Index (OMERO (OME Remote Objects) Server)

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
AbstractChecksumProvider - Class in ome.util.checksum: Abstract skeleton class implementing ChecksumProvider and providing implementations of the interface methods using a universal checksum class object.
AbstractChecksumProvider(HashFunction) - Constructor for class ome.util.checksum.AbstractChecksumProvider: Protected ctor.
AbstractClassIdsOptionsQuery - Class in ome.services.query: simple abstract class that provides a common Definitions containing: IdsQueryParameterDef, ome.services.query.OptionsQueryParameterDef, and ClassQueryParameterDef.
AbstractClassIdsOptionsQuery(Parameters) - Constructor for class ome.services.query.AbstractClassIdsOptionsQuery
AbstractCloseableAmdServant - Class in ome.services.blitz.impl: Base class for all servants that must guarantee proper clean-up of held resources on close.
AbstractCloseableAmdServant(ServiceInterface, BlitzExecutor) - Constructor for class ome.services.blitz.impl.AbstractCloseableAmdServant
AbstractExecFileTransfer - Class in ome.formats.importer.transfers: Local-only file transfer mechanism which makes use of soft-linking.
AbstractExecFileTransfer() - Constructor for class ome.formats.importer.transfers.AbstractExecFileTransfer
AbstractFileDeletions - Class in ome.services.delete.files: Base class for managing the removal of files from disk.
AbstractFileDeletions(AbstractFileSystemService, Set<Long>) - Constructor for class ome.services.delete.files.AbstractFileDeletions
AbstractFileExclusion - Class in ome.formats.importer.exclusions: Base FileExclusion implementation primarily providing a factory for FileExclusion implementations via AbstractFileExclusion.createExclusion(String).
AbstractFileExclusion() - Constructor for class ome.formats.importer.exclusions.AbstractFileExclusion
AbstractFileExclusion.Exclusion - Enum in ome.formats.importer.exclusions: Enum of well-known FileExclusion names.
AbstractFileSystemService - Class in ome.io.nio
AbstractFileSystemService(String) - Constructor for class ome.io.nio.AbstractFileSystemService
AbstractFileTransfer - Class in ome.formats.importer.transfers: Base FileTransfer implementation primarily providing the AbstractFileTransfer.start(TransferState) and AbstractFileTransfer.finish(TransferState, long) methods.
AbstractFileTransfer() - Constructor for class ome.formats.importer.transfers.AbstractFileTransfer
AbstractFileTransfer.Transfers - Enum in ome.formats.importer.transfers: Enum of well-known FileTransfer names.
AbstractHierarchyGraphSpec - Class in ome.services.graphs: Deprecated.
will be removed in OMERO 5.2, so use the new graphs implementation
AbstractHierarchyGraphSpec(List<String>) - Constructor for class ome.services.graphs.AbstractHierarchyGraphSpec: Deprecated.

Creates a new instance.
AbstractLevel1Service - Class in ome.logic: service level 1
AbstractLevel1Service() - Constructor for class ome.logic.AbstractLevel1Service
AbstractLevel2Service - Class in ome.logic: service level 2
AbstractLevel2Service() - Constructor for class ome.logic.AbstractLevel2Service
AbstractPyramidServant - Class in ome.services.blitz.impl: Specialization of AbstractAmdServant to be used by any services which provide the PyramidService interface.
AbstractPyramidServant(ServiceInterface, BlitzExecutor) - Constructor for class ome.services.blitz.impl.AbstractPyramidServant
AbstractRedirector - Class in ome.services.blitz.redirect: 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, Principal, String, PublicRepositoryI) - Constructor for class ome.services.blitz.repo.AbstractRepositoryI
AbstractRepositoryI(ObjectAdapter, Registry, Executor, Principal, FileMaker, PublicRepositoryI) - Constructor for class ome.services.blitz.repo.AbstractRepositoryI
AbstractSecurityFilter - Class in ome.security.basic: overrides FilterDefinitionFactoryBean in order to construct our security filter in code and not in XML.
AbstractSecurityFilter() - Constructor for class ome.security.basic.AbstractSecurityFilter: default constructor which calls all the necessary setters for this FactoryBean.
AbstractSecurityFilter(Roles) - Constructor for class ome.security.basic.AbstractSecurityFilter
AbstractSessionMessage - Class in ome.services.messages: InternalMessage implementations which carry relate to some Session bound event.
AbstractSessionMessage(Object, String) - Constructor for class ome.services.messages.AbstractSessionMessage
AbstractStatefulBean - Class in ome.services: Base bean implementation for stateful services.
AbstractStatefulBean() - Constructor for class ome.services.AbstractStatefulBean
AbstractStatsMessage - Class in ome.services.messages.stats: Published when some limit in user/group/session activity has been reached.
AbstractStatsMessage(Object) - Constructor for class ome.services.messages.stats.AbstractStatsMessage
AbstractStatsMessage(Object, boolean) - Constructor for class ome.services.messages.stats.AbstractStatsMessage
AbstractStepFactory - Class in ome.services.graphs: Deprecated.
will be removed in OMERO 5.2, so use the new graphs implementation
AbstractStepFactory() - Constructor for class ome.services.graphs.AbstractStepFactory: Deprecated.
AbstractThrottlingStrategy - Class in ome.services.throttling: Throttling implementation which uses the calling server Thread for execution.
AbstractThrottlingStrategy() - Constructor for class ome.services.throttling.AbstractThrottlingStrategy
accept(String, String) - Method in class ome.services.mail.MapAnnotationSubethaListener: Accepts all mails.
accept(Job) - Method in class ome.services.procs.ProcessorSkeleton
access(File) - Method in class omero.util.TempFileManager: Returns true if the current user can write to the give directory.
acl - Variable in class ome.tools.hibernate.ProxyCleanupFilter
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() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
acquireLock(String) - Method in class omero.util.ServantHolder: Acquires the given lock or if necessary creates a new one.
acquireProcessor(Job, int, Current) - Method in class ome.services.blitz.impl.SharedResourcesI
acquireProcessor(Job, int, Current) - Method in interface omero.grid.ParamsHelper.Acquirer
acquirer() - Method in class ome.services.blitz.impl.ScriptI
acquisitionData() - Method in class omero.sys.ParametersI: Sets the acquisition data parameter to true.
action(GraphStep.Callback, Session, SqlAction, GraphOpts) - Method in class ome.services.chgrp.ChgrpStep: Deprecated.
action(GraphStep.Callback, Session, SqlAction, GraphOpts) - Method in class ome.services.chown.ChownStep: Deprecated.
action(GraphStep.Callback, Session, SqlAction, GraphOpts) - Method in class ome.services.delete.DeleteStep: Deprecated.
action(GraphStep.Callback, Session, SqlAction, GraphOpts) - Method in class ome.services.export.ExporterStep: Deprecated.
action - Variable in class ome.services.graphs.GraphPolicy.Details: the current plan for the object, may be mutated by Policy#review(Map, Details, Map, Set)
action(GraphStep.Callback, Session, SqlAction, GraphOpts) - Method in class ome.services.graphs.GraphStep: Deprecated.

Primary action which should perform the main modifications required by the step.
action - Variable in class ome.services.messages.EventLogMessage
action - Variable in class ome.tools.hibernate.EventMethodInterceptor
activate(long) - Method in interface ome.api.IShare: Turns on the access control lists attached to the given share for the current session.
activate() - Method in interface ome.api.StatefulServiceInterface: Completely restore this service for active use from whatever passivation it has implemented.
activate() - Method in class ome.services.JobBean: Does almost nothing.
activate() - Method in class ome.services.RawFileBean
activate() - Method in class ome.services.RawPixelsBean
activate() - Method in class ome.services.RenderingBean
activate() - Method in class ome.services.SearchBean
activate(long) - Method in class ome.services.sharing.ShareBean
activate() - Method in class ome.services.ThumbnailBean
activate_async(AMD_StatefulServiceInterface_activate, Current) - Method in class ome.services.blitz.impl.AbstractAmdServant
activate_async(AMD_IShare_activate, long, Current) - Method in class ome.services.blitz.impl.ShareI
activate_async(AMD_StatefulServiceInterface_activate, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
activateAndWait(Current) - Method in class ome.services.blitz.impl.ProcessorCallbackI: Generates a UUID-based Identity with the category of PROCESSORCALLBACK.value and then calls {@link #activateAndWait(Current, Ice.Identity).
activateAndWait(Current, Identity) - Method in class ome.services.blitz.impl.ProcessorCallbackI: Primary method which adds this instance to IceStorm, waits for a response from any active processor services, and finally unregister itself before returning the first processor instance which responded.
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
adapter - Variable in class omero.cmd.SessionI
add(EventLog) - Method in class ome.services.eventlogs.EventBacklog: Adds the given EventLog instance to the end of a queue for later popping if no equivalent EventLog is present.
add(GraphStep, long[]) - Method in class ome.services.export.ExporterIndex: Deprecated.
add(Document, String, String, LuceneOptions) - Method in class ome.services.fulltext.BridgeHelper: Helper method which takes the parameters from the #set(String, Object, Document, Store, org.apache.lucene.document.Field.Index, Float) method (possibly modified) as well as the parsed String value which should be added to the index, and adds two fields.
add() - Method in class ome.services.graphs.GraphState: Deprecated.
add() - Method in interface ome.services.graphs.GraphStep.Callback: Deprecated.
add(GraphEntry, long[][]) - Method in class ome.services.graphs.GraphTables: Deprecated.
add(CodomainMapContext) - Method in class omeis.providers.re.codomain.CodomainChain: Adds a map context to the chain.
add(String, RType) - Method in class omero.sys.ParametersI
add(Resources.Entry) - Method in class omero.util.Resources
addAction(SearchAction) - Method in class ome.services.SearchBean
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
addCallback(CmdCallbackPrx, Current) - Method in class omero.cmd.HandleI
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.
addClientId(String) - Method in class omero.util.ServantHolder
addCodomainMap(CodomainMapContext) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
addCodomainMap(CodomainMapContext) - Method in interface omeis.providers.re.RenderingEngine: Adds the context to the mapping chain.
addCodomainMap_async(AMD_RenderingEngine_addCodomainMap, CodomainMapContext, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
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.
addEventLog(Class<? extends IObject>, long) - Method in class ome.services.eventlogs.EventLogQueue: Only schedule a new backlog event if there is no currently registered event of that type.
addFile(String) - Method in class ome.formats.importer.util.ErrorContainer
addGraphIds(GraphStep) - Method in class ome.services.graphs.GraphState: Deprecated.

Add the actually processed ids to the current savepoint.
addGraphIds(GraphStep) - Method in interface ome.services.graphs.GraphStep.Callback: Deprecated.
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.
addLocalFile(File, long) - Method in class ome.services.delete.files.AbstractFileDeletions: Called during the creation of instances if a particular file should be handled by AbstractFileDeletions.deleteLocal().
addLog(String, Class, Long) - Method in class ome.security.basic.BasicSecuritySystem
addLog(String, Class, Long) - Method in class ome.security.basic.CurrentDetails
addLong(String, long) - Method in class 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(Session, SqlAction, ServiceFactory, RepoFile, Long) - Method in class ome.services.scripts.ScriptRepoHelper
addParameters(Parameters) - Method in class ome.services.SearchBean
addProcess(ProcessContainer.Process) - Method in class ome.services.blitz.repo.ProcessContainer: Called once the ManagedImportProcessI service is created.
addProcessor(ProcessorPrx, Current) - Method in class ome.services.blitz.impl.SharedResourcesI
addProject(String, String) - Method in class ome.formats.OMEROMetadataStoreClient
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.
addToTargets(String, long) - Method in class omero.cmd.graphs.ChgrpFacadeI: Deprecated.

Add the given model object to the chgrp request's target objects.
addToTargets(String, long) - Method in class omero.cmd.graphs.ChmodFacadeI: Deprecated.

Add the given model object to the chmod request's target objects.
addToTargets(String, long) - Method in class omero.cmd.graphs.ChownFacadeI: Deprecated.

Add the given model object to the chown request's target objects.
addToTargets(String, long) - Method in class omero.cmd.graphs.DeleteFacadeI: Deprecated.

Add the given model object to the delete request's target objects.
addUser(long, Experimenter) - Method in interface ome.api.IShare: Adds experimenter to share
addUser(Set<String>, Experimenter) - Method in class ome.services.mail.MailSender
addUser(Set<String>, Experimenter) - Method in class ome.services.mail.ObjectMailSender
addUser(long, Experimenter) - Method in class ome.services.sharing.ShareBean
addUser_async(AMD_IShare_addUser, long, Experimenter, Current) - Method in class ome.services.blitz.impl.ShareI
addUsers(long, Experimenter...) - Method in interface ome.api.IShare: 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
adjustGraphPolicy(Function<GraphPolicy, GraphPolicy>) - Method in class omero.cmd.graphs.Chgrp2I
adjustGraphPolicy(Function<GraphPolicy, GraphPolicy>) - Method in class omero.cmd.graphs.Chmod2I
adjustGraphPolicy(Function<GraphPolicy, GraphPolicy>) - Method in class omero.cmd.graphs.Chown2I
adjustGraphPolicy(Function<GraphPolicy, GraphPolicy>) - Method in class omero.cmd.graphs.Delete2I
adjustGraphPolicy(Function<GraphPolicy, GraphPolicy>) - Method in interface omero.cmd.graphs.WrappableRequest: Transform the currently applicable graph policy for this request by the given function.
Adler32ChecksumProviderImpl - Class in ome.util.checksum: An implementation of the ChecksumProvider interface using Adler32 as the message digest algorithm.
Adler32ChecksumProviderImpl() - Constructor for class ome.util.checksum.Adler32ChecksumProviderImpl
admin - Variable in class ome.services.delete.DeleteBean
admin - Variable in class ome.services.sharing.ShareBean
AdminAction - Interface in ome.security: 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, ChmodStrategy, ChecksumProviderFactory) - Constructor for class ome.logic.AdminImpl
advices - Variable in class ome.services.util.Executor.Impl
advUsage() - Static method in class ome.formats.importer.cli.CommandLineImporter: Prints advanced usage to STDERR and exits with return code 1.
afs - Variable in class ome.services.delete.Deletion.Builder: Deprecated.
afs - Variable in class ome.services.delete.files.AbstractFileDeletions
afterPropertiesSet() - Method in class ome.security.KeyAndTrustStoreConfiguration
afterPropertiesSet() - Method in class ome.system.metrics.DefaultMetrics
afterTransactionBegin(Transaction) - Method in class ome.security.basic.OmeroInterceptor
afterTransactionCompletion(Transaction) - Method in class ome.security.basic.OmeroInterceptor
afterTransfer(int, List<String>) - Method in class ome.formats.importer.transfers.CopyFileTransfer: No cleanup action is taken.
afterTransfer(int, List<String>) - Method in class ome.formats.importer.transfers.CopyMoveFileTransfer: Deletes all copied files if there were no errors.
afterTransfer(int, List<String>) - Method in interface ome.formats.importer.transfers.FileTransfer: Callback which must be invoked after a related set of files has been processed.
afterTransfer(int, List<String>) - Method in class ome.formats.importer.transfers.HardlinkFileTransfer: No cleanup action is taken.
afterTransfer(int, List<String>) - Method in class ome.formats.importer.transfers.MoveFileTransfer: Deletes all hard-linked files if there were no errors.
afterTransfer(int, List<String>) - Method in class ome.formats.importer.transfers.SymlinkFileTransfer: No cleanup is needed for soft-linking.
afterTransfer(int, List<String>) - Method in class ome.formats.importer.transfers.UploadFileTransfer: Since the RawFileStorePrx instances are cleaned up after each transfer, there's no need to cleanup per File.
afterTransfer(int, List<String>) - Method in class ome.formats.importer.transfers.UploadRmFileTransfer: Deletes all uploaded files if there were no errors.
agent - Variable in class ome.formats.importer.ImportConfig
agent - Variable in class ome.services.sessions.SessionManager.CreationRequest
aggByQuery(String, String, String, Parameters) - Method in class ome.logic.QueryImpl
aggMapByQuery(String, String, String, String, Parameters) - Method in class ome.logic.QueryImpl
all(String[]) - Static method in class prefs: Calls Preferences.childrenNames() and returns the array.
ALL_PROJECTIONS - Static variable in class ome.services.search.FullText
AllEntitiesPseudoLogLoader<T extends 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.
allgroups - Variable in class ome.security.SecurityFilterHolder
AllGroupsSecurityFilter - Class in ome.security.basic: overrides FilterDefinitionFactoryBean in order to construct our security filter in code and not in XML.
AllGroupsSecurityFilter(SqlAction) - Constructor for class ome.security.basic.AllGroupsSecurityFilter: default constructor which calls all the necessary setters for this FactoryBean.
AllGroupsSecurityFilter(SqlAction, Roles) - Constructor for class ome.security.basic.AllGroupsSecurityFilter
allGrps() - Method in class omero.sys.ParametersI: Removes the group parameter from the map.
allObjects(Collection<Set<GraphPolicy.Details>>, GraphPolicy.Details, Collection<Set<GraphPolicy.Details>>) - Static method in class ome.services.graphs.GraphPolicy: Utility method to return all the objects for review as a single set of objects.
allow(ObjectPrx) - Method in class omero.cmd.SessionI
ALLOW_LEADING_WILDCARD - Static variable in interface ome.api.Search: Default leading-wildcard setting
allowAdministration() - Method in class ome.services.blitz.Router
allowAnnotate(IObject, Details) - Method in interface ome.security.ACLVoter: test whether the given object should be annotatable given the trusted details.
allowAnnotate(IObject, Details) - Method in class ome.security.basic.BasicACLVoter
allowAnnotate(IObject, Details) - Method in class ome.security.CompositeACLVoter
allowAnnotate(IObject, Details) - Method in class ome.security.sharing.SharingACLVoter
allowChmod(IObject) - Method in interface ome.security.ACLVoter: test whether the given object can have its Permissions changed within the current security context.
allowChmod(IObject) - Method in class ome.security.basic.BasicACLVoter
allowChmod(IObject) - Method in class ome.security.CompositeACLVoter
allowChmod(IObject) - Method in class ome.security.sharing.SharingACLVoter
allowCreation(IObject) - Method in interface ome.security.ACLVoter: test whether the given object should be insertable into the DB.
allowCreation(IObject) - Method in class ome.security.basic.BasicACLVoter
allowCreation(IObject) - Method in class ome.security.CompositeACLVoter
allowCreation(IObject) - Method in class ome.security.sharing.SharingACLVoter
allowDelete(IObject, Details) - Method in interface ome.security.ACLVoter: test whether the given object should be deleteable given the trusted details.
allowDelete(IObject, Details) - Method in class ome.security.basic.BasicACLVoter
allowDelete(IObject, Details) - Method in class ome.security.CompositeACLVoter
allowDelete(IObject, Details) - Method in class ome.security.sharing.SharingACLVoter
allowLoad(Session, Class<? extends IObject>, Details, long) - Method in interface ome.security.ACLVoter: test whether the object of the given Class with the given Details should be loadable in the current security context.
allowLoad(Session, Class<? extends IObject>, Details, long) - Method in class ome.security.basic.BasicACLVoter: delegates to SecurityFilter because that is where the logic is defined for the read filter Ignores the id for the moment.
allowLoad(Session, Class<? extends IObject>, Details, long) - Method in class ome.security.CompositeACLVoter
allowLoad(Session, Class<? extends IObject>, Details, long) - Method in class ome.security.sharing.SharingACLVoter
allowUpdate(IObject, Details) - Method in interface ome.security.ACLVoter: test whether the given object should be updateable given the trusted details.
allowUpdate(IObject, Details) - Method in class ome.security.basic.BasicACLVoter
allowUpdate(IObject, Details) - Method in class ome.security.CompositeACLVoter
allowUpdate(IObject, Details) - Method in class ome.security.sharing.SharingACLVoter
allTimes() - Method in class omero.sys.ParametersI: Removes the time parameters from the map.
allTypes() - Method in interface ome.api.Search: Permits all types to be returned.
allTypes() - Method in class ome.services.SearchBean
allTypes_async(AMD_Search_allTypes, Current) - Method in class ome.services.blitz.impl.SearchI
ALPHA_INDEX - Static variable in class ome.formats.model.ColorsFactory: Index of the red component of a color.
ALPHA_INDEX - Static variable in class omeis.providers.re.ColorsFactory: Index of the red component of a color.
ALPHA_TEXT - Static variable in class ome.formats.model.ChannelProcessor: Name of the blue component when it is a graphics image.
alphalessRendering - Variable in class omeis.providers.re.Optimizations: We can do alphaless rendering
alreadyRouted(Current) - Method in class ome.services.blitz.redirect.AbstractRedirector
alreadySeen(Object) - Method in class ome.tools.hibernate.UpdateFilter
alreadySucceeded(GraphStep) - Method in class ome.services.graphs.GraphSteps: Deprecated.
alreadyValidated(GraphStep) - Method in class ome.services.graphs.GraphSteps: Deprecated.
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: Deprecated.
will be removed in OMERO 5.2, so use the new graphs implementation
AnnotationGraphSpec(List<String>) - Constructor for class ome.services.graphs.AnnotationGraphSpec: Deprecated.

Creates a new instance.
AnnotationGraphSpec(Map<String, String>, List<String>) - Constructor for class ome.services.graphs.AnnotationGraphSpec: Deprecated.

