome.services.blitz.fire.SessionManagerI

getServiceInterface() - Method in class ome.logic.AdminImpl

getServiceInterface() - Method in class ome.logic.ConfigImpl

getServiceInterface() - Method in class ome.logic.LdapImpl

getServiceInterface() - Method in class ome.logic.MetadataImpl

Returns the Interface implemented by this class.

getServiceInterface() - Method in class ome.logic.PixelsImpl

Returns the interface this implementation is for.

getServiceInterface() - Method in class ome.logic.PojosImpl

Returns the Interface implemented by this class.

getServiceInterface() - Method in class ome.logic.QueryImpl

getServiceInterface() - Method in class ome.logic.RenderingSettingsImpl

Returns the interface this implementation is for.

getServiceInterface() - Method in class ome.logic.RepositoryInfoImpl

getServiceInterface() - Method in class ome.logic.TypesImpl

getServiceInterface() - Method in class ome.logic.UpdateImpl

getServiceInterface() - Method in class ome.services.delete.DeleteBean

getServiceInterface() - Method in class ome.services.JobBean

getServiceInterface() - Method in class ome.services.projection.ProjectionBean

Returns the interface this implementation is for.

getServiceInterface() - Method in class ome.services.RawFileBean

getServiceInterface() - Method in class ome.services.RawPixelsBean

getServiceInterface() - Method in class ome.services.RenderingBean

Returns the service corresponding to this class.

getServiceInterface() - Method in class ome.services.SearchBean

getServiceInterface() - Method in class ome.services.sessions.SessionBean

getServiceInterface() - Method in class ome.services.sharing.ShareBean

getServiceInterface() - Method in class ome.services.ThumbnailBean

getServiceInterface() - Method in interface ome.system.SelfConfigurableService

getServiceKey() - Method in class ome.services.blitz.util.ExpiredServantMessage

getSession(String) - Method in interface ome.api.ISession

Retrieves the session associated with this uuid, updating the last access time as well.

getSession(String) - Method in class ome.services.sessions.SessionBean

getSession() - Method in interface ome.services.sessions.SessionContext

getSession() - Method in class ome.services.sessions.SessionContextImpl

getSession() - Method in class ome.system.ServiceFactory

getSession() - Method in class ome.system.SessionInitializer

getSession() - Method in class ome.tools.hibernate.SessionFactory

Returns a session active for the current thread.

getSession() - Method in class omero.client

Returns the current active session or throws an exception if none has been created since the last client.closeSession()

getSession() - Method in class omero.util.RPSTileLoop

getSession_async(AMD_ISession_getSession, String, Current) - Method in class ome.services.blitz.impl.SessionI

getSessionCloseCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

getSessionContext(String) - Method in class ome.services.sessions.state.SessionCache

Retrieve a session possibly raising either RemovedSessionException or SessionTimeoutException.

getSessionFactory() - Method in class ome.logic.AbstractLevel1Service

delegates to HibernateDaoSupport to get the current SessionFactory

getSessionId() - Method in class ome.formats.importer.util.FileUploader

getSessionId() - Method in class ome.services.messages.AbstractSessionMessage

getSessionId() - Method in class omero.client

Returns the UUID for the current session without making a remote call.

getSessionInitializer() - Method in class ome.system.ServiceFactory

getSessionOpenCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

getSessionService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI

getSessionService() - Method in class ome.system.ServiceFactory

getSessionStats(String) - Method in interface ome.services.sessions.SessionManager

Return the SessionStats which are being counted for the given session or throw an exception if it has been removed.

getSessionStats(String) - Method in class ome.services.sessions.SessionManagerImpl

getSetting() - Method in interface ome.api.ILdap

Gets config value from properties.

getSetting() - Method in class ome.logic.LdapImpl

getSetting_async(AMD_ILdap_getSetting, Current) - Method in class ome.services.blitz.impl.LdapI

getSettings(long) - Method in class ome.services.ThumbnailCtx

Retrieves the RenderingDef object for a given Pixels ID.

getSha1() - Method in class ome.io.nio.RomioPixelBuffer

getShapeCount() - Method in class pojos.ROIData

Returns the number of shapes in the ROI.

getShapes(int, int) - Method in class pojos.ROIData

Returns the list of shapes on a given plane.

getShapeSettings() - Method in class pojos.ShapeData

Returns the settings associated to the shape.

getShapesInRange(ROICoordinate, ROICoordinate) - Method in class pojos.ROIData

Returns an iterator of the Shapes in the ROI in the range [start, end].

getShapeStats_async(AMD_IRoi_getShapeStats, long, Current) - Method in class ome.services.blitz.impl.RoiI

getShapeStatsList_async(AMD_IRoi_getShapeStatsList, List<Long>, Current) - Method in class ome.services.blitz.impl.RoiI

getShare(long) - Method in interface ome.api.IShare

Gets a share as a Session with all related: comments, members, fully loaded.

getShare(long) - Method in class ome.services.sharing.ShareBean

getShare_async(AMD_IShare_getShare, long, Current) - Method in class ome.services.blitz.impl.ShareI

getShareIfAccessible(long) - Method in class ome.services.sharing.ShareBean

Loads share and checks it's owner and member data against the current context (owner/member/admin).

getShares(long, boolean, boolean) - Method in class ome.services.sharing.BlobShareStore

getShares(long, boolean, boolean) - Method in class ome.services.sharing.FreezeShareStore

getShares(long, boolean, boolean) - Method in class ome.services.sharing.ShareStore

getShareService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI

getShareService() - Method in class ome.system.ServiceFactory

getSharesOwnedBy(Experimenter, boolean) - Method in interface ome.api.IShare

Gets all shares owned by the given Experimenter.

getSharesOwnedBy(Experimenter, boolean) - Method in class ome.services.sharing.ShareBean

getSharesOwnedBy_async(AMD_IShare_getSharesOwnedBy, Experimenter, boolean, Current) - Method in class ome.services.blitz.impl.ShareI

getSize() - Method in class ome.util.mem.CopiableArray

Returns the number of elements in the array.

getSizeC() - Method in class ome.io.bioformats.BfPixelBuffer

getSizeC() - Method in class ome.io.bioformats.BfPixelsWrapper

getSizeC() - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getSizeC() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getSizeC() - Method in interface ome.io.nio.PixelBuffer

Delegates to Pixels.getSizeC().

getSizeC() - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getSizeC() - Method in class pojos.PixelsData

Returns the number of channels.

getSizeT() - Method in class ome.io.bioformats.BfPixelBuffer

getSizeT() - Method in class ome.io.bioformats.BfPixelsWrapper

getSizeT() - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getSizeT() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getSizeT() - Method in interface ome.io.nio.PixelBuffer

Delegates to Pixels.getSizeT().

getSizeT() - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getSizeT() - Method in class pojos.PixelsData

Returns the number of time-points.

getSizeX() - Method in class ome.io.bioformats.BfPixelBuffer

getSizeX() - Method in class ome.io.bioformats.BfPixelsWrapper

getSizeX() - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getSizeX() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getSizeX() - Method in interface ome.io.nio.PixelBuffer

Delegates to Pixels.getSizeX().

getSizeX() - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getSizeX() - Method in class pojos.OTFData

Returns the size along the X-axis.

getSizeX() - Method in class pojos.PixelsData

Returns the number of pixels along the X-axis.

getSizeX1() - Method in class omeis.providers.re.RGBBuffer

Returns the number of pixels on the X1-axis.

getSizeX2() - Method in class omeis.providers.re.RGBBuffer

Returns the number of pixels on the X2-axis.

getSizeY() - Method in class ome.io.bioformats.BfPixelBuffer

getSizeY() - Method in class ome.io.bioformats.BfPixelsWrapper

getSizeY() - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getSizeY() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getSizeY() - Method in interface ome.io.nio.PixelBuffer

Delegates to Pixels.getSizeY().

getSizeY() - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getSizeY() - Method in class pojos.OTFData

Returns the size along the Y-axis.

getSizeY() - Method in class pojos.PixelsData

Returns the number of pixels along the Y-axis.

getSizeZ() - Method in class ome.io.bioformats.BfPixelBuffer

getSizeZ() - Method in class ome.io.bioformats.BfPixelsWrapper

getSizeZ() - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getSizeZ() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getSizeZ() - Method in interface ome.io.nio.PixelBuffer

Delegates to Pixels.getSizeZ().

getSizeZ() - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getSizeZ() - Method in class pojos.PixelsData

Returns the number of pixels along the Z-axis.

getSlice() - Method in class omeis.providers.re.data.PlaneDef

Returns an identifier to tell which kind of plane this object identifies.

getSourceObject(LSID) - Method in interface ome.formats.model.IObjectContainerStore

Retrieves an OMERO Blitz source object for a given LSID.

getSourceObject(LSID) - Method in class ome.formats.OMEROMetadataStoreClient

getSourceObjects(Class<T>) - Method in interface ome.formats.model.IObjectContainerStore

Retrieves all OMERO Blitz source objects of a given class.

getSourceObjects(Class<T>) - Method in class ome.formats.OMEROMetadataStoreClient

getSqlAction() - Method in class ome.services.util.Executor.SimpleWork

getStack(int, int) - Method in interface ome.api.RawPixelsStore

getStack(Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer

getStack(Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPixelsWrapper

getStack(Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getStack(Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getStack(Integer, Integer) - Method in interface ome.io.nio.PixelBuffer

Retrieves the the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel buffer.

getStack(Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getStack(int, int) - Method in class ome.services.RawPixelsBean

getStack_async(AMD_RawPixelsStore_getStack, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI

getStack_async(AMD_RawPixelsStore_getStack, int, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI

getStackDirect(Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPixelBuffer

getStackDirect(Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getStackDirect(Integer, Integer, byte[]) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getStackDirect(Integer, Integer, byte[]) - Method in interface ome.io.nio.PixelBuffer

Retrieves the the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel buffer.

getStackDirect(Integer, Integer, byte[]) - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getStackOffset(int, int) - Method in interface ome.api.RawPixelsStore

getStackOffset(Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer

getStackOffset(Integer, Integer) - Method in class ome.io.bioformats.BfPixelsWrapper

getStackOffset(Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getStackOffset(Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getStackOffset(Integer, Integer) - Method in interface ome.io.nio.PixelBuffer

Retrieves the offset for the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel buffer.

getStackOffset(Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getStackOffset(int, int) - Method in class ome.services.RawPixelsBean

getStackOffset_async(AMD_RawPixelsStore_getStackOffset, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI

getStackOffset_async(AMD_RawPixelsStore_getStackOffset, int, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI

getStackSize() - Method in interface ome.api.RawPixelsStore

getStackSize() - Method in class ome.io.bioformats.BfPixelBuffer

getStackSize() - Method in class ome.io.bioformats.BfPixelsWrapper

getStackSize() - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getStackSize() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getStackSize() - Method in interface ome.io.nio.PixelBuffer

Retrieves the in memory size of the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel buffer.

getStackSize() - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getStackSize(long) - Method in class ome.services.blitz.gateway.services.impl.RawPixelsStoreServiceImpl

getStackSize(long) - Method in interface ome.services.blitz.gateway.services.RawPixelsStoreService

Get the stack size of the current image.

getStackSize() - Method in class ome.services.RawPixelsBean

getStackSize_async(AMD_RawPixelsStore_getStackSize, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI

getStackSize_async(AMD_RawPixelsStore_getStackSize, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI

getStackTrace(Throwable) - Static method in class ome.formats.importer.util.ErrorHandler

Return stack trace from throwable

getStageLabelId() - Method in class pojos.ImageAcquisitionData

Returns the id of the StageLabel or -1 if not already linked to the image.

getStartTime() - Method in class omero.sys.ParametersI

Returns the value of the start time parameter.

getStartTime() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

getStartTime() - Method in class pojos.PlateAcquisitionData

Returns the time when the first image was collected.

getStartTime() - Method in class pojos.WellSampleData

Returns the time at which the field was acquired.

getStatefulServiceCount() - Method in class ome.services.blitz.impl.ServiceFactoryI

NB: Much of the logic here is similar to ServiceFactoryI.doClose and should be pushed down.

getStatefulServices() - Method in class omero.client

Returns all active StatefulServiceInterface proxies.

getStaticDisableHistory() - Method in class ome.formats.importer.ImportConfig

getStaticDisableHistory() - Method in class ome.formats.importer.util.IniFileLoader

getStaticDisableUpgradeCheck() - Method in class ome.formats.importer.ImportConfig

getStaticDisableUpgradeCheck() - Method in class ome.formats.importer.util.IniFileLoader

getStats() - Method in class ome.security.basic.CurrentDetails

getStats(List<Long>) - Method in class ome.services.roi.GeomTool

getStats() - Method in class omeis.providers.re.Renderer

Returns a RenderingStats object that the rendering strategy can use to track performance.

getStats() - Method in class omeis.providers.re.RenderingStats

Returns a stats report ready to be written to the log file.

getStatus() - Method in class ome.formats.importer.util.ErrorContainer

return the error status

getStatus() - Method in class pojos.PlateData

Returns the status of the plate.

getStatus() - Method in class pojos.WellData

Returns the status of the well.

getStore() - Method in class ome.services.fulltext.SimpleLuceneOptions

getStrategy(QuantumDef, PixelsType) - Method in class omeis.providers.re.quantum.QuantumFactory

Returns a strategy to carry out the quantization process whose context is defined by pd.

getStride() - Method in class omeis.providers.re.data.PlaneDef

Returns the stride.

getStroke() - Method in class pojos.ShapeSettingsData

Returns the color of the stroke.

getStrokeDashArray() - Method in class pojos.ShapeSettingsData

Returns the stroke dashes.

getStrokeWidth() - Method in class pojos.ShapeSettingsData

Returns the stroke's width.

getSubSpec() - Method in class ome.services.graphs.GraphEntry

getSubtypeValue(int, int, Object) - Method in class ome.tools.hibernate.ExtendedMetadata.Locks

uses the ClassMetadata for this ExtendedMetadata.Locks tp retrieve the component value.

getSuccessfulTransactionCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

getSuperSpec() - Method in class ome.services.graphs.BaseGraphSpec

getSuperSpec() - Method in class ome.services.graphs.GraphEntry

getSuperSpec() - Method in interface ome.services.graphs.GraphSpec

Specification of where this GraphSpec is attached under another .

getSupportedMetadataLevels() - Method in class ome.formats.importer.OMEROWrapper

getSystemGroupId() - Method in class ome.system.Roles

getSystemGroupName() - Method in class ome.system.Roles

getT() - Method in class omeis.providers.re.data.PlaneDef

Returns the timepoint.

getT() - Method in class pojos.ShapeData

Returns the time-point.

getTable() - Method in class ome.services.blitz.measurements.MeasurementStore

getTable() - Method in interface ome.services.blitz.measurements.OmeroMeasurementStore

Returns the Table proxy which is in use by this service.

getTable_async(AMD_IRoi_getTable, long, Current) - Method in class ome.services.blitz.impl.RoiI

getTagAnnotationCount() - Method in class ome.services.blitz.impl.OmeroMetadata

getTagAnnotationDescription(int) - Method in class ome.services.blitz.impl.OmeroMetadata

getTagAnnotationID(int) - Method in class ome.services.blitz.impl.OmeroMetadata

getTagAnnotationNamespace(int) - Method in class ome.services.blitz.impl.OmeroMetadata

getTagAnnotationValue(int) - Method in class ome.services.blitz.impl.OmeroMetadata

getTagDescription() - Method in class pojos.TagAnnotationData

Returns the description of the tag.

getTagDescriptions() - Method in class pojos.TagAnnotationData

Returns the descriptions linked to that tag.

getTaggedObjectsCount(Set<Long>, Parameters) - Method in interface ome.api.IMetadata

Returns a map whose key is a tag's id and the value the number of Projects, Datasets, and Images linked to that tag.

getTaggedObjectsCount(Set<Long>, Parameters) - Method in class ome.logic.MetadataImpl

Implemented as specified by the IMetadata I/F

getTaggedObjectsCount_async(AMD_IMetadata_getTaggedObjectsCount, List<Long>, Parameters, Current) - Method in class ome.services.blitz.impl.MetadataI

getTags() - Method in class pojos.TagAnnotationData

Returns the collection of tags related to this tag.

getTagValue() - Method in class pojos.TagAnnotationData

Returns the text of the tag.

getTarget() - Method in class ome.formats.importer.ImportContainer

getTarget(Class<T>, long) - Method in class ome.formats.OMEROMetadataStoreClient

Helper method to retrieve an object from iQuery

getTargetType(String) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl

Returns the IObject type which a given field points to.

getTempDir() - Method in class omero.util.TempFileManager

Returns the directory under which all temporary files and folders will be created.

gettempdir() - Static method in class omero.util.TempFileManager

Calls TempFileManager.getTempDir() on TempFileManager.manager.

getTemperature() - Method in class pojos.ImageAcquisitionData

Returns the temperature in Celcius.

getTerm() - Method in class pojos.TermAnnotationData

Returns the term.

getTermAnnotationCount() - Method in class ome.services.blitz.impl.OmeroMetadata

getTermAnnotationDescription(int) - Method in class ome.services.blitz.impl.OmeroMetadata

getTermAnnotationID(int) - Method in class ome.services.blitz.impl.OmeroMetadata

getTermAnnotationNamespace(int) - Method in class ome.services.blitz.impl.OmeroMetadata

getTermAnnotationValue(int) - Method in class ome.services.blitz.impl.OmeroMetadata

getTermDescription() - Method in class pojos.TermAnnotationData

Returns the description of the term.

getTermVector() - Method in class ome.services.fulltext.SimpleLuceneOptions

getTestIds() - Method in class ome.tools.RepositoryTask

Private method used for testing only.

getText() - Method in class pojos.EllipseData

Returns the text of the shape.

getText() - Method in class pojos.LineData

Returns the text of the shape.

getText() - Method in class pojos.MaskData

Returns the text of the shape.

getText() - Method in class pojos.PointData

Returns the text of the shape.

getText() - Method in class pojos.PolygonData

Returns the text of the shape.

getText() - Method in class pojos.PolylineData

Returns the text of the shape.

getText() - Method in class pojos.RectangleData

Returns the text of the shape.

getText() - Method in class pojos.TextData

Returns the text of the shape.

getText() - Method in class pojos.TextualAnnotationData

Returns the text of this annotation.

getText() - Method in class pojos.XMLAnnotationData

Returns the text of this annotation.

getThumbnail(Integer, Integer) - Method in interface ome.api.ThumbnailStore

Retrieves a thumbnail for a pixels set using a given set of rendering settings (RenderingDef).

getThumbnail(Thumbnail) - Method in class ome.io.nio.ThumbnailService

Return byte array of Thumbnail

getThumbnail(Thumbnail, byte[]) - Method in class ome.io.nio.ThumbnailService

Return byte array of Thumbnail, providing byte array

getThumbnail(long, RInt, RInt, Current) - Method in class ome.services.blitz.gateway.OmeroGateway

getThumbnail(long, RInt, RInt) - Method in interface ome.services.blitz.gateway.services.ImageService

Get the thumbnail of the image.

getThumbnail(long, RInt, RInt) - Method in class ome.services.blitz.gateway.services.impl.ImageServiceImpl

getThumbnail(long, RInt, RInt) - Method in class ome.services.blitz.gateway.services.impl.ThumbnailServiceImpl

getThumbnail(long, RInt, RInt) - Method in interface ome.services.blitz.gateway.services.ThumbnailService

Get the thumbnail of the image.

getThumbnail(String, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI

Get (the path of) the thumbnail image for an image file on the repository.

getThumbnail(Integer, Integer) - Method in class ome.services.ThumbnailBean

getThumbnail_async(AMD_ThumbnailStore_getThumbnail, RInt, RInt, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI

getThumbnailByIndex(String, int, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI

Get (the path of) the thumbnail image for an image file on the repository.

getThumbnailByLongestSide(Integer) - Method in interface ome.api.ThumbnailStore

Retrieves a thumbnail for a pixels set using a given set of rendering settings (RenderingDef).

getThumbnailByLongestSide(long, RInt) - Method in class ome.services.blitz.gateway.services.impl.ThumbnailServiceImpl

getThumbnailByLongestSide(long, RInt) - Method in interface ome.services.blitz.gateway.services.ThumbnailService

Get the thumbnail of the image, maintain aspect ratio.

getThumbnailByLongestSide(Integer) - Method in class ome.services.ThumbnailBean

getThumbnailByLongestSide_async(AMD_ThumbnailStore_getThumbnailByLongestSide, RInt, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI

getThumbnailByLongestSideDirect(Integer) - Method in interface ome.api.ThumbnailStore

Retrieves a thumbnail for a pixels set using a given set of rendering settings (RenderingDef).

getThumbnailByLongestSideDirect(Integer) - Method in class ome.services.ThumbnailBean

getThumbnailByLongestSideDirect_async(AMD_ThumbnailStore_getThumbnailByLongestSideDirect, RInt, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI

getThumbnailByLongestSideSet(Integer, Set<Long>) - Method in interface ome.api.ThumbnailStore

Retrieves a number of thumbnails for pixels sets using given sets of rendering settings (RenderingDef).

getThumbnailByLongestSideSet(RInt, List<Long>) - Method in class ome.services.blitz.gateway.services.impl.ThumbnailServiceImpl

getThumbnailByLongestSideSet(RInt, List<Long>) - Method in interface ome.services.blitz.gateway.services.ThumbnailService

Get a set of thumbnails, maintaining aspect ratio.

getThumbnailByLongestSideSet(Integer, Set<Long>) - Method in class ome.services.ThumbnailBean

getThumbnailByLongestSideSet_async(AMD_ThumbnailStore_getThumbnailByLongestSideSet, RInt, List<Long>, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI

getThumbnailDirect(Integer, Integer) - Method in interface ome.api.ThumbnailStore

Retrieves a thumbnail for a pixels set using a given set of rendering settings (RenderingDef).

getThumbnailDirect(Integer, Integer) - Method in class ome.services.ThumbnailBean

getThumbnailDirect_async(AMD_ThumbnailStore_getThumbnailDirect, RInt, RInt, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI

getThumbnailExists(Thumbnail) - Method in class ome.io.nio.ThumbnailService

Returns whether or not a thumbnail exists on disk.

getThumbnailForSectionByLongestSideDirect(int, int, Integer) - Method in interface ome.api.ThumbnailStore

Retrieves a thumbnail for a pixels set using a given set of rendering settings (RenderingDef) for a particular section.

getThumbnailForSectionByLongestSideDirect(int, int, Integer) - Method in class ome.services.ThumbnailBean

getThumbnailForSectionByLongestSideDirect_async(AMD_ThumbnailStore_getThumbnailForSectionByLongestSideDirect, int, int, RInt, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI

getThumbnailForSectionDirect(int, int, Integer, Integer) - Method in interface ome.api.ThumbnailStore

Retrieves a thumbnail for a pixels set using a given set of rendering settings (RenderingDef) for a particular section.

getThumbnailForSectionDirect(int, int, Integer, Integer) - Method in class ome.services.ThumbnailBean

getThumbnailForSectionDirect_async(AMD_ThumbnailStore_getThumbnailForSectionDirect, int, int, RInt, RInt, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI

getThumbnailIds() - Method in class ome.tools.RepositoryTask

This public method is used to return a list of thumbnail ids that require deletion from the disk repository.

getThumbnailLength(Thumbnail) - Method in class ome.io.nio.ThumbnailService

Returns length of Thumbnail on disk

getThumbnailOutputStream(Thumbnail) - Method in class ome.io.nio.ThumbnailService

Return FileOutputStream of Thumbnail

getThumbnailPath(Long) - Method in class ome.io.nio.AbstractFileSystemService

Returns a numbered path relative to the root of this service, but is ignorant of FS and similar constructs.

getThumbnailSet(Integer, Integer, Set<Long>) - Method in interface ome.api.ThumbnailStore

Retrieves a number of thumbnails for pixels sets using given sets of rendering settings (RenderingDef).

getThumbnailSet(RInt, RInt, List<Long>, Current) - Method in class ome.services.blitz.gateway.OmeroGateway

getThumbnailSet(RInt, RInt, List<Long>) - Method in interface ome.services.blitz.gateway.services.ImageService

Get a set of thumbnails.

getThumbnailSet(RInt, RInt, List<Long>) - Method in class ome.services.blitz.gateway.services.impl.ImageServiceImpl

getThumbnailSet(RInt, RInt, List<Long>) - Method in class ome.services.blitz.gateway.services.impl.ThumbnailServiceImpl

getThumbnailSet(RInt, RInt, List<Long>) - Method in interface ome.services.blitz.gateway.services.ThumbnailService

Get a set of thumbnails.

getThumbnailSet(Integer, Integer, Set<Long>) - Method in class ome.services.ThumbnailBean

getThumbnailSet_async(AMD_ThumbnailStore_getThumbnailSet, RInt, RInt, List<Long>, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI

getThumbnailStoreService() - Method in class ome.services.blitz.gateway.services.GatewayFactory

Return the thumbnail service.

getTie(Identity) - Method in class ome.services.blitz.impl.ServiceFactoryI

getTile(int, int, int, int, int, int, int) - Method in interface ome.api.RawPixelsStore

getTile(Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer

getTile(int, int, int, int, int, int, int, byte[]) - Method in class ome.io.bioformats.BfPixelsWrapper

getTile(Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getTile(Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getTile(Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer

Retrieves a tile from this pixel buffer.

getTile(Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer

getTile(int, int, int, int, int, int, int) - Method in class ome.services.RawPixelsBean

getTile(int, int, int, int, int, int, int) - Method in class omero.util.RPSTileData

getTile(int, int, int, int, int, int, int) - Method in interface omero.util.TileData

getTile_async(AMD_RawPixelsStore_getTile, int, int, int, int, int, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI

getTile_async(AMD_RawPixelsStore_getTile, int, int, int, int, int, int, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI

getTileDirect(Integer, Integer, Integer, Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPixelBuffer

getTileDirect(Integer, Integer, Integer, Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getTileDirect(Integer, Integer, Integer, Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getTileDirect(Integer, Integer, Integer, Integer, Integer, Integer, Integer, byte[]) - Method in interface ome.io.nio.PixelBuffer

Retrieves a tile from this pixel buffer.

getTileDirect(Integer, Integer, Integer, Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.nio.RomioPixelBuffer

getTileHeight() - Method in class ome.io.nio.ConfiguredTileSizes

getTileHeight() - Method in interface ome.io.nio.TileSizes

getTileSize() - Method in interface ome.api.RawPixelsStore

getTileSize(Long) - Method in class ome.formats.OMEROMetadataStoreClient

Retrieves the suggested tile size for a pixels set.

getTileSize() - Method in class ome.io.bioformats.BfPixelBuffer

getTileSize() - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getTileSize() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getTileSize() - Method in interface ome.io.nio.PixelBuffer

Retrieves the tile size for the pixel store.

getTileSize() - Method in class ome.io.nio.RomioPixelBuffer

getTileSize() - Method in class ome.services.RawPixelsBean

getTileSize() - Method in class ome.services.RenderingBean

getTileSize() - Method in class omeis.providers.re.Renderer

Retrieves the tile size for the pixel store.

getTileSize() - Method in interface omeis.providers.re.RenderingEngine

getTileSize_async(AMD_PyramidService_getTileSize, Current) - Method in class ome.services.blitz.impl.AbstractPyramidServant

getTileSize_async(AMD_PyramidService_getTileSize, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI

getTileSize_async(AMD_PyramidService_getTileSize, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI

getTileWidth() - Method in class ome.io.nio.ConfiguredTileSizes

getTileWidth() - Method in interface ome.io.nio.TileSizes

getTime() - Method in class pojos.TimeAnnotationData

Returns the time value.

getTimelineService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI

getTimepoint(int) - Method in interface ome.api.RawPixelsStore

getTimepoint(Integer) - Method in class ome.io.bioformats.BfPixelBuffer

getTimepoint(Integer, byte[]) - Method in class ome.io.bioformats.BfPixelsWrapper

getTimepoint(Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getTimepoint(Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getTimepoint(Integer) - Method in interface ome.io.nio.PixelBuffer

Retrieves the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel buffer.

getTimepoint(Integer) - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getTimepoint(int) - Method in class ome.services.RawPixelsBean

getTimePoint() - Method in class pojos.ROICoordinate

Returns the timepoint.

getTimepoint_async(AMD_RawPixelsStore_getTimepoint, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI

getTimepoint_async(AMD_RawPixelsStore_getTimepoint, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI

getTimepointDirect(Integer, byte[]) - Method in class ome.io.bioformats.BfPixelBuffer

getTimepointDirect(Integer, byte[]) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getTimepointDirect(Integer, byte[]) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getTimepointDirect(Integer, byte[]) - Method in interface ome.io.nio.PixelBuffer

Retrieves the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel buffer.

getTimepointDirect(Integer, byte[]) - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getTimepointOffset(int) - Method in interface ome.api.RawPixelsStore

getTimepointOffset(Integer) - Method in class ome.io.bioformats.BfPixelBuffer

getTimepointOffset(Integer) - Method in class ome.io.bioformats.BfPixelsWrapper

getTimepointOffset(Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getTimepointOffset(Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getTimepointOffset(Integer) - Method in interface ome.io.nio.PixelBuffer

Retrieves the in memory size of the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel buffer.

getTimepointOffset(Integer) - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getTimepointOffset(int) - Method in class ome.services.RawPixelsBean

getTimepointOffset_async(AMD_RawPixelsStore_getTimepointOffset, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI

getTimepointOffset_async(AMD_RawPixelsStore_getTimepointOffset, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI

getTimepointSize() - Method in interface ome.api.RawPixelsStore

getTimepointSize() - Method in class ome.io.bioformats.BfPixelBuffer

getTimepointSize() - Method in class ome.io.bioformats.BfPixelsWrapper

getTimepointSize() - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getTimepointSize() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getTimepointSize() - Method in interface ome.io.nio.PixelBuffer

Retrieves the in memory size of the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel buffer.

getTimepointSize() - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getTimepointSize(long) - Method in class ome.services.blitz.gateway.services.impl.RawPixelsStoreServiceImpl

getTimepointSize(long) - Method in interface ome.services.blitz.gateway.services.RawPixelsStoreService

Get the timepoint size of the current image.

getTimepointSize() - Method in class ome.services.RawPixelsBean

getTimepointSize_async(AMD_RawPixelsStore_getTimepointSize, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI

getTimepointSize_async(AMD_RawPixelsStore_getTimepointSize, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI

getTimestampAnnotationCount() - Method in class ome.services.blitz.impl.OmeroMetadata

getTimestampAnnotationDescription(int) - Method in class ome.services.blitz.impl.OmeroMetadata

getTimestampAnnotationID(int) - Method in class ome.services.blitz.impl.OmeroMetadata

getTimestampAnnotationNamespace(int) - Method in class ome.services.blitz.impl.OmeroMetadata

getTimestampAnnotationValue(int) - Method in class ome.services.blitz.impl.OmeroMetadata

getToken() - Method in class ome.formats.importer.util.ErrorContainer

getTokenUrl() - Method in class ome.formats.importer.ImportConfig

getTopicManager() - Method in class ome.services.blitz.util.BlitzConfiguration

getTotalFoundCount() - Method in class ome.services.graphs.GraphState

Return the total number of ids loaded into this instance.

getTotalProcessedCount() - Method in class ome.services.graphs.GraphState

Return the total number of ids which were processed.

getTotalSize() - Method in interface ome.api.RawPixelsStore

getTotalSize() - Method in class ome.io.bioformats.BfPixelBuffer

getTotalSize() - Method in class ome.io.bioformats.BfPixelsWrapper

getTotalSize() - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getTotalSize() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getTotalSize() - Method in interface ome.io.nio.PixelBuffer

Retrieves the in memory size of the entire pixel buffer.

getTotalSize() - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getTotalSize(long) - Method in class ome.services.blitz.gateway.services.impl.RawPixelsStoreServiceImpl

getTotalSize(long) - Method in interface ome.services.blitz.gateway.services.RawPixelsStoreService

Get the total size of the current image.

getTotalSize() - Method in class ome.services.RawPixelsBean

getTotalSize_async(AMD_RawPixelsStore_getTotalSize, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI

getTotalSize_async(AMD_RawPixelsStore_getTotalSize, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI

getTransactionAttribute(Method, Class) - Method in class ome.services.sharing.ShareRestrictionTransactionAttributeSource

getTransactionAttribute(Method, Class) - Method in class ome.tools.spring.ForceTransactionAttributeSource

getTransactionCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

getTransform() - Method in class pojos.ShapeData

Returns the transformation.

getTransmittance() - Method in class pojos.FilterData

Returns the cut out tolerance value or -1.

getType(MethodInvocation) - Method in class ome.tools.hibernate.EventMethodInterceptor.DisableAction

getType() - Method in class pojos.DetectorData

Returns the type of the detector.

getType() - Method in class pojos.FilterData

Returns the type.

getType() - Method in class pojos.LightSourceData

Returns the type of light.

getTypesService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI

getTypesService() - Method in class ome.system.ServiceFactory

getUIBounds() - Method in class ome.formats.importer.ImportConfig

getUIBounds() - Method in class ome.formats.importer.util.IniFileLoader

getUnique() - Method in class omero.sys.ParametersI

getUntied(Identity) - Method in class ome.services.blitz.util.ServantHolder

getUpdated() - Method in class pojos.DataObject

Returns the updated time of the object.

getUpdateEvent(Current) - Method in class omero.model.DetailsI

getUpdateService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI

getUpdateService() - Method in class ome.system.ServiceFactory

getUpgradeUrl() - Method in class ome.system.UpgradeCheck

getUploaderTokenURL() - Method in class ome.formats.importer.util.IniFileLoader

getUploaderUrl() - Method in class ome.formats.importer.ImportConfig

getUploaderURL() - Method in class ome.formats.importer.util.IniFileLoader

getUploadUrl() - Method in class ome.formats.importer.util.ErrorContainer

getUpperLimit() - Method in class omeis.providers.re.codomain.PlaneSlicingContext

Returns the constant level for bit-planes > planeSelected w.r.t the higher-order bits.

getUsageFraction() - Method in interface ome.api.IRepositoryInfo

This method returns a double of the used space divided by the free space.

getUsageFraction() - Method in class ome.logic.RepositoryInfoImpl

Deprecated.

getUsageFraction_async(AMD_IRepositoryInfo_getUsageFraction, Current) - Method in class ome.services.blitz.impl.RepositoryInfoI

getUsedFiles(String) - Method in class ome.formats.importer.ImportCandidates

Return string of files used by container item at path

getUsedFiles() - Method in class ome.formats.importer.ImportContainer

getUsedSpaceInKilobytes() - Method in interface ome.api.IRepositoryInfo

This method returns the total space in bytes for this file system including nested subdirectories.

getUsedSpaceInKilobytes() - Method in class ome.logic.RepositoryInfoImpl

Deprecated.

getUsedSpaceInKilobytes_async(AMD_IRepositoryInfo_getUsedSpaceInKilobytes, Current) - Method in class ome.services.blitz.impl.RepositoryInfoI

getUseMetadataFile() - Method in class ome.formats.importer.ImportContainer

Whether or not we're using an original metadata file.

getUseQuaqua() - Method in class ome.formats.importer.ImportConfig

getUseQuaqua() - Method in class ome.formats.importer.util.IniFileLoader

getUserAttribute(String) - Method in class ome.security.auth.LdapConfig

getUserDisableHistory() - Method in class ome.formats.importer.ImportConfig

getUserDisableHistory() - Method in class ome.formats.importer.util.IniFileLoader

getUserFilter() - Method in class ome.security.auth.LdapConfig

getUserFullPath() - Method in class ome.formats.importer.ImportConfig

getUserFullPath() - Method in class ome.formats.importer.util.IniFileLoader

getUserGroupId() - Method in class ome.system.Roles

getUserGroupName() - Method in class ome.system.Roles

getUserId() - Method in class ome.services.ThumbnailCtx

Retrieves the current user ID to use for queries.

getUserImages(Parameters) - Method in interface ome.api.IContainer

Retrieve a user's images.

getUserImages(Parameters) - Method in class ome.logic.PojosImpl

Implemented as specified by the IContainer I/F

getUserImages_async(AMD_IContainer_getUserImages, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI

getUserName() - Method in class pojos.ExperimenterData

Returns the last name of the experimenter.

getUserPasswordHash(Long) - Method in class ome.security.auth.PasswordUtil

getUserPixels() - Method in class ome.formats.importer.ImportContainer

getUserRoles(Experimenter) - Method in interface ome.api.local.LocalAdmin

Finds the group names for all groups for which the given Experimenter is a member.

getUserRoles(Experimenter) - Method in class ome.logic.AdminImpl

getUserRoles() - Method in interface ome.services.sessions.SessionContext

getUserRoles() - Method in class ome.services.sessions.SessionContextImpl

getUserRoles(String) - Method in interface ome.services.sessions.SessionManager

getUserRoles(String) - Method in class ome.services.sessions.SessionManagerImpl

getUserScripts_async(AMD_IScript_getUserScripts, List<IObject>, Current) - Method in class ome.services.blitz.impl.ScriptI

getUserSettingsDirectory() - Method in class ome.formats.importer.ImportConfig

getUserSettingsDirectory() - Method in class ome.formats.importer.util.IniFileLoader

getUserSpecifiedAnnotations() - Method in interface ome.formats.model.IObjectContainerStore

Returns the user specified annotations.

getUserSpecifiedAnnotations() - Method in class ome.formats.OMEROMetadataStoreClient

getUserSpecifiedImageDescription() - Method in interface ome.formats.model.IObjectContainerStore

Returns the user specified image description.

getUserSpecifiedImageDescription() - Method in class ome.formats.OMEROMetadataStoreClient

getUserSpecifiedImageName() - Method in interface ome.formats.model.IObjectContainerStore

Returns the user specified image name.

getUserSpecifiedImageName() - Method in class ome.formats.OMEROMetadataStoreClient

getUserSpecifiedPhysicalPixelSizes() - Method in interface ome.formats.model.IObjectContainerStore

Returns the user specified physical pixel sizes.

getUserSpecifiedPhysicalPixelSizes() - Method in class ome.formats.OMEROMetadataStoreClient

getUserSpecifiedPlateDescription() - Method in interface ome.formats.model.IObjectContainerStore

Returns the user specified plate description.

getUserSpecifiedPlateDescription() - Method in class ome.formats.OMEROMetadataStoreClient

getUserSpecifiedPlateName() - Method in interface ome.formats.model.IObjectContainerStore

Returns the user specified plate name.

getUserSpecifiedPlateName() - Method in class ome.formats.OMEROMetadataStoreClient

getUserSpecifiedTarget() - Method in interface ome.formats.model.IObjectContainerStore

Returns the user specified linkage target (usually a Dataset for Images and a Screen for Plates).

getUserSpecifiedTarget() - Method in class ome.formats.OMEROMetadataStoreClient

getUuid() - Method in class ome.services.db.DatabaseIdentity

getUuid() - Method in class ome.services.scripts.ScriptRepoHelper

Uuid of this repository.

getUuid() - Method in class ome.services.sessions.events.ChangeSecurityContextEvent

getValue() - Method in exception ome.formats.enums.EnumerationException

getValue() - Method in enum ome.formats.Index

getValue(Class<? extends IObject>, int) - Method in class ome.formats.OMEXMLModelComparator

Assigns a value to a particular class based on its location in the OME-XML hierarchy.

getValue() - Method in class pojos.BooleanAnnotationData

Returns the text of this annotation.

getVersion() - Method in interface ome.api.IConfig

Provides the release version.

getVersion() - Method in class ome.logic.ConfigImpl

see IConfig.getVersion()

getVersion() - Method in class pojos.DataObject

Returns the version of the object if the object is immutable, false otherwise.

getVersion_async(AMD_IConfig_getVersion, Current) - Method in class ome.services.blitz.impl.ConfigI

getVersionNote() - Method in class ome.formats.importer.util.IniFileLoader

getVersionNumber() - Method in class ome.formats.importer.ImportConfig

getVersionNumber() - Method in class ome.formats.importer.util.IniFileLoader

getVisibility() - Method in class ome.system.Preference

getVoltage() - Method in class pojos.DetectorData

Returns the voltage of the detector.

getWarmUpFactor() - Method in class ome.io.nio.SimpleBackOff

getWavelength() - Method in exception omeis.providers.re.quantum.QuantizationException

Returns the index of the wavelength that couldn't be rendered.

getWellOriginX() - Method in class pojos.PlateData

Returns the x-coordinate in 2D-space of the well.

getWellOriginY() - Method in class pojos.PlateData

Returns the y-coordinate in 2D-space of the well.

getWellSamples() - Method in class pojos.WellData

Returns the well samples linked to the well.

getWellType() - Method in class pojos.WellData

Returns a human readable identifier for the screening status e.g. empty, positive control, etc.

getWidth() - Method in class omeis.providers.re.data.RegionDef

Returns the width of the region.

getWidth() - Method in class pojos.MaskData

Returns the width of the mask.

getWidth() - Method in class pojos.RectangleData

Returns the width untransformed rectangle.

getWindowEnd() - Method in class omeis.providers.re.quantum.QuantumStrategy

Returns the upper bound of the input interval.

getWindowStart() - Method in class omeis.providers.re.quantum.QuantumStrategy

Returns the lower bound of the input interval.

getWorkingDistance() - Method in class pojos.ObjectiveData

Returns the working distance.

getX() - Method in class omeis.providers.re.data.PlaneDef

Returns the index of the plane in the set identified by this object.

getX() - Method in class omeis.providers.re.data.RegionDef

Returns the x-coordinate of the top-left corner.

getX() - Method in class pojos.EllipseData

Returns the x-coordinate of the center of the ellipse.

getX() - Method in class pojos.MaskData

Returns the x-coordinate of the top-left corner of the mask.

getX() - Method in class pojos.PointData

Returns the x-coordinate of the shape.

getX() - Method in class pojos.RectangleData

Returns the x-coordinate of the top-left corner of an untransformed rectangle.

getX() - Method in class pojos.TextData

Returns the x-coordinate text field.

getX1() - Method in class pojos.LineData

Returns the x-coordinate of the starting point of an untransformed line.

getX2() - Method in class pojos.LineData

Returns the x-coordinate of the end point of an untransformed line.

getXEnd() - Method in class omeis.providers.re.codomain.ContrastStretchingContext

Returns the x-coordinate of the pEnd point.

getXMLAnnotationCount() - Method in class ome.services.blitz.impl.OmeroMetadata

getXMLAnnotationDescription(int) - Method in class ome.services.blitz.impl.OmeroMetadata

getXMLAnnotationID(int) - Method in class ome.services.blitz.impl.OmeroMetadata

getXMLAnnotationNamespace(int) - Method in class ome.services.blitz.impl.OmeroMetadata

getXMLAnnotationValue(int) - Method in class ome.services.blitz.impl.OmeroMetadata

getXStart() - Method in class omeis.providers.re.codomain.ContrastStretchingContext

Returns the x-coordinate of the pStart point.

getY() - Method in class omeis.providers.re.data.PlaneDef

Returns the index of the plane in the set identified by this object.

getY() - Method in class omeis.providers.re.data.RegionDef

Returns the y-coordinate of the top-left corner.

getY() - Method in class pojos.EllipseData

Returns the y-coordinate of the center of the ellipse.

getY() - Method in class pojos.MaskData

Returns the y-coordinate of the top-left corner of the mask.

getY() - Method in class pojos.PointData

Returns the y coordinate of the shape.

getY() - Method in class pojos.RectangleData

Returns the y-coordinate of the top-left corner of an untransformed rectangle.

getY() - Method in class pojos.TextData

Returns the y-coordinate text field.

getY1() - Method in class pojos.LineData

Returns the y-coordinate of the starting point of an untransformed line.

getY2() - Method in class pojos.LineData

Returns the y-coordinate of the end point of an untransformed line.

getYEnd() - Method in class omeis.providers.re.codomain.ContrastStretchingContext

Returns the y-coordinate of the pEnd point.

getYStart() - Method in class omeis.providers.re.codomain.ContrastStretchingContext

Returns the y-coordinate of the pStart point.

getZ() - Method in class omeis.providers.re.data.PlaneDef

Returns the index of the plane in the set identified by this object.

getZ() - Method in class pojos.ShapeData

Returns the z-section.

getZoom() - Method in class pojos.DetectorData

Returns the offset of the detector.

getZSection() - Method in class pojos.ROICoordinate

Returns the z-section.

GlobalMulticaster - Class in ome.services.messages

Global ApplicationEventMulticaster which can be used to integrate parent and child OmeroContext instances.

GlobalMulticaster() - Constructor for class ome.services.messages.GlobalMulticaster

Keeps track of which instance this is.

granted(int, int) - Method in class omero.model.PermissionsI

GraphEntry - Class in ome.services.graphs

Single value of the map entries from spec.xml.

GraphEntry(GraphSpec, String) - Constructor for class ome.services.graphs.GraphEntry

GraphEntry(GraphSpec, String, GraphEntry) - Constructor for class ome.services.graphs.GraphEntry

GraphException - Exception in ome.services.graphs

Exception which will be thrown by activities within GraphSpec implementations.

GraphException(String) - Constructor for exception ome.services.graphs.GraphException

GraphOpts - Class in ome.services.graphs

Manager for option instances for an entire delete graph.

GraphOpts() - Constructor for class ome.services.graphs.GraphOpts

GraphOpts.Op - Enum in ome.services.graphs

GraphSpec - Interface in ome.services.graphs

Specification of a delete operation.

GraphSpecPostProcessor - Class in ome.services.graphs

post processor which should be included in all Spring context files with

GraphSpecPostProcessor() - Constructor for class ome.services.graphs.GraphSpecPostProcessor

GraphState - Class in ome.services.graphs

Tree-structure containing all scheduled deletes which closely resembles the tree structure of the GraphSpec itself.

GraphState(GraphStepFactory, SqlAction, Session, GraphSpec) - Constructor for class ome.services.graphs.GraphState

GraphStep - Class in ome.services.graphs

Single action performed by GraphState.

GraphStep(int, List<GraphStep>, GraphSpec, GraphEntry, long[]) - Constructor for class ome.services.graphs.GraphStep

GraphStep.Callback - Interface in ome.services.graphs

GraphStepFactory - Interface in ome.services.graphs

strategy interface which can be passed to GraphState to create the GraphStep instances needed.

GraphTables - Class in ome.services.graphs

algorithms for sorting and indexing the data returned by GraphSpec.queryBackupIds(Session, int, GraphEntry, QueryBuilder).

GraphTables() - Constructor for class ome.services.graphs.GraphTables

GREEN_INDEX - Static variable in class ome.formats.model.ColorsFactory

Index of the red component of a color.

GREEN_INDEX - Static variable in class omeis.providers.re.ColorsFactory

Index of the red component of a color.

GREEN_TEXT - Static variable in class ome.formats.model.ChannelProcessor

Name of the green component when it is a graphics image.

group - Variable in class ome.formats.importer.ImportConfig

group - Variable in class ome.system.Principal

GROUP_COLLAB_READ - Static variable in class ome.formats.importer.ImportEvent

GROUP_COLLAB_READ_LINK - Static variable in class ome.formats.importer.ImportEvent

GROUP_EXPERIMENTER_MAP - Static variable in class pojos.ExperimenterData

Identifies the Experimenter#GROUPEXPERIMENTERMAP field.

GROUP_EXPERIMENTER_MAP - Static variable in class pojos.GroupData

Identifies the ExperimenterGroup#GROUPEXPERIMENTERMAP field.

GROUP_PRIVATE - Static variable in class ome.formats.importer.ImportEvent

GROUP_PUBLIC - Static variable in class ome.formats.importer.ImportEvent

GROUP_SYSTEM - Static variable in class ome.formats.importer.ImportEvent

GroupAttributeMapper - Class in ome.security.auth

GroupAttributeMapper(LdapConfig) - Constructor for class ome.security.auth.GroupAttributeMapper

GroupData - Class in pojos

The data that makes up an OME Group along with the various members of the Group

GroupData() - Constructor for class pojos.GroupData

Creates a new instance.

GroupData(ExperimenterGroup) - Constructor for class pojos.GroupData

Creates a new instance.

groupName - Variable in class ome.formats.importer.ImportEvent.GROUP_SET

groupPermissions - Variable in class ome.system.SimpleEventContext

groupProxy(Long) - Method in interface ome.api.local.LocalAdmin

returns a possibly uninitialized proxy for the given group id.

groupProxy(String) - Method in interface ome.api.local.LocalAdmin

returns a possibly uninitialized proxy for the given group name.

groupProxy(Long) - Method in class ome.logic.AdminImpl

groupProxy(String) - Method in class ome.logic.AdminImpl

groups(String, LdapConfig, LdapOperations, RoleProvider, AttributeSet) - Method in class ome.security.auth.AttributeNewUserGroupBean

groups(String, LdapConfig, LdapOperations, RoleProvider, AttributeSet) - Method in interface ome.security.auth.NewUserGroupBean

groups(String, LdapConfig, LdapOperations, RoleProvider, AttributeSet) - Method in class ome.security.auth.QueryNewUserGroupBean

groupType - Variable in class ome.formats.importer.ImportEvent.GROUP_SET

grp(RLong) - Method in class omero.sys.ParametersI

Sets the value of the group parameter.

GUEST - Static variable in class ome.system.Login

CopyOfLogin constant which has username and password values set to null and other values set to their default.

GUEST - Static variable in class pojos.GroupData

Identifies the Guest group.

guests - Variable in class ome.services.sharing.data.ShareData

guests - Variable in class ome.services.sharing.data.ShareItem

H

handle(IObject) - Method in interface ome.formats.model.handler.ModelObjectHandler

Attempt to handle the model object of this type.

Handle - Class in ome.util.mem

Provides the basic machinery to share the same logical state across objects with different identities.

Handle(Copiable) - Constructor for class ome.util.mem.Handle

Subclasses use this constructor to specify the Body instance this handle will be paired up with.

handle - Variable in class omero.grid.DeleteCallbackI

Proxy passed to this instance on creation.

handle(int, int) - Method in interface omero.model.SmartShape.PointCallback

handleAnnotated(IAnnotated, Document, LuceneOptions) - Method in class ome.services.fulltext.bridges.TablesBridge

Responsible for iterating over any attached OMERO.tables and registering all appropriate row objects for later processing.

handleAnnotation(Annotation, TablesBridge.RowProcessor) - Method in class ome.services.fulltext.bridges.TablesBridge

Detects if the given annotation contains an OMERO.table and if so, passes it off for further processing.

handleContextRefreshedEvent(ContextRefreshedEvent) - Method in class ome.services.blitz.util.CheckAllJobs

handleContextRefreshedEvent(ContextRefreshedEvent) - Method in class ome.services.util.NamespaceCheck

handleContextRefreshedEvent(ContextRefreshedEvent) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl

Listener method which waits for a ContextRefreshedEvent and then extracts the SessionFactory from the ApplicationContext and pases it to ExtendedMetadata.Impl.setSessionFactory(SessionFactory).

handleContextRefreshedEvent(ContextRefreshedEvent) - Method in class ome.tools.spring.OnContextRefreshedEventListener

handleException(Throwable, String) - Static method in class ome.services.blitz.gateway.services.util.ServiceUtilities

Helper method to handle exceptions thrown by the connection library.

handleException(Throwable) - Method in class ome.services.blitz.impl.ServiceFactoryI

handleException(Throwable, OmeroContext) - Method in class omero.util.IceMapper

handleFile(File, int, Collection) - Method in class ome.formats.importer.ImportCandidates

Handle a file import

handleHdf5(String, TablesBridge.RowProcessor) - Method in class ome.services.fulltext.bridges.TablesBridge

Process a single OMERO.tables file.

handleImage(Image, Document, LuceneOptions) - Method in class ome.services.fulltext.bridges.TablesBridge

Processes any annotations attached to the following types which contain this image: Plate, Dataset

handleInput(Class<?>, Object) - Method in class omero.util.IceMapper

handleLsid(IObject) - Method in class ome.services.blitz.impl.OmeroMetadata

handleMissingPyramid(Pixels, String) - Method in class ome.io.nio.PixelsService

If the outer loop should continue, this method returns successfully; otherwise it throws a MissingPyramidException.

handleOutput(Class, Object) - Method in class omero.util.IceMapper

handleRingShutdown(Redirector.Context, String) - Method in class ome.services.blitz.redirect.ConfigRedirector

handleRingShutdown(Redirector.Context, String) - Method in class ome.services.blitz.redirect.NullRedirector

Does nothing.

handleRingShutdown(Redirector.Context, String) - Method in interface ome.services.blitz.redirect.Redirector

Gives the Redirector a chance to remove the current Ring when it is being shutdown.

handleRingShutdown(Redirector.Context, String) - Method in class ome.services.blitz.redirect.ScaleRedirector

Nothing needs to be done on shutdown, since the Ring implementation will properly disable the Node table queried during the next call to Redirector.getProxyOrNull(Context, String, Glacier2.SessionControlPrx, Ice.Current)

HardWiredInterceptor - Class in ome.logic

Extension point for interceptors which should be compiled in from third-party code.

HardWiredInterceptor() - Constructor for class ome.logic.HardWiredInterceptor

hasAlias(String) - Method in class ome.system.Preference

hasDectector() - Method in class pojos.ChannelAcquisitionData

Returns true if there is a detector for that channel, false otherwise.

hasEmissionData(ChannelData) - Static method in class ome.formats.model.ColorsFactory

Returns true if the channel has emission metadata, false otherwise.

hasEmissionData(LogicalChannel) - Static method in class omeis.providers.re.ColorsFactory

Returns true if the channel has emission metadata, false otherwise.

hasFilter() - Method in class pojos.ChannelAcquisitionData

Returns true if there is a filter set linked to the channel false otherwise.

hash - Variable in class ome.security.auth.ConfigurablePasswordProvider

Hash implementation to use for encoding passwords to check and changed passwords.

hashCode() - Method in class ome.tools.FileSystem

Public hashcode implementation based on String hash() return

hashCode(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType

hashCode() - Method in class ome.util.math.geom2D.Line

Overridden to reflect equality of abstract values (data object) as opposite to object identity.

hashCode() - Method in class ome.util.math.geom2D.PlanePoint

Overridden to reflect equality of abstract values (data object) as opposite to object identity.

hashCode() - Method in class ome.util.math.geom2D.Segment

Overridden to reflect equality of abstract values (data object) as opposite to object identity.

hashCode() - Method in class omeis.providers.re.data.PlaneDef

Overridden to reflect equality of abstract values (data object) as opposite to object identity.

hashCode() - Method in class pojos.ROICoordinate

Calculate the hashCode for the data, The hashcode is generated by bitshifting z by ZTBITSPLIT bits and adding t.

hasIris() - Method in class pojos.ObjectiveData

Returns a boolean flag if the value has been set, null otherwise.

hasLightPath() - Method in class pojos.ChannelAcquisitionData

Returns true if there is a light path described for that channel, false otherwise.

hasMetadata(long) - Method in class ome.services.ThumbnailCtx

Whether or not thumbnail metadata is available for a given Pixels ID.

hasNext() - Method in interface ome.api.Search

Returns true if another call to Search.next() is valid.

hasNext() - Method in class ome.services.eventlogs.EventLogLoader

Tests for available objects.

hasNext() - Method in class ome.services.graphs.BaseGraphSpec.SubSpecIterator

hasNext() - Method in class ome.services.SearchBean

hasNext_async(AMD_Search_hasNext, Current) - Method in class ome.services.blitz.impl.SearchI

hasntSeen(Object) - Method in class omero.util.IceMapper

hasOpticalAxisAveraged() - Method in class pojos.OTFData

Returns a boolean flag if the value has been set

hasPassword(MethodInvocation) - Method in class ome.logic.HardWiredInterceptor

hasPassword(String) - Method in class ome.security.auth.ConfigurablePasswordProvider

Always returns false, override with specific logic.

hasPassword(String) - Method in class ome.security.auth.FilePasswordProvider

hasPassword(String) - Method in class ome.security.auth.JdbcPasswordProvider

hasPassword(String) - Method in class ome.security.auth.LdapPasswordProvider

Only returns if the user is already in the database and has a DN value in the password table.

hasPassword(String) - Method in interface ome.security.auth.PasswordProvider

Returns true if this provider considers itself responsible for the given user name.

hasPassword(String) - Method in class ome.security.auth.PasswordProviders

hasPassword(String) - Method in class ome.security.auth.providers.LdapPasswordProvider431

Only returns if the user is already in the database and has a DN value in the password table.

hasPrivilegedToken(IObject) - Method in class ome.security.basic.BasicSecuritySystem

See {@link TokenHolder#hasPrivilegedToken(IObject)

hasPrivilegedToken(IObject) - Method in class ome.security.basic.TokenHolder

hasPrivilegedToken(IObject) - Method in interface ome.security.SecuritySystem

checks that the IObject argument has been granted a Token by the SecuritySystem.

hasPrivilegedToken(IObject) - Method in class ome.security.SecuritySystemHolder

hasPrivilegedToken(IObject) - Method in class ome.security.sharing.SharingSecuritySystem

hasPump() - Method in class pojos.LightSourceData

Returns true if the light source is a laser with a pump, false otherwise.

hasReference(LSID, LSID) - Method in interface ome.formats.model.IObjectContainerStore

Checks to see if there is currently an active reference for two LSIDs.

hasReference(LSID, LSID) - Method in class ome.formats.OMEROMetadataStoreClient

hasReplacement(Object) - Method in class ome.tools.hibernate.UpdateFilter

hasSavepoint() - Method in class ome.services.graphs.GraphStep

hasSession() - Method in class ome.system.SessionInitializer

hasSettings(long) - Method in class ome.services.ThumbnailCtx

Whether or not settings are available for a given Pixels ID.

hasShapes - Variable in class ome.services.roi.GeomTool

hasSubtypes(int) - Method in class ome.tools.hibernate.ExtendedMetadata.Locks

returns true if this offset points to a field which is an embedded component.

help(String[]) - Static method in class prefs

Returns a help string array.

helper - Variable in class ome.services.blitz.impl.ScriptI

Helper - Class in ome.services.blitz.measurements

Parallel type hierarchy to Column to facilitate (and speed-up) working with columns without adding methods to the slice definitions.

Helper() - Constructor for class ome.services.blitz.measurements.Helper

HibernateUtils - Class in ome.tools.hibernate

contains methods for reloading unloaded entities and nulled collections as well as determining the index of certain properties in a dehydrated Hiberante array.

HibernateUtils() - Constructor for class ome.tools.hibernate.HibernateUtils

Hidden - Annotation Type in ome.annotations

annotation which specifies that a method parameter (e.g. a password) must be hidden from logging output.

Hierarchy - Class in ome.services.query

single-point of entry for walking of OME container hierarchies.

Hierarchy() - Constructor for class ome.services.query.Hierarchy

HierarchyTransformations - Class in ome.tools

HierarchyTransformations() - Constructor for class ome.tools.HierarchyTransformations

hints - Variable in class ome.services.SVGRasterizer

The transcoder hints.

hostname - Variable in class ome.formats.importer.ImportConfig

HqlQuery - Class in ome.services.search

Delegate to IQuery.findAllByQuery(String, Parameters).

HqlQuery(SearchValues, String, Parameters) - Constructor for class ome.services.search.HqlQuery

HTM - Static variable in class pojos.FileAnnotationData

Identifies the HTM file formats.

HTML - Static variable in class pojos.FileAnnotationData

Identifies the HTML file formats.

HtmlMessenger - Class in ome.formats.importer.util

This class allows you to submit a URL and a String hash map of key-value pairs to be posted to the URL in question.

HtmlMessenger(String, List<Part>) - Constructor for class ome.formats.importer.util.HtmlMessenger

Instantiate html messenger

HtmlMessengerException - Exception in ome.formats.importer.util

HtmlMessengerException(String, Exception) - Constructor for exception ome.formats.importer.util.HtmlMessengerException

I

IAdmin - Interface in ome.api

Administration interface providing access to admin-only functionality as well as JMX-based server access and selected user functions.

IAnalysis - Interface in ome.api

Provides access to the model objects involved in analysis.

ic - Variable in class ome.services.sharing.ShareStore

ice_factory() - Static method in class ome.services.sharing.data.Obj

ice_factory() - Static method in class ome.services.sharing.data.ShareData

ice_factory() - Static method in class ome.services.sharing.data.ShareItem

ice_id() - Method in class ome.services.sharing.data.Obj

ice_id(Current) - Method in class ome.services.sharing.data.Obj

ice_id() - Method in class ome.services.sharing.data.ShareData

ice_id(Current) - Method in class ome.services.sharing.data.ShareData

ice_id() - Method in class ome.services.sharing.data.ShareItem

ice_id(Current) - Method in class ome.services.sharing.data.ShareItem

ice_ids() - Method in class ome.services.sharing.data.Obj

ice_ids(Current) - Method in class ome.services.sharing.data.Obj

ice_ids() - Method in class ome.services.sharing.data.ShareData

ice_ids(Current) - Method in class ome.services.sharing.data.ShareData

ice_ids() - Method in class ome.services.sharing.data.ShareItem

ice_ids(Current) - Method in class ome.services.sharing.data.ShareItem

ice_isA(String) - Method in class ome.services.sharing.data.Obj

ice_isA(String, Current) - Method in class ome.services.sharing.data.Obj

ice_isA(String) - Method in class ome.services.sharing.data.ShareData

ice_isA(String, Current) - Method in class ome.services.sharing.data.ShareData

ice_isA(String) - Method in class ome.services.sharing.data.ShareItem

ice_isA(String, Current) - Method in class ome.services.sharing.data.ShareItem

ice_staticId() - Static method in class ome.services.sharing.data.Obj

ice_staticId() - Static method in class ome.services.sharing.data.ShareData

ice_staticId() - Static method in class ome.services.sharing.data.ShareItem

IceMapper - Class in omero.util

Responsible for the mapping of ome.* types to omero.* types and back again.

IceMapper() - Constructor for class omero.util.IceMapper

IceMapper(IceMapper.ReturnMapping) - Constructor for class omero.util.IceMapper

IceMapper.ReturnMapping - Interface in omero.util

IceMethodInvoker - Class in ome.services.blitz.util

Method-cache primed either with an ServiceInterface instance or with a Class with generic type ServiceInterface.

IceMethodInvoker(ServiceInterface, OmeroContext) - Constructor for class ome.services.blitz.util.IceMethodInvoker

Create an IceMethodInvoker instance using the Class of the passed argument to call IceMethodInvoker#IceMethodInvoker(Class).

IceMethodInvoker(Class<S>, OmeroContext) - Constructor for class ome.services.blitz.util.IceMethodInvoker

Creates an IceMethodInvoker instance by using reflection on the Class argument.

IConfig - Interface in ome.api

Access to server configuration.

IContainer - Interface in ome.api

Provides methods for dealing with the core "Pojos" of OME.

id - Variable in class ome.services.graphs.BaseGraphSpec

The id of the root type which will be deleted.

id - Variable in class ome.services.graphs.GraphStep

The actual id to be deleted as opposed to GraphEntry.getId() which is the id of the root object.

id - Variable in class ome.services.sharing.data.Obj

id - Variable in class ome.services.sharing.data.ShareData

id - Variable in class ome.services.sharing.data.ShareItem

idCount(long) - Method in class ome.services.sharing.data.ShareMap

IDelete - Interface in ome.api

Provides simplifed methods for deleting instances from the database.

IdentityMapContext - Class in omeis.providers.re.codomain

An empty context for the identity map.