Creates a new instance.
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.
append(ILoggingEvent) - Method in class ome.util.logback.SiftingWhileRejectingDefaultAppender
appendDate(StringBuilder, Date) - Method in class ome.tools.hibernate.SqlArray
appendDbPoint(StringBuilder, Point) - Static method in class omero.model.SmartShape.Util
appendDbPoint(StringBuilder, double, double) - Static method in class omero.model.SmartShape.Util
appendSegement(StringBuilder, boolean, double, double) - Static method in class omero.model.SmartShape.Util
appendSpace() - Method in class ome.tools.hibernate.QueryBuilder
appendSvgPoint(StringBuilder, Point) - Static method in class omero.model.SmartShape.Util
appendSvgPoint(StringBuilder, double, double) - Static method in class omero.model.SmartShape.Util
apply(String) - Method in class ome.services.blitz.repo.path.MakePathComponentSafe
applyBeanPropertyValues(Object, String) - Method in class ome.system.OmeroContext: Uses the methods of this context's BeanFactory to autowire any Object based on the given beanName.
applyBeanPropertyValues(Object, Class<? extends ServiceInterface>) - Method in class ome.system.OmeroContext: Uses the methods of this context's BeanFactory to autowire any Object based on the service class.
applyContext(Details, boolean) - Method in class ome.security.basic.CurrentDetails
applyHardWiredInterceptors(List<HardWiredInterceptor>, AopContextInitializer) - Method in class ome.services.blitz.impl.AbstractAmdServant: Applies the hard-wired intercepting to this instance.
applyIfShareAccessible(QueryBuilder) - Method in class ome.services.sharing.ShareBean: If the current user is not an admin, then this methods adds a subclause to the HQL: AND ( share.owner.id = :userId or user.id = :userId ) QueryBuilder.where() should already have been called.
applySettingsToDataset(long, long) - Method in interface ome.api.IRenderingSettings: Applies rendering settings to all images in a given Dataset.
applySettingsToDataset(long, long) - Method in class ome.logic.RenderingSettingsImpl: Implemented as specified by the IRenderingSettings I/F.
applySettingsToDataset_async(AMD_IRenderingSettings_applySettingsToDataset, long, long, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
applySettingsToImage(long, long) - Method in interface ome.api.IRenderingSettings: Applies rendering settings to a given Image.
applySettingsToImage(long, long) - Method in class ome.logic.RenderingSettingsImpl: Implemented as specified by the IRenderingSettings I/F
applySettingsToImage_async(AMD_IRenderingSettings_applySettingsToImage, long, long, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
applySettingsToImages(long, List<Long>) - Method in interface ome.api.IRenderingSettings: Applies rendering settings to a given Image.
applySettingsToImages(long, List<Long>) - Method in class ome.logic.RenderingSettingsImpl: Implemented as specified by the IRenderingSettings I/F
applySettingsToImages_async(AMD_IRenderingSettings_applySettingsToImages, long, List<Long>, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
applySettingsToPixels(long, long) - Method in interface ome.api.IRenderingSettings: Applies rendering settings to a given Pixels.
applySettingsToPixels(long, long) - Method in class ome.logic.RenderingSettingsImpl: Implemented as specified by the IRenderingSettings I/F
applySettingsToPixels_async(AMD_IRenderingSettings_applySettingsToPixels, long, long, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
applySettingsToProject(long, long) - Method in interface ome.api.IRenderingSettings: Applies rendering settings to all images in all Datasets of a given Project.
applySettingsToProject(long, long) - Method in class ome.logic.RenderingSettingsImpl: Implemented as specified by the IRenderingSettings I/F.
applySettingsToProject_async(AMD_IRenderingSettings_applySettingsToProject, long, long, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
applySettingsToSet(long, Class<T>, Set<Long>) - Method in interface ome.api.IRenderingSettings: Applies rendering settings to one or many containers.
applySettingsToSet(long, Class<T>, Set<Long>) - Method in class ome.logic.RenderingSettingsImpl: Implemented as specified by the IRenderingSettings I/F.
applySettingsToSet_async(AMD_IRenderingSettings_applySettingsToSet, long, String, List<Long>, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
ARC - Static variable in class pojos.LightSourceData: Indicates that the light source is a arc.
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.
asOriginalFile(String) - Method in class ome.services.blitz.repo.CheckedPath: Creates an OriginalFile instance for the given CheckedPath even if it doesn't exist.
asPixels() - Method in class pojos.DataObject: Returns the hosted IObject as a Pixels.
asPlate() - Method in class pojos.DataObject: Returns the hosted IObject as a Plate.
asPoints() - Method in class omero.model.SmartEllipseI
asPoints() - Method in class omero.model.SmartLineI
asPoints() - Method in class omero.model.SmartMaskI
asPoints() - Method in class omero.model.SmartPathI
asPoints() - Method in class omero.model.SmartPointI
asPoints() - Method in class omero.model.SmartPolygonI
asPoints() - Method in class omero.model.SmartPolylineI
asPoints() - Method in class omero.model.SmartRectI
asPoints() - Method in interface omero.model.SmartShape: Provides some, possibly lossy, bounding polygon of this SmartShape via points.
asPoints() - Method in class omero.model.SmartTextI
asPojo(IObject) - Static method in class pojos.DataObject: Converts the passed IObject into its corresponding Pojo object.
asPojos(Collection) - Static method in class pojos.DataObject: Converts the collection of IObjects into the corresponding DataObjects
asPojos(Map) - Static method in class pojos.DataObject: Converts the map of IObjects into the corresponding DataObjects
asProject() - Method in class pojos.DataObject: Returns the hosted IObject as a Project.
asProperties() - Method in class ome.system.Login: produces a copy of the internal fields as a Properties instance.
asProperties() - Method in class ome.system.Server: produces a copy of the internal fields as a Properties instance.
asroot - Variable in class ome.services.sessions.SessionManagerImpl: A private session for use only by this instance for running methods via Executor.
asScreen() - Method in class pojos.DataObject: Returns the hosted IObject as a Screen.
assemble(Serializable, Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
assertManaged(IObject) - Method in class ome.logic.AdminImpl
assertMayProcess(String, long, Details) - Method in interface ome.services.graphs.GraphTraversal.Processor: Assert that an object with the given details may be processed.
assertMayProcess(String, long, Details) - Method in class omero.cmd.graphs.BaseGraphTraversalProcessor
assertMayProcess(String, long, Details) - Method in class omero.cmd.graphs.NullGraphTraversalProcessor
assertNodes(Set<String>) - Method in class ome.services.blitz.fire.Ring
assertResponse(int) - Method in class omero.cmd.Helper: Checks the given steps against the number of times that this method has been called on this instance and then increments the call count.
assertStep(int, int) - Method in class omero.cmd.Helper: Throws an exception if the current step is not the expected value.
assertStep(int) - Method in class omero.cmd.Helper: Checks the given steps against the number of times that this method has been called on this instance and then increments the call count.
asWell() - Method in class pojos.DataObject: Returns the hosted IObject as a Well.
asWellSample() - Method in class pojos.DataObject: Returns the hosted IObject as a Well.
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
AttributeNewUserGroupBean - Class in ome.security.auth: Handles the "*_attribute" specifiers from etc/omero.properties.
AttributeNewUserGroupBean(String, boolean, boolean) - Constructor for class ome.security.auth.AttributeNewUserGroupBean
AttributeSet - Class in ome.security.auth: Specialized handling of all the attributes, multi or single valued.
AttributeSet(DirContextAdapter) - Constructor for class ome.security.auth.AttributeSet
autoClose - Variable in class ome.formats.importer.ImportConfig
available() - Method in class ome.services.pixeldata.PersistentEventLogLoader
AWTScaleService - Class in ome.logic: Provides methods for scaling buffered images.
AWTScaleService() - Constructor for class ome.logic.AWTScaleService

B

B_BAND - Static variable in class omeis.providers.re.RGBBuffer: Index of the blue band in the image's data buffer.
BackOff - Interface in ome.io.nio: Strategy interface which is used by PixelsService to calculate the appropriate backoff to report to users when pixel data is not available.
backOff - Variable in class ome.io.nio.PixelsService: BackOff implementation for calculating MissingPyramidExceptions
base - Variable in class ome.util.mem.ReadOnlyByteArray: The original array.
BASE_SCRIPT_FILTER - Static variable in class ome.services.scripts.ScriptRepoHelper: IOFileFilter instance used during ScriptRepoHelper.iterate() to find the matching scripts in the given directory.
BaseGraphPolicyAdjuster - Class in omero.cmd.graphs: The base class assists adjustment of an existing graph traversal policy.
BaseGraphPolicyAdjuster(GraphPolicy) - Constructor for class omero.cmd.graphs.BaseGraphPolicyAdjuster: Construct a new graph policy adjuster.
BaseGraphSpec - Class in ome.services.graphs: Deprecated.
will be removed in OMERO 5.2, so use the new graphs implementation
BaseGraphSpec(String, String...) - Constructor for class ome.services.graphs.BaseGraphSpec: Deprecated.

Simplified constructor, primarily used for testing.
BaseGraphSpec(List<String>) - Constructor for class ome.services.graphs.BaseGraphSpec: Deprecated.
BaseGraphSpec.SubSpecIterator - Class in ome.services.graphs: Deprecated.

Iterator which walks returns all GraphSpecs which are reachable from the given spec, depth first including the spec itself.
BaseGraphSpec.SubSpecIterator(GraphSpec) - Constructor for class ome.services.graphs.BaseGraphSpec.SubSpecIterator: Deprecated.
BaseGraphTraversalProcessor - Class in omero.cmd.graphs: Useful methods for GraphTraversal.Processor instances to share.
BaseGraphTraversalProcessor(Session) - Constructor for class omero.cmd.graphs.BaseGraphTraversalProcessor
basename() - Method in class ome.services.scripts.RepoFile
BasePolicy - Class in ome.security.policy: Simple base class for Policy implementations which always returns true for BasePolicy.isRestricted(IObject) and always fails on BasePolicy.checkRestriction(IObject).
BasePolicy(Set<Class<IObject>>) - Constructor for class ome.security.policy.BasePolicy
basic - Variable in class ome.security.SecuritySystemHolder
BasicACLVoter - Class in ome.security.basic
BasicACLVoter(CurrentDetails, SystemTypes, TokenHolder, SecurityFilter, PolicyService) - Constructor for class ome.security.basic.BasicACLVoter
BasicACLVoter(CurrentDetails, SystemTypes, TokenHolder, SecurityFilter, PolicyService, Roles) - Constructor for class ome.security.basic.BasicACLVoter
BasicEventContext - Class in ome.security.basic: EventContext implementation for use within the security system.
BasicEventContext(Principal, SessionStats) - Constructor for class ome.security.basic.BasicEventContext
BasicEventContext(Principal, SessionStats, EventContext) - Constructor for class ome.security.basic.BasicEventContext: Copy-constructor to not have to allow the mutator SimpleEventContext.copy(EventContext) or BasicEventContext.copyContext(EventContext) out of the EventContext hierarchy.
BasicMethodSecurity - Class in ome.security.basic: Implementation of MethodSecurity which checks method security based on the RolesAllowed annotations of our implementation methods.
BasicMethodSecurity() - Constructor for class ome.security.basic.BasicMethodSecurity
BasicMethodSecurity(boolean) - Constructor for class ome.security.basic.BasicMethodSecurity
BasicSecuritySystem - Class in ome.security.basic: simplest implementation of SecuritySystem.
BasicSecuritySystem(OmeroInterceptor, SystemTypes, CurrentDetails, SessionManager, Roles, ServiceFactory, TokenHolder, SecurityFilter, PolicyService) - Constructor for class ome.security.basic.BasicSecuritySystem: Main public constructor for this SecuritySystem implementation.
BasicSecurityWiring - Class in ome.security.basic: Responsible for logging users in and out via the Principal before and after the actual invocation of OMERO methods.
BasicSecurityWiring() - Constructor for class ome.security.basic.BasicSecurityWiring
BasicSecurityWiring.CloseOnNoSessionContext - Class in ome.security.basic
BasicSecurityWiring.CloseOnNoSessionContext() - Constructor for class ome.security.basic.BasicSecurityWiring.CloseOnNoSessionContext
batch - Variable in class ome.services.fulltext.FullTextIndexer
batchSize - Variable in class ome.services.eventlogs.EventLogLoader
batchSize - Variable in class ome.services.search.SearchValues
batchTimer - Variable in class ome.services.fulltext.FullTextIndexer
be - Variable in class ome.services.blitz.impl.AbstractAmdServant
BeanHelper - Class in ome.services.util: Helper for all bean implementations.
BeanHelper(Class) - Constructor for class ome.services.util.BeanHelper
beforeTransactionCompletion(Transaction) - Method in class ome.security.basic.OmeroInterceptor
BfPixelBuffer - Class in ome.io.bioformats: PixelBuffer implementation which uses Bio-Formats to read pixels data directly from original files.
BfPixelBuffer(String, IFormatReader) - Constructor for class ome.io.bioformats.BfPixelBuffer: We may want a constructor that takes the id of an imported file or that takes a File object?
BfPixelsStoreI - Class in ome.services.blitz.repo
BfPixelsStoreI(String, ImageReader) - Constructor for class ome.services.blitz.repo.BfPixelsStoreI
BfPixelsWrapper - Class in ome.io.bioformats
BfPixelsWrapper(String, IFormatReader) - Constructor for class ome.io.bioformats.BfPixelsWrapper: We may want a constructor that takes the id of an imported file or that takes a File object?
BfPyramidPixelBuffer - Class in ome.io.bioformats: PixelBuffer implementation which uses Bio-Formats to read pixels data directly from original files.
BfPyramidPixelBuffer(Pixels, String, boolean) - Constructor for class ome.io.bioformats.BfPyramidPixelBuffer: We may want a constructor that takes the id of an imported file or that takes a File object?
BfPyramidPixelBuffer(TileSizes, Pixels, String, boolean) - Constructor for class ome.io.bioformats.BfPyramidPixelBuffer: Full constructor taking a TileSizes implementation which defines how large the pyramid tiles will be.
BfPyramidPixelBuffer(TileSizes, Pixels, String, boolean, boolean) - Constructor for class ome.io.bioformats.BfPyramidPixelBuffer
bfReader - Variable in class ome.io.bioformats.BfPixelBuffer
bfSetId(ReaderWrapper) - Method in class ome.services.blitz.repo.CheckedPath: Perform BioFormats ReaderWrapper.setId(String) for this file.
BinaryAccessPolicy - Class in ome.security.policy: Policy which should be checked anytime access to original binary files in OMERO is being attempted.
BinaryAccessPolicy(Set<Class<IObject>>, ACLVoter) - Constructor for class ome.security.policy.BinaryAccessPolicy
BinaryAccessPolicy(Set<Class<IObject>>, ACLVoter, String[]) - Constructor for class ome.security.policy.BinaryAccessPolicy
BinaryMaskQuantizer - Class in omeis.providers.re.quantum: Quantization process for binary masks.
BinaryMaskQuantizer(QuantumDef, Pixels) - Constructor for class omeis.providers.re.quantum.BinaryMaskQuantizer: Creates a new strategy.
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, int) - Constructor for class ome.services.blitz.util.BlitzConfiguration: Single constructor which builds all Ice instances needed for the server runtime based on arguments provided.
BlitzConfiguration(InitializationData, Ring, SessionManager, SecuritySystem, Executor, int) - Constructor for class ome.services.blitz.util.BlitzConfiguration: Like #BlitzConfiguration(ome.services.sessions.SessionManager, SecuritySystem, Executor) but allows properties to be specified via an InitializationData instance.
BlitzExecutor - Interface in ome.services.blitz.util: Single-point of execution for all AMD blitz calls.
BlitzInstanceProvider - Class in ome.formats.model: An instance provider which uses reflection to fulfill the contract of an InstanceProvider.
BlitzInstanceProvider(EnumerationProvider) - Constructor for class ome.formats.model.BlitzInstanceProvider: Default constructor.
BlitzOnly - Interface in ome.services.blitz.util: Marker interface which specifies that an servant should not be checked for api consistency via ApiConsistencyCheck.
BlobShareStore - Class in ome.services.sharing: Implements ShareStore and provides functionality to work with binary Ice data from the share.
BlobShareStore() - Constructor for class ome.services.sharing.BlobShareStore
block(long) - Method in class omero.cmd.CmdCallbackI: Blocks for the given number of milliseconds unless CmdCallbackI.finished(Response, Status, Current) has been called in which case it returns immediately with true.
block(long) - Method in class omero.grid.ProcessCallbackI: Should only be used if the default logic of the process methods is kept in place.
BLUE_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
buildLuceneQuery(List<String>, Date, Date, String, String) - Static method in class ome.util.search.LuceneQueryBuilder: Builds a query with the provided input terms over the given fields
buildLuceneQuery(List<String>, String) - Static method in class ome.util.search.LuceneQueryBuilder: Builds a query with the provided input terms over the given fields
buildOrObtainSession() - Method in class ome.tools.hibernate.CurrentSessionContext
buildParseJob(long) - Method in class omero.grid.ParamsHelper: Build a job for the script with id.
buildQuery(String[], GraphEntry, QueryBuilder, QueryBuilder, Session) - Method in class ome.services.graphs.BaseGraphSpec: Deprecated.
buildQuery(Session) - Method in class ome.services.query.CollectionCountQueryDefinition
buildQuery(Session) - Method in class ome.services.query.IObjectClassQuery
buildQuery(Session) - Method in class ome.services.query.PojosFindAnnotationsQueryDefinition
buildQuery(Session) - Method in class ome.services.query.PojosFindHierarchiesQueryDefinition
buildQuery(Session) - Method in class ome.services.query.PojosGetImagesByOptionsQueryDefinition
buildQuery(Session) - Method in class ome.services.query.PojosGetImagesQueryDefinition
buildQuery(Session) - Method in class ome.services.query.PojosGetUserImagesQueryDefinition
buildQuery(Session) - Method in class ome.services.query.PojosLoadHierarchyQueryDefinition
buildQuery(Session) - Method in class ome.services.query.Query: main point of entry for subclasses.
buildQuery(Session) - Method in class ome.services.query.StringQuery
buildQuery(QueryBuilder) - Method in class ome.services.scripts.ScriptRepoHelper: Adds a single clause of the form "AND (A OR B ...)" where each ScriptFileType A, B, etc. is given a chance to define its own clause.
buildResponse(int, Object) - Method in class ome.services.blitz.impl.commands.SaveI
buildResponse(int, Object) - Method in class ome.services.blitz.repo.ManagedImportRequestI
buildResponse(int, Object) - Method in class ome.services.blitz.repo.RawAccessRequestI
buildResponse(int, Object) - Method in class omero.cmd.admin.CurrentSessionsRequestI
buildResponse(int, Object) - Method in class omero.cmd.admin.ResetPasswordRequestI
buildResponse(int, Object) - Method in class omero.cmd.admin.UpdateSessionTimeoutRequestI
buildResponse(int, Object) - Method in class omero.cmd.basic.DoAllI
buildResponse(int, Object) - Method in class omero.cmd.basic.ListRequestsI
buildResponse(int, Object) - Method in class omero.cmd.basic.TimingI
buildResponse(int, Object) - Method in class omero.cmd.fs.ManageImageBinariesI
buildResponse(int, Object) - Method in class omero.cmd.fs.OriginalMetadataRequestI
buildResponse(int, Object) - Method in class omero.cmd.fs.UsedFilesRequestI
buildResponse(int, Object) - Method in class omero.cmd.graphs.Chgrp2I
buildResponse(int, Object) - Method in class omero.cmd.graphs.ChgrpFacadeI: Deprecated.
buildResponse(int, Object) - Method in class omero.cmd.graphs.ChgrpI: Deprecated.
buildResponse(int, Object) - Method in class omero.cmd.graphs.Chmod2I
buildResponse(int, Object) - Method in class omero.cmd.graphs.ChmodFacadeI: Deprecated.
buildResponse(int, Object) - Method in class omero.cmd.graphs.ChmodI: Deprecated.
buildResponse(int, Object) - Method in class omero.cmd.graphs.Chown2I
buildResponse(int, Object) - Method in class omero.cmd.graphs.ChownFacadeI: Deprecated.
buildResponse(int, Object) - Method in class omero.cmd.graphs.ChownI: Deprecated.
buildResponse(int, Object) - Method in class omero.cmd.graphs.Delete2I
buildResponse(int, Object) - Method in class omero.cmd.graphs.DeleteFacadeI: Deprecated.
buildResponse(int, Object) - Method in class omero.cmd.graphs.DeleteI: Deprecated.
buildResponse(int, Object) - Method in class omero.cmd.graphs.DiskUsageI
buildResponse(int, Object) - Method in class omero.cmd.graphs.GraphSpecListI: Deprecated.
buildResponse(int, Object) - Method in class omero.cmd.graphs.SkipHeadI
buildResponse(int, Object) - Method in interface omero.cmd.IRequest: Post-transaction chance to map from the return value of IRequest.step(int) to a Response object.
buildResponse(int, Object) - Method in class omero.cmd.mail.SendEmailRequestI
BULK_ANNOTATIONS_NS - Static variable in class pojos.FileAnnotationData: The name space used to indicate that the FileAnnotation is a Bulk Annotations file.
byAnnotatedWith(Annotation...) - Method in interface ome.api.Search: Finds entities annotated with an Annotation similar to the example.
byAnnotatedWith(Annotation...) - Method in class ome.services.SearchBean
byAnnotatedWith_async(AMD_Search_byAnnotatedWith, List<Annotation>, Current) - Method in class ome.services.blitz.impl.SearchI
byFullText(String) - Method in interface ome.api.Search: Passes the query as is to the Lucene backend.
byFullText(String) - Method in class ome.services.SearchBean
byFullText_async(AMD_Search_byFullText, String, Current) - Method in class ome.services.blitz.impl.SearchI
byGroupForTags(String) - Method in interface ome.api.Search: Returns transient (without ID) TagAnnotation instances which represent all the tags in the given group.
byGroupForTags(String) - Method in class ome.services.SearchBean
byGroupForTags_async(AMD_Search_byGroupForTags, String, Current) - Method in class ome.services.blitz.impl.SearchI
byHqlQuery(String, Parameters) - Method in interface ome.api.Search: Delegates to IQuery.findAllByQuery(String, Parameters) method to take advantage of the Search.and(), Search.or(), and Search.not() methods, or queue-semantics.
byHqlQuery(String, Parameters) - Method in class ome.services.SearchBean
byHqlQuery_async(AMD_Search_byHqlQuery, String, Parameters, Current) - Method in class ome.services.blitz.impl.SearchI
byLuceneQueryBuilder(String, String, String, String, String) - Method in interface ome.api.Search: Builds a Lucene query and passes it to the Lucene backend.
byLuceneQueryBuilder(String, String, String, String, String) - Method in class ome.services.SearchBean
byLuceneQueryBuilder_async(AMD_Search_byLuceneQueryBuilder, String, String, String, String, String, Current) - Method in class ome.services.blitz.impl.SearchI
byName - Static variable in enum omero.cmd.graphs.Preprocessor.TargetType: Deprecated.

lookup from initial-capital name to type, e.g.
bySimilarTerms(String...) - Method in interface ome.api.Search: Returns transient (without ID) TextAnnotation instances which represent terms which are similar to the give terms.
bySimilarTerms(String...) - Method in class ome.services.SearchBean
bySimilarTerms_async(AMD_Search_bySimilarTerms, List<String>, Current) - Method in class ome.services.blitz.impl.SearchI
bySomeMustNone(String[], String[], String[]) - Method in interface ome.api.Search: Builds a Lucene query and passes it to Search.byFullText(String).
bySomeMustNone(String[], String[], String[]) - Method in class ome.services.SearchBean
bySomeMustNone_async(AMD_Search_bySomeMustNone, List<String>, List<String>, List<String>, Current) - Method in class ome.services.blitz.impl.SearchI
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.
bytesPerPixel - Variable in class omeis.providers.re.data.Plane2D: How many bytes make up a pixel value.
byType - Static variable in enum omero.cmd.graphs.Preprocessor.TargetType: Deprecated.

lookup from type to initial-capital name, e.g.
byUUID(String[]) - Method in class ome.services.SearchBean

C

c2c() - Method in class 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
callback - Variable in class omero.cmd.SessionI
Callback2<R> - Class in ome.services.throttling: Callable-based callback which guarantees that ice_response or ice_exception is called.
Callback2(Current, Object, boolean, Callable<R>) - Constructor for class ome.services.throttling.Callback2
CallContext - Class in omero.cmd: Interceptor which takes any context provided by the client and calls setContext on CurrentDetails.
CallContext(OmeroContext, String) - Constructor for class omero.cmd.CallContext
CallContext(CurrentDetails, String) - Constructor for class omero.cmd.CallContext
callContextWrapper(Object) - Method in class omero.cmd.SessionI
callInvokerOnMappedArgs(IceMapper, Object, Current, Object...) - Method in class ome.services.blitz.impl.AbstractAmdServant
callInvokerOnRawArgs(Object, Current, Object...) - Method in class ome.services.blitz.impl.AbstractAmdServant
callInvokerOnRawArgs(ServiceInterface, IceMethodInvoker, Object, Current, Object...) - Method in interface ome.services.blitz.util.BlitzExecutor: Uses the given IceMethodInvoker to make the method call.
callInvokerOnRawArgs(ServiceInterface, IceMethodInvoker, Object, Current, Object...) - Method in class ome.services.throttling.InThreadThrottlingStrategy
callInvokerOnRawArgs(ServiceInterface, IceMethodInvoker, Object, Current, Object...) - Method in class ome.services.throttling.SerialThrottlingStrategy
callInvokerWithMappedArgs(ServiceInterface, IceMethodInvoker, IceMapper, Object, Current, Object...) - Method in interface ome.services.blitz.util.BlitzExecutor: Passes the given arguments to IceMethodInvoker with the assumption that all conversion from omero.* to ome.* has taken place.
callInvokerWithMappedArgs(ServiceInterface, IceMethodInvoker, IceMapper, Object, Current, Object...) - Method in class ome.services.throttling.InThreadThrottlingStrategy
callInvokerWithMappedArgs(ServiceInterface, IceMethodInvoker, IceMapper, Object, Current, Object...) - Method in class ome.services.throttling.SerialThrottlingStrategy
callWithRetries(String, String, boolean) - Method in class ome.services.db.SelfCorrectingDataSource
canAnnotate(IObject) - Method in interface ome.api.local.LocalAdmin: Companion to IAdmin#canUpdate(IObject) but not yet remotely accessible.
canAnnotate(IObject) - Method in class ome.logic.AdminImpl
canAnnotate(Current) - Method in class omero.model.PermissionsI
canAnnotate() - Method in class pojos.DataObject: Returns true if the object can be annotated false otherwise, depending on permissions level.
cancel() - Method in class ome.formats.importer.ImportCandidates.SCANNING: Can be called to cancel the current action.
cancel(Current) - Method in class ome.services.blitz.impl.ScriptProcessI
cancel() - Method in interface ome.services.procs.Process
cancel() - Method in class ome.services.procs.ProcessSkeleton
cancel(String) - Method in class ome.services.sessions.events.ChangeSecurityContextEvent
cancel(Current) - Method in class omero.cmd.HandleI
cancel(ERR, Throwable, String, String...) - Method in class omero.cmd.Helper: Calls #cancel(ERR, Throwable, String, Map) with the output of Helper.params(String...).
cancel(ERR, Throwable, String, Map<String, String>) - Method in class omero.cmd.Helper: Like #fail(ERR, String, String...) throws a HandleI.Cancel exception.
cancelJob() - Method in interface ome.api.JobHandle: Marks a job for cancellation.
cancelJob() - Method in class ome.services.JobBean
cancelJob_async(AMD_JobHandle_cancelJob, Current) - Method in class ome.services.blitz.impl.JobHandleI
CANCELLED - Static variable in interface ome.api.JobHandle
cancelUploads - Variable in class ome.formats.importer.util.ErrorHandler
canDelete(Current) - Method in class omero.model.PermissionsI
canDelete() - Method in class pojos.DataObject: Returns true if the object can be deleted by the user currently logged in, false otherwise, depending on permissions level.
canEdit() - Method in class ome.services.blitz.repo.CheckedPath
canEdit(Current) - Method in class omero.model.PermissionsI
canEdit() - Method in class pojos.DataObject: Returns true if the object can be edited by the user currently logged in false otherwise, depending on permissions level.
canLink(Current) - Method in class omero.model.PermissionsI
canLink() - Method in class pojos.DataObject: Returns true if the object can be linked e.g. image add to dataset, by the user currently logged in, false otherwise, depending on permissions level.
canLogin() - Method in class ome.formats.importer.ImportConfig: Confirm all information for login is supplied
canMapReturnValue() - Method in class omero.util.IceMapper: True if this instance has a IceMapper.ReturnMapping
canRead() - Method in class ome.services.blitz.repo.CheckedPath: Check if this file is actually readable on the underlying filesystem.
canRead(EventContext, String) - Method in class ome.system.PreferenceContext
canRunScript_async(AMD_IScript_canRunScript, long, Current) - Method in class ome.services.blitz.impl.ScriptI
canUpdate(IObject) - Method in interface ome.api.IAdmin: Returns true if the currently logged in user can modify the given IObject.
canUpdate(IObject) - Method in class ome.logic.AdminImpl
canUpdate(IObject, Current) - Method in interface ome.services.blitz.repo.RepositoryDao: Delegates to IAdmin#canUpdate
canUpdate(IObject, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
canUpdate_async(AMD_IAdmin_canUpdate, IObject, Current) - Method in class ome.services.blitz.impl.AdminI
canWriteParentDirectory(ServiceFactory, SqlAction, String, CheckedPath) - Method in class ome.services.blitz.repo.RepositoryDaoImpl: Throw a SecurityViolation if the current context cannot write to the parent directory.
caseSensitive - Variable in class ome.services.search.SearchValues
castChildOptions(Collection<ChildOption>) - Static method in class omero.cmd.graphs.ChildOptionI: Cast ChildOption[] to ChildOptionI[].
cb - Variable in class ome.services.throttling.Task
cd - Variable in class ome.security.basic.BasicSecuritySystem
cd - Variable in class ome.security.basic.EventLogListener
cd - Variable in class ome.security.SecurityFilterHolder
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.JdbcHashedPasswordProvider
changePassword(String, String) - Method in class ome.security.auth.JdbcPasswordProvider
changePassword(String, String, PasswordUtil.METHOD) - Method in class ome.security.auth.JdbcPasswordProvider: Actually perform the password change in the database and log the event against the user.
changePassword(String, String) - Method in interface ome.security.auth.PasswordProvider: Attempts to change the password for the given user.
changePassword(String, String) - Method in class ome.security.auth.PasswordProviders
changePassword_async(AMD_IAdmin_changePassword, RString, Current) - Method in class ome.services.blitz.impl.AdminI
changePasswordWithOldPassword(String, String) - Method in interface ome.api.IAdmin: change the password for the current user by passing the old password.
changePasswordWithOldPassword(String, String) - Method in class ome.logic.AdminImpl
changePasswordWithOldPassword_async(AMD_IAdmin_changePasswordWithOldPassword, RString, RString, Current) - Method in class ome.services.blitz.impl.AdminI
changePermissions(IObject, Permissions) - Method in interface ome.api.IAdmin: call defaults.setPermissions() on this instance.
changePermissions(IObject, Permissions) - Method in class ome.logic.AdminImpl: the implementation of this method is somewhat tricky in that Permissions changes must be allowed even when other updates are not.
changePermissions_async(AMD_IAdmin_changePermissions, IObject, Permissions, Current) - Method in class ome.services.blitz.impl.AdminI
ChangeSecurityContextEvent - Class in ome.services.sessions.events: InteralMessage published by the SessionManager when setSecurityContext() is called.
ChangeSecurityContextEvent(Object, String, IObject, IObject) - Constructor for class ome.services.sessions.events.ChangeSecurityContextEvent
changeUserPassword(String, String) - Method in interface ome.api.IAdmin: change the password for the a given user.
changeUserPassword(String, String) - Method in class ome.logic.AdminImpl
changeUserPassword_async(AMD_IAdmin_changeUserPassword, String, RString, Current) - Method in class ome.services.blitz.impl.AdminI
changeUserPasswordById(Long, String) - Method in class ome.security.auth.PasswordUtil: Calls {@link #changeUserPasswordById(Long, String, boolean) with "false" as the value of the salt argument in order to provide backwards compatibility.
changeUserPasswordById(Long, String, PasswordUtil.METHOD) - Method in class ome.security.auth.PasswordUtil: Calls either PasswordUtil.preparePassword(String) or PasswordUtil.prepareSaltedPassword(Long, String) and passes the resulting value to SqlAction.setUserPassword(Long, String).
Channel_EmissionWavelength - Static variable in class ome.formats.model.UnitsFactory
Channel_ExcitationWavelength - Static variable in class ome.formats.model.UnitsFactory
Channel_PinholeSize - Static variable in class ome.formats.model.UnitsFactory
ChannelAcquisitionData - Class in pojos: Object hosting the acquisition related to a logical channel.
ChannelAcquisitionData(LogicalChannel) - Constructor for class pojos.ChannelAcquisitionData: Creates a new instance.
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(IObject, Object) - Method in class ome.security.basic.GroupChmodStrategy: Here we used the checks returned from ExtendedMetadata to iterate through every non-system table and check that it has no FKs which point to back to its rows and violate the read permissions which are being reduced.
check(IObject, Object) - Method in interface ome.security.ChmodStrategy: Performs one of the checks returned by ChmodStrategy.getChecks(IObject obj, String permissions).
check(String) - Method in class ome.services.query.Query: check that there is a definition for this Query with the provided argument as its name.
check() - Method in interface omero.util.Resources.Entry: Called during each cycle.
CheckAllJobs - Class in ome.services.blitz.util
CheckAllJobs(Executor, ObjectAdapter, TopicManager) - Constructor for class ome.services.blitz.util.CheckAllJobs
CheckAllJobs(Executor, ObjectAdapter, TopicManager, long) - Constructor for class ome.services.blitz.util.CheckAllJobs
checkAndCollapseGraph() - Method in class ome.formats.OMEROMetadataStore: Checks the entire object graph for sections that may be collapsed if the data is derived from a Plate.
checkAndRegister() - Method in class ome.services.JobBean
checkArgs(Object...) - Method in class ome.services.graphs.GraphEntry: Deprecated.
checkBounds(Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer
checkBounds(Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelsWrapper
checkBounds(Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
checkBounds(Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
checkBounds(Integer, Integer, Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer: Checks to ensure that no one particular axis has an offset out of bounds.
checkBounds(Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer: Implemented as specified by PixelBuffer I/F.
checkCluster() - Method in class ome.services.blitz.fire.Ring: Method called during initialization to get all the active uuids within the cluster, and remove any dead nodes.
checkDatabase(String) - Method in class ome.system.PreferenceContext
checkDelayedCallContext(BasicEventContext) - Method in class ome.security.basic.CurrentDetails
CheckedPath - Class in ome.services.blitz.repo: To prevent frequently re-calculating paths and re-creating File objects, CheckedPath objects store various interpretations of paths that are passed in by users.
CheckedPath(ServerFilePathTransformer, String, ChecksumProviderFactory, ChecksumAlgorithm) - Constructor for class ome.services.blitz.repo.CheckedPath: Construct a CheckedPath from a relative "/"-delimited path rooted at the repository.
checkedPaths - Variable in class ome.services.blitz.repo.ManagedImportLocationI
checkImageDelete(long, boolean) - Method in interface ome.api.IDelete: Returns all entities which would prevent the given Image id from being deleted.
checkImageDelete(long, boolean) - Method in class ome.services.delete.DeleteBean
checkIndex(int) - Method in class ome.util.mem.ReadOnlyByteArray: Makes sure that i is in [0, length).
checkLocation(File, RawFileStorePrx) - Method in class ome.formats.importer.transfers.AbstractExecFileTransfer: Check that the target location: 1) doesn't exist and 2) is properly written to by the server.
checkManagedDetails(IObject, Details) - Method in class ome.security.basic.BasicSecuritySystem
checkManagedDetails(IObject, Details) - Method in class ome.security.basic.OmeroInterceptor
checkManagedDetails(IObject, Details, Details) - Method in class ome.security.basic.OmeroInterceptor: Like OmeroInterceptor.checkManagedDetails(IObject, Details, Details) but allows passing in a specific Details instance.
checkManagedDetails(IObject, Details) - Method in interface ome.security.SecuritySystem: checks that a non-privileged user has not attempted to edit the entity's security details.
checkManagedDetails(IObject, Details) - Method in class ome.security.SecuritySystemHolder
checkManagedDetails(IObject, Details) - Method in class ome.security.sharing.SharingSecuritySystem
checkMethod(Object, Method, Principal, boolean) - Method in class ome.security.basic.BasicMethodSecurity: See MethodSecurity#checkMethod(Object, Method, Principal)
checkMethod(Object, Method, Principal, boolean) - Method in interface ome.security.MethodSecurity: Throws a SecurityViolation exception if the given Principal does not have the proper permissions to execute the given method.
checkNonNull(List<Point>) - Static method in class omero.model.SmartShape.Util: Used from assert statements of the form: assert Util.checkNonNull(points) : "Null points in " + this; in all the implementations of SmartShape.asPoints().
checkParameters() - Method in class ome.services.query.Query: check the Parameters instance against the Definitions instance for this Query.
checkPassword(String, String, boolean) - Method in interface ome.api.local.LocalAdmin: Checks password for given user.
checkPassword(String, String, boolean) - Method in class ome.logic.AdminImpl: If ldap plugin turned, creates Ldap accounts and authentication by LDAP available.
checkPassword(String, String, boolean) - Method in class ome.security.auth.ConfigurablePasswordProvider: If ConfigurablePasswordProvider.ignoreUnknown is true, returns null, since the base class knows no users.
checkPassword(String, String, boolean) - Method in class ome.security.auth.FilePasswordProvider
checkPassword(String, String, boolean) - Method in class ome.security.auth.JdbcPasswordProvider: Retrieves password from the database and calls ConfigurablePasswordProvider.comparePasswords(String, String).
checkPassword(String, String, boolean) - Method in class ome.security.auth.LdapPasswordProvider
checkPassword(String, String, boolean) - Method in interface ome.security.auth.PasswordProvider: Authenticates the give user given the password token.
checkPassword(String, String, boolean) - Method in class ome.security.auth.PasswordProviders
checkPassword(String, String, boolean) - Method in class ome.security.auth.providers.LdapPasswordProvider431
checkPassword(String) - Method in class ome.services.blitz.fire.Ring: Currently only returns false since if the regular password check performed by SessionManager cannot find the session, then the cluster has no extra information.
checkPath(String, ChecksumAlgorithm, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI: Create a new CheckedPath object based on the given user input.
checkPermissions(String, String, StringHolder, Current) - Method in class ome.services.blitz.fire.PermissionsVerifierI
checkProperty(String, String) - Method in interface ome.api.local.LocalQuery: Checks if a property is defined on a mapped Hibernate type.
checkProperty(String, String) - Method in class ome.logic.PojosImpl
checkProperty(String, String) - Method in class ome.logic.QueryImpl
checkReady(String) - Method in class ome.security.basic.BasicSecuritySystem: calls BasicSecuritySystem.isReady() and if not throws an ApiUsageException.
checkRestriction(String, IObject) - Method in class ome.security.basic.BasicSecuritySystem
checkRestriction(IObject) - Method in class ome.security.policy.BasePolicy
checkRestriction(IObject) - Method in class ome.security.policy.BinaryAccessPolicy
checkRestriction(String, IObject) - Method in class ome.security.policy.DefaultPolicyService
checkRestriction(IObject) - Method in interface ome.security.policy.Policy: Like #isRestricted(Policy) but throws an appropriate SecurityViolation subclass if the restriction is active.
checkRestriction(String, IObject) - Method in interface ome.security.policy.PolicyService: Give each configured Policy instance the chance to throw a SecurityViolation from its Policy.checkRestriction(IObject) method.
checkRestriction(String, IObject) - Method in interface ome.security.SecuritySystem: Checks whether or not a ome.sercurity.Policy instance of matching name has been registered, considers itself active, and considers the passed context object to be restricted.
checkRestriction(String, IObject) - Method in class ome.security.SecuritySystemHolder
checkRestriction(String, IObject) - Method in class ome.security.sharing.SharingSecuritySystem
checkState() - Method in class ome.services.procs.ProcessSkeleton
checksum(String, ChecksumAlgorithm) - Method in class ome.formats.importer.exclusions.AbstractFileExclusion
CHECKSUM_ALGORITHM_NAMER - Static variable in class ome.services.blitz.util.ChecksumAlgorithmMapper
checksumAlgorithm - Variable in class ome.formats.importer.ImportConfig
ChecksumAlgorithmMapper - Class in ome.services.blitz.util: Work with ChecksumAlgorithm enumeration instances, including mapping their values back to ChecksumTypes.
ChecksumAlgorithmMapper() - Constructor for class ome.services.blitz.util.ChecksumAlgorithmMapper
checksumAlgorithms - Variable in class ome.services.blitz.repo.PublicRepositoryI
checksumAsBytes() - Method in class ome.util.checksum.AbstractChecksumProvider
checksumAsBytes() - Method in interface ome.util.checksum.ChecksumProvider: Returns a byte array representation of the calculated checksum.
checksumAsBytes() - Method in class ome.util.checksum.FileSizeChecksumProviderImpl
checksumAsString() - Method in class ome.util.checksum.AbstractChecksumProvider
checksumAsString() - Method in interface ome.util.checksum.ChecksumProvider: Returns a String representing the checksum in hex form.
checksumAsString() - Method in class ome.util.checksum.FileSizeChecksumProviderImpl
ChecksumProvider - Interface in ome.util.checksum: An interface producing checksums or message digests (depending on the implementing class) of a given type of input.
checksumProviderFactory - Variable in class ome.services.blitz.repo.PublicRepositoryI
ChecksumProviderFactory - Interface in ome.util.checksum: A factory producing throw-away objects of the ChecksumProvider type.
ChecksumProviderFactoryImpl - Class in ome.util.checksum: An implementation of the ChecksumProviderFactory interface.
ChecksumProviderFactoryImpl() - Constructor for class ome.util.checksum.ChecksumProviderFactoryImpl
checksums - Variable in class ome.formats.importer.ImportEvent.FILESET_UPLOAD_END
ChecksumType - Enum in ome.util.checksum: Enumeration defining the possible algorithms used for calculating checksums.
checkTarget(File, TransferState) - Method in class ome.formats.importer.transfers.AbstractExecFileTransfer: Check that the server can properly read the copied file.
checkType(String) - Method in interface ome.api.local.LocalQuery: Checks if a type has been mapped in Hibernate.
checkType(String) - Method in class ome.logic.PojosImpl
checkType(String) - Method in class ome.logic.QueryImpl
checkUpgrade - Variable in class ome.formats.importer.ImportConfig
checkWriteOperationAllowed(Session) - Method in class ome.tools.spring.ManualFlushHibernateTemplate
Chgrp2I - Class in omero.cmd.graphs: Request to move model objects to a different experiment group, reimplementing ChgrpI.
Chgrp2I(ACLVoter, SystemTypes, GraphPathBean, Deletion, GraphPolicy, SetMultimap<String, String>) - Constructor for class omero.cmd.graphs.Chgrp2I: Construct a new chgrp request; called from GraphRequestFactory.getRequest(Class).
ChgrpFacadeI - Class in omero.cmd.graphs: Deprecated.
will be removed in OMERO 5.3, so use the new graphs implementation
ChgrpFacadeI(GraphRequestFactory) - Constructor for class omero.cmd.graphs.ChgrpFacadeI: Deprecated.

Construct a new chgrp request; called from GraphRequestFactory.getRequest(Class).
ChgrpI - Class in omero.cmd.graphs: Deprecated.
will be removed in OMERO 5.2, so use the new graphs implementation
ChgrpI(Communicator, ChgrpStepFactory, ApplicationContext) - Constructor for class omero.cmd.graphs.ChgrpI: Deprecated.
chgrpQuery(EventContext, String, GraphOpts) - Method in class ome.services.graphs.BaseGraphSpec: Deprecated.
chgrpQuery(EventContext, String, GraphOpts) - Method in interface ome.services.graphs.GraphSpec: Deprecated.

Return a QueryBuilder which has been properly initialized to take the parameters "id" and "grp" and then have QueryBuilder.query(Session) called.
chgrpQuery(EventContext, String, GraphOpts) - Method in class ome.services.graphs.LightSourceGraphSpec: Deprecated.
ChgrpStep - Class in ome.services.chgrp: Deprecated.
will be removed in OMERO 5.2, so use the new graphs implementation
ChgrpStep(OmeroContext, ExtendedMetadata, Roles, int, List<GraphStep>, GraphSpec, GraphEntry, long[], long) - Constructor for class ome.services.chgrp.ChgrpStep: Deprecated.
ChgrpStepFactory - Class in ome.services.chgrp: Deprecated.
will be removed in OMERO 5.2, so use the new graphs implementation
ChgrpStepFactory(OmeroContext, ExtendedMetadata, Roles) - Constructor for class ome.services.chgrp.ChgrpStepFactory: Deprecated.
child(String) - Method in class ome.services.blitz.repo.CheckedPath: Returns a new CheckedPath that has the given path appended to the end of this instances path.
ChildOptionI - Class in omero.cmd.graphs: Child options adjust how child objects are treated according to their type and, if annotations, namespace, overriding the default graph traversal policy for orphans.
ChildOptionI(GraphPathBean, ImmutableSet<String>) - Constructor for class omero.cmd.graphs.ChildOptionI: Construct a new child option instance.
ChildOptionI(ChildOptionI) - Constructor for class omero.cmd.graphs.ChildOptionI: Construct a new child option instance identical to that given.
ChildOptionsPolicy - Class in omero.cmd.graphs: Adjust graph traversal policy for child objects according to their type and, if annotations, namespace.
ChildOptionsPolicy() - Constructor for class omero.cmd.graphs.ChildOptionsPolicy
chmod - Variable in class ome.logic.AdminImpl
chmod(IObject, String) - Method in class ome.security.basic.GroupChmodStrategy
chmod(IObject, String) - Method in interface ome.security.ChmodStrategy: Change the permissions for the given object.
Chmod2I - Class in omero.cmd.graphs: Request to change the permissions on model objects, reimplementing ChmodI.
Chmod2I(ACLVoter, SystemTypes, GraphPathBean, Deletion, GraphPolicy, SetMultimap<String, String>) - Constructor for class omero.cmd.graphs.Chmod2I: Construct a new chmod request; called from GraphRequestFactory.getRequest(Class).
ChmodFacadeI - Class in omero.cmd.graphs: Deprecated.
will be removed in OMERO 5.3, so use the new graphs implementation
ChmodFacadeI(GraphRequestFactory) - Constructor for class omero.cmd.graphs.ChmodFacadeI: Deprecated.

Construct a new chmod request; called from GraphRequestFactory.getRequest(Class).
ChmodI - Class in omero.cmd.graphs: Deprecated.
will be removed in OMERO 5.2, so use the new graphs implementation
ChmodI(Communicator, ChmodStrategy) - Constructor for class omero.cmd.graphs.ChmodI: Deprecated.
chmodQuery(EventContext, String, GraphOpts) - Method in class ome.services.graphs.BaseGraphSpec: Deprecated.
chmodQuery(EventContext, String, GraphOpts) - Method in interface ome.services.graphs.GraphSpec: Deprecated.
ChmodStrategy - Interface in ome.security: Strategy for changing the permissions of objects in the database as well as verifying that the permissions for the modified objects are sensible after the change.
choose() - Method in class ome.security.CompositeACLVoter
choose() - Method in class ome.security.SecurityFilterHolder
choose() - Method in class ome.security.SecuritySystemHolder
chooseNextRedirect(Redirector.Context, Set<String>) - Method in class ome.services.blitz.redirect.ConfigRedirector
chooseNextRedirect(Redirector.Context, Set<String>) - Method in class ome.services.blitz.redirect.NullRedirector: Does nothing.
chooseNextRedirect(Redirector.Context, Set<String>) - Method in interface ome.services.blitz.redirect.Redirector: Gives the Redirector a chance to configure the next appropriate redirect based on the Set of current Node uuids.
chooseNextRedirect(Redirector.Context, Set<String>) - Method in class ome.services.blitz.redirect.ScaleRedirector: Does nothing since all redirects are chosen during Redirector.getProxyOrNull(Context, String, Glacier2.SessionControlPrx, Ice.Current)
Chown2I - Class in omero.cmd.graphs: Request to give model objects to a different experimenter, reimplementing ChownI.
Chown2I(ACLVoter, SystemTypes, GraphPathBean, Deletion, GraphPolicy, SetMultimap<String, String>) - Constructor for class omero.cmd.graphs.Chown2I: Construct a new chown request; called from GraphRequestFactory.getRequest(Class).
ChownFacadeI - Class in omero.cmd.graphs: Deprecated.
will be removed in OMERO 5.3, so use the new graphs implementation
ChownFacadeI(GraphRequestFactory) - Constructor for class omero.cmd.graphs.ChownFacadeI: Deprecated.