IdentityMapContext() - Constructor for class omeis.providers.re.codomain.IdentityMapContext

idEqual(IObject, IObject) - Static method in class ome.tools.hibernate.HibernateUtils

returns true under the following circumstatnces: both arguments are null, or both arguments are identical (==), or both arguments have the same id value(equals)

IdMapHelper - Class in ome.services.sharing.data

IdMapHelper() - Constructor for class ome.services.sharing.data.IdMapHelper

IdMapHolder - Class in ome.services.sharing.data

IdMapHolder() - Constructor for class ome.services.sharing.data.IdMapHolder

IdMapHolder(Map<String, List<Long>>) - Constructor for class ome.services.sharing.data.IdMapHolder

idOnly - Variable in class ome.services.search.SearchValues

ids(Criteria) - Method in class ome.services.search.SearchAction

ids(QueryBuilder, String) - Method in class ome.services.search.SearchAction

idsInDb() - Method in class ome.services.scripts.ScriptRepoHelper

idsInDb(SqlAction) - Method in class ome.services.scripts.ScriptRepoHelper

idToUuid(long) - Method in class ome.services.sharing.ShareBean

idx - Variable in class ome.services.graphs.GraphStep

Location of this step in GraphState.steps.

IFD_TAG_PLANE_NUMBER - Static variable in class ome.io.bioformats.OmeroPixelsPyramidWriter

TIFF tag we're using to store the Bio-Formats plane number.

IFD_TAG_SERIES - Static variable in class ome.io.bioformats.OmeroPixelsPyramidWriter

TIFF tag we're using to store the Bio-Formats series.

ignoreUnknown - Variable in class ome.security.auth.ConfigurablePasswordProvider

If true, this implementation should return a null on #checkPassword(String, String) if the user is unknown, otherwise a Boolean.FALSE.

ILdap - Interface in ome.api

Administration interface providing access to admin-only functionality as well as JMX-based server access and selected user functions.

IllegalArgumentException - Exception in omero

IllegalArgumentException(String) - Constructor for exception omero.IllegalArgumentException

IMAGE - Static variable in class pojos.PixelsData

Identifies the Pixels#IMAGE field.

IMAGE_DESCRIPTION - Static variable in class ome.io.bioformats.OmeroPixelsPyramidWriter

Current TIFF image comment for OMERO pixels pyramid TIFFs.

IMAGE_LINKS - Static variable in class pojos.DatasetData

Identifies the Dataset#IMAGELINKS field.

IMAGE_QUERY - Static variable in class ome.services.delete.DeleteBean

Loads an Image graph including: Pixels, Channel, LogicalChannel, StatsInfo, PlaneInfo, Thumbnails, file maps, OriginalFiles, and Settings

ImageAcquisitionData - Class in pojos

Object hosting the acquisition metadata.

ImageAcquisitionData(Image) - Constructor for class pojos.ImageAcquisitionData

Creates a new instance.

imageCount - Variable in class ome.formats.importer.ImportSize

ImageData - Class in pojos

The data that makes up an OME Image along with links to its Pixels, enclosing Datasets, and the Experimenter that owns this Image.

ImageData() - Constructor for class pojos.ImageData

Creates a new instance.

ImageData(Image) - Constructor for class pojos.ImageData

Creates a new instance.

imageDescription - Variable in class ome.formats.importer.ImportConfig

imageName - Variable in class ome.formats.importer.ImportConfig

ImageNameMetadataStore - Class in ome.formats

Stores all Image names consumed by the interface.

ImageNameMetadataStore() - Constructor for class ome.formats.ImageNameMetadataStore

ImageService - Interface in ome.services.blitz.gateway.services

ImageServiceImpl - Class in ome.services.blitz.gateway.services.impl

ImageServiceImpl(GatewayFactory) - Constructor for class ome.services.blitz.gateway.services.impl.ImageServiceImpl

Instantiate the imageService with the serviceFactory.

IMetadata - Interface in ome.api

Provides method to interact with acquisition metadata and annotations.

img - Variable in class ome.services.SVGRasterizer

The image that represents the SVG document.

ImportableFiles - Class in ome.services.blitz.repo

A helper class used to obtain the import candidates

ImportCandidates - Class in ome.formats.importer

Utility class which given any File object will determine the correct number and members of a given import.

ImportCandidates(OMEROWrapper, String[], IObserver) - Constructor for class ome.formats.importer.ImportCandidates

Calls ImportCandidates.ImportCandidates(int, OMEROWrapper, String[], IObserver) with ImportCandidates.DEPTH as the first argument.

ImportCandidates(int, OMEROWrapper, String[], IObserver) - Constructor for class ome.formats.importer.ImportCandidates

Main constructor which iterates over all the paths calling DirectoryWalker.walk(File, Collection) and permitting a descent to the given depth.

importCandidates(ImportConfig, ImportCandidates) - Method in class ome.formats.importer.ImportLibrary

Primary user method for importing a number

ImportCandidates.CANCEL - Exception in ome.formats.importer

Marker exception raised if the ImportCandidates.SCANNING.cancel() method is called by an IObserver instance.

ImportCandidates.CANCEL() - Constructor for exception ome.formats.importer.ImportCandidates.CANCEL

ImportCandidates.SCANNING - Class in ome.formats.importer

Event raised during a pass through the directory structure given to ImportCandidates.

ImportCandidates.SCANNING(File, int, int, int) - Constructor for class ome.formats.importer.ImportCandidates.SCANNING

ImportConfig - Class in ome.formats.importer

Utility class which configures the Import.

ImportConfig() - Constructor for class ome.formats.importer.ImportConfig

Simplest constructor which use calls ImportConfig.ImportConfig(File) with null.

ImportConfig(File) - Constructor for class ome.formats.importer.ImportConfig

Calls ImportConfig#ImportConfig(Preferences, PreferenceContext, IniFileLoader, Properties) with user preferences, a local PreferenceContext, an IniFileLoader initialized with the given argument, and System.getProperties().

ImportConfig(Preferences, IniFileLoader, Properties) - Constructor for class ome.formats.importer.ImportConfig

Complete constructor.

ImportConfig.AnnotationListValue - Class in ome.formats.importer

ImportConfig.AnnotationListValue(String, ImportConfig, List<Annotation>) - Constructor for class ome.formats.importer.ImportConfig.AnnotationListValue

ImportConfig.BoolValue - Class in ome.formats.importer

ImportConfig.BoolValue(String, ImportConfig, boolean) - Constructor for class ome.formats.importer.ImportConfig.BoolValue

ImportConfig.DoubleArrayValue - Class in ome.formats.importer

ImportConfig.DoubleArrayValue(String, ImportConfig, Double[]) - Constructor for class ome.formats.importer.ImportConfig.DoubleArrayValue

ImportConfig.FileValue - Class in ome.formats.importer

ImportConfig.FileValue(String, ImportConfig) - Constructor for class ome.formats.importer.ImportConfig.FileValue

ImportConfig.IntValue - Class in ome.formats.importer

ImportConfig.IntValue(String, ImportConfig, int) - Constructor for class ome.formats.importer.ImportConfig.IntValue

ImportConfig.IntValue(String, ImportConfig, int, String) - Constructor for class ome.formats.importer.ImportConfig.IntValue

ImportConfig.LongValue - Class in ome.formats.importer

ImportConfig.LongValue(String, ImportConfig, long) - Constructor for class ome.formats.importer.ImportConfig.LongValue

ImportConfig.PassValue - Class in ome.formats.importer

ImportConfig.PassValue(String, ImportConfig) - Constructor for class ome.formats.importer.ImportConfig.PassValue

ImportConfig.StrValue - Class in ome.formats.importer

ImportConfig.StrValue(String, ImportConfig) - Constructor for class ome.formats.importer.ImportConfig.StrValue

ImportConfig.StrValue(String, ImportConfig, String) - Constructor for class ome.formats.importer.ImportConfig.StrValue

ImportConfig.StrValue(String, ImportConfig, String, String) - Constructor for class ome.formats.importer.ImportConfig.StrValue

ImportConfig.Value<T> - Class in ome.formats.importer

Container which thread-safely makes a generic configuration value available, without requiring getters and setters.

ImportContainer - Class in ome.formats.importer

ImportContainer(File, Long, IObject, Boolean, Double[], String, String[], Boolean) - Constructor for class ome.formats.importer.ImportContainer

importData(Long, String, int, ImportSize) - Method in class ome.formats.importer.ImportLibrary

saves the binary data to the server.

ImportEvent - Class in ome.formats.importer

Simple event base-class used by IObservable and IObserver implementations.

ImportEvent() - Constructor for class ome.formats.importer.ImportEvent

ImportEvent.ADD - Class in ome.formats.importer

ImportEvent.ADD() - Constructor for class ome.formats.importer.ImportEvent.ADD

ImportEvent.BEGIN_POST_PROCESS - Class in ome.formats.importer

ImportEvent.BEGIN_POST_PROCESS(int, String, IObject, Long, int, ImportSize) - Constructor for class ome.formats.importer.ImportEvent.BEGIN_POST_PROCESS

ImportEvent.BEGIN_SAVE_TO_DB - Class in ome.formats.importer

ImportEvent.BEGIN_SAVE_TO_DB(int, String, IObject, Long, int, ImportSize) - Constructor for class ome.formats.importer.ImportEvent.BEGIN_SAVE_TO_DB

ImportEvent.COUNT_EVENT - Class in ome.formats.importer

ImportEvent.DATA_STORED - Class in ome.formats.importer

ImportEvent.DATA_STORED(int, String, IObject, Long, int, ImportSize) - Constructor for class ome.formats.importer.ImportEvent.DATA_STORED

ImportEvent.DATASET_STORED - Class in ome.formats.importer

ImportEvent.DATASET_STORED(int, String, IObject, Long, int, ImportSize, Integer, Integer) - Constructor for class ome.formats.importer.ImportEvent.DATASET_STORED

ImportEvent.DEBUG_SEND - Class in ome.formats.importer

ImportEvent.DEBUG_SEND(boolean, boolean) - Constructor for class ome.formats.importer.ImportEvent.DEBUG_SEND

ImportEvent.END_POST_PROCESS - Class in ome.formats.importer

ImportEvent.END_POST_PROCESS(int, String, IObject, Long, int, ImportSize) - Constructor for class ome.formats.importer.ImportEvent.END_POST_PROCESS

ImportEvent.END_SAVE_TO_DB - Class in ome.formats.importer

ImportEvent.END_SAVE_TO_DB(int, String, IObject, Long, int, ImportSize) - Constructor for class ome.formats.importer.ImportEvent.END_SAVE_TO_DB

ImportEvent.ERRORS_CLEARED - Class in ome.formats.importer

ImportEvent.ERRORS_CLEARED(int) - Constructor for class ome.formats.importer.ImportEvent.ERRORS_CLEARED

ImportEvent.ERRORS_COMPLETE - Class in ome.formats.importer

ImportEvent.ERRORS_COMPLETE() - Constructor for class ome.formats.importer.ImportEvent.ERRORS_COMPLETE

ImportEvent.ERRORS_FAILED - Class in ome.formats.importer

ImportEvent.ERRORS_FAILED() - Constructor for class ome.formats.importer.ImportEvent.ERRORS_FAILED

ImportEvent.ERRORS_PENDING - Class in ome.formats.importer

ImportEvent.ERRORS_PENDING() - Constructor for class ome.formats.importer.ImportEvent.ERRORS_PENDING

ImportEvent.ERRORS_SEND - Class in ome.formats.importer

ImportEvent.ERRORS_SEND() - Constructor for class ome.formats.importer.ImportEvent.ERRORS_SEND

ImportEvent.ERRORS_UPLOAD_CANCELLED - Class in ome.formats.importer

ImportEvent.ERRORS_UPLOAD_CANCELLED() - Constructor for class ome.formats.importer.ImportEvent.ERRORS_UPLOAD_CANCELLED

ImportEvent.FILE_SIZE_STEP - Class in ome.formats.importer

ImportEvent.FILE_SIZE_STEP(long, long) - Constructor for class ome.formats.importer.ImportEvent.FILE_SIZE_STEP

ImportEvent.FILE_UPLOAD_BYTES - Class in ome.formats.importer

ImportEvent.FILE_UPLOAD_BYTES(String, int, int, Long, Long, Exception) - Constructor for class ome.formats.importer.ImportEvent.FILE_UPLOAD_BYTES

ImportEvent.FILE_UPLOAD_CANCELLED - Class in ome.formats.importer

ImportEvent.FILE_UPLOAD_CANCELLED(String, int, int, Long, Long, Exception) - Constructor for class ome.formats.importer.ImportEvent.FILE_UPLOAD_CANCELLED

ImportEvent.FILE_UPLOAD_COMPLETE - Class in ome.formats.importer

ImportEvent.FILE_UPLOAD_COMPLETE(String, int, int, Long, Long, Exception) - Constructor for class ome.formats.importer.ImportEvent.FILE_UPLOAD_COMPLETE

ImportEvent.FILE_UPLOAD_ERROR - Class in ome.formats.importer

ImportEvent.FILE_UPLOAD_ERROR(String, int, int, Long, Long, Exception) - Constructor for class ome.formats.importer.ImportEvent.FILE_UPLOAD_ERROR

ImportEvent.FILE_UPLOAD_EVENT - Class in ome.formats.importer

ImportEvent.FILE_UPLOAD_FAILED - Class in ome.formats.importer

ImportEvent.FILE_UPLOAD_FAILED(String, int, int, Long, Long, Exception) - Constructor for class ome.formats.importer.ImportEvent.FILE_UPLOAD_FAILED

ImportEvent.FILE_UPLOAD_FINISHED - Class in ome.formats.importer

ImportEvent.FILE_UPLOAD_FINISHED(String, int, int, Long, Long, Exception) - Constructor for class ome.formats.importer.ImportEvent.FILE_UPLOAD_FINISHED

ImportEvent.FILE_UPLOAD_STARTED - Class in ome.formats.importer

ImportEvent.FILE_UPLOAD_STARTED(String, int, int, Long, Long, Exception) - Constructor for class ome.formats.importer.ImportEvent.FILE_UPLOAD_STARTED

ImportEvent.GROUP_SET - Class in ome.formats.importer

ImportEvent.GROUP_SET(String, int) - Constructor for class ome.formats.importer.ImportEvent.GROUP_SET

ImportEvent.IMPORT_ARCHIVING - Class in ome.formats.importer

ImportEvent.IMPORT_ARCHIVING(int, String, IObject, Long, int, ImportSize) - Constructor for class ome.formats.importer.ImportEvent.IMPORT_ARCHIVING

ImportEvent.IMPORT_DONE - Class in ome.formats.importer

ImportEvent.IMPORT_DONE(int, String, IObject, Long, int, ImportSize, List<Pixels>) - Constructor for class ome.formats.importer.ImportEvent.IMPORT_DONE

ImportEvent.IMPORT_OVERLAYS - Class in ome.formats.importer

ImportEvent.IMPORT_OVERLAYS(int, String, IObject, Long, int, ImportSize) - Constructor for class ome.formats.importer.ImportEvent.IMPORT_OVERLAYS

ImportEvent.IMPORT_PROCESSING - Class in ome.formats.importer

ImportEvent.IMPORT_PROCESSING(int, String, IObject, Long, int, ImportSize) - Constructor for class ome.formats.importer.ImportEvent.IMPORT_PROCESSING

ImportEvent.IMPORT_QUEUE_DONE - Class in ome.formats.importer

ImportEvent.IMPORT_QUEUE_DONE() - Constructor for class ome.formats.importer.ImportEvent.IMPORT_QUEUE_DONE

ImportEvent.IMPORT_QUEUE_STARTED - Class in ome.formats.importer

ImportEvent.IMPORT_QUEUE_STARTED() - Constructor for class ome.formats.importer.ImportEvent.IMPORT_QUEUE_STARTED

ImportEvent.IMPORT_STEP - Class in ome.formats.importer

ImportEvent.IMPORT_STEP(int, int, int) - Constructor for class ome.formats.importer.ImportEvent.IMPORT_STEP

ImportEvent.LOADED_IMAGE - Class in ome.formats.importer

ImportEvent.LOADED_IMAGE(String, Integer, Integer, Integer) - Constructor for class ome.formats.importer.ImportEvent.LOADED_IMAGE

ImportEvent.LOADING_IMAGE - Class in ome.formats.importer

ImportEvent.LOADING_IMAGE(String, Integer, Integer, Integer) - Constructor for class ome.formats.importer.ImportEvent.LOADING_IMAGE

ImportEvent.LOGGED_IN - Class in ome.formats.importer

ImportEvent.LOGGED_IN() - Constructor for class ome.formats.importer.ImportEvent.LOGGED_IN

ImportEvent.LOGGED_OUT - Class in ome.formats.importer

ImportEvent.LOGGED_OUT() - Constructor for class ome.formats.importer.ImportEvent.LOGGED_OUT

ImportEvent.PROGRESS_EVENT - Class in ome.formats.importer

ImportEvent.QUICKBAR_UPDATE - Class in ome.formats.importer

ImportEvent.QUICKBAR_UPDATE() - Constructor for class ome.formats.importer.ImportEvent.QUICKBAR_UPDATE

ImportEvent.REIMPORT - Class in ome.formats.importer

ImportEvent.REIMPORT() - Constructor for class ome.formats.importer.ImportEvent.REIMPORT

importFile(File, String, Map<Integer, Image>) - Method in class ome.services.blitz.repo.PublicRepositoryI

importFileSet(OriginalFile, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI

Import an image set's metadata.

ImportFixture - Class in ome.formats.importer

test fixture for importing files without a GUI.

ImportFixture(OMEROMetadataStoreClient, OMEROWrapper) - Constructor for class ome.formats.importer.ImportFixture

importImage(ImportContainer, int, int, int) - Method in class ome.formats.importer.ImportLibrary

Perform an image import.

ImportLibrary - Class in ome.formats.importer

support class for the proper usage of OMEROMetadataStoreClient and FormatReader instances.

ImportLibrary(OMEROMetadataStoreClient, OMEROWrapper) - Constructor for class ome.formats.importer.ImportLibrary

The library will not close the client instance.

ImportProcessor - Class in ome.services.procs

ImportProcessor() - Constructor for class ome.services.procs.ImportProcessor

ImportSize - Class in ome.formats.importer

Calculates the various dimensions of an image from a Pixels instance.

ImportSize(String, Pixels, String) - Constructor for class ome.formats.importer.ImportSize

in(PixelsType, String[]) - Static method in class omeis.providers.re.data.PlaneFactory

A static helper method to check if a type is one of the elements in an array.

include(int) - Method in class ome.tools.hibernate.ExtendedMetadata.Locks

returns true if this offset points to a field which may contain an IObject instance

increment() - Method in class ome.services.sessions.SessionContext.Count

Increment the current reference count and return the new value atomically.

increment(int) - Method in class ome.services.sessions.stats.LongCounter

index - Variable in class ome.formats.importer.ImportEvent.COUNT_EVENT

index - Variable in class ome.formats.importer.ImportEvent.ERRORS_CLEARED

index - Variable in class ome.formats.importer.ImportEvent.PROGRESS_EVENT

Index - Enum in ome.formats

index(String, String[]) - Static method in class ome.tools.hibernate.HibernateUtils

indexAllEvents() - Static method in class ome.services.fulltext.Main

indexByClass(Set<String>) - Static method in class ome.services.fulltext.Main

indexer - Variable in class ome.services.fulltext.FullTextThread

indexFullDb() - Static method in class ome.services.fulltext.Main

indexObject(IObject) - Method in interface ome.api.IUpdate

Initiates full-text indexing for the given object.

indexObject(IObject) - Method in class ome.logic.UpdateImpl

indexObject_async(AMD_IUpdate_indexObject, IObject, Current) - Method in class ome.services.blitz.impl.UpdateI

IniFileLoader - Class in ome.formats.importer.util

This class loads in the default importer.ini file (or one specified from the command line when starting the app)

IniFileLoader(File) - Constructor for class ome.formats.importer.util.IniFileLoader

Load given file

init(ObjectAdapter, String) - Method in class ome.services.blitz.fire.Ring

Typically called from within BlitzConfiguration after the communicator and adapter have been properly setup.

init(String) - Method in class ome.services.blitz.repo.FileMaker

init() - Static method in class ome.services.fulltext.Main

init() - Method in class ome.services.sessions.SessionManagerImpl

Initialization method called by the Spring run-time to acquire an initial Session.

init() - Method in class ome.services.sharing.ShareStore

Calls ShareStore.doInit() within a transaction with a session available to all HibernateTemplate callbacks.

initFile(String) - Method in class ome.io.bioformats.OmeroPixelsPyramidReader

initFile(String) - Method in class ome.services.formats.OmeroReader

INITIAL_DELAY - Static variable in class ome.logic.RepositoryInfoImpl

Time (2 minutes) between successive calls to RepositoryInfoImpl.sanityCheckRepository() needed to trigger an actual call to RepositoryInfoImpl.getUsageFraction()

initialize(Object) - Method in interface ome.api.local.LocalQuery

Uses the Hibernate static method initialize to prepare an object for shipping over the wire.

initialize(ServiceFactoryPrx) - Method in class ome.formats.OMEROMetadataStoreClient

Initializes the MetadataStore with an already logged in, ready to go service factory.

initialize(client) - Method in class ome.formats.OMEROMetadataStoreClient

Initializes the MetadataStore with an already logged in, ready to go service factory.

initialize(String, String, String, int) - Method in class ome.formats.OMEROMetadataStoreClient

Initializes the MetadataStore taking string parameters to feed to the OMERO Blitz client object.

initialize(String, String, String, int, boolean) - Method in class ome.formats.OMEROMetadataStoreClient

Initializes the MetadataStore taking string parameters to feed to the OMERO Blitz client object.

initialize(String, String, String, int, long, boolean) - Method in class ome.formats.OMEROMetadataStoreClient

Initializes the MetadataStore taking string parameters to feed to the OMERO Blitz client object.

initialize(String, int, String) - Method in class ome.formats.OMEROMetadataStoreClient

Initializes the MetadataStore by joining an existing session.

initialize(String, int, String, boolean) - Method in class ome.formats.OMEROMetadataStoreClient

Initializes the MetadataStore by joining an existing session.

initialize(ServiceFactoryPrx, List<Pixels>, List<Long>) - Method in class ome.formats.OverlayMetadataStore

Initializes the metadata store implementation.

initialize(Object) - Method in class ome.logic.QueryImpl

initialize(Session) - Method in class ome.services.blitz.impl.OmeroMetadata

initialize(String[], String[], Class[], Map<String, Object>) - Method in class ome.services.blitz.measurements.MeasurementStore

initialize(String[], String[], Class[], Map<String, Object>) - Method in interface ome.services.blitz.measurements.OmeroMeasurementStore

initialize() - Method in class ome.services.eventlogs.PersistentEventLogLoader

Called when the configuration database does not contain a valid current_id.

initialize() - Method in class ome.services.fulltext.PersistentEventLogLoader

Called when the configuration database does not contain a valid current_id.

initialize(long, String, Map<String, String>) - Method in class ome.services.graphs.AnnotationGraphSpec

initialize(long, String, Map<String, String>) - Method in class ome.services.graphs.BaseGraphSpec

initialize(long, String, Map<String, String>) - Method in class ome.services.graphs.GraphEntry

Called during GraphSpec.initialize(long, String, Map) to give the entry a chance to modify its #op based on the options and to initialize subspecs.

initialize(long, String, Map<String, String>) - Method in interface ome.services.graphs.GraphSpec

Called as each delete command is started.

initialize() - Method in class ome.services.pixeldata.PersistentEventLogLoader

initializeRedirect(Redirector.Context, String) - Method in class ome.services.blitz.redirect.AbstractRedirector

Set the new redirect value if null, or if the uuid is null or empty, then the existing redirect will be removed.

initializeUserAttributes(MethodInvocation, ServiceFactory, Principal, AtomicBoolean) - Static method in class ome.logic.HardWiredInterceptor

Adds the given environment context objects to the ReflectiveMethodInvocation.getUserAttributes() Map for lookup in subclasses

inMemoryCache(String) - Method in interface ome.services.sessions.SessionManager

Returns after possibly creating an in-memory cache which can be used throughout the session.

inMemoryCache(String) - Method in class ome.services.sessions.SessionManagerImpl

inMemoryCache(String) - Method in class ome.services.sessions.state.SessionCache

InMemoryPlanarPixelBuffer - Class in ome.io.nio

Class implementation of the PixelBuffer interface for in memory planar pixel data.

InMemoryPlanarPixelBuffer(Pixels, byte[][][][]) - Constructor for class ome.io.nio.InMemoryPlanarPixelBuffer

Constructs an in memory pixel buffer based on a defined dimensionality.

INNER_JOIN - Static variable in class ome.services.query.Query

imported constant for ease of use

input - Variable in class ome.services.SVGRasterizer

The transcoder input.

inputEnvironment(String) - Method in interface ome.services.sessions.SessionManager

Returns a copy of the input environment.

inputEnvironment(String) - Method in class ome.services.sessions.SessionManagerImpl

insertEntity(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

INSIGHT_PUBLISHED_NS - Static variable in class pojos.BooleanAnnotationData

The name space used to indicate that the tag is used a tag set.

INSIGHT_RATING_NS - Static variable in class pojos.RatingAnnotationData

The name space used to identify the archived annotation linked to a set of pixels.

INSIGHT_TAGSET_NS - Static variable in class pojos.TagAnnotationData

The name space used to indicate that the tag is used a tag set.

InstanceProvider - Interface in ome.formats.model

An instance provider, whose job is to make OMERO Blitz classes available to a consumer based on a set of criteria.

instantiate(String, EntityMode, Serializable) - Method in class ome.security.basic.OmeroInterceptor

default logic, but we may want to use them eventually for dependency-injection.

INSTITUTION - Static variable in class pojos.ExperimenterData

Identifies the Experimenter#INSTITUTION field.

InstrumentData - Class in pojos

Hosts the instrument used to capture an image.

InstrumentData(Instrument) - Constructor for class pojos.InstrumentData

Creates a new instance.

InstrumentProcessor - Class in ome.formats.model

Processes the members of an Instrument (Objective, OTF, Arc Laser and Filament) and ensures that the Instrument containers are present in the container cache, adding them if they are missing.

InstrumentProcessor() - Constructor for class ome.formats.model.InstrumentProcessor

INT - Static variable in class omeis.providers.re.data.PlaneFactory

Identifies the type used to store pixel values.

INT16 - Static variable in class omeis.providers.re.data.PlaneFactory

Identifies the INT16 data type used to store pixel values, as per OME spec.

INT16_TYPE - Static variable in class pojos.PixelsData

Identifies the type used to store pixel values.

INT32 - Static variable in class omeis.providers.re.data.PlaneFactory

Identifies the INT32 data type used to store pixel values, as per OME spec.

INT32_TYPE - Static variable in class pojos.PixelsData

Identifies the type used to store pixel values.

INT8 - Static variable in class omeis.providers.re.data.PlaneFactory

Identifies the INT8 data type used to store pixel values, as per OME spec.

INT8_TYPE - Static variable in class pojos.PixelsData

Identifies the type used to store pixel values.

INT_16 - Static variable in class omerojava.util.PixelTypes

Identifies the type used to store pixel values.

INT_32 - Static variable in class omerojava.util.PixelTypes

Identifies the type used to store pixel values.

INT_8 - Static variable in class omerojava.util.PixelTypes

Identifies the type used to store pixel values.

IntConverter - Class in omerojava.util

Packs a sequence of bytes representing a signed (2's complement) big-endian integer into an integer value of appropriate integer value.

IntConverter() - Constructor for class omerojava.util.IntConverter

INTEGER(Connection, List<Integer>) - Method in interface ome.tools.hibernate.ListAsSQLArrayUserType.ArrayFactory

InteractiveProcessorI - Class in omero.grid

Processor implementation which delegates to an omero.grid.Processor servant.

InteractiveProcessorI(Principal, SessionManager, Executor, ProcessorPrx, Job, long, SessionControlPrx, ParamsHelper) - Constructor for class omero.grid.InteractiveProcessorI

interceptor - Variable in class ome.security.basic.BasicSecuritySystem

internalDelete(IObject, UpdateFilter, Session) - Method in class ome.logic.UpdateImpl

internalMerge(IObject, UpdateFilter, Session) - Method in class ome.logic.UpdateImpl

Note if we use anything other than merge here, functionality from ome.tools.hibernate.MergeEventListener needs to be moved to UpdateFilter or to another event listener.

InternalMessage - Class in ome.util.messages

Message which can be published via OmeroContext.publishEvent(ApplicationEvent) or OmeroContext.publishMessage(InternalMessage).

InternalMessage(Object) - Constructor for class ome.util.messages.InternalMessage

Sole constructor which takes the "source" of this EventObject.

InternalRepositoryConfig - Class in ome.services.blitz.repo

Simple configuration class which is created via repository.xml Spring configuration file after the OMERO.repository context is loaded.

InternalRepositoryConfig(String) - Constructor for class ome.services.blitz.repo.InternalRepositoryConfig

InternalRepositoryI - Class in ome.services.blitz.repo

Standalone repository service.

InternalRepositoryI(ObjectAdapter, Registry, Executor, SqlAction, String, String) - Constructor for class ome.services.blitz.repo.InternalRepositoryI

internalSave(IObject, ReloadFilter, Session) - Method in class ome.logic.UpdateImpl

Note if we use anything other than merge here, functionality from ome.tools.hibernate.MergeEventListener needs to be moved to UpdateFilter or to another event listener.

InternalServiceFactory - Class in ome.tools.spring

subclass of ome.system.ServiceFactory which retrieves unmanaged ("internal") service-instances.

InternalServiceFactory() - Constructor for class ome.tools.spring.InternalServiceFactory

default construtor

InternalServiceFactory(OmeroContext) - Constructor for class ome.tools.spring.InternalServiceFactory

internalSession - Variable in class ome.services.sessions.SessionManagerImpl

Internal SessionContext created during SessionManagerImpl.init() which is used for all method calls internal to the session manager (see execute* methods)

Intersection - Class in ome.services.search

Intersection SearchAction which combines two other search actions into one logical unit, e.g.

Intersection(SearchValues, SearchAction, SearchAction) - Constructor for class ome.services.search.Intersection

intersects(double, double, double, double) - Method in class ome.util.math.geom2D.EllipseArea

Required by the Shape I/F.

intersects(Rectangle2D) - Method in class ome.util.math.geom2D.EllipseArea

Required by the Shape I/F.

intersects(double, double, double, double) - Method in class ome.util.math.geom2D.RectangleArea

Required by the Shape I/F.

intersects(Rectangle2D) - Method in class ome.util.math.geom2D.RectangleArea

Required by the Shape I/F.

intervalEnd - Variable in class omeis.providers.re.codomain.CodomainMapContext

The upper bound of the codomain interval.

intervalStart - Variable in class omeis.providers.re.codomain.CodomainMapContext

The lower bound of the codomain interval.

InThreadThrottlingStrategy - Class in ome.services.throttling

Throttling implementation which uses the calling server Thread for execution.

InThreadThrottlingStrategy(CurrentDetails) - Constructor for class ome.services.throttling.InThreadThrottlingStrategy

invalidateConnection(long, Experimenter) - Method in interface ome.api.IShare

Makes the connection invalid for share for specifiec user.

invalidateConnection(long, Experimenter) - Method in class ome.services.sharing.ShareBean

invalidateConnection_async(AMD_IShare_invalidateConnection, long, Experimenter, Current) - Method in class ome.services.blitz.impl.ShareI

invalidateCurrentEventContext() - Method in class ome.security.basic.CurrentDetails

It suffices to set the Details to a new instance to make this context unusable.

invalidateEventContext() - Method in class ome.security.basic.BasicSecuritySystem

invalidateEventContext() - Method in interface ome.security.SecuritySystem

Clears the content of the EventContextso that the SecuritySystem will no longer return true for SecuritySystem.isReady().

invalidateEventContext() - Method in class ome.security.SecuritySystemHolder

invalidateEventContext() - Method in class ome.security.sharing.SharingSecuritySystem

invertPDI(Set<Image>, CBlock<T>) - Static method in class ome.tools.HierarchyTransformations

invoke(MethodInvocation) - Method in class ome.security.basic.BasicSecurityWiring

Wraps all OMERO invocations with login/logout semantics.

invoke(MethodInvocation) - Method in class ome.security.basic.EventHandler

invocation interceptor for prepairing this Thread for execution and subsequently reseting it.

invoke(MethodInvocation) - Method in class ome.security.basic.NullEventHandler

invoke(MethodInvocation) - Method in class ome.services.blitz.fire.AopContextInitializer

invoke(Object, Current, IceMapper, Object...) - Method in class ome.services.blitz.util.IceMethodInvoker

Calls the method named in Current.operation with the arguments provided mapped via the IceMapper instance.

invoke(MethodInvocation) - Method in class ome.services.util.ServiceHandler

invoke(MethodInvocation) - Method in class ome.tools.hibernate.EventMethodInterceptor

invoke(MethodInvocation) - Method in class ome.tools.hibernate.ProxyCleanupFilter.Interceptor

invoke(MethodInvocation) - Method in class ome.tools.hibernate.SessionFactory

Wraps all invocations to Session to prevent certain usages.

invoke(MethodInvocation) - Method in class ome.tools.hibernate.SessionHandler

delegates to HibernateInterceptor or manages sessions internally, based on the type of service.

invoker - Variable in class ome.services.blitz.impl.AbstractAmdServant

If a service is provided, then an invoker will be created to cache all of its methods.

IObjectClassQuery - Class in ome.services.query

simple query subclass which uses the Parameters.CLASS parameter value to create a Criteria and then adds Expression instances based on all other parameter names.

IObjectClassQuery(Parameters) - Constructor for class ome.services.query.IObjectClassQuery

IObjectContainerStore - Interface in ome.formats.model

An object that handles the storage and manipulation of IObject containers and their references.

iObjectType - Variable in class ome.services.graphs.GraphStep

Type of object which is being deleted, using during GraphState#release(String) to send an EventLogMessage.

IObservable - Interface in ome.formats.importer

IObserver - Interface in ome.formats.importer

IPixels - Interface in ome.api

Metadata gateway for the RenderingEngine and clients.

iPixels - Variable in class ome.services.projection.ProjectionBean

Reference to the service used to retrieve the pixels metadata.

IProcessManager - Interface in ome.services.procs

Manages asynchronous processing logic for all Job instances created

IProjection - Interface in ome.api

Provides methods for performing projections of Pixels sets.

IQuery - Interface in ome.api

Provides methods for directly querying object graphs.

iQuery - Variable in class ome.logic.AbstractLevel2Service

iQuery - Variable in class ome.services.AbstractStatefulBean

IQueryEnumProvider - Class in ome.formats.enums

An enumeration provider which uses IQuery and a cache to fulfill the contract of an EnumerationProvider.

IQueryEnumProvider(IQueryPrx) - Constructor for class ome.formats.enums.IQueryEnumProvider

Default IQuery based enumeration provider constructor.

IRenderingSettings - Interface in ome.api

Provides method to apply rendering settings to a collection of images.

IRepositoryInfo - Interface in ome.api

Provides methods for obtaining information for server repository disk space allocation.

IResults - Interface in ome.api

Provides methods for storing, quering, and retrieving analysis results.

IResults.PixelSet - Class in ome.api

IResults.PixelSet() - Constructor for class ome.api.IResults.PixelSet

IResults.Result - Interface in ome.api

is_adminorpi - Static variable in class ome.tools.hibernate.SecurityFilter

is_nonprivate - Static variable in class ome.tools.hibernate.SecurityFilter

is_share - Static variable in class ome.tools.hibernate.SecurityFilter

isAccepted(boolean, String, String, Current) - Method in class ome.services.blitz.impl.ProcessorCallbackI

Callback method called by the remote processor instance.

isActive() - Method in class ome.security.basic.BasicMethodSecurity

See MethodSecurity.isActive()

isActive() - Method in interface ome.security.MethodSecurity

Indicates whether or not method security is active.

isActive(Long, int) - Method in class ome.services.blitz.gateway.services.impl.RenderingServiceImpl

isActive(Long, int) - Method in interface ome.services.blitz.gateway.services.RenderingService

Is the channel active.

isActive() - Method in interface ome.services.procs.Process

isActive() - Method in class ome.services.procs.ProcessSkeleton

isActive(int) - Method in class ome.services.RenderingBean

Implemented as specified by the RenderingEngine interface.

isActive(int) - Method in interface omeis.providers.re.RenderingEngine

Returns true if the channel is mapped, false otherwise.

isActive() - Method in class pojos.ExperimenterData

Returns true if the experimenter is active, false otherwise.

isActive_async(AMD_RenderingEngine_isActive, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI

isActive_async(AMD_RenderingEngine_isActive, int, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI

isAdmin - Variable in class ome.system.SimpleEventContext

isAllowLeadingWildcard() - Method in interface ome.api.Search

Returns the current leading-wildcard setting.

isAllowLeadingWildcard() - Method in class ome.services.SearchBean

isAllowLeadingWildcard_async(AMD_Search_isAllowLeadingWildcard, Current) - Method in class ome.services.blitz.impl.SearchI

isAlphalessRendering() - Method in class omeis.providers.re.Optimizations

Returns true if the alphaless rendering optimization is enabled, and false if it is not.

isArchived() - Method in class pojos.ImageData

Returns true if the image has been archived, false otherwise.

isAutoCloseEnabled() - Method in class ome.tools.hibernate.CurrentSessionContext

IScale - Interface in ome.api

Provides methods for performing scaling (change of the image size through interpolation or other means) on BufferedImages.

isCaseSensitive() - Method in interface ome.api.Search

Returns the current case sensitivity setting.

isCaseSensitive() - Method in class ome.services.SearchBean

isCaseSensitive_async(AMD_Search_isCaseSensitive, Current) - Method in class ome.services.blitz.impl.SearchI

isClientObject() - Method in class pojos.ShapeData

Returns true if the object one that has been created client side.

isClientSide() - Method in class pojos.ROIData

Returns true if the object a client-side object, false otherwise.

IsConstant() - Method in class omeis.providers.re.codomain.PlaneSlicingContext

Returns the type of bit-planes mapping.

isCurrentUserAdmin() - Method in class ome.services.sessions.SessionContextImpl

isCurrentUserAdmin() - Method in interface ome.system.EventContext

isCurrentUserAdmin() - Method in class ome.system.SimpleEventContext

isDb() - Method in class ome.system.Preference

isDebugConsole() - Method in class ome.formats.importer.util.IniFileLoader

isDebugUI() - Method in class ome.formats.importer.util.IniFileLoader

isDetectorSettingsDirty() - Method in class pojos.ChannelAcquisitionData

Returns true if the detector settings has been updated, false otherwise.

isDirectory() - Method in class pojos.FileData

Returns true if the file is a directory, false otherwise.

isDirty() - Method in class pojos.DataObject

Returns true if setter value has modified the value of the stored IObject, false otherwise.

isDisabled(String) - Method in class ome.security.basic.BasicSecuritySystem

isDisabled(String) - Method in class ome.security.basic.CurrentDetails

isDisabled(String) - Method in interface ome.security.SecuritySystem

checks if the listed id is disabled for the current Thread.

isDisabled(String) - Method in class ome.security.SecuritySystemHolder

isDisabled(String) - Method in class ome.security.sharing.SharingSecuritySystem

isDiskSpaceChecking() - Method in class ome.services.RawFileBean

getter disk overflow checking

isDiskSpaceChecking() - Method in class ome.services.RawPixelsBean

isDiskSpaceChecking() - Method in class ome.services.ThumbnailBean

isEmpty() - Method in class ome.services.query.Definitions

isEmptyEventContext() - Method in class ome.security.sharing.SharingSecuritySystem

isEnabled() - Method in class ome.security.auth.LdapConfig

isEncryptedConnection() - Method in class ome.formats.OMEROMetadataStoreClient

isEndTime() - Method in class omero.sys.ParametersI

Returns true if the map contains the end time parameter, false otherwise.

ISession - Interface in ome.api

Start here: Session creation service for OMERO.

isExceptionThrown() - Method in class ome.system.UpgradeCheck

isExperimenter() - Method in class omero.sys.ParametersI

Returns true if the filter contains and ownerId parameter, false otherwise.

isExtendedGraphCritical(Set<Long>) - Method in class ome.services.ThumbnailCtx

Whether or not we're extended graph critical for a given set of dimension pools.

isf - Variable in class ome.services.util.Executor.Impl

isFloat() - Method in interface ome.api.RawPixelsStore

isFloat() - Method in class ome.io.bioformats.BfPixelBuffer

isFloat() - Method in class ome.io.bioformats.BfPixelsWrapper

isFloat() - Method in class ome.io.bioformats.BfPyramidPixelBuffer

isFloat() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

isFloat() - Method in interface ome.io.nio.PixelBuffer

Returns whether or not the pixel buffer has floating point pixels.

isFloat() - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

isFloat(long) - Method in class ome.services.blitz.gateway.services.impl.RawPixelsStoreServiceImpl

isFloat(long) - Method in interface ome.services.blitz.gateway.services.RawPixelsStoreService

Are the bytes in the image floats.

isFloat() - Method in class ome.services.RawPixelsBean

isFloat_async(AMD_RawPixelsStore_isFloat, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI

isFloat_async(AMD_RawPixelsStore_isFloat, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI

isFontBold() - Method in class pojos.ShapeSettingsData

Returns true if it is bold, false otherwise.

isFontItalic() - Method in class pojos.ShapeSettingsData

Returns true if it is italic, false otherwise.

isForce() - Method in class ome.services.graphs.GraphOpts

isGranted(Permissions.Role, Permissions.Right) - Static method in class ome.tools.hibernate.SecurityFilter

isGraphCritical() - Method in class ome.security.basic.BasicSecuritySystem

isGraphCritical() - Method in class ome.security.basic.CurrentDetails

isGraphCritical() - Method in interface ome.security.SecuritySystem

Determines if the current security context has the possibility of corrupting consistent graphs.

isGraphCritical() - Method in class ome.security.SecuritySystemHolder

isGraphCritical() - Method in class ome.security.sharing.SharingSecuritySystem

isGroup() - Method in class omero.sys.ParametersI

Returns true if the filter contains an groupId, false otherwise.

isGroupRead(Current) - Method in class omero.model.PermissionsI

isGroupRead() - Method in class pojos.PermissionData

Returns true if the group has read access, false otherwise.

isGroupWrite(Current) - Method in class omero.model.PermissionsI

isGroupWrite() - Method in class pojos.PermissionData

Returns true if the group has write access, false otherwise.

isHard() - Method in class ome.services.messages.stats.AbstractStatsMessage

IShare - Interface in ome.api

Provides method for sharing - collaboration process for images, datasets, projects.

isHidden() - Method in class pojos.FileData

Returns true if the file is hidden, false otherwise.

isImagingEnvironmentDirty() - Method in class pojos.ImageAcquisitionData

Returns true if the StageLabel has been updated, false otherwise.

isImmutable(Object) - Method in class omero.util.IceMapper

isInRepo(long) - Method in class ome.services.scripts.ScriptRepoHelper

isInRepo(SqlAction, long) - Method in class ome.services.scripts.ScriptRepoHelper

isInSystemGroup(Long) - Method in class ome.security.SystemTypes

isInSystemGroup(Details) - Method in class ome.security.SystemTypes

isInUserGroup(Long) - Method in class ome.security.SystemTypes

isInUserGroup(Details) - Method in class ome.security.SystemTypes

isKeep() - Method in class ome.services.graphs.GraphEntry

isLeicaReader() - Method in class ome.formats.importer.OMEROWrapper

isLifetime() - Method in class pojos.ImageData

Returns true if the image is a lifetime image, false otherwise.

isLightSourceSettingsDirty() - Method in class pojos.ChannelAcquisitionData

Returns true if the light source settings has been updated, false otherwise.

isLittleEndian() - Method in class ome.io.bioformats.BfPixelBuffer

Delegates to IFormatReader.isLittleEndian().

isLoaded() - Method in class pojos.DataObject

Returns true if the object is loaded, false otherwise.

isMergedBatches() - Method in interface ome.api.Search

Returns the current merged-batches setting.

isMergedBatches() - Method in class ome.services.SearchBean

isMergedBatches_async(AMD_Search_isMergedBatches, Current) - Method in class ome.services.blitz.impl.SearchI

isMetadataOnly() - Method in class ome.formats.importer.ImportLibrary

Retrieves the metadata only flag.

isMinMaxSet() - Method in class ome.formats.importer.OMEROWrapper

isModified() - Method in class ome.services.AbstractStatefulBean

isMovieFile() - Method in class pojos.FileAnnotationData

Returns true if it is a movie file.

isMutable() - Method in class ome.tools.hibernate.ListAsSQLArrayUserType

isNoiseReduction() - Method in class omeis.providers.re.metadata.StatsFactory

Returns true if the flag is on, false otherwise.

isNull() - Method in class ome.services.graphs.GraphEntry

isNullablePrimitive(Class<?>) - Static method in class omero.util.IceMapper

isObjectiveSettingsDirty() - Method in class pojos.ImageAcquisitionData

Returns true if the objective settings has been updated, false otherwise.

isOwnerOrSupervisor(IObject) - Method in class ome.security.basic.BasicSecuritySystem

tests whether or not the current user is either the owner of this entity, or the superivsor of this entity, for example as root or as group owner.

isOwnerOrSupervisor(IObject) - Method in class ome.security.basic.CurrentDetails

isPagination() - Method in class omero.sys.ParametersI

Returns true if the filter contains a limit OR a offset, false otherwise.

isPixelsTypeSigned() - Method in class ome.services.RenderingBean

Implemented as specified by the RenderingEngine interface.

isPixelsTypeSigned() - Method in class omeis.providers.re.Renderer

Returns true if the pixels type is signed, false otherwise.

isPixelsTypeSigned() - Method in interface omeis.providers.re.RenderingEngine

Returns true if the pixels type is signed, false otherwise.

isPixelsTypeSigned_async(AMD_RenderingEngine_isPixelsTypeSigned, Current) - Method in class ome.services.blitz.impl.RenderingEngineI

isPixelsTypeSigned_async(AMD_RenderingEngine_isPixelsTypeSigned, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI

isPrefs() - Method in class ome.system.Preference

isPrimaryColorEnabled() - Method in class omeis.providers.re.Optimizations

Returns true if the primary color optimization is enabled, and false if it is not.

isPrimitive(Class<?>) - Method in class omero.util.IceMapper

isReadOnly() - Method in class ome.services.sessions.SessionContextImpl

isReadOnly() - Method in interface ome.system.EventContext

isReadOnly - Variable in class ome.system.SimpleEventContext

isReadOnly() - Method in class ome.system.SimpleEventContext

isReadOnly() - Method in class pojos.ShapeData

Returns true if the object a read-only object, false otherwise.

isReady() - Method in class ome.security.basic.BasicSecuritySystem

implements SecuritySystem.isReady().

isReady() - Method in class ome.security.basic.CurrentDetails

Checks if the current Thread has non-null Experimenter, Event, and , required for proper functioning of the security system.

isReady() - Method in interface ome.security.SecuritySystem

checks if this SecuritySystem instance is in a valid state.

isReady() - Method in class ome.security.SecuritySystemHolder

isReady() - Method in class ome.security.sharing.SharingSecuritySystem

isRepeatable() - Method in class ome.formats.importer.util.FileUploadCounter

isRetry() - Method in class ome.io.messages.MissingPyramidMessage

isReturnUnloaded() - Method in interface ome.api.Search

Returns the current return-unloaded setting.

isReturnUnloaded() - Method in class ome.services.SearchBean

isReturnUnloaded_async(AMD_Search_isReturnUnloaded, Current) - Method in class ome.services.blitz.impl.SearchI

isRootUser(Experimenter) - Method in class ome.system.Roles

isSame(long) - Method in class omerojava.util.DataSink

Returns true if a data source has already been created for the specified pixels set, false otherwise.

isSecure() - Method in class omero.client

Specifies whether or not this client was created via a call to client.createClient(boolean) with a boolean of false.

isSend(int) - Method in class ome.formats.importer.util.ErrorHandler

Check if files need sending at error container index

isSet(Permissions.Flag) - Static method in class ome.tools.hibernate.SecurityFilter

isSigned() - Method in interface ome.api.RawPixelsStore

isSigned() - Method in class ome.io.bioformats.BfPixelBuffer

isSigned() - Method in class ome.io.bioformats.BfPixelsWrapper

isSigned() - Method in class ome.io.bioformats.BfPyramidPixelBuffer

isSigned() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

isSigned() - Method in interface ome.io.nio.PixelBuffer

Returns whether or not the pixel buffer has signed pixels.

isSigned() - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

isSigned(long) - Method in class ome.services.blitz.gateway.services.impl.RawPixelsStoreServiceImpl

isSigned(long) - Method in interface ome.services.blitz.gateway.services.RawPixelsStoreService

Are the bytes in the image signed.

isSigned() - Method in class ome.services.RawPixelsBean

isSigned_async(AMD_RawPixelsStore_isSigned, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI

isSigned_async(AMD_RawPixelsStore_isSigned, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI

isSingleton() - Method in class ome.security.basic.EventListenersFactoryBean

being a singleton implies that this FactoryBean will only ever create one instance.

isSoft() - Method in class ome.services.graphs.GraphEntry

isSPWReader() - Method in class ome.formats.importer.OMEROWrapper

isStageLabelDirty() - Method in class pojos.ImageAcquisitionData

Returns true if the position has been updated, false otherwise.

isStartTime() - Method in class omero.sys.ParametersI

Returns true if the map contains the start time parameter, false otherwise.

isStatisticsEnabled() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

Are statistics logged

isSyncOnLogin() - Method in class ome.security.auth.LdapConfig

isSystemGroup(ExperimenterGroup) - Method in class ome.system.Roles

isSystemType(Class<? extends IObject>) - Method in class ome.security.basic.BasicSecuritySystem

classes which cannot be created by regular users.

isSystemType(Class<? extends IObject>) - Method in interface ome.security.SecuritySystem

checks if instances of the given type are "System-Types".

isSystemType(Class<? extends IObject>) - Method in class ome.security.SecuritySystemHolder

isSystemType(Class<? extends IObject>) - Method in class ome.security.sharing.SharingSecuritySystem

isSystemType(Class<?>) - Method in class ome.security.SystemTypes

classes which cannot be created by regular users.

isThisType(String, boolean) - Method in class ome.io.bioformats.OmeroPixelsPyramidReader

isThisType(String, boolean) - Method in class ome.services.formats.OmeroReader

isThisType(RandomAccessInputStream) - Method in class ome.services.formats.OmeroReader

isThreadSafe() - Method in class ome.services.messages.AbstractSessionMessage

isThreadSafe() - Method in class ome.util.messages.InternalMessage

Returns true if this message can safely be passed to another Thread.

isThumbnailCached(long) - Method in class ome.services.ThumbnailCtx

Checks to see if a thumbnail is in the on disk cache or not.

isTransient(Object) - Method in class ome.security.basic.OmeroInterceptor

isTypeSigned(PixelsType) - Static method in class omeis.providers.re.data.PlaneFactory

A static helper method to retrieve pixel byte signage.

isUnloaded(Object) - Static method in class ome.tools.hibernate.HibernateUtils

isUpgradeNeeded() - Method in class ome.formats.importer.ImportConfig

Check online to see if this is the current version

isUpgradeNeeded() - Method in class ome.system.UpgradeCheck

isUseProjections() - Method in interface ome.api.Search

Returns the current use-projection setting.

isUseProjections() - Method in class ome.services.SearchBean

isUseProjections_async(AMD_Search_isUseProjections, Current) - Method in class ome.services.blitz.impl.SearchI

isUserGroup(ExperimenterGroup) - Method in class ome.system.Roles

isUserRead(Current) - Method in class omero.model.PermissionsI

isUserRead() - Method in class pojos.PermissionData

Returns true if the user has read access, false otherwise.

isUserWrite(Current) - Method in class omero.model.PermissionsI

isUserWrite() - Method in class pojos.PermissionData

Returns true if the user has write access, false otherwise.

isVisible() - Method in class pojos.ShapeData

Returns true if the shape is visible, false otherwise.

isVoid(Current) - Method in class ome.services.blitz.util.IceMethodInvoker

Checks for a void return type, which is needed to know what type of ice_response() method to invoke.

isVoid - Variable in class ome.services.throttling.Task

isVoid() - Method in class omero.util.IceMapper

Returns true only if the current mapping is the IceMapper.VOID mapping.

isWorldRead(Current) - Method in class omero.model.PermissionsI

isWorldRead() - Method in class pojos.PermissionData

Returns true if the world has read access, false otherwise.

isWorldWrite(Current) - Method in class omero.model.PermissionsI

isWorldWrite() - Method in class pojos.PermissionData

Returns true if the world has write access, false otherwise.

isWrapperArray(Class<?>) - Static method in class omero.util.IceMapper

isWrite() - Method in class ome.io.bioformats.BfPyramidPixelBuffer

Wether or not this instance is in writing-mode.

isXYPlanar() - Method in class omeis.providers.re.data.Plane2D

Returns true if the plane is an XY-plane, false otherwise.

iterate() - Method in class ome.services.scripts.ScriptRepoHelper

iterator() - Method in class ome.services.eventlogs.EventLogLoader

iterator() - Method in class ome.services.messages.ShapeChangeMessage

ITypes - Interface in ome.api

Access to reflective type information.

IUpdate - Interface in ome.api

Provides methods for directly updating object graphs.

iUpdate - Variable in class ome.logic.AbstractLevel2Service

iUpdate - Variable in class ome.services.AbstractStatefulBean

J

JavaImageScalingService - Class in ome.logic

Provides methods for scaling buffered images using Java Image Scaling.

JavaImageScalingService() - Constructor for class ome.logic.JavaImageScalingService

javaType - Variable in class omeis.providers.re.data.Plane2D

The Java type that we're using for pixel value retrieval

JdbcPasswordProvider - Class in ome.security.auth

Central PasswordProvider which uses the "password" table in the central OMERO database.

JdbcPasswordProvider(PasswordUtil) - Constructor for class ome.security.auth.JdbcPasswordProvider

JdbcPasswordProvider(PasswordUtil, boolean) - Constructor for class ome.security.auth.JdbcPasswordProvider

job(ServiceFactory, long) - Method in class ome.services.procs.ProcessManager.Work

JobBean - Class in ome.services

Provides methods for submitting asynchronous tasks.

JobBean() - Constructor for class ome.services.JobBean

default constructor

jobError() - Method in interface ome.api.JobHandle

Returns true if the Job has thrown an error.

jobError() - Method in class ome.services.JobBean

jobError_async(AMD_JobHandle_jobError, Current) - Method in class ome.services.blitz.impl.JobHandleI

jobFinished() - Method in interface ome.api.JobHandle

jobFinished() - Method in class ome.services.JobBean

jobFinished_async(AMD_JobHandle_jobFinished, Current) - Method in class ome.services.blitz.impl.JobHandleI

JobHandle - Interface in ome.api

Allows submission of asynchronous jobs.

JobHandleI - Class in ome.services.blitz.impl

Implementation of the JobHandle service.

JobHandleI(JobHandle, BlitzExecutor) - Constructor for class ome.services.blitz.impl.JobHandleI

jobMessage() - Method in interface ome.api.JobHandle

jobMessage() - Method in class ome.services.JobBean

jobMessage_async(AMD_JobHandle_jobMessage, Current) - Method in class ome.services.blitz.impl.JobHandleI

jobRunning() - Method in interface ome.api.JobHandle

Returns true if the Job is running, i.e. has an attached Process.

jobRunning() - Method in class ome.services.JobBean

jobRunning_async(AMD_JobHandle_jobRunning, Current) - Method in class ome.services.blitz.impl.JobHandleI

jobStatus() - Method in interface ome.api.JobHandle

jobStatus() - Method in class ome.services.JobBean

jobStatus_async(AMD_JobHandle_jobStatus, Current) - Method in class ome.services.blitz.impl.JobHandleI

join(QueryBuilder, String, String, String, String) - Method in class ome.services.graphs.BaseGraphSpec

Used to generate a join statement on the QueryBuilder making use of {@link ExtendedMetadata#getRelationship(String, String).

join(String) - Method in interface ome.services.sessions.SessionCallback

join(String) - Method in class ome.services.sessions.SessionCallback.SimpleCloseCallback

join(String, String, boolean, boolean) - Method in class ome.tools.hibernate.QueryBuilder

join(String...) - Static method in class prefs

Joins all the String arguments given into a single String (joined with " "), and returns that String as the first element of a new array.

joinChildren(Criteria, Class, int) - Static method in class ome.services.query.Hierarchy

joinParents(Criteria, Class, int) - Static method in class ome.services.query.Hierarchy

joinSession(String) - Method in class omero.client

Uses the given session uuid as name and password to rejoin a running session.

K

keepAlive(Current) - Method in class ome.services.blitz.gateway.OmeroGateway

Keep service alive.

keepAlive() - Method in class ome.services.blitz.gateway.services.GatewayFactory

keepAlive() - Method in interface ome.services.blitz.gateway.services.GatewayService

Keep service alive.

keepAlive(ServiceInterfacePrx, Current) - Method in class ome.services.blitz.impl.ServiceFactoryI

Currently ignoring the individual proxies

keepAllAlive(ServiceInterfacePrx[], Current) - Method in class ome.services.blitz.impl.ServiceFactoryI

key(String) - Method in class ome.security.auth.AttributeSet

key - Variable in class ome.services.eventlogs.PersistentEventLogLoader

Key used to look configuration value; 'name'

KeyAndTrustStoreConfiguration - Class in ome.security

Calls System.setProperty(String, String) for the "javax.net.ssl" properties needed to configure a trust store and a keystore for the Java process.

KeyAndTrustStoreConfiguration() - Constructor for class ome.security.KeyAndTrustStoreConfiguration

keys() - Method in class ome.services.sharing.BlobShareStore

keys() - Method in class ome.services.sharing.FreezeShareStore

keys() - Method in class ome.services.sharing.ShareStore

keys(String[]) - Static method in class prefs

Returns Preferences.keys()

keySet() - Method in class ome.services.query.Definitions

kill(Current) - Method in class ome.services.blitz.impl.ScriptProcessI

killSession() - Method in class omero.client

Calls ISession.closeSession(omero.model.Session) until the returned reference count is greater than zero.

knownManagers() - Method in class ome.services.blitz.fire.Ring

L

LASER - Static variable in class pojos.LightSourceData

Indicates that the light source is a laser.

lastEventLog() - Method in class ome.services.eventlogs.EventLogLoader

lastModified() - Method in class pojos.FileData

Returns when the file was last modified.

LASTNAME - Static variable in class pojos.ExperimenterData

Identifies the Experimenter#LASTNAME field.

lastPlane() - Method in class pojos.ROIData

Returns the last plane that the ROI ends on.

lastresultsAsWorkingGroup() - Method in class ome.services.SearchBean

launchProcessing() - Method in class ome.formats.OMEROMetadataStoreClient

LdapConfig - Class in ome.security.auth

Static methods for dealing with LDAP (DN) and the "password" table.

LdapConfig(boolean, String, String, String, String, String) - Constructor for class ome.security.auth.LdapConfig

Passes all values to LdapConfig.LdapConfig(boolean, String, String, String, String, String, boolean) but sets LdapConfig.syncOnLogin to false.

LdapConfig(boolean, String, String, String, String, String, boolean) - Constructor for class ome.security.auth.LdapConfig

Base constructor which stores all LdapConfig.parse(String) and stores all values for later lookup.

LdapI - Class in ome.services.blitz.impl

Implementation of the ILdap service.

LdapI(ILdap, BlitzExecutor) - Constructor for class ome.services.blitz.impl.LdapI

LdapImpl - Class in ome.logic

Provides methods for administering user accounts, passwords, as well as methods which require special privileges.

LdapImpl(ContextSource, LdapOperations, Roles, LdapConfig, RoleProvider, SqlAction) - Constructor for class ome.logic.LdapImpl

LdapPasswordProvider - Class in ome.security.auth

LDAP PasswordProvider which can create users on request to synchronize with an LDAP directory.

LdapPasswordProvider(PasswordUtil, LdapImpl) - Constructor for class ome.security.auth.LdapPasswordProvider

LdapPasswordProvider(PasswordUtil, LdapImpl, boolean) - Constructor for class ome.security.auth.LdapPasswordProvider

LdapPasswordProvider431 - Class in ome.security.auth.providers

LDAP PasswordProvider which can create users on request to synchronize with an LDAP directory.

LdapPasswordProvider431(PasswordUtil, LdapImpl) - Constructor for class ome.security.auth.providers.LdapPasswordProvider431

LdapPasswordProvider431(PasswordUtil, LdapImpl, boolean) - Constructor for class ome.security.auth.providers.LdapPasswordProvider431

ldapUtil - Variable in class ome.logic.AdminImpl

ldapUtil - Variable in class ome.security.auth.LdapPasswordProvider

ldapUtil - Variable in class ome.security.auth.providers.LdapPasswordProvider431

leaderOfGroups - Variable in class ome.system.SimpleEventContext

leadingWildcard - Variable in class ome.services.search.SearchValues

leaves() - Method in class omero.sys.ParametersI

Sets the leaf parameter to true.

LEFT_JOIN - Static variable in class ome.services.query.Query

imported constant for ease of use

LegacyRepositoryI - Class in ome.services.blitz.repo

Repository which makes the ${omero.data.dir} directory available via the standard Repository API.

LegacyRepositoryI(ObjectAdapter, Registry, Executor, SqlAction, String, String) - Constructor for class ome.services.blitz.repo.LegacyRepositoryI

LegacyRepositoryI(ObjectAdapter, Registry, Executor, SqlAction, String, FileMaker) - Constructor for class ome.services.blitz.repo.LegacyRepositoryI

length() - Method in class ome.services.scripts.RepoFile.FsFile

length() - Method in class ome.services.scripts.RepoFile

length - Variable in class ome.util.mem.ReadOnlyByteArray

The length of the slice.

length - Variable in class omerojava.util.ReadOnlyByteArray

The length of the slice.

LEVEL_FIVE - Static variable in class pojos.RatingAnnotationData

Indicates the object is rated with five stars.

LEVEL_FOUR - Static variable in class pojos.RatingAnnotationData

Indicates the object is rated with four stars.

LEVEL_ONE - Static variable in class pojos.RatingAnnotationData

Indicates the object is rated with one star.

LEVEL_THREE - Static variable in class pojos.RatingAnnotationData

Indicates the object is rated with three stars.

LEVEL_TWO - Static variable in class pojos.RatingAnnotationData

Indicates the object is rated with two stars.

LEVEL_ZERO - Static variable in class pojos.RatingAnnotationData

Indicates the object is not rated.

lies(PlanePoint) - Method in class ome.util.math.geom2D.Line

Tells whether the specified point lies on this line.

lies(PlanePoint, boolean) - Method in class ome.util.math.geom2D.Line

Tells whether the specified point lies on this line and within the specified orientation.

lies(double, double) - Method in class ome.util.math.geom2D.Segment

Tells whether a specified point lies on this line.

LIGHT_EMITTING_DIODE - Static variable in class pojos.LightSourceData

Indicates that the light source is a light emitting diode.

LightPathData - Class in pojos

Object hosting a light path.

LightPathData(LightPath) - Constructor for class pojos.LightPathData

Creates a new instance.

LightSourceData - Class in pojos

Object hosting a light source: filament, arc, laser or light emitting diode

LightSourceData(LightSource) - Constructor for class pojos.LightSourceData

Creates a new instance.

Line - Class in ome.util.math.geom2D

An orientated line in the Euclidean space R².

Line(PlanePoint, PlanePoint) - Constructor for class ome.util.math.geom2D.Line

Creates a new object to represent the line passing through the o and p points.

Line(PlanePoint, PlanePoint, PlanePoint) - Constructor for class ome.util.math.geom2D.Line

Creates a new object to represent the line passing through o and having direction pq.

LINE_CAP_BUTT - Static variable in class pojos.ShapeSettingsData

The Butt descriptor.

LINE_CAP_ROUND - Static variable in class pojos.ShapeSettingsData

The Round descriptor.

LINE_CAP_SQUARE - Static variable in class pojos.ShapeSettingsData

The Square descriptor.

LINEAR - Static variable in class omeis.providers.re.quantum.QuantumFactory

Flag to select a linear map for the quantization process.

LineData - Class in pojos

Represents a line in the Euclidean space R².

LineData(Shape) - Constructor for class pojos.LineData

Creates a new instance.