Construct a new chown request; called from GraphRequestFactory.getRequest(Class).
ChownI - Class in omero.cmd.graphs: Deprecated.
will be removed in OMERO 5.2, so use the new graphs implementation
ChownI(Communicator, ChownStepFactory, ApplicationContext) - Constructor for class omero.cmd.graphs.ChownI: Deprecated.
ChownStep - Class in ome.services.chown: Deprecated.
will be removed in OMERO 5.2, so use the new graphs implementation
ChownStep(OmeroContext, ExtendedMetadata, Roles, int, List<GraphStep>, GraphSpec, GraphEntry, long[], long) - Constructor for class ome.services.chown.ChownStep: Deprecated.
ChownStepFactory - Class in ome.services.chown: Deprecated.
will be removed in OMERO 5.2, so use the new graphs implementation
ChownStepFactory(OmeroContext, ExtendedMetadata, Roles) - Constructor for class ome.services.chown.ChownStepFactory: Deprecated.
classes - Variable in class ome.services.fulltext.FullTextBridge
ClassQuerySource - Class in ome.services.query: creates a query based on the id string by interpreting it as a Class.
ClassQuerySource() - Constructor for class ome.services.query.ClassQuerySource
clean() - Method in class ome.services.RawFileBean
clean() - Method in class ome.services.RawPixelsBean
cleanServants(boolean) - Method in class omero.cmd.SessionI: Use SessionI.cleanServants(boolean, String, ServantHolder, Ice.ObjectAdapter) to clean up.
cleanServants(boolean, String, ServantHolder, ObjectAdapter) - Static method in class omero.cmd.SessionI: Clean all servants that are in the current holder and remove them from the adapter.
cleanTempDir() - Method in class omero.util.TempFileManager: Deletes TempFileManager.dir
cleanThread() - Method in class ome.tools.hibernate.SessionHandler
cleanup() - Method in class ome.formats.importer.cli.CommandLineImporter: Cleans up after a successful or unsuccessful image import.
cleanup() - Method in class ome.services.util.ServiceHandler
cleanup() - Method in class omero.util.Resources
cleanup() - Method in interface omero.util.Resources.Entry: Gives an Resources.Entry a chance to cleanup resources before it is removed from checking.
cleanup() - Method in class omero.util.TempFileManager: Releases TempFileManager.lock and deletes TempFileManager.dir.
CleanupFailure - Exception in ome.formats.importer.transfers: Exception thrown when cleaning up resources after transfer fails partially or completely.
CleanupFailure(List<File>) - Constructor for exception ome.formats.importer.transfers.CleanupFailure
cleanupSelf() - Method in class omero.cmd.SessionI: Called if this isn't a kill-everything event.
cleanupUpload(RawFileStorePrx, FileInputStream) - Method in class ome.formats.importer.transfers.AbstractFileTransfer: Utility method for closing resources.
cleanUserDir() - Method in class omero.util.TempFileManager: Attempts to delete all directories under self.userdir other than the one owned by this process.
clear() - Method in interface ome.api.local.LocalQuery
clear() - Method in class ome.formats.importer.ImportLibrary
clear() - Method in class ome.logic.QueryImpl
clear() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl: reset all statistics
clearDisabled() - Method in class ome.security.basic.CurrentDetails
clearErrors(int) - Method in class ome.formats.importer.util.ErrorHandler
clearFiles() - Method in class ome.formats.importer.util.ErrorContainer: Clear the list of files to upload.
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 - Variable in class omero.model.DetailsI
CLIENT_CONTEXT - Static variable in class ome.system.OmeroContext: identifier for an OmeroContext configured in classpath*:beanRefContext.xml for use by remote (via JNDI/RMI) clients.
ClientError - Exception in omero: abstract superclass of all Omero exceptions.
ClientError(String) - Constructor for exception omero.ClientError
ClientFilePathTransformer - Class in ome.services.blitz.repo.path: Transform client-local File to repository FsFile path.
ClientFilePathTransformer(Function<String, String>) - Constructor for class ome.services.blitz.repo.path.ClientFilePathTransformer: Construct a new client-side file path transformer.
clientId - Variable in class omero.cmd.SessionI
clientId(Current) - Static method in class omero.cmd.SessionI: Helpers method to extract the CLIENTUUID out of the given Ice.Current.
clientIds - Variable in class omero.util.ServantHolder: An internal mapping to all client ids from SessionI for a given DB session since there is no method on ObjectAdapter to retrieve all servants.
ClientKeepAlive - Class in ome.formats.importer.util: A Runnable which keeps a Connector's server side resources from timing out.
ClientKeepAlive() - Constructor for class ome.formats.importer.util.ClientKeepAlive
clone() - Method in class ome.services.sessions.state.CacheListener
close(boolean) - Method in class loci.ome.io.OmeroReader
close() - Method in interface ome.api.StatefulServiceInterface: signals the end of the service lifecycle.
close() - Method in class ome.formats.importer.OMEROWrapper
close() - Method in class ome.io.bioformats.BfPixelBuffer
close() - Method in class ome.io.bioformats.BfPixelsWrapper
close() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
close() - Method in class ome.io.bioformats.OmeroPixelsPyramidReader
close() - Method in class ome.io.bioformats.OmeroPixelsPyramidWriter
close() - Method in class ome.io.nio.FileBuffer: Closes the buffer, cleaning up file state.
close() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
close() - Method in interface ome.io.nio.PixelBuffer: Closes the buffer, cleaning up file state.
close() - Method in class ome.io.nio.RomioPixelBuffer: Closes the buffer, cleaning up file state.
close(Current) - Method in class ome.services.blitz.impl.AbstractCloseableAmdServant
close(boolean, Current) - Method in class ome.services.blitz.impl.ScriptProcessI
close(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI: Deprecated.
close() - Method in class ome.services.blitz.repo.AbstractRepositoryI
close() - Method in class ome.services.blitz.repo.FileMaker
close() - Method in class ome.services.formats.OmeroReader
close(Signal, Integer) - Static method in class ome.services.fulltext.Main
close() - Method in class ome.services.JobBean
close() - Method in class ome.services.messages.ParserOpenFileMessage: Used to close the passed in resource.
close() - Method in class ome.services.messages.RegisterServiceCleanupMessage: Used to close the passed in resource.
close() - Method in class ome.services.RawFileBean
close() - Method in class ome.services.RawPixelsBean
close() - Method in class ome.services.RenderingBean
close() - Method in class ome.services.SearchBean
close() - Method in interface ome.services.sessions.SessionCallback
close(String) - Method in interface ome.services.sessions.SessionManager: If reference count for the session is less than 1, close the session.
close(String) - Method in class ome.services.sessions.SessionManagerImpl
close() - Method in class ome.services.sharing.ShareStore
close() - Method in class ome.services.ThumbnailBean
close() - Method in class omeis.providers.re.Renderer: Closes the buffer, cleaning up file state.
close(boolean) - Method in class omero.cmd.CmdCallbackI: First removes self from the adapter so as to no longer receive notifications, and the calls close on the remote handle if requested.
close(Current) - Method in class omero.cmd.HandleI
close(Current) - Method in class omero.grid.InteractiveProcessorI
close() - Method in class omero.grid.ProcessCallbackI
close(Current) - Method in interface omero.util.CloseableServant
close() - Method in class omero.util.RPSTileData
close() - Method in interface omero.util.TileData
close_async(AMD_StatefulServiceInterface_close, Current) - Method in class ome.services.blitz.impl.AbstractCloseableAmdServant: SessionHandler also specially catches close() calls, but cannot remove the servant from the ObjectAdapter and thereby prevent any further communication.
close_async(AMD_StatefulServiceInterface_close, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
CloseableServant - Interface in omero.util: Marker interface which distinguishes a servant which wants to have CloseableServant.close(Ice.Current) called on SessionI.doDestroy()
closeAll() - Method in interface ome.services.sessions.SessionManager: Close all sessions with checking for the necessary reference counts.
closeAll() - Method in class ome.services.sessions.SessionManagerImpl
closeAll() - Method in class ome.system.OmeroContext: closes all the nested OmeroContexts within this instance.
closeCalled(int) - Method in class ome.services.blitz.repo.ManagedImportProcessI
closeCompleted(ImportConfig) - Static method in class ome.formats.importer.cli.CommandLineImporter: Look for all ImportProcessPrx in the current session and close them if they return a non-null Response (i.e. they are done).
closeOnDestroy(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
closeParsedFiles() - Method in class ome.services.fulltext.ParserSession
closeRaf() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
closeServices() - Method in class ome.formats.OMEROMetadataStoreClient: Closes all stateful services.
closeSession(Session) - Method in interface ome.api.ISession: Closes session and releases all resources.
closeSession(Session) - Method in class ome.services.sessions.SessionBean
closeSession() - Method in class ome.system.ServiceFactory
closeSession() - Method in class omero.client: Closes the session and nulls out the communicator.
closeSession() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
closeSession_async(AMD_ISession_closeSession, Session, Current) - Method in class ome.services.blitz.impl.SessionI
closeShare(long) - Method in interface ome.api.IShare: Closes share.
closeShare(long) - Method in class ome.services.sharing.ShareBean
closeShare_async(AMD_IShare_closeShare, long, Current) - Method in class ome.services.blitz.impl.ShareI
closeStatement() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
closeUploader() - Method in class ome.formats.importer.transfers.TransferState: Call StatefulServiceInterfacePrx.close() on the cached TransferState.prx instance if non-null and null the instance.
closeWriter() - Method in class ome.io.bioformats.BfPyramidPixelBuffer: This method should never exit without releasing the lock.
CmdCallbackI - Class in omero.cmd: Callback servant used to wait until a HandlePrx would return non-null on getReponse.
CmdCallbackI(client, HandlePrx) - Constructor for class omero.cmd.CmdCallbackI
CmdCallbackI(ObjectAdapter, String, HandlePrx) - Constructor for class omero.cmd.CmdCallbackI
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: Deprecated.
collapse(boolean) - Method in interface ome.services.graphs.GraphStep.Callback: Deprecated.
collect(UnloadedCollector, Image) - Method in class ome.services.delete.DeleteBean: Walks the Image graph collecting unloaded instances of all entities for later delete.
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: Deprecated.

Returns all column sets where the first LENGTH - 1 members of "match" coincide with the values of the columns in the set.
COMBINED - Static variable in class ome.services.fulltext.BridgeHelper: Name of the Field which contains the union of all fields.
combineFacadeRequests(List<Request>) - Static method in class omero.cmd.graphs.GraphUtil: Deprecated.
because facade classes are deprecated
combineFilePathRestrictions(FilePathRestrictions...) - Static method in class ome.services.blitz.repo.path.FilePathRestrictions: Combine sets of rules to form a set that satisfies them all and that include transformations away from Unicode control characters.
CommandLineImporter - Class in ome.formats.importer.cli: The base entry point for the CLI version of the OMERO importer.
CommandLineImporter(ImportConfig, String[], boolean) - Constructor for class ome.formats.importer.cli.CommandLineImporter: Legacy constructor which uses a UploadFileTransfer.
CommandLineImporter(ImportConfig, String[], boolean, FileTransfer, int) - Constructor for class ome.formats.importer.cli.CommandLineImporter: Legacy constructor without any file exclusions.
CommandLineImporter(ImportConfig, String[], boolean, FileTransfer, List<FileExclusion>, int) - Constructor for class ome.formats.importer.cli.CommandLineImporter: Main entry class for the application.
commonRoot(List<FsFile>) - Method in class ome.services.blitz.repo.ManagedRepositoryI: From a list of paths, calculate the common root path that all share.
COMPANION_FILE_NS - Static variable in class pojos.FileAnnotationData: The name space used to indicate that the FileAnnotation is a companion file.
compare(LSID, LSID) - Method in class ome.formats.OMEXMLModelComparator
compare(Dataset, Dataset) - Method in class ome.formats.SortDatasetsByName
compare(Project, Project) - Method in class ome.formats.SortProjectsByName
compare(Object, Object) - Method in class pojos.ROICoordinate: Implemented as specified by the Comparator I/F.
comparePasswords(String, String) - Method in class ome.security.auth.ConfigurablePasswordProvider: Compares the password provided by the user (unhashed) against the given trusted password.
comparePasswords(Long, String, String) - Method in class ome.security.auth.ConfigurablePasswordProvider: Compares the password provided by the user (unhashed) against the given trusted password.
comparePasswords(Long, String, String, PasswordUtil) - Method in class ome.security.auth.ConfigurablePasswordProvider
comparePasswords(String, String) - Method in interface ome.security.auth.PasswordUtility
Complement - Class in ome.services.search: Complement SearchAction which combines two other search actions into one logical unit, e.g.
Complement(SearchValues, SearchAction, SearchAction) - Constructor for class ome.services.search.Complement
complete() - Method in class ome.formats.OverlayMetadataStore: Completes overlay population, flushing in memory ROI.
completeFast - Variable in class ome.services.fulltext.FullTextIndexer
completeSlow - Variable in class ome.services.fulltext.FullTextIndexer
COMPLEX_TYPE - Static variable in class pojos.PixelsData: Identifies the type used to store pixel values.
CompositeACLVoter - Class in ome.security
CompositeACLVoter(CurrentDetails, BasicACLVoter, SharingACLVoter) - Constructor for class ome.security.CompositeACLVoter
CompressImpl - Class in ome.logic
CompressImpl() - Constructor for class ome.logic.CompressImpl
compressToStream(BufferedImage, OutputStream) - Method in interface ome.api.local.LocalCompress: Compresses a buffered image to an output stream.
compressToStream(BufferedImage, OutputStream) - Method in class ome.logic.CompressImpl
computeLocationStats(Pixels, PixelBuffer, PlaneDef, int) - Method in class omeis.providers.re.metadata.StatsFactory: Helper object to determine the location of the pixels' values, the inputWindow i.e.
concatenate(FsFile...) - Static method in class ome.services.blitz.repo.path.FsFile: Concatenate paths.
ConcurrentStatisticsImpl - Class in org.hibernate.stat: Implementation of Statistics, as well as StatisticsImplementor, based on the java.util.concurrent package introduced in Java 5.
ConcurrentStatisticsImpl() - Constructor for class org.hibernate.stat.ConcurrentStatisticsImpl
ConcurrentStatisticsImpl(SessionFactoryImplementor) - Constructor for class org.hibernate.stat.ConcurrentStatisticsImpl
config - Variable in class ome.formats.importer.cli.CommandLineImporter: Configuration used by all components
config - Variable in class ome.formats.importer.util.ErrorHandler
configGroup(EventContext, List<Long>) - Method in class ome.security.basic.AllGroupsSecurityFilter
ConfigI - Class in ome.services.blitz.impl: Implementation of the IConfig service.
ConfigI(IConfig, BlitzExecutor) - Constructor for class ome.services.blitz.impl.ConfigI
ConfigImpl - Class in ome.logic: implementation of the IConfig service interface.
ConfigImpl() - Constructor for class ome.logic.ConfigImpl
ConfigRedirector - Class in ome.services.blitz.redirect: Redirector implementation which uses the REDIRECT config key via LocalConfig to know which Node is currently active.
ConfigRedirector(Executor) - Constructor for class ome.services.blitz.redirect.ConfigRedirector
ConfigurablePasswordProvider - Class in ome.security.auth: Base class for most PasswordProvider implementations, providing configuration for default behaviors.
ConfigurablePasswordProvider(PasswordUtil) - Constructor for class ome.security.auth.ConfigurablePasswordProvider: Call ConfigurablePasswordProvider.ConfigurablePasswordProvider(PasswordUtil, boolean) with "ignoreUnknown" equal to false.
ConfigurablePasswordProvider(PasswordUtil, boolean) - Constructor for class ome.security.auth.ConfigurablePasswordProvider: Call ConfigurablePasswordProvider.ConfigurablePasswordProvider(PasswordUtil, boolean, boolean) with "salt" equal to false.
ConfigurablePasswordProvider(PasswordUtil, boolean, boolean) - Constructor for class ome.security.auth.ConfigurablePasswordProvider
configure(List<HardWiredInterceptor>, OmeroContext) - Static method in class ome.logic.HardWiredInterceptor
configure(SelfConfigurableService) - Method in class ome.services.util.BeanHelper
configure(Type, Properties, Dialect) - Method in class ome.tools.hibernate.MySeqGenerator: If the parameters do not contain a SequenceGenerator.SEQUENCE name, we assign one based on the table name.
configureDebug(String) - Method in class ome.formats.importer.ImportConfig: Modifies the logging level of everything under the ome.formats, ome.services.blitz, ome.system and loci packages hierarchically.
ConfiguredTileSizes - Class in ome.io.nio: Implementation which has all values injected during configuration.
ConfiguredTileSizes() - Constructor for class ome.io.nio.ConfiguredTileSizes
ConfiguredTileSizes(int, int, int, int) - Constructor for class ome.io.nio.ConfiguredTileSizes
configureServant(Object) - Method in class omero.cmd.SessionI: Apply proper AOP and call setters for any known injection properties.
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
container - Variable in class ome.formats.importer.ImportEvent.PROGRESS_EVENT
ContainerI - Class in ome.services.blitz.impl: Implementation of the IContainer service.
ContainerI(IContainer, BlitzExecutor) - Constructor for class ome.services.blitz.impl.ContainerI
contains(Object) - Method in interface ome.api.local.LocalQuery: Tests if an object is currently contained in the session.
contains(Object) - Method in class ome.logic.QueryImpl
contains(long, Class<T>, long) - Method in class ome.services.sharing.ShareStore
contains(double, double) - Method in class ome.util.math.geom2D.EllipseArea: Required by the Shape I/F.
contains(double, double, double, double) - Method in class ome.util.math.geom2D.EllipseArea: Required by the Shape I/F.
contains(Point2D) - Method in class ome.util.math.geom2D.EllipseArea: Required by the Shape I/F.
contains(Rectangle2D) - Method in class ome.util.math.geom2D.EllipseArea: Required by the Shape I/F.
contains(double, double) - Method in class ome.util.math.geom2D.RectangleArea: Required by the Shape I/F.
contains(double, double, double, double) - Method in class ome.util.math.geom2D.RectangleArea: Required by the Shape I/F.
contains(Point2D) - Method in class ome.util.math.geom2D.RectangleArea: Required by the Shape I/F.
contains(Rectangle2D) - Method in class ome.util.math.geom2D.RectangleArea: Required by the Shape I/F.
contains(String) - Method in class pojos.WorkflowData: Returns true if the keyword exist in the workflow, false otherwise.
containsKey(Object) - Method in class ome.services.query.Definitions
contentLength - Variable in class ome.formats.importer.ImportEvent.FILE_UPLOAD_EVENT
context - Variable in class ome.logic.AdminImpl
context - Variable in class ome.services.blitz.fire.SessionManagerI
context - Variable in class ome.services.blitz.repo.PublicRepositoryI
context - Variable in class ome.services.fulltext.FileParser
context - Variable in class ome.services.fulltext.FullTextIndexer
context - Variable in class ome.services.messages.ContextMessage
context - Variable in class ome.services.sessions.SessionManagerImpl
context - Variable in class ome.services.util.Executor.Impl
context - Variable in class omero.cmd.SessionI
ContextMessage - Class in ome.services.messages
ContextMessage(Object, Map<String, String>) - Constructor for class ome.services.messages.ContextMessage
ContextMessage.Pop - Class in ome.services.messages: Published when an internal service is finished with the context previously signaled through publishing a ContextMessage.Push.
ContextMessage.Pop(Object, Map<String, String>) - Constructor for class ome.services.messages.ContextMessage.Pop
ContextMessage.Push - Class in ome.services.messages: Published when an internal service would like to modify the current EventContext.
ContextMessage.Push(Object, Map<String, String>) - Constructor for class ome.services.messages.ContextMessage.Push
contexts - Variable in class omero.cmd.admin.CurrentSessionsRequestI
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 omero.cmd.SessionI
convert(ElectricPotential) - Static method in class omero.model.ElectricPotentialI: FIXME: this should likely take a default so that locations which don't want an exception can have log.warn("Using new PositiveFloat(1.0)!"
convert(Frequency) - Static method in class omero.model.FrequencyI: FIXME: this should likely take a default so that locations which don't want an exception can have log.warn("Using new PositiveFloat(1.0)!"
convert(Length) - Static method in class omero.model.LengthI: FIXME: this should likely take a default so that locations which don't want an exception can have log.warn("Using new PositiveFloat(1.0)!"
convert(Power) - Static method in class omero.model.PowerI: FIXME: this should likely take a default so that locations which don't want an exception can have log.warn("Using new PositiveFloat(1.0)!"
convert(Pressure) - Static method in class omero.model.PressureI: FIXME: this should likely take a default so that locations which don't want an exception can have log.warn("Using new PositiveFloat(1.0)!"
convert(Temperature) - Static method in class omero.model.TemperatureI: FIXME: this should likely take a default so that locations which don't want an exception can have log.warn("Using new PositiveFloat(1.0)!"
convert(Time) - Static method in class omero.model.TimeI: FIXME: this should likely take a default so that locations which don't want an exception can have log.warn("Using new PositiveFloat(1.0)!"
convert(IceMapper) - Method in interface omero.rtypes.Conversion: Convert the "val" field on the given RType instance to an ome.model.* representation.
convert(EventContext) - Static method in class omero.util.IceMapper
convert(RGBBuffer) - Static method in class omero.util.IceMapper
convert(PlaneDef) - Static method in class omero.util.IceMapper: Converts the passed Ice Object and returns the converted object.
convert(Principal) - Static method in class omero.util.IceMapper
convert(Roles) - Static method in class omero.util.IceMapper
convert(Date) - Static method in class omero.util.IceMapper
convert(RTime) - Static method in class omero.util.IceMapper
convert(Parameters) - Method in class omero.util.IceMapper
convert(String, Object) - Method in class omero.util.IceMapper
convert(Options) - Static method in class omero.util.IceMapper
convert(Filter) - Static method in class omero.util.IceMapper
convert(Permissions) - Static method in class omero.util.IceMapper
convert(Permissions) - Static method in class omero.util.IceMapper
convertElectricPotential(ElectricPotential) - Static method in class ome.formats.model.UnitsFactory: Convert a Bio-Formats ElectricPotential to an OMERO ElectricPotential.
convertElectricPotential(ElectricPotential) - Static method in class ome.formats.model.UnitsFactory
convertElectricPotential(ElectricPotential, Unit<ElectricPotential>) - Static method in class ome.formats.model.UnitsFactory
convertElectricPotentialXML(ElectricPotential, String) - Static method in class ome.formats.model.UnitsFactory
convertFrequency(Frequency) - Static method in class ome.formats.model.UnitsFactory: Convert a Bio-Formats Frequency to an OMERO Frequency.
convertFrequency(Frequency) - Static method in class ome.formats.model.UnitsFactory
convertFrequency(Frequency, Unit<Frequency>) - Static method in class ome.formats.model.UnitsFactory
convertFrequencyXML(Frequency, String) - Static method in class ome.formats.model.UnitsFactory
convertLength(Length) - Static method in class ome.formats.model.UnitsFactory: Convert a Bio-Formats Length to an OMERO Length.
convertLength(Length) - Static method in class ome.formats.model.UnitsFactory
convertLength(Length, Unit<Length>) - Static method in class ome.formats.model.UnitsFactory
convertLengthXML(Length, String) - Static method in class ome.formats.model.UnitsFactory
convertMapPairs(List<MapPair>) - Static method in class omero.util.IceMapper
convertNamedValueList(List<NamedValue>) - Static method in class omero.util.IceMapper
convertPower(Power) - Static method in class ome.formats.model.UnitsFactory: Convert a Bio-Formats Power to an OMERO Power.
convertPower(Power) - Static method in class ome.formats.model.UnitsFactory
convertPower(Power, Unit<Power>) - Static method in class ome.formats.model.UnitsFactory
convertPowerXML(Power, String) - Static method in class ome.formats.model.UnitsFactory
convertPressure(Pressure) - Static method in class ome.formats.model.UnitsFactory: Convert a Bio-Formats Pressure to an OMERO Pressure.
convertPressure(Pressure) - Static method in class ome.formats.model.UnitsFactory
convertPressure(Pressure, Unit<Pressure>) - Static method in class ome.formats.model.UnitsFactory
convertPressureXML(Pressure, String) - Static method in class ome.formats.model.UnitsFactory
convertStringStringMap(Map<String, String>) - Static method in class omero.util.IceMapper: Convert a String→String map's values to RStrings.
convertTemperature(Temperature) - Static method in class ome.formats.model.UnitsFactory: Convert a Bio-Formats Temperature to an OMERO Temperature.
convertTemperature(Temperature) - Static method in class ome.formats.model.UnitsFactory
convertTemperature(Temperature, Unit<Temperature>) - Static method in class ome.formats.model.UnitsFactory
convertTemperatureXML(Temperature, String) - Static method in class ome.formats.model.UnitsFactory
convertTime(Time) - Static method in class ome.formats.model.UnitsFactory: Convert a Bio-Formats Time to an OMERO Time.
convertTime(Time) - Static method in class ome.formats.model.UnitsFactory
convertTime(Time, Unit<Time>) - Static method in class ome.formats.model.UnitsFactory
convertTimeXML(Time, String) - Static method in class ome.formats.model.UnitsFactory
ConvertToBlitzExceptionMessage - Class in ome.services.blitz.util: Internal event which gives third party services a chance to map their exceptions to a blitz exception.
ConvertToBlitzExceptionMessage(Object, Throwable) - Constructor for class ome.services.blitz.util.ConvertToBlitzExceptionMessage
convertXml(MetadataRetrieve) - Method in class ome.services.blitz.impl.ExporterI
Copiable - Interface in ome.util.mem: Requires an implementing class to provide deep copies of its instances.
CopiableArray - Class in ome.util.mem: This abstract class provides an implementation of the Copiable interface.
CopiableArray(int) - Constructor for class ome.util.mem.CopiableArray: Creates a new instance.
copy(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.
copy() - Method in class omero.cmd.graphs.ChgrpI: Deprecated.
copy() - Method in class omero.cmd.graphs.ChmodI: Deprecated.
copy() - Method in class omero.cmd.graphs.ChownI: Deprecated.
copy() - Method in class omero.cmd.graphs.DeleteI: Deprecated.
copy() - Method in interface omero.cmd.graphs.IGraphModifyRequest: Deprecated.

Produce a clone of this object.
copy(Current) - Method in class omero.model.ElectricPotentialI
copy(Current) - Method in class omero.model.FrequencyI
copy(Current) - Method in class omero.model.LengthI
copy(Current) - Method in class omero.model.PowerI
copy(Current) - Method in class omero.model.PressureI
copy(Current) - Method in class omero.model.TemperatureI
copy(Current) - Method in class omero.model.TimeI
copyAndResizeImage(long, Integer, Integer, Integer, Integer, List<Integer>, String, boolean) - Method in interface ome.api.IPixels: Copies the metadata, and only the metadata linked to a Image object into a new Image object of equal or differing size across one or many of its three physical dimensions or temporal dimension.
copyAndResizeImage(long, Integer, Integer, Integer, Integer, List<Integer>, String, boolean) - Method in class ome.logic.PixelsImpl
copyAndResizeImage_async(AMD_IPixels_copyAndResizeImage, long, RInt, RInt, RInt, RInt, List<Integer>, String, boolean, Current) - Method in class ome.services.blitz.impl.PixelsI
copyAndResizePixels(long, Integer, Integer, Integer, Integer, List<Integer>, String, boolean) - Method in interface ome.api.IPixels: Copies the metadata, and only the metadata linked to a Pixels object into a new Pixels object of equal or differing size across one or many of its three physical dimensions or temporal dimension.
copyAndResizePixels(long, Integer, Integer, Integer, Integer, List<Integer>, String, boolean) - Method in class ome.logic.PixelsImpl
copyAndResizePixels_async(AMD_IPixels_copyAndResizePixels, long, RInt, RInt, RInt, RInt, List<Integer>, String, boolean, Current) - Method in class ome.services.blitz.impl.PixelsI
copyClassListToArray(List<Class>) - Static method in class ome.services.search.SearchValues
copyDetails(Details) - Static method in class ome.services.search.SearchValues
copyFieldsTo(Chgrp2) - Method in class omero.cmd.graphs.Chgrp2I
copyFieldsTo(Chmod2) - Method in class omero.cmd.graphs.Chmod2I
copyFieldsTo(Chown2) - Method in class omero.cmd.graphs.Chown2I
copyFieldsTo(Delete2) - Method in class omero.cmd.graphs.Delete2I
copyFieldsTo(X) - Method in interface omero.cmd.graphs.WrappableRequest: Copy the fields of this request to that of the given request.
CopyFileTransfer - Class in ome.formats.importer.transfers: Local-only file transfer mechanism which makes use of the plaform copy command.
CopyFileTransfer() - Constructor for class ome.formats.importer.transfers.CopyFileTransfer
copyGroup(ExperimenterGroup) - Method in class ome.security.auth.SimpleRoleProvider
copyList(List<T>) - Static method in class ome.services.search.SearchValues
CopyMoveFileTransfer - Class in ome.formats.importer.transfers: Local-only file transfer mechanism which makes use of the local copy command followed by the deletion of the original source file.
CopyMoveFileTransfer() - Constructor for class ome.formats.importer.transfers.CopyMoveFileTransfer
copyObject(Filterable, ModelMapper) - Method in class omero.model.DetailsI
copyObject(Filterable, ModelMapper) - Method in class omero.model.ElectricPotentialI
copyObject(Filterable, ModelMapper) - Method in class omero.model.FrequencyI
copyObject(Filterable, ModelMapper) - Method in class omero.model.LengthI
copyObject(Filterable, ModelMapper) - Method in class omero.model.PermissionsI
copyObject(Filterable, ModelMapper) - Method in class omero.model.PowerI
copyObject(Filterable, ModelMapper) - Method in class omero.model.PressureI
copyObject(Filterable, ModelMapper) - Method in class omero.model.TemperatureI
copyObject(Filterable, ModelMapper) - Method in class omero.model.TimeI
copyOfValues() - Method in class ome.services.search.SearchAction
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 class ome.services.messages.DeleteLogMessage
count() - Method in interface ome.services.sessions.SessionContext: Returns the SessionContext.Count instance held by this context.
count() - Method in class ome.services.sessions.SessionContextImpl
count - Variable in class ome.services.sessions.stats.LongCounter
countAnnotationsUsedNotOwned(Class, long) - Method in interface ome.api.IMetadata: Counts the number of annotation of a given type used by the specified user but not owned by the user.
countAnnotationsUsedNotOwned(Class, long) - Method in class ome.logic.MetadataImpl: Implemented as specified by the IMetadata I/F
countAnnotationsUsedNotOwned_async(AMD_IMetadata_countAnnotationsUsedNotOwned, String, long, Current) - Method in class ome.services.blitz.impl.MetadataI
countByPeriod_async(AMD_ITimeline_countByPeriod, List<String>, RTime, RTime, Parameters, Current) - Method in class ome.services.blitz.impl.TimelineI
countCachedContainers(Class<? extends IObject>, int...) - Method in interface ome.formats.model.IObjectContainerStore: Counts the number of containers the MetadataStore has of a given class and at a given index of the hierarchy if specified.
countCachedContainers(Class<? extends IObject>, int...) - Method in class ome.formats.OMEROMetadataStoreClient
countCachedReferences(Class<? extends IObject>, Class<? extends IObject>) - Method in interface ome.formats.model.IObjectContainerStore: Counts the number of references the MetadataStore has between objects of two classes.
countCachedReferences(Class<? extends IObject>, Class<? extends IObject>) - Method in class ome.formats.OMEROMetadataStoreClient
Counter - Interface in ome.system.metrics: Thin wrapper around Counter
counter(Object, String) - Method in class ome.system.metrics.DefaultMetrics
counter(Object, String) - Method in interface ome.system.metrics.Metrics
counter(Object, String) - Method in class ome.system.metrics.NullMetrics
CounterFactory - Class in ome.services.sessions.stats: Factory for creating counter objects.
CounterFactory() - Constructor for class ome.services.sessions.stats.CounterFactory
countInDb() - Method in class ome.services.scripts.ScriptRepoHelper
countInDb(SqlAction) - Method in class ome.services.scripts.ScriptRepoHelper
countLocks(Session, Long, String[][], String) - Method in interface ome.tools.hibernate.ExtendedMetadata: Takes the lock checks returned by ExtendedMetadata.getLockChecks(Class) and performs the actual check returning a map from class to total number of locks.
countLocks(Session, Long, String[][], String) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
countOnDisk() - Method in class ome.services.scripts.ScriptRepoHelper: Returns the number of files which match ScriptRepoHelper.scriptFilter in ScriptRepoHelper.dir.
countSpecifiedAnnotations(Class, Set<String>, Set<String>, Parameters) - Method in interface ome.api.IMetadata: Counts the number of annotation of a given type.
countSpecifiedAnnotations(Class, Set<String>, Set<String>, Parameters) - Method in class ome.logic.MetadataImpl: Implemented as specified by the IMetadata I/F
countSpecifiedAnnotations_async(AMD_IMetadata_countSpecifiedAnnotations, String, List<String>, List<String>, Parameters, Current) - Method in class ome.services.blitz.impl.MetadataI
countTiles(Pixels) - Method in class ome.io.nio.SimpleBackOff
cpf - Variable in class ome.logic.AdminImpl
cpf - Variable in class ome.services.blitz.impl.ScriptI
CRC32ChecksumProviderImpl - Class in ome.util.checksum: An implementation of the ChecksumProvider interface using CRC32 as the message digest algorithm.
CRC32ChecksumProviderImpl() - Constructor for class ome.util.checksum.CRC32ChecksumProviderImpl
create(String, SessionControlPrx, Current) - Method in class ome.services.blitz.fire.SessionManagerI
create(int, List<GraphStep>, GraphSpec, GraphEntry, long[]) - Method in class ome.services.chgrp.ChgrpStepFactory: Deprecated.
create(int, List<GraphStep>, GraphSpec, GraphEntry, long[]) - Method in class ome.services.chown.ChownStepFactory: Deprecated.
create(int, List<GraphStep>, GraphSpec, GraphEntry, long[]) - Method in class ome.services.delete.DeleteStepFactory: Deprecated.
create(int, List<GraphStep>, GraphSpec, GraphEntry, long[]) - Method in class ome.services.export.ExporterStepFactory: Deprecated.
create(int, List<GraphStep>, GraphSpec, GraphEntry, long[]) - Method in interface ome.services.graphs.GraphStepFactory: Deprecated.
create(String) - Method in class omero.util.ObjectFactoryRegistry.ObjectFactory
create(File) - Method in class omero.util.TempFileManager: If the given directory doesn't exist, creates it and returns true.
create_path() - Static method in class omero.util.TempFileManager: Calls TempFileManager.createPath(String, String, boolean) on TempFileManager.manager with defaults of "omero", ".tmp", and false.
create_path(String) - Static method in class omero.util.TempFileManager: 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.
createBfReader() - Method in class ome.io.nio.PixelsService: Create an IFormatReader with the appropriate ReaderWrapper instances and IFormatReader.setFlattenedResolutions(boolean) set to false.
createBufferedImage() - Method in class ome.services.SVGRasterizer: Returns the image that represents the SVG document.
createByName(String, Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
createCache(CacheEventListener...) - Method in class ome.services.sessions.state.CacheFactory
createCache(String, boolean, int) - Method in class ome.services.sessions.state.SessionCache
createCallback(ImportProcessPrx, HandlePrx, ImportContainer) - Method in class ome.formats.importer.ImportLibrary
createChildOption() - Method in class omero.cmd.graphs.GraphRequestFactory
createClient(boolean) - Method in class omero.client: Creates a possibly insecure client instance and calls client.joinSession(String) using the current session id.
createCommunicator() - Method in class ome.services.blitz.util.BlitzConfiguration
createCommunicator(String, String[]) - Method in class ome.services.blitz.util.BlitzConfiguration
createData() - Method in class omero.util.RPSTileLoop
createData() - Method in class omero.util.TileLoop: Subclasses must provide a fresh instance of TileData.
createDataObject(T, Parameters) - Method in interface ome.api.IContainer: Creates the specified data object.
createDataObject(IObject, Parameters) - Method in class ome.logic.PojosImpl: Implemented as specified by the IContainer I/F
createDataObject_async(AMD_IContainer_createDataObject, IObject, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI
createDataObjects(IObject[], Parameters) - Method in interface ome.api.IContainer: convenience method to save network calls.
createDataObjects(IObject[], Parameters) - Method in class ome.logic.PojosImpl: Implemented as specified by the IContainer I/F
createDataObjects_async(AMD_IContainer_createDataObjects, List<IObject>, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI
createDetails() - Method in class ome.security.basic.CurrentDetails: Creates a Details object for the current security context.
createDirectories() - Method in class ome.services.util.ServerDirectoryCheck
createdOrModified(Class, Criteria) - Method in class ome.services.search.SearchAction
createdOrModified(Class, QueryBuilder, String) - Method in class ome.services.search.SearchAction
createdStart - Variable in class ome.services.search.SearchValues
createdStop - Variable in class ome.services.search.SearchValues
createEnumeration(T) - Method in interface ome.api.ITypes
createEnumeration(T) - Method in class ome.logic.TypesImpl
createEnumeration_async(AMD_ITypes_createEnumeration, IObject, Current) - Method in class ome.services.blitz.impl.TypesI
createException(MethodInvocation) - Method in class ome.tools.hibernate.EventMethodInterceptor.DisableAction
createExclusion(String) - Static method in class ome.formats.importer.exclusions.AbstractFileExclusion: Factory method for instantiating FileTransfer objects from a string.
createExperimenter(Experimenter, ExperimenterGroup, ExperimenterGroup...) - Method in interface ome.api.IAdmin: create and return a new user in the given groups.
createExperimenter(Experimenter, ExperimenterGroup, ExperimenterGroup...) - Method in class ome.logic.AdminImpl
createExperimenter(Experimenter, ExperimenterGroup, ExperimenterGroup...) - Method in interface ome.security.auth.RoleProvider
createExperimenter(Experimenter, ExperimenterGroup, ExperimenterGroup...) - Method in class ome.security.auth.SimpleRoleProvider
createExperimenter_async(AMD_IAdmin_createExperimenter, Experimenter, ExperimenterGroup, List<ExperimenterGroup>, Current) - Method in class ome.services.blitz.impl.AdminI
createExperimenterWithPassword(Experimenter, String, ExperimenterGroup, ExperimenterGroup...) - Method in interface ome.api.IAdmin: create and return a new user in the given groups with password.
createExperimenterWithPassword(Experimenter, String, ExperimenterGroup, ExperimenterGroup...) - Method in class ome.logic.AdminImpl
createExperimenterWithPassword_async(AMD_IAdmin_createExperimenterWithPassword, Experimenter, RString, ExperimenterGroup, List<ExperimenterGroup>, Current) - Method in class ome.services.blitz.impl.AdminI
createExporter(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
createFactories(Communicator) - Method in class ome.services.blitz.impl.commands.RequestObjectFactoryRegistry
createFactories(Communicator) - Method in class ome.services.blitz.repo.RequestObjectFactoryRegistry
createFactories(Communicator) - Method in class ome.services.roi.RoiTypes.RoiTypesObjectFactoryRegistry
createFactories(Communicator) - Method in class omero.cmd.admin.CurrentSessionsRequestI.Factory
createFactories(Communicator) - Method in class omero.cmd.admin.UpdateSessionTimeoutRequestI.Factory
createFactories(Communicator) - Method in class omero.cmd.RequestObjectFactoryRegistry
createFactories(Communicator) - Method in class omero.rtypes.RTypeObjectFactoryRegistry
createFactories(Communicator) - Method in class omero.util.ObjectFactoryRegistry
createFromRequest(SessionManager.CreationRequest) - Method in interface ome.services.sessions.SessionManager
createFromRequest(SessionManager.CreationRequest) - Method in class ome.services.sessions.SessionManagerImpl
createFullTextThread(EventLogLoader) - Static method in class ome.services.fulltext.Main
createFullTextThread(EventLogLoader, boolean) - Static method in class ome.services.fulltext.Main
createGroup(ExperimenterGroup) - Method in interface ome.api.IAdmin: create and return a new group.
createGroup(ExperimenterGroup) - Method in class ome.logic.AdminImpl
createGroup(ExperimenterGroup) - Method in interface ome.security.auth.RoleProvider
createGroup(String, Permissions, boolean) - Method in interface ome.security.auth.RoleProvider
createGroup(String, Permissions, boolean, boolean) - Method in interface ome.security.auth.RoleProvider
createGroup(String, Permissions, boolean) - Method in class ome.security.auth.SimpleRoleProvider
createGroup(String, Permissions, boolean, boolean) - Method in class ome.security.auth.SimpleRoleProvider
createGroup(ExperimenterGroup) - Method in class ome.security.auth.SimpleRoleProvider
createGroup_async(AMD_IAdmin_createGroup, ExperimenterGroup, Current) - Method in class ome.services.blitz.impl.AdminI
createHandle(Request) - Method in class omero.cmd.HandleFactory
createImage(int, int, int, int, List<Integer>, PixelsType, String, String) - Method in interface ome.api.IPixels: Creates the metadata, and only the metadata linked to an Image object.
createImage(int, int, int, int, List<Integer>, PixelsType, String, String) - Method in class ome.logic.PixelsImpl
createImage(int, int) - Method in class ome.services.SVGRasterizer.Rasterizer
createImage_async(AMD_IPixels_createImage, int, int, int, int, List<Integer>, PixelsType, String, String, Current) - Method in class ome.services.blitz.impl.PixelsI
createImport(ImportContainer) - Method in class ome.formats.importer.ImportLibrary: Provide initial configuration to the server in order to create the ImportProcessPrx which will manage state server-side.
createImportProcess(Fileset, ImportLocation, ImportSettings, Current) - Method in class ome.services.blitz.repo.ManagedRepositoryI: Creating the process will register itself in an appropriate container (i.e. a SessionI or similar) for the current user and therefore this instance no longer needs to worry about the maintenance of the object.
createInstance() - Method in class ome.security.basic.EventListenersFactoryBean: First, adds all default listeners.
createInstance() - Method in class ome.services.delete.Deletion.Builder: Deprecated.
createJob(ServiceFactory) - Method in class ome.services.scripts.ScriptFinder: Returns a fresh (unsaved) ScriptJob which can be passed to acquireProcessor for background processing.
createJobHandle(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
createJobHandle() - Method in class ome.system.ServiceFactory: create a new JobHandle proxy.
createJPEG(OutputStream) - Method in class ome.services.SVGRasterizer: Returns the image that represents the SVG document as a JPEG.
createMinMaxBfPixelBuffer(String, int, IMinMaxStore) - Method in class ome.io.nio.PixelsService: Helper method to properly log any exceptions raised by Bio-Formats and add a min/max calculator wrapper to the reader stack.
createNewRenderingDef(Pixels) - Method in interface ome.api.IRenderingSettings: Creates a new rendering definition object along with its sub-objects.
createNewRenderingDef(Pixels) - Method in class ome.logic.RenderingSettingsImpl: Implemented as specified by the IRenderingSettings I/F
createNewRenderingDef_async(AMD_IRenderingSettings_createNewRenderingDef, Pixels, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
createOrFixUserDir(String, List<CheckedPath>, Session, ServiceFactory, SqlAction) - Method in interface ome.services.blitz.repo.RepositoryDao: Checks that the given CheckedPath objects exist (via RepositoryDao.findRepoFile(String, CheckedPath, String, Ice.Current)) and are in the "user" group.
createOrFixUserDir(String, List<CheckedPath>, Session, ServiceFactory, SqlAction) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
createOriginalFile(ServiceFactory, SqlAction, String, List<CheckedPath>, ChecksumAlgorithm, String) - Method in class ome.services.blitz.repo.RepositoryDaoImpl: Primary location for creating original files from a CheckedPath instance.
createPath(String, String, boolean) - Method in class omero.util.TempFileManager: Uses File.createTempFile(String, String, File) to create temporary files and folders under TempFileManager.dir.
createPixelBuffer(Pixels) - Method in class ome.io.nio.PixelsService: Creates a PixelBuffer for a given pixels set.
createPlane(PlaneDef, int, Pixels, PixelBuffer) - Static method in class omeis.providers.re.data.PlaneFactory: Factory method to fetch plane data and create an object to access it.
createPrincipal() - Method in class ome.system.SessionInitializer
createProcessBuilder(File, File) - Method in class ome.formats.importer.transfers.AbstractExecFileTransfer: Creates a ProcessBuilder instance ready to have ProcessBuilder.start() called on it.
createProcessBuilder(File, File) - Method in class ome.formats.importer.transfers.CopyFileTransfer: Executes "cp file location" (Unix) or "cp file location" (Windows) and fails on non-0 return codes.
createProcessBuilder(File, File) - Method in class ome.formats.importer.transfers.HardlinkFileTransfer: Executes "ln file location" (Unix) or "mklink /H location file" (Windows) and fails on non-0 return codes.
createProcessBuilder(File, File) - Method in class ome.formats.importer.transfers.SymlinkFileTransfer: Executes "ln -s file location" (Unix) or "mklink location file" (Windows) and fails on non-0 return codes.
createPyramidPixelBuffer(Pixels, String, boolean) - Method in class ome.io.nio.PixelsService: Helper method to properly log any exceptions raised by Bio-Formats.
createQueryBuilder(String[], GraphEntry) - Method in class ome.services.graphs.BaseGraphSpec: Deprecated.
createRawFileStore(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
createRawFileStore(OriginalFile, Current) - Method in class ome.services.blitz.repo.AbstractRepositoryI
createRawFileStore() - Method in class ome.system.ServiceFactory: create a new RawFileStore proxy.
createRawPixelsStore(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
createRawPixelsStore(OriginalFile, Current) - Method in class ome.services.blitz.repo.AbstractRepositoryI
createRawPixelsStore() - Method in class ome.system.ServiceFactory: create a new RawPixelsStore proxy.
createRenderingEngine(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
createRenderingEngine(OriginalFile, Current) - Method in class ome.services.blitz.repo.AbstractRepositoryI
createRenderingEngine() - Method in class ome.system.ServiceFactory: create a new RenderingEngine proxy.
createRepoRFS(CheckedPath, String, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI: Create, initialize, and register an RepoRawFileStoreI with the proper setting (read or write).
createRomioPixelBuffer(String, Pixels, boolean) - Method in class ome.io.nio.PixelsService: Helper method to properlty create a RomioPixelBuffer.
createRoot() - Method in class ome.formats.OMEROMetadataStore
createRoot() - Method in class ome.formats.OMEROMetadataStoreClient
createRoot_async(AMD_MetadataStore_createRoot, Current) - Method in class ome.services.blitz.impl.MetadataStoreI
createSafeInputStream(Communicator, byte[]) - Static method in class ome.services.util.IceUtil: Creates an InputStream with the appropriate encoding.
createSafeOutputStream(Communicator) - Static method in class ome.services.util.IceUtil: Creates an OutputStream with the appropriate encoding.
createSearchService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
createSearchService() - Method in class ome.system.ServiceFactory: create a new Search proxy.
createServantDelegate(String) - Method in class omero.cmd.SessionI: Creates a proxy according to the ServantDefinition for the given name.
createSession(Principal, String) - Method in interface ome.api.ISession: Creates a new session and returns it to the user.
createSession(Principal, String) - Method in class ome.services.sessions.SessionBean
createSession() - Method in class omero.client: 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).
createTemplatePath(Object, Current) - Method in class ome.services.blitz.repo.ManagedRepositoryI: Expand the template path and create its directories with the correct ownership.
createThumbnail(Integer, Integer) - Method in interface ome.api.ThumbnailStore: Creates a thumbnail for a pixels set using a given set of rendering settings (RenderingDef) in the on-disk cache.
createThumbnail(Thumbnail, byte[]) - Method in class ome.io.nio.ThumbnailService: Creates thumbnail on disk using byte array
createThumbnail(Integer, Integer) - Method in class ome.services.ThumbnailBean
createThumbnail_async(AMD_ThumbnailStore_createThumbnail, RInt, RInt, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
createThumbnailMetadata(Pixels, Dimension) - Method in class ome.services.ThumbnailCtx: Creates metadata for a thumbnail of a given set of pixels set and X-Y dimensions.
createThumbnails() - Method in interface ome.api.ThumbnailStore: Creates thumbnails for a pixels set using a given set of rendering settings (RenderingDef) in the on-disk cache for every sizeX/sizeY combination already cached.
createThumbnails() - Method in class ome.services.ThumbnailBean
createThumbnails_async(AMD_ThumbnailStore_createThumbnails, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
createThumbnailsByLongestSideSet(Integer, Set<Long>) - Method in interface ome.api.ThumbnailStore: Creates thumbnails for a number of pixels sets using a given set of rendering settings (RenderingDef) in the on-disk cache.
createThumbnailsByLongestSideSet(Integer, Set<Long>) - Method in class ome.services.ThumbnailBean
createThumbnailsByLongestSideSet_async(AMD_ThumbnailStore_createThumbnailsByLongestSideSet, RInt, List<Long>, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
createThumbnailService() - Method in class ome.system.ServiceFactory: create a new ThumbnailStore proxy.
createThumbnailStore(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
createThumbnailStore(OriginalFile, Current) - Method in class ome.services.blitz.repo.AbstractRepositoryI
createTransfer(String) - Static method in class ome.formats.importer.transfers.AbstractFileTransfer: Factory method for instantiating FileTransfer objects from a string.
createUploadProcess(Fileset, ImportLocation, ImportSettings, Current, boolean) - Method in class ome.services.blitz.repo.ManagedRepositoryI: Creating the process will register itself in an appropriate container (i.e. a SessionI or similar) for the current user and therefore this instance no longer needs to worry about the maintenance of the object.
createUser(Experimenter, String) - Method in interface ome.api.IAdmin: create and return a new user.
createUser(String) - Method in interface ome.api.ILdap: Creates an Experimenter entry in the OMERO DB based on the supplied LDAP username.
createUser(Experimenter, String) - Method in class ome.logic.AdminImpl
createUser(String) - Method in class ome.logic.LdapImpl: Creates an Experimenter based on the supplied LDAP username.
createUser(String, String) - Method in class ome.logic.LdapImpl: Creates an Experimenter based on the supplied LDAP username.
createUser(String, String, boolean) - Method in class ome.logic.LdapImpl: Creates an Experimenter based on the supplied LDAP username.
createUser_async(AMD_IAdmin_createUser, Experimenter, String, Current) - Method in class ome.services.blitz.impl.AdminI
createUser_async(AMD_ILdap_createUser, String, Current) - Method in class ome.services.blitz.impl.LdapI
createUserFromLdap(String, String) - Method in class ome.logic.LdapImpl: Deprecated.
createUserSession(long, long, String) - Method in interface ome.api.ISession: Allows a user to open up another session for him/herself with the given defaults without needing to re-enter password.
createUserSession(long, long, String) - Method in class ome.services.sessions.SessionBean
createUserSession_async(AMD_ISession_createUserSession, long, long, String, Current) - Method in class ome.services.blitz.impl.SessionI
createWithAgent(Principal, String, String, String) - Method in interface ome.services.sessions.SessionManager
createWithAgent(Principal, String, String) - Method in interface ome.services.sessions.SessionManager
createWithAgent(Principal, String, String, String) - Method in class ome.services.sessions.SessionManagerImpl
createWithAgent(Principal, String, String) - Method in class ome.services.sessions.SessionManagerImpl
credentials - Variable in class ome.services.sessions.SessionManager.CreationRequest
credentials - Variable in class ome.system.SessionInitializer
CRITICAL_USAGE - Static variable in class ome.logic.RepositoryInfoImpl: Percentage (100.0 - 0.0) of disk use which will cause an exception during RepositoryInfoImpl.sanityCheckRepository()
csId - Variable in class ome.system.SimpleEventContext
csName - Variable in class ome.system.SimpleEventContext
CSV - Static variable in class pojos.FileAnnotationData: Identifies the CSV file formats.
ctx - Variable in class ome.security.auth.ConfigurablePasswordProvider
ctx - Variable in class ome.security.basic.BasicSecuritySystem
ctx - Variable in class ome.services.blitz.impl.AbstractAmdServant
ctx - Variable in class ome.services.delete.Deletion.Builder: Deprecated.
ctx - Variable in class ome.services.sharing.BlobShareStore
ctx - Variable in class ome.services.throttling.AbstractThrottlingStrategy
ctx - Variable in class ome.system.ServiceFactory: the context instance which this ServiceFactory uses to look up all of its state.
cuId - Variable in class ome.system.SimpleEventContext
cuName - Variable in class ome.system.SimpleEventContext
curr - Variable in class ome.services.blitz.util.FindServiceFactoryMessage
current - Variable in class ome.security.SecurityFilterHolder
current - Variable in class ome.security.SecuritySystemHolder
current - Variable in class ome.services.throttling.Task
current - Variable in class ome.tools.hibernate.ProxyCleanupFilter
current - Variable in class omero.cmd.admin.CurrentSessionsRequestI
current - Variable in class omero.cmd.admin.UpdateSessionTimeoutRequestI
current_group - Static variable in class ome.security.basic.OneGroupSecurityFilter
current_user - Static variable in interface ome.security.SecurityFilter
currentContext(Principal) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
CurrentDetails - Class in ome.security.basic: Stores information related to the security context of the current thread.
CurrentDetails() - Constructor for class ome.security.basic.CurrentDetails: Default constructor.
CurrentDetails(SessionCache) - Constructor for class ome.security.basic.CurrentDetails
CurrentDetails(SessionCache, Roles) - Constructor for class ome.security.basic.CurrentDetails
currentMetadata() - Method in interface ome.api.Search: Provides access to the extra query information (for example Lucene score and boost values) for a single call to Search.next().
currentMetadata() - Method in class ome.services.SearchBean
currentMetadata_async(AMD_Search_currentMetadata, Current) - Method in class ome.services.blitz.impl.SearchI
currentMetadataList() - Method in interface ome.api.Search: Provides access to the extra query information (for example Lucene score and boost values) for a single call to Search.results().
currentMetadataList() - Method in class ome.services.SearchBean
currentMetadataList_async(AMD_Search_currentMetadataList, Current) - Method in class ome.services.blitz.impl.SearchI
CurrentPlatform - Class in ome.services.blitz.util: Test under which platform OMERO is currently running.
CurrentPlatform() - Constructor for class ome.services.blitz.util.CurrentPlatform
CurrentSessionContext - Class in ome.tools.hibernate: Implementation of Hibernate's current_session_context_class extension point.
CurrentSessionContext(SessionFactoryImplementor) - Constructor for class ome.tools.hibernate.CurrentSessionContext
CurrentSessionsRequestI - Class in omero.cmd.admin
CurrentSessionsRequestI(CurrentDetails, SessionManager) - Constructor for class omero.cmd.admin.CurrentSessionsRequestI
CurrentSessionsRequestI.Factory - Class in omero.cmd.admin
CurrentSessionsRequestI.Factory(CurrentDetails, SessionManager) - Constructor for class omero.cmd.admin.CurrentSessionsRequestI.Factory
CurrentSessionStats - Class in ome.services.sessions.stats: Wrapper which delegates to a SessionStats instance acquired during construction.
CurrentSessionStats(CurrentDetails, SessionManager) - Constructor for class ome.services.sessions.stats.CurrentSessionStats
currentUser - Variable in class ome.security.basic.BasicACLVoter
currentUser(Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl

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
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.
DATE(Connection, List<Date>) - Method in interface ome.tools.hibernate.ListAsSQLArrayUserType.ArrayFactory
DATE_ACQUISITION - Static variable in class ome.util.search.LuceneQueryBuilder
DATE_IMPORT - Static variable in class ome.util.search.LuceneQueryBuilder
DATE_TYPE_ACQUISITION - Static variable in interface ome.api.Search: Treat date range as acquisition date
DATE_TYPE_IMPORT - Static variable in interface ome.api.Search: Treat date range as import date
DBEnumCheck - Class in ome.services.util: Hook run by the context to guarantee that various enumerations are up to date.
DBEnumCheck(Executor, PreferenceContext) - Constructor for class ome.services.util.DBEnumCheck
DBPatchCheck - Class in ome.services.util: Hook run by the context.
DBPatchCheck(SqlAction, PreferenceContext) - Constructor for class ome.services.util.DBPatchCheck
dbPath(Shape) - Method in class ome.services.roi.GeomTool
DBUnicodeUnitsCheck - Class in ome.services.util: Checks that the database contains correctly encoded enumerations for units of measure.
DBUnicodeUnitsCheck(Executor, PreferenceContext) - Constructor for class ome.services.util.DBUnicodeUnitsCheck
DBUserCheck - Class in ome.services.util: Hook run by the context.
DBUserCheck(SqlAction, PreferenceContext) - Constructor for class ome.services.util.DBUserCheck
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(String, Object...) - Method in class omero.cmd.Helper
DEBUG - Static variable in class prefs: Activated by setting DBEUG=true in the environment.
debugAll - Variable in class ome.security.basic.EventListenersFactoryBean
dec() - Method in interface ome.system.metrics.Counter
dec() - Method in class ome.system.metrics.DefaultCounter
DECILE - Static variable in class omeis.providers.re.quantum.QuantumStrategy: Determines the number of sub-intervals of the [globalMin, globalMax] interval.
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: Deprecated.
DEFAULT - Static variable in class pojos.GroupData: Identifies the default group.
DEFAULT - Static variable in class prefs: Key (and default value) of the property under prefs.ROOT which defines which "profile" (subnode} is in effect.
DEFAULT_BATCH_SIZE - Static variable in interface ome.api.Search: Default batch size
DEFAULT_BATCH_SIZE - Static variable in class ome.services.eventlogs.EventLogLoader: Currently 100.
DEFAULT_CASE_SENSITIVTY - Static variable in interface ome.api.Search: Default case sensitivity
DEFAULT_COMPRESSION_QUALITY - Static variable in class ome.services.ThumbnailBean: The default compression quality in fractional percent.
DEFAULT_ENCODING - Static variable in class ome.security.auth.PasswordUtil: The default encoding for converting plain text passwords to byte arrays (UTF-8)
DEFAULT_FILL_COLOUR - Static variable in class pojos.ShapeSettingsData: The default fill color.
DEFAULT_FILL_COLOUR_ALPHA - Static variable in class pojos.ShapeSettingsData: The default fill color.
DEFAULT_FONT_FAMILY - Static variable in class pojos.ShapeSettingsData: The default font family.
DEFAULT_FONT_SIZE - Static variable in class pojos.ShapeSettingsData: The default font size in "pt".
DEFAULT_MAX - Static variable in class ome.services.eventlogs.EventLogQueue: Default maximum for the number of rows that will be loaded in a single call to SqlAction.getEventLogPartitions(java.util.Collection, java.util.Collection, long, long) .
DEFAULT_MERGED_BATCHES - Static variable in interface ome.api.Search: Default 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 loci.ome.io.OmeroReader
DEFAULT_PORT - Static variable in class ome.services.mail.SubethaSMTP
DEFAULT_PORT - Static variable in class ome.system.Server
DEFAULT_QABASEURL - Static variable in class ome.formats.importer.ImportConfig
DEFAULT_REPORTING_LOOPS - Static variable in class ome.services.fulltext.FullTextIndexer: Default number of loops to wait if no external value is set.
DEFAULT_RETURN_UNLOADED - Static variable in interface ome.api.Search: Default 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.services.blitz.impl.SharedResourcesI: If no value is passed to this instance, this is the time (1 hour) which will be used for a script session.
DEFAULT_TIMEOUT - Static variable in class ome.system.UpgradeCheck: Default timeout is 10 seconds.
DEFAULT_USE_PROJECTIONS - Static variable in interface ome.api.Search: Default use-projections
DEFAULT_WAIT - Static variable in class ome.formats.importer.cli.CommandLineImporter
DEFAULT_X_WIDTH - Static variable in class ome.services.ThumbnailBean: The default X-width for a thumbnail.
DEFAULT_Y_WIDTH - Static variable in class ome.services.ThumbnailBean: The default Y-width for a thumbnail.
DefaultCounter - Class in ome.system.metrics: Thin wrapper around Counter
DefaultCounter(Counter) - Constructor for class ome.system.metrics.DefaultCounter
DefaultHistogram - Class in ome.system.metrics: Thin wrapper around Histogram
DefaultHistogram(Histogram) - Constructor for class ome.system.metrics.DefaultHistogram
DefaultMetrics - Class in ome.system.metrics: Spring bean for configuring metrics in this JVM.
DefaultMetrics() - Constructor for class ome.system.metrics.DefaultMetrics
DefaultPolicyService - Class in ome.security.policy: PolicyService which is configured with all Policy instances which are discovered in the Spring context and only focuses on a small subset of IObject types as specified by DefaultPolicyService.filterObject(IObject).
DefaultPolicyService() - Constructor for class ome.security.policy.DefaultPolicyService
DefaultSnapshot - Class in ome.system.metrics: Thin wrapper around Snapshot
DefaultSnapshot(Snapshot) - Constructor for class ome.system.metrics.DefaultSnapshot
DefaultTimer - Class in ome.system.metrics: Thin wrapper around Timer
DefaultTimer(Timer) - Constructor for class ome.system.metrics.DefaultTimer
DefaultTimer.Context - Class in ome.system.metrics
DefaultTimer.Context(Timer.Context) - Constructor for class ome.system.metrics.DefaultTimer.Context
defaultTimeToIdle - Variable in class ome.services.sessions.SessionManagerImpl
defaultTimeToLive - Variable in class ome.services.sessions.SessionManagerImpl
DEFAULTWORKFLOW - Static variable in class pojos.WorkflowData: The default workflow, i.e. nothing .
define(Session, String, String, long, SessionManager.CreationRequest) - Method in class ome.services.sessions.SessionManagerImpl
define(Session, String, String, long, long, long, String, String, String) - Method in class ome.services.sessions.SessionManagerImpl
Definitions - Class in ome.services.query: container for QueryParameterDef instances.
Definitions(QueryParameterDef...) - Constructor for class ome.services.query.Definitions
defs - Variable in class ome.services.query.Query: container of QueryParameterDef instances.
DelegatingStats - Class in ome.services.sessions.stats: Delegates to a SessionStats which is acquired from DelegatingStats.stats().
DelegatingStats() - Constructor for class ome.services.sessions.stats.DelegatingStats
DelegatingStats(SessionStats[]) - Constructor for class ome.services.sessions.stats.DelegatingStats
delete(long) - Method in class ome.services.scripts.ScriptRepoHelper
delete(String) - Method in class ome.tools.hibernate.QueryBuilder
Delete2I - Class in omero.cmd.graphs: Request to delete model objects, reimplementing DeleteI.
Delete2I(ACLVoter, SystemTypes, GraphPathBean, Deletion, GraphPolicy, SetMultimap<String, String>) - Constructor for class omero.cmd.graphs.Delete2I: Construct a new delete request; called from GraphRequestFactory.getRequest(Class).
deleteAnnotationLinks(AnnotationGraphSpec, Session, List<Long>) - Method in class ome.services.graphs.GraphStep: Deprecated.
DeleteBean - Class in ome.services.delete: Strict implementation of the IDelete service interface which will use the SecuritySystem via SecuritySystem.runAsAdmin(AdminAction) to forcibly delete instances.
DeleteBean(LocalAdmin, SessionFactory) - Constructor for class ome.services.delete.DeleteBean
deleteChannels(long) - Method in class ome.services.delete.DeleteBean
deleteComment(Annotation) - Method in interface ome.api.IShare: Deletes comment from the database.
deleteComment(Annotation) - Method in class ome.services.sharing.ShareBean
deleteComment_async(AMD_IShare_deleteComment, Annotation, Current) - Method in class ome.services.blitz.impl.ShareI
deleteCurrentId() - Method in class ome.services.eventlogs.PersistentEventLogLoader
deleteDataObject(IObject, Parameters) - Method in class ome.logic.PojosImpl: Implemented as specified by the IContainer I/F
deleteDataObjects(IObject[], Parameters) - Method in class ome.logic.PojosImpl: Implemented as specified by the IContainer I/F
deletedIds - Variable in class ome.services.delete.files.AbstractFileDeletions
deleteEntity(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
deleteEnumeration(T) - Method in interface ome.api.ITypes: deletes enumeration value specified by object
deleteEnumeration(T) - Method in class ome.logic.TypesImpl
deleteEnumeration_async(AMD_ITypes_deleteEnumeration, IObject, Current) - Method in class ome.services.blitz.impl.TypesI
DeleteException - Exception in ome.services.delete: 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
DeleteFacadeI - Class in omero.cmd.graphs: Deprecated.
will be removed in OMERO 5.3, so use the new graphs implementation
DeleteFacadeI(GraphRequestFactory) - Constructor for class omero.cmd.graphs.DeleteFacadeI: Deprecated.

Construct a new delete request; called from GraphRequestFactory.getRequest(Class).
deleteFiles() - Method in class ome.services.delete.Deletion: Deprecated.

For each Report use the map of tables to deleted ids to remove the files under Files, Pixels and Thumbnails if the ids no longer exist in the db.
deleteFiles(SetMultimap<String, Long>) - Method in class ome.services.delete.Deletion: Deprecated.

For each Report use the map of tables to deleted ids to remove the files under Files, Pixels and Thumbnails if the ids no longer exist in the db.
deleteFilesFromRepository(ImportContainer) - Method in class ome.formats.importer.ImportLibrary: Delete files from the managed repository.
deleteGroup(ExperimenterGroup) - Method in interface ome.api.IAdmin: removes a group by first removing all users in the group, and then deleting the actual ExperimenterGroup instance.
deleteGroup(ExperimenterGroup) - Method in class ome.logic.AdminImpl
deleteGroup_async(AMD_IAdmin_deleteGroup, ExperimenterGroup, Current) - Method in class ome.services.blitz.impl.AdminI
DeleteI - Class in omero.cmd.graphs: Deprecated.
will be removed in OMERO 5.2, so use the new graphs implementation
DeleteI(Communicator, Deletion) - Constructor for class omero.cmd.graphs.DeleteI: Deprecated.
deleteImage(long, boolean) - Method in interface ome.api.IDelete: Deletes an Image and all related (subordinate) metadata as defined below.
deleteImage(long, boolean) - Method in class ome.services.delete.DeleteBean
deleteImages(Set<Long>, boolean) - Method in interface ome.api.IDelete: Deletes several Image instances within a single transaction via the IDelete.deleteImage(long, boolean) method.
deleteImages(Set<Long>, boolean) - Method in class ome.services.delete.DeleteBean
deleteImagesByDataset(long, boolean) - Method in interface ome.api.IDelete: Deletes the user-visible Image instances of the given Dataset within a single transaction via the IDelete.deleteImage(long, boolean).
deleteImagesByDataset(long, boolean) - Method in class ome.services.delete.DeleteBean
deleteInstances(String, Collection<Long>) - Method in interface ome.services.graphs.GraphTraversal.Processor: Delete the given instances.
deleteInstances(String, Collection<Long>) - Method in class omero.cmd.graphs.BaseGraphTraversalProcessor
deleteInstances(String, Collection<Long>) - Method in class omero.cmd.graphs.NullGraphTraversalProcessor
deleteLocal() - Method in class ome.services.delete.files.AbstractFileDeletions: Helper to delete and log.
DeleteLogMessage - Class in ome.services.messages
DeleteLogMessage(Object, long) - Constructor for class ome.services.messages.DeleteLogMessage
DeleteLogsMessage - Class in ome.services.messages
DeleteLogsMessage(Object, List<Long>) - Constructor for class ome.services.messages.DeleteLogsMessage
deleteObject(IObject) - Method in interface ome.api.IUpdate: Deletes a single entity.
deleteObject(IObject) - Method in class ome.logic.UpdateImpl
deleteObject_async(AMD_IUpdate_deleteObject, IObject, Current) - Method in class ome.services.blitz.impl.UpdateI
deleteObserver(IObserver) - Method in class ome.formats.importer.ImportLibrary
deleteObserver(IObserver) - Method in interface ome.formats.importer.IObservable: Delete observer
deleteObserver(IObserver) - Method in class ome.formats.importer.util.ClientKeepAlive
deleteObserver(IObserver) - Method in class ome.formats.importer.util.ErrorHandler
deleteObserver(IObserver) - Method in class ome.formats.importer.util.FileUploader
deletePaths(String[], boolean, boolean, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI: Delete paths recursively as described in Repositories.ice.
deletePlate(long) - Method in interface ome.api.IDelete: Deletes all the images contained in a plate as if deleted by: deleteImage(id, true) so that all Dataset and Annotation links are broken, with WellSamples removed first.
deletePlate(long) - Method in class ome.services.delete.DeleteBean
deleteQuery(EventContext, String, GraphOpts) - Method in class ome.services.graphs.BaseGraphSpec: Deprecated.
deleteQuery(EventContext, String, GraphOpts) - Method in interface ome.services.graphs.GraphSpec: Deprecated.
deleteQuery(EventContext, String, GraphOpts) - Method in class ome.services.graphs.RenderingDefGraphSpec: Deprecated.

Uses direct SQL in order to workaround any security filters which may be in place since rdefs are considered outside of the security system.
deleteRepoDeleteLogs(SqlAction.DeleteLog, Current) - Method in interface ome.services.blitz.repo.RepositoryDao: Call SqlAction.deleteRepoDeleteLogs(DeleteLog) with the current context.
deleteRepoDeleteLogs(List<SqlAction.DeleteLog>, Current) - Method in interface ome.services.blitz.repo.RepositoryDao: Call SqlAction.deleteRepoDeleteLogs(DeleteLog) with the current context for a number of templates.
deleteRepoDeleteLogs(SqlAction.DeleteLog, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
deleteRepoDeleteLogs(List<SqlAction.DeleteLog>, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
deleteScript_async(AMD_IScript_deleteScript, long, Current) - Method in class ome.services.blitz.impl.ScriptI: Delete the script with id from the server.
deleteSettings(long) - Method in interface ome.api.IDelete: Deletes all rendering settings for the given Pixel id.
deleteSettings(long) - Method in class ome.services.delete.DeleteBean
DeleteStep - Class in ome.services.delete: Deprecated.
will be removed in OMERO 5.2, so use the new graphs implementation
DeleteStep(ExtendedMetadata, OmeroContext, int, List<GraphStep>, GraphSpec, GraphEntry, long[]) - Constructor for class ome.services.delete.DeleteStep: Deprecated.
DeleteStepFactory - Class in ome.services.delete: Deprecated.
will be removed in OMERO 5.2, so use the new graphs implementation
DeleteStepFactory(OmeroContext, ExtendedMetadata) - Constructor for class ome.services.delete.DeleteStepFactory: Deprecated.
deleteTransferredFiles(int, List<String>) - Method in class ome.formats.importer.transfers.AbstractFileTransfer: Method used by subclasses during #afterTransfer(int, List) if they would like to remove all the files transferred in the set.
Deletion - Class in ome.services.delete: Deprecated.
all except setup and Deletion.deleteFiles(SetMultimap) will be removed in OMERO 5.2, so use the new graphs implementation
Deletion(ApplicationContext, DeleteStepFactory, AbstractFileSystemService, OmeroContext) - Constructor for class ome.services.delete.Deletion: Deprecated.
Deletion.Builder - Class in ome.services.delete: Deprecated.

Inner class which can be used to generate a Deletion.
Deletion.Builder(AbstractFileSystemService, ExtendedMetadata) - Constructor for class ome.services.delete.Deletion.Builder: Deprecated.
deliver(String, String, InputStream) - Method in class ome.services.mail.MapAnnotationSubethaListener: Stores each email as a map annotation with MapAnnotationSubethaListener.NAMESPACE set.
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() - Method in class ome.services.blitz.util.BlitzConfiguration
destroy() - Method in class ome.services.throttling.Queue
destroy() - Method in class ome.services.util.SleepTimer: This method is called by Spring during server shut-down.
destroy() - Method in class ome.tools.spring.ShutdownSafeEhcacheManagerFactoryBean
destroy(Current) - Method in class omero.cmd.SessionI: Destruction simply decrements the reference count for a session to allow reconnecting to it.
destroy() - Method in class omero.util.ObjectFactoryRegistry.ObjectFactory
DestroySessionMessage - Class in ome.services.messages: Published before a session destruction.
DestroySessionMessage(Object, String) - Constructor for class ome.services.messages.DestroySessionMessage
detach(String) - Method in interface ome.services.sessions.SessionManager: Allows decrementing the reference count for a session without calling the actual SessionManager.close(String) logic.
detach(String) - Method in class ome.services.sessions.SessionManagerImpl
detachOnDestroy(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
DetailsI - Class in omero.model
DetailsI() - Constructor for class omero.model.DetailsI
DetailsI(client) - Constructor for class omero.model.DetailsI
detailsIndex(String[]) - Static method in class ome.tools.hibernate.HibernateUtils
Detector_Voltage - Static variable in class ome.formats.model.UnitsFactory
DetectorData - Class in pojos: Hosts a detector.
DetectorData(Detector) - Constructor for class pojos.DetectorData: Creates a new instance.
DetectorSettings_ReadOutRate - Static variable in class ome.formats.model.UnitsFactory
DetectorSettings_Voltage - Static variable in class ome.formats.model.UnitsFactory
determineColor(Length) - 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.
DIRECTORY_MIMETYPE - Static variable in class ome.services.blitz.repo.PublicRepositoryI: Mimetype used to connote a directory OriginalFile object.
dirname() - Method in class ome.services.scripts.RepoFile
dirtyMetadata(long) - Method in class ome.services.ThumbnailCtx: Whether or not the thumbnail metadata for a given Pixels ID is dirty (the RenderingDef has been updated since the Thumbnail was).
disable(Session) - Method in class ome.security.basic.AbstractSecurityFilter
disable(String...) - Method in class ome.security.basic.BasicSecuritySystem
disable(Session) - Method in interface ome.security.SecurityFilter: Reverts the call to SecurityFilter.enable(Session, EventContext).
disable(Session) - Method in class ome.security.SecurityFilterHolder
disable(String...) - Method in interface ome.security.SecuritySystem: disables components of the backend for the current Thread.
disable(String...) - Method in class ome.security.SecuritySystemHolder
disable(String...) - Method in class ome.security.sharing.SharingSecuritySystem
disableBaseFilters(Session) - Method in class ome.security.basic.AbstractSecurityFilter
disabled(MethodInvocation) - Method in class ome.tools.hibernate.EventMethodInterceptor.DisableAction
disableFilters(Session) - Method in class ome.services.query.Query: turns the filters off that are listed in Query.newlyEnabledFilters
disableReadFilter(Object) - Method in class ome.security.basic.BasicSecuritySystem: disable this filer.
disassemble(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
discover() - Method in interface ome.api.ILdap: Discovers and lists Experimenters who are present in the remote LDAP server and in the local DB but have the ldap property set to false.
discover() - Method in class ome.logic.LdapImpl
discover_async(AMD_ILdap_discover, Current) - Method in class ome.services.blitz.impl.LdapI
discoverGroups() - Method in interface ome.api.ILdap: Discovers and lists ExperimenterGroups which are present in the remote LDAP server and in the local DB but have the ldap property set to false.
discoverGroups() - Method in class ome.logic.LdapImpl
discoverGroups_async(AMD_ILdap_discoverGroups, Current) - Method in class ome.services.blitz.impl.LdapI
discriminator(String) - Method in class ome.services.roi.GeomTool: Maps from multiple possible user-provided names of shapes (e.g.
DiskUsageI - Class in omero.cmd.graphs: Calculate the disk usage entailed by the given objects.
DiskUsageI(PixelsService, ThumbnailService, GraphPathBean) - Constructor for class omero.cmd.graphs.DiskUsageI: Construct a disk usage request.
dispatch(String[]) - Static method in class prefs: Uses the first string in the argument array to reflectively invoke another method with the same signature on prefs.
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
DoAllI - Class in omero.cmd.basic: Permits performing multiple operations
DoAllI(OmeroContext) - Constructor for class omero.cmd.basic.DoAllI
doCheck() - Method in class ome.services.util.DBEnumCheck
doCheck() - Method in class ome.services.util.DBUnicodeUnitsCheck
doCheckPassword(String, String, Properties, boolean) - Method in class ome.security.auth.FilePasswordProvider
doClose() - Method in class ome.services.sharing.BlobShareStore
doClose() - Method in class ome.services.sharing.ShareStore
doClose - Variable in class omero.cmd.SessionI
doContains(long, Class<T>, long) - Method in class ome.services.sharing.BlobShareStore
doContains(ShareData, Class<T>, long) - Method in class ome.services.sharing.BlobShareStore
doContains(long, Class<T>, long) - Method in class ome.services.sharing.ShareStore
doDestroy() - Method in class omero.cmd.SessionI: Performs the actual cleanup operation on all the resources shared between this and other ServiceFactoryI instances in the same Session.
doFilter(String, Object) - Method in class ome.tools.hibernate.ProxyCleanupFilter
doFilter(String, Filterable) - Method in class ome.tools.hibernate.ProxySafeFilter
doFilter(String, Collection) - Method in class ome.tools.hibernate.ProxySafeFilter
doImport() - Method in class ome.formats.importer.ImportFixture: runs import by looping through all files and then calling: ImportLibrary#open(String) ImportLibrary#calculateImageCount(String) ImportLibrary#importMetadata() ImportLibrary#importData(long, String)
doImport() - Method in class ome.formats.importer.util.TinyImportFixture
doImport() - Method in class ome.formats.OMEROImportFixture: runs import by looping through all files and then calling: ImportLibrary#open(String) ImportLibrary#calculateImageCount(String) ImportLibrary#importMetadata() ImportLibrary#importData(long, String, ome.formats.testclient.ImportLibrary.Step)
doIndexing(FullTextSession) - Method in class ome.services.fulltext.FullTextIndexer
doInHibernate(Session) - Method in class ome.services.query.Query: template method defined by HibernateTemplate.
doInit() - Method in class ome.services.sharing.BlobShareStore
doInit() - Method in class ome.services.sharing.ShareStore
doLogin(boolean, boolean) - Method in class ome.security.basic.EventHandler
doLookup(String, String, Long) - Method in class ome.services.query.HierarchyNavigator: Look up which objects of a given type relate to the given query object.
doLookup(T, E) - Method in class ome.services.query.HierarchyNavigatorWrap: Look up which objects of a given type relate to the given query object.
doMore(int) - Method in class ome.services.fulltext.FullTextIndexer: Default implementation suggests doing more if fewer than FullTextIndexer.reps runs have been made and if there are still more than EventLogLoader.batchSize x 100 backlog entries.
doParse(File) - Method in class ome.services.fulltext.FileParser: Template method to parse a File into manageable chunks.
doParse(File) - Method in class ome.services.fulltext.PdfParser
doRun() - Method in class ome.services.fulltext.FullTextThread: Passes the FullTextIndexer instance to Executor.Work#doWork(org.springframework.transaction.TransactionStatus, org.hibernate.Session, ome.system.ServiceFactory) between calls to DetailsFieldBridge.lock() and DetailsFieldBridge.unlock() in order to guarantee that no other FieldBridge can edit the property.
doRun() - Method in class ome.services.pixeldata.PixelDataThread: Loads event logs from the PixelDataHandler processing them all then in a background thread via a ExecutorCompletionService.
doRun() - Method in class ome.services.procs.ProcessManager
doRun() - Method in class ome.services.util.ExecutionThread
doSet(Share, ShareData, List<ShareItem>) - Method in class ome.services.sharing.BlobShareStore
doSet(Share, ShareData, List<ShareItem>) - Method in class ome.services.sharing.ShareStore
doStop() - Method in class omero.grid.InteractiveProcessorI
dot(PlanePoint) - Method in class ome.util.math.geom2D.PlanePoint: Calulates the dot product of this vector by the specified argument.
doThumbnails - Variable in class ome.formats.importer.ImportConfig
DOUBLE(Connection, List<Double>) - Method in interface ome.tools.hibernate.ListAsSQLArrayUserType.ArrayFactory
DOUBLE - Static variable in class omeis.providers.re.data.PlaneFactory: Identifies the type used to store pixel values.
DOUBLE_COMPLEX_TYPE - Static variable in class pojos.PixelsData: Identifies the type used to store pixel values.
DOUBLE_TYPE - Static variable in class omeis.providers.re.data.PlaneFactory: Identifies the DOUBLE data type used to store pixel values, as per OME spec.
DOUBLE_TYPE - Static variable in class pojos.PixelsData: Identifies the type used to store pixel values.
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.
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: Loads #rep EventLog instances and returns them.
doWork(Session, ServiceFactory) - Method in class ome.services.procs.ProcessManager.Work
doWork(Session, ServiceFactory) - Method in class ome.services.search.AnnotatedWith
doWork(Session, ServiceFactory) - Method in class ome.services.search.Complement
doWork(Session, ServiceFactory) - Method in class ome.services.search.FullText
doWork(Session, ServiceFactory) - Method in class ome.services.search.HqlQuery
doWork(Session, ServiceFactory) - Method in class ome.services.search.Intersection
doWork(Session, ServiceFactory) - Method in class ome.services.search.SimilarTerms
doWork(Session, ServiceFactory) - Method in class ome.services.search.TagsAndGroups
doWork(Session, ServiceFactory) - Method in class ome.services.search.Union
doWork(SqlAction) - Method in interface ome.services.util.Executor.SqlWork
doWork(Session, ServiceFactory) - Method in interface ome.services.util.Executor.Work: Work method.
drop(String[]) - Static method in class prefs: Drops the entire profile (subnode) via Preferences.removeNode().
dryRun - Variable in class ome.services.fulltext.FullTextIndexer
dsAllQuery - Static variable in class ome.services.delete.QueryConstraints
dsNotOwnQuery - Static variable in class ome.services.delete.QueryConstraints