LineData() - Constructor for class pojos.LineData

Create a new instance of LineData, creating a new LineI Object.

LineData(double, double, double, double) - Constructor for class pojos.LineData

Create a new instance of the LineData,

link(ILink[], Parameters) - Method in interface ome.api.IContainer

Convenience method for creating links.

link(ILink[], Parameters) - Method in class ome.logic.PojosImpl

Implemented as specified by the IContainer I/F

link_async(AMD_IContainer_link, List<IObject>, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI

linkGroupAndUser(ExperimenterGroup, Experimenter, boolean) - Method in class ome.security.auth.SimpleRoleProvider

list(List<Obj>) - Method in class ome.services.sharing.ShareBean

ListAsSQLArrayUserType<T> - Class in ome.tools.hibernate

Hibernate type to store Lists of primitives using SQL ARRAY.

ListAsSQLArrayUserType() - Constructor for class ome.tools.hibernate.ListAsSQLArrayUserType

ListAsSQLArrayUserType.ArrayFactory - Interface in ome.tools.hibernate

ListAsSQLArrayUserType.BOOLEAN - Class in ome.tools.hibernate

To use, define : hibernate.property type="ome.tools.hibernate.ListAsSQLArrayUserType$BOOLEAN" hibernate.column name="fieldName" sql-type="bool[]"

ListAsSQLArrayUserType.BOOLEAN() - Constructor for class ome.tools.hibernate.ListAsSQLArrayUserType.BOOLEAN

ListAsSQLArrayUserType.DATE - Class in ome.tools.hibernate

To use, define : hibernate.property type="ome.tools.hibernate.ListAsSQLArrayUserType$DATE" hibernate.column name="fieldName" sql-type="timestamp[]"

ListAsSQLArrayUserType.DATE() - Constructor for class ome.tools.hibernate.ListAsSQLArrayUserType.DATE

ListAsSQLArrayUserType.DOUBLE - Class in ome.tools.hibernate

To use, define : hibernate.property type="ome.tools.hibernate.ListAsSQLArrayUserType$DOUBLE" hibernate.column name="fieldName" sql-type="float8[]"

ListAsSQLArrayUserType.DOUBLE() - Constructor for class ome.tools.hibernate.ListAsSQLArrayUserType.DOUBLE

ListAsSQLArrayUserType.ENUM<E extends Enum<E>> - Class in ome.tools.hibernate

Warning, this one is special.

ListAsSQLArrayUserType.ENUM(E[]) - Constructor for class ome.tools.hibernate.ListAsSQLArrayUserType.ENUM

ListAsSQLArrayUserType.FLOAT - Class in ome.tools.hibernate

To use, define : hibernate.property type="ome.tools.hibernate.ListAsSQLArrayUserType$FLOAT" hibernate.column name="fieldName" sql-type="real[]"

ListAsSQLArrayUserType.FLOAT() - Constructor for class ome.tools.hibernate.ListAsSQLArrayUserType.FLOAT

ListAsSQLArrayUserType.INTEGER - Class in ome.tools.hibernate

To use, define : hibernate.property type="ome.tools.hibernate.ListAsSQLArrayUserType$INTEGER" hibernate.column name="fieldName" sql-type="int[]"

ListAsSQLArrayUserType.INTEGER() - Constructor for class ome.tools.hibernate.ListAsSQLArrayUserType.INTEGER

ListAsSQLArrayUserType.STRING - Class in ome.tools.hibernate

To use, define : hibernate.property type="ome.tools.hibernate.ListAsSQLArrayUserType$STRING" hibernate.column name="fieldName" sql-type="text[]"

ListAsSQLArrayUserType.STRING() - Constructor for class ome.tools.hibernate.ListAsSQLArrayUserType.STRING

ListAsSQLArrayUserType.STRING2 - Class in ome.tools.hibernate

To use, define : hibernate.property type="ome.tools.hibernate.ListAsSQLArrayUserType$STRING2" hibernate.column name="fieldName" sql-type="text[]" Added by Josh

ListAsSQLArrayUserType.STRING2() - Constructor for class ome.tools.hibernate.ListAsSQLArrayUserType.STRING2

listFiles(String, RepositoryListConfig, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI

listFileSets(String, RepositoryListConfig, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI

Get a list of those files as importable and non-importable list.

LISTOBJECTARRAY_TO_RTYPESEQSEQ - Static variable in class omero.util.IceMapper

ln(double, double, double, double) - Method in class ome.services.roi.GeomTool

load() - Method in class ome.formats.importer.ImportConfig.Value

Loads properties from various locations.

load(String, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI

Interface methods yet TODO

load() - Method in class ome.services.RenderingBean

Implemented as specified by the RenderingEngine interface.

load(long, boolean) - Method in class ome.services.scripts.ScriptRepoHelper

load(long, Session, SqlAction, boolean) - Method in class ome.services.scripts.ScriptRepoHelper

load() - Method in interface omeis.providers.re.RenderingEngine

Creates a instance of the rendering engine.

load(String[]) - Static method in class prefs

Loads a profile from Properties files, or properly formatted System.in input if no files are given.

load_async(AMD_RenderingEngine_load, Current) - Method in class ome.services.blitz.impl.RenderingEngineI

load_async(AMD_RenderingEngine_load, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI

load_nowarn(String[]) - Static method in class prefs

Performs the same actions as prefs.load(String[]) but does not throw prefs.CONFLICT if a key already exists.

loadAll() - Method in class ome.formats.importer.ImportConfig

Loads all the values for which it makes sense to have a preferences values.

loadAll(boolean) - Method in class ome.services.scripts.ScriptRepoHelper

Walks all files in the repository (via ScriptRepoHelper.iterate() and adds them if not found in the database.

loadAllMetadata(long) - Method in class ome.services.ThumbnailCtx

Retrieves all thumbnail metadata available in the database for a given Pixels ID.

loadAndPrepareMetadata(Set<Long>, int) - Method in class ome.services.ThumbnailCtx

Bulk loads and prepares metadata for a group of pixels sets.

loadAndPrepareMetadata(Set<Long>, Dimension) - Method in class ome.services.ThumbnailCtx

Bulk loads and prepares metadata for a group of pixels sets.

loadAndPrepareRenderingSettings(Set<Long>) - Method in class ome.services.ThumbnailCtx

Bulk loads a set of rendering settings for a group of pixels sets and prepares our internal data structures.

loadAndPrepareRenderingSettings(long, long) - Method in class ome.services.ThumbnailCtx

Loads and prepares a rendering settings for a Pixels ID and RenderingDef ID.

loadAnnotation(Set<Long>) - Method in interface ome.api.IMetadata

Loads the specified annotations.

loadAnnotation(Set<Long>) - Method in class ome.logic.MetadataImpl

Implemented as specified by the IMetadata I/F

loadAnnotation_async(AMD_IMetadata_loadAnnotation, List<Long>, Current) - Method in class ome.services.blitz.impl.MetadataI

loadAnnotations(Class<T>, Set<Long>, Set<String>, Set<Long>, Parameters) - Method in interface ome.api.IMetadata

Loads all the annotations of given types, that have been attached to the specified rootNodes for the specified annotatorIds.

loadAnnotations(Class<T>, Set<Long>, Set<String>, Set<Long>, Parameters) - Method in class ome.logic.MetadataImpl

Implemented as specified by the IMetadata I/F

loadAnnotations_async(AMD_IMetadata_loadAnnotations, String, List<Long>, List<String>, List<Long>, Parameters, Current) - Method in class ome.services.blitz.impl.MetadataI

loadAnnotationsUsedNotOwned(Class, long) - Method in interface ome.api.IMetadata

Loads the annotations of a given type used by the specified user but not owned by the user.

loadAnnotationsUsedNotOwned(Class, long) - Method in class ome.logic.MetadataImpl

Implemented as specified by the IMetadata I/F

loadAnnotationsUsedNotOwned_async(AMD_IMetadata_loadAnnotationsUsedNotOwned, String, long, Current) - Method in class ome.services.blitz.impl.MetadataI

loadChannelAcquisitionData(Set<Long>) - Method in interface ome.api.IMetadata

Loads the logical channels and the acquisition metadata related to them.

loadChannelAcquisitionData(Set<Long>) - Method in class ome.logic.MetadataImpl

Implemented as specified by the IMetadata I/F

loadChannelAcquisitionData_async(AMD_IMetadata_loadChannelAcquisitionData, List<Long>, Current) - Method in class ome.services.blitz.impl.MetadataI

loadCollection(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

loadContainerHierarchy(Class<T>, Set<Long>, Parameters) - Method in interface ome.api.IContainer

Retrieves hierarchy trees rooted by a given node (unless orphan is specified -- See below) This method also retrieves the Experimenters linked to the objects in the tree.

loadContainerHierarchy(Class, Set, Parameters) - Method in class ome.logic.PojosImpl

Implemented as speficied by the IContainer I/F

loadContainerHierarchy_async(AMD_IContainer_loadContainerHierarchy, String, List<Long>, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI

loaded - Variable in class ome.services.blitz.fire.SessionManagerI

loadedObjects(int) - Method in class ome.services.sessions.stats.DelegatingStats

loadedObjects(int) - Method in class ome.services.sessions.stats.NullSessionStats

loadedObjects(int) - Method in interface ome.services.sessions.stats.SessionStats

loadedObjects(int) - Method in class ome.services.sessions.stats.SimpleSessionStats

loadEntity(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

loader - Variable in class ome.services.fulltext.FullTextIndexer

loader - Variable in class ome.services.pixeldata.PixelDataHandler

loadEventContext(boolean) - Method in class ome.security.basic.BasicSecuritySystem

loadEventContext(boolean, boolean) - Method in class ome.security.basic.BasicSecuritySystem

loadEventContext(boolean) - Method in interface ome.security.SecuritySystem

Prepares the current EventContext instance with the current Principal.

loadEventContext(boolean) - Method in class ome.security.SecuritySystemHolder

loadEventContext(boolean) - Method in class ome.security.sharing.SharingSecuritySystem

loadGui() - Method in class ome.formats.importer.ImportConfig

Loads gui specific values for which it makes sense to have a preferences values.

loadInstrument(long) - Method in interface ome.api.IMetadata

Loads the instrument and its components i.e. detectors, objectives, etc.

loadInstrument(long) - Method in class ome.logic.MetadataImpl

Implemented as specified by the IMetadata I/F

loadInstrument_async(AMD_IMetadata_loadInstrument, long, Current) - Method in class ome.services.blitz.impl.MetadataI

loadLdapGroups(String, DistinguishedName) - Method in class ome.logic.LdapImpl

loadMeasuredRois(Session, long, long) - Method in class ome.services.blitz.impl.RoiI

loadMembers(ShareData) - Method in class ome.services.sharing.ShareBean

loadRenderingDef(long) - Method in class ome.services.RenderingBean

Implemented as specified by the RenderingEngine interface.

loadRenderingDef(long) - Method in interface omeis.providers.re.RenderingEngine

Loads a specific set of rendering settings that does not necessarily have to be linked to the given Pixels set.

loadRenderingDef_async(AMD_RenderingEngine_loadRenderingDef, long, Current) - Method in class ome.services.blitz.impl.RenderingEngineI

loadRenderingDef_async(AMD_RenderingEngine_loadRenderingDef, long, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI

loadRndSettings(long) - Method in interface ome.api.IPixels

Loads a specific set of rendering settings with the following objects pre-linked: renderingDef.quantization renderingDef.model renderingDef.waveRendering renderingDef.waveRendering.color renderingDef.waveRendering.family renderingDef.spatialDomainEnhancement

loadRndSettings(long) - Method in class ome.logic.PixelsImpl

Implemented as specified by the IPixels I/F.

loadRndSettings_async(AMD_IPixels_loadRndSettings, long, Current) - Method in class ome.services.blitz.impl.PixelsI

loadScripts(ServiceFactory, Parameters) - Method in class ome.services.scripts.ScriptFinder

Load all scripts that match the name, sha1, and format for script

loadSpecifiedAnnotations(Class, Set<String>, Set<String>, Parameters) - Method in interface ome.api.IMetadata

Loads the annotations of a given type.

loadSpecifiedAnnotations(Class, Set<String>, Set<String>, Parameters) - Method in class ome.logic.MetadataImpl

Implemented as specified by the IMetadata I/F

loadSpecifiedAnnotations_async(AMD_IMetadata_loadSpecifiedAnnotations, String, List<String>, List<String>, Parameters, Current) - Method in class ome.services.blitz.impl.MetadataI

loadSpecs() - Method in class ome.services.blitz.impl.DeleteI

loadTagContent(Set<Long>, Parameters) - Method in interface ome.api.IMetadata

Loads the Tag Set if the id is specified otherwise loads all the Tag Set.

loadTagContent(Set<Long>, Parameters) - Method in class ome.logic.MetadataImpl

Implemented as specified by the IMetadata I/F

loadTagContent_async(AMD_IMetadata_loadTagContent, List<Long>, Parameters, Current) - Method in class ome.services.blitz.impl.MetadataI

loadTagSets(Parameters) - Method in interface ome.api.IMetadata

Loads all the tag Sets.

loadTagSets(Parameters) - Method in class ome.logic.MetadataImpl

Implemented as specified by the IMetadata I/F

loadTagSets_async(AMD_IMetadata_loadTagSets, Parameters, Current) - Method in class ome.services.blitz.impl.MetadataI

LocalAdmin - Interface in ome.api.local

Provides local (internal) extensions for administration

LocalCompress - Interface in ome.api.local

Provides methods for performing scaling (change of the image size through interpolation or other means) on BufferedImages.

LocalConfig - Interface in ome.api.local

Provides local (internal) extensions for configuration.

LocalQuery - Interface in ome.api.local

Provides local (internal) extensions for querying

localQuery - Variable in class ome.logic.UpdateImpl

LocalShare - Interface in ome.api.local

Provides local (internal) extensions for shares

LocalUpdate - Interface in ome.api.local

Provides local (internal) extensions for updating

log - Variable in class ome.formats.importer.util.ErrorHandler

log - Variable in class ome.security.auth.ConfigurablePasswordProvider

log(String) - Method in class ome.security.basic.OmeroInterceptor

log - Variable in class ome.services.blitz.impl.AbstractAmdServant

log - Variable in class ome.services.blitz.redirect.AbstractRedirector

log - Static variable in class ome.services.delete.DeleteBean

log - Variable in class ome.services.eventlogs.EventLogLoader

log - Variable in class ome.services.fulltext.BridgeHelper

log(String) - Method in class ome.services.graphs.GraphEntry

Similar to GraphEntry.toString() but used to

log - Variable in class ome.services.roi.GeomTool

log - Variable in class ome.services.roi.PixelData

log - Variable in class ome.services.scripts.ScriptFinder

log - Variable in class ome.services.scripts.ScriptRepoHelper

log - Static variable in class ome.services.sharing.ShareBean

log - Variable in class ome.services.sharing.ShareStore

log - Variable in class ome.services.throttling.AbstractThrottlingStrategy

log - Static variable in class ome.services.util.DBEnumCheck

log - Static variable in class ome.services.util.DBPatchCheck

log - Static variable in class ome.services.util.DropBoxDirectoryCheck

log - Static variable in class ome.services.util.NamespaceCheck

log - Static variable in class ome.services.util.ServerDirectoryCheck

log - Static variable in class ome.services.util.ServerVersionCheck

log(String) - Method in class ome.tools.hibernate.EventMethodInterceptor

LOGARITHMIC - Static variable in class omeis.providers.re.quantum.QuantumFactory

Flag to select a logarithmic map for the quantization process.

LogarithmicMap - Class in omeis.providers.re.quantum

This class implements the QuantumMap interface.

LogarithmicMap() - Constructor for class omeis.providers.re.quantum.LogarithmicMap

LOGFILE - Static variable in class ome.formats.importer.util.IniFileLoader

Public in order to configure LogAppenderProxy, but then the value might as well be configured in the log4j.properties file

logger() - Method in class ome.services.fulltext.BridgeHelper

login(String, String, String) - Method in class ome.formats.importer.util.HtmlMessenger

Login to website

login(Principal) - Method in class ome.security.basic.BasicSecuritySystem

login(Principal) - Method in class ome.security.basic.CurrentDetails

login(BasicEventContext) - Method in class ome.security.basic.CurrentDetails

Login method which can be used by the security system to replace the existing BasicEventContext.

login(Principal) - Method in interface ome.security.basic.PrincipalHolder

Add a new principal context to the stack.

login(Principal) - Method in interface ome.security.SecuritySystem

stores this Principal instance in the current thread context for authenticating and authorizing all actions.

login(Principal) - Method in class ome.security.SecuritySystemHolder

login(Principal) - Method in class ome.security.sharing.SharingSecuritySystem

Login - Class in ome.system

Provides simplified handling of login properties when creating a ServiceFactory.

Login(String, String) - Constructor for class ome.system.Login

standard constructor which leaves OMERO_GROUP and OMERO_EVENT null.

Login(String, String, String, String) - Constructor for class ome.system.Login

extended constructor.

loginAttempt(String, Boolean) - Method in class ome.security.auth.ConfigurablePasswordProvider

LoginAttemptListener - Class in ome.security.auth

Listens for any LoginAttemptMessage.

LoginAttemptListener(int, long) - Constructor for class ome.security.auth.LoginAttemptListener

LoginAttemptMessage - Class in ome.services.messages

Published when any check is performed against a password.

LoginAttemptMessage(Object, String, Boolean) - Constructor for class ome.services.messages.LoginAttemptMessage

logout() - Method in class ome.formats.OMEROMetadataStoreClient

Destroys the sessionFactory and closes the client.

logout() - Method in class ome.security.basic.BasicSecuritySystem

logout() - Method in class ome.security.basic.CurrentDetails

logout() - Method in interface ome.security.basic.PrincipalHolder

Pop the last created principal context and return the number of active contexts remaining.

logout() - Method in interface ome.security.SecuritySystem

clears the top Principal instance from the current thread context.

logout() - Method in class ome.security.SecuritySystemHolder

logout() - Method in class ome.security.sharing.SharingSecuritySystem

logs - Variable in class ome.services.messages.ShapeChangeMessage

logSummary() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

log in info level the main statistics

logVersionInfo(String) - Method in class ome.formats.OMEROMetadataStoreClient

LONG - Static variable in class omeis.providers.re.data.PlaneFactory

Identifies the type used to store pixel values.

LongAnnotationData - Class in pojos

Wraps a long annotation.

LongAnnotationData(long) - Constructor for class pojos.LongAnnotationData

Creates a new instance.

LongAnnotationData() - Constructor for class pojos.LongAnnotationData

Creates a new instance.

LongAnnotationData(LongAnnotation) - Constructor for class pojos.LongAnnotationData

Creates a new instance.

LongCounter - Class in ome.services.sessions.stats

Counter object which increments an internal long by some integer value, and according to some strategy publishes an InternalMessage subclass.

LongCounter(int) - Constructor for class ome.services.sessions.stats.LongCounter

LongSeqHelper - Class in ome.services.sharing.data

LongSeqHelper() - Constructor for class ome.services.sharing.data.LongSeqHelper

LongSeqHolder - Class in ome.services.sharing.data

LongSeqHolder() - Constructor for class ome.services.sharing.data.LongSeqHolder

LongSeqHolder(List<Long>) - Constructor for class ome.services.sharing.data.LongSeqHolder

lookup(long) - Method in class ome.services.procs.ProcessorSkeleton

lookup(String, Parameters) - Method in class ome.services.query.ClassQuerySource

lookup(String, Parameters) - Method in class ome.services.query.NullQuerySource

lookup(String, Parameters) - Method in class ome.services.query.QueryFactory

lookup(String, Parameters) - Method in class ome.services.query.QuerySource

map the queryID argument to some Query instance (including null).

lookup(String, Parameters) - Method in class ome.services.query.StringQuerySource

lookup(String, ApplicationContext) - Method in class ome.system.OmeroContext.Locator

uses ContextSingletonBeanFactoryLocator.createDefinition(java.lang.String, java.lang.String) and ContextSingletonBeanFactoryLocator.initializeDefinition(org.springframework.beans.factory.BeanFactory) to create a new context from a given definition.

lookupClusterNodes() - Method in class ome.services.blitz.fire.Registry.Impl

lookupClusterNodes() - Method in interface ome.services.blitz.fire.Registry

Returns all found cluster nodes or null if something goes wrong during lookup (null QueryPrx for example)

lookupExperimenter(String) - Method in interface ome.api.IAdmin

look up an Experimenter and all related groups by name.

lookupExperimenter(String) - Method in class ome.logic.AdminImpl

lookupExperimenter_async(AMD_IAdmin_lookupExperimenter, String, Current) - Method in class ome.services.blitz.impl.AdminI

lookupExperimenters() - Method in interface ome.api.IAdmin

Looks up all experimenters present and all related groups.

lookupExperimenters() - Method in class ome.logic.AdminImpl

lookupExperimenters_async(AMD_IAdmin_lookupExperimenters, Current) - Method in class ome.services.blitz.impl.AdminI

lookupGroup(String) - Method in interface ome.api.IAdmin

look up an ExperimenterGroup and all contained users by name.

lookupGroup(String) - Method in class ome.logic.AdminImpl

lookupGroup_async(AMD_IAdmin_lookupGroup, String, Current) - Method in class ome.services.blitz.impl.AdminI

lookupGroups() - Method in interface ome.api.IAdmin

Looks up all groups present and all related experimenters.

lookupGroups() - Method in class ome.logic.AdminImpl

lookupGroups_async(AMD_IAdmin_lookupGroups, Current) - Method in class ome.services.blitz.impl.AdminI

lookupLdapAuthExperimenter(long) - Method in interface ome.api.IAdmin

Looks up experimenters who uses LDAP authentication (has set dn on password table).

lookupLdapAuthExperimenter(long) - Method in class ome.logic.AdminImpl

lookupLdapAuthExperimenter(Long) - Method in class ome.logic.LdapImpl

lookupLdapAuthExperimenter_async(AMD_IAdmin_lookupLdapAuthExperimenter, long, Current) - Method in class ome.services.blitz.impl.AdminI

lookupLdapAuthExperimenters() - Method in interface ome.api.IAdmin

Looks up all id of experimenters who uses LDAP authentication (has set dn on password table).

lookupLdapAuthExperimenters() - Method in class ome.logic.AdminImpl

lookupLdapAuthExperimenters() - Method in class ome.logic.LdapImpl

lookupLdapAuthExperimenters_async(AMD_IAdmin_lookupLdapAuthExperimenters, Current) - Method in class ome.services.blitz.impl.AdminI

lookupMonitorServers() - Method in class ome.services.blitz.fire.Registry.Impl

lookupMonitorServers() - Method in interface ome.services.blitz.fire.Registry

lookupPixels(long) - Method in class ome.services.RenderingBean

Implemented as specified by the RenderingEngine interface.

lookupPixels(long) - Method in interface omeis.providers.re.RenderingEngine

Loads the Pixels set this Rendering Engine is for.

lookupPixels_async(AMD_RenderingEngine_lookupPixels, long, Current) - Method in class ome.services.blitz.impl.RenderingEngineI

lookupPixels_async(AMD_RenderingEngine_lookupPixels, long, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI

lookupProcessors() - Method in class ome.services.blitz.fire.Registry.Impl

lookupProcessors() - Method in interface ome.services.blitz.fire.Registry

lookupRenderingDef(long) - Method in class ome.services.RenderingBean

Implemented as specified by the RenderingEngine interface.

lookupRenderingDef(long) - Method in interface omeis.providers.re.RenderingEngine

Loads the rendering settings associated to the specified pixels set.

lookupRenderingDef_async(AMD_RenderingEngine_lookupRenderingDef, long, Current) - Method in class ome.services.blitz.impl.RenderingEngineI

lookupRenderingDef_async(AMD_RenderingEngine_lookupRenderingDef, long, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI

lookupRepositories() - Method in class ome.services.blitz.fire.Registry.Impl

lookupRepositories() - Method in interface ome.services.blitz.fire.Registry

lookupTables() - Method in class ome.services.blitz.fire.Registry.Impl

lookupTables() - Method in interface ome.services.blitz.fire.Registry

loop(int, long) - Method in class omero.grid.DeleteCallbackI

Calls DeleteCallbackI.block(long) "loops" number of times with the "ms" argument.

loop - Variable in class omero.util.RPSTileData

lowestEntityId - Variable in class ome.services.pixeldata.PersistentEventLogLoader

The lowest entity id from a single dataPerUser set.

lsid(Class, long) - Method in class ome.services.db.DatabaseIdentity

lsid(Class, long, long) - Method in class ome.services.db.DatabaseIdentity

lsid(String, String) - Method in class ome.services.db.DatabaseIdentity

lsid(String, String, String) - Method in class ome.services.db.DatabaseIdentity

LsidUtils - Class in ome.tools.lsid

LsidUtils() - Constructor for class ome.tools.lsid.LsidUtils

M

mailSender - Variable in class ome.logic.AdminImpl

main(String[]) - Static method in class ome.formats.importer.util.FileUploader

Main for testing (debugging only)

main(String[]) - Static method in class ome.security.auth.PasswordUtil

Main method which takes exactly one argument, passes it to PasswordUtil.preparePassword(String) and prints the results on System.out.

main(String[]) - Static method in class ome.services.blitz.Entry

Entry point to the server.

main(String[]) - Static method in class ome.services.blitz.Status

Uses the passed args to create an Communicator.

Main - Class in ome.services.fulltext

Commandline entry-point for various full text actions.

Main() - Constructor for class ome.services.fulltext.Main

main(String[]) - Static method in class ome.services.fulltext.Main

main(String[]) - Static method in class ome.tools.FileSystem

main(String[]) - Static method in class omero.util.TempFileManager

Command-line interface to the global TempFileManager instance ( #manger).

main(String[]) - Static method in class prefs

Entry point to the prefs command line too.

makeAndLaunchHandle(Identity, DeleteCommand...) - Method in class ome.services.blitz.impl.DeleteI

makeAndRun(Identity, DeleteCommand...) - Method in class ome.services.blitz.impl.DeleteI

makeNew(int) - Method in class ome.util.mem.CopiableArray

Creates a new array of the speficied size.

makeNew(Pixels, ImageService) - Static method in class omerojava.util.DataSink

Factory method to create a new DataSink to handle access to the metadata associated with the specified pixels set.

makePyramid(Pixels) - Method in class ome.io.nio.PixelsService

Creates a pixels pyramid for a given set of pixels.

MANAGED_CONTEXT - Static variable in class ome.system.OmeroContext

identifier for an OmeroContext configured in classpath*:beanRefContext.xml for use by server-side processes.

managedEvent(boolean, IObject, Details, Details, Details) - Method in class ome.security.basic.OmeroInterceptor

managedExternalInfo(boolean, IObject, Details, Details, Details) - Method in class ome.security.basic.OmeroInterceptor

responsible for guaranteeing that external info is not modified by any users, including rot.

managedGroup(boolean, IObject, Details, Details, Details, BasicEventContext) - Method in class ome.security.basic.OmeroInterceptor

managedOwner(boolean, IObject, Details, Details, Details, BasicEventContext) - Method in class ome.security.basic.OmeroInterceptor

managedPermissions(boolean, IObject, Details, Details, Details, boolean) - Method in class ome.security.basic.OmeroInterceptor

responsible for properly copying user-requested permissions taking into account the Flag#LOCKED status.

ManagedServiceFactory - Class in ome.tools.spring

subclass of ome.system.ServiceFactory which retrieves managed service-instances.

ManagedServiceFactory() - Constructor for class ome.tools.spring.ManagedServiceFactory

manager - Variable in class ome.services.util.ExecutionThread

managerOrNull() - Method in class ome.services.blitz.fire.TopicManager.Impl

ManualFlushHibernateTemplate - Class in ome.tools.spring

ManualFlushHibernateTemplate() - Constructor for class ome.tools.spring.ManualFlushHibernateTemplate

map() - Method in class ome.formats.importer.ImportConfig

map(Map<String, List<Long>>) - Method in class ome.services.sharing.ShareBean

map() - Method in class omero.sys.ParametersI

Deprecated.

map(Filterable[]) - Method in class omero.util.IceMapper

mapFlexServer(String, String) - Method in class ome.formats.importer.util.IniFileLoader

Append kep to server map

mapFromAttributes(Attributes) - Method in class ome.security.auth.GroupAttributeMapper

mapFromContext(Object) - Method in class ome.security.auth.PersonContextMapper

mapReturnValue(IceMapper, Object) - Method in class ome.services.blitz.impl.RoiI.RoiResultMapReturnMapper

mapReturnValue(IceMapper, Object) - Method in class ome.services.blitz.impl.RoiI.RoiResultReturnMapper

mapReturnValue(Object) - Method in class omero.util.IceMapper

Convert the given Object via the set IceMapper.ReturnMapping.

mapReturnValue(IceMapper, Object) - Method in interface omero.util.IceMapper.ReturnMapping

mapServerToClient(byte[], int, int, String) - Static method in class omerojava.util.DataSink

mapServerToClient(byte[], int, int, String, boolean) - Static method in class omerojava.util.DataSink

mapUserGroups() - Method in class ome.formats.OMEROMetadataStoreClient

Maps the user's groups for use by ScreenLogin.registerGroup() Also strips system groups from this map

markAndSweep() - Method in class ome.services.db.SelfCorrectingDataSource

First removes all entries in SelfCorrectingDataSource.errorTimes that are older than some given time and then uses the remaining number of errors to determine the backoff : (#^1/2)*1000 milliseconds.

MaskData - Class in pojos

Represents an Mask in the Euclidean space R².

MaskData(Shape) - Constructor for class pojos.MaskData

Creates a new instance.

MaskData() - Constructor for class pojos.MaskData

Creates a new instance of MaskData.

MaskData(double, double, double, double, byte[]) - Constructor for class pojos.MaskData

Creates a new instance of the MaskData.

matches(Class, Class) - Static method in class ome.services.blitz.util.ApiConsistencyCheck

Defines what Class types match.

matches(File) - Method in class ome.services.scripts.RepoFile

MAX - Static variable in class omeis.providers.re.quantum.QuantumStrategy

Maximum value (255) allowed for the upper bound of the codomain interval.

MAX_CHANNELS - Static variable in class omeis.providers.re.Renderer

The maximum number of channels.

MAXIMUM_BUFFER_SIZE - Static variable in class ome.io.nio.RomioPixelBuffer

Default maximum buffer size for planar data transfer. (1MB)

MAXIMUM_INTENSITY - Static variable in interface ome.api.IProjection

Maximum intensity projection (MIP)

maxUserTimeToIdle - Variable in class ome.services.sessions.SessionManagerImpl

maxUserTimeToLive - Variable in class ome.services.sessions.SessionManagerImpl

MEAN_INTENSITY - Static variable in interface ome.api.IProjection

Mean intensity projection

MEASUREMENT_NS - Static variable in class pojos.FileAnnotationData

The name space used to indicate that the FileAnnotation is a Measurement file.

MeasurementStore - Class in ome.services.blitz.measurements

Parser API implementation for storing result measurements from SPW companion files as ROIs and OMERO.tables.

MeasurementStore(LocalUpdate, TablePrx) - Constructor for class ome.services.blitz.measurements.MeasurementStore

memberOfGroups - Variable in class ome.system.SimpleEventContext

members - Variable in class ome.services.sharing.data.ShareData

members - Variable in class ome.services.sharing.data.ShareItem

MERGE_EVENT - Static variable in class ome.security.basic.MergeEventListener

mergedBatches - Variable in class ome.services.search.SearchValues

MergeEventListener - Class in ome.security.basic

responsible for responding to merge events. in particular in load/re-loading certain types to make use by clients easier.

MergeEventListener(CurrentDetails, TokenHolder) - Constructor for class ome.security.basic.MergeEventListener

main constructor.

message - Variable in exception ome.io.nio.PixelBufferException

message - Variable in exception ome.services.graphs.GraphException

message() - Method in class ome.services.sessions.stats.LongCounter

message() - Method in class ome.services.sessions.stats.MethodCounter

message() - Method in class ome.services.sessions.stats.ObjectsReadCounter

message() - Method in class ome.services.sessions.stats.ObjectsWrittenCounter

message() - Method in class ome.services.sessions.stats.SessionsCreatedCounter

MessageException - Exception in ome.util.messages

Message which wraps a Throwable instance since OmeroContext.publishEvent(org.springframework.context.ApplicationEvent) cannot throw a checked exception.

MessageException(String, Throwable) - Constructor for exception ome.util.messages.MessageException

Create an instance.

meta - Variable in class ome.services.roi.PixelData

metadata - Variable in class ome.logic.AbstractLevel2Service

METADATA_LEVEL - Static variable in class ome.formats.importer.ImportCandidates

MetadataI - Class in ome.services.blitz.impl

Implementation of the IMetadata service.

MetadataI(IMetadata, BlitzExecutor) - Constructor for class ome.services.blitz.impl.MetadataI

Creates a new instance.

MetadataImpl - Class in ome.logic

Implement the IMetadata I/F.

MetadataImpl() - Constructor for class ome.logic.MetadataImpl

MetadataStoreI - Class in ome.services.blitz.impl

MetadataStoreI(BlitzExecutor, PopulateRoiJob, SqlAction, OriginalFilesService, String) - Constructor for class ome.services.blitz.impl.MetadataStoreI

methodCount() - Method in class ome.services.sessions.stats.DelegatingStats

methodCount() - Method in class ome.services.sessions.stats.NullSessionStats

methodCount() - Method in interface ome.services.sessions.stats.SessionStats

methodCount() - Method in class ome.services.sessions.stats.SimpleSessionStats

MethodCounter - Class in ome.services.sessions.stats

Counter for active methods for a given session.

MethodCounter(int) - Constructor for class ome.services.sessions.stats.MethodCounter

methodHardLimit - Variable in class ome.services.sessions.stats.CounterFactory

methodIn() - Method in class ome.services.sessions.stats.DelegatingStats

methodIn() - Method in class ome.services.sessions.stats.NullSessionStats

methodIn() - Method in interface ome.services.sessions.stats.SessionStats

methodIn() - Method in class ome.services.sessions.stats.SimpleSessionStats

METHODOLOGY_STRINGS - Static variable in interface ome.api.IProjection

Methodology strings

methodOut() - Method in class ome.services.sessions.stats.DelegatingStats

methodOut() - Method in class ome.services.sessions.stats.NullSessionStats

methodOut() - Method in interface ome.services.sessions.stats.SessionStats

methodOut() - Method in class ome.services.sessions.stats.SimpleSessionStats

methodSecurity - Variable in class ome.security.basic.BasicSecurityWiring

MethodSecurity - Interface in ome.security

Interface which allows security interceptors to check if a method should be executable for a given user.

MethodStatsMessage - Class in ome.services.messages.stats

Published when more than the specified number of active method calls is reached.

MethodStatsMessage(Object, long) - Constructor for class ome.services.messages.stats.MethodStatsMessage

MIDDLENAME - Static variable in class pojos.ExperimenterData

Identifies the Experimenter#MIDDLENAME field.

mimetype(String, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI

Get the mimetype for a file.

MIN - Static variable in class omeis.providers.re.quantum.QuantumStrategy

Minimum value (0) allowed for the lower bound of the codomain interval.

minMaxSet - Variable in class ome.formats.importer.OMEROWrapper

MissingPyramidMessage - Class in ome.io.messages

Published when an request is made for a pixels pyramid when the file does not yet exist.

MissingPyramidMessage(Object, long) - Constructor for class ome.io.messages.MissingPyramidMessage

MODEL_GREYSCALE - Static variable in class omeis.providers.re.Renderer

Identifies the type used to store model values.

MODEL_HSB - Static variable in class omeis.providers.re.Renderer

Identifies the type used to store model values.

MODEL_RGB - Static variable in class omeis.providers.re.Renderer

Identifies the type used to store model values.

ModelException - Exception in ome.formats.model

Exception thrown when there is an object instantiation error or error processing the model.

ModelException(String) - Constructor for exception ome.formats.model.ModelException

Default constructor.

ModelException(String, Class<? extends IObject>, Exception) - Constructor for exception ome.formats.model.ModelException

Default constructor.

ModelObjectHandler - Interface in ome.formats.model.handler

A model object handler whose purpose is to provide extra logic, such as enumeration not-null constraint fulfilment.

ModelObjectHandlerFactory - Class in ome.formats.model.handler

Factory for all available model handlers.

ModelObjectHandlerFactory(EnumerationProvider) - Constructor for class ome.formats.model.handler.ModelObjectHandlerFactory

Default constructor.

ModelProcessor - Interface in ome.formats.model

An object which performs post-processing on an IObjectContainerStore.

modificationCheck() - Method in class ome.services.scripts.ScriptRepoHelper

Checks if

modified - Variable in class ome.services.AbstractStatefulBean

True if any write operation took place on this bean.

modified() - Method in class ome.services.AbstractStatefulBean

modifiedStart - Variable in class ome.services.search.SearchValues

modifiedStop - Variable in class ome.services.search.SearchValues

more() - Method in class ome.services.eventlogs.AllEntitiesPseudoLogLoader

Returns the number of classes which are still unprocessed as a proxy for how much is left to process.

more() - Method in class ome.services.eventlogs.AllEventsLogLoader

more() - Method in class ome.services.eventlogs.EventLogLoader

Should return an estimate of how many more EventLog instances are available for processing.

more() - Method in class ome.services.eventlogs.PersistentEventLogLoader

moveToCommonSpace(IObject...) - Method in interface ome.api.IAdmin

Moves the given objects into the "user" group to make them visible and linkable from all security contexts.

moveToCommonSpace(IObject...) - Method in class ome.logic.AdminImpl

moveToCommonSpace_async(AMD_IAdmin_moveToCommonSpace, List<IObject>, Current) - Method in class ome.services.blitz.impl.AdminI

MOVIE_MPEG_NS - Static variable in interface ome.api.IMetadata

The name space used to indicate that the FileAnnotation is an MPEG file.

MOVIE_NS - Static variable in class pojos.FileAnnotationData

The name space used to indicate that the FileAnnotation is a movie.

MOVIE_QT_NS - Static variable in interface ome.api.IMetadata

The name space used to indicate that the FileAnnotation is an QT file.

MOVIE_WMV_NS - Static variable in interface ome.api.IMetadata

The name space used to indicate that the FileAnnotation is an WMV file.

MS_EXCEL - Static variable in class pojos.FileAnnotationData

Identifies the Excel file formats.

MS_POWER_POINT - Static variable in class pojos.FileAnnotationData

Identifies the Power point file formats.

MS_POWER_POINT_SHOW - Static variable in class pojos.FileAnnotationData

Identifies the Power point file formats.

MS_POWER_POINT_X - Static variable in class pojos.FileAnnotationData

Identifies the Power point file formats.

MS_WORD - Static variable in class pojos.FileAnnotationData

Identifies the Word file formats.

MS_WORD_X - Static variable in class pojos.FileAnnotationData

Identifies the Word file formats.

multicastEvent(ApplicationEvent) - Method in class ome.services.messages.GlobalMulticaster

Multicast only if this instance was the first created.

MultiImageData - Class in pojos

Handle image file composed of multiples files e.g. lei.

MultiImageData(OriginalFile) - Constructor for class pojos.MultiImageData

Creates a new instance.

mutex - Variable in class ome.system.SessionInitializer

MySeqGenerator - Class in ome.tools.hibernate

http://www.hibernate.org/296.html

MySeqGenerator() - Constructor for class ome.tools.hibernate.MySeqGenerator

N

name - Variable in class ome.services.query.QueryParameterDef

name of this parameter.

name - Variable in class ome.services.scripts.RepoFile.FsFile

name - Variable in class ome.system.Principal

NAME - Static variable in class pojos.DatasetData

Identifies the Dataset#NAME field.

NAME - Static variable in class pojos.GroupData

Identifies the ExperimenterGroup#NAME field.

NAME - Static variable in class pojos.ImageData

Identifies the Image#NAME field.

NAME - Static variable in class pojos.PlateData

Identifies the Plate#NAME field.

NAME - Static variable in class pojos.ProjectData

Identifies the Project#NAME field.

NAME - Static variable in class pojos.ScreenData

Identifies the Screen#NAME field.

nameById(long) - Method in interface ome.security.auth.RoleProvider

nameById(long) - Method in class ome.security.auth.SimpleRoleProvider

NamespaceCheck - Class in ome.services.util

Hook run by the context.

NamespaceCheck(Executor, String, Roles) - Constructor for class ome.services.util.NamespaceCheck

needsInit() - Method in class ome.services.blitz.repo.FileMaker

needsSanityCheck() - Method in class ome.logic.RepositoryInfoImpl

Calculates based on the cached usage and the elapsed time whether or not a real RepositoryInfoImpl.sanityCheckRepository() should be calculated.

newBlueColor() - Static method in class ome.formats.model.ColorsFactory

Creates a new Blue Color object.

newBlueColor() - Static method in class omeis.providers.re.ColorsFactory

Creates a new Blue Color object.

newEvent(Session, EventType, TokenHolder) - Method in class ome.security.basic.CurrentDetails

newGreenColor() - Static method in class ome.formats.model.ColorsFactory

Creates a new Green Color object.

newGreenColor() - Static method in class omeis.providers.re.ColorsFactory

Creates a new Green Color object.

newGreyColor() - Static method in class ome.formats.model.ColorsFactory

Creates a new Grey Color object.

newGreyColor() - Static method in class omeis.providers.re.ColorsFactory

Creates a new Grey Color object.

newlyEnabledFilters - Variable in class ome.services.query.Query

the set of filters that is being or has been enabled for this Query.

newRedColor() - Static method in class ome.formats.model.ColorsFactory

Creates a new Red Color object.

newRedColor() - Static method in class omeis.providers.re.ColorsFactory

Creates a new Red Color object.

newTable(long, String, Current) - Method in class ome.services.blitz.impl.SharedResourcesI

newTransientDetails(IObject) - Method in class ome.security.basic.BasicSecuritySystem

newTransientDetails(IObject) - Method in class ome.security.basic.OmeroInterceptor

newTransientDetails(IObject) - Method in interface ome.security.SecuritySystem

creates a new secure details for transient entities.

newTransientDetails(IObject) - Method in class ome.security.SecuritySystemHolder

newTransientDetails(IObject) - Method in class ome.security.sharing.SharingSecuritySystem

NewUserGroupBean - Interface in ome.security.auth

Strategy for finding the appropriate groups for a given user in LDAP.

newWhiteColor() - Static method in class ome.formats.model.ColorsFactory

Creates a new White Color object.

newWhiteColor() - Static method in class omeis.providers.re.ColorsFactory

Creates a new White Color object.

next() - Method in interface ome.api.Search

Returns the next entity from the current query.

next() - Method in class ome.services.eventlogs.EventLogLoader

Returns the current EventLogLoader.log instance which may be loaded by a call to EventLogLoader.hasNext() if necessary.

next() - Method in class ome.services.graphs.BaseGraphSpec.SubSpecIterator

next() - Method in class ome.services.SearchBean

next_async(AMD_Search_next, Current) - Method in class ome.services.blitz.impl.SearchI

nextEventLog(long) - Method in class ome.services.eventlogs.EventLogLoader

Returns the EventLog with the next id after the given argument or null if none exists.

noAcquisitionData() - Method in class omero.sys.ParametersI

Sets the acquisition data parameter to false.

nodeProxyQuery(Redirector.Context, String, String) - Method in class ome.services.blitz.redirect.AbstractRedirector

NOISE_REDUCTION - Static variable in class omeis.providers.re.quantum.QuantumFactory

Default value.

noLeaves() - Method in class omero.sys.ParametersI

Sets the leaf parameter to false.

noOrphan() - Method in class omero.sys.ParametersI

Sets the orphan parameter to false.

noPage() - Method in class omero.sys.ParametersI

Nulls both the Filter.limit and Filter.offset values.

norm(String) - Static method in class ome.services.scripts.RepoFile

Somewhat complicated method to turn any path into a unique like path rooted at "/".

norm() - Method in class ome.util.math.geom2D.PlanePoint

Calculates the Euclidian norm of this vector.

normalize() - Method in class ome.util.math.geom2D.PlanePoint

Calculates the unit vector of this vector, provided this is not the null vector.

not() - Method in interface ome.api.Search

Applies the next by* method to the previous by* method, so that a call Search.hasNext(), Search.next(), or Search.results() sees only the intersection of the two calls.

not() - Method in class ome.services.SearchBean

not_async(AMD_Search_not, Current) - Method in class ome.services.blitz.impl.SearchI

notAnnotatedBy(Details) - Method in interface ome.api.Search

Restricts entities by who has not annotated them with an Annotation matching the other filters.

notAnnotatedBy - Variable in class ome.services.search.SearchValues

notAnnotatedBy(Details) - Method in class ome.services.SearchBean

notAnnotatedBy_async(AMD_Search_notAnnotatedBy, Details, Current) - Method in class ome.services.blitz.impl.SearchI

notifications(String) - Method in class ome.services.sessions.SessionManagerImpl

notifyElementEvicted(Ehcache, Element) - Method in class ome.services.sessions.state.CacheListener

notifyElementExpired(Ehcache, Element) - Method in class ome.services.sessions.state.CacheListener

notifyElementPut(Ehcache, Element) - Method in class ome.services.sessions.state.CacheListener

notifyElementRemoved(Ehcache, Element) - Method in class ome.services.sessions.state.CacheListener

notifyElementUpdated(Ehcache, Element) - Method in class ome.services.sessions.state.CacheListener

notifyObservers(ImportEvent) - Method in class ome.formats.importer.ImportLibrary

notifyObservers(ImportEvent) - Method in interface ome.formats.importer.IObservable

Notify observers of event

notifyObservers(ImportEvent) - Method in class ome.formats.importer.util.ClientKeepAlive

notifyObservers(ImportEvent) - Method in class ome.formats.importer.util.ErrorHandler

notifyObservers(ImportEvent) - Method in class ome.formats.importer.util.FileUploader

notifyRemoveAll(Ehcache) - Method in class ome.services.sessions.state.CacheListener

NotNull - Annotation Type in ome.annotations

annotation used for determining the types of a Set

notNull(String[]) - Static method in class prefs

Returns an empty array if the argument is null.

notNullOrLikeOrEqual(QueryBuilder, String, Class, Object, boolean, boolean) - Static method in class ome.services.search.SearchAction

notNullOrLikeOrEqual(String, Class, Object, boolean, boolean) - Static method in class ome.services.search.SearchAction

notOwnedBy(Details) - Method in interface ome.api.Search

Uses the Details.getOwner() and Details.getGroup() information to restrict the entities which will be returned.

notOwnedBy - Variable in class ome.services.search.SearchValues

notOwnedBy(Details) - Method in class ome.services.SearchBean

notOwnedBy_async(AMD_Search_notOwnedBy, Details, Current) - Method in class ome.services.blitz.impl.SearchI

noUnique() - Method in class omero.sys.ParametersI

NS_COMMENT - Static variable in class ome.services.sharing.ShareBean

NS_ENABLED - Static variable in class ome.services.sharing.ShareBean

NS_IMPORTER_ARCHIVED - Static variable in interface ome.api.IMetadata

The name space indicating that the Boolean annotation indicated if an archived image is imported with the image.

NS_INSIGHT_RATING - Static variable in interface ome.api.IMetadata

The name space indicating that the Long annotation is a rating annotation i.e. an integer in the interval [0, 5].

NS_INSIGHT_TAG_SET - Static variable in interface ome.api.IMetadata

The name space indicating that the tag is used a tag set.

nsExcludes - Static variable in class ome.services.graphs.AnnotationGraphSpec

Collection of namespace values (defined as AnnotationGraphSpec.nsIncludes) which will be omitted from deletes by default.

NSEXPERIMENTERPHOTO - Static variable in class ome.logic.AdminImpl

nsIncludes - Static variable in class ome.services.graphs.AnnotationGraphSpec

Collection of namespace values (or LIKE values if they contain '%' or '?')

NULL_PLANE_SIZE - Static variable in class ome.io.nio.PixelsService

Null plane size constant.

NULL_RENDERER - Static variable in class ome.services.RenderingBean

Message if the rendering engine is not ready.

nullDetails() - Method in class pojos.DataObject

Returns true if the details are null otherwise false otherwise.

NullEventHandler - Class in ome.security.basic

Provides only the bare minimum of functionality to allow methods to succeed.

NullEventHandler(SecuritySystem, SessionFactory) - Constructor for class ome.security.basic.NullEventHandler

nullPlane - Static variable in class ome.io.nio.PixelsService

Null plane byte array.

NullQuerySource - Class in ome.services.query

always returns null for any id.

NullQuerySource() - Constructor for class ome.services.query.NullQuerySource

NullRedirector - Class in ome.services.blitz.redirect

Redirector implementation to effectively disable redirects.

NullRedirector() - Constructor for class ome.services.blitz.redirect.NullRedirector

nullSafe(Integer) - Method in class pojos.DataObject

nullSafe(RInt) - Method in class pojos.DataObject

nullSafe(Long) - Method in class pojos.DataObject

nullSafe(Double) - Method in class pojos.DataObject

nullSafe(Float) - Method in class pojos.DataObject

nullSafe(RFloat) - Method in class pojos.DataObject

nullSafe(RDouble) - Method in class pojos.DataObject

nullSafeGet(ResultSet, String[], Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType

nullSafeGroupId(IObject) - Static method in class ome.tools.hibernate.HibernateUtils

returns the id of the group of this entity, or null if: (1) the object is null, (2) the Details is null, (3) the group is null.

nullSafeOwnerId(IObject) - Static method in class ome.tools.hibernate.HibernateUtils

returns the id of the owner of this entity, or null if: (1) the object is null, (2) the Details is null, (3) the owner is null.

nullSafeSet(PreparedStatement, Object, int) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType

NullSessionStats - Class in ome.services.sessions.stats

Implementation of SimpleStats which does nothing.

NullSessionStats() - Constructor for class ome.services.sessions.stats.NullSessionStats

numberOfSubtypes(int) - Method in class ome.tools.hibernate.ExtendedMetadata.Locks

returns the number of subtypes for iterating over this secondary array.

numDone - Variable in class ome.formats.importer.ImportEvent.COUNT_EVENT

numDone - Variable in class ome.formats.importer.ImportEvent.PROGRESS_EVENT

numFiles - Variable in class ome.formats.importer.ImportCandidates.SCANNING

numOfDirectories - Variable in class ome.formats.importer.ImportConfig

O

Obj - Class in ome.services.sharing.data

Obj() - Constructor for class ome.services.sharing.data.Obj

Obj(String, long) - Constructor for class ome.services.sharing.data.Obj

OBJECT_TO_RTYPE - Static variable in class omero.util.IceMapper

OBJECTARRAY_TO_RTYPESEQ - Static variable in class omero.util.IceMapper

ObjectFactories - Static variable in class ome.services.roi.RoiTypes

ObjectFactories - Static variable in class omero.rtypes

ObjectiveData - Class in pojos

Hosts an objective used to capture an image.

ObjectiveData(Objective) - Constructor for class pojos.ObjectiveData

Creates a new instance.

objectList - Variable in class ome.services.sharing.data.ShareData

objectMap - Variable in class ome.services.sharing.data.ShareData

objects - Variable in class ome.services.messages.ReindexMessage

ObjectsReadCounter - Class in ome.services.sessions.stats

Counter for all the objects read in a session.

ObjectsReadCounter(int) - Constructor for class ome.services.sessions.stats.ObjectsReadCounter

objectsReadHardLimit - Variable in class ome.services.sessions.stats.CounterFactory

ObjectsReadStatsMessage - Class in ome.services.messages.stats

Published when some limit in user/group/session activity has been reached.

ObjectsReadStatsMessage(Object, long) - Constructor for class ome.services.messages.stats.ObjectsReadStatsMessage

ObjectsWrittenCounter - Class in ome.services.sessions.stats

Counter for all the objects read in a session.

ObjectsWrittenCounter(int) - Constructor for class ome.services.sessions.stats.ObjectsWrittenCounter

objectsWrittenHardLimit - Variable in class ome.services.sessions.stats.CounterFactory

ObjectsWrittenStatsMessage - Class in ome.services.messages.stats

ObjectsWrittenStatsMessage(Object, long) - Constructor for class ome.services.messages.stats.ObjectsWrittenStatsMessage

ObjHolder - Class in ome.services.sharing.data

ObjHolder() - Constructor for class ome.services.sharing.data.ObjHolder

ObjHolder(Obj) - Constructor for class ome.services.sharing.data.ObjHolder

ObjHolder.Patcher - Class in ome.services.sharing.data

ObjHolder.Patcher() - Constructor for class ome.services.sharing.data.ObjHolder.Patcher

ObjPrx - Interface in ome.services.sharing.data

ObjPrxHelper - Class in ome.services.sharing.data

ObjPrxHelper() - Constructor for class ome.services.sharing.data.ObjPrxHelper

ObjPrxHolder - Class in ome.services.sharing.data

ObjPrxHolder() - Constructor for class ome.services.sharing.data.ObjPrxHolder

ObjPrxHolder(ObjPrx) - Constructor for class ome.services.sharing.data.ObjPrxHolder

ObjSeqHelper - Class in ome.services.sharing.data

ObjSeqHelper() - Constructor for class ome.services.sharing.data.ObjSeqHelper

ObjSeqHolder - Class in ome.services.sharing.data

ObjSeqHolder() - Constructor for class ome.services.sharing.data.ObjSeqHolder

ObjSeqHolder(List<Obj>) - Constructor for class ome.services.sharing.data.ObjSeqHolder

observers - Variable in class ome.formats.importer.util.ErrorHandler

obtainProxy(String, Redirector.Context, String, SessionControlPrx, Current) - Method in class ome.services.blitz.redirect.AbstractRedirector

OCTETSTREAM - Static variable in class omero.grid.ParamsHelper

offset - Variable in class ome.util.mem.ReadOnlyByteArray

Marks the start of the slice.

offset - Variable in class omerojava.util.ReadOnlyByteArray

Marks the start of the slice.

ome.annotations - package ome.annotations

Runtime source annotation package for the OMERO server This includes classes that annotate source code and check metadata at runtime for server API calls.

ome.api - package ome.api

Contains the central verbs of the Omero System.

ome.api.local - package ome.api.local

Non-client service API for OMERO This includes interfaces for the local administration of the OMERO server.

ome.formats - package ome.formats

ome.formats.enums - package ome.formats.enums

ome.formats.enums.handler - package ome.formats.enums.handler

ome.formats.importer - package ome.formats.importer

ome.formats.importer.util - package ome.formats.importer.util

ome.formats.model - package ome.formats.model

ome.formats.model.handler - package ome.formats.model.handler

ome.io.bioformats - package ome.io.bioformats

ome.io.messages - package ome.io.messages

ome.io.nio - package ome.io.nio

New Input/Output handling for the OMERO server This includes interfaces/classes for the input and output handling of data within the OMERO server.

ome.logic - package ome.logic

The central repository of implementations which will be accessible through this server.

ome.security - package ome.security

JBoss and OMERO security handling This includes classes that provide security for the execution and usage of the OMERO server on a JBoss platform.

ome.security.auth - package ome.security.auth

ome.security.auth.providers - package ome.security.auth.providers

ome.security.basic - package ome.security.basic

Basic OMERO security contextual classes Basic classes that provide security context objects necessary to secure the implementation of the OMERO server on a JBoss platform.

ome.security.sharing - package ome.security.sharing

ome.services - package ome.services

Base services package for OMERO API services This includes classes that implement OMERO API services described as interfaces in the OMERO Common component.

ome.services.blitz - package ome.services.blitz

ome.services.blitz.fire - package ome.services.blitz.fire

ome.services.blitz.gateway - package ome.services.blitz.gateway

ome.services.blitz.gateway.services - package ome.services.blitz.gateway.services

ome.services.blitz.gateway.services.impl - package ome.services.blitz.gateway.services.impl

ome.services.blitz.gateway.services.util - package ome.services.blitz.gateway.services.util

ome.services.blitz.impl - package ome.services.blitz.impl

ome.services.blitz.measurements - package ome.services.blitz.measurements

ome.services.blitz.redirect - package ome.services.blitz.redirect

ome.services.blitz.repo - package ome.services.blitz.repo

ome.services.blitz.util - package ome.services.blitz.util

ome.services.db - package ome.services.db

ome.services.delete - package ome.services.delete

Implementations of the ome.api.IDelete service.

ome.services.eventlogs - package ome.services.eventlogs

ome.services.export - package ome.services.export

Helpers for implementing the necessary interfaces from Bio-Formats for mapping OMERO objects (ome.model.*) to OME-XML and OME-TIFF

ome.services.formats - package ome.services.formats

ome.services.fulltext - package ome.services.fulltext

All necessary classes for background indexing of metadata and attached binary files.

ome.services.fulltext.bridges - package ome.services.fulltext.bridges

Custom FieldBridge implementations which can be configured to be run on each indexing activity.

ome.services.graphs - package ome.services.graphs

Server classes for handling complicated graphs of model objects.

ome.services.messages - package ome.services.messages

Message implementations used throughout the server for internal communication.

ome.services.messages.stats - package ome.services.messages.stats

ome.services.pixeldata - package ome.services.pixeldata

ome.services.procs - package ome.services.procs

Internal process and process management This includes interfaces and classes that provide thread process management for internal processes critical to the operation of the OMERO server.

ome.services.procs.scripts - package ome.services.procs.scripts

Script processor infrastructure.

ome.services.projection - package ome.services.projection

ome.services.query - package ome.services.query

facilitates the creation of Hibernate Queries and Criteria.

ome.services.roi - package ome.services.roi

ome.services.scheduler - package ome.services.scheduler

ome.services.scripts - package ome.services.scripts

ome.services.search - package ome.services.search

Internal search implementation classes.

ome.services.sessions - package ome.services.sessions

ome.services.sessions.events - package ome.services.sessions.events

ome.services.sessions.state - package ome.services.sessions.state

ome.services.sessions.stats - package ome.services.sessions.stats

ome.services.sharing - package ome.services.sharing

ome.api.IShare support infrastructure.

ome.services.sharing.data - package ome.services.sharing.data

ome.services.throttling - package ome.services.throttling

ome.services.util - package ome.services.util

Helper classes to support OMERO service beans Instead of abstract classes, IOC methods and dependency injection is used to provide service interception for the Service (binary) bean classes.

ome.system - package ome.system

Provides the necessary container structure for the entire Omero system.

ome.tools - package ome.tools

OMERO Server Utility and Spring/Hibernate Tools Classes/Interfaces that implement File, Hibernate, Spring, Annotation, Hierarchy, etc. method mechanics for the OMERO server Related Documentation For more information, please see: TODO

ome.tools.hibernate - package ome.tools.hibernate

Hibernate specific tools for the OMERO Server Classes/Interfaces that implement Hibernate method mechanics for the OMERO server Related Documentation For more information, please see: TODO

ome.tools.lsid - package ome.tools.lsid

Life Science Identifier (LSID) tools Classes/Interfaces that manage conversions and creation of LSID unique identifiers Related Documentation For more information, please see: TODO

ome.tools.spring - package ome.tools.spring

OMERO Server tools specific to Spring Classes/Interfaces that implement AOP, Post-processing injection, session flushing, and factory management.

ome.util.math.geom2D - package ome.util.math.geom2D

Plane geometry data structures for OMERO This includes a several implementations of various two dimensional simple geometry classes to represent these structures within the OMERO system.

ome.util.mem - package ome.util.mem

Dynamic object instance and state management for OMERO This includes various implementations of copy and clonable operations.

ome.util.messages - package ome.util.messages

Messages package for specialized exception handling for OMERO.

omeis.providers.re - package omeis.providers.re

Red-Green-Blue (RGB) data structures and Image Rendering Service This package provides basic data structures to represent an RGB pixel set and provide a service for the rendering of this pixel set.

omeis.providers.re.codomain - package omeis.providers.re.codomain

Provides codomain pixel set data structures for Maps and Contexts.

omeis.providers.re.data - package omeis.providers.re.data

Provides classes needed to define XY planes within a dynamic 3D context.

omeis.providers.re.metadata - package omeis.providers.re.metadata

omeis.providers.re.quantum - package omeis.providers.re.quantum

OMENAME - Static variable in class pojos.ExperimenterData

Identifies the Experimenter#OMENAME field.

omero - package omero

omero.grid - package omero.grid

omero.model - package omero.model

omero.sys - package omero.sys

omero.util - package omero.util

OMERO_EMISSION_FILTER_SUFFIX - Static variable in class ome.formats.OMEROMetadataStoreClient

Emission filter LSID suffix.

OMERO_EVENT - Static variable in class ome.system.Login

Java property name for use in configuration of client login.

OMERO_EXCITATION_FILTER_SUFFIX - Static variable in class ome.formats.OMEROMetadataStoreClient

Excitation filter LSID suffix.

OMERO_GROUP - Static variable in class ome.system.Login

Java property name for use in configuration of client login.

OMERO_HOST - Static variable in class ome.system.Server

Java property name for use in configuration of the client connection.

OMERO_PASS - Static variable in class ome.system.Login

Java property name for use in configuration of client login.

OMERO_PORT - Static variable in class ome.system.Server

Java property name for use in configuration of the client connection.

OMERO_TABLE - Variable in class ome.services.fulltext.bridges.TablesBridge

Mimetype set on OriginalFile.mimetype (or in previous version, OriginalFile.format.value).

OMERO_USER - Static variable in class ome.system.Login

Java property name for use in configuration of client login.

omeroClass(String, boolean) - Static method in class omero.util.IceMapper

OmeroContext - Class in ome.system

Provides static access for the creation of singleton and non-singleton application contexts.

OmeroContext(String) - Constructor for class ome.system.OmeroContext

OmeroContext(String[]) - Constructor for class ome.system.OmeroContext

OmeroContext(String[], boolean) - Constructor for class ome.system.OmeroContext

OmeroContext(String[], ApplicationContext) - Constructor for class ome.system.OmeroContext

OmeroContext(String[], boolean, ApplicationContext) - Constructor for class ome.system.OmeroContext

OmeroContext.Locator - Class in ome.system

provides access to the protected methods of ContextSingletonBeanFactoryLocator which cannot be used externally.

OmeroContext.Locator() - Constructor for class ome.system.OmeroContext.Locator

omeroDataDir - Variable in class ome.services.blitz.impl.MetadataStoreI

omeroDataDir - Variable in class ome.services.OmeroFilePathResolver

The server's OMERO data directory.

OmeroFilePathResolver - Class in ome.services

OMERO server based resolver for file paths.

OmeroFilePathResolver(SqlAction, String) - Constructor for class ome.services.OmeroFilePathResolver

Constructor.

OmeroGateway - Class in ome.services.blitz.gateway

OmeroGateway(BlitzExecutor) - Constructor for class ome.services.blitz.gateway.OmeroGateway

OMEROImportFixture - Class in ome.formats

test fixture for importing files without a GUI.

OMEROImportFixture(OMEROMetadataStoreClient, OMEROWrapper) - Constructor for class ome.formats.OMEROImportFixture

OmeroInterceptor - Class in ome.security.basic

implements Interceptor for controlling various aspects of the Hibernate runtime.

OmeroInterceptor(Roles, SystemTypes, ExtendedMetadata, CurrentDetails, TokenHolder, SessionStats) - Constructor for class ome.security.basic.OmeroInterceptor

omerojava.util - package omerojava.util

OmeroMeasurementStore - Interface in ome.services.blitz.measurements

Sub-interface of MeasurementStore with extended life-cycle methods for handling exceptions during saving the measurements to multiple stores.

OmeroMetadata - Class in ome.services.blitz.impl

An implementation for MetadataStore and MetadataRetrieve that knows how to read and write the OMERO object model.

OmeroMetadata(DatabaseIdentity) - Constructor for class ome.services.blitz.impl.OmeroMetadata

OMEROMetadataStore - Class in ome.formats

An OMERO metadata store.

OMEROMetadataStore() - Constructor for class ome.formats.OMEROMetadataStore

Empty constructor for testing purposes.