E

ec - Variable in class ome.services.graphs.GraphStep: Deprecated.

An event context which has been initialized for a particular group, i.e.
editScript_async(AMD_IScript_editScript, OriginalFile, String, Current) - Method in class ome.services.blitz.impl.ScriptI
ElectricPotentialI - Class in omero.model: Blitz wrapper around the ElectricPotential class.
ElectricPotentialI() - Constructor for class omero.model.ElectricPotentialI
ElectricPotentialI(double, UnitsElectricPotential) - Constructor for class omero.model.ElectricPotentialI
ElectricPotentialI(double, Unit<ElectricPotential>) - Constructor for class omero.model.ElectricPotentialI
ElectricPotentialI(ElectricPotential, Unit<ElectricPotential>) - Constructor for class omero.model.ElectricPotentialI: Copy constructor that converts the given ElectricPotential based on the given ome-xml enum
ElectricPotentialI(double, UnitsElectricPotential) - Constructor for class omero.model.ElectricPotentialI: Copy constructor that converts the given ElectricPotential based on the given ome.model enum
ElectricPotentialI(ElectricPotential, String) - Constructor for class omero.model.ElectricPotentialI: Copy constructor that converts the given ElectricPotential based on the given enum string.
ElectricPotentialI(ElectricPotential, UnitsElectricPotential) - Constructor for class omero.model.ElectricPotentialI: Copy constructor that converts between units if possible.
ElectricPotentialI(ElectricPotential) - Constructor for class omero.model.ElectricPotentialI: Convert a Bio-Formats Length to an OMERO Length.
elementType - Variable in class ome.services.query.CollectionQueryParameterDef
ellipse(double, double, double, double) - Method in class ome.services.roi.GeomTool
ellipse(double, double, double, double, int, int) - Method in class ome.services.roi.GeomTool
EllipseArea - Class in ome.util.math.geom2D: Represents an ellipse in the Euclidean space R².
EllipseArea(float, float, float, float) - Constructor for class ome.util.math.geom2D.EllipseArea: Creates a new instance.
EllipseData - Class in pojos: Represents an ellipse in the Euclidean space R².
EllipseData(Shape) - Constructor for class pojos.EllipseData: Creates a new instance of Ellipse data from an existing shape.
EllipseData() - Constructor for class pojos.EllipseData: Creates a new instance of EllipseData.
EllipseData(double, double, double, double) - Constructor for class pojos.EllipseData: Creates a new instance of the EllipseData.
em - Variable in class ome.services.delete.Deletion.Builder: Deprecated.
em - Variable in class ome.services.graphs.BaseGraphSpec: Deprecated.
em - Variable in class ome.services.graphs.GraphStep: Deprecated.
email - Variable in class ome.formats.importer.ImportConfig
EMAIL - 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.
emptyPath - Static variable in class ome.services.blitz.repo.path.FsFile: the FsFile that has no path components
enable(Session, EventContext) - Method in class ome.security.basic.AllGroupsSecurityFilter: Since we assume that the group is "-1" for this method, we have to pass in lists of all groups as we did before group permissions (~4.2).
enable(String...) - Method in class ome.security.basic.BasicSecuritySystem
enable(Session, EventContext) - Method in class ome.security.basic.OneGroupSecurityFilter
enable(Session, EventContext) - Method in interface ome.security.SecurityFilter: Enables this filter with the settings from this filter.
enable(Session, EventContext) - Method in class ome.security.SecurityFilterHolder
enable(String...) - Method in interface ome.security.SecuritySystem: enables components of the backend for the current Thread.
enable(String...) - Method in class ome.security.SecuritySystemHolder
enable(String...) - Method in class ome.security.sharing.SharingSecuritySystem
enableBaseFilters(Session, int, Long) - Method in class ome.security.basic.AbstractSecurityFilter
enableFilters(Session) - Method in class ome.services.query.PojosFindHierarchiesQueryDefinition
enableFilters(Session) - Method in class ome.services.query.PojosGetImagesByOptionsQueryDefinition
enableFilters(Session) - Method in class ome.services.query.PojosGetImagesQueryDefinition
enableFilters(Session) - Method in class ome.services.query.PojosGetUserImagesQueryDefinition
enableFilters(Session) - Method in class ome.services.query.PojosLoadHierarchyQueryDefinition
enableFilters(Session) - Method in class ome.services.query.Query: does nothing by default, but can be overridden by subclasses to enable particular filters.
enableKeepAlive(int) - Method in class omero.client: Resets the "omero.keep_alive" property on the current Communicator which is used on initialization to determine the time-period between checks.
enableReadFilter(Object) - Method in class ome.security.basic.BasicSecuritySystem: enables the read filter such that graph queries will have non-visible entities silently removed from the return value.
encodePassword(String) - Method in class ome.security.auth.ConfigurablePasswordProvider: Encodes the password as it would be encoded for a check by ConfigurablePasswordProvider.comparePasswords(String, String)
encodePassword(Long, String, boolean, PasswordUtil) - Method in class ome.security.auth.ConfigurablePasswordProvider
encodePassword(String) - Method in interface ome.security.auth.PasswordUtility
encodeSaltedPassword(Long, String) - Method in class ome.security.auth.ConfigurablePasswordProvider: Encodes the password as it would be encoded for a check by ConfigurablePasswordProvider.comparePasswords(String, String) salting the password with the given userId if it's provided.
encryptedConnection - Variable in class ome.formats.importer.ImportConfig
endIO(int) - Method in class omeis.providers.re.RenderingStats: Notifies the end of pixels data retrieval for the specified wavelength (channel).
endMalloc() - Method in class omeis.providers.re.RenderingStats: Notifies the end of the allocation of an RGB memory buffers for the rendering process.
endRendering() - Method in class omeis.providers.re.RenderingStats: Notifies the end of the trasnformation of the raw pixels data.
endTime(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
entityToStringLong(E) - Method in class ome.services.query.HierarchyNavigatorWrap: Convert a model object to the type string and database ID expected by HierarchyNavigator.
entityType - Variable in class ome.services.messages.EventLogMessage
entries - Variable in class ome.services.graphs.BaseGraphSpec: Deprecated.

The paths which make up this graph specification.
entries() - Method in class ome.services.graphs.BaseGraphSpec: Deprecated.
entries() - Method in interface ome.services.graphs.GraphSpec: Deprecated.

Returns a copy of the list of GraphEntry instances contained in this GraphSpec
Entry - Class in ome.services.blitz: OMERO.blitz startup code.
Entry(String) - Constructor for class ome.services.blitz.Entry: Stores name of the OmeroContext which is to be used by this instance.
entry - Variable in class ome.services.graphs.GraphStep: Deprecated.

GraphEntry instance which is active for this step.
entrySet() - Method in class ome.services.graphs.GraphState: Deprecated.
entrySet() - Method in interface ome.services.graphs.GraphStep.Callback: Deprecated.
EnumerationException - Exception in ome.formats.enums
EnumerationException(String, Class<? extends IObject>, String) - Constructor for exception ome.formats.enums.EnumerationException
EnumerationHandler - Interface in ome.formats.enums.handler: An enumeration handler whose purpose is to provide extra logic, such as regular expression matching, for the lookup of enumerations for a specific type.
EnumerationProvider - Interface in ome.formats.enums: An enumeration provider, whose job is to make OMERO enumerations available to a consumer based on a set of criteria.
EnumHandlerFactory - Class in ome.formats.enums.handler: Factory for all available enumeration handlers.
EnumHandlerFactory() - Constructor for class ome.formats.enums.handler.EnumHandlerFactory
env() - Method in class omero.client: Helper method to access session environment
ENV - Static variable in class prefs: Environment variable which can be set to override the current, active profile.
environment(String, String) - Method in class ome.services.sessions.SessionManagerImpl
EPSILON - Static variable in class ome.logic.RenderingSettingsImpl: The value used to compare double and float.
equals(Object) - Method in class ome.services.blitz.repo.CheckedPath: Instances are equal if their string representations match.
equals(Object) - Method in class ome.services.blitz.repo.path.FsFile: Instances are equal if their string representations match.
equals(Object) - Method in class ome.tools.FileSystem: Public equals implementation based on name only (very loose equals)
equals(Object, Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
equals(Object) - Method in class ome.util.math.geom2D.Line: Overridden to reflect equality of abstract values (data object) as opposite to object identity.
equals(Object) - Method in class ome.util.math.geom2D.PlanePoint: Overridden to reflect equality of abstract values (data object) as opposite to object identity.
equals(double, double) - Method in class ome.util.math.geom2D.PlanePoint: Check to see if the point values are equal.
equals(double, double, double) - Method in class ome.util.math.geom2D.Segment: Performs an equality test based on a point on this line defined by k as in getPoint() and another given point.
equals(Object) - Method in class ome.util.math.geom2D.Segment: Overridden to reflect equality of abstract values (data object) as opposite to object identity.
equals(Object) - Method in class omeis.providers.re.codomain.CodomainMapContext: This method is overridden so that objects of the same class are considered the same.
equals(Object) - Method in class omeis.providers.re.data.PlaneDef: Overridden to reflect equality of abstract values (data object) as opposite to object identity.
equals(Object) - Method in class omero.cmd.graphs.Preprocessor.GraphModifyTarget: Deprecated.
equals(Object) - Method in class omero.model.ElectricPotentialI
equals(Object) - Method in class omero.model.FrequencyI
equals(Object) - Method in class omero.model.LengthI
equals(Object) - Method in class omero.model.PowerI
equals(Object) - Method in class omero.model.PressureI
equals(Object) - Method in class omero.model.TemperatureI
equals(Object) - Method in class omero.model.TimeI
equals(Object) - Method in class pojos.ROICoordinate: Overridden to control if the passed object equals the current one.
ERROR - Static variable in interface ome.api.JobHandle
error() - Method in class ome.services.delete.Deletion: Deprecated.
error(SqlAction.DeleteLog, Throwable) - Method in class ome.services.messages.DeleteLogMessage
error(String, Object...) - Method in class omero.cmd.Helper
error(Throwable, String, Object...) - Method in class omero.cmd.Helper
ErrorContainer - Class in ome.formats.importer.util: Container for errors
ErrorContainer() - Constructor for class ome.formats.importer.util.ErrorContainer
errorCount - Variable in class ome.formats.importer.ImportEvent.IMPORT_SUMMARY
errorCount() - Method in class ome.formats.importer.util.ErrorHandler
ErrorHandler - Class in ome.formats.importer.cli: IObserver based on the gui ErrorHandler code which collects all exceptions during ImportLibrary.importCandidates(ome.formats.importer.ImportConfig, ome.formats.importer.ImportCandidates) and after the import is finished offers to submit them via the feedback system.
ErrorHandler(ImportConfig) - Constructor for class ome.formats.importer.cli.ErrorHandler
ErrorHandler - Class in ome.formats.importer.util: Top of the error handling hierarchy.
ErrorHandler(ImportConfig) - Constructor for class ome.formats.importer.util.ErrorHandler: Initialize
ErrorHandler.EXCEPTION_EVENT - Class in ome.formats.importer.util
ErrorHandler.EXCEPTION_EVENT(Exception) - Constructor for class ome.formats.importer.util.ErrorHandler.EXCEPTION_EVENT
ErrorHandler.FILE_EXCEPTION - Class in ome.formats.importer.util: ErrorHandler.FILE_EXCEPTIONs are thrown any time in the context of a particular file and otherwise unspecified exception takes place.
ErrorHandler.FILE_EXCEPTION(String, Exception, String[], String) - Constructor for class ome.formats.importer.util.ErrorHandler.FILE_EXCEPTION
ErrorHandler.INTERNAL_EXCEPTION - Class in ome.formats.importer.util
ErrorHandler.INTERNAL_EXCEPTION(String, Exception, String[], String) - Constructor for class ome.formats.importer.util.ErrorHandler.INTERNAL_EXCEPTION
ErrorHandler.MISSING_LIBRARY - Class in ome.formats.importer.util: A ErrorHandler.FILE_EXCEPTION caused specifically by some library (native or otherwise) not being installed locally.
ErrorHandler.MISSING_LIBRARY(String, MissingLibraryException, String[], String) - Constructor for class ome.formats.importer.util.ErrorHandler.MISSING_LIBRARY
ErrorHandler.UNKNOWN_FORMAT - Class in ome.formats.importer.util: Unlike ErrorHandler.FILE_EXCEPTION, UNKNOWN_FORMAT does not have a reader since bio-formats is telling us that it does not know how to handle the given file.
ErrorHandler.UNKNOWN_FORMAT(String, Exception, Object) - Constructor for class ome.formats.importer.util.ErrorHandler.UNKNOWN_FORMAT
ErrorHandler.UNREADABLE_FILE - Class in ome.formats.importer.util: Similar to ErrorHandler.UNKNOWN_FORMAT UNREADABLE_FILE specifies that the file which is being accessed is unreadable (does not exist or canRead is false), so if the user is specifically saying that the file should be imported, there may be some underlying issue.
ErrorHandler.UNREADABLE_FILE(String, Exception, Object) - Constructor for class ome.formats.importer.util.ErrorHandler.UNREADABLE_FILE
errorIfInvalid(QueryParameter) - Method in class ome.services.query.CollectionQueryParameterDef
errorIfInvalid(QueryParameter) - Method in class ome.services.query.QueryParameterDef: validation method called by Query.checkParameters().
errorIfInvalidState() - Method in class ome.services.JobBean
errorIfInvalidState() - Method in class ome.services.RenderingBean
errorIfInvalidState() - Method in class ome.services.ThumbnailBean
errorIfNullPixels() - Method in class ome.services.RenderingBean: Throws an ApiUsageException if the pixels are not set.
errorIfNullPixels() - Method in class ome.services.ThumbnailBean
errorIfNullPixelsAndRenderingDef() - Method in class ome.services.ThumbnailBean
errorIfNullRenderer() - Method in class ome.services.RenderingBean: Reloads the rendering engine if null and has been made passive or throws an ApiUsageException if the rendering engine is not set.
errorIfNullRenderingDef() - Method in class ome.services.RenderingBean: Throws an ApiUsageException if the rendering settings are not set.
errorIfNullRenderingDef() - Method in class ome.services.ThumbnailBean
errorOnViolation(Class, Method, Object[]) - Static method in class ome.annotations.ApiConstraintChecker
errors - Variable in class ome.formats.importer.util.ErrorHandler
evaluateLinkages(IObject) - Method in class ome.security.basic.OmeroInterceptor: Checks the details of the objects which the given object links to in order to guarantee that linkages are valid.
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
EventLogFailure - Class in ome.services.eventlogs: Signifies that the processing of a EventLog has failed.
EventLogFailure(EventLogLoader, EventLog, Throwable) - Constructor for class ome.services.eventlogs.EventLogFailure
EventLogListener - Class in ome.security.basic: responsible for responding to all Hibernate Events.
EventLogListener(CurrentDetails) - Constructor for class ome.security.basic.EventLogListener: main constructor.
EventLogLoader - Class in ome.services.eventlogs: Data access object for the FullTextIndexer which provides an Iterator interface for EventLog instances to be properly indexed.
EventLogLoader() - Constructor for class ome.services.eventlogs.EventLogLoader
EventLogMessage - Class in ome.services.messages: Published only when an event log should be saved at the end of a transaction.
EventLogMessage(Object, String, Class<? extends IObject>, List<Long>) - Constructor for class ome.services.messages.EventLogMessage
EventLogQueue - Class in ome.services.eventlogs: PersistentEventLogLoader implementation which loads many rows at the same time, culling out duplicates in order to speed up indexing.
EventLogQueue() - Constructor for class ome.services.eventlogs.EventLogQueue
EventLogQueue(Metrics, int, String[], String[]) - Constructor for class ome.services.eventlogs.EventLogQueue
EventLogsMessage - Class in ome.services.messages: Published with the final collection of EventLog instances which will be saved.
EventLogsMessage(Object, Multimap<String, EventLog>) - Constructor for class ome.services.messages.EventLogsMessage
EventMethodInterceptor - Class in ome.tools.hibernate: filter which can be added to any event type in order to catch execution.
EventMethodInterceptor() - Constructor for class ome.tools.hibernate.EventMethodInterceptor
EventMethodInterceptor(EventMethodInterceptor.Action) - Constructor for class ome.tools.hibernate.EventMethodInterceptor
EventMethodInterceptor.Action - Class in ome.tools.hibernate
EventMethodInterceptor.Action() - Constructor for class ome.tools.hibernate.EventMethodInterceptor.Action
EventMethodInterceptor.DisableAction - Class in ome.tools.hibernate
EventMethodInterceptor.DisableAction() - Constructor for class ome.tools.hibernate.EventMethodInterceptor.DisableAction
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.
exclusions - Variable in class ome.formats.importer.cli.CommandLineImporter: FileExclusion mechanisms for skipping candidates
exec(File, File) - Method in class ome.formats.importer.transfers.AbstractExecFileTransfer: Executes a local command and fails on non-0 return codes.
execute(HibernateCallback) - Method in interface ome.api.local.LocalQuery: Executes a HibernateCallback
execute(Query<T>) - Method in interface ome.api.local.LocalQuery: Executes a locally defined Query.
execute(String[]) - Method in class ome.formats.importer.ImportCandidates: Method called during ImportCandidates.ImportCandidates(OMEROWrapper, String[], IObserver) to operate on all the given paths.
execute(HibernateCallback) - Method in class ome.logic.QueryImpl
execute(Query<T>) - Method in class ome.logic.QueryImpl
execute(int) - Method in class ome.services.delete.Deletion: Deprecated.
execute(int) - Method in class ome.services.graphs.GraphState: Deprecated.
execute(Principal, Executor.Work) - Method in interface ome.services.util.Executor: Call #execute(Map, Principal, Work) with a null call context.
execute(Map<String, String>, Principal, Executor.Work) - Method in interface ome.services.util.Executor: Executes a Executor.Work instance wrapped in two layers of AOP.
execute(Principal, Executor.Work) - Method in class ome.services.util.Executor.Impl: Call #execute(Map, Principal, Work) with a null call context.
execute(Map<String, String>, Principal, Executor.Work) - Method in class ome.services.util.Executor.Impl: Executes a Executor.Work instance wrapped in two layers of AOP.
execute(RMap, Current) - Method in class omero.grid.InteractiveProcessorI
executePasswordCheck(String, String) - Method in interface ome.services.sessions.SessionManager: Executes a password check using the Executor framework.
executePasswordCheck(String, String) - Method in class ome.services.sessions.SessionManagerImpl
executePost(String, Map<String, String>) - Method in class ome.formats.importer.util.ErrorHandler: Execute a post with the given post list.
executePost() - Method in class ome.formats.importer.util.HtmlMessenger: Execute a post action and retrieve server reply This method executes the post created when this class is instantiated
executeSql(Executor.SqlWork) - Method in interface ome.services.util.Executor: Executes a Executor.SqlWork wrapped with a transaction.
executeSql(Executor.SqlWork) - Method in class ome.services.util.Executor.Impl: Executes a SqkWork in transaction.
ExecutionThread - Class in ome.services.util: Thread which can be started and will appropriately acquire a session, then use the Executor to complete its work.
ExecutionThread(SessionManager, Executor, Executor.Work, Principal) - Constructor for class ome.services.util.ExecutionThread: Main constructor.
executor - Variable in class ome.logic.UpdateImpl
executor - Variable in class ome.services.blitz.fire.SessionManagerI
executor - Variable in class ome.services.blitz.redirect.AbstractRedirector
executor - Variable in class ome.services.blitz.repo.RepositoryDaoImpl
executor - Variable in class ome.services.sessions.SessionManagerImpl
executor - Variable in class ome.services.sharing.ShareBean
executor - Variable in class ome.services.util.ExecutionThread
Executor - Interface in ome.services.util: Simple execution/work interface which can be used for internal tasks which need to have a full working implementation.
executor - Variable in class omero.cmd.SessionI: Executor to be used by servant implementations which do not delegate to the server package where all instances are wrapped with AOP for dealing with Hibernate.
Executor.Descriptive - Class in ome.services.util
Executor.Descriptive(Object, String, Object...) - Constructor for class ome.services.util.Executor.Descriptive
Executor.Descriptive(String, String, Object...) - Constructor for class ome.services.util.Executor.Descriptive
Executor.Impl - Class in ome.services.util
Executor.Impl(CurrentDetails, SessionFactory, SqlAction, String[]) - Constructor for class ome.services.util.Executor.Impl
Executor.Impl(CurrentDetails, SessionFactory, SqlAction, String[], ExecutorService) - Constructor for class ome.services.util.Executor.Impl
Executor.Priority - Enum in ome.services.util
Executor.SimpleSqlWork - Class in ome.services.util: Simple adapter which takes a String for Executor.Descriptive.description
Executor.SimpleSqlWork(Object, String, Object...) - Constructor for class ome.services.util.Executor.SimpleSqlWork
Executor.SimpleWork - Class in ome.services.util: Simple adapter which takes a String for Executor.Descriptive.description
Executor.SimpleWork(Object, String, Object...) - Constructor for class ome.services.util.Executor.SimpleWork
Executor.SqlWork - Interface in ome.services.util: Work SPI to perform actions related to stateless sessions.
Executor.StatefulWork - Interface in ome.services.util: In the case of a stateful work order, the bean itself needs to be associated with the sessionHandler and thread rather than the word instance itself.
Executor.Work<X> - Interface in ome.services.util: Work SPI to perform actions within the server as if they were fully wrapped in our service logic.
executorWorkCall(Executor.Work) - Method in class ome.services.blitz.impl.AbstractAmdServant
exists() - Method in interface ome.api.RawFileStore: Checks to see if a raw file exists with the file ID that the service was initialized with.
exists(OriginalFile) - Method in class ome.io.nio.OriginalFilesService: Returns whether or not an OriginalFile exists on disk.
exists() - Method in class ome.services.blitz.repo.CheckedPath: Check if this file actually exists on the underlying filesystem.
exists() - Method in class ome.services.RawFileBean
exists_async(AMD_RawFileStore_exists, Current) - Method in class ome.services.blitz.impl.RawFileStoreI
exit(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.
expandTemplateRootOwnedPath(EventContext, ServiceFactory) - Method in class ome.services.blitz.repo.ManagedRepositoryI: Expand the root-owned segment of the template path.
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: Deprecated.
will be removed in OMERO 5.2, so use the new graphs implementation
ExporterIndex(int) - Constructor for class ome.services.export.ExporterIndex: Deprecated.
ExporterStep - Class in ome.services.export: Deprecated.
will be removed in OMERO 5.2, so use the new graphs implementation
ExporterStep(ExtendedMetadata, int, List<GraphStep>, GraphSpec, GraphEntry, long[]) - Constructor for class ome.services.export.ExporterStep: Deprecated.
ExporterStepFactory - Class in ome.services.export: Deprecated.
will be removed in OMERO 5.2, so use the new graphs implementation
ExporterStepFactory(Executor, Principal, ExtendedMetadata) - Constructor for class ome.services.export.ExporterStepFactory: Deprecated.
ExtendedMetadata - Interface in ome.tools.hibernate: extension of the model metadata provided by SessionFactory.
ExtendedMetadata.Immutables - Class in ome.tools.hibernate
ExtendedMetadata.Impl - Class in ome.tools.hibernate: Sole implementation of ExtendedMetadata.
ExtendedMetadata.Impl() - Constructor for class ome.tools.hibernate.ExtendedMetadata.Impl
ExtendedMetadata.Locks - Class in ome.tools.hibernate: inner class which wraps the information (index number, path, etc) related to what fields a particular object can lock.
ExtendedMetadata.Relationship - Class in ome.tools.hibernate: Simple value class to maintain all of the state for use by ExtendedMetadata.getRelationship(String, String) and ExtendedMetadata.getSQLJoin(String, String, String, String).