OMEROMetadataStore(ServiceFactory) - Constructor for class ome.formats.OMEROMetadataStore

Creates a new instance.

OMEROMetadataStoreClient - Class in ome.formats

Client side implementation of the Bio-Formats MetadataStore.

OMEROMetadataStoreClient() - Constructor for class ome.formats.OMEROMetadataStoreClient

OmeroPixelsPyramidReader - Class in ome.io.bioformats

File format reader for OMERO pixels pyramid files.

OmeroPixelsPyramidReader() - Constructor for class ome.io.bioformats.OmeroPixelsPyramidReader

OmeroPixelsPyramidWriter - Class in ome.io.bioformats

File format writer for OMERO pixels pyramid files.

OmeroPixelsPyramidWriter() - Constructor for class ome.io.bioformats.OmeroPixelsPyramidWriter

OmeroReader - Class in ome.services.formats

Implementation of IFormatReader for use in export.

OmeroReader(RawPixelsStore, Pixels) - Constructor for class ome.services.formats.OmeroReader

OmeroReader(RawPixelsStorePrx, Pixels) - Constructor for class ome.services.formats.OmeroReader

OMEROWrapper - Class in ome.formats.importer

OMEROWrapper(ImportConfig) - Constructor for class ome.formats.importer.OMEROWrapper

Wrapper for bio-formats

OMEXMLModelComparator - Class in ome.formats

This comparator takes into account the OME-XML data model hierarchy and uses that to define equivalence.

OMEXMLModelComparator() - Constructor for class ome.formats.OMEXMLModelComparator

onAddError(ErrorContainer, String) - Method in class ome.formats.importer.util.ErrorHandler

Action to take on adding an error to container

onApplicationEvent(LoginAttemptMessage) - Method in class ome.security.auth.LoginAttemptListener

onApplicationEvent(EventLogMessage) - Method in class ome.security.basic.BasicSecuritySystem

onApplicationEvent(ApplicationEvent) - Method in class ome.services.blitz.fire.SessionManagerI

onApplicationEvent(ApplicationEvent) - Method in class ome.services.blitz.fire.TopicManager.Impl

onApplicationEvent(ApplicationEvent) - Method in class ome.services.eventlogs.EventLogLoader

onApplicationEvent(MissingPyramidMessage) - Method in class ome.services.pixeldata.PixelDataThread

onApplicationEvent(ContextRefreshedEvent) - Method in class ome.services.scheduler.SchedulerFactoryBean

onApplicationEvent(ApplicationEvent) - Method in class ome.services.sessions.SessionManagerImpl

onApplicationEvent(ApplicationEvent) - Method in class ome.services.throttling.AbstractThrottlingStrategy

onApplicationEvent(ApplicationEvent) - Method in class ome.services.util.DropBoxDirectoryCheck

onApplicationEvent(ApplicationEvent) - Method in class ome.services.util.ServiceHandler

onApplicationEvent(ContextRefreshedEvent) - Method in class ome.tools.spring.OnContextRefreshedEventListener

onBoundaries(double, double) - Method in class ome.util.math.geom2D.EllipseArea

Implemented as specified by the PlaneArea I/F.

onBoundaries(double, double) - Method in interface ome.util.math.geom2D.PlaneArea

Controls if a specified point is on the boundary of the PlaneArea.

onBoundaries(double, double) - Method in class ome.util.math.geom2D.RectangleArea

Implemented as specified by the PlaneArea I/F.

onCancel() - Method in class ome.formats.importer.util.ErrorHandler

action to take on cancel

onCollectionRecreate(Object, Serializable) - Method in class ome.security.basic.OmeroInterceptor

onCollectionRemove(Object, Serializable) - Method in class ome.security.basic.OmeroInterceptor

onCollectionUpdate(Object, Serializable) - Method in class ome.security.basic.OmeroInterceptor

OnContextRefreshedEventListener - Class in ome.tools.spring

ApplicationListener which only listens for ContextRefreshedEvent and only responds to the first one.

OnContextRefreshedEventListener() - Constructor for class ome.tools.spring.OnContextRefreshedEventListener

OnContextRefreshedEventListener(boolean, int) - Constructor for class ome.tools.spring.OnContextRefreshedEventListener

onDelete(Object, Serializable, Object[], String[], Type[]) - Method in class ome.security.basic.OmeroInterceptor

default logic

onDiskCache(String) - Method in interface ome.services.sessions.SessionManager

Returns after possibly creating an on-disk cache which can be used throughout the session.

onDiskCache(String) - Method in class ome.services.sessions.SessionManagerImpl

onDiskCache(String) - Method in class ome.services.sessions.state.SessionCache

onException(Exception) - Method in class ome.formats.importer.util.ErrorHandler

Action to take on exception

onFlushDirty(Object, Serializable, Object[], Object[], String[], Type[]) - Method in class ome.security.basic.OmeroInterceptor

callsback to BasicSecuritySystem.checkManagedDetails(IObject, Details) for properly setting Details.

onHearbeat(Runnable) - Method in class omero.client

onLoad(Object, Serializable, Object[], String[], Type[]) - Method in class ome.security.basic.OmeroInterceptor

default logic.

onlyAnnotatedBetween(Timestamp, Timestamp) - Method in interface ome.api.Search

Restricts entities by the time in which any annotation (which matches the other filters) was added them.

onlyAnnotatedBetween(Timestamp, Timestamp) - Method in class ome.services.SearchBean

onlyAnnotatedBetween_async(AMD_Search_onlyAnnotatedBetween, RTime, RTime, Current) - Method in class ome.services.blitz.impl.SearchI

onlyAnnotatedBy(Details) - Method in interface ome.api.Search

Restricts entities by who has annotated them with an Annotation matching the other filters.

onlyAnnotatedBy(Details) - Method in class ome.services.SearchBean

onlyAnnotatedBy_async(AMD_Search_onlyAnnotatedBy, Details, Current) - Method in class ome.services.blitz.impl.SearchI

onlyAnnotatedWith(Class...) - Method in interface ome.api.Search

Restricts entities to having an Annotation of all the given types.

onlyAnnotatedWith - Variable in class ome.services.search.SearchValues

onlyAnnotatedWith(Class...) - Method in class ome.services.SearchBean

onlyAnnotatedWith_async(AMD_Search_onlyAnnotatedWith, List<String>, Current) - Method in class ome.services.blitz.impl.SearchI

onlyCreatedBetween(Timestamp, Timestamp) - Method in interface ome.api.Search

Restricts the time between which an entity may have been created.

onlyCreatedBetween(Timestamp, Timestamp) - Method in class ome.services.SearchBean

onlyCreatedBetween_async(AMD_Search_onlyCreatedBetween, RTime, RTime, Current) - Method in class ome.services.blitz.impl.SearchI

onlyIds(Long...) - Method in interface ome.api.Search

Restricts the set of ids which will be checked.

onlyIds - Variable in class ome.services.search.SearchValues

onlyIds(Long...) - Method in class ome.services.SearchBean

onlyIds_async(AMD_Search_onlyIds, List<Long>, Current) - Method in class ome.services.blitz.impl.SearchI

onlyModifiedBetween(Timestamp, Timestamp) - Method in interface ome.api.Search

Restricts the time between which an entity may have last been modified.

onlyModifiedBetween(Timestamp, Timestamp) - Method in class ome.services.SearchBean

onlyModifiedBetween_async(AMD_Search_onlyModifiedBetween, RTime, RTime, Current) - Method in class ome.services.blitz.impl.SearchI

onlyOwnedBy(Details) - Method in interface ome.api.Search

Uses the Details.getOwner() and Details.getGroup() information to restrict the entities which will be returned.

onlyOwnedBy(Details) - Method in class ome.services.SearchBean

onlyOwnedBy_async(AMD_Search_onlyOwnedBy, Details, Current) - Method in class ome.services.blitz.impl.SearchI

onlyPermissionsChanged(Details, Details) - Static method in class ome.tools.hibernate.HibernateUtils

onlyType(Class<T>) - Method in interface ome.api.Search

Restricts the search to a single type.

onlyType(Class<T>) - Method in class ome.services.SearchBean

onlyType_async(AMD_Search_onlyType, String, Current) - Method in class ome.services.blitz.impl.SearchI

onlyTypes(Class<T>...) - Method in interface ome.api.Search

Restricts searches to a set of types.

onlyTypes - Variable in class ome.services.search.SearchValues

onlyTypes(Class<T>...) - Method in class ome.services.SearchBean

onlyTypes_async(AMD_Search_onlyTypes, List<String>, Current) - Method in class ome.services.blitz.impl.SearchI

onMerge(MergeEvent) - Method in class ome.security.basic.MergeEventListener

onMerge(MergeEvent, Map) - Method in class ome.security.basic.MergeEventListener

onNotSending(int, String) - Method in class ome.formats.importer.util.ErrorHandler

onPostDelete(PostDeleteEvent) - Method in class ome.security.ACLEventListener

unused

onPostDelete(PostDeleteEvent) - Method in class ome.security.basic.EventLogListener

onPostInsert(PostInsertEvent) - Method in class ome.security.ACLEventListener

unused

onPostInsert(PostInsertEvent) - Method in class ome.security.basic.EventLogListener

onPostLoad(PostLoadEvent) - Method in class ome.security.ACLEventListener

catches all load events after the fact, and tests the current users permissions to read that object.

onPostUpdate(PostUpdateEvent) - Method in class ome.security.ACLEventListener

unused

onPostUpdate(PostUpdateEvent) - Method in class ome.security.basic.EventLogListener

onPreDelete(PreDeleteEvent) - Method in class ome.security.ACLEventListener

onPreInsert(PreInsertEvent) - Method in class ome.security.ACLEventListener

onPreLoad(PreLoadEvent) - Method in class ome.security.ACLEventListener

unused

onPrepareStatement(String) - Method in class ome.security.basic.OmeroInterceptor

onPreUpdate(PreUpdateEvent) - Method in class ome.security.ACLEventListener

onPreUpdate(PreUpdateEvent) - Method in class ome.security.basic.UpdateEventListener

updates the update event field of an IObject instance.

onRefresh() - Method in class ome.system.OmeroContext

onRefresh(RefreshEvent) - Method in class ome.tools.hibernate.ReloadingRefreshEventListener

onRefresh(RefreshEvent, Map) - Method in class ome.tools.hibernate.ReloadingRefreshEventListener

onRelease(Class<IObject>, Set<Long>) - Method in class ome.services.delete.DeleteStep

onRelease(Class<IObject>, Set<Long>) - Method in class ome.services.export.ExporterStep

onRelease(Class<IObject>, Set<Long>) - Method in class ome.services.graphs.GraphStep

onSave(Object, Serializable, Object[], String[], Type[]) - Method in class ome.security.basic.OmeroInterceptor

callsback to BasicSecuritySystem.newTransientDetails(IObject) for properly setting Details

onSaveOrUpdate(SaveOrUpdateEvent) - Method in class ome.security.basic.SaveEventListener

onSending(int) - Method in class ome.formats.importer.util.ErrorHandler

onSent(int) - Method in class ome.formats.importer.util.ErrorHandler

onSessionClosed(Runnable) - Method in class omero.client

onSetOmeroContext(OmeroContext) - Method in class ome.services.blitz.impl.AbstractAmdServant

To be overridden by subclasses.

onSetOmeroContext(OmeroContext) - Method in class ome.services.blitz.impl.MetadataStoreI

onShutdown(Runnable) - Method in class omero.client

onUpdate(IObservable, ImportEvent) - Method in class ome.formats.importer.util.ErrorHandler

abstract on update method

onWindowChange() - Method in class omeis.providers.re.quantum.BinaryMaskQuantizer

onWindowChange() - Method in class omeis.providers.re.quantum.Quantization_8_16_bit

The input window size changed, rebuild the LUT.

onWindowChange() - Method in class omeis.providers.re.quantum.QuantumStrategy

Notifies when the input interval has changed or the mapping strategy has changed.

openBytes(int, byte[], int, int, int, int) - Method in class ome.services.formats.OmeroReader

openPlane2D(String, int, byte[]) - Method in class ome.formats.importer.OMEROWrapper

Obtains an object which represents a given sub-image of a plane within the file.

openPlane2D(String, int, byte[], int, int, int, int) - Method in class ome.formats.importer.OMEROWrapper

Obtains an object which represents a given sub-image of a plane within the file.

openSession() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

openTable(OriginalFile, Current) - Method in class ome.services.blitz.impl.SharedResourcesI

optimisticFailure(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

Optimizations - Class in omeis.providers.re

A container for any potential optimizations that the renderer can enable based on the data and rendering settings it has been fed.

Optimizations() - Constructor for class omeis.providers.re.Optimizations

optional - Variable in class ome.services.query.QueryParameterDef

whether or not this QueryParameter can be omitted or its value null.

options - Variable in class ome.services.graphs.BaseGraphSpec

Options passed to the #initialize(long, Map) method, which may be used during #delete(Session, int) to alter behavior.

optlock - Variable in class ome.services.sharing.data.ShareData

or() - Method in interface ome.api.Search

Applies the next by* method to the previous by* method, so that a call Search.hasNext(), Search.next(), or Search.results() sees only the union of the two calls.

or() - Method in class ome.services.SearchBean

or(String) - Method in class ome.tools.hibernate.QueryBuilder

Appends "or" plus your string unless this is the first where-spec in which case it is simply appended.

or_async(AMD_Search_or, Current) - Method in class ome.services.blitz.impl.SearchI

order(String, boolean) - Method in class ome.tools.hibernate.QueryBuilder

orderBy - Variable in class ome.services.search.SearchValues

orderByAscending(String) - Static method in class ome.services.search.SearchAction

orderByPath(String) - Static method in class ome.services.search.SearchAction

org.hibernate.stat - package org.hibernate.stat

origin - Variable in class ome.util.math.geom2D.Line

The origin point of the line.

ORIGINAL_METADATA_NAME - Static variable in class pojos.FileAnnotationData

The default name for the original metadata file.

OriginalFilesService - Class in ome.io.nio

Raw file service which provides access to FileBuffers.

OriginalFilesService(String) - Constructor for class ome.io.nio.OriginalFilesService

Constructor

originX1 - Variable in class ome.util.math.geom2D.Segment

The origin of the segment's first element.

originX2 - Variable in class ome.util.math.geom2D.Segment

The origin of the segment's first element.

orphan() - Method in class omero.sys.ParametersI

Sets the orphan parameter to true.

osf - Variable in class ome.logic.AdminImpl

OTFData - Class in pojos

Hosts an OTF.

OTFData(OTF) - Constructor for class pojos.OTFData

Creates a new instance.

outputEnvironment(String) - Method in interface ome.services.sessions.SessionManager

Returns a copy of the output environment.

outputEnvironment(String) - Method in class ome.services.sessions.SessionManagerImpl

OverlayMetadataStore - Class in ome.formats

Client side metadata store implementation that only deals with overlays.

OverlayMetadataStore() - Constructor for class ome.formats.OverlayMetadataStore

overrideKeep() - Method in class ome.services.graphs.AnnotationGraphSpec

Returns true to prevent skipping of the entire subspec if there were any "excludes" passed in with the options.

overrideKeep() - Method in class ome.services.graphs.BaseGraphSpec

Always returns false.

overrideKeep() - Method in interface ome.services.graphs.GraphSpec

For some GraphSpec type/option combinations, a "KEEP" setting may need to be overridden.

overrides() - Method in class ome.security.basic.EventListenersFactoryBean

own(String) - Method in class ome.services.db.DatabaseIdentity

ownedBy - Variable in class ome.services.search.SearchValues

owner - Variable in class ome.services.sharing.data.ShareData

ownerCount(long) - Method in class ome.services.sharing.data.ShareMap

ownerOrGroup(Class, Criteria) - Method in class ome.services.search.SearchAction

ownerOrGroup(Class, QueryBuilder, String) - Method in class ome.services.search.SearchAction

ownerOrGroupFilters(Session, String[], String[]) - Method in class ome.services.query.Query

standard filter used by many subclasses which uses the PojoOptions#isExperimenter() and PojoOptions#isGroup() booleans to see if a filter should be turned on.

P

pack(ReadOnlyByteArray, int, int) - Method in class omerojava.util.DoubleConverter

Implemented as specified by BytesConverter

pack(ReadOnlyByteArray, int, int) - Method in class omerojava.util.FloatConverter

Implemented as specified by BytesConverter

pack(ReadOnlyByteArray, int, int) - Method in class omerojava.util.IntConverter

Implemented as specified by BytesConverter

pack(ReadOnlyByteArray, int, int) - Method in class omerojava.util.UintConverter

Implemented as specified by BytesConverter

page(int, int) - Method in class omero.sys.ParametersI

Sets both the Filter.limit and Filter.offset values by wrapping the arguments in RInt and passing the values to ParametersI.page(RInt, RInt)

page(RInt, RInt) - Method in class omero.sys.ParametersI

Creates a Filter if necessary and sets both Filter.limit and Filter.offset.

param(String, Object) - Method in class ome.tools.hibernate.QueryBuilder

ParametersI - Class in omero.sys

Helper subclass of Parameters for simplifying method parameter creation.

ParametersI() - Constructor for class omero.sys.ParametersI

Default constructor creates the ParametersI.map() instance to prevent later NullPointerExceptions.

ParametersI(Map<String, RType>) - Constructor for class omero.sys.ParametersI

Uses (and does not copy) the given Map as the named parameter store in this instance.

paramList(String, Collection) - Method in class ome.tools.hibernate.QueryBuilder

params - Variable in class ome.services.query.Query

container of QueryParameter instances.

params(Parameters) - Method in class ome.tools.hibernate.QueryBuilder

params(Current) - Method in class omero.grid.InteractiveProcessorI

ParamsHelper - Class in omero.grid

ParamsHelper(ParamsHelper.Acquirer, Executor, Principal) - Constructor for class omero.grid.ParamsHelper

ParamsHelper.Acquirer - Interface in omero.grid

Interface added in order to allow ParamHelper instances to use methods from SharedResourcesI.

parent - Variable in class ome.services.graphs.GraphStep

Final member of GraphStep.stack which is the direct ancestor of this step.

parse(String[]) - Static method in class ome.logic.HardWiredInterceptor

Produces a List of instantiated interceptors from a list of HardWiredInterceptor subclass names.

parse(String) - Method in class ome.security.auth.LdapConfig

parse(OriginalFile, OriginalFilesService, Map<String, FileParser>) - Method in class ome.services.fulltext.BridgeHelper

Attempts to parse the given OriginalFile.

parse(File) - Method in class ome.services.fulltext.FileParser

Uses FileParser.doParse(File) to create manageable chunks of a file for indexing.

parse(String[], String[], String[]) - Static method in class ome.services.search.SomeMustNone

parse(ShareData) - Method in class ome.services.sharing.ShareStore

parse(long, byte[]) - Method in class ome.services.sharing.ShareStore

parseAndSetInt(InitializationData, String, int) - Method in class omero.client

parseAwtPath(String) - Static method in class omero.model.SmartShape.Util

parseData(Map) - Method in interface ome.api.IResults

server-side parsing of data maps

parseField(String) - Static method in class ome.tools.lsid.LsidUtils

takes a field identifier as code-generated in each IObject class and produces a back-end useable name.

parseFilter(Criteria, Filter) - Method in class ome.logic.QueryImpl

responsible for applying the information provided in a Filter to a org.hibernate.Critieria instance.

parseFlexMaps(Preferences) - Method in class ome.formats.importer.util.IniFileLoader

Parse Flex reader server maps

parsePoints(String) - Static method in class omero.model.SmartShape.Util

parsePointsToIntegerList(String) - Method in class pojos.ShapeData

Parses the points list from the string to a list of integer objects.

parsePointsToPath(String, boolean) - Static method in class omero.model.SmartShape.Util

parsePointsToPoint2DList(String) - Method in class pojos.ShapeData

Parses the points list from the string to a list of point2d objects.

parsers - Variable in class ome.services.fulltext.FullTextBridge

parseType(String) - Static method in class ome.tools.lsid.LsidUtils

takes a field identifier as code-generated in each IObject class and produces a back-end useable type name.

passesFilter(Details, Long, Long, boolean, boolean, boolean) - Method in class ome.tools.hibernate.SecurityFilter

tests that the Details argument passes the security test that this filter defines.

passivate() - Method in interface ome.api.StatefulServiceInterface

Perform whatever passivation is possible or throw an exception.

passivate() - Method in class ome.services.JobBean

Does nothing.

passivate() - Method in class ome.services.RawFileBean

passivate() - Method in class ome.services.RawPixelsBean

passivate() - Method in class ome.services.RenderingBean

passivate() - Method in class ome.services.SearchBean

passivate() - Method in class ome.services.ThumbnailBean

passivate_async(AMD_StatefulServiceInterface_passivate, Current) - Method in class ome.services.blitz.impl.AbstractAmdServant

passivate_async(AMD_StatefulServiceInterface_passivate, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI

passivate_async(AMD_StatefulServiceInterface_passivate, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI

passivationNotAllowed() - Method in class ome.services.util.BeanHelper

password - Variable in class ome.formats.importer.ImportConfig

PasswordChangeException - Exception in ome.security.auth

Caught exception thrown from PasswordProvider.changePassword(String, String) to allow read-only implementations to refuse an action.

PasswordChangeException(String) - Constructor for exception ome.security.auth.PasswordChangeException

passwordDigest(String) - Method in class ome.security.auth.PasswordUtil

Creates an MD5 hash of the given clear text and base64 encodes it.

passwordProvider - Variable in class ome.logic.AdminImpl

PasswordProvider - Interface in ome.security.auth

Authentication interface responsible for checking and changing passwords.

PasswordProviders - Class in ome.security.auth

Composite class which delegates to each of the configured providers in turn.

PasswordProviders(PasswordProvider...) - Constructor for class ome.security.auth.PasswordProviders

passwordUtil - Variable in class ome.logic.AdminImpl

PasswordUtil - Class in ome.security.auth

Static methods for dealing with password hashes and the "password" table.

PasswordUtil(SqlAction) - Constructor for class ome.security.auth.PasswordUtil

PasswordUtility - Interface in ome.security.auth

Extension interface to PasswordProvider for methods which may or may not be available from a provider implementation.

patch(Object) - Method in class ome.services.sharing.data.ObjHolder.Patcher

patch(Object) - Method in class ome.services.sharing.data.ShareDataHolder.Patcher

patch(Object) - Method in class ome.services.sharing.data.ShareItemHolder.Patcher

path(String) - Method in class ome.services.graphs.GraphEntry

path - Variable in class ome.services.scripts.RepoFile.FsFile

pathMsg - Variable in class ome.services.graphs.GraphStep

String representation of the path to this GraphEntry used for logging.

PDF - Static variable in class pojos.FileAnnotationData

Identifies the PDF file formats.

PdfParser - Class in ome.services.fulltext

FileParser for "application/pdf" files using PDFBox.

PdfParser() - Constructor for class ome.services.fulltext.PdfParser

PermissionData - Class in pojos

Simple data object to wrap a Permissions instance.

PermissionData() - Constructor for class pojos.PermissionData

Creates a new instance.

PermissionData(Permissions) - Constructor for class pojos.PermissionData

Creates a new instance.

permissions(Class<T>) - Method in class ome.logic.TypesImpl

permissionsClause(EventContext, QueryBuilder) - Static method in class ome.services.graphs.GraphState

Appends a clause to the QueryBuilder based on the current user.

PermissionsI - Class in omero.model

Blitz wrapper around the Permissions class.

PermissionsI() - Constructor for class omero.model.PermissionsI

PermissionsI(String) - Constructor for class omero.model.PermissionsI

PermissionsVerifierI - Class in ome.services.blitz.fire

PermissionsVerifierI(Ring, SessionManager, Executor, String) - Constructor for class ome.services.blitz.fire.PermissionsVerifierI

PermitAll - Annotation Type in ome.annotations

Security annotation which allows a method to be called by all users regardless of their status.

PerSessionStats - Class in ome.services.sessions.stats

Delegates to a SessionStats which is acquired on every method invocation.

PerSessionStats(CurrentDetails) - Constructor for class ome.services.sessions.stats.PerSessionStats

PersistentEventLogLoader - Class in ome.services.eventlogs

EventLogLoader implementation which keeps tracks of the last EventLog instance, and always provides the next unindexed instance.

PersistentEventLogLoader() - Constructor for class ome.services.eventlogs.PersistentEventLogLoader

PersistentEventLogLoader - Class in ome.services.fulltext

EventLogLoader implementation which keeps tracks of the last EventLog instance, and always provides the next unindexed instance.

PersistentEventLogLoader() - Constructor for class ome.services.fulltext.PersistentEventLogLoader

PersistentEventLogLoader - Class in ome.services.pixeldata

EventLogLoader implementation which keeps tracks of the last EventLog instance, and always provides the next unindexed instance.

PersistentEventLogLoader(String) - Constructor for class ome.services.pixeldata.PersistentEventLogLoader

PersonContextMapper - Class in ome.security.auth

Specialized OME Experimenter context mapper.

PersonContextMapper(LdapConfig, String) - Constructor for class ome.security.auth.PersonContextMapper

PersonContextMapper(LdapConfig, String, String) - Constructor for class ome.security.auth.PersonContextMapper

PerThreadStats - Class in ome.services.sessions.stats

Delegates to a SessionStats which is acquired on every method invocation.

PerThreadStats(CurrentDetails) - Constructor for class ome.services.sessions.stats.PerThreadStats

PHOTOMETRIC_MONOCHROME - Static variable in class omeis.providers.re.Renderer

Identifies the type used to store photometric interpretation values.

pid() - Method in class omero.util.TempFileManager

Returns some representation of the current process's id

ping() - Method in class ome.formats.OMEROMetadataStoreClient

Pings all registered OMERO Blitz proxies.

PixelBuffer - Interface in ome.io.nio

This interface declares the I/O responsibilities of a buffer, file or otherwise, that contains a 5-dimensional Pixel array (XYZCT).

PixelBufferException - Exception in ome.io.nio

PixelBufferException(String) - Constructor for exception ome.io.nio.PixelBufferException

PixelData - Class in ome.services.roi

Strategy for loading and optionally caching pixel data.

PixelData(PixelsService, IPixels) - Constructor for class ome.services.roi.PixelData

PixelDataHandler - Class in ome.services.pixeldata

Simple action which can be done in an asynchronous thread in order to process PIXELDATA event logs.

PixelDataHandler(PersistentEventLogLoader, PixelsService) - Constructor for class ome.services.pixeldata.PixelDataHandler

PixelDataThread - Class in ome.services.pixeldata

PixelDataThread(SessionManager, Executor, PixelDataHandler, String) - Constructor for class ome.services.pixeldata.PixelDataThread

Uses default Principal for processing

PixelDataThread(SessionManager, Executor, PixelDataHandler, Principal, String) - Constructor for class ome.services.pixeldata.PixelDataThread

Main constructor.

pixelMap - Static variable in class omerojava.util.PixelTypes

Set the pixels Map containing the byte size of the map.

pixels - Variable in class ome.formats.importer.ImportEvent.IMPORT_DONE

pixels - Variable in class ome.formats.importer.ImportSize

pixels(String, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI

pixels - Variable in class omero.util.RPSTileLoop

Instance will be replaced on RawPixelsStorePrx.save()

PIXELS - Static variable in class pojos.ImageData

Identifies the Image#PIXELS field.

PIXELS_PATH - Static variable in class ome.io.nio.AbstractFileSystemService

PixelsCache - Class in omerojava.util

Caches Plane2D data, within a given pixels set, that have been rendered.

PixelsCache(int, int) - Constructor for class omerojava.util.PixelsCache

Creates a new instance.

pixelsData - Variable in class ome.logic.RenderingSettingsImpl

Reference to the service used to retrieve the pixels data.

PixelsData - Class in pojos

The data that makes up an OME Pixels object along with a back pointer to the Image that owns this Pixels.

PixelsData() - Constructor for class pojos.PixelsData

Creates a new instance.

PixelsData(Pixels) - Constructor for class pojos.PixelsData

Creates a new instance.

PixelsI - Class in ome.services.blitz.impl

Implementation of the IPixels service.

PixelsI(IPixels, BlitzExecutor) - Constructor for class ome.services.blitz.impl.PixelsI

pixelsID - Variable in class ome.io.messages.MissingPyramidMessage

PixelsImpl - Class in ome.logic

implementation of the Pixels service interface.

PixelsImpl() - Constructor for class ome.logic.PixelsImpl

pixelsMetadata - Variable in class ome.logic.RenderingSettingsImpl

Reference to the service used to retrieve the pixels metadata.

PixelsProcessor - Class in ome.formats.model

Processes the pixels sets of an IObjectContainerStore and ensures that the physical pixel dimensions are updated if they were specified by the user.

PixelsProcessor() - Constructor for class ome.formats.model.PixelsProcessor

PixelsService - Class in ome.io.nio

PixelsService(String) - Constructor for class ome.io.nio.PixelsService

Constructor.

PixelsService(String, FilePathResolver) - Constructor for class ome.io.nio.PixelsService

Constructor.

PixelsService(String, FilePathResolver, BackOff, TileSizes) - Constructor for class ome.io.nio.PixelsService

Constructor.

pixelsService - Variable in class ome.services.pixeldata.PixelDataHandler

pixelsService - Variable in class ome.services.projection.ProjectionBean

Reference to the service used to retrieve the pixels data.

PixelTypes - Class in omerojava.util

PixelTypes() - Constructor for class omerojava.util.PixelTypes

pixId - Variable in class ome.formats.importer.ImportEvent.PROGRESS_EVENT

Plane1D - Class in omerojava.util

Plane1D(ReadOnlyByteArray, int, int, int, BytesConverter) - Constructor for class omerojava.util.Plane1D

Creates a new intance.

Plane2D - Class in omeis.providers.re.data

Plane2D(PlaneDef, Pixels, PixelData) - Constructor for class omeis.providers.re.data.Plane2D

Constructor that sub-classes must call.

Plane2D - Class in omerojava.util

Holds structure used to mapped the raw pixels data.

Plane2D(ReadOnlyByteArray, int, int, int, BytesConverter) - Constructor for class omerojava.util.Plane2D

Creates a new intance.

PlaneArea - Interface in ome.util.math.geom2D

Interface that all areas of the Euclidean space R² must implement.

planeDef - Variable in class omeis.providers.re.data.Plane2D

The type of plane.

PlaneDef - Class in omeis.providers.re.data

Identifies a 2D-plane in the XYZ moving frame of the 3D stack.

PlaneDef(int, int) - Constructor for class omeis.providers.re.data.PlaneDef

Creates a new instance.

PlaneFactory - Class in omeis.providers.re.data

Encapsulates access to the image raw data.

PlaneFactory() - Constructor for class omeis.providers.re.data.PlaneFactory

PlaneInfoProcessor - Class in ome.formats.model

Processes the plane info sets of an IObjectContainerStore and removes entities of this rapidly exploding object that have no metadata populated.

PlaneInfoProcessor() - Constructor for class ome.formats.model.PlaneInfoProcessor

PlanePoint - Class in ome.util.math.geom2D

Represents a point in the Euclidean space R².

PlanePoint(double, double) - Constructor for class ome.util.math.geom2D.PlanePoint

Creates a new instance.

planes - Variable in class ome.services.formats.OmeroReader

PlaneSlicingContext - Class in omeis.providers.re.codomain

We consider that the image is composed of eight 1-bit planes ranging from bit-plane 0 for the least significant bit to bit-plane 7 for the most significant bit.

PlaneSlicingContext(int, int, boolean) - Constructor for class omeis.providers.re.codomain.PlaneSlicingContext

Creates a new instance.

PLATE_LINKS - Static variable in class pojos.ScreenData

Identifies the Screen#PLATELINKS field.

PlateAcquisitionData - Class in pojos

The data that makes up an OME PlateAcquisition.

PlateAcquisitionData() - Constructor for class pojos.PlateAcquisitionData

Creates a new instance.

PlateAcquisitionData(PlateAcquisition) - Constructor for class pojos.PlateAcquisitionData

Creates a new instance.

PlateData - Class in pojos

The data that makes up an OME Plate along with links to its contained Well and enclosing Screen as well as the Experimenter that owns this Plate.

PlateData() - Constructor for class pojos.PlateData

Creates a new instance.

PlateData(Plate) - Constructor for class pojos.PlateData

Creates a new instance.

plateDescription - Variable in class ome.formats.importer.ImportConfig

PLATEIMAGES_QUERY - Static variable in class ome.services.delete.DeleteBean

plateName - Variable in class ome.formats.importer.ImportConfig

PointData - Class in pojos

Represents a point in the Euclidean space R².

PointData(Shape) - Constructor for class pojos.PointData

Creates a new instance.

PointData() - Constructor for class pojos.PointData

Create a new instance of PointData, creating a new pointI Object.

PointData(double, double) - Constructor for class pojos.PointData

Create a new instance of the PointData,

points(double, double, double, double) - Static method in class omero.model.SmartShape.Util

Returns the four corner points of a rectangle

pointsByBoundingBox(Shape, Rectangle2D, SmartShape.PointCallback) - Static method in class omero.model.SmartShape.Util

pointsToPath(List<Point>, boolean) - Static method in class omero.model.SmartShape.Util

pojos - package pojos

pojos.util - package pojos.util

PojosFindAnnotationsQueryDefinition - Class in ome.services.query

PojosFindAnnotationsQueryDefinition(Parameters) - Constructor for class ome.services.query.PojosFindAnnotationsQueryDefinition

PojosFindHierarchiesQueryDefinition - Class in ome.services.query

walks up the hierarchy tree starting at Image nodes while fetching various information.

PojosFindHierarchiesQueryDefinition(Parameters) - Constructor for class ome.services.query.PojosFindHierarchiesQueryDefinition

PojosGetImagesByOptionsQueryDefinition - Class in ome.services.query

PojosGetImagesByOptionsQueryDefinition(Parameters) - Constructor for class ome.services.query.PojosGetImagesByOptionsQueryDefinition

PojosGetImagesQueryDefinition - Class in ome.services.query

PojosGetImagesQueryDefinition(Parameters) - Constructor for class ome.services.query.PojosGetImagesQueryDefinition

PojosGetUserImagesQueryDefinition - Class in ome.services.query

PojosGetUserImagesQueryDefinition(Parameters) - Constructor for class ome.services.query.PojosGetUserImagesQueryDefinition

PojosImpl - Class in ome.logic

implementation of the Pojos service interface.

PojosImpl() - Constructor for class ome.logic.PojosImpl

PojosLoadHierarchyQueryDefinition - Class in ome.services.query

PojosLoadHierarchyQueryDefinition(Parameters) - Constructor for class ome.services.query.PojosLoadHierarchyQueryDefinition

poll(Current) - Method in class ome.services.blitz.impl.ScriptProcessI

PolygonData - Class in pojos

Represents an Polygon shape in the Euclidean space R².

PolygonData(Shape) - Constructor for class pojos.PolygonData

Creates a new instance.

PolygonData() - Constructor for class pojos.PolygonData

Creates a new instance of PolygonData.

PolygonData(List<Point2D.Double>, List<Point2D.Double>, List<Point2D.Double>, List<Integer>) - Constructor for class pojos.PolygonData

Creates a new instance of the PolygonData, set the points in the polygon.

PolylineData - Class in pojos

Represents an Polyline shape in the Euclidean space R².

PolylineData(Shape) - Constructor for class pojos.PolylineData

Creates a new instance.

PolylineData() - Constructor for class pojos.PolylineData

Creates a new instance of polyline, creating a new PolylineI Object.

PolylineData(List<Point2D.Double>, List<Point2D.Double>, List<Point2D.Double>, List<Integer>) - Constructor for class pojos.PolylineData

Create a new instance of the PolylineData, set the points in the polyline.

POLYNOMIAL - Static variable in class omeis.providers.re.quantum.QuantumFactory

Flag to select a polynomial map for the quantization process.

PolynomialMap - Class in omeis.providers.re.quantum

This class implements the QuantumMap interface.

PolynomialMap() - Constructor for class omeis.providers.re.quantum.PolynomialMap

pop(GraphOpts) - Method in class ome.services.graphs.GraphEntry

pop() - Method in class ome.services.graphs.GraphOpts

pop(GraphOpts) - Method in class ome.services.graphs.GraphStep

pop() - Method in class ome.services.pixeldata.PersistentEventLogLoader

pop(List<IObject>) - Method in class ome.services.SearchBean

Wrapper method which should be called on all results for the user.

pop(String[]) - Static method in class prefs

Creates a new subarray from the argument, effectively popping off the first element.

popRoi - Variable in class ome.services.blitz.impl.MetadataStoreI

populateMinMax(double[][][]) - Method in class ome.formats.OMEROMetadataStore

Synchronize the minimum and maximum intensity values with those specified by the client and save them in the DB.

populateMinMax() - Method in class ome.formats.OMEROMetadataStoreClient

Sends all the minimums and maximums for all images processed so far to the server.

populateMinMax_async(AMD_MetadataStore_populateMinMax, double[][][], Current) - Method in class ome.services.blitz.impl.MetadataStoreI

PopulateRoiJob - Class in ome.services.roi

Start-up task which guarantees that lib/python/populateroi.py is added as a script to the server.

PopulateRoiJob(Roles, String, Executor) - Constructor for class ome.services.roi.PopulateRoiJob

PopulateRoiJob(Roles, String, Executor, File) - Constructor for class ome.services.roi.PopulateRoiJob

PopulateRoiJob(Roles, Principal, Executor, File) - Constructor for class ome.services.roi.PopulateRoiJob

port - Variable in class ome.formats.importer.ImportConfig

postFlush(Iterator) - Method in class ome.security.basic.OmeroInterceptor

postProcess() - Method in class ome.formats.OMEROMetadataStoreClient

Post processes the internal structure of the client side MetadataStore.

postProcess() - Method in class ome.io.bioformats.OmeroPixelsPyramidWriter

Performs re-compression post processing on the pixel pyramid.

postProcess(ListableBeanFactory) - Method in class ome.services.graphs.BaseGraphSpec

postProcess(ListableBeanFactory) - Method in class ome.services.graphs.GraphEntry

Load the spec which has the same name as this entry, but do not load the spec if the name matches GraphEntry.name.

postProcess(ListableBeanFactory) - Method in interface ome.services.graphs.GraphSpec

Gives all specs a chance to reference subspecs.

postProcess_async(AMD_MetadataStore_postProcess, Current) - Method in class ome.services.blitz.impl.MetadataStoreI

Called after some number of Passes the #savedPixels to a background processor for further work.

postProcessAfterInitialization(Object, String) - Method in class ome.services.blitz.util.ApiConsistencyCheck

postProcessAfterInitialization(Object, String) - Method in class ome.services.graphs.GraphSpecPostProcessor

postProcessBeforeInitialization(Object, String) - Method in class ome.services.blitz.util.ApiConsistencyCheck

No-op

postProcessBeforeInitialization(Object, String) - Method in class ome.services.graphs.GraphSpecPostProcessor

preClose() - Method in class ome.services.blitz.gateway.OmeroGateway

preClose() - Method in class ome.services.blitz.impl.AbstractAmdServant

preClose() - Method in class ome.services.blitz.impl.ExporterI

preClose() - Method in class ome.services.blitz.impl.MetadataStoreI

preClose() - Method in class ome.services.blitz.impl.SharedResourcesI

preClose() - Method in class ome.services.blitz.repo.RepoRawFileStoreI

Preference - Class in ome.system

Definition of a server configuration variable ("preference") along with its mutability, visibility, aliases and other important information.

Preference() - Constructor for class ome.system.Preference

By default, configures this instance for PropertyPlaceholderConfigurer.SYSTEM_PROPERTIES_MODE_OVERRIDE as well as ignoring unfound resources.

Preference(String, boolean, Preference.Visibility, String[]) - Constructor for class ome.system.Preference

Preference.Visibility - Enum in ome.system

PreferenceContext - Class in ome.system

Central configuration for OMERO properties from (in order): Any injected Properties instances Java System.getProperties() Any configured property files As of OMERO 4.2, server configurations are not stored in Java's Preferences API but in an IceGrid xml file under etc/grid of the server installation.

PreferenceContext() - Constructor for class ome.system.PreferenceContext

By default, configures this instance for PropertyPlaceholderConfigurer.SYSTEM_PROPERTIES_MODE_OVERRIDE as well as ignoring unfound resources.

preFlush(Iterator) - Method in class ome.security.basic.OmeroInterceptor

prefs - Class in <Unnamed>

Command-line (and static) utility for working with the omero.prefs Preferences node in order to store Java properties-file like values on a user basis.

prefs() - Constructor for class prefs

prepare(Set<Long>) - Method in interface ome.api.RawPixelsStore

Prepares the stateful service with a cache of loaded Pixels objects.

prepare(Map<Integer, Image>) - Method in class ome.formats.importer.ImportLibrary

Prepares the metadata store using existing metadata that has been pre-registered by OMERO.fs.

prepare(Map<Integer, Image>) - Method in class ome.formats.OMEROMetadataStoreClient

Prepares the metadata store using existing metadata that has been pre-registered by OMERO.fs.

prepare(Set<Long>) - Method in class ome.services.RawPixelsBean

prepare_async(AMD_RawPixelsStore_prepare, List<Long>, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI

prepare_async(AMD_RawPixelsStore_prepare, List<Long>, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI

preparePassword(String) - Method in class ome.security.auth.PasswordUtil

preparePixelsStore(List<Long>) - Method in class ome.formats.OMEROMetadataStoreClient

Prepares the server side RawPixelsStore.

prepareReload() - Method in class ome.services.sessions.SessionManagerImpl

prepareStatement() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

previewImageDelete(long, boolean) - Method in interface ome.api.IDelete

Returns all entities which would be deleted by a call to IDelete.deleteImage(long, boolean).

previewImageDelete(long, boolean) - Method in class ome.services.delete.DeleteBean

This uses DeleteBean.IMAGE_QUERY to load all the subordinate metadata of the Image which will be deleted.

previewImageDelete_async(AMD_IDelete_previewImageDelete, long, boolean, Current) - Method in class ome.services.blitz.impl.DeleteI

primaryColorEnabled - Variable in class omeis.providers.re.Optimizations

The channel bindings are only "primary" colors.

PRIMITIVE - Static variable in class omero.util.IceMapper

PRIMITIVE_FILTERABLE_COLLECTION_MAP - Static variable in class omero.util.IceMapper

PRIMITIVE_MAP - Static variable in class omero.util.IceMapper

principal - Variable in class ome.services.blitz.fire.Ring

principal() - Method in class ome.services.blitz.fire.Ring

principal() - Method in interface ome.services.blitz.redirect.Redirector.Context

Principal instance which can be used for internal calls the Executor.

principal - Variable in class ome.services.util.ExecutionThread

principal() - Method in class ome.services.util.Executor.Impl

principal() - Method in interface ome.services.util.Executor

Returns a Principal representing your current session or null, if none is active.

Principal - Class in ome.system

implementation of Principal.

Principal(String) - Constructor for class ome.system.Principal

Creates a Principal with null group and event type.

Principal(String, String, String) - Constructor for class ome.system.Principal

principal - Variable in class ome.system.SessionInitializer

Principal given by the user

principalHolder - Variable in class ome.security.basic.BasicSecurityWiring

PrincipalHolder - Interface in ome.security.basic

Stack of active Principal instances.

principalHolder - Variable in class ome.services.sessions.SessionManagerImpl

principalHolder - Variable in class ome.services.util.Executor.Impl

print() - Method in class ome.formats.importer.ImportCandidates

Prints the "standard" representation of the groups, which is parsed by other software layers.

print(String) - Method in class ome.services.blitz.util.CommonsLoggingAdapter

print(String[]) - Static method in class prefs

Prints the arg array and returns an empty array (for exit purposes)

printDebug(String[]) - Static method in class prefs

Delegates to prefs.printErr(String[]) iff prefs.DEBUG is true.

printErr(String[]) - Static method in class prefs

Prints the arg array and returns the input array (for exit purposes)

printErrorText(Throwable) - Static method in class ome.services.blitz.gateway.services.util.ServiceUtilities

Utility method to print the error message

process(IObjectContainerStore) - Method in class ome.formats.model.ChannelProcessor

Processes the OMERO client side metadata store.

process(IObjectContainerStore) - Method in class ome.formats.model.InstrumentProcessor

Processes the OMERO client side metadata store.

process(IObjectContainerStore) - Method in interface ome.formats.model.ModelProcessor

Processes the an IObjectContainerStore.

process(IObjectContainerStore) - Method in class ome.formats.model.PixelsProcessor

Processes the OMERO client side metadata store.

process(IObjectContainerStore) - Method in class ome.formats.model.PlaneInfoProcessor

Processes the OMERO client side metadata store.

process(IObjectContainerStore) - Method in class ome.formats.model.ReferenceProcessor

process(IObjectContainerStore) - Method in class ome.formats.model.ShapeProcessor

Processes the OMERO client side metadata store.

process(IObjectContainerStore) - Method in class ome.formats.model.TargetProcessor

Processes the OMERO client side metadata store.

process(IObjectContainerStore) - Method in class ome.formats.model.WellProcessor

Processes the OMERO client side metadata store.

process(Long, ServiceFactory, Session) - Method in class ome.services.pixeldata.PixelDataHandler

Here we assume that our log loader will only return us the proper types, since we are using the specific type defined in this package.

process(long) - Method in class ome.services.procs.ImportProcessor

Process - Interface in ome.services.procs

process(long) - Method in interface ome.services.procs.Processor

process(long) - Method in class ome.services.procs.ProcessorSkeleton

process(Job) - Method in class ome.services.procs.ProcessorSkeleton

process - Variable in class omero.grid.ProcessCallbackI

Proxy passed to this instance on creation.

ProcessCallback - Interface in ome.services.procs

ProcessCallbackI - Class in omero.grid

ProcessCallbackI(client, ProcessPrx) - Constructor for class omero.grid.ProcessCallbackI

ProcessCallbackI(client, ProcessPrx, boolean) - Constructor for class omero.grid.ProcessCallbackI

ProcessCallbackI(ObjectAdapter, ProcessPrx) - Constructor for class omero.grid.ProcessCallbackI

ProcessCallbackI(ObjectAdapter, ProcessPrx, boolean) - Constructor for class omero.grid.ProcessCallbackI

ProcessCallbackI.Action - Enum in omero.grid

processCancelled(Process) - Method in class ome.services.JobBean

processCancelled(Process) - Method in interface ome.services.procs.ProcessCallback

processCancelled(boolean, Current) - Method in class omero.grid.ProcessCallbackI

processFinished(Process) - Method in class ome.services.JobBean

processFinished(Process) - Method in interface ome.services.procs.ProcessCallback

processFinished(int, Current) - Method in class omero.grid.ProcessCallbackI

processKilled(boolean, Current) - Method in class omero.grid.ProcessCallbackI

ProcessManager - Class in ome.services.procs

ProcessManager(SessionManager, SecuritySystem, Executor, Processor...) - Constructor for class ome.services.procs.ProcessManager

main constructor which takes a non-null array of Processor instances as its only argument.

ProcessManager.Work - Class in ome.services.procs

Task performed by the ProcessManager on each invocation of ExecutionThread.run().

ProcessManager.Work(SecuritySystem, Processor...) - Constructor for class ome.services.procs.ProcessManager.Work

processor() - Method in interface ome.services.procs.Process

Processor - Interface in ome.services.procs

processor() - Method in class ome.services.procs.ProcessSkeleton

ProcessorCallbackI - Class in ome.services.blitz.impl

Callback used to lookup active processors via IceStorm.

ProcessorCallbackI(ServiceFactoryI) - Constructor for class ome.services.blitz.impl.ProcessorCallbackI

Simplified constructor used to see if any usermode processor is active for either the current group or the current user.

ProcessorCallbackI(ServiceFactoryI, ResultHolder<String>, Job) - Constructor for class ome.services.blitz.impl.ProcessorCallbackI

Primary constructor.

processors - Variable in class ome.services.procs.ProcessManager.Work

processors available for processing.

ProcessorSkeleton - Class in ome.services.procs

ProcessorSkeleton() - Constructor for class ome.services.procs.ProcessorSkeleton

ProcessSkeleton - Class in ome.services.procs

ProcessSkeleton(Processor) - Constructor for class ome.services.procs.ProcessSkeleton

procMap - Variable in class ome.services.procs.ProcessManager.Work

Map of all active processes.

PROJECT_LINKS - Static variable in class pojos.DatasetData

Identifies the Dataset#PROJECTLINKS field.

ProjectData - Class in pojos

The data that makes up an OME Project along with links to its contained Datasets and the Experimenter that owns this Project.

ProjectData() - Constructor for class pojos.ProjectData

Creates a new instance.

ProjectData(Project) - Constructor for class pojos.ProjectData

Creates a new instance.

projection(String, Parameters) - Method in interface ome.api.IQuery

Return a list of Java Object instances (not IObject instances).

projection(String, Parameters) - Method in class ome.logic.QueryImpl

projection_async(AMD_IQuery_projection, String, Parameters, Current) - Method in class ome.services.blitz.impl.QueryI

ProjectionBean - Class in ome.services.projection

Implements projection functionality for Pixels sets as declared in IProjection.

ProjectionBean() - Constructor for class ome.services.projection.ProjectionBean

ProjectionI - Class in ome.services.blitz.impl

Implementation of the IProjection service.

ProjectionI(ServiceInterface, BlitzExecutor) - Constructor for class ome.services.blitz.impl.ProjectionI

projectPixels(long, PixelsType, int, int, int, List<Integer>, int, int, int, String) - Method in interface ome.api.IProjection

Performs a projection through selected optical sections and optical sections for a given set of time points of a Pixels set.

projectPixels(long, PixelsType, int, int, int, List<Integer>, int, int, int, String) - Method in class ome.services.projection.ProjectionBean

projectPixels_async(AMD_IProjection_projectPixels, long, PixelsType, ProjectionType, int, int, List<Integer>, int, int, int, String, Current) - Method in class ome.services.blitz.impl.ProjectionI

projectStack(long, PixelsType, int, int, int, int, int, int) - Method in interface ome.api.IProjection

Performs a projection through the optical sections of a particular wavelength at a given time point of a Pixels set.

projectStack(long, PixelsType, int, int, int, int, int, int) - Method in class ome.services.projection.ProjectionBean

projectStack_async(AMD_IProjection_projectStack, long, PixelsType, ProjectionType, int, int, int, int, int, Current) - Method in class ome.services.blitz.impl.ProjectionI

ProjectWithImageNameBridge - Class in ome.services.fulltext.bridges

Example custom FieldBridge implementation which parses all Image names from a Project and inserts them into the index for that Project.

ProjectWithImageNameBridge() - Constructor for class ome.services.fulltext.bridges.ProjectWithImageNameBridge

prompt(ImportConfig.Value, String, boolean) - Method in class ome.formats.importer.ImportConfig

Build prompt

propagateHiddenValues(IObject, IObject) - Method in class ome.security.basic.MergeEventListener

proxy() - Method in class ome.services.blitz.impl.ServiceFactoryI

ProxyCleanupFilter - Class in ome.tools.hibernate

removes all proxies from a return graph to prevent ClassCastExceptions and Session Closed exceptions.

ProxyCleanupFilter() - Constructor for class ome.tools.hibernate.ProxyCleanupFilter

Passes null to ProxyCleanupFilter.ProxyCleanupFilter(CurrentDetails) such that all restricted objects will be unloaded.

ProxyCleanupFilter(CurrentDetails) - Constructor for class ome.tools.hibernate.ProxyCleanupFilter

Constructor take a CurrentDetails object in order to check the security restrictions on certain objects.

ProxyCleanupFilter.Interceptor - Class in ome.tools.hibernate

wraps a filter for each invocation

ProxyCleanupFilter.Interceptor() - Constructor for class ome.tools.hibernate.ProxyCleanupFilter.Interceptor

proxyForSession(Redirector.Context, String) - Method in class ome.services.blitz.redirect.AbstractRedirector

proxyNames - Variable in class ome.services.util.Executor.Impl

ProxySafeFilter - Class in ome.tools.hibernate

extension to ContextFilter to check for uninitialized Hibernate proxies before stepping into an entity or collection.

ProxySafeFilter() - Constructor for class ome.tools.hibernate.ProxySafeFilter

pt(double, double) - Method in class ome.services.roi.GeomTool

PublicRepositoryI - Class in ome.services.blitz.repo

An implementation of he PublicRepository interface

PublicRepositoryI(File, long, Executor, SqlAction, Principal) - Constructor for class ome.services.blitz.repo.PublicRepositoryI

publisher - Variable in class ome.services.fulltext.BridgeHelper

publisher - Variable in class ome.services.sessions.stats.CounterFactory

publisherOrNull(String) - Method in class ome.services.blitz.fire.TopicManager.Impl

publishEvent(ApplicationEvent) - Method in class ome.system.OmeroContext

publishMessage(InternalMessage) - Method in class ome.system.OmeroContext

Convenience method around OmeroContext.publishEvent(org.springframework.context.ApplicationEvent) which catches all MessageException and unwraps the contained Throwable instance and rethrows.

purgeNode(String) - Method in class ome.services.blitz.fire.Ring

push(GraphOpts, EventContext) - Method in class ome.services.graphs.GraphEntry

push(GraphOpts.Op, boolean, EventContext) - Method in class ome.services.graphs.GraphOpts

Adds the given operation to the current list if the user has permissions to do so.

push(GraphOpts) - Method in class ome.services.graphs.GraphStep

put(File, Dataset) - Method in class ome.formats.importer.ImportFixture

put(String, String) - Method in class ome.security.auth.AttributeSet

put(Identity, Object) - Method in class ome.services.blitz.util.ServantHolder

put(Callback) - Method in class ome.services.throttling.Queue

putAll(Map<File, Dataset>) - Method in class ome.formats.importer.ImportFixture

putSession(String, SessionContext) - Method in class ome.services.sessions.state.SessionCache

Puts a session blindly into the context.

PYR_LOCK_EXT - Static variable in class ome.io.bioformats.BfPyramidPixelBuffer

PYRAMID_SUFFIX - Static variable in class ome.io.nio.PixelsService

Suffix for an the image pyramid of a given pixels set.

PYTHONSCRIPT - Static variable in class omero.grid.ParamsHelper

The text representation of the format in a python script.

Q

qDef - Variable in class omeis.providers.re.quantum.QuantumStrategy

Reference to a quantumDef object.

Quantization_8_16_bit - Class in omeis.providers.re.quantum

Quantization process.

Quantization_8_16_bit(QuantumDef, PixelsType) - Constructor for class omeis.providers.re.quantum.Quantization_8_16_bit

Creates a new strategy.

QuantizationException - Exception in omeis.providers.re.quantum

This exception is thrown during the quantization process if something goes wrong.

QuantizationException() - Constructor for exception omeis.providers.re.quantum.QuantizationException

Creates a new exception.

QuantizationException(String) - Constructor for exception omeis.providers.re.quantum.QuantizationException

Constructs a new exception with the specified detail message.

QuantizationException(Throwable) - Constructor for exception omeis.providers.re.quantum.QuantizationException

Constructs a new exception with the specified cause.

QuantizationException(String, Throwable) - Constructor for exception omeis.providers.re.quantum.QuantizationException

Constructs a new exception with the specified detail message and cause.

quantize(double) - Method in class omeis.providers.re.quantum.BinaryMaskQuantizer

Implemented as specified in QuantumStrategy.

quantize(double) - Method in class omeis.providers.re.quantum.Quantization_8_16_bit

Implemented as specified in QuantumStrategy.

quantize(double) - Method in class omeis.providers.re.quantum.QuantumStrategy

Maps a value from [windowStart, windowEnd] to a value in the codomain interval.

QuantumFactory - Class in omeis.providers.re.quantum

Factory to create objects to carry out quantization for a given context.

QuantumFactory(List<Family>) - Constructor for class omeis.providers.re.quantum.QuantumFactory

Default constructor.

QuantumMap - Interface in omeis.providers.re.quantum

Provides methods to map value.

QuantumStrategy - Class in omeis.providers.re.quantum

Subclasses Work on explicit pixel types.

QuantumStrategy(QuantumDef, PixelsType) - Constructor for class omeis.providers.re.quantum.QuantumStrategy

Creates a new instance.

query() - Method in class ome.services.eventlogs.AllEntitiesPseudoLogLoader

query() - Method in class ome.services.eventlogs.AllEventsLogLoader

query() - Method in class ome.services.eventlogs.EventLogLoader

query() - Method in class ome.services.eventlogs.PersistentEventLogLoader

query() - Method in class ome.services.pixeldata.PersistentEventLogLoader

Uses data from the PersistentEventLogLoader.dataPerUser "queue" to allow new requests to be processed even if one user adds a large number of PIXELDATA events.

Query<T> - Class in ome.services.query

base Query type to facilitate the creation of ORM queries.

Query(Definitions, Parameters) - Constructor for class ome.services.query.Query

main constructor used by subclasses.

query(Session) - Method in class ome.tools.hibernate.QueryBuilder

queryBackupIds(Session, int, GraphEntry, QueryBuilder) - Method in class ome.services.graphs.AnnotationGraphSpec

queryBackupIds(Session, int, GraphEntry, QueryBuilder) - Method in class ome.services.graphs.BaseGraphSpec

queryBackupIds(Session, int, GraphEntry, QueryBuilder) - Method in interface ome.services.graphs.GraphSpec

If a given path is deleted before its sub-path, this points to a one-to-one relationship.

QueryBuilder - Class in ome.tools.hibernate

Very thin wrapper around a StringBuilder to generate HQL queries.

QueryBuilder() - Constructor for class ome.tools.hibernate.QueryBuilder

QueryBuilder(int) - Constructor for class ome.tools.hibernate.QueryBuilder

queryCacheHit(String, String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

queryCacheMiss(String, String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

queryCachePut(String, String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

QueryConstraints - Class in ome.services.delete

AdminAction which queries all datasets and annotations belonging to the given Image

QueryConstraints(LocalAdmin, LocalQuery, long, boolean) - Constructor for class ome.services.delete.QueryConstraints

QueryException - Exception in ome.services.query

something failed in looking up a query

QueryException(String) - Constructor for exception ome.services.query.QueryException

queryExecuted(String, int, long) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

queryFactory - Variable in class ome.logic.AbstractLevel1Service

queryFactory - Variable in class ome.logic.AbstractLevel2Service

QueryFactory - Class in ome.services.query

query locator which is configured by Spring.

QueryFactory(QuerySource...) - Constructor for class ome.services.query.QueryFactory

main constructor which takes a non-null array of query sources as its only argument.

QueryI - Class in ome.services.blitz.impl

Implementation of the IQuery service.

QueryI(IQuery, BlitzExecutor) - Constructor for class ome.services.blitz.impl.QueryI

QueryImpl - Class in ome.logic

Provides methods for directly querying object graphs.

QueryImpl() - Constructor for class ome.logic.QueryImpl

QueryNewUserGroupBean - Class in ome.security.auth

Handles the ":query:" specifier from etc/omero.properties.

QueryNewUserGroupBean(String) - Constructor for class ome.security.auth.QueryNewUserGroupBean

QueryParameterDef - Class in ome.services.query

definition of a slot into which a QueryParameter must fit.

QueryParameterDef(String, Class, boolean) - Constructor for class ome.services.query.QueryParameterDef

main constructor.

queryResults(Class, Set, String[], boolean[], int, int) - Method in interface ome.api.IResults

querying for IResults

queryResultsPrimitive(String, int[], String[], boolean[], int, int) - Method in interface ome.api.IResults

queryService - Variable in class ome.services.eventlogs.EventLogLoader

QuerySource - Class in ome.services.query

contract for any source of queries.

QuerySource() - Constructor for class ome.services.query.QuerySource

queryString() - Method in class ome.tools.hibernate.QueryBuilder

Returns the current query as a String.

Queue - Class in ome.services.throttling

Manages AMD-based method dispatches from blitz

Queue(OmeroContext) - Constructor for class ome.services.throttling.Queue

QUEUED - Static variable in interface ome.api.JobHandle

queueDelete_async(AMD_IDelete_queueDelete, DeleteCommand[], Current) - Method in class ome.services.blitz.impl.DeleteI

R

R_BAND - Static variable in class omeis.providers.re.RGBBuffer

Index of the red band in the image's data buffer.

random(int) - Method in class ome.services.roi.GeomTool

randomize(Random) - Method in class omero.model.SmartEllipseI

randomize(Random) - Method in class omero.model.SmartLineI

randomize(Random) - Method in class omero.model.SmartMaskI

randomize(Random) - Method in class omero.model.SmartPathI

randomize(Random) - Method in class omero.model.SmartPointI

randomize(Random) - Method in class omero.model.SmartPolygonI

randomize(Random) - Method in class omero.model.SmartPolylineI

randomize(Random) - Method in class omero.model.SmartRectI

randomize(Random) - Method in interface omero.model.SmartShape

Initializes this shape with completely random data.

randomize(Random) - Method in class omero.model.SmartTextI

rarray(RType...) - Static method in class omero.rtypes

rarray(Collection<RType>) - Static method in class omero.rtypes

RatingAnnotationData - Class in pojos

Annotation used to rate an object.

RatingAnnotationData() - Constructor for class pojos.RatingAnnotationData

Creates a new instance of value LEVEL_ZERO.

RatingAnnotationData(int) - Constructor for class pojos.RatingAnnotationData

Creates a new instance.

RatingAnnotationData(LongAnnotation) - Constructor for class pojos.RatingAnnotationData

Creates a new instance.

RawFileBean - Class in ome.services

Raw file gateway which provides access to the OMERO file repository.

RawFileBean() - Constructor for class ome.services.RawFileBean

default constructor

RawFileBean(boolean) - Constructor for class ome.services.RawFileBean

overriden to allow Spring to set boolean

RawFileStore - Interface in ome.api

Raw file gateway which provides access to the OMERO file repository.

RawFileStoreI - Class in ome.services.blitz.impl

Implementation of the RawFileStore service.

RawFileStoreI(RawFileStore, BlitzExecutor) - Constructor for class ome.services.blitz.impl.RawFileStoreI

RawFileStoreService - Interface in ome.services.blitz.gateway.services

RawFileStoreServiceImpl - Class in ome.services.blitz.gateway.services.impl

RawFileStoreServiceImpl(RawFileStorePrx) - Constructor for class ome.services.blitz.gateway.services.impl.RawFileStoreServiceImpl

Create the ImageService passing the gateway.

RawPixelsBean - Class in ome.services

Implementation of the RawPixelsStore stateful service.

RawPixelsBean() - Constructor for class ome.services.RawPixelsBean

default constructor

RawPixelsBean(boolean, String) - Constructor for class ome.services.RawPixelsBean

overriden to allow Spring to set boolean

RawPixelsStore - Interface in ome.api

Binary data provider.

RawPixelsStoreI - Class in ome.services.blitz.impl

Implementation of the RawPixelsStore service.

RawPixelsStoreI(RawPixelsStore, BlitzExecutor) - Constructor for class ome.services.blitz.impl.RawPixelsStoreI

RawPixelsStoreService - Interface in ome.services.blitz.gateway.services

RawPixelsStoreServiceImpl - Class in ome.services.blitz.gateway.services.impl

RawPixelsStoreServiceImpl(RawPixelsStorePrx) - Constructor for class ome.services.blitz.gateway.services.impl.RawPixelsStoreServiceImpl

Create the ImageService passing the gateway.

rbool(boolean) - Static method in class omero.rtypes

rclass(String) - Static method in class omero.rtypes

rdouble(double) - Static method in class omero.rtypes

read(long, int) - Method in interface ome.api.RawFileStore

Delegates to FileBuffer

read(ByteBuffer) - Method in class ome.io.nio.FileBuffer

Delegates to FileChannel

read(ByteBuffer, long) - Method in class ome.io.nio.FileBuffer

Delegates to FileChannel

read(long, long, int) - Method in class ome.services.blitz.gateway.services.impl.RawFileStoreServiceImpl

read(long, long, int) - Method in interface ome.services.blitz.gateway.services.RawFileStoreService

Read from the file in the rawFileStore.

read(String, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI

read(long, int) - Method in class ome.services.RawFileBean

read(String) - Method in class ome.services.scripts.ScriptRepoHelper

read(BasicStream) - Static method in class ome.services.sharing.data.IdMapHelper

read(BasicStream) - Static method in class ome.services.sharing.data.LongSeqHelper

read(BasicStream) - Static method in class ome.services.sharing.data.ObjSeqHelper

read(BasicStream) - Static method in class ome.services.sharing.data.StringSeqHelper

read_async(AMD_Exporter_read, long, int, Current) - Method in class ome.services.blitz.impl.ExporterI

read_async(AMD_RawFileStore_read, long, int, Current) - Method in class ome.services.blitz.impl.RawFileStoreI

read_async(AMD_RawFileStore_read, long, int, Current) - Method in class ome.services.blitz.repo.RepoRawFileStoreI

readBytes(int) - Method in class ome.services.sessions.stats.DelegatingStats

readBytes(int) - Method in class ome.services.sessions.stats.NullSessionStats

readBytes(int) - Method in interface ome.services.sessions.stats.SessionStats

readBytes(int) - Method in class ome.services.sessions.stats.SimpleSessionStats

reader - Variable in class ome.formats.importer.util.ErrorHandler.FILE_EXCEPTION

reader - Variable in class ome.formats.importer.util.ErrorHandler.INTERNAL_EXCEPTION

reader - Variable in class ome.io.bioformats.BfPixelBuffer

reader() - Method in class ome.io.bioformats.BfPixelBuffer

reader - Variable in class ome.io.bioformats.BfPyramidPixelBuffer

Bio-Formats implementation the delegate uses to read the backing TIFF.

readerClass - Static variable in class ome.services.util.DBEnumCheck

READERS_KEY - Static variable in class ome.formats.importer.ImportConfig

Lookup key for System.getProperty(String).

readersPath - Variable in class ome.formats.importer.ImportConfig

readOnly - Variable in class ome.security.basic.EventHandler

readOnly - Variable in class ome.services.sessions.SessionManagerImpl

READONLY_FLAG - Static variable in class pojos.ShapeData

Flag stating that the ROI is read only.

ReadOnlyByteArray - Class in ome.util.mem

A read-only slice of a given array.

ReadOnlyByteArray(byte[], int, int) - Constructor for class ome.util.mem.ReadOnlyByteArray

Creates a read-only slice of base.

ReadOnlyByteArray - Class in omerojava.util

A read-only slice of a given array.

ReadOnlyByteArray(byte[], int, int) - Constructor for class omerojava.util.ReadOnlyByteArray

Creates a read-only slice of base.

reapSession(String) - Method in class ome.services.blitz.fire.SessionManagerI

Destroys all the ServiceFactoryI instances based on the given sessionId.

recompressSeries(TiffReader, int) - Method in class ome.io.bioformats.OmeroPixelsPyramidWriter

Re-compresses a source series, that is JPEG 2000 compressed, via its resolution level.

recreate(Connection, String, Comparator, Map) - Static method in class ome.services.sharing.data.ShareItems

recreate(Connection, String, Comparator) - Static method in class ome.services.sharing.data.ShareItems

recreate(Connection, String, Comparator, Map) - Static method in class ome.services.sharing.data.ShareMap

recreate(Connection, String, Comparator) - Static method in class ome.services.sharing.data.ShareMap

recreateCollection(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

rect(double, double, double, double) - Method in class ome.services.roi.GeomTool

RectangleArea - Class in ome.util.math.geom2D

Represents a rectangle in the Euclidean space R².

RectangleArea() - Constructor for class ome.util.math.geom2D.RectangleArea

Constructs a new RectangleAreaAdapter whose top-left corner is (0, 0) and whose width and height are both zero.

RectangleArea(int, int, int, int) - Constructor for class ome.util.math.geom2D.RectangleArea

Constructs a new RectangleAreaAdapter whose top-left corner is specified as (x, y) and whose width and height are specified by the arguments of the same name.

RectangleData - Class in pojos

Represents a rectangle in the Euclidean space R².

RectangleData(Shape) - Constructor for class pojos.RectangleData

Creates a new instance.

RectangleData() - Constructor for class pojos.RectangleData

Creates a new instance with a default rectangle.

RectangleData(double, double, double, double) - Constructor for class pojos.RectangleData

Creates a new instance of the RectangleData.

RED_INDEX - Static variable in class ome.formats.model.ColorsFactory

Index of the red component of a color.

RED_INDEX - Static variable in class omeis.providers.re.ColorsFactory

Index of the red component of a color.

RED_TEXT - Static variable in class ome.formats.model.ChannelProcessor

Name of the red component when it is a graphics image.

Redirector - Interface in ome.services.blitz.redirect

Strategy interface for helping a Ring instance decide whether to redirect SessionPrx creation to another SessionManagerI instance.

Redirector.Context - Interface in ome.services.blitz.redirect

Interface implemented by Ring instances to allow passing in the context necessary for making strategy decisions.

ReferenceProcessor - Class in ome.formats.model

Processes the references of an IObjectContainerStore and ensures that container references are consistent with the LSID stored in the IObjectContainer itself.

ReferenceProcessor() - Constructor for class ome.formats.model.ReferenceProcessor

refresh(T) - Method in interface ome.api.IQuery

refreshes an entire IObject graph, recursive loading all data for the managed instances in the graph from the database.

refresh(T) - Method in class ome.logic.QueryImpl

refresh(String, SessionContext) - Method in class ome.services.sessions.state.SessionCache

Used externally to refresh the SessionContext instance associated with the session uuid

refresh_async(AMD_IQuery_refresh, IObject, Current) - Method in class ome.services.blitz.impl.QueryI

refreshAll() - Method in class ome.system.OmeroContext

refreshes all the nested OmeroContexts within this instance.

refreshAllIfNecessary() - Method in class ome.system.OmeroContext

Calls #refreshAll() if {@link #isRunning()} throws an {@link IllegalStateException}.

RegionDef - Class in omeis.providers.re.data

Identifies a rectangular region.

RegionDef() - Constructor for class omeis.providers.re.data.RegionDef

Creates a default instance.

RegionDef(int, int, int, int) - Constructor for class omeis.providers.re.data.RegionDef

Creates a rectangular region.

register(String, ObjectPrx, boolean) - Method in class ome.services.blitz.fire.TopicManager.Impl

register(String, ObjectPrx, boolean) - Method in interface ome.services.blitz.fire.TopicManager

Enforces no security constraints.

register(String, RString, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI

Register an OriginalFile using its path

register(Communicator) - Method in class ome.services.roi.RoiTypes.ObjectFactory

register(Communicator) - Method in class omero.rtypes.ObjectFactory

registerAll(Ehcache, CacheEventListener...) - Method in class ome.services.sessions.state.CacheFactory

registerCallback(ProcessCallbackPrx, Current) - Method in class ome.services.blitz.impl.ScriptProcessI

registerCallback(ProcessCallback) - Method in interface ome.services.procs.Process

registerCallback(ProcessCallback) - Method in class ome.services.procs.ProcessSkeleton

registerFileSet(OriginalFile, List<Image>, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI

Register the Images in a list of Images, a single image will be a one-element list

registerObjectFactory(Map<String, ObjectFactory>) - Method in class ome.services.blitz.util.BlitzConfiguration

Registers both the code generated ObjectFactory for all the omero.model.* classes as well as all the classes which the server would like to receive from clients.

registerOriginalFile(OriginalFile, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI

Register an OriginalFile object

registerServant(Identity, Object) - Method in class ome.services.blitz.impl.ServiceFactoryI

Registers the servant with the adapter (or throws an exception if one is already registered) as well as configures the servant in any post-Spring way necessary, based on the type of the servant.

RegisterServantMessage - Class in ome.services.blitz.util

InternalMessage raised when a servant should be registered for clean.

RegisterServantMessage(Object, Object, Current) - Constructor for class ome.services.blitz.util.RegisterServantMessage

RegisterServiceCleanupMessage - Class in ome.services.messages

Published when some resource must be cleaned up after method execution.

RegisterServiceCleanupMessage(Object, Object) - Constructor for class ome.services.messages.RegisterServiceCleanupMessage

registerTrigger(String, Trigger) - Method in class ome.services.scheduler.SchedulerFactoryBean

Registers a JobDetailAwareTrigger.

Registry - Interface in ome.services.blitz.fire

Helper class which makes the RegistryPrx available within OmeroBlitz.

registry - Variable in class ome.services.blitz.fire.SessionManagerI

Registry.Impl - Class in ome.services.blitz.fire

Registry.Impl(Communicator) - Constructor for class ome.services.blitz.fire.Registry.Impl

reindex(T) - Method in class ome.services.fulltext.BridgeHelper

Publishes a ReindexMessage which will get processed asynchronously.

reindexAll(List<T>) - Method in class ome.services.fulltext.BridgeHelper

Publishes a ReindexMessage which will get processed asynchronously.

ReindexMessage<T extends ome.model.IObject> - Class in ome.services.messages

Published when one or more IObject instances must be re-indexed.

ReindexMessage(Object, List<T>) - Constructor for class ome.services.messages.ReindexMessage

release(String, int) - Method in class ome.services.graphs.GraphState

release(String, int) - Method in interface ome.services.graphs.GraphStep.Callback

release(GraphStep.Callback) - Method in class ome.services.graphs.GraphStep

releaseDate - Static variable in class ome.formats.importer.Version

The data of the last release date.

releaseLock(String) - Method in class ome.services.blitz.util.ServantHolder

Releases the given lock if found, otherwise throws an InternalException

reload(String) - Method in interface ome.services.sessions.SessionManager

Similar to SessionManager.getEventContext(Principal) but uses the internal reload logic to get a fresh representation of the context.

reload(String) - Method in class ome.services.sessions.SessionManagerImpl

reload(SessionContext) - Method in class ome.services.sessions.SessionManagerImpl

Will be called in a synchronized block by SessionCache in order to allow for an update.

reload(String) - Method in class ome.services.sessions.state.SessionCache

Provides the reloading logic of the SessionCache for the SessionManagerImpl to use.

reload(SessionContext) - Method in interface ome.services.sessions.state.SessionCache.StaleCacheListener

Method called for every active session in the cache.

ReloadFilter - Class in ome.tools.hibernate

UpdateFilter subclass specialized for use with the Session.save(Object) (as opposed to Session.merge(Object)) method.

ReloadFilter(Session) - Constructor for class ome.tools.hibernate.ReloadFilter

ReloadingRefreshEventListener - Class in ome.tools.hibernate

responsible for responding to RefreshEvent. in particular in reloading the unloaded entities.

ReloadingRefreshEventListener() - Constructor for class ome.tools.hibernate.ReloadingRefreshEventListener

remove() - Method in interface ome.api.Search

Unsupported operation.

remove(Identity) - Method in class ome.services.blitz.util.ServantHolder

remove() - Method in class ome.services.eventlogs.EventBacklog

Removes and returns the next EventLog instance or null if none is present.

remove() - Method in class ome.services.eventlogs.EventLogLoader

remove() - Method in class ome.services.graphs.BaseGraphSpec.SubSpecIterator

remove() - Method in class ome.services.SearchBean

remove() - Method in class omeis.providers.re.codomain.CodomainChain

Removes all CodomainMapContexts except the identity and resets the interval.

remove(CodomainMapContext) - Method in class omeis.providers.re.codomain.CodomainChain

Removes a map context from the chain.

remove(Resources.Entry) - Method in class omero.util.Resources

remove_async(AMD_Search_remove, Current) - Method in class ome.services.blitz.impl.SearchI

remove_path(File) - Static method in class omero.util.TempFileManager

Calls TempFileManager.removePath(File) on TempFileManager.manager.

removeAllDisabled(String...) - Method in class ome.security.basic.CurrentDetails

removeAllListeners() - Method in class ome.services.messages.GlobalMulticaster

removeApplicationListener(ApplicationListener) - Method in class ome.services.messages.GlobalMulticaster

removeApplicationListenerBean(String) - Method in class ome.services.messages.GlobalMulticaster

removeCodomainMap(CodomainMapContext) - Method in class ome.services.RenderingBean

Implemented as specified by the RenderingEngine interface.

removeCodomainMap(CodomainMapContext) - Method in interface omeis.providers.re.RenderingEngine

Removes the specified context from the chain.

removeCodomainMap_async(AMD_RenderingEngine_removeCodomainMap, CodomainMapContext, Current) - Method in class ome.services.blitz.impl.RenderingEngineI

removeCodomainMap_async(AMD_RenderingEngine_removeCodomainMap, CodomainMapContext, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI

removeCollection(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

removeDisabled(String) - Method in class ome.security.basic.CurrentDetails

removeFiles(List<Long>) - Method in class ome.io.nio.OriginalFilesService

Removes files from data repository based on a parameterized List of Long file ids

removeGroupOwners(ExperimenterGroup, Experimenter...) - Method in interface ome.api.IAdmin

removes the given users from the owner list for this group.

removeGroupOwners(ExperimenterGroup, Experimenter...) - Method in class ome.logic.AdminImpl

removeGroupOwners_async(AMD_IAdmin_removeGroupOwners, ExperimenterGroup, List<Experimenter>, Current) - Method in class ome.services.blitz.impl.AdminI

removeGroups(Experimenter, ExperimenterGroup...) - Method in interface ome.api.IAdmin

removes a user from the given groups.

removeGroups(Experimenter, ExperimenterGroup...) - Method in class ome.logic.AdminImpl

removeGroups(Experimenter, ExperimenterGroup...) - Method in interface ome.security.auth.RoleProvider

removeGroups(Experimenter, ExperimenterGroup...) - Method in class ome.security.auth.SimpleRoleProvider

removeGroups_async(AMD_IAdmin_removeGroups, Experimenter, List<ExperimenterGroup>, Current) - Method in class ome.services.blitz.impl.AdminI

removeGuest(long, String) - Method in interface ome.api.IShare

Removes guest email address from share.

removeGuest(long, String) - Method in class ome.services.sharing.ShareBean

removeGuest_async(AMD_IShare_removeGuest, long, String, Current) - Method in class ome.services.blitz.impl.ShareI

removeGuests(long, String...) - Method in interface ome.api.IShare

Removes guest email addresses from the share.

removeGuests(long, String...) - Method in class ome.services.sharing.ShareBean

removeGuests_async(AMD_IShare_removeGuests, long, List<String>, Current) - Method in class ome.services.blitz.impl.ShareI

removeIObjectContainer(LSID) - Method in interface ome.formats.model.IObjectContainerStore

Removes an IObject container from within the OME-XML data model store.

removeIObjectContainer(LSID) - Method in class ome.formats.OMEROMetadataStoreClient

removeMissingFilesFromDb(SqlAction, Session, List<OriginalFile>) - Method in class ome.services.scripts.ScriptRepoHelper

Given the current files on disk, #unregister(Long, Session) all files which have been removed from disk.

removeModelProcessor(ModelProcessor) - Method in class ome.formats.OMEROMetadataStoreClient

Removes a model processor from use.

removeNamespace(String) - Method in class pojos.ROIData

Removes the namespace from the ROI.

removeObject(long, T) - Method in interface ome.api.IShare

Removes existing item from the share.

removeObject(Identity) - Method in class ome.services.blitz.fire.Registry.Impl

removeObject(Identity) - Method in interface ome.services.blitz.fire.Registry

removeObject(long, T) - Method in class ome.services.sharing.ShareBean

removeObject_async(AMD_IShare_removeObject, long, IObject, Current) - Method in class ome.services.blitz.impl.ShareI

removeObjects(long, T...) - Method in interface ome.api.IShare

Remove existing items from the share.

removeObjects(long, T...) - Method in class ome.services.sharing.ShareBean

removeObjects_async(AMD_IShare_removeObjects, long, List<IObject>, Current) - Method in class ome.services.blitz.impl.ShareI

removeObjectSafely(Identity) - Method in class ome.services.blitz.fire.Registry.Impl

removeObjectSafely(Identity) - Method in interface ome.services.blitz.fire.Registry

removePath(File) - Method in class omero.util.TempFileManager

If the given file is under TempFileManager.dir, then it is deleted whether file or folder.

removePixels(List<Long>) - Method in class ome.io.nio.PixelsService

Removes files from data repository based on a parameterized List of Long pixels ids

removeProcessor(ProcessorPrx, Current) - Method in class ome.services.blitz.impl.SharedResourcesI

removeServer(String) - Method in class ome.formats.importer.ImportConfig

removeSession(String) - Method in class ome.services.sessions.state.SessionCache

removeSessionCallback(String, SessionCallback) - Method in class ome.services.sessions.state.SessionCache

removeShapeData(ShapeData) - Method in class pojos.ROIData

Removes the ShapeData object from ROIData.

removeThumbnails(List<Long>) - Method in class ome.io.nio.ThumbnailService

Removes files from data repository based on a parameterized List of Long thumbnail ids

removeUnusedFiles() - Method in interface ome.api.IRepositoryInfo

Removes all files from the server that do not have an OriginalFile complement in the database, all the Pixels that do not have a complement in the database and all the Thumbnail's that do not have a complement in the database.

removeUnusedFiles() - Method in class ome.logic.RepositoryInfoImpl

removeUnusedFiles_async(AMD_IRepositoryInfo_removeUnusedFiles, Current) - Method in class ome.services.blitz.impl.RepositoryInfoI

removeUser(long, Experimenter) - Method in interface ome.api.IShare

Removes experimenter from share

removeUser(long, Experimenter) - Method in class ome.services.sharing.ShareBean

removeUser_async(AMD_IShare_removeUser, long, Experimenter, Current) - Method in class ome.services.blitz.impl.ShareI

removeUsers(long, List<Experimenter>) - Method in interface ome.api.IShare

Removes experimenters from share

removeUsers(long, List<Experimenter>) - Method in class ome.services.sharing.ShareBean

removeUsers_async(AMD_IShare_removeUsers, long, List<Experimenter>, Current) - Method in class ome.services.blitz.impl.ShareI

removingOnly() - Method in class ome.services.eventlogs.EventBacklog

Check the current state of the EventBacklog.

rename(String, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI

render(String, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI

render(PlaneDef) - Method in class ome.services.RenderingBean

Implemented as specified by the RenderingEngine interface.

render(PlaneDef) - Method in class omeis.providers.re.Renderer

Renders the data selected by pd according to the current rendering settings.

render(PlaneDef) - Method in interface omeis.providers.re.RenderingEngine

Renders the data selected by pd according to the current rendering settings.

render_async(AMD_RenderingEngine_render, PlaneDef, Current) - Method in class ome.services.blitz.impl.RenderingEngineI

render_async(AMD_RenderingEngine_render, PlaneDef, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI

renderAsPackedInt(Long, int, int) - Method in class ome.services.blitz.gateway.services.impl.RenderingServiceImpl

renderAsPackedInt(Long, int, int) - Method in interface ome.services.blitz.gateway.services.RenderingService

Render as a packedInt

renderAsPackedInt(PlaneDef) - Method in class ome.services.RenderingBean

Implemented as specified by the RenderingEngine interface.

renderAsPackedInt(PlaneDef, PixelBuffer) - Method in class omeis.providers.re.Renderer

Renders the data selected by pd according to the current rendering settings.

renderAsPackedInt(PlaneDef) - Method in interface omeis.providers.re.RenderingEngine

Renders the data selected by pd according to the current rendering settings.

renderAsPackedInt_async(AMD_RenderingEngine_renderAsPackedInt, PlaneDef, Current) - Method in class ome.services.blitz.impl.RenderingEngineI

renderAsPackedInt_async(AMD_RenderingEngine_renderAsPackedInt, PlaneDef, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI

renderAsPackedIntAsRGBA(long, int, int, Current) - Method in class ome.services.blitz.gateway.OmeroGateway

renderAsPackedIntAsRGBA(long, int, int) - Method in interface ome.services.blitz.gateway.services.ImageService

Render image as Buffered image.

renderAsPackedIntAsRGBA(long, int, int) - Method in class ome.services.blitz.gateway.services.impl.ImageServiceImpl

renderAsPackedIntAsRGBA(long, int, int) - Method in class ome.services.blitz.gateway.services.impl.RenderingServiceImpl

renderAsPackedIntAsRGBA(long, int, int) - Method in interface ome.services.blitz.gateway.services.RenderingService

Render image as Buffered image.

renderAsPackedIntAsRGBA(PlaneDef) - Method in class ome.services.RenderingBean

Implemented as specified by the RenderingEngine interface.

renderAsPackedIntAsRGBA(PlaneDef, PixelBuffer) - Method in class omeis.providers.re.Renderer

Renders the data selected by pd according to the current rendering settings.

renderAsPackedIntAsRGBA(PlaneDef) - Method in interface omeis.providers.re.RenderingEngine

Renders the data selected by pd according to the current rendering settings.

renderAsPackedIntAsRGBA_async(AMD_RenderingEngine_renderAsPackedIntAsRGBA, PlaneDef, Current) - Method in class ome.services.blitz.impl.RenderingEngineI

renderAsPackedIntAsRGBA_async(AMD_RenderingEngine_renderAsPackedIntAsRGBA, PlaneDef, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI

renderCompressed(PlaneDef) - Method in class ome.services.RenderingBean

Implemented as specified by the RenderingEngine interface.

renderCompressed(PlaneDef) - Method in interface omeis.providers.re.RenderingEngine

Renders the data selected by pd according to the current rendering settings and compresses the resulting RGBA composite image.

renderCompressed_async(AMD_RenderingEngine_renderCompressed, PlaneDef, Current) - Method in class ome.services.blitz.impl.RenderingEngineI

renderCompressed_async(AMD_RenderingEngine_renderCompressed, PlaneDef, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI

Renderer - Class in omeis.providers.re

Transforms raw image data into an RGB image that can be displayed on screen.

Renderer(QuantumFactory, List<RenderingModel>, Pixels, RenderingDef, PixelBuffer) - Constructor for class omeis.providers.re.Renderer

Creates a new instance to render the specified pixels set and get this new instance ready for rendering.

RENDERING_DEF_QUERY_PREFIX - Static variable in class ome.logic.PixelsImpl

Standard rendering definition HQL query prefix

RenderingBean - Class in ome.services

Provides the RenderingEngine service.

RenderingBean(PixelsService, LocalCompress, Executor, SecuritySystem) - Constructor for class ome.services.RenderingBean

Compression service Bean injector.

RenderingEngine - Interface in omeis.providers.re

Defines a service to render a given pixels set.

RenderingEngineI - Class in ome.services.blitz.impl

Implementation of the RenderingEngine service.

RenderingEngineI(RenderingEngine, BlitzExecutor) - Constructor for class ome.services.blitz.impl.RenderingEngineI

RenderingService - Interface in ome.services.blitz.gateway.services

RenderingServiceImpl - Class in ome.services.blitz.gateway.services.impl

RenderingServiceImpl(RenderingEnginePrx) - Constructor for class ome.services.blitz.gateway.services.impl.RenderingServiceImpl

Create the ImageService passing the gateway.

RenderingSettingsI - Class in ome.services.blitz.impl

Implementation of the IRenderingSettings service.

RenderingSettingsI(IRenderingSettings, BlitzExecutor) - Constructor for class ome.services.blitz.impl.RenderingSettingsI

RenderingSettingsImpl - Class in ome.logic

Implementation of the IRenderingSettings I/F.

RenderingSettingsImpl() - Constructor for class ome.logic.RenderingSettingsImpl

RenderingStats - Class in omeis.providers.re

Exposes methods to time the various steps in the rendering process and provides a stats report.

RenderingStats(Renderer, PlaneDef) - Constructor for class omeis.providers.re.RenderingStats

Creates a new instance.

RenderingTask - Interface in omeis.providers.re

This interface represents a rendering operation task.

renderProjectedAsPackedInt(int, int, int, int, int) - Method in class ome.services.RenderingBean

Implemented as specified by the RenderingEngine interface.

renderProjectedAsPackedInt(int, int, int, int, int) - Method in interface omeis.providers.re.RenderingEngine

Performs a projection through selected optical sections of a particular timepoint with the currently active channels and renders the data for display.

renderProjectedAsPackedInt_async(AMD_RenderingEngine_renderProjectedAsPackedInt, ProjectionType, int, int, int, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI

renderProjectedAsPackedInt_async(AMD_RenderingEngine_renderProjectedAsPackedInt, ProjectionType, int, int, int, int, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI

renderProjectedCompressed(int, int, int, int, int) - Method in class ome.services.RenderingBean

Implemented as specified by the RenderingEngine interface.

renderProjectedCompressed(int, int, int, int, int) - Method in interface omeis.providers.re.RenderingEngine

Performs a projection through selected optical sections of a particular timepoint with the currently active channels, renders the data for display and compresses the resulting RGBA composite image.

renderProjectedCompressed_async(AMD_RenderingEngine_renderProjectedCompressed, ProjectionType, int, int, int, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI

renderProjectedCompressed_async(AMD_RenderingEngine_renderProjectedCompressed, ProjectionType, int, int, int, int, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI

ReorderedPixelData - Class in ome.io.nio

Represents a block of pixel data that needs to be re-ordered in accordance with a DeltaVision file.

ReorderedPixelData(String, ByteBuffer, int) - Constructor for class ome.io.nio.ReorderedPixelData

Default constructor.

replace(Object, Object, Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType

repo - Variable in class ome.services.pixeldata.PersistentEventLogLoader

RepoFile - Class in ome.services.scripts

File type wrapper for paths which are intended for being stored in the database as a part of this repository.

RepoFile(File, String) - Constructor for class ome.services.scripts.RepoFile

Assumes that path is relative under root, and constructs a new RepoFile.FsFile and calls RepoFile.RepoFile(File, File)

RepoFile(File, File) - Constructor for class ome.services.scripts.RepoFile

Both root and file are absolute paths to files.

RepoFile.FsFile - Class in ome.services.scripts

File type wrapper for actual OS files.

RepoRawFileStoreI - Class in ome.services.blitz.repo

An implementation of the RepoRawFileStore interface

RepoRawFileStoreI(long, File) - Constructor for class ome.services.blitz.repo.RepoRawFileStoreI

report(Current) - Method in class ome.services.blitz.impl.DeleteHandleI

reportForgottenPassword(String, String) - Method in interface ome.api.IAdmin

Can be used after repeated AuthenticationException instances are thrown, to request that an email with a temporary password be sent.

reportForgottenPassword(String, String) - Method in class ome.logic.AdminImpl

reportForgottenPassword_async(AMD_IAdmin_reportForgottenPassword, String, String, Current) - Method in class ome.services.blitz.impl.AdminI

repositories(Current) - Method in class ome.services.blitz.impl.SharedResourcesI

RepositoryInfoI - Class in ome.services.blitz.impl

Implementation of the IRepositoryInfo service.

RepositoryInfoI(IRepositoryInfo, BlitzExecutor) - Constructor for class ome.services.blitz.impl.RepositoryInfoI

RepositoryInfoImpl - Class in ome.logic

Class implementation of the IRepositoryInfo service interface.

RepositoryInfoImpl() - Constructor for class ome.logic.RepositoryInfoImpl

RepositoryTask - Class in ome.tools

Class implementation of various mechanised tasks, database queries, file I/O, etc.

RepositoryTask(SqlAction) - Constructor for class ome.tools.RepositoryTask

Constructor

reps - Variable in class ome.services.fulltext.FullTextIndexer

reps - Variable in class ome.services.pixeldata.PixelDataHandler

requestFromUser() - Method in class ome.formats.importer.ImportConfig

if can't log in request needed information

requestHeartBeats() - Method in class ome.services.blitz.fire.SessionManagerI

Destroys all the ServiceFactoryI instances based on the given sessionId.

REQUEUED - Static variable in interface ome.api.JobHandle

requiresCompanion(String) - Static method in class ome.services.util.DBEnumCheck

requiresPixelsPyramid() - Method in interface ome.api.RawPixelsStore

requiresPixelsPyramid(Pixels) - Method in class ome.io.nio.PixelsService

Returns true if a pyramid should be used for the given Pixels.

requiresPixelsPyramid() - Method in class ome.services.RawPixelsBean

requiresPixelsPyramid() - Method in class ome.services.RenderingBean

requiresPixelsPyramid() - Method in interface omeis.providers.re.RenderingEngine

requiresPixelsPyramid_async(AMD_PyramidService_requiresPixelsPyramid, Current) - Method in class ome.services.blitz.impl.AbstractPyramidServant

requiresPixelsPyramid_async(AMD_PyramidService_requiresPixelsPyramid, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI

requiresPixelsPyramid_async(AMD_PyramidService_requiresPixelsPyramid, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI

resetCacheSize(int) - Method in class omerojava.util.PixelsCache

Resets the size of the cache.

resetCallGroup() - Method in class ome.security.basic.CurrentDetails

resetCallGroup() - Method in class ome.services.util.Executor.Impl

resetCallGroup() - Method in interface ome.services.util.Executor

Delegates to CurrentDetails.resetCallGroup().

resetDefaults(RenderingDef, Pixels) - Method in interface ome.api.IRenderingSettings

Resets the given rendering settings to those that are specified by the rendering engine intelligent pretty good image (PG) logic for the pixels set linked to that set of rendering settings.

resetDefaults() - Method in interface ome.api.Search

Resets all settings (non-query state) to the original default values, as if the instance had just be created.

resetDefaults() - Method in interface ome.api.ThumbnailStore

Resets the rendering definition for the active pixels set to its default settings.

resetDefaults(RenderingDef, Pixels) - Method in class ome.logic.RenderingSettingsImpl

Implemented as specified by the IRenderingSettings I/F

resetDefaults() - Method in class ome.services.RenderingBean

Implemented as specified by the RenderingEngine interface.

resetDefaults() - Method in class ome.services.SearchBean

resetDefaults() - Method in class ome.services.ThumbnailBean

resetDefaults() - Method in interface omeis.providers.re.RenderingEngine

Resets the default settings i.e. the default values internal to the Rendering engine.

resetDefaults_async(AMD_RenderingEngine_resetDefaults, Current) - Method in class ome.services.blitz.impl.RenderingEngineI

resetDefaults_async(AMD_IRenderingSettings_resetDefaults, RenderingDef, Pixels, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI

resetDefaults_async(AMD_Search_resetDefaults, Current) - Method in class ome.services.blitz.impl.SearchI

resetDefaults_async(AMD_ThumbnailStore_resetDefaults, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI

resetDefaults_async(AMD_RenderingEngine_resetDefaults, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI

resetDefaultsAndGenerateThumbnails(List<Long>, List<Long>) - Method in class ome.formats.OMEROMetadataStoreClient

Resets the defaults and generates thumbnails for a given set of Pixels IDs.

resetDefaultsByOwnerInSet(Class<T>, Set<Long>) - Method in interface ome.api.IRenderingSettings

Resets the rendering settings of a given group of containers based on the owner's (essentially a copy).

resetDefaultsByOwnerInSet(Class<T>, Set<Long>) - Method in class ome.logic.RenderingSettingsImpl

Implemented as specified by the IRenderingSettings I/F.

resetDefaultsByOwnerInSet_async(AMD_IRenderingSettings_resetDefaultsByOwnerInSet, String, List<Long>, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI

resetDefaultsForPixels(long) - Method in interface ome.api.IRenderingSettings

Resets a Pixels' default rendering settings back to those that are specified by the rendering engine intelligent pretty good image (PG) logic.

resetDefaultsForPixels(long) - Method in class ome.logic.RenderingSettingsImpl

Implemented as specified by the IRenderingSettings I/F.

resetDefaultsForPixels_async(AMD_IRenderingSettings_resetDefaultsForPixels, long, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI

resetDefaultsInDataset(long) - Method in interface ome.api.IRenderingSettings

Resets a dataset's rendering settings back to those that are specified by the rendering engine intelligent pretty good image (PG) logic.

resetDefaultsInDataset(long) - Method in class ome.logic.RenderingSettingsImpl

Implemented as specified by the IRenderingSettings I/F.

resetDefaultsInDataset_async(AMD_IRenderingSettings_resetDefaultsInDataset, long, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI

resetDefaultsInImage(long) - Method in interface ome.api.IRenderingSettings

Resets an image's default rendering settings back to those that are specified by the rendering engine intelligent pretty good image (PG) logic.

resetDefaultsInImage(long) - Method in class ome.logic.RenderingSettingsImpl

Implemented as specified by the IRenderingSettings I/F.

resetDefaultsInImage_async(AMD_IRenderingSettings_resetDefaultsInImage, long, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI

resetDefaultsInSet(Class<T>, Set<Long>) - Method in interface ome.api.IRenderingSettings

Resets a rendering settings back to one or many containers that are specified by the rendering engine intelligent pretty good image (PG) logic.

resetDefaultsInSet(Class<T>, Set<Long>) - Method in class ome.logic.RenderingSettingsImpl

Implemented as specified by the IRenderingSettings I/F.

resetDefaultsInSet_async(AMD_IRenderingSettings_resetDefaultsInSet, String, List<Long>, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI

resetDefaultsNoSave(RenderingDef, Pixels) - Method in interface ome.api.IRenderingSettings

Resets the given rendering settings to those that are specified by the rendering engine intelligent pretty good image (PG) logic for the pixels set linked to that set of rendering settings.

resetDefaultsNoSave(RenderingDef, Pixels) - Method in class ome.logic.RenderingSettingsImpl

Implemented as specified by the IRenderingSettings I/F

resetDefaultsNoSave() - Method in class ome.services.RenderingBean

Implemented as specified by the RenderingEngine interface.

resetDefaultsNoSave() - Method in interface omeis.providers.re.RenderingEngine

Resets the default settings i.e. the default values internal to the Rendering engine.

resetDefaultsNoSave_async(AMD_RenderingEngine_resetDefaultsNoSave, Current) - Method in class ome.services.blitz.impl.RenderingEngineI

resetDefaultsNoSave_async(AMD_IRenderingSettings_resetDefaultsNoSave, RenderingDef, Pixels, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI

resetDefaultsNoSave_async(AMD_RenderingEngine_resetDefaultsNoSave, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI

resetDetails(IObject, Object[], Object[], int) - Method in class ome.security.basic.OmeroInterceptor

asks BasicSecuritySystem to create a new managed Details based on the previous state of this entity.

resetEnumerations(Class<T>) - Method in interface ome.api.ITypes

resetEnumerations(Class<T>) - Method in class ome.logic.TypesImpl

resetEnumerations_async(AMD_ITypes_resetEnumerations, String, Current) - Method in class ome.services.blitz.impl.TypesI

resetMinMaxInSet(Class<T>, Set<Long>) - Method in interface ome.api.IRenderingSettings

Resets a the channel windows for one or many containers back to their global minimum and global maximum for the channel.

resetMinMaxInSet(Class<T>, Set<Long>) - Method in class ome.logic.RenderingSettingsImpl

Implemented as specified by the IRenderingSettings I/F.

resetMinMaxInSet_async(AMD_IRenderingSettings_resetMinMaxInSet, String, List<Long>, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI

resetReadFilter(Session) - Method in interface ome.api.local.LocalShare

resetReadFilter(Session) - Method in class ome.services.sharing.ShareBean

resolveAlias(String) - Method in class ome.system.PreferenceContext

resolveConfigFile(String) - Method in class ome.services.blitz.util.BlitzConfiguration

Resolve the given config file to a concrete location, possibly throwing an exception if stored in a jar.

resolver - Variable in class ome.io.nio.PixelsService

Resolver of archived original file paths for pixels sets.

resource - Variable in class ome.services.messages.RegisterServiceCleanupMessage

Resources - Class in omero.util

Container class for storing resources which should be cleaned up on close and periodically checked.

Resources() - Constructor for class omero.util.Resources

As Resources.Resources(int) but specifies a 60 second sleep period between task execution.

Resources(int) - Constructor for class omero.util.Resources

As Resources#Resources(int, ExecutorService) but uses a Executors.newSingleThreadExecutor().

Resources(int, ScheduledExecutorService) - Constructor for class omero.util.Resources

Resources.Entry - Interface in omero.util

Interface to be implemented by any object which wants to be managed by the Resources class.

response - Variable in class ome.services.throttling.Task

response(Object, OmeroContext) - Method in class ome.services.throttling.Task

Calls the response method

responseRunning(List<Long>, Current) - Method in class ome.services.blitz.impl.ProcessorCallbackI

Callback method which should not be called for this instance.

restartIfNeeded() - Method in class ome.services.scheduler.SchedulerFactoryBean

Similar to the SchedulerFactoryBean.isRunning() method, but properly handles the situation where the Scheduler has been completely shutdown and therefore must be replaced.

RESUBMITTED - Static variable in interface ome.api.JobHandle

ResultHolder<U> - Class in ome.services.blitz.util

ResultHolder(long) - Constructor for class ome.services.blitz.util.ResultHolder

results() - Method in interface ome.api.Search

Returns up to batch size number of results along with the related query metadata.

results() - Method in class ome.services.SearchBean

results_async(AMD_Search_results, Current) - Method in class ome.services.blitz.impl.SearchI

retrieveAllRndSettings(long, long) - Method in interface ome.api.IPixels

Retrieves all the rendering settings for a given pixels set and the passed user with the following objects pre-linked: renderingDef.quantization renderingDef.model renderingDef.waveRendering renderingDef.waveRendering.color renderingDef.waveRendering.family renderingDef.spatialDomainEnhancement

retrieveAllRndSettings(long, long) - Method in class ome.logic.PixelsImpl

Implemented as specified by the IPixels I/F.

retrieveAllRndSettings_async(AMD_IPixels_retrieveAllRndSettings, long, long, Current) - Method in class ome.services.blitz.impl.PixelsI

retrieveCollection(IObject, String, Parameters) - Method in interface ome.api.IContainer

Retrieves a collection with all members initialized ("loaded").

retrieveCollection(IObject, String, Parameters) - Method in class ome.logic.PojosImpl

Implemented as specified by the IContainer I/F

retrieveCollection_async(AMD_IContainer_retrieveCollection, IObject, String, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI

retrievePixDescription(long) - Method in interface ome.api.IPixels

Retrieves the pixels metadata with the following objects pre-linked: pixels.pixelsType pixels.pixelsDimensions pixels.channels pixels.channnels.statsInfo pixels.channnels.colorComponent pixels.channnels.logicalChannel pixels.channnels.logicalChannel.photometricInterpretation

retrievePixDescription(long) - Method in class ome.logic.PixelsImpl

retrievePixDescription_async(AMD_IPixels_retrievePixDescription, long, Current) - Method in class ome.services.blitz.impl.PixelsI

retrieveResult(int, List) - Method in interface ome.api.IResults

retrieving data for PixelSet

retrieveResultPrimitive(int, String[]) - Method in interface ome.api.IResults

retrieveResultsBulk(int[], List[]) - Method in interface ome.api.IResults

retrieveResultsBulkPrimitive(int[], String[][]) - Method in interface ome.api.IResults

retrieveRndSettings(long) - Method in interface ome.api.IPixels

Retrieves the rendering settings for a given pixels set and the currently logged in user with the following objects pre-linked: renderingDef.quantization renderingDef.model renderingDef.waveRendering renderingDef.waveRendering.color renderingDef.waveRendering.family renderingDef.spatialDomainEnhancement

retrieveRndSettings(long) - Method in class ome.logic.PixelsImpl

Implemented as specified by the IPixels I/F.

retrieveRndSettings_async(AMD_IPixels_retrieveRndSettings, long, Current) - Method in class ome.services.blitz.impl.PixelsI

retrieveRndSettingsFor(long, long) - Method in interface ome.api.IPixels

Retrieves the rendering settings for a given pixels set and the passed user with the following objects pre-linked: renderingDef.quantization renderingDef.model renderingDef.waveRendering renderingDef.waveRendering.color renderingDef.waveRendering.family renderingDef.spatialDomainEnhancement

retrieveRndSettingsFor(long, long) - Method in class ome.logic.PixelsImpl

Implemented as specified by the IPixels I/F.

retrieveRndSettingsFor_async(AMD_IPixels_retrieveRndSettingsFor, long, long, Current) - Method in class ome.services.blitz.impl.PixelsI

returnedClass() - Method in class ome.tools.hibernate.ListAsSQLArrayUserType

returnSeen(Object) - Method in class ome.tools.hibernate.UpdateFilter

returnUnloaded - Variable in class ome.services.search.SearchValues

reverse(Object) - Method in class omero.util.IceMapper

reverse(Collection) - Method in class omero.util.IceMapper

Copied from ModelMapper.findCollection(Collection) This could be unified in that a method findCollection(Collection, Map) was added with ModelMapper calling findCollection(source,model2target) and #reverseCollection(Collection) calling findCollection(source,target2model).

reverse(Collection, Class) - Method in class omero.util.IceMapper

Creates a collection assignable to the given type.

reverse(Map) - Method in class omero.util.IceMapper

reverse(ModelBased) - Method in class omero.util.IceMapper

Copied from ReverseModelMapper#map(ModelBased)

reverseArray(List, Class) - Method in class omero.util.IceMapper

Supports the separate case of reversing for arrays.

ReverseIntensityContext - Class in omeis.providers.re.codomain

The empty context of the reverse intensity map.

ReverseIntensityContext() - Constructor for class omeis.providers.re.codomain.ReverseIntensityContext

revision - Static variable in class ome.formats.importer.Version

The repository revision.

RevisionDate - Annotation Type in ome.annotations

annotation used for tracking source code changes.

revisionDate - Static variable in class ome.formats.importer.Version

The data of the last repository revision.

RevisionNumber - Annotation Type in ome.annotations

annotation used for tracking source code changes.

rfloat(float) - Static method in class omero.rtypes

RGBAIntBuffer - Class in omeis.providers.re

Holds the data of an RGBA image.

RGBAIntBuffer(int, int) - Constructor for class omeis.providers.re.RGBAIntBuffer

Creates a new 4-band packed integer buffer.

RGBBuffer - Class in omeis.providers.re

Holds the data of an RGB image.

RGBBuffer() - Constructor for class omeis.providers.re.RGBBuffer

Simple constructor to avoid memory allocations.

RGBBuffer(int, int) - Constructor for class omeis.providers.re.RGBBuffer

Creates a new 3-band buffer.

RGBIntBuffer - Class in omeis.providers.re

Holds the data of an RGB image.

RGBIntBuffer(int, int) - Constructor for class omeis.providers.re.RGBIntBuffer

Creates a new 3-band packed integer buffer.

Ring - Class in ome.services.blitz.fire

Distributed ring of BlitzConfiguration objects which manages lookups of sessions and other resources from all the blitzes which take part in the cluster.

Ring(String, Executor) - Constructor for class ome.services.blitz.fire.Ring

Ring(String, Executor, Redirector) - Constructor for class ome.services.blitz.fire.Ring

ring - Variable in class ome.services.blitz.fire.SessionManagerI

rint(int) - Static method in class omero.rtypes

rinternal(Internal) - Static method in class omero.rtypes

rlist(RType...) - Static method in class omero.rtypes

rlist(Collection<RType>) - Static method in class omero.rtypes

rlong(long) - Static method in class omero.rtypes

rmap() - Static method in class omero.rtypes

rmap(Map<String, RType>) - Static method in class omero.rtypes

rmap(String, RType) - Static method in class omero.rtypes

robject(IObject) - Static method in class omero.rtypes

ROIComponent - Class in pojos.util

Component hosting the ROI.

ROIComponent(long) - Constructor for class pojos.util.ROIComponent

Instantiate the ROIComponent.

ROICoordinate - Class in pojos

Defines a plane.

ROICoordinate() - Constructor for class pojos.ROICoordinate

Creates a default instance.

ROICoordinate(int, int) - Constructor for class pojos.ROICoordinate

Creates a new instance.

ROIData - Class in pojos

Converts the ROI object.

ROIData(Roi) - Constructor for class pojos.ROIData

Creates a new instance.

ROIData() - Constructor for class pojos.ROIData

Create a new instance of an ROIData object.

RoiI - Class in ome.services.blitz.impl

implementation of the IRoi service interface.

RoiI(BlitzExecutor, GeomTool, SqlAction) - Constructor for class ome.services.blitz.impl.RoiI

RoiI.RoiResultMapper - Class in ome.services.blitz.impl

RoiI.RoiResultMapper(RoiOptions) - Constructor for class ome.services.blitz.impl.RoiI.RoiResultMapper

RoiI.RoiResultMapReturnMapper - Class in ome.services.blitz.impl

RoiI.RoiResultMapReturnMapper(RoiOptions) - Constructor for class ome.services.blitz.impl.RoiI.RoiResultMapReturnMapper

RoiI.RoiResultReturnMapper - Class in ome.services.blitz.impl

RoiI.RoiResultReturnMapper(RoiOptions) - Constructor for class ome.services.blitz.impl.RoiI.RoiResultReturnMapper

RoiTypes - Class in ome.services.roi

Intelligent server-side representations of the Roi and Shape types.

RoiTypes() - Constructor for class ome.services.roi.RoiTypes

RoiTypes.ObjectFactory - Class in ome.services.roi

RoiTypes.ObjectFactory(String) - Constructor for class ome.services.roi.RoiTypes.ObjectFactory

roleProvider - Variable in class ome.logic.AdminImpl

RoleProvider - Interface in ome.security.auth

Provides user and group creation, deletion, and modification for use by services.

roles - Variable in class ome.security.basic.BasicSecuritySystem

roles - Variable in class ome.services.sessions.SessionManagerImpl

Roles - Class in ome.system

encapsulates the naming scheme for critical system groups and accounts.

Roles() - Constructor for class ome.system.Roles

default constructor which assigns hard-coded values to all roles

Roles(long, String, long, String, long, String) - Constructor for class ome.system.Roles

constructor which allows full specification of all roles

RolesAllowed - Annotation Type in ome.annotations

Security annotation which specifies a list of user roles which will be permitted to execute this method.

rollback(EventLog) - Method in class ome.services.eventlogs.EventLogLoader

rollback(String, int) - Method in class ome.services.graphs.GraphState

rollback(String, int) - Method in interface ome.services.graphs.GraphStep.Callback

rollback(GraphStep.Callback) - Method in class ome.services.graphs.GraphStep

rollbackOnly() - Method in class ome.services.graphs.GraphStep

RomioPixelBuffer - Class in ome.io.nio

Class implementation of the PixelBuffer interface for standard "proprietary" ROMIO/OMEIS data format.

RomioPixelBuffer(String, Pixels) - Constructor for class ome.io.nio.RomioPixelBuffer

Creates a new instance.

RomioPixelBuffer(String, Pixels, boolean) - Constructor for class ome.io.nio.RomioPixelBuffer

Creates a new instance, with manual setting of RomioPixelBuffer.permitModification.

root(Current) - Method in class ome.services.blitz.repo.PublicRepositoryI

ROOT - Static variable in class prefs

"omero.prefs", the value of the root Preferences node used for all configuration work.

ROOT_DEFAULT - Static variable in class ome.io.nio.AbstractFileSystemService

ROUTED_FROM - Static variable in class ome.services.blitz.redirect.AbstractRedirector

Router - Class in ome.services.blitz

Wrapper around a call to 'glacier2router' to permit Java control over the process.

Router() - Constructor for class ome.services.blitz.Router

rps - Variable in class omero.util.RPSTileData

RPSTileData - Class in omero.util

Access strategy which can be implemented by diverse resources

RPSTileData(RPSTileLoop, RawPixelsStorePrx) - Constructor for class omero.util.RPSTileData

RPSTileLoop - Class in omero.util

Helper subclass of TileLoop which handles unloaded Pixels instances and manages the creation of the RPSTileData.

RPSTileLoop(ServiceFactoryPrx, Pixels) - Constructor for class omero.util.RPSTileLoop

rset(RType...) - Static method in class omero.rtypes

rset(Collection<RType>) - Static method in class omero.rtypes

rstring(String) - Static method in class omero.rtypes

RTF - Static variable in class pojos.FileAnnotationData

Identifies the RTF file formats.

rtime(long) - Static method in class omero.rtypes

rtime(Date) - Static method in class omero.rtypes

rtime_max() - Static method in class omero.rtypes

rtime_min() - Static method in class omero.rtypes

rtime_str(String) - Static method in class omero.rtypes

rtype() - Method in class omero.rtypes.ObjectFactory

rtype(Object) - Static method in class omero.rtypes

Attempts to dispatch to the other omero.rtypes.* static methods to create a proper RType subclass by checking the type of the input.

RTYPEDICT - Static variable in class omero.util.IceMapper

RTypeMapper - Class in omero.util

Extension of IceMapper which guarantees that RCollection and RMap instances are properly created.

RTypeMapper(IceMapper.ReturnMapping) - Constructor for class omero.util.RTypeMapper

rtypes - Class in omero

Abstract class similar to Arrays or Collections which is responsible for creating RTypes from static factory methods.

rtypes() - Constructor for class omero.rtypes

rtypes.Conversion - Interface in omero

SPI-style interface which helps the omero server to properly convert omero.RType objects into Java-native objects for use in Hibernate.

rtypes.ObjectFactory - Class in omero

rtypes.ObjectFactory(String) - Constructor for class omero.rtypes.ObjectFactory

run() - Method in class ome.formats.importer.util.ClientKeepAlive

run(int, int, int, int, int, int, int, int) - Method in interface ome.io.nio.TileLoopIteration

Invoke a single loop iteration.

run() - Method in class ome.services.blitz.impl.DeleteHandleI

NB: only executes if DeleteHandleI.state is State#CREATED.

run() - Method in class ome.services.blitz.Status

run() - Method in class ome.services.blitz.util.CheckAllJobs

run() - Method in interface ome.services.procs.IProcessManager

Runs the processing phase as root.

run(OmeroContext) - Method in class ome.services.throttling.Adapter

run(OmeroContext) - Method in class ome.services.throttling.Callback

run(OmeroContext) - Method in class ome.services.throttling.Callback2

run() - Method in class ome.services.throttling.Slot

run(OmeroContext) - Method in class ome.services.throttling.Task

run() - Method in class ome.services.util.DropBoxDirectoryCheck

Synchronizes the ${omero.data.dir}/DropBox directory by creating a directory for any user who does not have one.

run() - Method in class ome.services.util.ExecutionThread

Initializes the Session for this Thread if necessary, then calls ExecutionThread.doRun().

run() - Method in class ome.services.util.ServerDirectoryCheck

Synchronizes the ${omero.data.dir}/Server directory by creating a directory for any user who does not have one.

run() - Method in class ome.system.UpgradeCheck

If the UpgradeCheck.url has been set to null or the empty string, then no upgrade check will be performed (silently).

run(TileData, int, int, int, int, int, int, int, int) - Method in interface omero.util.TileLoopIteration

Invoke a single loop iteration.

runAsAdmin() - Method in interface ome.security.AdminAction

executes with special privilegs within the SecuritySystem.

runAsAdmin(AdminAction) - Method in class ome.security.basic.BasicSecuritySystem

merge event is disabled for BasicSecuritySystem.runAsAdmin(AdminAction) because passing detached (client-side) entities to this method is particularly dangerous.

runAsAdmin(AdminAction) - Method in interface ome.security.SecuritySystem

Allows actions to be performed with the EventContext.isCurrentUserAdmin() flag enabled but without changing the value of EventContext.getCurrentUserId(), so that ownerships are properly handled.

runAsAdmin(AdminAction) - Method in class ome.security.SecuritySystemHolder

runAsAdmin(AdminAction) - Method in class ome.security.sharing.SharingSecuritySystem

runAsAdmin() - Method in class ome.services.delete.QueryConstraints

runnableCall(Current, Task) - Method in class ome.services.blitz.impl.AbstractAmdServant

runnableCall(Current, Task) - Method in interface ome.services.blitz.util.BlitzExecutor

runnableCall(Current, Task) - Method in class ome.services.throttling.InThreadThrottlingStrategy

runnableCall(Current, Task) - Method in class ome.services.throttling.SerialThrottlingStrategy

RUNNING - Static variable in interface ome.api.JobHandle

runningProcess(long) - Method in interface ome.services.procs.IProcessManager

Returns a running Process for the id or null.

runningProcess(long) - Method in class ome.services.procs.ProcessManager

runScript_async(AMD_IScript_runScript, long, Map<String, RType>, RInt, Current) - Method in class ome.services.blitz.impl.ScriptI

runTopLevel(Session, List<Long>) - Method in class ome.services.graphs.AnnotationGraphSpec

runTopLevel(Session, List<Long>) - Method in class ome.services.graphs.BaseGraphSpec

runTopLevel(Session, List<Long>) - Method in interface ome.services.graphs.GraphSpec

Workaround for the removal of GraphSpec#delete when refactoring to GraphState.

S

safeRunnableCall(Current, Object, boolean, Callable<R>) - Method in class ome.services.blitz.impl.AbstractAmdServant

safeRunnableCall(Current, Object, boolean, Callable<R>) - Method in interface ome.services.blitz.util.BlitzExecutor

safeRunnableCall(Current, Object, boolean, Callable<R>) - Method in class ome.services.throttling.InThreadThrottlingStrategy

safeRunnableCall(Current, Object, boolean, Callable<R>) - Method in class ome.services.throttling.SerialThrottlingStrategy

sanityCheckPixels(Pixels, Pixels) - Method in interface ome.api.IRenderingSettings

Checks if the specified sets of pixels are compatible.

sanityCheckPixels(Pixels, Pixels) - Method in class ome.logic.RenderingSettingsImpl

Implemented as specified by the IRenderingSettings I/F

sanityCheckPixels_async(AMD_IRenderingSettings_sanityCheckPixels, Pixels, Pixels, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI

sanityCheckRepository() - Method in interface ome.api.IRepositoryInfo

Checks that image data repository has not exceeded 95% disk space use level.

sanityCheckRepository() - Method in class ome.logic.RepositoryInfoImpl

sanityCheckRepository_async(AMD_IRepositoryInfo_sanityCheckRepository, Current) - Method in class ome.services.blitz.impl.RepositoryInfoI

save() - Method in interface ome.api.RawFileStore

Saves the OriginalFile associated with the service if it has been modified.

save() - Method in interface ome.api.RawPixelsStore

save() - Method in class ome.services.blitz.measurements.MeasurementStore

save() - Method in interface ome.services.blitz.measurements.OmeroMeasurementStore

save() - Method in class ome.services.RawFileBean

save() - Method in class ome.services.RawPixelsBean

save_async(AMD_RawFileStore_save, Current) - Method in class ome.services.blitz.impl.RawFileStoreI

save_async(AMD_RawPixelsStore_save, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI

save_async(AMD_RawPixelsStore_save, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI

save_async(AMD_RawFileStore_save, Current) - Method in class ome.services.blitz.repo.RepoRawFileStoreI

SAVE_EVENT - Static variable in class ome.security.basic.SaveEventListener

saveAll() - Method in class ome.formats.importer.ImportConfig

saveAndReturnArray(IObject[]) - Method in interface ome.api.IUpdate

saveAndReturnArray(IObject[]) - Method in class ome.logic.UpdateImpl

saveAndReturnArray(List<IObject>, Current) - Method in class ome.services.blitz.gateway.OmeroGateway

saveAndReturnArray(List<IObject>) - Method in interface ome.services.blitz.gateway.services.DataService

Save and return the array.

saveAndReturnArray(List<IObject>) - Method in class ome.services.blitz.gateway.services.impl.DataServiceImpl

saveAndReturnArray_async(AMD_IUpdate_saveAndReturnArray, List<IObject>, Current) - Method in class ome.services.blitz.impl.UpdateI

saveAndReturnIds(IObject[]) - Method in interface ome.api.IUpdate

Logic differs from other methods.

saveAndReturnIds(IObject[]) - Method in class ome.logic.UpdateImpl

saveAndReturnIds_async(AMD_IUpdate_saveAndReturnIds, List<IObject>, Current) - Method in class ome.services.blitz.impl.UpdateI

saveAndReturnObject(T) - Method in interface ome.api.IUpdate

saveAndReturnObject(IObject) - Method in class ome.logic.UpdateImpl

saveAndReturnObject(IObject, Current) - Method in class ome.services.blitz.gateway.OmeroGateway

saveAndReturnObject(IObject) - Method in interface ome.services.blitz.gateway.services.DataService

Save and return the Object.

saveAndReturnObject(IObject) - Method in class ome.services.blitz.gateway.services.impl.DataServiceImpl

saveAndReturnObject_async(AMD_IUpdate_saveAndReturnObject, IObject, Current) - Method in class ome.services.blitz.impl.UpdateI

saveArray(IObject[]) - Method in interface ome.api.IUpdate

saveArray(IObject[]) - Method in class ome.logic.UpdateImpl

saveArray(List<IObject>, Current) - Method in class ome.services.blitz.gateway.OmeroGateway

saveArray(List<IObject>) - Method in interface ome.services.blitz.gateway.services.DataService

Save the array.

saveArray(List<IObject>) - Method in class ome.services.blitz.gateway.services.impl.DataServiceImpl

saveArray_async(AMD_IUpdate_saveArray, List<IObject>, Current) - Method in class ome.services.blitz.impl.UpdateI

saveCollection(Collection<IObject>) - Method in interface ome.api.IUpdate

saveCollection(Collection) - Method in class ome.logic.UpdateImpl

saveCollection_async(AMD_IUpdate_saveCollection, List<IObject>, Current) - Method in class ome.services.blitz.impl.UpdateI

saveCurrentSettings() - Method in class ome.services.RenderingBean

Implemented as specified by the RenderingEngine interface.

saveCurrentSettings() - Method in interface omeis.providers.re.RenderingEngine

Saves the current rendering settings in the database.

saveCurrentSettings_async(AMD_RenderingEngine_saveCurrentSettings, Current) - Method in class ome.services.blitz.impl.RenderingEngineI

saveCurrentSettings_async(AMD_RenderingEngine_saveCurrentSettings, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI

savedDataset - Variable in class ome.formats.importer.ImportConfig

savedDirectory - Variable in class ome.formats.importer.ImportConfig

savedPlates - Variable in class ome.services.blitz.impl.MetadataStoreI

savedProject - Variable in class ome.formats.importer.ImportConfig

savedScreen - Variable in class ome.formats.importer.ImportConfig

SaveEventListener - Class in ome.security.basic

event listener which will only handle newly created (transient) objects in a given graph.

SaveEventListener(CurrentDetails, TokenHolder) - Constructor for class ome.security.basic.SaveEventListener

main constructor.

saveGui() - Method in class ome.formats.importer.ImportConfig

Saves gui specific values for which it makes sense to have a preferences values.

saveObject(IObject) - Method in interface ome.api.IUpdate

saveObject(IObject) - Method in class ome.logic.UpdateImpl

saveObject(IObject, Current) - Method in class ome.services.blitz.gateway.OmeroGateway

saveObject(IObject) - Method in interface ome.services.blitz.gateway.services.DataService

Save the object to the db .

saveObject(IObject) - Method in class ome.services.blitz.gateway.services.impl.DataServiceImpl

saveObject_async(AMD_IUpdate_saveObject, IObject, Current) - Method in class ome.services.blitz.impl.UpdateI

savepoint(String) - Method in class ome.services.graphs.GraphState

savepoint(String) - Method in interface ome.services.graphs.GraphStep.Callback

savepoint(GraphStep.Callback) - Method in class ome.services.graphs.GraphStep

saveRndSettings(RenderingDef) - Method in interface ome.api.IPixels

Saves the specified rendering settings.

saveRndSettings(RenderingDef) - Method in class ome.logic.PixelsImpl

saveRndSettings_async(AMD_IPixels_saveRndSettings, RenderingDef, Current) - Method in class ome.services.blitz.impl.PixelsI

saveToDB() - Method in class ome.formats.OMEROMetadataStore

Saves the current object graph to the database.

saveToDB() - Method in class ome.formats.OMEROMetadataStoreClient

Updates the server side MetadataStore with a list of our objects and references and saves them into the database.

saveToDB_async(AMD_MetadataStore_saveToDB, Current) - Method in class ome.services.blitz.impl.MetadataStoreI

scalar(double) - Method in class ome.util.math.geom2D.PlanePoint

Multiplies this vector by the specified scalar.

scale(double) - Method in class ome.util.math.geom2D.EllipseArea

Implemented as specified by the PlaneArea I/F.

scale(double) - Method in interface ome.util.math.geom2D.PlaneArea

Resets the bounding Rectangle of the planeArea according to the specified scaling factor.

scale(double) - Method in class ome.util.math.geom2D.RectangleArea

Implemented as specified by the PlaneArea I/F.

scaleBufferedImage(BufferedImage, float, float) - Method in interface ome.api.IScale

Scales a buffered image using defined X and Y axis scale factors.

scaleBufferedImage(BufferedImage, float, float) - Method in class ome.logic.AWTScaleService

scaleBufferedImage(BufferedImage, float, float) - Method in class ome.logic.JavaImageScalingService

ScaleRedirector - Class in ome.services.blitz.redirect

Planned implementation (NYI): will use the "Node.scale" column to randomly choose a target.

ScaleRedirector(Executor) - Constructor for class ome.services.blitz.redirect.ScaleRedirector

scalingFactor - Variable in class ome.io.nio.SimpleBackOff

SchedulerFactoryBean - Class in ome.services.scheduler

Produces a SchedulerFactoryBean() - Constructor for class ome.services.scheduler.SchedulerFactoryBean

SCORE - Static variable in interface ome.api.Search

String constant used to look up the score value of Lucene queries returned by this interface.

SCREEN_LINKS - Static variable in class pojos.PlateData

Identifies the Plate#SCREENLINKS field.

ScreenData - Class in pojos

The data that makes up an OME Screen along with links to its contained Plates and the Experimenter that owns this Screen.

ScreenData() - Constructor for class pojos.ScreenData

Creates a new instance.

ScreenData(Screen) - Constructor for class pojos.ScreenData

Creates a new instance.

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.

SCRIPT_REPO - Static variable in class ome.services.scripts.ScriptRepoHelper

Id used by all script repositories.

ScriptFinder - Class in ome.services.scripts

Looks up an official script based on path for internal use.

ScriptFinder(Roles, String, Executor, File) - Constructor for class ome.services.scripts.ScriptFinder

ScriptFinder(Roles, Principal, Executor, File) - Constructor for class ome.services.scripts.ScriptFinder

ScriptI - Class in ome.services.blitz.impl

implementation of the IScript service interface.

ScriptI(BlitzExecutor, ScriptRepoHelper) - Constructor for class ome.services.blitz.impl.ScriptI

ScriptProcess - Class in ome.services.procs.scripts

ScriptProcess(Processor) - Constructor for class ome.services.procs.scripts.ScriptProcess

ScriptProcessI - Class in ome.services.blitz.impl

ScriptProcessI(ServiceFactoryI, Current, InteractiveProcessorPrx, InteractiveProcessorI, ProcessPrx) - Constructor for class ome.services.blitz.impl.ScriptProcessI

ScriptProcessor - Class in ome.services.procs.scripts

ScriptProcessor() - Constructor for class ome.services.procs.scripts.ScriptProcessor

ScriptRepoHelper - Class in ome.services.scripts

Strategy used by the ScriptRepository for registering, loading, and saving files.

ScriptRepoHelper(Executor, String, Roles) - Constructor for class ome.services.scripts.ScriptRepoHelper

ScriptRepoHelper(File, Executor, Principal, Roles) - Constructor for class ome.services.scripts.ScriptRepoHelper

ScriptRepoHelper(String, File, Executor, Principal, Roles) - Constructor for class ome.services.scripts.ScriptRepoHelper

ScriptRepositoryI - Class in ome.services.blitz.repo

Repository which makes the included script files available to users.

ScriptRepositoryI(ObjectAdapter, Registry, Executor, SqlAction, String, ScriptRepoHelper) - Constructor for class ome.services.blitz.repo.ScriptRepositoryI

scripts - Variable in class ome.services.blitz.impl.ScriptI

Search - Interface in ome.api

Central search interface, allowing Web2.0 style queries.

SearchAction - Class in ome.services.search

Serializable action used by SearchBean to generate results lazily.

SearchAction(SearchValues) - Constructor for class ome.services.search.SearchAction

searchAll() - Method in interface ome.api.ILdap

Searchs all Experimenter list on LDAP for attribute objectClass = person.

searchAll() - Method in class ome.logic.LdapImpl

searchAll_async(AMD_ILdap_searchAll, Current) - Method in class ome.services.blitz.impl.LdapI

SearchBean - Class in ome.services

Implements the Search interface.

SearchBean(Executor, Class<? extends Analyzer>) - Constructor for class ome.services.SearchBean

SearchBean() - Constructor for class ome.services.SearchBean

Empty constructor required by EJB and self configuration.

searchByAttribute(String, String, String) - Method in interface ome.api.ILdap

Searchs all Experimenter in LDAP for specyfied attribute

searchByAttribute(String, String, String) - Method in class ome.logic.LdapImpl

searchByAttribute_async(AMD_ILdap_searchByAttribute, String, String, String, Current) - Method in class ome.services.blitz.impl.LdapI

searchByAttributes(String, String[], String[]) - Method in interface ome.api.ILdap

Searchs all Experimenter in LDAP for specyfied attributes.

searchByAttributes(String, String[], String[]) - Method in class ome.logic.LdapImpl

searchByAttributes_async(AMD_ILdap_searchByAttributes, String, List<String>, List<String>, Current) - Method in class ome.services.blitz.impl.LdapI

searchByDN(String) - Method in interface ome.api.ILdap

Searchs one Experimenter in LDAP for specyfied Distinguished Name - String

searchByDN(String) - Method in class ome.logic.LdapImpl

searchByDN_async(AMD_ILdap_searchByDN, String, Current) - Method in class ome.services.blitz.impl.LdapI

searchDnInGroups(String, String) - Method in interface ome.api.ILdap

Searchs Distinguished Name - String in groups

searchDnInGroups(String, String) - Method in class ome.logic.LdapImpl

searchDnInGroups_async(AMD_ILdap_searchDnInGroups, String, String, Current) - Method in class ome.services.blitz.impl.LdapI

SearchI - Class in ome.services.blitz.impl

Implementation of the Search service.

SearchI(Search, BlitzExecutor) - Constructor for class ome.services.blitz.impl.SearchI

SearchValues - Class in ome.services.search

Values used by SearchBean to store user requests.

SearchValues() - Constructor for class ome.services.search.SearchValues

sec - Variable in class ome.logic.AbstractLevel2Service

sec - Variable in class ome.security.auth.SimpleRoleProvider

sec - Variable in class ome.services.AbstractStatefulBean

sec - Variable in class ome.services.procs.ProcessManager.Work

SecuritySystem in order to perform a secure save on the Job instance.

secondLevelCacheHit(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

secondLevelCacheMiss(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

secondLevelCachePut(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

secSys - Variable in class ome.security.basic.EventHandler

SecureAction - Interface in ome.security

action for passing to SecuritySystem#doAction(IObject, SecureAction).

SecureMerge - Class in ome.tools.hibernate

Helper originally from SimpleRoleProvider for merging admin objects.

SecureMerge(Session) - Constructor for class ome.tools.hibernate.SecureMerge

SecureMerge(Session, boolean) - Constructor for class ome.tools.hibernate.SecureMerge

securityFilter - Variable in class ome.security.basic.BasicACLVoter

SecurityFilter - Class in ome.tools.hibernate

overrides FilterDefinitionFactoryBean in order to construct our security filter in code and not in XML.

SecurityFilter() - Constructor for class ome.tools.hibernate.SecurityFilter

default constructor which calls all the necessary setters for this FactoryBean.

SecurityFilter(Roles) - Constructor for class ome.tools.hibernate.SecurityFilter

SecuritySystem - Interface in ome.security

central security interface.

securitySystem - Variable in class ome.services.blitz.fire.SessionManagerI

SecuritySystemHolder - Class in ome.security

Security dispatcher holding each currently active SecuritySystem instance and allowing dispatching between them.

SecuritySystemHolder(BasicSecuritySystem, SharingSecuritySystem) - Constructor for class ome.security.SecuritySystemHolder

Segment - Class in ome.util.math.geom2D

A segment in the Euclidean space R².

Segment(double, double, double, double) - Constructor for class ome.util.math.geom2D.Segment

Creates a new instance.

select(String...) - Method in class ome.tools.hibernate.QueryBuilder

SelfConfigurableService - Interface in ome.system

selfConfigure() - Method in class ome.logic.AbstractLevel1Service

This method was previously called by the EJB container, but is no longer needed.

selfConfigure() - Method in class ome.logic.AbstractLevel2Service

This method was previously called by the EJB container, but is no longer needed.

selfConfigure(OmeroContext) - Method in class ome.logic.HardWiredInterceptor

Calls OmeroContext.applyBeanPropertyValues(Object, String) to have properties injected.

selfConfigure(SessionManager, ServiceFactory) - Static method in class ome.security.basic.BasicSecuritySystem

Simpilifed factory method which generates all the security primitives internally.

selfConfigure() - Method in class ome.services.AbstractStatefulBean

selfConfigure() - Method in interface ome.system.SelfConfigurableService

SelfCorrectingDataSource - Class in ome.services.db

DataSource delegate which wraps the

SelfCorrectingDataSource(DataSource, long) - Constructor for class ome.services.db.SelfCorrectingDataSource

SelfCorrectingDataSource(DataSource, long, int, long) - Constructor for class ome.services.db.SelfCorrectingDataSource

sendData(OutputStream) - Method in class ome.formats.importer.util.ErrorFilePart

sendErrors() - Method in class ome.formats.importer.util.ErrorHandler

Send existing errors in ErrorContainer array to server

sendFiles - Variable in class ome.formats.importer.ImportConfig

sendFiles - Variable in class ome.formats.importer.ImportEvent.DEBUG_SEND

sendFiles - Variable in class ome.formats.importer.util.ErrorHandler

sendLogFile - Variable in class ome.formats.importer.ImportConfig

sendLogs - Variable in class ome.formats.importer.ImportEvent.DEBUG_SEND

sendLogs - Variable in class ome.formats.importer.util.ErrorHandler

sendReport - Variable in class ome.formats.importer.ImportConfig

SerialThrottlingStrategy - Class in ome.services.throttling

Throttling implementation which only allows a single invocation to be run at any given time.

SerialThrottlingStrategy(OmeroContext) - Constructor for class ome.services.throttling.SerialThrottlingStrategy

series - Variable in class ome.formats.importer.ImportEvent.IMPORT_STEP

series - Variable in class ome.formats.importer.ImportEvent.PROGRESS_EVENT

seriesCount - Variable in class ome.formats.importer.ImportEvent.IMPORT_STEP

ServantHolder - Class in ome.services.blitz.util

Manager for all active servants in a single ServiceFactoryI.

ServantHolder() - Constructor for class ome.services.blitz.util.ServantHolder

Server - Class in ome.system

Provides simplified handling of server properties when creating a ServiceFactory.

Server(String) - Constructor for class ome.system.Server

standard constructor which users Server.DEFAULT_PORT.

Server(String, int) - Constructor for class ome.system.Server

extended constructor.

SERVER_NAME_SEPARATOR - Static variable in class ome.formats.importer.ImportConfig

Delimiter used to encode multiple servers in one preferences value.

ServerDirectoryCheck - Class in ome.services.util

Hook run by the context at startup to create needed directories for the server.

ServerDirectoryCheck(String) - Constructor for class ome.services.util.ServerDirectoryCheck

serverList - Variable in class ome.formats.importer.ImportConfig

ServerVersionCheck - Class in ome.services.util

Hook run by the context.

ServerVersionCheck(String) - Constructor for class ome.services.util.ServerVersionCheck

service - Variable in class ome.services.blitz.impl.AbstractAmdServant

If there is no undering ome.* service, then this value can be null.

service - Variable in class ome.services.util.Executor.Impl

ServiceFactory - Class in ome.system

Entry point for all client calls.

ServiceFactory() - Constructor for class ome.system.ServiceFactory

default constructor which obtains the global static client context from OmeroContext.

ServiceFactory(Login) - Constructor for class ome.system.ServiceFactory

constructor which obtains a new (non-static) client context, passing in the Properties representation of the Login for configuration.

ServiceFactory(Server) - Constructor for class ome.system.ServiceFactory

constructor which obtains a new (non-static) client context, passing in the Properties representation of the Server for configuration.

ServiceFactory(Server, Login) - Constructor for class ome.system.ServiceFactory

constructor which obtains a new (non-static) client context, passing in the Properties representation of both the Server and the Login for configuration.

ServiceFactory(Properties) - Constructor for class ome.system.ServiceFactory

constructor which obtains a new client context, passing in the provided properties for configuration.

ServiceFactory(OmeroContext) - Constructor for class ome.system.ServiceFactory

constructor which uses the provided OmeroContext for all loookups.

ServiceFactory(String) - Constructor for class ome.system.ServiceFactory

constructor which finds the global static OmeroContext with the given name.

ServiceFactoryAware - Interface in ome.services.blitz.util

Servant which is aware of the ServiceFactoryI-instance which it belongs to and will have it injected on instantiation.

ServiceFactoryI - Class in ome.services.blitz.impl

Responsible for maintaining all servants for a single session.

ServiceFactoryI(Current, SessionControlPrx, OmeroContext, SessionManager, Executor, Principal, List<HardWiredInterceptor>, TopicManager, Registry) - Constructor for class ome.services.blitz.impl.ServiceFactoryI

ServiceFactoryI(boolean, Current, SessionControlPrx, OmeroContext, SessionManager, Executor, Principal, List<HardWiredInterceptor>, TopicManager, Registry) - Constructor for class ome.services.blitz.impl.ServiceFactoryI

ServiceHandler - Class in ome.services.util

ServiceHandler(CurrentDetails) - Constructor for class ome.services.util.ServiceHandler

ServiceHandler(CurrentDetails, long, long) - Constructor for class ome.services.util.ServiceHandler

ServiceInterface - Interface in ome.api

Marker interface representing an OMERO API Interface.

ServiceUtilities - Class in ome.services.blitz.gateway.services.util

ServiceUtilities() - Constructor for class ome.services.blitz.gateway.services.util.ServiceUtilities

session - Variable in class ome.system.SessionInitializer

session - Variable in class omero.util.RPSTileLoop

SessionBean - Class in ome.services.sessions

Implementation of ISession.

SessionBean(SessionManager, Executor, CurrentDetails) - Constructor for class ome.services.sessions.SessionBean

SessionCache - Class in ome.services.sessions.state

Synchronized and lockable state for the SessionManager.

SessionCache() - Constructor for class ome.services.sessions.state.SessionCache

SessionCache.StaleCacheListener - Interface in ome.services.sessions.state

Observer pattern used to refresh sessions in doUpdate.

SessionCallback - Interface in ome.services.sessions

SessionCallback.SimpleCloseCallback - Class in ome.services.sessions

Assumes that only close() will be called.

SessionCallback.SimpleCloseCallback() - Constructor for class ome.services.sessions.SessionCallback.SimpleCloseCallback

SessionContext - Interface in ome.services.sessions

Extends EventContext to hold a Session.

SessionContext.Count - Class in ome.services.sessions

Synchronized counter which can be passed between SessionContext instances as they are recreated.

SessionContext.Count(String) - Constructor for class ome.services.sessions.SessionContext.Count

SessionContextImpl - Class in ome.services.sessions

SessionContextImpl(Session, List<Long>, List<Long>, List<String>, SessionStats, SessionContext) - Constructor for class ome.services.sessions.SessionContextImpl

SessionContextImpl(Session, List<Long>, List<Long>, List<String>, SessionStats, Roles, SessionContext) - Constructor for class ome.services.sessions.SessionContextImpl

sessionFactory - Variable in class ome.logic.AbstractLevel1Service

SessionFactory - Class in ome.tools.hibernate

Simple source of Thread-aware Session instances.

SessionFactory(SessionFactory, SqlAction) - Constructor for class ome.tools.hibernate.SessionFactory

SessionHandler - Class in ome.tools.hibernate

interceptor which delegates to HibernateInterceptor for stateless services but which keeps a WeakHashMap of sessions keyed by the stateful service reference.

SessionHandler(SessionFactory) - Constructor for class ome.tools.hibernate.SessionHandler

constructor taking a DataSource and a SessionFactory.

SessionI - Class in ome.services.blitz.impl

Implementation of the ISession service.

SessionI(ISession, BlitzExecutor) - Constructor for class ome.services.blitz.impl.SessionI

sessionId(String, String) - Static method in class ome.services.blitz.impl.ServiceFactoryI

Definition of session ids: "session-/"

sessionId() - Method in class ome.services.blitz.impl.ServiceFactoryI

Returns the Identity for this instance as defined by ServiceFactoryI.sessionId(String, String)

sessionInit() - Method in class ome.services.util.ExecutionThread

SessionInitializer - Class in ome.system

Manages the creation of a single Session created via the injected ISession service.

SessionInitializer() - Constructor for class ome.system.SessionInitializer

sessionKey - Variable in class ome.formats.importer.ImportConfig

sessionManager - Variable in class ome.logic.UpdateImpl

sessionManager - Variable in class ome.security.basic.BasicSecuritySystem

sessionManager - Variable in class ome.services.blitz.fire.SessionManagerI

SessionManager - Interface in ome.services.sessions

Responsible for holding onto Session instances for optimized login.

sessionManager - Variable in class ome.services.sharing.ShareBean

SessionManagerI - Class in ome.services.blitz.fire

Central login logic for all OMERO.blitz clients.

SessionManagerI(Ring, ObjectAdapter, SecuritySystem, SessionManager, Executor, TopicManager, Registry) - Constructor for class ome.services.blitz.fire.SessionManagerI

SessionManagerImpl - Class in ome.services.sessions

Is for ISession a cache and will be kept there in sync?

SessionManagerImpl() - Constructor for class ome.services.sessions.SessionManagerImpl

sessions - Variable in class ome.system.SessionInitializer

SessionsCreatedCounter - Class in ome.services.sessions.stats

Counter for all the objects read in a session.

SessionsCreatedCounter(int) - Constructor for class ome.services.sessions.stats.SessionsCreatedCounter

SessionsCreatedStatsMessage - Class in ome.services.messages.stats

Published when some limit in user/group/session activity has been reached.

SessionsCreatedStatsMessage(Object, long) - Constructor for class ome.services.messages.stats.SessionsCreatedStatsMessage

SessionStats - Interface in ome.services.sessions.stats

Thread-safe counter for all

sessionToClientIds - Variable in class ome.services.blitz.fire.SessionManagerI

An internal mapping to all ServiceFactoryI instances for a given session since there is no method on ObjectAdapter to retrieve all servants.

set(T) - Method in class ome.formats.importer.ImportConfig.Value

Sets the in-memory value, which will get persisted on ImportConfig.Value.store() when ImportConfig.saveAll() is called.

set(U) - Method in class ome.services.blitz.util.ResultHolder

set(String, Object, Document, LuceneOptions) - Method in class ome.services.fulltext.BridgeHelper

Method to be implemented by all bridges.

set(String, Object, Document, LuceneOptions) - Method in class ome.services.fulltext.bridges.ProjectWithImageNameBridge

If the "value" argument is a Project, this bridge gathers all images and adds them to the index with a slightly reduced boost value.

set(String, Object, Document, LuceneOptions) - Method in class ome.services.fulltext.bridges.TablesBridge

Primary entry point for all bridges.

set(String, Object, Document, LuceneOptions) - Method in class ome.services.fulltext.FullTextBridge

Default implementation of the #set(String, Object, Document, Store, org.apache.lucene.document.Field.Index, Float) method which calls #set_file(String, IObject, Document, Store, org.apache.lucene.document.Field.Index, Float) #set_annotations(String, Object, Document, Store, org.apache.lucene.document.Field.Index, Float), #set_details(String, Object, Document, Store, org.apache.lucene.document.Field.Index, Float), and finally #set_custom(String, Object, Document, Store, org.apache.lucene.document.Field.Index, Float).

set(Share, long, List<T>, List<Long>, List<String>, boolean) - Method in class ome.services.sharing.ShareStore

set(int, byte) - Method in class ome.util.mem.ByteArray

Writes value into the element at the index position within this slice.

set(int, byte[]) - Method in class ome.util.mem.ByteArray

Copies the values in buf into this slice, starting from index.

set(int, int, InputStream) - Method in class ome.util.mem.ByteArray

Writes up to maxLength bytes from the supplied stream into this slice, starting from index.

set(Copiable, int) - Method in class ome.util.mem.CopiableArray

Replaces the element at the specified position with the specified Copiable.

set(int, int, boolean) - Method in class omero.model.PermissionsI

set(String[]) - Static method in class prefs

Takes an array of length 2, using args[0] as the key and args[1] as the value to be set.

set_annotations(String, IObject, Document, LuceneOptions) - Method in class ome.services.fulltext.FullTextBridge

Walks the various Annotation instances attached to the object argument and adds various levels to the index.

set_custom(String, IObject, Document, LuceneOptions) - Method in class ome.services.fulltext.FullTextBridge

Loops over each field bridge class and calls its FieldBridge#set(String, Object, Document, Store, org.apache.lucene.document.Field.Index, Float) method.

set_details(String, IObject, Document, LuceneOptions) - Method in class ome.services.fulltext.FullTextBridge

Parses all ownership and time-based details to the index for the given object.

set_file(String, IObject, Document, LuceneOptions) - Method in class ome.services.fulltext.FullTextBridge

Uses #parse(OriginalFile) to get a Reader for the given file which is then passed to #add(Document, String, Reader, Float) using the field name "file".

setAbsolutePath(String) - Method in class ome.formats.importer.util.ErrorContainer

set path for file

setActive(long, boolean) - Method in interface ome.api.IShare

setActive(long, int, boolean, Current) - Method in class ome.services.blitz.gateway.OmeroGateway

setActive(Long, int, boolean) - Method in interface ome.services.blitz.gateway.services.ImageService

Set the active channels in the pixels.

setActive(Long, int, boolean) - Method in class ome.services.blitz.gateway.services.impl.ImageServiceImpl

setActive(Long, int, boolean) - Method in class ome.services.blitz.gateway.services.impl.RenderingServiceImpl

setActive(Long, int, boolean) - Method in interface ome.services.blitz.gateway.services.RenderingService

Set the active channels in the pixels.

setActive(int, boolean) - Method in class ome.services.RenderingBean

Implemented as specified by the RenderingEngine interface.

setActive(long, boolean) - Method in class ome.services.sharing.ShareBean

setActive(int, boolean) - Method in class omeis.providers.re.Renderer

Makes a particular channel active or inactive.

setActive(int, boolean) - Method in interface omeis.providers.re.RenderingEngine

Maps the specified channel if true, unmaps the channel otherwise.

setActive_async(AMD_RenderingEngine_setActive, int, boolean, Current) - Method in class ome.services.blitz.impl.RenderingEngineI

setActive_async(AMD_IShare_setActive, long, boolean, Current) - Method in class ome.services.blitz.impl.ShareI

setActive_async(AMD_RenderingEngine_setActive, int, boolean, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI

setAgent(String) - Method in class omero.client

Sets the user agent string for this client.

setAirPressure(double) - Method in class pojos.ImageAcquisitionData

Sets the air pressure.

setAliases(String[]) - Method in class ome.system.Preference

Setter injector

setAllowLeadingWildcard(boolean) - Method in interface ome.api.Search

Permits full-text queries with a leading query if true.

setAllowLeadingWildcard(boolean) - Method in class ome.services.SearchBean

setAllowLeadingWildcard_async(AMD_Search_setAllowLeadingWildcard, boolean, Current) - Method in class ome.services.blitz.impl.SearchI

setAllPixels(List<PixelsData>) - Method in class pojos.ImageData

Sets the set of pixels related to this image.

setAlpha(Integer) - Method in class pojos.WellData

Sets the alpha component of the color associated to the well.

setAlphalessRendering(boolean) - Method in class omeis.providers.re.Optimizations

Enable or disable the alphaless rendering optimization.

setAlternateStylesheet(String) - Method in class ome.services.SVGRasterizer

Sets the alternate stylesheet to use.

setAnalyzer(Class<? extends Analyzer>) - Method in class ome.logic.QueryImpl

setAnalyzer(Class<? extends Analyzer>) - Method in class ome.services.SearchBean

Injector used by Spring.

setAnnotations(Set) - Method in class pojos.DatasetData

Sets the annotations related to this dataset.

setAnnotations(Set) - Method in class pojos.ImageData

Sets the image's annotations.

setApplicationContext(ApplicationContext) - Method in class ome.logic.AdminImpl

setApplicationContext(ApplicationContext) - Method in class ome.logic.LdapImpl

setApplicationContext(ApplicationContext) - Method in class ome.security.auth.ConfigurablePasswordProvider

setApplicationContext(ApplicationContext) - Method in class ome.security.basic.BasicSecuritySystem

setApplicationContext(ApplicationContext) - Method in class ome.services.blitz.fire.SessionManagerI

setApplicationContext(ApplicationContext) - Method in class ome.services.blitz.impl.AbstractAmdServant

Creates an IceMethodInvoker for this instance if AbstractAmdServant.service is non-null.

setApplicationContext(ApplicationContext) - Method in class ome.services.fulltext.FileParser

setApplicationContext(ApplicationContext) - Method in class ome.services.graphs.GraphSpecPostProcessor

setApplicationContext(ApplicationContext) - Method in class ome.services.procs.ImportProcessor

setApplicationContext(ApplicationContext) - Method in class ome.services.scheduler.SchedulerFactoryBean

setApplicationContext(ApplicationContext) - Method in class ome.services.sessions.SessionManagerImpl

setApplicationContext(ApplicationContext) - Method in class ome.services.sessions.state.CacheFactory

setApplicationContext(ApplicationContext) - Method in class ome.services.sessions.state.SessionCache

Context injector.

setApplicationContext(ApplicationContext) - Method in class ome.services.sharing.BlobShareStore

Because there is a cyclical dependency SF->ACLVoter->BlobStore->SF we have to lazy-load the session factory via the context.

setApplicationContext(ApplicationContext) - Method in class ome.services.throttling.AbstractThrottlingStrategy

setApplicationContext(ApplicationContext) - Method in class ome.services.util.Executor.Impl

setApplicationContext(ApplicationContext) - Method in class ome.tools.hibernate.SessionHandler

setApplicationContext(ApplicationContext) - Method in class ome.tools.spring.InternalServiceFactory

simple injector for the ApplicationContext

setApplicationContext(ApplicationContext) - Method in class ome.tools.spring.ManagedServiceFactory

simple injector for the ApplicationContext

setApplicationContext(ApplicationContext) - Method in class ome.tools.spring.OnContextRefreshedEventListener

setApplicationEventPublisher(ApplicationEventPublisher) - Method in class ome.io.nio.PixelsService

setApplicationEventPublisher(ApplicationEventPublisher) - Method in class ome.services.fulltext.BridgeHelper

setApplicationEventPublisher(ApplicationEventPublisher) - Method in class ome.services.fulltext.bridges.TablesBridge

setApplicationEventPublisher(ApplicationEventPublisher) - Method in class ome.services.sessions.stats.CounterFactory

setApplicationEventPublisher(ApplicationEventPublisher) - Method in class ome.services.sessions.stats.LongCounter

setAppVersion(String) - Method in class ome.formats.importer.util.ErrorContainer

setArchive(boolean) - Method in class ome.formats.importer.ImportContainer

setArchive(boolean, boolean) - Method in class ome.formats.OMEROMetadataStoreClient

Populates archive flags on all images currently processed links relevant original metadata files as requested and performs graph logic to have the scaffolding in place for later original file upload.

setArchiveScreeningDomain(boolean) - Method in class ome.formats.OMEROMetadataStoreClient

Populates archive flags on all images currently processed links relevant original metadata files as requested and performs graph logic to have the scafolding in place for later original file upload if we are of the HCS domain.

setArcID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setArcLotNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setArcManufacturer(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setArcModel(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setArcPower(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setArcSerialNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setArcType(ArcType, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setBackgroundColor(Paint) - Method in class ome.services.SVGRasterizer

Sets the Paint to use for the background of the image.

setBatchSize(int) - Method in interface ome.api.Search

Sets the maximum number of results that will be returned by one call to Search.results().

setBatchSize(int) - Method in class ome.services.eventlogs.EventLogLoader

Set the number of EventLog instances will be loaded in a single run.

setBatchSize(int) - Method in class ome.services.SearchBean

setBatchSize_async(AMD_Search_setBatchSize, int, Current) - Method in class ome.services.blitz.impl.SearchI

setBeanFactory(BeanFactory) - Method in class ome.services.messages.GlobalMulticaster

setBeanName(String) - Method in class ome.services.graphs.BaseGraphSpec

setBeanName(String) - Method in class ome.system.Preference

Setter injector

setBfImageCount(Integer) - Method in class ome.formats.importer.ImportContainer

setBfImageNames(List<String>) - Method in class ome.formats.importer.ImportContainer

setBfPixels(List<Pixels>) - Method in class ome.formats.importer.ImportContainer

setBinaryOnlyMetadataFile(String) - Method in class ome.formats.OMEROMetadataStoreClient

setBinaryOnlyUUID(String) - Method in class ome.formats.OMEROMetadataStoreClient

setBit(byte[], int, int) - Method in class pojos.MaskData

Sets the bit value in a byte array at position bit to be the value value.

setBlue(Integer) - Method in class pojos.WellData

Sets the blue component of the color associated to the well.

setBlueValue(int, int) - Method in class omeis.providers.re.RGBAIntBuffer

Sets the Blue value for a particular pixel index.

setBlueValue(int, int) - Method in class omeis.providers.re.RGBBuffer

Sets the Blue value for a particular pixel index.

setBlueValue(int, int) - Method in class omeis.providers.re.RGBIntBuffer

Sets the Blue value for a particular pixel index.

setBooleanAnnotationAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setBooleanAnnotationDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setBooleanAnnotationID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setBooleanAnnotationNamespace(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setBooleanAnnotationValue(Boolean, int) - Method in class ome.formats.OMEROMetadataStoreClient

setBounds(int, int, int, int) - Method in class ome.util.math.geom2D.EllipseArea

Implemented as specified in the PlaneArea I/F.

setBounds(int, int, int, int) - Method in interface ome.util.math.geom2D.PlaneArea

Sets the bounding Rectangle of the planeArea to the specified x, y, width, and height.

setBounds(int, int, int, int) - Method in class ome.util.math.geom2D.RectangleArea

Implemented as specified by the PlaneArea I/F.

setByteOrder(ByteOrder) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

Sets the pixel byte order.

setC(int) - Method in class pojos.ShapeData

Sets the channel.

setCacheEventListeners(CacheEventListener[]) - Method in class ome.services.sessions.state.CacheFactory

setCacheManager(CacheManager) - Method in class ome.services.sessions.state.SessionCache

Injection method, also performs the creation of SessionCache.sessions

setCallback(ClientCallbackPrx, Current) - Method in class ome.services.blitz.impl.ServiceFactoryI

setCallGroup(Long) - Method in class ome.security.basic.CurrentDetails

setCallGroup(long) - Method in class ome.services.util.Executor.Impl

setCallGroup(long) - Method in interface ome.services.util.Executor

Delegates to CurrentDetails.setCallGroup(Long) to permit thread-specific setting of the group.

setCaseSentivice(boolean) - Method in interface ome.api.Search

Sets the case sensitivity on all queries where case-sensitivity is supported.

setCaseSentivice(boolean) - Method in class ome.services.SearchBean

setCaseSentivice_async(AMD_Search_setCaseSentivice, boolean, Current) - Method in class ome.services.blitz.impl.SearchI

setChannelAcquisitionMode(AcquisitionMode, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setChannelAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setChannelColor(Integer, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setChannelContrastMethod(ContrastMethod, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setChannelEmissionWavelength(PositiveInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setChannelExcitationWavelength(PositiveInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

(non-Javadoc)

setChannelFilterSetRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setChannelFluor(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setChannelGlobalMinMax(long, int, double, double) - Method in interface ome.api.IPixels

Sets the channel global (all 2D optical sections corresponding to a particular channel) minimum and maximum for a Pixels set.

setChannelGlobalMinMax(int, double, double, int) - Method in class ome.formats.OMEROMetadataStoreClient

setChannelGlobalMinMax(long, int, double, double) - Method in class ome.logic.PixelsImpl

setChannelGlobalMinMax_async(AMD_IPixels_setChannelGlobalMinMax, long, int, double, double, Current) - Method in class ome.services.blitz.impl.PixelsI

setChannelID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setChannelIlluminationType(IlluminationType, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setChannelLightSourceSettingsAttenuation(PercentFraction, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setChannelLightSourceSettingsID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setChannelLightSourceSettingsWavelength(PositiveInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setChannelName(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setChannelNDFilter(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setChannelOTFRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setChannelPinholeSize(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setChannelPockelCellSetting(Integer, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setChannelSamplesPerPixel(PositiveInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setChannelWindow(Long, int, double, double) - Method in class ome.services.blitz.gateway.services.impl.RenderingServiceImpl

setChannelWindow(Long, int, double, double) - Method in interface ome.services.blitz.gateway.services.RenderingService

Set the channel min, max.

setChannelWindow(int, double, double) - Method in class ome.services.RenderingBean

Implemented as specified by the RenderingEngine interface.

setChannelWindow(int, double, double) - Method in class omeis.providers.re.Renderer

Sets the pixels intensity interval for the specified channel.

setChannelWindow(int, double, double) - Method in interface omeis.providers.re.RenderingEngine

Returns the pixels intensity interval.

setChannelWindow_async(AMD_RenderingEngine_setChannelWindow, int, double, double, Current) - Method in class ome.services.blitz.impl.RenderingEngineI

setChannelWindow_async(AMD_RenderingEngine_setChannelWindow, int, double, double, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI

setClasses(Set<String>) - Method in class ome.services.eventlogs.AllEntitiesPseudoLogLoader

setClient(OMEROMetadataStoreClient) - Method in class ome.formats.importer.util.ClientKeepAlive

setClientEndpoints(String, int) - Method in class ome.services.blitz.Router

setClientObject(boolean) - Method in class pojos.ShapeData

Sets to true if the object one that has been created client side, false otherwise.

setClientSide(boolean) - Method in class pojos.ROIData

Sets the flag indicating if the object is a client-side object or not.

setCo2Percent(double) - Method in class pojos.ImageAcquisitionData

Sets the co2 level.

setCodomain(int, int) - Method in class omeis.providers.re.codomain.CodomainMapContext

Sets the codomain interval.

setCodomainInterval(int, int) - Method in class ome.services.RenderingBean

Implemented as specified by the RenderingEngine interface.

setCodomainInterval(int, int) - Method in class omeis.providers.re.Renderer

Sets the codomain interval i.e. a sub-interval of [0, 255].

setCodomainInterval(int, int) - Method in interface omeis.providers.re.RenderingEngine

Sets the sub-interval of the device space i.e. a discrete sub-interval of [0, 255]

setCodomainInterval_async(AMD_RenderingEngine_setCodomainInterval, int, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI

setCodomainInterval_async(AMD_RenderingEngine_setCodomainInterval, int, int, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI

setComment(String) - Method in class ome.formats.importer.util.ErrorContainer

setCommentAnnotationAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setCommentAnnotationDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setCommentAnnotationID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setCommentAnnotationNamespace(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setCommentAnnotationValue(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setCommentType(String) - Method in class ome.formats.importer.util.ErrorContainer

setComponents(List<ImageData>) - Method in class pojos.MultiImageData

Sets the images composing the file.

setCompressionLevel(float) - Method in interface ome.api.local.LocalCompress

Sets the current compression level for the service.

setCompressionLevel(float) - Method in class ome.logic.CompressImpl

setCompressionLevel(float) - Method in class ome.services.RenderingBean

Implemented as specified by the RenderingEngine interface.

setCompressionLevel(float) - Method in interface omeis.providers.re.RenderingEngine

Sets the current compression level for the service.

setCompressionLevel_async(AMD_RenderingEngine_setCompressionLevel, float, Current) - Method in class ome.services.blitz.impl.RenderingEngineI

setCompressionLevel_async(AMD_RenderingEngine_setCompressionLevel, float, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI

setCompressionService(LocalCompress) - Method in class ome.services.ThumbnailBean

Compression service Bean injector.

setConfigValue(String, String) - Method in interface ome.api.IConfig

set a configuration value in the backend store.

setConfigValue(String, String) - Method in class ome.logic.ConfigImpl

see IConfig.setConfigValue(String, String)

setConfigValue_async(AMD_IConfig_setConfigValue, String, String, Current) - Method in class ome.services.blitz.impl.ConfigI

setConfigValueIfEquals(String, String, String) - Method in interface ome.api.IConfig

Calls IConfig.setConfigValue(String, String) if and only if the configuration property is currently equal to the test argument.

setConfigValueIfEquals(String, String, String) - Method in class ome.logic.ConfigImpl

see IConfig.setConfigValueIfEquals(String, String, String)

setConfigValueIfEquals_async(AMD_IConfig_setConfigValueIfEquals, String, String, String, Current) - Method in class ome.services.blitz.impl.ConfigI

setConstant(boolean) - Method in class omeis.providers.re.codomain.PlaneSlicingContext

Sets the type of mapping.

setContent(Object) - Method in class pojos.AnnotationData

Sets the annotation value.

setContent(Object) - Method in class pojos.BooleanAnnotationData

Sets the text annotation.

setContent(Object) - Method in class pojos.DoubleAnnotationData

Sets the text annotation.

setContent(Object) - Method in class pojos.FileAnnotationData

Sets the text annotation.

setContent(Object) - Method in class pojos.LongAnnotationData

Sets the text annotation.

setContent(Object) - Method in class pojos.RatingAnnotationData

Sets the text annotation.

setContent(Object) - Method in class pojos.TagAnnotationData

Sets the text annotation.

setContent(Object) - Method in class pojos.TermAnnotationData

Sets the text annotation.

setContent(Object) - Method in class pojos.TextualAnnotationData

Sets the text annotation.

setContent(Object) - Method in class pojos.TimeAnnotationData

Sets the time annotation.

setContent(Object) - Method in class pojos.XMLAnnotationData

Sets the annotation.

setContext(Map<String, String>) - Method in class ome.security.basic.CurrentDetails

setContext(CodomainMapContext) - Method in interface omeis.providers.re.codomain.CodomainMap

Sets the parameters used to write the equation of the specified codomain transformation.

setContrastMethod(ContrastMethod) - Method in class pojos.ChannelData

Sets the contrast method value.

setCoordinates(int, int, int, int) - Method in class omeis.providers.re.codomain.ContrastStretchingContext

Sets the coordinates of the points used to determine the equations of the lines.

setCorrectionCollar(double) - Method in class pojos.ImageAcquisitionData

Sets the correction of the objective.

setCounterFactory(CounterFactory) - Method in class ome.services.sessions.SessionManagerImpl

setCreationEvent(Event, Current) - Method in class omero.model.DetailsI

setCredentials(String) - Method in class ome.system.SessionInitializer

setCriteria(Criteria) - Method in class ome.services.query.Query

provide this Query instance with a Criteria to be used for retrieving data.

setCurrentDetails(CurrentDetails) - Method in class ome.logic.ConfigImpl

PreferenceContext setter for dependency injection.

setCurrentDetails(CurrentDetails) - Method in class ome.services.graphs.BaseGraphSpec

setCurrentDetails(CurrentDetails) - Method in class ome.tools.hibernate.ProxyCleanupFilter.Interceptor

setCurrentGroup(long) - Method in class ome.formats.OMEROMetadataStoreClient

Changes the default group of the currently logged in user.

setCurrentId(long) - Method in class ome.services.eventlogs.PersistentEventLogLoader

setCustomAnnotationList(List<Annotation>) - Method in class ome.formats.importer.ImportContainer

Sets the list of custom, user specified, annotations to link to all images represented by this container.

setCustomImageDescription(String) - Method in class ome.formats.importer.ImportContainer

Sets the custom image description for import.

setCustomImageName(String) - Method in class ome.formats.importer.ImportContainer

Sets the custom image name for import.

setCustomImageNaming(boolean) - Method in class ome.formats.importer.ImportConfig

setCustomImageNaming(boolean) - Method in class ome.formats.importer.util.IniFileLoader

setCustomPlateDescription(String) - Method in class ome.formats.importer.ImportContainer

Sets the custom plate description for import.

setCustomPlateName(String) - Method in class ome.formats.importer.ImportContainer

Sets the custom plate name for import.

setDatabaseIdentity(DatabaseIdentity) - Method in class ome.logic.ConfigImpl

setDatadir(String) - Method in class ome.logic.RepositoryInfoImpl

Bean injection setter for data repository directory

setDataObjects(Set<DataObject>) - Method in class pojos.TagAnnotationData

Sets the collection of data objects related to that tag.

setDatasetAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setDatasetDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setDatasetExperimenterRef(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setDatasetGroupRef(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setDatasetID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setDatasetName(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setDatasetProjectRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setDatasets(Set) - Method in class pojos.ImageData

Sets the datasets containing the image.

setDatasets(Set<DatasetData>) - Method in class pojos.ProjectData

Sets the datasets contained in this project.

setDataValue(double) - Method in class pojos.DoubleAnnotationData

Sets the rating value.

setDataValue(long) - Method in class pojos.LongAnnotationData

Sets the rating value.

setDb(boolean) - Method in class ome.system.Preference

Setter injector

setDebug(boolean) - Method in class ome.tools.hibernate.EventMethodInterceptor

setDebugAll(boolean) - Method in class ome.security.basic.EventListenersFactoryBean

for setter injection

setDebugLevel(int) - Method in class ome.formats.importer.ImportConfig

setDebugLevel(int) - Method in class ome.formats.importer.util.IniFileLoader

Set debug level for application

setDefaultGroup(Experimenter, ExperimenterGroup) - Method in interface ome.api.IAdmin

sets the default group for a given user.

setDefaultGroup(Experimenter, ExperimenterGroup) - Method in class ome.logic.AdminImpl

setDefaultGroup(Experimenter, ExperimenterGroup) - Method in interface ome.security.auth.RoleProvider

setDefaultGroup(Experimenter, ExperimenterGroup) - Method in class ome.security.auth.SimpleRoleProvider

setDefaultGroup_async(AMD_IAdmin_setDefaultGroup, Experimenter, ExperimenterGroup, Current) - Method in class ome.services.blitz.impl.AdminI

setDefaultPixels(PixelsData) - Method in class pojos.ImageData

Sets the default set of pixels.

setDefaultSample(int) - Method in class pojos.PlateData

Sets the default sample.

setDefaultT(Long, int) - Method in class ome.services.blitz.gateway.services.impl.RenderingServiceImpl

setDefaultT(Long, int) - Method in interface ome.services.blitz.gateway.services.RenderingService

Set the default timepoint of the image.

setDefaultT(int) - Method in class ome.services.RenderingBean

Implemented as specified by the RenderingEngine interface.

setDefaultT(int) - Method in class omeis.providers.re.Renderer

Sets the default timepoint index.

setDefaultT(int) - Method in interface omeis.providers.re.RenderingEngine

Sets the default timepoint index.

setDefaultT_async(AMD_RenderingEngine_setDefaultT, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI

setDefaultT_async(AMD_RenderingEngine_setDefaultT, int, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI

setDefaultTimeToIdle(long) - Method in class ome.services.sessions.SessionManagerImpl

setDefaultTimeToLive(long) - Method in class ome.services.sessions.SessionManagerImpl

setDefaultZ(Long, int) - Method in class ome.services.blitz.gateway.services.impl.RenderingServiceImpl

setDefaultZ(Long, int) - Method in interface ome.services.blitz.gateway.services.RenderingService

Set the default Z section of the image.

setDefaultZ(int) - Method in class ome.services.RenderingBean

Implemented as specified by the RenderingEngine interface.

setDefaultZ(int) - Method in class omeis.providers.re.Renderer

Sets the index of the default focal section.

setDefaultZ(int) - Method in interface omeis.providers.re.RenderingEngine

Sets the index of the default focal section.

setDefaultZ_async(AMD_RenderingEngine_setDefaultZ, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI

setDefaultZ_async(AMD_RenderingEngine_setDefaultZ, int, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI

setDescription(long, String) - Method in interface ome.api.IShare

setDescription(long, String) - Method in class ome.services.sharing.ShareBean

setDescription(String) - Method in class pojos.DatasetData

Sets the description of the dataset.

setDescription(String) - Method in class pojos.FileAnnotationData

Sets the description of the annotation.

setDescription(String) - Method in class pojos.FileData

Sets the description.

setDescription(String) - Method in class pojos.GroupData

Sets the name of the group.

setDescription(String) - Method in class pojos.ImageData

Sets the description of the image.

setDescription(String) - Method in class pojos.PlateAcquisitionData

Sets the name of the acquisition.

setDescription(String) - Method in class pojos.PlateData

Sets the description of the plate.

setDescription(String) - Method in class pojos.ProjectData

Sets the description of the project.

setDescription(String) - Method in class pojos.ScreenData

Sets the description of the screen.

setDescription(String) - Method in class pojos.XMLAnnotationData

Sets the description of the annotation.

setDescription_async(AMD_IShare_setDescription, long, String, Current) - Method in class ome.services.blitz.impl.ShareI

setDetach(boolean, Current) - Method in class omero.grid.InteractiveProcessorI

setDetectorAmplificationGain(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setDetectorGain(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setDetectorID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setDetectorLotNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setDetectorManufacturer(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setDetectorModel(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setDetectorOffset(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setDetectorSerialNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setDetectorSettingBinning(Binning) - Method in class pojos.ChannelAcquisitionData

Sets the detector's binning.

setDetectorSettingOffset(double) - Method in class pojos.ChannelAcquisitionData

Sets the detector's setting offset.

setDetectorSettingsBinning(Binning, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setDetectorSettingsGain(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setDetectorSettingsGain(double) - Method in class pojos.ChannelAcquisitionData

Sets the detector setting's gain.

setDetectorSettingsID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setDetectorSettingsOffset(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setDetectorSettingsReadOutRate(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setDetectorSettingsReadOutRate(double) - Method in class pojos.ChannelAcquisitionData

Sets the detector setting's read out rate.

setDetectorSettingsVoltage(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setDetectorSettingsVoltage(double) - Method in class pojos.ChannelAcquisitionData

Sets the detector setting's voltage.

setDetectorType(DetectorType, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setDetectorVoltage(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setDetectorZoom(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setDichroicID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setDichroicLotNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setDichroicManufacturer(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setDichroicModel(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setDichroicSerialNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setDirty(boolean) - Method in class pojos.DataObject

Sets to true if the value has been modified, otherwise.

setDirty(boolean) - Method in class pojos.ShapeData

Sets to true if the figure been changed from the server side version, false otherwise.

setDiskSpaceChecking(boolean) - Method in class ome.services.RawFileBean

setter disk overflow checking

setDiskSpaceChecking(boolean) - Method in class ome.services.RawPixelsBean

setDiskSpaceChecking(boolean) - Method in class ome.services.ThumbnailBean

setDN(Long, String) - Method in interface ome.api.ILdap

Searchs all Experimenter in LDAP for objectClass = person

setDN(Long, String) - Method in class ome.logic.LdapImpl

setDN_async(AMD_ILdap_setDN, RLong, String, Current) - Method in class ome.services.blitz.impl.LdapI

setDoThumbnails(boolean) - Method in class ome.formats.importer.ImportContainer

Sets whether or not we are performing thumbnail creation upon import completion.

setDoubleAnnotationAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setDoubleAnnotationDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setDoubleAnnotationID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setDoubleAnnotationNamespace(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setDoubleAnnotationValue(Double, int) - Method in class ome.formats.OMEROMetadataStoreClient

setEllipseDescription(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setEllipseFill(Integer, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setEllipseFontSize(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setEllipseID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setEllipseLabel(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setEllipseName(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setEllipseRadiusX(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setEllipseRadiusY(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setEllipseStroke(Integer, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setEllipseStrokeDashArray(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setEllipseStrokeWidth(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setEllipseTheC(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setEllipseTheT(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setEllipseTheZ(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setEllipseTransform(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setEllipseX(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setEllipseY(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setEmail(String) - Method in class ome.formats.importer.util.ErrorContainer

setEmail(String) - Method in class pojos.ExperimenterData

Sets the e-mail of the experimenter.

setEmissionWavelength(int) - Method in class pojos.ChannelData

Sets the emission wavelength.

setEncryptedConnection(boolean) - Method in class ome.formats.OMEROMetadataStoreClient

setEnumerationProvider(EnumerationProvider) - Method in class ome.formats.OMEROMetadataStoreClient

Sets the active enumeration provider.

setError(Throwable) - Method in class ome.formats.importer.util.ErrorContainer

setExcitationWavelength(int) - Method in class pojos.ChannelData

Sets the excitation wavelength.

setExcludes(String[]) - Method in class ome.services.eventlogs.EventLogLoader

Spring injector

setExecutor(Executor) - Method in class ome.logic.UpdateImpl

setExecutor(Executor) - Method in class ome.services.SearchBean

Injector used by Spring, currently, since SelfConfigurableService.selfConfigure() requires it.

setExecutor(Executor) - Method in class ome.services.sessions.SessionManagerImpl

setExperimentDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setExperimenterAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setExperimenterDisplayName(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setExperimenterEmail(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setExperimenterFirstName(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setExperimenterGroupRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setExperimenterID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setExperimenterInstitution(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setExperimenterLastName(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setExperimenterMiddleName(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setExperimenters(Set<ExperimenterData>) - Method in class pojos.GroupData

Sets the experimenters contained in this group.

setExperimenterUserName(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setExperimentExperimenterRef(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setExperimentID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setExperimentType(ExperimentType, int) - Method in class ome.formats.OMEROMetadataStoreClient

setExpiration(long, Timestamp) - Method in interface ome.api.IShare

setExpiration(long, Timestamp) - Method in class ome.services.sharing.ShareBean

setExpiration_async(AMD_IShare_setExpiration, long, RTime, Current) - Method in class ome.services.blitz.impl.ShareI

setExtendedMetadata(ExtendedMetadata) - Method in class ome.logic.AbstractLevel2Service

setExtendedMetadata(ExtendedMetadata) - Method in class ome.services.graphs.AnnotationGraphSpec

Performs sanity checks on the annotation entries found in ExtendedMetadata.

setExtendedMetadata(ExtendedMetadata) - Method in class ome.services.graphs.BaseGraphSpec

setExtent(double, double) - Method in class omeis.providers.re.quantum.QuantumStrategy

Sets the maximum range of the input window.

setExternalDescription(String) - Method in class pojos.WellData

Sets the external description of the well.

setExternalIdentifier(String) - Method in class pojos.PlateData

Sets the external identifier.

setExternalInfo(ExternalInfo, Current) - Method in class omero.model.DetailsI

setExtra(String) - Method in class ome.formats.importer.util.ErrorContainer

setFilamentID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setFilamentLotNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setFilamentManufacturer(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setFilamentModel(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setFilamentPower(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setFilamentSerialNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setFilamentType(FilamentType, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setFile(File) - Method in class ome.formats.OMEROImportFixture

setFileAnnotationAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setFileAnnotationBinaryFileFileName(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setFileAnnotationBinaryFileMIMEType(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setFileAnnotationBinaryFileSize(NonNegativeLong, int) - Method in class ome.formats.OMEROMetadataStoreClient

setFileAnnotationDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setFileAnnotationID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setFileAnnotationNamespace(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setFileId(long) - Method in interface ome.api.RawFileStore

This method manages the state of the service.

setFileId(long) - Method in class ome.services.RawFileBean

setFileId_async(AMD_RawFileStore_setFileId, long, Current) - Method in class ome.services.blitz.impl.RawFileStoreI

setFileId_async(AMD_RawFileStore_setFileId, long, Current) - Method in class ome.services.blitz.repo.RepoRawFileStoreI

setFilePathResolver(FilePathResolver) - Method in class ome.io.nio.PixelsService

setFiles(String[]) - Method in class ome.formats.importer.util.ErrorContainer

setFileService(OriginalFilesService) - Method in class ome.logic.RepositoryInfoImpl

Bean injection setter for ROMIO file service

setFileType(String) - Method in class ome.formats.importer.util.ErrorContainer

setFill(Color) - Method in class pojos.ShapeSettingsData

Set the fill colour.

setFillRule(String) - Method in class pojos.ShapeSettingsData

Set the fill rule.

setFilterFilterWheel(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setFilterID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setFilterLotNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setFilterManufacturer(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setFilterModel(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setFilterSerialNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setFilterSetDichroicRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setFilterSetEmissionFilterRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setFilterSetExcitationFilterRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setFilterSetID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setFilterSetLotNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setFilterSetManufacturer(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setFilterSetModel(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setFilterSetSerialNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setFilterType(FilterType, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setFirstName(String) - Method in class pojos.ExperimenterData

Sets the first name of the experimenter.

setFluor(String) - Method in class pojos.ChannelData

Sets the fluor.

setFontFamily(String) - Method in class pojos.ShapeSettingsData

Returns the stroke.

setFontSize(int) - Method in class pojos.ShapeSettingsData

Set the size of the font.

setFontStyle(String) - Method in class pojos.ShapeSettingsData

Sets the style of the font.

setFullTextBridge(FullTextBridge) - Method in class ome.logic.UpdateImpl

setGreen(Integer) - Method in class pojos.WellData

Sets the green component of the color associated to the well.

setGreenValue(int, int) - Method in class omeis.providers.re.RGBAIntBuffer

Sets the Green value for a particular pixel index.

setGreenValue(int, int) - Method in class omeis.providers.re.RGBBuffer

Sets the Green value for a particular pixel index.

setGreenValue(int, int) - Method in class omeis.providers.re.RGBIntBuffer

Sets the Green value for a particular pixel index.

setGroup(ExperimenterGroup, Current) - Method in class omero.model.DetailsI

setGroupContact(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setGroupDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setGroupID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setGroupLeader(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setGroupName(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setGroupOwner(ExperimenterGroup, Experimenter) - Method in interface ome.api.IAdmin

adds the user to the owner list for this group.

setGroupOwner(ExperimenterGroup, Experimenter) - Method in class ome.logic.AdminImpl

setGroupOwner_async(AMD_IAdmin_setGroupOwner, ExperimenterGroup, Experimenter, Current) - Method in class ome.services.blitz.impl.AdminI

setGroupRead(boolean, Current) - Method in class omero.model.PermissionsI

setGroupRead(boolean) - Method in class pojos.PermissionData

Sets to true if the group has read access, false otherwise.

setGroups(List<GroupData>) - Method in class pojos.ExperimenterData

Sets the groups the experimenter is a member of.

setGroupWrite(boolean, Current) - Method in class omero.model.PermissionsI

setGroupWrite(boolean) - Method in class pojos.PermissionData

Sets to true if the group has write access, false otherwise.

setHeight(int) - Method in class omeis.providers.re.data.RegionDef

Sets the height of the region.

setHeight(double) - Method in class pojos.MaskData

Sets the height of an untransformed mask.

setHeight(double) - Method in class pojos.RectangleData

Sets the height of an untransformed rectangle.

setHumidity(double) - Method in class pojos.ImageAcquisitionData

Sets the humidity.

setIContainer(IContainer) - Method in class ome.logic.MetadataImpl

IContainer bean injector.

setId(String) - Method in class ome.io.bioformats.OmeroPixelsPyramidReader

setId(String) - Method in class ome.io.bioformats.OmeroPixelsPyramidWriter

setId(long) - Method in class pojos.DataObject

Sets the database id.

setIdOnly() - Method in class ome.services.SearchBean

setIllumination(Illumination) - Method in class pojos.ChannelData

Sets the illumination value.

setImage(ImageData) - Method in class pojos.PixelsData

Sets the image linked to this pixels' set.

setImage(Image) - Method in class pojos.ROIData

Sets the imageId for the ROI.

setImage(ImageData) - Method in class pojos.WellSampleData

Sets the image linked to this well sample.

setImageAcquiredDate(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setImageAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setImageDatasetRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setImageDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setImageExperimenterRef(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setImageExperimentRef(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setImageGroupRef(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setImageHeight(float) - Method in class ome.services.SVGRasterizer

Sets the height of the image to rasterize.

setImageID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setImageInstrumentRef(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setImageMicrobeamManipulationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setImageName(String, int) - Method in class ome.formats.ImageNameMetadataStore

setImageName(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setImageObjectiveSettingsCorrectionCollar(Double, int) - Method in class ome.formats.OMEROMetadataStoreClient

setImageObjectiveSettingsID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setImageObjectiveSettingsMedium(Medium, int) - Method in class ome.formats.OMEROMetadataStoreClient

setImageObjectiveSettingsRefractiveIndex(Double, int) - Method in class ome.formats.OMEROMetadataStoreClient

setImageROIRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setImageROIRef(String, int, int) - Method in class ome.formats.OverlayMetadataStore

setImages(Set<ImageData>) - Method in class pojos.DatasetData

Sets the images contained in this dataset.

setImageWidth(float) - Method in class ome.services.SVGRasterizer

Sets the width of the image to rasterize.

setImagingEnvironmentAirPressure(Double, int) - Method in class ome.formats.OMEROMetadataStoreClient

setImagingEnvironmentCO2Percent(PercentFraction, int) - Method in class ome.formats.OMEROMetadataStoreClient

setImagingEnvironmentHumidity(PercentFraction, int) - Method in class ome.formats.OMEROMetadataStoreClient

setImagingEnvironmentTemperature(Double, int) - Method in class ome.formats.OMEROMetadataStoreClient

setIndex(int) - Method in class ome.formats.importer.util.ErrorContainer

Set index

setInProgressImageResource(Resource) - Method in class ome.services.ThumbnailBean

In-progress image resource Bean injector.

setInput(String, String, Object) - Method in interface ome.api.ISession

Places an entry in the given session's input environment.

setInput(String, String, Object) - Method in class ome.services.sessions.SessionBean

setInput(String, String, Object) - Method in interface ome.services.sessions.SessionManager

Places the argument in the input environment under the given key, possibly initializing the Map Throws an exception if there is no Session with the given identifier.

setInput(String, String, Object) - Method in class ome.services.sessions.SessionManagerImpl

setInput(String, RType) - Method in class omero.client

Sets an item in the "input" shared (session) memory under the given name.

setInput_async(AMD_ISession_setInput, String, String, RType, Current) - Method in class ome.services.blitz.impl.SessionI

setInstanceProvider(InstanceProvider) - Method in class ome.formats.OMEROMetadataStoreClient

Sets the active instance provider.

setInstitution(String) - Method in class pojos.ExperimenterData

Sets the institution where the experimenter works.

setInstrumentID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setInterval(int, int) - Method in class omeis.providers.re.codomain.CodomainChain

Sets the codomain interval.

setIoService(ThumbnailService) - Method in class ome.services.ThumbnailBean

I/O service (ThumbnailService) Bean injector.

setIPixels(IPixels) - Method in class ome.services.projection.ProjectionBean

IPixels bean injector.

setIPixels(IPixels) - Method in class ome.services.ThumbnailBean

Pixels service Bean injector.

setIRepositoryInfo(IRepositoryInfo) - Method in class ome.services.RawFileBean

Disk Space Usage service Bean injector

setIRepositoryInfo(IRepositoryInfo) - Method in class ome.services.RawPixelsBean

Disk Space Usage service Bean injector

setIRepositoryInfo(IRepositoryInfo) - Method in class ome.services.ThumbnailBean

Disk Space Usage service Bean injector

setIsSPW(Boolean) - Method in class ome.formats.importer.ImportContainer

setJavaClasspath(String) - Method in class ome.formats.importer.util.ErrorContainer

setJavaVersion(String) - Method in class ome.formats.importer.util.ErrorContainer

setKey(String) - Method in class ome.services.eventlogs.PersistentEventLogLoader

setKeyStore(String) - Method in class ome.security.KeyAndTrustStoreConfiguration

setKeyStorePassword(String) - Method in class ome.security.KeyAndTrustStoreConfiguration

setKeywords(String) - Method in class pojos.WorkflowData

Sets the keywords of the workflow.

setKeywords(List<String>) - Method in class pojos.WorkflowData

Sets the keywords of the workflow.

setLabelName(String) - Method in class pojos.ImageAcquisitionData

Sets the name of the stage label.

setLanguages(String) - Method in class ome.services.SVGRasterizer

Sets the preferred language to use.

setLaserFrequencyMultiplication(PositiveInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setLaserID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setLaserLaserMedium(LaserMedium, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setLaserLotNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setLaserManufacturer(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setLaserModel(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setLaserPockelCell(Boolean, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setLaserPower(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setLaserPulse(Pulse, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setLaserPump(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setLaserRepetitionRate(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setLaserSerialNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setLaserTuneable(Boolean, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setLaserType(LaserType, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setLaserWavelength(PositiveInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setLastName(String) - Method in class pojos.ExperimenterData

Sets the last name of the experimenter.

setLightEmittingDiodeID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setLightEmittingDiodeLotNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setLightEmittingDiodeManufacturer(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setLightEmittingDiodeModel(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setLightEmittingDiodePower(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setLightEmittingDiodeSerialNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setLightPathDichroicRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setLightPathEmissionFilterRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setLightPathExcitationFilterRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setLightSource(LightSourceData) - Method in class pojos.ChannelAcquisitionData

Sets the light source associated to the settings.

setLigthSettingsAttenuation(double) - Method in class pojos.ChannelAcquisitionData

Sets the attenuation of the light settings.

setLigthSettingsWavelength(int) - Method in class pojos.ChannelAcquisitionData

Returns the wavelength of the light source.

setLimits(int, int) - Method in class omeis.providers.re.codomain.PlaneSlicingContext

Set the limits.

setLineCap(int) - Method in class pojos.ShapeSettingsData

Sets the line cap.

setLineDescription(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setLineFill(Integer, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setLineFontSize(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setLineID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setLineLabel(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setLineName(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setLineStroke(Integer, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setLineStrokeDashArray(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setLineStrokeWidth(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setLineTheC(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setLineTheT(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setLineTheZ(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setLineTransform(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setLineX1(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setLineX2(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setLineY1(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setLineY2(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setListAnnotationAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setListAnnotationDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setListAnnotationID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setListAnnotationNamespace(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setLongAnnotationAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setLongAnnotationDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setLongAnnotationID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setLongAnnotationNamespace(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setLongAnnotationValue(Long, int) - Method in class ome.formats.OMEROMetadataStoreClient

setLowerLimit(int) - Method in class omeis.providers.re.codomain.PlaneSlicingContext

Sets the value (in [intervalStart, intervalEnd]) used to set the level of the bit-plane < bit-plane selected.

setMap(QuantumMap) - Method in class omeis.providers.re.quantum.QuantumStrategy

Sets the quantum map.

setMapping(Family, double, boolean) - Method in class omeis.providers.re.quantum.QuantumStrategy

Sets the selected family, the curve coefficient and the noise reduction flag.

setMarkerEnd(String) - Method in class pojos.ShapeSettingsData

Returns the marker end.

setMarkerStart(String) - Method in class pojos.ShapeSettingsData

Returns the marker start.

setMask(byte[]) - Method in class pojos.MaskData

Sets the mask image.

setMask(BufferedImage) - Method in class pojos.MaskData

Sets the mask from the bufferedImage.

setMaskBinData(byte[], int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setMaskBinData(byte[], int, int) - Method in class ome.formats.OverlayMetadataStore

setMaskDescription(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setMaskFill(Integer, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setMaskFontSize(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setMaskHeight(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setMaskHeight(Double, int, int) - Method in class ome.formats.OverlayMetadataStore

setMaskID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setMaskLabel(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setMaskName(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setMaskStroke(Integer, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setMaskStroke(Integer, int, int) - Method in class ome.formats.OverlayMetadataStore

setMaskStrokeDashArray(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setMaskStrokeWidth(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setMaskTheC(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setMaskTheT(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setMaskTheZ(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setMaskTransform(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setMaskWidth(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setMaskWidth(Double, int, int) - Method in class ome.formats.OverlayMetadataStore

setMaskX(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setMaskX(Double, int, int) - Method in class ome.formats.OverlayMetadataStore

setMaskY(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setMaskY(Double, int, int) - Method in class ome.formats.OverlayMetadataStore

setMaxClauseCount(Integer) - Method in class ome.services.SearchBean

Injector used by Spring.

setMedia(String) - Method in class ome.services.SVGRasterizer

Sets the media to rasterize.

setMedium(Medium) - Method in class pojos.ImageAcquisitionData

Sets the medium of the objective.

setMergedBatches(boolean) - Method in interface ome.api.Search

Set whether or not results from two separate queries can be returned in the same call to Search.results().

setMergedBatches(boolean) - Method in class ome.services.SearchBean

setMergedBatches_async(AMD_Search_setMergedBatches, boolean, Current) - Method in class ome.services.blitz.impl.SearchI

setMessage(String) - Method in interface ome.api.JobHandle

Sets the job's message string, and returns the previous value.

setMessage(String, Current) - Method in class ome.services.blitz.impl.ScriptProcessI

setMessage(String) - Method in class ome.services.JobBean

setMessage_async(AMD_JobHandle_setMessage, String, Current) - Method in class ome.services.blitz.impl.JobHandleI

setMetadataOnly(boolean) - Method in class ome.formats.importer.ImportContainer

Sets the metadata only flag.

setMetadataOnly(boolean) - Method in class ome.formats.importer.ImportLibrary

Sets the metadata only flag.

setMetadataOptions(MetadataOptions) - Method in class ome.formats.importer.OMEROWrapper

setMethodHardLimit(int) - Method in class ome.services.sessions.stats.CounterFactory

setMethodSecurity(MethodSecurity) - Method in class ome.security.basic.BasicSecurityWiring

Setter injection.

setMicrobeamManipulationDescription(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setMicrobeamManipulationExperimenterRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setMicrobeamManipulationID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setMicrobeamManipulationLightSourceSettingsAttenuation(PercentFraction, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setMicrobeamManipulationLightSourceSettingsID(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setMicrobeamManipulationLightSourceSettingsWavelength(PositiveInteger, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setMicrobeamManipulationROIRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setMicrobeamManipulationType(MicrobeamManipulationType, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setMicroscopeLotNumber(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setMicroscopeManufacturer(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setMicroscopeModel(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setMicroscopeSerialNumber(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setMicroscopeType(MicroscopeType, int) - Method in class ome.formats.OMEROMetadataStoreClient

setMiddleName(String) - Method in class pojos.ExperimenterData

Sets the middle name of the experimenter.

setMode(AcquisitionMode) - Method in class pojos.ChannelData

Sets the acquisition mode value.

setModel(RenderingModel) - Method in class ome.services.RenderingBean

Implemented as specified by the RenderingEngine interface.

setModel(RenderingModel) - Method in class omeis.providers.re.Renderer

Specifies the model that dictates how transformed raw data has to be mapped onto a color space.

setModel(RenderingModel) - Method in interface omeis.providers.re.RenderingEngine

Specifies the model that dictates how transformed raw data has to be mapped onto a color space.

setModel_async(AMD_RenderingEngine_setModel, RenderingModel, Current) - Method in class ome.services.blitz.impl.RenderingEngineI

setModel_async(AMD_RenderingEngine_setModel, RenderingModel, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI

setModelProcessors(List<ModelProcessor>) - Method in class ome.formats.OMEROMetadataStoreClient

Sets the current set of model processors.

setMutable(boolean) - Method in class ome.system.Preference

Setter injector

setName(String) - Method in class ome.formats.OMEROImportFixture

setName(String) - Method in class pojos.ChannelData

Sets the name of the logical channel.

setName(String) - Method in class pojos.DatasetData

Sets the name of the dataset.

setName(String) - Method in class pojos.GroupData

Sets the name of the group.

setName(String) - Method in class pojos.ImageData

Sets the name of the image.

setName(String) - Method in class pojos.PlateAcquisitionData

Sets the name of the acquisition.

setName(String) - Method in class pojos.PlateData

Sets the name of the plate.

setName(String) - Method in class pojos.ProjectData

Sets the name of the project.

setName(String) - Method in class pojos.ScreenData

Sets the name of the screen.

setNameSpace(String) - Method in class pojos.AnnotationData

Sets the name space of the underlying Annotation instance.

setNameSpace(String) - Method in class pojos.TermAnnotationData

Returns the namespace of the term.

setNamespace(String) - Method in class pojos.WorkflowData

Sets the namespace of the workflow.

setNamespaceKeywords(String, String[]) - Method in class pojos.ROIData

Sets the namespace and keywords.

setNamespaceMap(Map<String, List<String>>) - Method in class pojos.ROIData

Sets the namespaces and keywords of the ROI from the map.

setNDFilter(double) - Method in class pojos.ChannelData

Sets the ND filter.

setNumOfDirectories(int) - Method in class ome.formats.importer.ImportConfig

setNumOfDirectories(int) - Method in class ome.formats.importer.util.IniFileLoader

setObjectiveCalibratedMagnification(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setObjectiveCorrection(Correction, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setObjectiveID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setObjectiveImmersion(Immersion, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setObjectiveIris(Boolean, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setObjectiveLensNA(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setObjectiveLotNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setObjectiveManufacturer(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setObjectiveModel(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setObjectiveNominalMagnification(PositiveInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setObjectiveSerialNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setObjectiveWorkingDistance(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setObjectsReadHardLimit(int) - Method in class ome.services.sessions.stats.CounterFactory

setObjectsWrittenHardLimit(int) - Method in class ome.services.sessions.stats.CounterFactory

setOrder(ByteOrder) - Method in class ome.io.nio.ReorderedPixelData

Set the byte order of the backing buffer.

setOriginalFilesService(OriginalFilesService) - Method in class ome.services.RawFileBean

I/O service (OriginalFilesService) Bean injector.

setOriginalSettingsForPixels(long) - Method in interface ome.api.IRenderingSettings

Resets an Pixels' default rendering settings back to channel global minimum and maximum.

setOriginalSettingsForPixels(long) - Method in class ome.logic.RenderingSettingsImpl

Implemented as specified by the IRenderingSettings I/F.

setOriginalSettingsForPixels_async(AMD_IRenderingSettings_setOriginalSettingsForPixels, long, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI

setOriginalSettingsInDataset(long) - Method in interface ome.api.IRenderingSettings

Resets a dataset's rendering settings back to channel global minimum and maximum.

setOriginalSettingsInDataset(long) - Method in class ome.logic.RenderingSettingsImpl

Implemented as specified by the IRenderingSettings I/F.

setOriginalSettingsInDataset_async(AMD_IRenderingSettings_setOriginalSettingsInDataset, long, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI

setOriginalSettingsInImage(long) - Method in interface ome.api.IRenderingSettings

Resets an image's default rendering settings back to channel global minimum and maximum.

setOriginalSettingsInImage(long) - Method in class ome.logic.RenderingSettingsImpl

Implemented as specified by the IRenderingSettings I/F.

setOriginalSettingsInImage_async(AMD_IRenderingSettings_setOriginalSettingsInImage, long, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI

setOriginalSettingsInSet(Class<T>, Set<Long>) - Method in interface ome.api.IRenderingSettings

Resets a rendering settings back to channel global minimum and maximum for the specified containers.

setOriginalSettingsInSet(Class<T>, Set<Long>) - Method in class ome.logic.RenderingSettingsImpl

Implemented as specified by the IRenderingSettings I/F.

setOriginalSettingsInSet_async(AMD_IRenderingSettings_setOriginalSettingsInSet, String, List<Long>, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI

setOSArch(String) - Method in class ome.formats.importer.util.ErrorContainer

setOSName(String) - Method in class ome.formats.importer.util.ErrorContainer

setOSVersion(String) - Method in class ome.formats.importer.util.ErrorContainer

setOTFBinaryFileFileName(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setOTFBinaryFileMIMEType(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setOTFBinaryFileSize(NonNegativeLong, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setOTFFilterSetRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setOTFID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setOTFObjectiveSettingsCorrectionCollar(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setOTFObjectiveSettingsID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setOTFObjectiveSettingsMedium(Medium, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setOTFObjectiveSettingsRefractiveIndex(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setOTFOpticalAxisAveraged(Boolean, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setOTFSizeX(PositiveInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setOTFSizeY(PositiveInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setOTFType(PixelType, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setOutput(String, String, Object) - Method in interface ome.api.ISession

Places an entry in the given session's output environment.

setOutput(String, String, Object) - Method in class ome.services.sessions.SessionBean

setOutput(String, String, Object) - Method in interface ome.services.sessions.SessionManager

Places the argument in the output environment under the given key, possibly initializing the Map Throws an exception if there is no Session with the given identifier.

setOutput(String, String, Object) - Method in class ome.services.sessions.SessionManagerImpl

setOutput(String, RType) - Method in class omero.client

Sets an item in the "output" shared (session) memory under the given name.

setOutput_async(AMD_ISession_setOutput, String, String, RType, Current) - Method in class ome.services.blitz.impl.SessionI

setOverlays(Map<byte[], Integer>) - Method in class ome.services.RenderingBean

Implemented as specified by the RenderingEngine interface.

setOverlays(Map<byte[], Integer>) - Method in class omeis.providers.re.Renderer

Sets a map of overlays to be rendered.

setOverlays(Map<byte[], Integer>) - Method in interface omeis.providers.re.RenderingEngine

Informs the rendering engine that it should render a set of overlays on each rendered frame.

setOverlays_async(AMD_RenderingEngine_setOverlays, RLong, RLong, Map<Long, Integer>, Current) - Method in class ome.services.blitz.impl.RenderingEngineI

setOverlays_async(AMD_RenderingEngine_setOverlays, RLong, RLong, Map<Long, Integer>, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI

setOwner(Experimenter, Current) - Method in class omero.model.DetailsI

setParameterValues(Properties) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType

setParentFilePath(String, int) - Method in class pojos.ImageData

Sets the path to the file hosting the image.

setPathDefinition(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPathDescription(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPathFill(Integer, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPathFontSize(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPathID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPathLabel(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPathName(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPathStroke(Integer, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPathStrokeDashArray(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPathStrokeWidth(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPathTheC(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPathTheT(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPathTheZ(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPathToFile(String) - Method in class pojos.ImageData

Sets the path to the file.

setPathTransform(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPerm1(long, Current) - Method in class omero.model.PermissionsI

setPerm1(Long) - Method in class omero.model.PermissionsI

setPermissions(Permissions, Current) - Method in class omero.model.DetailsI

setPermissionsVerifier(String, int) - Method in class ome.services.blitz.Router

setPinholeSize(double) - Method in class pojos.ChannelData

Sets the pinhole size.

setPixelDataService(PixelsService) - Method in class ome.services.ThumbnailBean

Pixels service Bean injector.

setPixels(Pixels) - Method in class omero.util.RPSTileLoop

Called by the TileData implementation to update the RPSTileLoop.pixels instance for re-use by the client.

setPixelsAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPixelsBinDataBigEndian(Boolean, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPixelsData(PixelsService) - Method in class ome.logic.RenderingSettingsImpl

Sets injector.

setPixelsData(PixelsService) - Method in class ome.services.RawPixelsBean

setPixelsDimensionOrder(DimensionOrder, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPixelsId(long, boolean) - Method in interface ome.api.RawPixelsStore

Initializes the stateful service for a given Pixels set.

setPixelsId(long) - Method in interface ome.api.ThumbnailStore

This method manages the state of the service; it must be invoked before using any other methods.

setPixelsID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPixelsId(long) - Method in class ome.services.blitz.gateway.services.impl.ThumbnailServiceImpl

Lookup the pixels for the renderingEngine for pixelsId

setPixelsId(long, boolean) - Method in class ome.services.RawPixelsBean

setPixelsId(long) - Method in class ome.services.ThumbnailBean

setPixelsId_async(AMD_RawPixelsStore_setPixelsId, long, boolean, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI

setPixelsId_async(AMD_ThumbnailStore_setPixelsId, long, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI

setPixelsId_async(AMD_RawPixelsStore_setPixelsId, long, boolean, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI

setPixelSizeX(double) - Method in class pojos.PixelsData

Sets the dimension of a pixel along the X-axis, dimension is in microns.

setPixelSizeY(double) - Method in class pojos.PixelsData

Sets the dimension of a pixel along the Y-axis, dimension is in microns.

setPixelSizeZ(double) - Method in class pojos.PixelsData

Sets the dimension of a pixel along the Z-axis, dimension is in microns.

setPixelsMetadata(IPixels) - Method in class ome.logic.RenderingSettingsImpl

Sets injector.

setPixelsMetadata(IPixels) - Method in class ome.services.RawPixelsBean

setPixelsParams(long, int) - Method in class ome.formats.OMEROMetadataStoreClient

Sets extended the properties on a pixel set.

setPixelsParams_async(AMD_MetadataStore_setPixelsParams, long, boolean, Map<String, String>, Current) - Method in class ome.services.blitz.impl.MetadataStoreI

setPixelsPhysicalSizeX(PositiveFloat, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPixelsPhysicalSizeY(PositiveFloat, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPixelsPhysicalSizeZ(PositiveFloat, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPixelsService(PixelsService) - Method in class ome.logic.RepositoryInfoImpl

Bean injection setter for ROMIO pixels service

setPixelsService(PixelsService) - Method in class ome.services.projection.ProjectionBean

PixelsService bean injector.

setPixelsSizeC(PositiveInteger, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPixelsSizeT(PositiveInteger, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPixelsSizeX(PositiveInteger, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPixelsSizeY(PositiveInteger, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPixelsSizeZ(PositiveInteger, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPixelsTimeIncrement(Double, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPixelsType(PixelType, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPixelToMMFactor(float) - Method in class ome.services.SVGRasterizer

Sets the unit conversion factor to the specified value.

setPlane(byte[], int, int, int) - Method in interface ome.api.RawPixelsStore

setPlane(Long, byte[], int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

Writes a plane to the server.

setPlane(ByteBuffer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer

setPlane(byte[], Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer

setPlane(ByteBuffer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

setPlane(byte[], Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

setPlane(ByteBuffer, Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

setPlane(byte[], Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

setPlane(ByteBuffer, Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer

Sets a particular 2D image plane in this pixel buffer.

setPlane(byte[], Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer

Sets a particular 2D image plane in this pixel buffer.

setPlane(ByteBuffer, Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

setPlane(byte[], Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

setPlane(long, byte[], int, int, int) - Method in class ome.services.blitz.gateway.services.impl.RawPixelsStoreServiceImpl

setPlane(long, byte[], int, int, int) - Method in interface ome.services.blitz.gateway.services.RawPixelsStoreService

set the plane at z, c, t to the bytes of buf.

setPlane(byte[], int, int, int) - Method in class ome.services.RawPixelsBean

setPlane_async(AMD_RawPixelsStore_setPlane, byte[], int, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI

setPlane_async(AMD_RawPixelsStore_setPlane, byte[], int, int, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI

setPlaneAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPlaneDeltaT(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPlaneExposureTime(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPlaneHashSHA1(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPlanePositionX(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPlanePositionY(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPlanePositionZ(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPlanes(int, int) - Method in class omeis.providers.re.codomain.PlaneSlicingContext

Sets the value of the selected planes i.e. the previous plane and the selected one.

setPlaneTheC(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPlaneTheT(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPlaneTheZ(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPlateAcquisition(Set<PlateAcquisitionData>) - Method in class pojos.PlateData

Sets the plate acquisition linked to the plate.

setPlateAcquisitionAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPlateAcquisitionDescription(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPlateAcquisitionEndTime(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPlateAcquisitionID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPlateAcquisitionMaximumFieldCount(PositiveInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPlateAcquisitionName(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPlateAcquisitionStartTime(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPlateAcquisitionWellSampleRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPlateAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPlateColumnNamingConvention(NamingConvention, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPlateColumns(PositiveInteger, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPlateDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPlateExternalIdentifier(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPlateID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPlateName(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPlateRowNamingConvention(NamingConvention, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPlateRows(PositiveInteger, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPlates(Set<PlateData>) - Method in class pojos.ScreenData

Sets the plates contained in this screen.

setPlateScreenRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPlateStatus(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPlateWellOriginX(Double, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPlateWellOriginY(Double, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPockelCell(int) - Method in class pojos.ChannelData

Sets the pockel cell.

setPointDescription(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPointFill(Integer, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPointFontSize(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPointID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPointLabel(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPointName(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPoints(List<Point2D.Double>, List<Point2D.Double>, List<Point2D.Double>, List<Integer>) - Method in class pojos.PolygonData

Sets the points in the polygon.

setPoints(List<Point2D.Double>, List<Point2D.Double>, List<Point2D.Double>, List<Integer>) - Method in class pojos.PolylineData

Sets the points in the polyline.

setPointStroke(Integer, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPointStrokeDashArray(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPointStrokeWidth(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPointTheC(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPointTheT(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPointTheZ(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPointTransform(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPointX(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPointY(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPolylineClosed(Boolean, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPolylineDescription(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPolylineFill(Integer, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPolylineFontSize(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPolylineID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPolylineLabel(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPolylineName(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPolylinePoints(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPolylineStroke(Integer, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPolylineStrokeDashArray(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPolylineStrokeWidth(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPolylineTheC(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPolylineTheT(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPolylineTheZ(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPolylineTransform(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setPositionX(double) - Method in class pojos.ImageAcquisitionData

Sets the x-position.

setPositionY(double) - Method in class pojos.ImageAcquisitionData

Sets the y-position.

setPositionZ(double) - Method in class pojos.ImageAcquisitionData

Sets the z-position.

setPreferenceContext(PreferenceContext) - Method in class ome.logic.ConfigImpl

PreferenceContext setter for dependency injection.

setPreferences(List<Preference>) - Method in class ome.system.PreferenceContext

setPrefs(boolean) - Method in class ome.system.Preference

setPrimaryColorEnabled(boolean) - Method in class omeis.providers.re.Optimizations

Enable or disable the primary color optimization.

setPrincipal(Principal) - Method in class ome.system.SessionInitializer

setPrincipalHolder(PrincipalHolder) - Method in class ome.security.basic.BasicSecurityWiring

Setter injection.

setPrincipalHolder(PrincipalHolder) - Method in class ome.services.sessions.SessionManagerImpl

setProcessManager(IProcessManager) - Method in class ome.services.JobBean

Process Manager Bean injector.

setProjectAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setProjectDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setProjectExperimenterRef(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setProjectGroupRef(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setProjectID(Long) - Method in class ome.formats.importer.ImportContainer

setProjectID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setProjectName(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setProjects(Set<ProjectData>) - Method in class pojos.DatasetData

Sets the projects containing the dataset.

setProperty(String, String) - Method in class ome.system.PreferenceContext

With ticket:2214, preferences are no longer mutable.

setProtocolDescription(String) - Method in class pojos.ScreenData

Sets the description of the protocol.

setProtocolIdentifier(String) - Method in class pojos.ScreenData

Sets the identifier of the protocol.

setProxy(ObjectPrx) - Method in class ome.services.blitz.util.RegisterServantMessage

setQuality(float) - Method in class ome.services.SVGRasterizer

Sets the quality of the image to rasterize when rasterizing to a JPEG.

setQuantizationMap(int, Family, double, boolean) - Method in class ome.services.RenderingBean

Implemented as specified by the RenderingEngine interface.

setQuantizationMap(Family, double, boolean) - Method in class omeis.providers.re.quantum.QuantumStrategy

Sets the selected family, the curve coefficient and the noise reduction flag and rebuilds the look-up table.

setQuantizationMap(int, Family, double, boolean) - Method in class omeis.providers.re.Renderer

Sets the mapping strategy for the specified channel.

setQuantizationMap(int, Family, double, boolean) - Method in interface omeis.providers.re.RenderingEngine

Sets the quantization map, one per channel.

setQuantizationMap_async(AMD_RenderingEngine_setQuantizationMap, int, Family, double, boolean, Current) - Method in class ome.services.blitz.impl.RenderingEngineI

setQuantizationMap_async(AMD_RenderingEngine_setQuantizationMap, int, Family, double, boolean, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI

setQuantumStrategy(int) - Method in class ome.services.RenderingBean

Implemented as specified by the RenderingEngine interface.

setQuantumStrategy(int) - Method in class omeis.providers.re.Renderer

Sets the bit resolution.

setQuantumStrategy(int) - Method in interface omeis.providers.re.RenderingEngine

Sets the quantization strategy.

setQuantumStrategy_async(AMD_RenderingEngine_setQuantumStrategy, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI

setQuantumStrategy_async(AMD_RenderingEngine_setQuantumStrategy, int, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI

setQuery(Query) - Method in class ome.services.query.Query

provide this Query instance with a Query to be used for retrieving data.

setQueryFactory(QueryFactory) - Method in class ome.logic.AbstractLevel1Service

setQueryFactory(QueryFactory) - Method in class ome.logic.AbstractLevel2Service

setQueryService(LocalQuery) - Method in class ome.logic.AbstractLevel2Service

setQueryService(LocalQuery) - Method in class ome.logic.UpdateImpl

setQueryService(LocalQuery) - Method in class ome.services.AbstractStatefulBean

Query service Bean injector.

setQueryService(IQuery) - Method in class ome.services.eventlogs.EventLogLoader

Spring injector

setQueryService(IQuery) - Method in class ome.services.procs.ProcessorSkeleton

setRadiusX(double) - Method in class pojos.EllipseData

Sets the radius along the X-axis.

setRadiusY(double) - Method in class pojos.EllipseData

Sets the radius along the Y-axis.

setRating(int) - Method in class pojos.RatingAnnotationData

Sets the rating value.

setReader(String) - Method in class ome.formats.importer.ImportContainer

setReader(IFormatReader) - Method in interface ome.formats.model.IObjectContainerStore

Sets the Bio-Formats reader that will be used to populate the container store.

setReader(IFormatReader) - Method in class ome.formats.OMEROMetadataStoreClient

setReaderType(String) - Method in class ome.formats.importer.util.ErrorContainer

set file format for import

setReadOnly(boolean) - Method in class ome.services.sessions.SessionManagerImpl

setReadOnly(boolean) - Method in class pojos.ShapeData

Sets to true if the object is a read-only object, false otherwise.

setReagentAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setReagentDescription(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setReagentID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setReagentName(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setReagentReagentIdentifier(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setReagentSetDescripion(String) - Method in class pojos.ScreenData

Sets the identifier of the reagent.

setReagentSetIdentifier(String) - Method in class pojos.ScreenData

Sets the identifier of the reagent.

setRectangleDescription(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setRectangleFill(Integer, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setRectangleFontSize(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setRectangleHeight(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setRectangleID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setRectangleLabel(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setRectangleName(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setRectangleStroke(Integer, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setRectangleStrokeDashArray(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setRectangleStrokeWidth(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setRectangleTheC(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setRectangleTheT(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setRectangleTheZ(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setRectangleTransform(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setRectangleWidth(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setRectangleX(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setRectangleY(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setRed(Integer) - Method in class pojos.WellData

Sets the red component of the color associated to the well.

setRedValue(int, int) - Method in class omeis.providers.re.RGBAIntBuffer

Sets the Red value for a particular pixel index.

setRedValue(int, int) - Method in class omeis.providers.re.RGBBuffer

Sets the Red value for a particular pixel index.

setRedValue(int, int) - Method in class omeis.providers.re.RGBIntBuffer

Sets the Red value for a particular pixel index.

setReference(OriginalFile) - Method in class pojos.ImageData

Sets the reference to the file to register.

setReferenceStringCache(Map<String, String[]>) - Method in interface ome.formats.model.IObjectContainerStore

Sets the string based reference cache for this container store.

setReferenceStringCache(Map<String, String[]>) - Method in class ome.formats.OMEROMetadataStoreClient

setRefPlateId(long) - Method in class pojos.PlateAcquisitionData

Sets the id of the plate this plate acquisition is for.

setRefractiveIndex(double) - Method in class pojos.ImageAcquisitionData

Sets the refractive index of the objective.

setRegion(int, long, byte[]) - Method in interface ome.api.RawPixelsStore

setRegion(Integer, Long, byte[]) - Method in class ome.io.bioformats.BfPixelBuffer

setRegion(Integer, Long, ByteBuffer) - Method in class ome.io.bioformats.BfPixelBuffer

setRegion(Integer, Long, byte[]) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

setRegion(Integer, Long, ByteBuffer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

setRegion(Integer, Long, byte[]) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

setRegion(Integer, Long, ByteBuffer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

setRegion(Integer, Long, byte[]) - Method in interface ome.io.nio.PixelBuffer

Sets a region in this pixel buffer.

setRegion(Integer, Long, ByteBuffer) - Method in interface ome.io.nio.PixelBuffer

Sets a region in this pixel buffer.

setRegion(Integer, Long, byte[]) - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

setRegion(Integer, Long, ByteBuffer) - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

setRegion(int, long, byte[]) - Method in class ome.services.RawPixelsBean

setRegion(RegionDef) - Method in class omeis.providers.re.data.PlaneDef

Sets the region to render.

setRegion_async(AMD_RawPixelsStore_setRegion, int, long, byte[], Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI

setRegion_async(AMD_RawPixelsStore_setRegion, int, long, byte[], Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI

setRegisteredFile(OriginalFile) - Method in class pojos.FileData

Sets the registered file.

setRegisteredFile(Image) - Method in class pojos.ImageData

Sets the registered file.

setRegistry(Registry) - Method in class ome.services.blitz.fire.Ring

Sets the Registry for this instance.

setRenderingDefId(long) - Method in interface ome.api.ThumbnailStore

This method manages the state of the service; it should be invoked directly after setPixelsId.

setRenderingDefId(long, long) - Method in class ome.services.blitz.gateway.services.impl.ThumbnailServiceImpl

setRenderingDefId(long, long) - Method in interface ome.services.blitz.gateway.services.ThumbnailService

Set the rendering def from the default to another.

setRenderingDefId(long) - Method in class ome.services.ThumbnailBean

setRenderingDefId_async(AMD_ThumbnailStore_setRenderingDefId, long, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI

setRepetitions(int) - Method in class ome.services.fulltext.FullTextIndexer

Spring injector.

setRepetitions(int) - Method in class ome.services.pixeldata.PixelDataHandler

Spring injector.

setRepositoryPath(String) - Method in class pojos.FileData

Sets the path to the parent.

setResolutionLevel(int) - Method in interface ome.api.RawPixelsStore

setResolutionLevel(int) - Method in class ome.io.bioformats.BfPixelBuffer

setResolutionLevel(int) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

setResolutionLevel(IFD) - Method in class ome.io.bioformats.OmeroPixelsPyramidReader

setResolutionLevel(int) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

setResolutionLevel(int) - Method in interface ome.io.nio.PixelBuffer

Sets the active resolution level.

setResolutionLevel(int) - Method in class ome.io.nio.RomioPixelBuffer

setResolutionLevel(int) - Method in class ome.services.RawPixelsBean

setResolutionLevel(int) - Method in class ome.services.RenderingBean

setResolutionLevel(int) - Method in class omeis.providers.re.Renderer

Sets the active resolution level.

setResolutionLevel(int) - Method in interface omeis.providers.re.RenderingEngine

setResolutionLevel_async(AMD_PyramidService_setResolutionLevel, int, Current) - Method in class ome.services.blitz.impl.AbstractPyramidServant

setResolutionLevel_async(AMD_PyramidService_setResolutionLevel, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI

setResolutionLevel_async(AMD_PyramidService_setResolutionLevel, int, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI

setRetry() - Method in class ome.io.messages.MissingPyramidMessage

setReturnUnloaded(boolean) - Method in interface ome.api.Search

Determines if all results should be returned as unloaded objects.

setReturnUnloaded(boolean) - Method in class ome.services.SearchBean

setReturnUnloaded_async(AMD_Search_setReturnUnloaded, boolean, Current) - Method in class ome.services.blitz.impl.SearchI

setRGBA(int, int, int, int, int) - Method in class ome.services.RenderingBean

Implemented as specified by the RenderingEngine interface.

setRGBA(int, int, int, int, int) - Method in class omeis.providers.re.Renderer

Sets the color associated to the specified channel.

setRGBA(int, int, int, int, int) - Method in interface omeis.providers.re.RenderingEngine

Sets the four components composing the color associated to the specified channel.

setRGBA_async(AMD_RenderingEngine_setRGBA, int, int, int, int, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI

setRGBA_async(AMD_RenderingEngine_setRGBA, int, int, int, int, int, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI

setROIAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setROICoordinate(ROICoordinate) - Method in class pojos.ShapeData

Sets the ROICoordinate for the ShapeData

setROIDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setROIID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setROIID(String, int) - Method in class ome.formats.OverlayMetadataStore

setROIName(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setROINamespace(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setRoles(Roles) - Method in class ome.services.sessions.SessionManagerImpl

setRoot(Object) - Method in class ome.formats.OMEROMetadataStoreClient

setRow(byte[], int, int, int, int) - Method in interface ome.api.RawPixelsStore

setRow(ByteBuffer, Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer

setRow(ByteBuffer, Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

setRow(ByteBuffer, Integer, Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

setRow(ByteBuffer, Integer, Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer

Sets a particular row or scanline in this pixel buffer.

setRow(ByteBuffer, Integer, Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

setRow(byte[], int, int, int, int) - Method in class ome.services.RawPixelsBean

setRow_async(AMD_RawPixelsStore_setRow, byte[], int, int, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI

setRow_async(AMD_RawPixelsStore_setRow, byte[], int, int, int, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI

setScaleService(IScale) - Method in class ome.services.ThumbnailBean

Scale service Bean injector.

setScreenAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setScreenDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setScreenID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setScreenName(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setScreenPlateRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setScreenProtocolDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setScreenProtocolIdentifier(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setScreenReagentSetDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setScreenReagentSetIdentifier(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setScreens(Set<ScreenData>) - Method in class pojos.PlateData

Sets the screens containing the plate.

setScreenType(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setSecurityContext(IObject, Current) - Method in class ome.services.blitz.impl.ServiceFactoryI

setSecurityContext(Principal, IObject) - Method in interface ome.services.sessions.SessionManager

Sets the context for the current session to the given value.

setSecurityContext(Principal, IObject) - Method in class ome.services.sessions.SessionManagerImpl

setSecurityPassword(String, Current) - Method in class ome.services.blitz.impl.ServiceFactoryI

setSecuritySystem(SecuritySystem) - Method in class ome.logic.AbstractLevel2Service

setSecuritySystem(SecuritySystem) - Method in class ome.services.AbstractStatefulBean

setSecuritySystem(SecuritySystem) - Method in class ome.services.blitz.impl.TimelineI

setSelectedFile(File) - Method in class ome.formats.importer.util.ErrorContainer

setSeries(int) - Method in class ome.io.bioformats.BfPixelBuffer

Sets the current series in the underlying Bio-Formats reader.

setServerEndpoints(String, int) - Method in class ome.services.blitz.Router

setServiceFactory(ServiceFactoryI) - Method in class ome.services.blitz.gateway.OmeroGateway

Initialize the service factory which creates the gateway and services and links the different services together.

setServiceFactory(ServiceFactoryI) - Method in class ome.services.blitz.impl.DeleteI

setServiceFactory(ServiceFactoryI) - Method in class ome.services.blitz.impl.ExporterI

setServiceFactory(ServiceFactoryI) - Method in class ome.services.blitz.impl.MetadataStoreI

setServiceFactory(ServiceFactoryI) - Method in class ome.services.blitz.impl.RawFileStoreI

setServiceFactory(ServiceFactoryI) - Method in class ome.services.blitz.impl.RenderingEngineI

setServiceFactory(ServiceFactoryI) - Method in class ome.services.blitz.impl.RoiI

setServiceFactory(ServiceFactoryI) - Method in class ome.services.blitz.impl.ScriptI

setServiceFactory(ServiceFactoryI) - Method in class ome.services.blitz.impl.SharedResourcesI

setServiceFactory(ServiceFactoryI) - Method in class ome.services.blitz.impl.TimelineI

setServiceFactory(ServiceFactoryI) - Method in interface ome.services.blitz.util.ServiceFactoryAware

setSession(Session) - Method in class ome.system.ServiceFactory

setSession(Session) - Method in class ome.system.SessionInitializer

setSessionCache(SessionCache) - Method in class ome.services.sessions.SessionManagerImpl

setSessionFactory(SessionFactory) - Method in class ome.logic.AbstractLevel1Service

delegates to HibernateDaoSupport.

setSessionFactory(SessionFactory) - Method in class ome.logic.TypesImpl

injector for usage by the container.

setSessionFactory(SessionFactory) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl

Initializes the metadata needed by this instance.

setSessionHandler(SessionHandler) - Method in class ome.tools.hibernate.ProxyCleanupFilter.Interceptor

setSessionId(String) - Method in class ome.formats.importer.util.FileUploader

Set specific sessionID

setSessionManager(SessionManager) - Method in class ome.logic.UpdateImpl

setSessionManager(SessionManager) - Method in class ome.security.basic.BasicMethodSecurity

setSessionManager(SessionManager) - Method in class ome.services.blitz.impl.TimelineI

setSessionManager(String, int) - Method in class ome.services.blitz.Router

setSessionService(ISession) - Method in class ome.system.SessionInitializer

setSettingsService(IRenderingSettings) - Method in class ome.services.ThumbnailBean

Rendering settings service Bean injector.

setShapeSettings(Shape) - Method in class pojos.ShapeData

Set the settings associated to the shape.

setShareId(Long) - Method in interface ome.api.local.LocalShare

setShareId(Long) - Method in interface ome.services.sessions.SessionContext

The Share id is the only mutable bit in the SessionContext.

setShareId(Long) - Method in class ome.services.sessions.SessionContextImpl

setShareId(Long) - Method in class ome.services.sharing.ShareBean

Not in the public interface (since it allows setting to -1 which makes everything readable, but used internally similar to a LocalShare interface.

setSizeC(int) - Method in class pojos.PixelsData

Sets the number of channels.

setSizeT(int) - Method in class pojos.PixelsData

Sets the number of time-points.

setSizeX(int) - Method in class pojos.PixelsData

Sets the number of pixels along the X-axis.

setSizeY(int) - Method in class pojos.PixelsData

Sets the number of pixels along the Y-axis.

setSizeZ(int) - Method in class pojos.PixelsData

Sets the number of pixels along the Z-axis.

setSqlAction(SqlAction) - Method in class ome.logic.ConfigImpl

SqlAction setter for dependency injection.

setSqlAction(SqlAction) - Method in class ome.logic.RepositoryInfoImpl

Bean injection setter for SQL operations

setSqlAction(SqlAction) - Method in class ome.services.eventlogs.PersistentEventLogLoader

setSqlAction(SqlAction) - Method in class ome.services.fulltext.FullTextIndexer

Since these instances are used repeatedly, we need to check for already set SqlAction

setSqlAction(SqlAction) - Method in class ome.services.pixeldata.PixelDataHandler

Since these instances are used repeatedly, we need to check for already set SqlAction

setSqlAction(SqlAction) - Method in class ome.services.RawPixelsBean

SQL action Bean injector

setSqlAction(SqlAction) - Method in class ome.services.util.Executor.SimpleWork

setStack(byte[], int, int, int) - Method in interface ome.api.RawPixelsStore

setStack(ByteBuffer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer

setStack(byte[], Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer

setStack(ByteBuffer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

setStack(byte[], Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

setStack(ByteBuffer, Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

setStack(byte[], Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

setStack(ByteBuffer, Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer

Sets the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel buffer.

setStack(byte[], Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer

Sets the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel buffer.

setStack(ByteBuffer, Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

setStack(byte[], Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

setStack(byte[], int, int, int) - Method in class ome.services.RawPixelsBean

setStack_async(AMD_RawPixelsStore_setStack, byte[], int, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI

setStack_async(AMD_RawPixelsStore_setStack, byte[], int, int, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI

setStageLabelName(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setStageLabelX(Double, int) - Method in class ome.formats.OMEROMetadataStoreClient

setStageLabelY(Double, int) - Method in class ome.formats.OMEROMetadataStoreClient

setStageLabelZ(Double, int) - Method in class ome.formats.OMEROMetadataStoreClient

setStaleCacheListener(SessionCache.StaleCacheListener) - Method in class ome.services.sessions.state.SessionCache

setStatisticsEnabled(boolean) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

Enable statistics logs (this is a dynamic parameter)

setStatus(String) - Method in interface ome.api.JobHandle

Updates the JobStatus for the current job.

setStatus(int) - Method in class ome.formats.importer.util.ErrorContainer

set the status for this error

setStatus(String) - Method in class ome.services.JobBean

setStatus(String) - Method in class pojos.PlateData

Sets the status.

setStatus(String) - Method in class pojos.WellData

Sets the status of the well.

setStatus_async(AMD_JobHandle_setStatus, String, Current) - Method in class ome.services.blitz.impl.JobHandleI

setStatusAndMessage(String, String) - Method in interface ome.api.JobHandle

Like JobHandle.setStatus(String) but also sets the message.

setStatusAndMessage(String, String) - Method in class ome.services.JobBean

setStatusAndMessage_async(AMD_JobHandle_setStatusAndMessage, String, RString, Current) - Method in class ome.services.blitz.impl.JobHandleI

setStride(int) - Method in class omeis.providers.re.data.PlaneDef

Returns the stride.

setStroke(Color) - Method in class pojos.ShapeSettingsData

Set the stroke colour.

setStrokeDashArray(double[]) - Method in class pojos.ShapeSettingsData

Set the stroke dashes.

setStrokeWidth(double) - Method in class pojos.ShapeSettingsData

Set the stroke width.

setT(int) - Method in class pojos.ShapeData

Sets the time-point.

setTagAnnotationAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setTagAnnotationDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setTagAnnotationID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setTagAnnotationNamespace(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setTagAnnotationValue(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setTagDescription(String) - Method in class pojos.TagAnnotationData

Sets the description of the tag.

setTagDescriptions(List<TextualAnnotationData>) - Method in class pojos.TagAnnotationData

Sets the tag's descriptions.

setTagValue(String) - Method in class pojos.TagAnnotationData

Sets the value of the tag.

setTarget(IObject) - Method in class ome.formats.importer.ImportContainer

setTemperature(double) - Method in class pojos.ImageAcquisitionData

Sets the temperature.

setTerm(String) - Method in class pojos.TermAnnotationData

Sets the term.

setTermAnnotationAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setTermAnnotationDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setTermAnnotationID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setTermAnnotationNamespace(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setTermAnnotationValue(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setText(String) - Method in class pojos.EllipseData

Sets the text of the shape.

setText(String) - Method in class pojos.LineData

Sets the text of the shape.

setText(String) - Method in class pojos.MaskData

Sets the text of the shape.

setText(String) - Method in class pojos.PointData

Sets the text of the shape.

setText(String) - Method in class pojos.PolygonData

Sets the text of the shape.

setText(String) - Method in class pojos.PolylineData

Sets the text of the shape.

setText(String) - Method in class pojos.RectangleData

Sets the text of the shape.

setText(String) - Method in class pojos.TextData

Sets the text of the shape.

setText(String) - Method in class pojos.TextualAnnotationData

Sets the text.

setText(String) - Method in class pojos.XMLAnnotationData

Sets the text value.

setTextDescription(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setTextFill(Integer, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setTextFontSize(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setTextID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setTextLabel(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setTextName(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setTextStroke(Integer, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setTextStrokeDashArray(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setTextStrokeWidth(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setTextTheC(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setTextTheT(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setTextTheZ(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setTextTransform(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setTextValue(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setTextX(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setTextY(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setThumbnailService(ThumbnailService) - Method in class ome.logic.RepositoryInfoImpl

Bean injection setter for ROMIO thumbnail service

setTie(TieBase) - Method in class ome.services.blitz.impl.RawFileStoreI

setTie(TieBase) - Method in interface ome.services.blitz.util.TieAware

setTiffDataFirstC(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setTiffDataFirstT(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setTiffDataFirstZ(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setTiffDataIFD(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setTiffDataPlaneCount(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setTile(byte[], int, int, int, int, int, int, int) - Method in interface ome.api.RawPixelsStore

setTile(Long, byte[], int, int, int, int, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

Writes a tile of pixels to the server.

setTile(byte[], Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer

setTile(byte[], Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

setTile(byte[], Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

setTile(byte[], Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer

Sets a tile in this pixel buffer.

setTile(byte[], Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer

setTile(byte[], int, int, int, int, int, int, int) - Method in class ome.services.RawPixelsBean

setTile(byte[], int, int, int, int, int, int, int) - Method in class omero.util.RPSTileData

setTile(byte[], int, int, int, int, int, int, int) - Method in interface omero.util.TileData

setTile_async(AMD_RawPixelsStore_setTile, byte[], int, int, int, int, int, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI

setTile_async(AMD_RawPixelsStore_setTile, byte[], int, int, int, int, int, int, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI

setTimeout(int) - Method in class ome.services.blitz.Router

setTimepoint(byte[], int) - Method in interface ome.api.RawPixelsStore

setTimepoint(ByteBuffer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer

setTimepoint(byte[], Integer) - Method in class ome.io.bioformats.BfPixelBuffer

setTimepoint(ByteBuffer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

setTimepoint(byte[], Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

setTimepoint(ByteBuffer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

setTimepoint(byte[], Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

setTimepoint(ByteBuffer, Integer) - Method in interface ome.io.nio.PixelBuffer

Sets the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel buffer.

setTimepoint(byte[], Integer) - Method in interface ome.io.nio.PixelBuffer

Sets the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel buffer.

setTimepoint(ByteBuffer, Integer) - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

setTimepoint(byte[], Integer) - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

setTimepoint(byte[], int) - Method in class ome.services.RawPixelsBean

setTimepoint_async(AMD_RawPixelsStore_setTimepoint, byte[], int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI

setTimepoint_async(AMD_RawPixelsStore_setTimepoint, byte[], int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI

setTimestampAnnotationAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setTimestampAnnotationDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setTimestampAnnotationID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setTimestampAnnotationNamespace(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setTimestampAnnotationValue(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

settings - Variable in class pojos.ShapeData

The representation of the shape.

SETTINGSID_QUERY - Static variable in class ome.services.delete.DeleteBean

setToken(String) - Method in class ome.formats.importer.util.ErrorContainer

setToken(GraphHolder) - Method in class ome.security.basic.TokenHolder

setTransform(String) - Method in class pojos.ShapeData

Sets the Affine transform of the shape.

setTransmittanceRangeCutIn(PositiveInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setTransmittanceRangeCutInTolerance(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setTransmittanceRangeCutOut(PositiveInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setTransmittanceRangeCutOutTolerance(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setTransmittanceRangeTransmittance(PercentFraction, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setTrustStore(String) - Method in class ome.security.KeyAndTrustStoreConfiguration

setTrustStorePassword(String) - Method in class ome.security.KeyAndTrustStoreConfiguration

setTypes(ITypes) - Method in class ome.services.eventlogs.PersistentEventLogLoader

setTypesService(ITypes) - Method in class ome.services.JobBean

Types service Bean injector.

setTypesService(ITypes) - Method in class ome.services.procs.ProcessorSkeleton

setUIBounds(Rectangle) - Method in class ome.formats.importer.ImportConfig

setUIBounds(Rectangle) - Method in class ome.formats.importer.util.IniFileLoader

Set ui bounds for application

setUp() - Method in class ome.formats.importer.ImportFixture

checks for the necessary fields and initializes the ImportLibrary

setUp() - Method in class ome.formats.importer.util.TinyImportFixture

checks for the necessary fields and initializes the ImportLibrary

setUp() - Method in class ome.formats.OMEROImportFixture

checks for the necessary fields and initializes the ImportLibrary

setUpdateEvent(Event, Current) - Method in class omero.model.DetailsI

setUpdateInterval(long) - Method in class ome.services.sessions.state.SessionCache

Inject time in milliseconds between updates.

setUpdateService(LocalUpdate) - Method in class ome.logic.AbstractLevel2Service

setUpdateService(LocalUpdate) - Method in class ome.services.AbstractStatefulBean

setUpdateService(IUpdate) - Method in class ome.services.procs.ProcessorSkeleton

setUploadUrl(String) - Method in class ome.formats.importer.util.ErrorContainer

setUpperLimit(int) - Method in class omeis.providers.re.codomain.PlaneSlicingContext

Sets the value (in [intervalStart, intervalEnd]) used to set the level of the bit-plane > bit-plane selected.

setUsedFiles(String[]) - Method in class ome.formats.importer.ImportContainer

setUseMetadataFile(boolean) - Method in class ome.formats.importer.ImportContainer

Sets whether or not we're using an original metadata file.

setUseProjections(boolean) - Method in interface ome.api.Search

Determines if Lucene queries should not hit the database.

setUseProjections(boolean) - Method in class ome.services.SearchBean

setUseProjections_async(AMD_Search_setUseProjections, boolean, Current) - Method in class ome.services.blitz.impl.SearchI

setUseQuaqua(boolean) - Method in class ome.formats.importer.ImportConfig

setUseQuaqua(boolean) - Method in class ome.formats.importer.util.IniFileLoader

setUserDisableHistory(boolean) - Method in class ome.formats.importer.ImportConfig

setUserDisableHistory(boolean) - Method in class ome.formats.importer.util.IniFileLoader

Set debug level for application

setUserFullPath(boolean) - Method in class ome.formats.importer.ImportConfig

setUserFullPath(boolean) - Method in class ome.formats.importer.util.IniFileLoader

setUserId(long) - Method in class ome.services.ThumbnailCtx

Sets the user ID to use for queries.

setUserPixels(Double[]) - Method in class ome.formats.importer.ImportContainer

setUserRead(boolean, Current) - Method in class omero.model.PermissionsI

setUserRead(boolean) - Method in class pojos.PermissionData

Sets to true if the user has read access, false otherwise.

setUserSpecifiedAnnotations(List<Annotation>) - Method in interface ome.formats.model.IObjectContainerStore

Sets the user specified image annotations.

setUserSpecifiedAnnotations(List<Annotation>) - Method in class ome.formats.OMEROMetadataStoreClient

setUserSpecifiedImageDescription(String) - Method in interface ome.formats.model.IObjectContainerStore

Sets the user specified image description.

setUserSpecifiedImageDescription(String) - Method in class ome.formats.OMEROMetadataStoreClient

setUserSpecifiedImageName(String) - Method in interface ome.formats.model.IObjectContainerStore

Sets the user specified image name.

setUserSpecifiedImageName(String) - Method in class ome.formats.OMEROMetadataStoreClient

setUserSpecifiedPhysicalPixelSizes(Double, Double, Double) - Method in interface ome.formats.model.IObjectContainerStore

Sets the user specified physical pixel sizes.

setUserSpecifiedPhysicalPixelSizes(Double, Double, Double) - Method in class ome.formats.OMEROMetadataStoreClient

setUserSpecifiedPlateDescription(String) - Method in interface ome.formats.model.IObjectContainerStore

Sets the user specified plate description.

setUserSpecifiedPlateDescription(String) - Method in class ome.formats.OMEROMetadataStoreClient

setUserSpecifiedPlateName(String) - Method in interface ome.formats.model.IObjectContainerStore

Sets the user specified plate name.

setUserSpecifiedPlateName(String) - Method in class ome.formats.OMEROMetadataStoreClient

setUserSpecifiedTarget(IObject) - Method in interface ome.formats.model.IObjectContainerStore

Sets the user specified linkage target (usually a Dataset for Images and a Screen for Plates).

setUserSpecifiedTarget(IObject) - Method in class ome.formats.OMEROMetadataStoreClient

setUserStyleSheetURI(String) - Method in class ome.services.SVGRasterizer

Sets the uri of the user stylesheet.

setUserWrite(boolean, Current) - Method in class omero.model.PermissionsI

setUserWrite(boolean) - Method in class pojos.PermissionData

Sets to true if the user has write access, false otherwise.

setUUID(String) - Method in class ome.formats.OMEROMetadataStoreClient

setUuid(String) - Method in class ome.services.sessions.SessionManagerImpl

setUUIDFileName(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setUUIDValue(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setValue(boolean) - Method in class pojos.BooleanAnnotationData

Returns the text.

setValue(IObject) - Method in class pojos.DataObject

Sets the IObject.

setVersion(int) - Method in class pojos.DataObject

Sets the version of the object if it is immutable.

setVersionNumber(String) - Method in class ome.formats.importer.ImportConfig

setVisibility(Preference.Visibility) - Method in class ome.system.Preference

Setter injector

setVisible(boolean) - Method in class pojos.ShapeData

Sets to true if the shape is visible, false otherwise.

setWavelength(int) - Method in exception omeis.providers.re.quantum.QuantizationException

Sets the index of the wavelength that couldn't be rendered.

setWellAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setWellColor(Integer, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setWellColumn(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setWellExternalDescription(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setWellExternalIdentifier(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setWellID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setWellReagentRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setWellRow(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setWellSampleAnnotationRef(String, int, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setWellSampleID(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setWellSampleImageRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setWellSampleIndex(NonNegativeInteger, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setWellSamplePositionX(Double, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setWellSamplePositionY(Double, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setWellSamples(List<WellSampleData>) - Method in class pojos.WellData

Sets the well samples linked to the well.

setWellSampleTimepoint(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setWellStatus(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setWellType(String) - Method in class pojos.WellData

Sets a human readable identifier for the screening status e.g. empty, positive control, etc.

setWidth(int) - Method in class omeis.providers.re.data.RegionDef

Sets the width of the region.

setWidth(double) - Method in class pojos.MaskData

Sets the width of an untransformed mask.

setWidth(double) - Method in class pojos.RectangleData

Sets width of an untransformed rectangle.

setWindow(double, double) - Method in class omeis.providers.re.quantum.QuantumStrategy

Sets the input window interval.

setWorldRead(boolean, Current) - Method in class omero.model.PermissionsI

setWorldRead(boolean) - Method in class pojos.PermissionData

Sets to true if the world has read access, false otherwise.

setWorldWrite(boolean, Current) - Method in class omero.model.PermissionsI

setWorldWrite(boolean) - Method in class pojos.PermissionData

Sets to true if the world has write access, false otherwise.

setX(int) - Method in class omeis.providers.re.data.PlaneDef

Selects a plane in the set identified by this object.

setX(int) - Method in class omeis.providers.re.data.RegionDef

Sets the x-coordinate of the top-left corner.

setX(double) - Method in class pojos.EllipseData

Sets the x-coordinate of the center of the ellipse.

setX(double) - Method in class pojos.MaskData

Sets the x-coordinate top-left corner of an untransformed mask.

setX(double) - Method in class pojos.PointData

set the x-coordinate of the shape.

setX(double) - Method in class pojos.RectangleData

Sets the x-coordinate of the top-left corner of an untransformed rectangle.

setX(double) - Method in class pojos.TextData

Sets the x-coordinate of the text field.

setX1(double) - Method in class pojos.LineData

Set the x-coordinate of the starting point of an untransformed line.

setX2(double) - Method in class pojos.LineData

Set the x-coordinate of the end point of an untransformed line.

setXEnd(int) - Method in class omeis.providers.re.codomain.ContrastStretchingContext

Sets the x-coodinate of the pEnd point.

setXMLAnnotationAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient

setXMLAnnotationDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setXMLAnnotationID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setXMLAnnotationNamespace(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setXMLAnnotationValue(String, int) - Method in class ome.formats.OMEROMetadataStoreClient

setXMLParserValidating(boolean) - Method in class ome.services.SVGRasterizer

Sets whether or not the XML parser used to parse SVG document should be validating or not, depending on the specified parameter.

setXStart(int) - Method in class omeis.providers.re.codomain.ContrastStretchingContext

Sets the x-coodinate of the pStart point.

setY(int) - Method in class omeis.providers.re.data.PlaneDef

Selects a plane in the set identified by this object.

setY(int) - Method in class omeis.providers.re.data.RegionDef

Sets the y-coordinate of the top-left corner.

setY(double) - Method in class pojos.EllipseData

Sets the y-coordinate of the center of the ellipse.

setY(double) - Method in class pojos.MaskData

Sets the y-coordinate top-left corner of an untransformed mask.

setY(double) - Method in class pojos.PointData

set the y-coordinate of the shape.

setY(double) - Method in class pojos.RectangleData

Sets the y-coordinate of the top-left corner of an untransformed rectangle.

setY(double) - Method in class pojos.TextData

Sets the y-coordinate of the text field.

setY1(double) - Method in class pojos.LineData

Set the y-coordinate of the starting point of an untransformed line.

setY2(double) - Method in class pojos.LineData

Set the y-coordinate of the end point of an untransformed line.

setYEnd(int) - Method in class omeis.providers.re.codomain.ContrastStretchingContext

Sets the y-coodinate of the pEnd point.

setYStart(int) - Method in class omeis.providers.re.codomain.ContrastStretchingContext

Sets the y-coodinate of the pStart point.

setZ(int) - Method in class omeis.providers.re.data.PlaneDef

Selects a plane in the set identified by this object.

setZ(int) - Method in class pojos.ShapeData

Sets the z-section.

sf - Variable in class ome.logic.TypesImpl

sf - Variable in class ome.security.auth.SimpleRoleProvider

sf - Variable in class ome.security.basic.BasicSecuritySystem

sf - Variable in class ome.services.blitz.impl.MetadataStoreI

sf - Variable in class ome.services.delete.DeleteBean

sha1() - Method in class ome.services.scripts.RepoFile.FsFile

sha1() - Method in class ome.services.scripts.RepoFile

sha1(File) - Method in class omero.client

Calculates the local sha1 for a file.

shape() - Method in class ome.services.roi.RoiTypes.ObjectFactory

ShapeChangeMessage - Class in ome.services.messages

Published on any modification to a Shape.

ShapeChangeMessage(Object, List<EventLog>) - Constructor for class ome.services.messages.ShapeChangeMessage

ShapeData - Class in pojos

Hosts a shape.

ShapeData(Shape, boolean) - Constructor for class pojos.ShapeData

Creates a new instance.

ShapeData(Shape) - Constructor for class pojos.ShapeData

Creates a new instance.

ShapeProcessor - Class in ome.formats.model

Processes the shapes of a IObjectContainerStore and ensures that the ROI containers are present.

ShapeProcessor() - Constructor for class ome.formats.model.ShapeProcessor

ShapeSettingsData - Class in pojos

Stores the settings related to a given shape.

share - Variable in class ome.services.sharing.data.ShareItem

ShareBean - Class in ome.services.sharing

Note: SessionManager should not be used to obtain the Share data since it may not be completely in sync. i.e.

ShareBean(LocalAdmin, SessionManager, ShareStore, Executor) - Constructor for class ome.services.sharing.ShareBean

shareCount(long) - Method in class ome.services.sharing.data.ShareItems

ShareData - Class in ome.services.sharing.data

ShareData() - Constructor for class ome.services.sharing.data.ShareData

ShareData(long, long, List<Long>, List<String>, Map<String, List<Long>>, List<Obj>, boolean, long) - Constructor for class ome.services.sharing.data.ShareData

ShareDataHolder - Class in ome.services.sharing.data

ShareDataHolder() - Constructor for class ome.services.sharing.data.ShareDataHolder

ShareDataHolder(ShareData) - Constructor for class ome.services.sharing.data.ShareDataHolder

ShareDataHolder.Patcher - Class in ome.services.sharing.data

ShareDataHolder.Patcher() - Constructor for class ome.services.sharing.data.ShareDataHolder.Patcher

ShareDataPrx - Interface in ome.services.sharing.data

ShareDataPrxHelper - Class in ome.services.sharing.data

ShareDataPrxHelper() - Constructor for class ome.services.sharing.data.ShareDataPrxHelper

ShareDataPrxHolder - Class in ome.services.sharing.data

ShareDataPrxHolder() - Constructor for class ome.services.sharing.data.ShareDataPrxHolder

ShareDataPrxHolder(ShareDataPrx) - Constructor for class ome.services.sharing.data.ShareDataPrxHolder

sharedResources(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI

SharedResourcesI - Class in ome.services.blitz.impl

Implementation of the SharedResources interface.

SharedResourcesI(BlitzExecutor, TopicManager, Registry, ScriptRepoHelper) - Constructor for class ome.services.blitz.impl.SharedResourcesI

SharedResourcesI(BlitzExecutor, TopicManager, Registry, ScriptRepoHelper, long) - Constructor for class ome.services.blitz.impl.SharedResourcesI

ShareI - Class in ome.services.blitz.impl

Implementation of the IShare service.

ShareI(IShare, BlitzExecutor) - Constructor for class ome.services.blitz.impl.ShareI

shareId - Variable in class ome.system.SimpleEventContext

ShareItem - Class in ome.services.sharing.data

ShareItem() - Constructor for class ome.services.sharing.data.ShareItem

ShareItem(long, String, long, List<Long>, List<String>) - Constructor for class ome.services.sharing.data.ShareItem

ShareItemHolder - Class in ome.services.sharing.data

ShareItemHolder() - Constructor for class ome.services.sharing.data.ShareItemHolder

ShareItemHolder(ShareItem) - Constructor for class ome.services.sharing.data.ShareItemHolder

ShareItemHolder.Patcher - Class in ome.services.sharing.data

ShareItemHolder.Patcher() - Constructor for class ome.services.sharing.data.ShareItemHolder.Patcher

ShareItemPrx - Interface in ome.services.sharing.data

ShareItemPrxHelper - Class in ome.services.sharing.data

ShareItemPrxHelper() - Constructor for class ome.services.sharing.data.ShareItemPrxHelper

ShareItemPrxHolder - Class in ome.services.sharing.data

ShareItemPrxHolder() - Constructor for class ome.services.sharing.data.ShareItemPrxHolder

ShareItemPrxHolder(ShareItemPrx) - Constructor for class ome.services.sharing.data.ShareItemPrxHolder

ShareItems - Class in ome.services.sharing.data

ShareItems(Connection, String, boolean, Comparator, Map) - Constructor for class ome.services.sharing.data.ShareItems

ShareItems(Connection, String, boolean, Comparator) - Constructor for class ome.services.sharing.data.ShareItems

ShareItems(Connection, String, boolean) - Constructor for class ome.services.sharing.data.ShareItems

ShareItems(Connection, String) - Constructor for class ome.services.sharing.data.ShareItems

ShareMap - Class in ome.services.sharing.data

ShareMap(Connection, String, boolean, Comparator, Map) - Constructor for class ome.services.sharing.data.ShareMap

ShareMap(Connection, String, boolean, Comparator) - Constructor for class ome.services.sharing.data.ShareMap

ShareMap(Connection, String, boolean) - Constructor for class ome.services.sharing.data.ShareMap

ShareMap(Connection, String) - Constructor for class ome.services.sharing.data.ShareMap

ShareRestrictionTransactionAttributeSource - Class in ome.services.sharing

Prevents methods from setting the transaction to readOnly = false when a share is activated.

ShareRestrictionTransactionAttributeSource(CurrentDetails, SessionCache) - Constructor for class ome.services.sharing.ShareRestrictionTransactionAttributeSource

ShareStore - Class in ome.services.sharing

Entry to the Ice code generated data/ directory.

ShareStore() - Constructor for class ome.services.sharing.ShareStore

sharesToSessions(List<ShareData>) - Method in class ome.services.sharing.ShareBean

shareToSession(ShareData) - Method in class ome.services.sharing.ShareBean

sharing - Variable in class ome.security.SecuritySystemHolder

SharingACLVoter - Class in ome.security.sharing

SharingACLVoter(CurrentDetails, SystemTypes, ShareStore) - Constructor for class ome.security.sharing.SharingACLVoter

SharingSecuritySystem - Class in ome.security.sharing

central security interface.

SharingSecuritySystem() - Constructor for class ome.security.sharing.SharingSecuritySystem

SHORT - Static variable in class omeis.providers.re.data.PlaneFactory

Identifies the type used to store pixel values.

shortName - Variable in class ome.formats.importer.ImportEvent.COUNT_EVENT

shouldBeOmitted(String) - Static method in class ome.services.util.DBEnumCheck

shutdown(boolean) - Method in class ome.services.blitz.Entry

Calls OmeroContext.closeAll() to recursively close all OMERO.blitz resources in the reverse order that they were created.

shutdown(Current) - Method in class ome.services.blitz.impl.ScriptProcessI

shutdown(Communicator) - Method in class ome.services.blitz.Router

Uses the administrative interface for the Glacier2 router to call AdminPrx.shutdown().

ShutdownSafeEhcacheManagerFactoryBean - Class in ome.tools.spring

Workaround for the Spring/EHCache shutdown sequence.

ShutdownSafeEhcacheManagerFactoryBean() - Constructor for class ome.tools.spring.ShutdownSafeEhcacheManagerFactoryBean

signed - Variable in class omeis.providers.re.data.Plane2D

The sign of the type

SimilarTerms - Class in ome.services.search

Search to find similar terms to some given terms.

SimilarTerms(SearchValues, String...) - Constructor for class ome.services.search.SimilarTerms

SimpleBackOff - Class in ome.io.nio

Basic BackOff implementation which attempts several writes of the default block size on startup, and uses that as a scaling factor for all subsequent calculations.

SimpleBackOff() - Constructor for class ome.io.nio.SimpleBackOff

SimpleBackOff(TileSizes) - Constructor for class ome.io.nio.SimpleBackOff

SimpleEventContext - Class in ome.system

simple, non-thread-safe, serializable EventContext

SimpleEventContext() - Constructor for class ome.system.SimpleEventContext

Constructor for subclasses

SimpleEventContext(EventContext) - Constructor for class ome.system.SimpleEventContext

copy constructor.

SimpleLuceneOptions - Class in ome.services.fulltext

Implementation of LuceneOptions which takes an existing instance and possible overrides for each of the values.

SimpleLuceneOptions(LuceneOptions, Float) - Constructor for class ome.services.fulltext.SimpleLuceneOptions

SimpleLuceneOptions(LuceneOptions, Field.Store) - Constructor for class ome.services.fulltext.SimpleLuceneOptions

SimpleLuceneOptions(LuceneOptions, Field.Index, Field.Store) - Constructor for class ome.services.fulltext.SimpleLuceneOptions

SimpleLuceneOptions(LuceneOptions, Float, Field.Index, Field.Store) - Constructor for class ome.services.fulltext.SimpleLuceneOptions

SimpleRoleProvider - Class in ome.security.auth

Implements RoleProvider.

SimpleRoleProvider(SecuritySystem, SessionFactory) - Constructor for class ome.security.auth.SimpleRoleProvider

SimpleSessionStats - Class in ome.services.sessions.stats

SimpleSessionStats(ObjectsReadCounter, ObjectsWrittenCounter, MethodCounter) - Constructor for class ome.services.sessions.stats.SimpleSessionStats

singleFile(File, ImportConfig) - Method in class ome.formats.importer.ImportCandidates

Return an import container for a single file

size() - Method in interface ome.api.RawFileStore

Returns the size of the file on disk (not as stored in the database since that value will only be updated on RawFileStore.save().

size() - Method in class ome.formats.importer.ImportCandidates

size - Variable in class ome.formats.importer.ImportEvent.PROGRESS_EVENT

size() - Method in class ome.io.nio.FileBuffer

size(String) - Method in class ome.security.auth.AttributeSet

size() - Method in class ome.security.basic.CurrentDetails

size() - Method in interface ome.security.basic.PrincipalHolder

Get the number of active principal contexts.

size() - Method in class ome.services.export.ExporterIndex

size() - Method in class ome.services.graphs.GraphState

size() - Method in interface ome.services.graphs.GraphStep.Callback

size() - Method in class ome.services.query.Definitions

size() - Method in class ome.services.RawFileBean

size() - Method in class ome.services.scheduler.ThreadPool

size() - Method in class ome.tools.hibernate.ExtendedMetadata.Locks

the total number of fields for this entity.

size() - Method in class omero.util.Resources

size_async(AMD_RawFileStore_size, Current) - Method in class ome.services.blitz.impl.RawFileStoreI

size_async(AMD_RawFileStore_size, Current) - Method in class ome.services.blitz.repo.RepoRawFileStoreI

sizeC - Variable in class ome.formats.importer.ImportSize

sizeC - Variable in class ome.services.formats.OmeroReader

sizeImages() - Method in class ome.services.blitz.impl.OmeroMetadata

sizes - Variable in class ome.io.nio.PixelsService

TileSizes implementation for default values

sizes - Variable in class ome.io.nio.SimpleBackOff

sizeT - Variable in class ome.formats.importer.ImportSize

sizeT - Variable in class ome.services.formats.OmeroReader

sizeX - Variable in class ome.formats.importer.ImportSize

sizeX - Variable in class ome.services.formats.OmeroReader

sizeX - Variable in class omeis.providers.re.data.Plane2D

Number of pixels along the X-axis.

sizeY - Variable in class ome.formats.importer.ImportSize

sizeY - Variable in class ome.services.formats.OmeroReader

sizeY - Variable in class omeis.providers.re.data.Plane2D

Number of pixels along the Y-axis.

sizeZ - Variable in class ome.formats.importer.ImportSize

sizeZ - Variable in class ome.services.formats.OmeroReader

skip() - Method in class ome.services.graphs.GraphEntry

A KEEP setting is a way of putting a KEEP suggestion to vote.

skipFrom() - Method in class ome.tools.hibernate.QueryBuilder

skipWhere() - Method in class ome.tools.hibernate.QueryBuilder

slice - Variable in class omeis.providers.re.data.Plane2D

The slice we're working with

Slot - Class in ome.services.throttling

Worker which consumes from the Queue.

Slot(Queue) - Constructor for class ome.services.throttling.Slot

sm - Variable in class ome.services.blitz.impl.TimelineI

SmartEllipseI - Class in omero.model

SmartEllipseI() - Constructor for class omero.model.SmartEllipseI

SmartLineI - Class in omero.model

SmartLineI() - Constructor for class omero.model.SmartLineI

SmartMaskI - Class in omero.model

SmartMaskI() - Constructor for class omero.model.SmartMaskI

SmartPathI - Class in omero.model

SmartPathI() - Constructor for class omero.model.SmartPathI

SmartPointI - Class in omero.model

SmartPointI() - Constructor for class omero.model.SmartPointI

SmartPolygonI - Class in omero.model

SmartPolygonI() - Constructor for class omero.model.SmartPolygonI

SmartPolylineI - Class in omero.model

SmartPolylineI() - Constructor for class omero.model.SmartPolylineI

SmartRectI - Class in omero.model

SmartRectI() - Constructor for class omero.model.SmartRectI

SmartShape - Interface in omero.model

Orthogonal interface hierarchy of types for working with the Shape hierarchy.

SmartShape.PointCallback - Interface in omero.model

Callback interface passed every point which is within the area of this shape.

SmartShape.Util - Class in omero.model

Utility class used as a mixin by all of the SmartShape implementations.

SmartShape.Util() - Constructor for class omero.model.SmartShape.Util

SmartTextI - Class in omero.model

THIS CLASS IS CURRENTLY BROKEN.

SmartTextI() - Constructor for class omero.model.SmartTextI

SmtpAuthenticator - Class in ome.security

SmtpAuthenticator(String, String) - Constructor for class ome.security.SmtpAuthenticator

SomeMustNone - Class in ome.services.search

FullText subclass which parses 3 arrays of strings into into a single Lucene query.

SomeMustNone(SearchValues, String[], String[], String[], Class<? extends Analyzer>) - Constructor for class ome.services.search.SomeMustNone

SortDatasetsByName - Class in ome.formats

SortDatasetsByName() - Constructor for class ome.formats.SortDatasetsByName

SortProjectsByName - Class in ome.formats

SortProjectsByName() - Constructor for class ome.formats.SortProjectsByName

source - Variable in class ome.formats.importer.util.ErrorHandler.UNKNOWN_FORMAT

source - Variable in class ome.formats.importer.util.ErrorHandler.UNREADABLE_FILE

sources - Variable in class ome.services.query.QueryFactory

sources available for lookups.

spec - Variable in class ome.services.graphs.GraphStep

GraphSpec instance which is active for this step.

sql - Variable in class ome.logic.AdminImpl

sql - Variable in class ome.security.basic.EventHandler

sql - Variable in class ome.services.blitz.impl.MetadataStoreI

sql - Variable in class ome.services.blitz.impl.RoiI

sql - Variable in class ome.services.eventlogs.PersistentEventLogLoader

sql - Variable in class ome.services.OmeroFilePathResolver

SQL action instance for this class.

sql - Variable in class ome.services.roi.GeomTool

sqlAction - Variable in class ome.services.util.Executor.Impl

SqlArray<T> - Class in ome.tools.hibernate

Hibernate type to store a java array using SQL ARRAY.

SqlArray(List<T>, int) - Constructor for class ome.tools.hibernate.SqlArray

SqlArray(List<T>, int, String) - Constructor for class ome.tools.hibernate.SqlArray

SqlArray.BOOLEAN - Class in ome.tools.hibernate

SqlArray.BOOLEAN(List<Boolean>) - Constructor for class ome.tools.hibernate.SqlArray.BOOLEAN

SqlArray.DATE - Class in ome.tools.hibernate

SqlArray.DATE(List<Date>) - Constructor for class ome.tools.hibernate.SqlArray.DATE

SqlArray.DOUBLE - Class in ome.tools.hibernate

SqlArray.DOUBLE(List<Double>) - Constructor for class ome.tools.hibernate.SqlArray.DOUBLE

SqlArray.FLOAT - Class in ome.tools.hibernate

SqlArray.FLOAT(List<Float>) - Constructor for class ome.tools.hibernate.SqlArray.FLOAT

SqlArray.INTEGER - Class in ome.tools.hibernate

SqlArray.INTEGER(List<Integer>) - Constructor for class ome.tools.hibernate.SqlArray.INTEGER

SqlArray.STRING - Class in ome.tools.hibernate

SqlArray.STRING(List<String>) - Constructor for class ome.tools.hibernate.SqlArray.STRING

SqlArray.STRING2 - Class in ome.tools.hibernate

SqlArray.STRING2(List<String[]>) - Constructor for class ome.tools.hibernate.SqlArray.STRING2

sqlTypes() - Method in class ome.tools.hibernate.ListAsSQLArrayUserType

ss - Variable in class ome.services.blitz.impl.TimelineI

stack - Variable in class ome.services.graphs.GraphStep

Stack of other GraphStep instances which show where this step is in the entire graph.

stackAsString(Throwable) - Static method in class omero.util.IceMapper

standalone(String[]) - Static method in class ome.services.fulltext.Main

Starts up and simply waits until told by the grid to disconnect.

start() - Method in class ome.services.blitz.Entry

Obtains the named OmeroContext, creating it if necessary, and then delegates to _CommunicatorOperationsNC.waitForShutdown() until either it is externally shutdown, or until a signal is caught.

start() - Method in class ome.services.blitz.Router

start() - Method in class ome.services.fulltext.FullTextThread

Called by Spring on creation.

start(GraphStep.Callback) - Method in class ome.services.graphs.GraphStep

start() - Method in class ome.services.pixeldata.PixelDataThread

Called by Spring on creation.

start() - Method in class ome.services.util.DBEnumCheck

start() - Method in class ome.services.util.DBPatchCheck

start() - Method in class ome.services.util.ServerVersionCheck

Prints simple banner with OMERO version.

Start() - Method in class omerojava.util.GatewayHeartbeat

Start the heartbeat thread.

startIO(int) - Method in class omeis.providers.re.RenderingStats

Notifies the start of pixels data retrieval for the specified wavelength (channel).

startMalloc() - Method in class omeis.providers.re.RenderingStats

Notifies the start of the allocation of an RGB memory buffer for the rendering process.

startProcess(ServiceFactory, long) - Method in class ome.services.procs.ProcessManager.Work

startRendering() - Method in class omeis.providers.re.RenderingStats

Notifies the start of the trasnformation of the raw pixels data.

startTime(RTime) - Method in class omero.sys.ParametersI

Sets the value of the start time parameter.

StatefulServiceInterface - Interface in ome.api

OMERO API Interface with stateful semantics.

stats() - Method in interface ome.services.sessions.SessionContext

Return a SessionStats implementation for this session.

stats() - Method in class ome.services.sessions.SessionContextImpl

stats() - Method in class ome.services.sessions.stats.CurrentSessionStats

stats() - Method in class ome.services.sessions.stats.DelegatingStats

Intended to be overwritten by subclasses.

stats() - Method in class ome.services.sessions.stats.PerSessionStats

stats() - Method in class ome.services.sessions.stats.PerThreadStats

StatsFactory - Class in omeis.providers.re.metadata

Computes two types of statistics: The PixelsStats and the location stats.

StatsFactory() - Constructor for class omeis.providers.re.metadata.StatsFactory

status() - Method in class ome.services.blitz.Entry

Status - Class in ome.services.blitz

Status check for OMERO.blitz.

Status(String[]) - Constructor for class ome.services.blitz.Status

STDIN - Static variable in class prefs

Storing the standard in as a Properties instance as early as possible to prevent lost data.

step - Variable in class ome.formats.importer.ImportEvent.IMPORT_STEP

steps(SqlAction, Session, DeleteHandleI.Report) - Method in class ome.services.blitz.impl.DeleteHandleI

stop() - Method in class ome.services.fulltext.FullTextThread

Called by Spring on destruction.

stop() - Method in class ome.services.pixeldata.PixelDataThread

Called by Spring on destruction.

stop() - Method in class ome.services.util.ServerVersionCheck

Prints simple banner with "Stopping OMERO"

stop() - Method in class omeis.providers.re.RenderingStats

Notifies this object that the rendering process has finished.

stop(Current) - Method in class omero.grid.InteractiveProcessorI

Cancels the current process, nulls the value, and returns immediately if detach is false.

Stop() - Method in class omerojava.util.GatewayHeartbeat

Stop the the OmeroJava service and kill the heartbeat thread.

store(int, Class, int, IResults.Result) - Method in interface ome.api.IResults

storing results.

store() - Method in class ome.formats.importer.ImportConfig.PassValue

store() - Method in class ome.formats.importer.ImportConfig.Value

Stores the current value back to some medium.

store - Variable in class ome.formats.OMEROImportFixture

store - Variable in class ome.services.blitz.impl.MetadataStoreI

store - Variable in class ome.services.sharing.ShareBean

store(Object, Object) - Method in class omero.util.IceMapper

storeMultiBulk(int, Class[], int[], IResults.Result[]) - Method in interface ome.api.IResults

storeMultiBulkPrimitive(int, String[], int[], Map[]) - Method in interface ome.api.IResults

storePrimitive(int, String, int, Map) - Method in interface ome.api.IResults

storeShareData(long, ShareData) - Method in class ome.services.sharing.ShareBean

storeSingleBulk(int, Class, int, IResults.Result[]) - Method in interface ome.api.IResults

storeSingleBulkPrimitive(int, Class, int, Map[]) - Method in interface ome.api.IResults

STRING - Static variable in class ome.services.query.StringQuery

parameter name for the definition of the HQL string.

STRING(Connection, List<String>) - Method in interface ome.tools.hibernate.ListAsSQLArrayUserType.ArrayFactory

STRING2(Connection, List<String[]>) - Method in interface ome.tools.hibernate.ListAsSQLArrayUserType.ArrayFactory

STRING_TO_RSTRING - Static variable in class omero.util.IceMapper

stringFromSvnString(String) - Static method in class ome.system.Version

Parses the given String to remove the leading "$", keyword name, and colons.

StringQuery - Class in ome.services.query

simple HQL query.

StringQuery(Parameters) - Constructor for class ome.services.query.StringQuery

StringQuerySource - Class in ome.services.query

interprets the query id as an HQL query.

StringQuerySource() - Constructor for class ome.services.query.StringQuerySource

StringSeqHelper - Class in ome.services.sharing.data

StringSeqHelper() - Constructor for class ome.services.sharing.data.StringSeqHelper

StringSeqHolder - Class in ome.services.sharing.data

StringSeqHolder() - Constructor for class ome.services.sharing.data.StringSeqHolder

StringSeqHolder(List<String>) - Constructor for class ome.services.sharing.data.StringSeqHolder

StringUtils - Class in ome.tools

StringUtils() - Constructor for class ome.tools.StringUtils

submit(Job) - Method in interface ome.api.JobHandle

Submits a Job and returns its database id.

submit(Job) - Method in class ome.services.JobBean

submit(Callable<T>) - Method in class ome.services.util.Executor.Impl

submit(Callable<T>) - Method in interface ome.services.util.Executor

Simple submission method which can be used in conjunction with a call to Executor.execute(Principal, Work) to overcome the no-multiple-login rule.

submit_async(AMD_JobHandle_submit, Job, Current) - Method in class ome.services.blitz.impl.JobHandleI

SUBMITTED - Static variable in interface ome.api.JobHandle

subscribe(String, ObjectPrx, Current) - Method in class ome.services.blitz.impl.ServiceFactoryI

subselect(QueryBuilder) - Method in class ome.tools.hibernate.QueryBuilder

Appends the string representation of the QueryBuilder argument inside of parentheses.

subtypeEquals(int, int, String) - Method in class ome.tools.hibernate.ExtendedMetadata.Locks

returns true is the indexed subtype returns the same class type as the klass argument.

subtypeName(int, int) - Method in class ome.tools.hibernate.ExtendedMetadata.Locks

retrieves the full Hibernate path for this component field.

success - Variable in class ome.services.messages.LoginAttemptMessage

sum(PlanePoint) - Method in class ome.util.math.geom2D.PlanePoint

Calculates the sum of this vector with the specified argument.

SUM_INTENSITY - Static variable in interface ome.api.IProjection

Sum intensity projection

superspec - Variable in class ome.services.graphs.BaseGraphSpec

Path of the superspec.

SVGRasterizer - Class in ome.services

This class provides a simple and method based API for converting a SVG document fragment to a BufferedImage.

SVGRasterizer(String) - Constructor for class ome.services.SVGRasterizer

Constructs a new SVGRasterizer.

SVGRasterizer(URL) - Constructor for class ome.services.SVGRasterizer

Constructs a new SVGRasterizer.

SVGRasterizer(InputStream) - Constructor for class ome.services.SVGRasterizer

Constructs a new SVGRasterizer converter.

SVGRasterizer(Reader) - Constructor for class ome.services.SVGRasterizer

Constructs a new SVGRasterizer converter.

SVGRasterizer.Rasterizer - Class in ome.services

An image transcoder that stores the resulting image.

SVGRasterizer.Rasterizer() - Constructor for class ome.services.SVGRasterizer.Rasterizer

SVN_DATE_FORMAT - Static variable in class ome.system.Version

Date format used by Subversions "Date" keyword.

swapIfRequired(byte[]) - Method in class ome.io.bioformats.BfPixelsWrapper

cgb - stolen from ImportLibrary - slightly modified Examines a byte array to see if it needs to be byte swapped and modifies the byte array directly.

synchronizeJobs() - Method in class ome.services.blitz.util.CheckAllJobs

synchronizeLdapUser(String) - Method in class ome.logic.LdapImpl

synchronizeLoginCache() - Method in interface ome.api.IAdmin

uses JMX to refresh the login cache if supported.

synchronizeLoginCache() - Method in class ome.logic.AdminImpl

synchronizeLoginCache_async(AMD_IAdmin_synchronizeLoginCache, Current) - Method in class ome.services.blitz.impl.AdminI

sys(String[]) - Static method in class prefs

Replaces the user Preferences instance with the system Preferences and continues dispatching.

SYSTEM - Static variable in class pojos.GroupData

Identifies the System group.

SystemTypes - Class in ome.security

Defines what IObject classes are considered "system" types.

SystemTypes() - Constructor for class ome.security.SystemTypes

SystemTypes(Roles) - Constructor for class ome.security.SystemTypes

sysTypes - Variable in class ome.security.basic.BasicACLVoter

sysTypes - Variable in class ome.security.basic.BasicSecuritySystem

T

t - Variable in exception ome.util.messages.MessageException

table - Variable in class ome.services.graphs.GraphStep

Parsed table name used for the SQL/HQL statements.

TablesBridge - Class in ome.services.fulltext.bridges

Bridge for parsing OMERO.tables attached to container types.

TablesBridge() - Constructor for class ome.services.fulltext.bridges.TablesBridge

TagAnnotationData - Class in pojos

A tag annotation can either be related to an image or a tag but not to both at the same time.

TagAnnotationData(String, boolean) - Constructor for class pojos.TagAnnotationData

Creates a new instance.

TagAnnotationData(String) - Constructor for class pojos.TagAnnotationData

Creates a new instance.

TagAnnotationData(String, String) - Constructor for class pojos.TagAnnotationData

Creates a new instance.

TagAnnotationData(String, String, boolean) - Constructor for class pojos.TagAnnotationData

Creates a new instance.

TagAnnotationData(TagAnnotation) - Constructor for class pojos.TagAnnotationData

Creates a new instance.

TagAnnotationData(TagAnnotation, List<CommentAnnotation>) - Constructor for class pojos.TagAnnotationData

Creates a new instance.

TagsAndGroups - Class in ome.services.search

Query template used by SearchBean to store user requests.

TagsAndGroups(SearchValues, String, boolean) - Constructor for class ome.services.search.TagsAndGroups

take() - Method in class ome.services.throttling.Queue

takeover() - Method in class ome.services.blitz.repo.AbstractRepositoryI

Method called in a background thread which may end up waiting indefinitely on the repository lock file ("${omero.data.dir}/.omero/repository/${omero.db.uuid}/repo_uuid").

target - Variable in class ome.formats.importer.ImportEvent.PROGRESS_EVENT

target2model - Variable in class omero.util.IceMapper

targetClass - Variable in class ome.formats.importer.ImportConfig

targetId - Variable in class ome.formats.importer.ImportConfig

TargetProcessor - Class in ome.formats.model

Processes the IObjectContainerStore and populates references for the linkage target object of choice.

TargetProcessor() - Constructor for class ome.formats.model.TargetProcessor

Task - Class in ome.services.throttling

Simple base task which contains logic for routing calls reflectively to ice_response and ice_exception of any AMD callback.

Task(Object, Current, boolean) - Constructor for class ome.services.throttling.Task

tearDown() - Method in class ome.formats.importer.ImportFixture

sets ImportLibrary, OMEROMetadataStoreClient, and file array to null.

tearDown() - Method in class ome.formats.importer.util.TinyImportFixture

tearDown() - Method in class ome.formats.OMEROImportFixture

sets ImportLibrary, OMEROMetadataStore, and file array to null.

TempFileManager - Class in omero.util

Creates temporary files and folders and makes a best effort to remove them on exit (or sooner).

TempFileManager() - Constructor for class omero.util.TempFileManager

Default constructor, passes "omero" to TempFileManager.TempFileManager(String)

TempFileManager(String) - Constructor for class omero.util.TempFileManager

Initializes a TempFileManager instance with a userDir containing the given prefix value.

templateMessage - Variable in class ome.logic.AdminImpl

TemporaryRepositoryI - Class in ome.services.blitz.repo

Simple repository service to make the ${java.io.tmpdir} available at runtime.

TemporaryRepositoryI(ObjectAdapter, Registry, Executor, SqlAction, String) - Constructor for class ome.services.blitz.repo.TemporaryRepositoryI

TermAnnotationData - Class in pojos

Defines a Term Annotation.

TermAnnotationData(String) - Constructor for class pojos.TermAnnotationData

Creates a new instance.

TermAnnotationData(TermAnnotation) - Constructor for class pojos.TermAnnotationData

Creates a new instance.

test(String[]) - Static method in class prefs

Simple test framework, callable from the command line via "java prefs test"

TEXT - Static variable in class pojos.FileAnnotationData

Identifies the Text file formats.

TextData - Class in pojos

Represents a Text in the Euclidean space R².

TextData(Shape) - Constructor for class pojos.TextData

Creates a new instance of Text data from an existing shape.

TextData() - Constructor for class pojos.TextData

Creates a new instance of TextData, creating a new TextI Object.

TextData(String, double, double) - Constructor for class pojos.TextData

Creates a new instance of the TextData, sets the centre and major, minor axes.

TextualAnnotationData - Class in pojos

Basic textual annotation used to add comments to a given object.

TextualAnnotationData() - Constructor for class pojos.TextualAnnotationData

Creates a new instance.

TextualAnnotationData(String) - Constructor for class pojos.TextualAnnotationData

Creates a new instance.

TextualAnnotationData(CommentAnnotation) - Constructor for class pojos.TextualAnnotationData

Creates a new instance.

ThreadPool - Class in ome.services.scheduler

Produces a ThreadPool(int, int, long) - Constructor for class ome.services.scheduler.ThreadPool

threadSafe - Variable in class ome.util.messages.InternalMessage

ThrottlingStrategy - Interface in ome.services.throttling

Strategy interface for controlling the execution of blitz methods.

throwCreationViolation(IObject) - Method in interface ome.security.ACLVoter

throws a SecurityViolation based on the given IObject and the context of the current user.

throwCreationViolation(IObject) - Method in class ome.security.basic.BasicACLVoter

throwCreationViolation(IObject) - Method in class ome.security.CompositeACLVoter

throwCreationViolation(IObject) - Method in class ome.security.sharing.SharingACLVoter

throwDeleteViolation(IObject) - Method in interface ome.security.ACLVoter

throws a SecurityViolation based on the given IObject and the context of the current user.

throwDeleteViolation(IObject) - Method in class ome.security.basic.BasicACLVoter

throwDeleteViolation(IObject) - Method in class ome.security.CompositeACLVoter

throwDeleteViolation(IObject) - Method in class ome.security.sharing.SharingACLVoter

throwDisabled(String) - Method in class ome.security.sharing.SharingACLVoter

throwIfAlreadySet(Object, Object) - Method in class ome.services.util.BeanHelper

throwIfCancelled() - Method in class ome.services.sessions.events.ChangeSecurityContextEvent

throwIfInitialized(Object) - Method in class ome.services.blitz.util.BlitzConfiguration

If this configuration is finished and BlitzConfiguration.communicator is not-null, throw a IllegalStateException

throwLoadViolation(IObject) - Method in interface ome.security.ACLVoter

throws a SecurityViolation based on the given IObject and the context of the current user.

throwLoadViolation(IObject) - Method in class ome.security.basic.BasicACLVoter

throwLoadViolation(IObject) - Method in class ome.security.CompositeACLVoter

throwLoadViolation(IObject) - Method in class ome.security.sharing.SharingACLVoter

throwMissingPyramidException(String, Pixels) - Method in interface ome.io.nio.BackOff

throwMissingPyramidException(String, Pixels) - Method in class ome.io.nio.SimpleBackOff

throwOnNullData(long, ShareData) - Method in class ome.services.sharing.ShareBean

throwUpdateViolation(IObject) - Method in interface ome.security.ACLVoter

throws a SecurityViolation based on the given IObject and the context of the current user.

throwUpdateViolation(IObject) - Method in class ome.security.basic.BasicACLVoter

throwUpdateViolation(IObject) - Method in class ome.security.CompositeACLVoter

throwUpdateViolation(IObject) - Method in class ome.security.sharing.SharingACLVoter

throwUsage() - Method in class ome.tools.hibernate.QueryBuilder

ThumbnailBean - Class in ome.services

Provides methods for directly querying object graphs.

ThumbnailBean() - Constructor for class ome.services.ThumbnailBean

default constructor

ThumbnailBean(boolean) - Constructor for class ome.services.ThumbnailBean

overriden to allow Spring to set boolean

ThumbnailCtx - Class in ome.services

ThumbnailCtx(IQuery, IUpdate, IPixels, IRenderingSettings, ThumbnailService, SecuritySystem, long) - Constructor for class ome.services.ThumbnailCtx

Default constructor.

thumbnailExists(Integer, Integer) - Method in interface ome.api.ThumbnailStore

Checks if a thumbnail of a particular size exists for a pixels set.

thumbnailExists(Integer, Integer) - Method in class ome.services.ThumbnailBean

thumbnailExists_async(AMD_ThumbnailStore_thumbnailExists, RInt, RInt, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI

THUMBNAILS_PATH - Static variable in class ome.io.nio.AbstractFileSystemService

ThumbnailService - Class in ome.io.nio

ThumbnailService(String) - Constructor for class ome.io.nio.ThumbnailService

Constructor

ThumbnailService - Interface in ome.services.blitz.gateway.services

ThumbnailServiceImpl - Class in ome.services.blitz.gateway.services.impl

ThumbnailServiceImpl(ThumbnailStorePrx) - Constructor for class ome.services.blitz.gateway.services.impl.ThumbnailServiceImpl

Create the ThumbnailService passing the gateway.

ThumbnailStore - Interface in ome.api

Provides methods for dealing with thumbnails.

ThumbnailStoreI - Class in ome.services.blitz.impl

Implementation of the ThumbnailStore service.

ThumbnailStoreI(ThumbnailStore, BlitzExecutor) - Constructor for class ome.services.blitz.impl.ThumbnailStoreI

thumbs(String, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI

TieAware - Interface in ome.services.blitz.util

Servant which is aware of the TieBase-instance which it belongs to and will have it injected on instantiation.

TileData - Interface in omero.util

Access strategy which can be implemented by diverse resources

TileLoop - Class in omero.util

TileLoop() - Constructor for class omero.util.TileLoop

TileLoopIteration - Interface in ome.io.nio

A single iteration of a tile for each loop.

TileLoopIteration - Interface in omero.util

A single iteration of a tile for each loop.

TileSizes - Interface in ome.io.nio

Strategy interface which is used by PixelsService to specify the default tile sizes as well as when tiling is necessary.

TimeAnnotationData - Class in pojos

Basic time annotation.

TimeAnnotationData() - Constructor for class pojos.TimeAnnotationData

Creates a default instance.

TimeAnnotationData(TimestampAnnotation) - Constructor for class pojos.TimeAnnotationData

Creates a new instance.

TimelineI - Class in ome.services.blitz.impl

implementation of the ITimeline service interface.

TimelineI(BlitzExecutor) - Constructor for class ome.services.blitz.impl.TimelineI

timeOfEvent(Event) - Method in class pojos.DataObject

TinyImportFixture - Class in ome.formats.importer.util

test fixture which uses a hard-coded file ("tinyTest.d3d.dv") from the classpath, and adds them to a new UUID-named dataset.

TinyImportFixture(ServiceFactory) - Constructor for class ome.formats.importer.util.TinyImportFixture

tmpdir() - Method in class omero.util.TempFileManager

Returns a platform-specific user-writable temporary directory.

to - Variable in class ome.services.blitz.util.ConvertToBlitzExceptionMessage

toBufferedImage(Pixels, int[]) - Static method in class omerojava.util.GatewayUtils

Convert the raw integer(4byte colour data) to a bufferedImage, for pixels object pixels.

toJavaType(RInt) - Method in class ome.services.blitz.impl.MetadataStoreI

Transforms an OMERO RType into the corresponding Java type.

toJavaType(RLong) - Method in class ome.services.blitz.impl.MetadataStoreI

Transforms an OMERO RType into the corresponding Java type.

toJavaType(RBool) - Method in class ome.services.blitz.impl.MetadataStoreI

Transforms an OMERO RType into the corresponding Java type.

toJavaType(RFloat) - Method in class ome.services.blitz.impl.MetadataStoreI

Transforms an OMERO RType into the corresponding Java type.

toJavaType(RDouble) - Method in class ome.services.blitz.impl.MetadataStoreI

Transforms an OMERO RType into the corresponding Java type.

toJavaType(RString) - Method in class ome.services.blitz.impl.MetadataStoreI

Transforms an OMERO RType into the corresponding Java type.

tokenHolder - Variable in class ome.security.basic.BasicACLVoter

tokenHolder - Variable in class ome.security.basic.BasicSecuritySystem

TokenHolder - Class in ome.security.basic

Manages a special token (a unique object) which can be inserted into IObject instances for special almost-administrative handling.

TokenHolder() - Constructor for class ome.security.basic.TokenHolder

tokenStream(String, Reader) - Method in class ome.services.fulltext.FullTextAnalyzer

Returns a LowercaseAlphaNumericTokenizer

toLog() - Method in class ome.formats.importer.ImportCandidates.SCANNING

toLog() - Method in class ome.formats.importer.ImportEvent.IMPORT_STEP

toLog() - Method in class ome.formats.importer.ImportEvent.LOADED_IMAGE

toLog() - Method in class ome.formats.importer.ImportEvent.LOADING_IMAGE

toLog() - Method in class ome.formats.importer.ImportEvent

toLog() - Method in class ome.formats.importer.util.ErrorHandler.FILE_EXCEPTION

toLog() - Method in class ome.formats.importer.util.ErrorHandler.INTERNAL_EXCEPTION

toLog() - Method in class ome.formats.importer.util.ErrorHandler.UNKNOWN_FORMAT

toLog() - Method in class ome.formats.importer.util.ErrorHandler.UNREADABLE_FILE

toNumber(double) - Static method in class pojos.ShapeData

Returns a double array as a number attribute value.

topicManager - Variable in class ome.services.blitz.fire.SessionManagerI

TopicManager - Interface in ome.services.blitz.fire

Local dispatcher to TopicManager

TopicManager.Impl - Class in ome.services.blitz.fire

TopicManager.Impl(Communicator) - Constructor for class ome.services.blitz.fire.TopicManager.Impl

TopicManager.TopicMessage - Class in ome.services.blitz.fire

TopicManager.TopicMessage(Object, String, ObjectPrxHelperBase, String, Object...) - Constructor for class ome.services.blitz.fire.TopicManager.TopicMessage

topicOrNull(String) - Method in class ome.services.blitz.fire.TopicManager.Impl

toPoints(Point2D.Double[]) - Static method in class pojos.ShapeData

Returns a Point2D.Double array as a Points attribute value. as specified in http://www.w3.org/TR/SVGMobile12/shapes.html#PointsBNF

toRType(Integer) - Method in class ome.formats.OMEROMetadataStoreClient

Transforms a Java type into the corresponding OMERO RType.

toRType(NonNegativeInteger) - Method in class ome.formats.OMEROMetadataStoreClient

Transforms a Java type into the corresponding OMERO RType.

toRType(NonNegativeLong) - Method in class ome.formats.OMEROMetadataStoreClient

Transforms a Java type into the corresponding OMERO RType.

toRType(PositiveFloat) - Method in class ome.formats.OMEROMetadataStoreClient

Transforms a Java type into the corresponding OMERO RType.

toRType(PercentFraction) - Method in class ome.formats.OMEROMetadataStoreClient

Transforms a Java type into the corresponding OMERO RType.

toRType(Long) - Method in class ome.formats.OMEROMetadataStoreClient

Transforms a Java type into the corresponding OMERO RType.

toRType(String) - Method in class ome.formats.OMEROMetadataStoreClient

Transforms a Java type into the corresponding OMERO RType.

toRType(Boolean) - Method in class ome.formats.OMEROMetadataStoreClient

Transforms a Java type into the corresponding OMERO RType.

toRType(Double) - Method in class ome.formats.OMEROMetadataStoreClient

Transforms a Java type into the corresponding OMERO RType.

toRType(Float) - Method in class ome.formats.OMEROMetadataStoreClient

Transforms a Java type into the corresponding OMERO RType.

toRType(Timestamp) - Method in class ome.formats.OMEROMetadataStoreClient

Transforms a Java type into the corresponding OMERO RType.

toRType(NamingConvention) - Method in class ome.formats.OMEROMetadataStoreClient

Transforms a Java type into the corresponding OMERO RType.

toRType(Object) - Method in class omero.util.IceMapper

toString() - Method in exception ome.formats.enums.EnumerationException

toString() - Method in class ome.formats.importer.ImportConfig.Value

toString() - Method in enum ome.formats.Index

toString() - Method in exception ome.formats.model.ModelException

toString() - Method in class ome.io.nio.AbstractBuffer

toString() - Method in class ome.io.nio.ConfiguredTileSizes

toString() - Method in class ome.io.nio.SimpleBackOff

toString() - Method in class ome.services.blitz.impl.ServiceFactoryI

toString() - Method in class ome.services.graphs.BaseGraphSpec

toString() - Method in class ome.services.graphs.GraphEntry

toString() - Method in exception ome.services.graphs.GraphException

toString() - Method in class ome.services.graphs.GraphState

toString() - Method in class ome.services.graphs.GraphTables

toString() - Method in class ome.services.scripts.RepoFile.FsFile

toString() - Method in class ome.services.scripts.RepoFile

toString() - Method in class ome.services.throttling.Task

toString() - Method in class ome.system.Principal

returns only the name of the instance because that is the expected behavior of Principal implementations

toString() - Method in class ome.tools.FileSystem

Public toString implementation

toString() - Method in class ome.tools.hibernate.QueryBuilder

toString() - Method in class ome.tools.hibernate.SqlArray

toString() - Method in class ome.tools.spring.InternalServiceFactory

toString() - Method in class omeis.providers.re.codomain.CodomainChain

Overrides the toString method.

toString() - Method in class omeis.providers.re.data.PlaneDef

Overrides generic toString method to provide a specific string representation of this object.

toString() - Method in class omeis.providers.re.data.RegionDef

Overridden to return the region as a string.

toString() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

toString() - Method in class pojos.DataObject

Overridden to return the name of the class and the object id.

toString() - Method in class pojos.ROICoordinate

Returns the string of the coordinates.

total - Variable in class ome.formats.importer.ImportEvent.COUNT_EVENT

total - Variable in class ome.formats.importer.ImportEvent.PROGRESS_EVENT

total() - Method in class ome.tools.hibernate.ExtendedMetadata.Locks

as opposed to ExtendedMetadata.Locks.size(), the returns the actual number of fields that will need to be checked.

total_files - Variable in class ome.formats.importer.ImportEvent.FILE_SIZE_STEP

total_files_length - Variable in class ome.formats.importer.ImportEvent.FILE_SIZE_STEP

totalErrors - Variable in class ome.formats.importer.util.ErrorHandler

totalFiles - Variable in class ome.formats.importer.ImportCandidates.SCANNING

totalSharedItems() - Method in class ome.services.sharing.BlobShareStore

totalSharedItems() - Method in class ome.services.sharing.FreezeShareStore

totalSharedItems() - Method in class ome.services.sharing.ShareStore

totalShares() - Method in class ome.services.sharing.BlobShareStore

totalShares() - Method in class ome.services.sharing.FreezeShareStore

totalShares() - Method in class ome.services.sharing.ShareStore

trace(String, String) - Method in class ome.services.blitz.util.CommonsLoggingAdapter

transfer(String, RepositoryPrx, String, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI

transform(int) - Method in class omeis.providers.re.codomain.CodomainChain

Applies the transformation.

transform(int) - Method in interface omeis.providers.re.codomain.CodomainMap

Performs the transformation.

transform(int, double) - Method in class omeis.providers.re.quantum.ExponentialMap

Implemented as specified in QuantumMap.

transform(double, double) - Method in class omeis.providers.re.quantum.ExponentialMap

Implemented as specified in QuantumMap.

transform(float, double) - Method in class omeis.providers.re.quantum.ExponentialMap

Implemented as specified in QuantumMap.

transform(int, double) - Method in class omeis.providers.re.quantum.LogarithmicMap

Implemented as specified in QuantumMap.

transform(double, double) - Method in class omeis.providers.re.quantum.LogarithmicMap

Implemented as specified in QuantumMap.

transform(float, double) - Method in class omeis.providers.re.quantum.LogarithmicMap

Implemented as specified in QuantumMap.

transform(int, double) - Method in class omeis.providers.re.quantum.PolynomialMap

Implemented as specified in QuantumMap.

transform(double, double) - Method in class omeis.providers.re.quantum.PolynomialMap

Implemented as specified in QuantumMap.

transform(float, double) - Method in class omeis.providers.re.quantum.PolynomialMap

Implemented as specified in QuantumMap.

transform(int, double) - Method in interface omeis.providers.re.quantum.QuantumMap

Maps the specified value.

transform(double, double) - Method in interface omeis.providers.re.quantum.QuantumMap

Maps the specified value.

transform(float, double) - Method in interface omeis.providers.re.quantum.QuantumMap

Maps the specified value.

translateException(Throwable) - Method in class ome.services.util.BeanHelper

truncate(long) - Method in interface ome.api.RawFileStore

Limits the size of a file to the given length.

truncate(long) - Method in class ome.io.nio.FileBuffer

truncate(long) - Method in class ome.services.RawFileBean

truncate_async(AMD_RawFileStore_truncate, long, Current) - Method in class ome.services.blitz.impl.RawFileStoreI

truncate_async(AMD_RawFileStore_truncate, long, Current) - Method in class ome.services.blitz.repo.RepoRawFileStoreI

tSize - Variable in class ome.formats.importer.ImportSize

txSource - Variable in class ome.security.basic.EventHandler

type - Variable in class ome.services.query.QueryParameterDef

type of this parameter.

type - Variable in class ome.services.sharing.data.Obj

type() - Method in class ome.services.sharing.data.ObjHolder.Patcher

type() - Method in class ome.services.sharing.data.ShareDataHolder.Patcher

type - Variable in class ome.services.sharing.data.ShareItem

type() - Method in class ome.services.sharing.data.ShareItemHolder.Patcher

type - Variable in class ome.system.Principal

type - Variable in class omeis.providers.re.quantum.QuantumStrategy

The type of pixels this strategy is for.

type() - Method in interface omero.rtypes.Conversion

Specifies the type that can be expected from the rtypes.Conversion.convert(IceMapper) method.

typeCount(String) - Method in class ome.services.sharing.data.ShareItems

types - Variable in class ome.services.eventlogs.PersistentEventLogLoader

TypesI - Class in ome.services.blitz.impl

Implementation of the ITypes service.

TypesI(ITypes, BlitzExecutor) - Constructor for class ome.services.blitz.impl.TypesI

TypesImpl - Class in ome.logic

implementation of the ITypes service interface.

TypesImpl() - Constructor for class ome.logic.TypesImpl

U

UINT16 - Static variable in class omeis.providers.re.data.PlaneFactory

Identifies the UINT16 data type used to store pixel values, as per OME spec.

UINT16_TYPE - Static variable in class pojos.PixelsData

Identifies the type used to store pixel values.

UINT32 - Static variable in class omeis.providers.re.data.PlaneFactory

Identifies the UINT32 data type used to store pixel values, as per OME spec.

UINT32_TYPE - Static variable in class pojos.PixelsData

Identifies the type used to store pixel values.

UINT8 - Static variable in class omeis.providers.re.data.PlaneFactory

Identifies the UINT8 data type used to store pixel values, as per OME spec.

UINT8_TYPE - Static variable in class pojos.PixelsData

Identifies the type used to store pixel values.

UINT_16 - Static variable in class omerojava.util.PixelTypes

Identifies the type used to store pixel values.

UINT_32 - Static variable in class omerojava.util.PixelTypes

Identifies the type used to store pixel values.

UINT_8 - Static variable in class omerojava.util.PixelTypes

Identifies the type used to store pixel values.

UintConverter - Class in omerojava.util

Packs a sequence of bytes representing an unsigned big-endian integer into an integer value of appropriate integer type.

UintConverter() - Constructor for class omerojava.util.UintConverter

umask - Variable in class ome.system.SimpleEventContext

uncheckedCast(ObjectPrx) - Static method in class ome.services.sharing.data.ObjPrxHelper

uncheckedCast(ObjectPrx, String) - Static method in class ome.services.sharing.data.ObjPrxHelper

uncheckedCast(ObjectPrx) - Static method in class ome.services.sharing.data.ShareDataPrxHelper

uncheckedCast(ObjectPrx, String) - Static method in class ome.services.sharing.data.ShareDataPrxHelper

uncheckedCast(ObjectPrx) - Static method in class ome.services.sharing.data.ShareItemPrxHelper

uncheckedCast(ObjectPrx, String) - Static method in class ome.services.sharing.data.ShareItemPrxHelper

Union - Class in ome.services.search

Union SearchAction which combines two other search actions into one logical unit, e.g.

Union(SearchValues, SearchAction, SearchAction) - Constructor for class ome.services.search.Union

unique() - Method in class omero.sys.ParametersI

unique_alias(String) - Method in class ome.tools.hibernate.QueryBuilder

Obtain a unique alias to be used in the SQL.

UNKNOWN - Static variable in class pojos.FileAnnotationData

Indicates that the format is not recognized.

unlink(ILink[], Parameters) - Method in interface ome.api.IContainer

Removes links between OmeroDataObjects e.g Project-Dataset, Dataset-Image Note that the objects themselves aren't deleted, only the Link objects.

unlink(ILink[], Parameters) - Method in class ome.logic.PojosImpl

Implemented as specified by the IContainer I/F

unlink_async(AMD_IContainer_unlink, List<IObject>, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI

unload(Current) - Method in class omero.model.DetailsI

unload(Current) - Method in class omero.model.PermissionsI

UnloadedCollectionException - Exception in omero

UnloadedCollectionException(String) - Constructor for exception omero.UnloadedCollectionException

UnloadedEntityException - Exception in omero

UnloadedEntityException(String) - Constructor for exception omero.UnloadedEntityException

unloadedObjectCache - Variable in class ome.tools.hibernate.ProxyCleanupFilter

unloadReplacedObjects() - Method in class ome.tools.hibernate.UpdateFilter

provides an external hook to unload all files which have already been merged.

UNMAPPED - Static variable in class omero.util.IceMapper

Specifies a return type which should not be parsed.

unordered() - Method in interface ome.api.Search

Removes the current stack of order statements.

unordered() - Method in class ome.services.SearchBean

unordered_async(AMD_Search_unordered, Current) - Method in class ome.services.blitz.impl.SearchI

unregister(String, ObjectPrx) - Method in class ome.services.blitz.fire.TopicManager.Impl

unregister(String, ObjectPrx) - Method in interface ome.services.blitz.fire.TopicManager

unregister(Long, SqlAction) - Method in class ome.services.scripts.ScriptRepoHelper

Unregisters a given file from the script repository by setting its Repo uuid to null.

unregisterCallback(ProcessCallbackPrx, Current) - Method in class ome.services.blitz.impl.ScriptProcessI

unregisterCallback(ProcessCallback) - Method in interface ome.services.procs.Process

unregisterCallback(ProcessCallback) - Method in class ome.services.procs.ProcessSkeleton

unregisterServant(Identity) - Method in class ome.services.blitz.impl.ServiceFactoryI

Reverts all the additions made by #registerServant(ServantInterface, Ice.Current, Ice.Identity) Now called by SessionManagerI in response to an UnregisterServantMessage

UnregisterServantMessage - Class in ome.services.blitz.util

InternalMessage raised when a servant should be removed from the adapter.

UnregisterServantMessage(Object, Current) - Constructor for class ome.services.blitz.util.UnregisterServantMessage

unsetGroupOwner(ExperimenterGroup, Experimenter) - Method in interface ome.api.IAdmin

removes the user from the owner list for this group.

unsetGroupOwner(ExperimenterGroup, Experimenter) - Method in class ome.logic.AdminImpl

unsetGroupOwner_async(AMD_IAdmin_unsetGroupOwner, ExperimenterGroup, Experimenter, Current) - Method in class ome.services.blitz.impl.AdminI

update(IObservable, ImportEvent) - Method in interface ome.formats.importer.IObserver

Update observable on event

update(IObservable, ImportEvent) - Method in class ome.formats.importer.util.ErrorHandler

update(long) - Method in interface ome.formats.importer.util.FileUploadCounter.ProgressListener

update(IObservable, ImportEvent) - Method in class ome.services.blitz.repo.ImportableFiles

update(RepoFile, Long) - Method in class ome.services.scripts.ScriptRepoHelper

update(Session) - Method in interface ome.services.sessions.SessionManager

See ISession#updateSession(Session) for the logic that's implemented here.

update(Session, boolean) - Method in interface ome.services.sessions.SessionManager

Same as SessionManager.update(Session) but some security checks can be overriden.

update(Session) - Method in class ome.services.sessions.SessionManagerImpl

update(Session, boolean) - Method in class ome.services.sessions.SessionManagerImpl

update(Share, ShareData) - Method in class ome.services.sharing.ShareStore

update(String) - Method in class ome.tools.hibernate.QueryBuilder

update(CodomainMapContext) - Method in class omeis.providers.re.codomain.CodomainChain

Updates a map context in the chain.

UPDATE_EVENT - Static variable in class ome.security.basic.UpdateEventListener

updateCodomainMap(CodomainMapContext) - Method in class ome.services.RenderingBean

Implemented as specified by the RenderingEngine interface.

updateCodomainMap(CodomainMapContext) - Method in interface omeis.providers.re.RenderingEngine

Updates the specified context.

updateCodomainMap_async(AMD_RenderingEngine_updateCodomainMap, CodomainMapContext, Current) - Method in class ome.services.blitz.impl.RenderingEngineI

updateCodomainMap_async(AMD_RenderingEngine_updateCodomainMap, CodomainMapContext, Current) - Method in class ome.services.blitz.repo.BfRenderingEngineI

updateCollection(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

updateDataObject(T, Parameters) - Method in interface ome.api.IContainer

Updates a data object.

updateDataObject(IObject, Parameters) - Method in class ome.logic.PojosImpl

Implemented as specified by the IContainer I/F

updateDataObject_async(AMD_IContainer_updateDataObject, IObject, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI

updateDataObjects(IObject[], Parameters) - Method in interface ome.api.IContainer

convenience method to save network calls.

updateDataObjects(IObject[], Parameters) - Method in class ome.logic.PojosImpl

Implemented as specified by the IContainer I/F

updateDataObjects_async(AMD_IContainer_updateDataObjects, List<IObject>, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI

updatedObjects(int) - Method in class ome.services.sessions.stats.DelegatingStats

updatedObjects(int) - Method in class ome.services.sessions.stats.NullSessionStats

updatedObjects(int) - Method in interface ome.services.sessions.stats.SessionStats

updatedObjects(int) - Method in class ome.services.sessions.stats.SimpleSessionStats

updateEntity(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl

updateEnumeration(T) - Method in interface ome.api.ITypes

updates enumeration value specified by object

updateEnumeration(T) - Method in class ome.logic.TypesImpl

updateEnumeration_async(AMD_ITypes_updateEnumeration, IObject, Current) - Method in class ome.services.blitz.impl.TypesI

updateEnumerations(List<T>) - Method in interface ome.api.ITypes

updates enumeration value specified by object

updateEnumerations(List<T>) - Method in class ome.logic.TypesImpl

updateEnumerations_async(AMD_ITypes_updateEnumerations, List<IObject>, Current) - Method in class ome.services.blitz.impl.TypesI

updateEvent(UserGroupUpdateEvent) - Method in class ome.services.sessions.state.SessionCache

Marks a new update request in State#lastUpdateRequest.

UpdateEventListener - Class in ome.security.basic

responsible for setting the updat event on all events shortly before being saved.

UpdateEventListener(CurrentDetails) - Constructor for class ome.security.basic.UpdateEventListener

main constructor. controls access to individual db rows..

updateExperimenter(Experimenter) - Method in interface ome.api.IAdmin

Updates an experimenter if admin or owner of group.

updateExperimenter(Experimenter) - Method in class ome.logic.AdminImpl

updateExperimenter_async(AMD_IAdmin_updateExperimenter, Experimenter, Current) - Method in class ome.services.blitz.impl.AdminI

updateExperimenterWithPassword(Experimenter, String) - Method in interface ome.api.IAdmin

Updates an experimenter if admin or owner of group.

updateExperimenterWithPassword(Experimenter, String) - Method in class ome.logic.AdminImpl

updateExperimenterWithPassword_async(AMD_IAdmin_updateExperimenterWithPassword, Experimenter, RString, Current) - Method in class ome.services.blitz.impl.AdminI

UpdateFilter - Class in ome.tools.hibernate

responsible for correlating entity identities during multiple calls to merge.

UpdateFilter() - Constructor for class ome.tools.hibernate.UpdateFilter

updateFlexReaderServerMaps() - Method in class ome.formats.importer.util.IniFileLoader

Updates the Flex reader server maps from the configuration file.

updateGroup(ExperimenterGroup) - Method in interface ome.api.IAdmin

Updates an experimenter group if admin or owner of group.

updateGroup(ExperimenterGroup) - Method in class ome.logic.AdminImpl

updateGroup_async(AMD_IAdmin_updateGroup, ExperimenterGroup, Current) - Method in class ome.services.blitz.impl.AdminI

UpdateI - Class in ome.services.blitz.impl

Implementation of the IUpdate service.

UpdateI(IUpdate, BlitzExecutor) - Constructor for class ome.services.blitz.impl.UpdateI

UpdateImpl - Class in ome.logic

implementation of the IUpdate service interface

UpdateImpl() - Constructor for class ome.logic.UpdateImpl

updateMinMax(int, byte[], int) - Method in class ome.formats.importer.OMEROWrapper

updateObject(String, IObject, Map<String, Integer>) - Method in class ome.formats.OMEROMetadataStore

Updates a given model object in our object graph.

updateObject(T...) - Method in interface ome.security.SecureAction

executes with special privilegs within the SecuritySystem.

updateObject(T...) - Method in class ome.tools.hibernate.SecureMerge

updateObjects_async(AMD_MetadataStore_updateObjects, IObjectContainer[], Current) - Method in class ome.services.blitz.impl.MetadataStoreI

updatePixels(List<Pixels>) - Method in class ome.formats.OMEROMetadataStoreClient

Updates a list of Pixels.

updatePixels(Pixels, Current) - Method in class ome.services.blitz.gateway.OmeroGateway

updatePixels(Pixels) - Method in interface ome.services.blitz.gateway.services.DataService

Update the pixels object in the server.

updatePixels(Pixels) - Method in class ome.services.blitz.gateway.services.impl.DataServiceImpl

updateQuantumManager() - Method in class omeis.providers.re.Renderer

Updates the QuantumManager and configures it according to the current quantum definition.

updateReadFilter(Session) - Method in class ome.security.basic.BasicSecuritySystem

updateReferences(Map<String, String[]>) - Method in class ome.formats.OMEROMetadataStore

Updates our object graph references.

updateReferences_async(AMD_MetadataStore_updateReferences, Map<String, String[]>, Current) - Method in class ome.services.blitz.impl.MetadataStoreI

updateSelf(Experimenter) - Method in interface ome.api.IAdmin

Allows a user to update his/her own information.

updateSelf(Experimenter) - Method in class ome.logic.AdminImpl

updateSelf_async(AMD_IAdmin_updateSelf, Experimenter, Current) - Method in class ome.services.blitz.impl.AdminI

updateServerList(String) - Method in class ome.formats.importer.ImportConfig

Save the current serverList if the currentServer is not on the list.

updateSession(Session) - Method in class ome.services.sessions.SessionBean

UpgradeCheck - Class in ome.system

Contacts a given URL which should be an OME server which will return either an empty String or a URL which points to a needed upgrade.

UpgradeCheck(String, String, String) - Constructor for class ome.system.UpgradeCheck

Calls UpgradeCheck.UpgradeCheck(String, String, String, int) using UpgradeCheck.DEFAULT_TIMEOUT

UpgradeCheck(String, String, String, int) - Constructor for class ome.system.UpgradeCheck

Main constructor.

upload(File) - Method in class omero.client

upload(File, OriginalFile) - Method in class omero.client

upload(File, OriginalFile, Integer) - Method in class omero.client

Utility method to upload a file to the server

uploadedBytes - Variable in class ome.formats.importer.ImportEvent.FILE_UPLOAD_EVENT

uploadFiles(String, int, ErrorContainer) - Method in class ome.formats.importer.util.FileUploader

Upload files from error container to url

UploadMask - Class in pojos.util

Uploaded for masks.

UploadMask(long) - Constructor for class pojos.util.UploadMask

Creates a new instance.

uploadMask_async(AMD_IRoi_uploadMask, long, int, int, byte[], Current) - Method in class ome.services.blitz.impl.RoiI

uploadMyUserPhoto(String, String, byte[]) - Method in interface ome.api.IAdmin

Uploads a photo for the user which will be displayed on his/her profile.

uploadMyUserPhoto(String, String, byte[]) - Method in class ome.logic.AdminImpl

uploadMyUserPhoto_async(AMD_IAdmin_uploadMyUserPhoto, String, String, byte[], Current) - Method in class ome.services.blitz.impl.AdminI

uploadOfficialScript_async(AMD_IScript_uploadOfficialScript, String, String, Current) - Method in class ome.services.blitz.impl.ScriptI

uploadPlane(long, int, int, int, byte[], Current) - Method in class ome.services.blitz.gateway.OmeroGateway

uploadPlane(long, int, int, int, byte[]) - Method in interface ome.services.blitz.gateway.services.ImageService

Upload the plane to the server, on pixels id with channel and the time, + z section. the data is the client 2d data values.

uploadPlane(long, int, int, int, byte[]) - Method in class ome.services.blitz.gateway.services.impl.ImageServiceImpl

Upload the plane to the server, on pixels id with channel and the time, + z section. the data is the client 2d data values.

uploadScript_async(AMD_IScript_uploadScript, String, String, Current) - Method in class ome.services.blitz.impl.ScriptI

Upload script to the server.

usage() - Static method in class ome.services.fulltext.Main

usage(String[]) - Static method in class prefs

Returns a usage string array.

useCustomImageNaming - Variable in class ome.formats.importer.ImportConfig

usedFiles - Variable in class ome.formats.importer.util.ErrorHandler.FILE_EXCEPTION

usedFiles - Variable in class ome.formats.importer.util.ErrorHandler.INTERNAL_EXCEPTION

useFullPath - Variable in class ome.formats.importer.ImportConfig

useProjections - Variable in class ome.services.search.SearchValues

user - Variable in class ome.services.messages.LoginAttemptMessage

USER - Static variable in class pojos.GroupData

Identifies the User group.

userGroups(String) - Method in class ome.security.auth.PasswordUtil

UserGroupUpdateEvent - Class in ome.services.sessions.events

InteralMessage published by the SecuritySystem when an Experimenter, ExperimenterGroup, or GroupExperimenterMap is inserted or updated.

UserGroupUpdateEvent(Object) - Constructor for class ome.services.sessions.events.UserGroupUpdateEvent

userId(String) - Method in class ome.security.auth.PasswordUtil

username - Variable in class ome.formats.importer.ImportConfig

username() - Method in class omero.util.TempFileManager

Returns the current OS-user's name.

usernameFilter(String) - Method in class ome.security.auth.LdapConfig

userPixels - Variable in class ome.formats.importer.ImportConfig

userProxy(String) - Method in interface ome.api.local.LocalAdmin

returns a possibly uninitialized proxy for the given user name.

userProxy(Long) - Method in interface ome.api.local.LocalAdmin

returns a possibly uninitialized proxy for the given user id.

userProxy(Long) - Method in class ome.logic.AdminImpl

userProxy(String) - Method in class ome.logic.AdminImpl

util - Variable in class ome.security.auth.ConfigurablePasswordProvider

Utils - Class in ome.io.nio

General utility methods for working with ROMIO classes.

Utils() - Constructor for class ome.io.nio.Utils

uuid - Variable in class ome.services.blitz.fire.Ring

UUID for this cluster node.

uuid() - Method in class ome.services.blitz.fire.Ring

uuid() - Method in interface ome.services.blitz.redirect.Redirector.Context

The UUID for the local node which will be used as the redirect lookup string for this Redirector.Context.

uuid - Variable in class ome.services.roi.GeomTool

V

valid(String) - Method in class ome.services.db.DatabaseIdentity

Validate - Annotation Type in ome.annotations

annotation used for determining the types of a Set

validatePassword(String, String) - Method in class ome.logic.LdapImpl

Validates password for base.

validateScript_async(AMD_IScript_validateScript, Job, List<IObject>, Current) - Method in class ome.services.blitz.impl.ScriptI

value(String) - Method in class ome.services.query.Query

get the Object value for this name argument.

value - Variable in class ome.services.sharing.data.IdMapHolder

value - Variable in class ome.services.sharing.data.LongSeqHolder

value - Variable in class ome.services.sharing.data.ObjHolder

value - Variable in class ome.services.sharing.data.ObjPrxHolder

value - Variable in class ome.services.sharing.data.ObjSeqHolder

value - Variable in class ome.services.sharing.data.ShareDataHolder

value - Variable in class ome.services.sharing.data.ShareDataPrxHolder

value - Variable in class ome.services.sharing.data.ShareItemHolder

value - Variable in class ome.services.sharing.data.ShareItemPrxHolder

value - Variable in class ome.services.sharing.data.StringSeqHolder

valueMapper - Variable in class omeis.providers.re.quantum.QuantumStrategy

Reference to the value mapper.

valueOf(String) - Static method in enum ome.formats.Index

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ome.services.graphs.GraphOpts.Op

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ome.system.Preference.Visibility

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum omero.grid.ProcessCallbackI.Action

Returns the enum constant of this type with the specified name.

values() - Method in class ome.formats.importer.ImportConfig

values() - Static method in enum ome.formats.Index

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum ome.services.graphs.GraphOpts.Op

Returns an array containing the constants of this enum type, in the order they are declared.

values - Variable in class ome.services.search.SearchAction

values() - Static method in enum ome.system.Preference.Visibility

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum omero.grid.ProcessCallbackI.Action

Returns an array containing the constants of this enum type, in the order they are declared.

vec(PlanePoint) - Method in class ome.util.math.geom2D.PlanePoint

Calculates the vector associated to this point and the specified argument.

vec(double, double) - Method in class ome.util.math.geom2D.PlanePoint

Calculates the vector associated to this point and the specified argument.

verbose - Variable in class ome.tools.hibernate.EventMethodInterceptor

Version - Class in ome.formats.importer

Version() - Constructor for class ome.formats.importer.Version

Version - Class in ome.system

static utililty for checking Omero classes for revision number and date.

Version() - Constructor for class ome.system.Version

VERSION_REGEX - Static variable in interface ome.api.IConfig

Defines how the omero.version Preference will be parsed into the form: Major.minor.patch for IConfig.getVersion()

versionNote - Static variable in class ome.formats.importer.Version

VOID - Static variable in class omero.util.IceMapper

W

waitForLock - Variable in class ome.services.fulltext.FullTextThread

WAITING - Static variable in interface ome.api.JobHandle

walk() - Method in class ome.services.graphs.BaseGraphSpec

walk() - Method in interface ome.services.graphs.GraphSpec

Returns an iterator over all subspecs and their subspecs, depth-first.

warmUpFactor - Variable in class ome.io.nio.SimpleBackOff

warning(String) - Method in class ome.services.blitz.util.CommonsLoggingAdapter

wasCancelled() - Method in class ome.formats.importer.ImportCandidates

WellData - Class in pojos

The data that makes up an OME Well and the Experimenter that owns this Well.

WellData() - Constructor for class pojos.WellData

Creates a new instance.

WellData(Well) - Constructor for class pojos.WellData

Creates a new instance.

WellProcessor - Class in ome.formats.model

Processes the Wells of an IObjectContainerStore and ensures that the Plate has been populated and that it is validated and that if any PlateAcquisition objects are in the hierarchy that they have a name.

WellProcessor() - Constructor for class ome.formats.model.WellProcessor

WELLS - Static variable in class pojos.PlateData

Identifies the Plate#WELLS field.

WellSampleData - Class in pojos

The data that makes up an OME WellSample along with links to its images and the Experimenter that owns this WellSample.

WellSampleData() - Constructor for class pojos.WellSampleData

Creates a new instance.

WellSampleData(WellSample) - Constructor for class pojos.WellSampleData

Creates a new instance.

where() - Method in class ome.tools.hibernate.QueryBuilder

Marks the end of all fetches by adding a "where" clause to the string.

work - Variable in class ome.services.util.ExecutionThread

WorkflowData - Class in pojos

The data that makes up an OME worflow object.

WorkflowData(Namespace) - Constructor for class pojos.WorkflowData

Creates a new instance.

WorkflowData(String, List<String>) - Constructor for class pojos.WorkflowData

Creates a new instance.

WorkflowData(String, String) - Constructor for class pojos.WorkflowData

Creates a new instance.

WorkflowData() - Constructor for class pojos.WorkflowData

Creates a new instance.

wrap(String, IObject) - Method in class ome.services.eventlogs.AllEntitiesPseudoLogLoader

wrap(Iterator<Reader>) - Method in class ome.services.fulltext.FileParser

Wraps an Iterator with an Iterable instance.

wrap(Reader) - Method in class ome.services.fulltext.FileParser

write(byte[], long, int) - Method in interface ome.api.RawFileStore

Delegates to FileBuffer

write(byte[], int, int) - Method in class ome.formats.importer.util.FileUploadCounter.OutputStreamCounter

write(int) - Method in class ome.formats.importer.util.FileUploadCounter.OutputStreamCounter

write(ByteBuffer, long) - Method in class ome.io.nio.FileBuffer

Delegates to FileChannel

write(ByteBuffer) - Method in class ome.io.nio.FileBuffer

Delegates to FileChannel

write(long, byte[], long, int) - Method in class ome.services.blitz.gateway.services.impl.RawFileStoreServiceImpl

write(long, byte[], long, int) - Method in interface ome.services.blitz.gateway.services.RawFileStoreService

Write the contents of the buffer to the the file starting from position and for length bytes.

write(String, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI

write(byte[], long, int) - Method in class ome.services.RawFileBean

write(String, String) - Method in class ome.services.scripts.ScriptRepoHelper

write(RepoFile, String) - Method in class ome.services.scripts.ScriptRepoHelper

write(BasicStream, Map<String, List<Long>>) - Static method in class ome.services.sharing.data.IdMapHelper

write(BasicStream, List<Long>) - Static method in class ome.services.sharing.data.LongSeqHelper

write(BasicStream, List<Obj>) - Static method in class ome.services.sharing.data.ObjSeqHelper

write(BasicStream, List<String>) - Static method in class ome.services.sharing.data.StringSeqHelper

write_async(AMD_RawFileStore_write, byte[], long, int, Current) - Method in class ome.services.blitz.impl.RawFileStoreI

write_async(AMD_RawFileStore_write, byte[], long, int, Current) - Method in class ome.services.blitz.repo.RepoRawFileStoreI

writeFilesToFileStore(List<File>, Map<String, OriginalFile>) - Method in class ome.formats.OMEROMetadataStoreClient

Writes binary original file data to the OMERO server.

writeImage(BufferedImage, TranscoderOutput) - Method in class ome.services.SVGRasterizer.Rasterizer

writeLine(String) - Method in class ome.services.blitz.repo.FileMaker

writer - Variable in class ome.io.bioformats.BfPyramidPixelBuffer

Bio-Formats implementation used to write to the backing TIFF.

writeRequest(OutputStream) - Method in class ome.formats.importer.util.FileUploadCounter

writtenBytes(int) - Method in class ome.services.sessions.stats.DelegatingStats

writtenBytes(int) - Method in class ome.services.sessions.stats.NullSessionStats

writtenBytes(int) - Method in interface ome.services.sessions.stats.SessionStats

writtenBytes(int) - Method in class ome.services.sessions.stats.SimpleSessionStats

wSize - Variable in class ome.formats.importer.ImportSize

X

x1 - Variable in class ome.util.math.geom2D.PlanePoint

The first element.

x2 - Variable in class ome.util.math.geom2D.PlanePoint

The second element.

XML - Static variable in class pojos.FileAnnotationData

Identifies the XML file formats.

XMLAnnotationData - Class in pojos

Defines an XML Annotation.

XMLAnnotationData() - Constructor for class pojos.XMLAnnotationData

Creates a new instance.

XMLAnnotationData(String) - Constructor for class pojos.XMLAnnotationData

Creates a new instance.

XMLAnnotationData(XmlAnnotation) - Constructor for class pojos.XMLAnnotationData

Creates a new instance.

XY - Static variable in class omeis.providers.re.data.PlaneDef

Flag to identify an XY-plane.

XZ - Static variable in class omeis.providers.re.data.PlaneDef

Flag to identify an XZ-plane.

Z

zero() - Method in class omeis.providers.re.RGBAIntBuffer

zero() - Method in class omeis.providers.re.RGBBuffer

Zeros out (sets every pixel offset to zero) each band.

zero() - Method in class omeis.providers.re.RGBIntBuffer

zSize - Variable in class ome.formats.importer.ImportSize

ZY - Static variable in class omeis.providers.re.data.PlaneDef

Flag to identify an YZ-plane.

_

__createDelegateD() - Method in class ome.services.sharing.data.ObjPrxHelper

__createDelegateD() - Method in class ome.services.sharing.data.ShareDataPrxHelper

__createDelegateD() - Method in class ome.services.sharing.data.ShareItemPrxHelper

__createDelegateM() - Method in class ome.services.sharing.data.ObjPrxHelper

__createDelegateM() - Method in class ome.services.sharing.data.ShareDataPrxHelper

__createDelegateM() - Method in class ome.services.sharing.data.ShareItemPrxHelper

__del__() - Method in class omero.client

Calls closeSession() and ignores any exceptions.

__dont_use_me_factory - Variable in class ome.services.sharing.BlobShareStore

Used indirectly to obtain sessions for querying and updating the store during normal operation.

__ids - Static variable in class ome.services.sharing.data.Obj

__ids - Static variable in class ome.services.sharing.data.ShareData

__ids - Static variable in class ome.services.sharing.data.ShareItem

__read(BasicStream, boolean) - Method in class ome.services.sharing.data.Obj

__read(InputStream, boolean) - Method in class ome.services.sharing.data.Obj

__read(BasicStream) - Static method in class ome.services.sharing.data.ObjPrxHelper

__read(BasicStream, boolean) - Method in class ome.services.sharing.data.ShareData

__read(InputStream, boolean) - Method in class ome.services.sharing.data.ShareData

__read(BasicStream) - Static method in class ome.services.sharing.data.ShareDataPrxHelper

__read(BasicStream, boolean) - Method in class ome.services.sharing.data.ShareItem

__read(InputStream, boolean) - Method in class ome.services.sharing.data.ShareItem

__read(BasicStream) - Static method in class ome.services.sharing.data.ShareItemPrxHelper

__redirect(long, _RawFileStoreTie, Current) - Method in class ome.services.blitz.impl.RawFileStoreI

__write(BasicStream) - Method in class ome.services.sharing.data.Obj

__write(OutputStream) - Method in class ome.services.sharing.data.Obj

__write(BasicStream, ObjPrx) - Static method in class ome.services.sharing.data.ObjPrxHelper

__write(BasicStream) - Method in class ome.services.sharing.data.ShareData

__write(OutputStream) - Method in class ome.services.sharing.data.ShareData

__write(BasicStream, ShareDataPrx) - Static method in class ome.services.sharing.data.ShareDataPrxHelper

__write(BasicStream) - Method in class ome.services.sharing.data.ShareItem

__write(OutputStream) - Method in class ome.services.sharing.data.ShareItem

__write(BasicStream, ShareItemPrx) - Static method in class ome.services.sharing.data.ShareItemPrxHelper

_addGraph(ShareData, ShareBean.Graph) - Method in class ome.services.sharing.ShareBean

_ObjDel - Interface in ome.services.sharing.data

_ObjDelD - Class in ome.services.sharing.data

_ObjDelD() - Constructor for class ome.services.sharing.data._ObjDelD

_ObjDelM - Class in ome.services.sharing.data

_ObjDelM() - Constructor for class ome.services.sharing.data._ObjDelM

_ShareDataDel - Interface in ome.services.sharing.data

_ShareDataDelD - Class in ome.services.sharing.data

_ShareDataDelD() - Constructor for class ome.services.sharing.data._ShareDataDelD

_ShareDataDelM - Class in ome.services.sharing.data

_ShareDataDelM() - Constructor for class ome.services.sharing.data._ShareDataDelM

_ShareItemDel - Interface in ome.services.sharing.data

_ShareItemDelD - Class in ome.services.sharing.data

_ShareItemDelD() - Constructor for class ome.services.sharing.data._ShareItemDelD

_ShareItemDelM - Class in ome.services.sharing.data

_ShareItemDelM() - Constructor for class ome.services.sharing.data._ShareItemDelM

_wait(Current) - Method in class ome.services.blitz.impl.ScriptProcessI

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