F

factory - Variable in class ome.security.basic.EventHandler
factory - Variable in class ome.services.blitz.impl.RoiI
factory - Variable in class ome.services.blitz.impl.ScriptI
factory - Variable in class ome.services.blitz.impl.TimelineI
factory - Variable in class ome.services.roi.GeomTool
factory - Variable in class ome.services.sessions.SessionManagerImpl
factory - Variable in class ome.services.util.Executor.Impl
factory - Variable in class ome.tools.hibernate.ListAsSQLArrayUserType
FACTORY - Static variable in class ome.tools.hibernate.SqlArray
Factory - Static variable in class omero.model.DetailsI
Factory - Static variable in class omero.model.ElectricPotentialI
Factory - Static variable in class omero.model.FrequencyI
Factory - Static variable in class omero.model.LengthI
Factory - Static variable in class omero.model.PermissionsI
Factory - Static variable in class omero.model.PowerI
Factory - Static variable in class omero.model.PressureI
Factory - Static variable in class omero.model.TemperatureI
Factory - Static variable in class omero.model.TimeI
fail(File, Long, Long) - Method in class ome.services.delete.files.AbstractFileDeletions
fail(ERR, Throwable, String, String...) - Method in class omero.cmd.Helper: Calls #fail(ERR, String, Map) with the output of Helper.params(String...).
fail(ERR, Throwable, String, Map<String, String>) - Method in class omero.cmd.Helper: Sets the status.flags and the ERR properties appropriately and also stores the message and stacktrace of the throwable in the parameters.
FailedLoginMailSender - Class in ome.services.mail: On an LoginAttemptMessage potentially send an email to administrators or the user herself to alert of possible security issues.
FailedLoginMailSender() - Constructor for class ome.services.mail.FailedLoginMailSender
failingChecksums - Variable in class ome.formats.importer.ImportEvent.FILESET_UPLOAD_END
failLocationCheck(File, String) - Method in class ome.formats.importer.transfers.AbstractExecFileTransfer
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(String, String, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
file() - Method in class ome.services.scripts.RepoFile
FILE_TRANSFER_NS - Static variable in class pojos.AnnotationData: The name space used to identify the file transfer type.
FileAnnotationData - Class in pojos: Annotation to upload files to the server.
FileAnnotationData(File) - Constructor for class pojos.FileAnnotationData: Creates a new instance.
FileAnnotationData(FileAnnotation) - Constructor for class pojos.FileAnnotationData: Creates a new instance.
FileBuffer - Class in ome.io.nio: Raw file buffer which provides I/O operations within the OMERO file repository.
FileBuffer(String, String) - Constructor for class ome.io.nio.FileBuffer: Default constructor allowing to pass in a non-"rw" file mode.
fileById(long, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
fileContext(long, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl: Create a String-String map which can be used as the context for a call to Executor.execute based on the group of the file object.
FileData - Class in pojos: DataObject used to handle the file visible via FS.
FileData(OriginalFile) - Constructor for class pojos.FileData: Creates a new instance.
FileData(OriginalFile, boolean) - Constructor for class pojos.FileData: Creates a new instance.
FileData(OriginalFile, boolean, boolean) - Constructor for class pojos.FileData: Creates a new instance.
FileDeleter - Class in ome.services.delete.files: Helper class which sorts through a number of file-based deletions before processing them.
FileDeleter(OmeroContext, AbstractFileSystemService, SetMultimap<String, Long>) - Constructor for class ome.services.delete.files.FileDeleter
FileDeleterGraphState - Class in ome.services.delete.files: Deprecated.
will be removed in OMERO 5.2, so use the new graphs implementation
FileDeleterGraphState(OmeroContext, AbstractFileSystemService, GraphState, String, long) - Constructor for class ome.services.delete.files.FileDeleterGraphState: Deprecated.
FileExclusion - Interface in ome.formats.importer.exclusions: Voter given the opportunity by the ImportLibrary to cancel the importing of a given file.
fileExists(String, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
fileIndex - Variable in class ome.formats.importer.ImportEvent.FILE_UPLOAD_EVENT
FileMaker - Class in ome.services.blitz.repo: Utility class for creating and cleaning up a repository lock file.
FileMaker(String) - Constructor for class ome.services.blitz.repo.FileMaker
filename - Variable in class ome.formats.importer.ImportEvent.FILE_UPLOAD_EVENT
fileName - Variable in class ome.formats.importer.ImportSize
filename - Variable in class ome.formats.importer.util.ErrorHandler.FILE_EXCEPTION
filename - Variable in class ome.formats.importer.util.ErrorHandler.INTERNAL_EXCEPTION
filename - Variable in class ome.formats.importer.util.ErrorHandler.UNKNOWN_FORMAT
filename - Variable in class ome.formats.importer.util.ErrorHandler.UNREADABLE_FILE
FILENAME - Static variable in class ome.formats.importer.util.TinyImportFixture: Hard-coded filename of the image to be imported
FilenameExclusion - Class in ome.formats.importer.exclusions: Voter which checks the filename (not full path) of a given File along with the checksum to detect duplicates.
FilenameExclusion() - Constructor for class ome.formats.importer.exclusions.FilenameExclusion
FileParser - Class in ome.services.fulltext: Object which attempts to parse any file given to it.
FileParser() - Constructor for class ome.services.fulltext.FileParser
FilePasswordProvider - Class in ome.security.auth: Example password provider which uses the given file as password lookup.
FilePasswordProvider(PasswordUtil, File) - Constructor for class ome.security.auth.FilePasswordProvider
FilePasswordProvider(PasswordUtil, File, boolean) - Constructor for class ome.security.auth.FilePasswordProvider
filePath - Variable in class ome.io.bioformats.BfPixelBuffer
FilePathNamingValidator - Class in ome.services.blitz.repo.path
FilePathNamingValidator(FilePathRestrictions...) - Constructor for class ome.services.blitz.repo.path.FilePathNamingValidator
FilePathResolver - Interface in ome.io.nio: Resolver for file paths and related metadata.
FilePathRestrictionInstance - Enum in ome.services.blitz.repo.path
FilePathRestrictions - Class in ome.services.blitz.repo.path: Capture a set of rules by which local files may not be named on the file-system.
FilePathRestrictions(SetMultimap<Integer, Integer>, Set<String>, Set<String>, Set<String>, Set<Character>) - Constructor for class ome.services.blitz.repo.path.FilePathRestrictions: Construct a set of rules by which local files may not be named on the file-system.
filePathRestrictions - Variable in class ome.services.blitz.repo.PublicRepositoryI
files - Variable in class ome.services.fulltext.FullTextBridge
FILES_PATH - Static variable in class ome.io.nio.AbstractFileSystemService
fileset - Variable in class ome.formats.importer.ImportEvent.IMPORT_DONE
FilesetData - Class in pojos: Wraps a file set object.
FilesetData(Fileset) - Constructor for class pojos.FilesetData: Creates a new instance.
FileSizeChecksumProviderImpl - Class in ome.util.checksum: Trivial checksum provider whose hash is simply the number of bytes that were put into the calculation.
FileSizeChecksumProviderImpl() - Constructor for class ome.util.checksum.FileSizeChecksumProviderImpl
filesService - Variable in class ome.services.blitz.impl.MetadataStoreI
filesToString(File...) - Static method in class omero.client
FileSystem - Class in ome.tools: Extends Sun Microsystems java.io.File for J2SE 5 only.
FileSystem(String) - Constructor for class ome.tools.FileSystem: pass-thru constructor
FileSystem(URI) - Constructor for class ome.tools.FileSystem: pass-thru constructor
FileSystem(String, String) - Constructor for class ome.tools.FileSystem: pass-thru constructor
FileSystem(File, String) - Constructor for class ome.tools.FileSystem: pass-thru constructor
fileTotal - Variable in class ome.formats.importer.ImportEvent.FILE_UPLOAD_EVENT
FileTransfer - Interface in ome.formats.importer.transfers: Abstracted concept of "getting the file to the server".
FileUploader - Class in ome.formats.importer.util
FileUploader(CloseableHttpClient) - Constructor for class ome.formats.importer.util.FileUploader: Initialize upload with httpClient
fileUploadErrors - Variable in class ome.formats.importer.util.ErrorHandler
fillData(ImportSettings, Fileset, ClientFilePathTransformer) - Method in class ome.formats.importer.ImportContainer
fillData(ImportSettings, Fileset, ClientFilePathTransformer, FileTransfer) - Method in class ome.formats.importer.ImportContainer
fillData(ImportConfig, ImportSettings, Fileset, ClientFilePathTransformer) - Method in class ome.formats.importer.ImportContainer
fillData(ImportConfig, ImportSettings, Fileset, ClientFilePathTransformer, FileTransfer) - Method in class ome.formats.importer.ImportContainer
fillObject(ReverseModelMapper) - Method in class omero.model.DetailsI
fillObject(ReverseModelMapper) - Method in class omero.model.ElectricPotentialI
fillObject(ReverseModelMapper) - Method in class omero.model.FrequencyI
fillObject(ReverseModelMapper) - Method in class omero.model.LengthI
fillObject(ReverseModelMapper) - Method in class omero.model.PermissionsI
fillObject(ReverseModelMapper) - Method in class omero.model.PowerI
fillObject(ReverseModelMapper) - Method in class omero.model.PressureI
fillObject(ReverseModelMapper) - Method in class omero.model.TemperatureI
fillObject(ReverseModelMapper) - Method in class omero.model.TimeI
fillRelationships(SessionFactoryImplementor, Map<String, ExtendedMetadata.Relationship>) - Method in class ome.tools.hibernate.ExtendedMetadata.Locks: For each of the fields contained in this ExtendedMetadata.Locks object, parse out the type and the field name and store those as the key and value in the "value" argument.
fillReplacement(MergeEvent) - Method in class ome.security.basic.MergeEventListener
fillServerError(ServerError, Throwable) - Static method in class omero.util.IceMapper
fillVersionInfo(List<NamedValue>) - Method in class ome.formats.importer.ImportConfig: Note useful version information that can be extracted from this system, as provenance that is useful for debugging.
filter - Variable in class ome.security.basic.BasicSecuritySystem
filter(String, Filterable) - Method in class ome.tools.hibernate.ProxyCleanupFilter
filter(String, Collection) - Method in class ome.tools.hibernate.ProxyCleanupFilter
filter(String, Map) - Method in class ome.tools.hibernate.ProxyCleanupFilter
filter(String, Filter) - Method in class ome.tools.hibernate.QueryBuilder
filter(String, Filterable) - Method in class ome.tools.hibernate.ReloadFilter
filter(String, Object) - Method in class ome.tools.hibernate.UpdateFilter: overrides ContextFilter.filter(String, Object) to allow only certain types to enter the Hibernate system
filter(String, Filterable) - Method in class ome.tools.hibernate.UpdateFilter: overrides ContextFilter.filter(String, Filterable) to return previously merged or previously checked items.
filter(String, Collection) - Method in class ome.tools.hibernate.UpdateFilter: overrides ContextFilter.filter(String, Collection) to return previously checked collections.
filter(String, Map) - Method in class ome.tools.hibernate.UpdateFilter: Prevents CountPerOwner from being loaded unnecessarily.
filter(String, Filterable) - Method in class 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
filterByType(Collection<Preprocessor.GraphModifyTarget>, Preprocessor.TargetType) - Static method in class omero.cmd.graphs.Preprocessor.GraphModifyTarget: Deprecated.

Return only the targets of the given type.
FilterData - Class in pojos: Object hosting a filter.
FilterData(Filter) - Constructor for class pojos.FilterData: Creates a new instance.
filterFilesByRepository(String, List<Long>, Current) - Method in interface ome.services.blitz.repo.RepositoryDao: Find the original file IDs among those given that are in the given repository.
filterFilesByRepository(String, List<Long>, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
filterName - Static variable in class ome.security.basic.AllGroupsSecurityFilter
filterNow() - Method in class ome.tools.hibernate.QueryBuilder: In order to support the order() method in addition to a filter, we allow applying the filter and nulling the instance eagerly before the user calls order.
filterObject(IObject) - Method in class ome.security.policy.DefaultPolicyService: Limit the objects to which Policy instances are applied.
FilterSetData - Class in pojos: Object hosting a filterSet.
FilterSetData(FilterSet) - Constructor for class pojos.FilterSetData: Creates a new instance.
finalize() - Method in class omero.cmd.fs.UsedFilesRequestI
finalizePixelStore() - Method in class ome.formats.OMEROMetadataStoreClient: Closes the active raw pixels store.
find(Class<T>, long) - Method in interface ome.api.IQuery: lookup an entity by class and id.
find(Class, long) - Method in class ome.logic.QueryImpl
find(String) - Method in interface ome.services.sessions.SessionManager
find(String) - Method in class ome.services.sessions.SessionManagerImpl
find_async(AMD_IQuery_find, String, long, Current) - Method in class ome.services.blitz.impl.QueryI
findAll(Class<T>, Filter) - Method in interface ome.api.IQuery: lookup all entities that belong to this class and match filter.
findAll(Class<T>, Filter) - Method in class ome.logic.QueryImpl
findAll_async(AMD_IQuery_findAll, String, Filter, Current) - Method in class ome.services.blitz.impl.QueryI
findAllByExample(T, Filter) - Method in interface ome.api.IQuery: search based on provided example entity.
findAllByExample(T, Filter) - Method in class ome.logic.QueryImpl
findAllByExample_async(AMD_IQuery_findAllByExample, IObject, Filter, Current) - Method in class ome.services.blitz.impl.QueryI
findAllByFullText(Class<T>, String, Parameters) - Method in interface ome.api.IQuery: executes a full text search based on Lucene.
findAllByFullText(Class<T>, String, Parameters) - Method in class ome.logic.QueryImpl
findAllByFullText_async(AMD_IQuery_findAllByFullText, String, String, Parameters, Current) - Method in class ome.services.blitz.impl.QueryI
findAllByQuery(String, Parameters) - Method in interface ome.api.IQuery: executes the stored query with the given name.
findAllByQuery(String, Parameters) - Method in class ome.logic.QueryImpl
findAllByQuery_async(AMD_IQuery_findAllByQuery, String, Parameters, Current) - Method in class ome.services.blitz.impl.QueryI
findAllByString(Class<T>, String, String, boolean, Filter) - Method in interface ome.api.IQuery: search a given field matching against a String.
findAllByString(Class<T>, String, String, boolean, Filter) - Method in class ome.logic.QueryImpl
findAllByString_async(AMD_IQuery_findAllByString, String, String, String, boolean, Filter, Current) - Method in class ome.services.blitz.impl.QueryI
findByExample(T) - Method in interface ome.api.IQuery: search based on provided example entity.
findByExample(T) - Method in class ome.logic.QueryImpl
findByExample_async(AMD_IQuery_findByExample, IObject, Current) - Method in class ome.services.blitz.impl.QueryI
findByImage_async(AMD_IRoi_findByImage, long, RoiOptions, Current) - Method in class ome.services.blitz.impl.RoiI
findByMimetype(String) - Method in class ome.services.scripts.ScriptRepoHelper: Search through all ScriptFileType instances and find one with a matching mimetype string.
findByPlane_async(AMD_IRoi_findByPlane, long, int, int, RoiOptions, Current) - Method in class ome.services.blitz.impl.RoiI
findByQuery(String, Parameters) - Method in interface ome.api.IQuery: executes the stored query with the given name.
findByQuery(String, Parameters) - Method in class ome.logic.QueryImpl
findByQuery_async(AMD_IQuery_findByQuery, String, Parameters, Current) - Method in class ome.services.blitz.impl.QueryI
findByRoi_async(AMD_IRoi_findByRoi, long, RoiOptions, Current) - Method in class ome.services.blitz.impl.RoiI
findByString(Class<T>, String, String) - Method in interface ome.api.IQuery: search a given field matching against a String.
findByString(Class<T>, String, String) - Method in class ome.logic.QueryImpl
findByString_async(AMD_IQuery_findByString, String, String, String, Current) - Method in class ome.services.blitz.impl.QueryI
findByUser(String) - Method in interface ome.services.sessions.SessionManager
findByUser(String) - Method in class ome.services.sessions.SessionManagerImpl
findByUserAndAgent(String, String...) - Method in interface ome.services.sessions.SessionManager: Returns a non-null, possibly empty list of session instances belonging to the given user and with one of the given agents.
findByUserAndAgent(String, String...) - Method in class ome.services.sessions.SessionManagerImpl
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 specified 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: Searches unique Distinguished Name - String in LDAP for Common Name equals username.
findDN(String) - Method in class ome.logic.LdapImpl
findDN_async(AMD_ILdap_findDN, String, Current) - Method in class ome.services.blitz.impl.LdapI
findEnumeration(HashMap<String, IObject>, String) - Method in interface ome.formats.enums.handler.EnumerationHandler: Attempt to find an enumeration from an existing set of enumeration values.
findExperimenter(String) - Method in interface ome.api.ILdap: Searches Experimenter by unique Distinguished Name - String in LDAP for Common Name equals username.
findExperimenter(String) - Method in class ome.logic.LdapImpl
findExperimenter_async(AMD_ILdap_findExperimenter, String, Current) - Method in class ome.services.blitz.impl.LdapI
findGroup(String) - Method in interface ome.api.ILdap: Looks up a specific ExperimenterGroup in LDAP using the provided group name.
findGroup(String) - Method in class ome.logic.LdapImpl
findGroup_async(AMD_ILdap_findGroup, String, Current) - Method in class ome.services.blitz.impl.LdapI
findGroupDN(String) - Method in interface ome.api.ILdap: Looks up the DN for a group.
findGroupDN(String) - Method in class ome.logic.LdapImpl
findGroupDN_async(AMD_ILdap_findGroupDN, String, Current) - Method in class ome.services.blitz.impl.LdapI
findImproperIncomingLinks(Session, String[]) - Method in class ome.services.chgrp.ChgrpStep: Deprecated.
findImproperIncomingLinks(Session, String[]) - Method in class ome.services.chown.ChownStep: Deprecated.
findImproperIncomingLinks(Session, String[]) - Method in class ome.services.delete.DeleteStep: Deprecated.
findImproperIncomingLinks(Session, String[]) - Method in class ome.services.graphs.GraphStep: Deprecated.
findInDb(CheckedPath, String, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI: Find the given path in the DB or create.
findInDb(String, boolean) - Method in class ome.services.scripts.ScriptRepoHelper
findInDb(RepoFile, boolean) - Method in class ome.services.scripts.ScriptRepoHelper
findInDb(SqlAction, RepoFile, boolean) - Method in class ome.services.scripts.ScriptRepoHelper: Looks to see if a path is contained in the repository.
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.
findOrCreateInDb(CheckedPath, String, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
findOrCreateInDb(CheckedPath, String, String, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
findParameterAnnotations(Class, Method) - Static method in class ome.annotations.AnnotationUtils: finds all parameter annotations for the given class including on all implemented interfaces.
findProxy(Redirector.Context, String) - Method in class ome.services.blitz.redirect.AbstractRedirector
findRepoDeleteLogs(SqlAction.DeleteLog, Current) - Method in interface ome.services.blitz.repo.RepositoryDao: Call SqlAction.findRepoDeleteLogs(DeleteLog) with the current context.
findRepoDeleteLogs(List<SqlAction.DeleteLog>, Current) - Method in interface ome.services.blitz.repo.RepositoryDao: As #findRepoDeleteLogs(DeleteLog, Current) but for a collection of templates.
findRepoDeleteLogs(SqlAction.DeleteLog, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
findRepoDeleteLogs(List<SqlAction.DeleteLog>, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
findRepoFile(String, CheckedPath, String, Current) - Method in interface ome.services.blitz.repo.RepositoryDao: Delegate to SqlAction.findRepoFile(String, String, String, String) for looking up the id of the file, and then load it normally via IQuery.
findRepoFile(ServiceFactory, SqlAction, String, CheckedPath, String) - Method in interface ome.services.blitz.repo.RepositoryDao: As RepositoryDao.findRepoFile(String, CheckedPath, String, Current) but can be called from within a transaction.
findRepoFile(String, CheckedPath, String, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
findRepoFile(ServiceFactory, SqlAction, String, CheckedPath, String) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
FindServiceFactoryMessage - Class in ome.services.blitz.util: InternalMessage raised when a servant needs to find the ServiceFactoryI instance that the current user is working with.
FindServiceFactoryMessage(Object, Current) - Constructor for class ome.services.blitz.util.FindServiceFactoryMessage
finish(TransferState, long) - Method in class ome.formats.importer.transfers.AbstractFileTransfer: Save the current state to disk and finish all timing and logging.
finish() - Method in class ome.services.blitz.impl.commands.SaveI
finish() - Method in class ome.services.blitz.repo.ManagedImportRequestI
finish() - Method in class ome.services.blitz.repo.RawAccessRequestI
finish() - Method in class ome.services.delete.Deletion: Deprecated.

Should be called within the transaction boundaries but as the last processing step.
finish() - Method in interface ome.services.procs.Process
finish() - Method in class ome.services.procs.ProcessSkeleton
finish() - Method in class omero.cmd.admin.CurrentSessionsRequestI
finish() - Method in class omero.cmd.admin.ResetPasswordRequestI
finish() - Method in class omero.cmd.admin.UpdateSessionTimeoutRequestI
finish() - Method in class omero.cmd.basic.DoAllI
finish() - Method in class omero.cmd.basic.ListRequestsI
finish() - Method in class omero.cmd.basic.TimingI
finish() - Method in class omero.cmd.fs.ManageImageBinariesI
finish() - Method in class omero.cmd.fs.OriginalMetadataRequestI
finish() - Method in class omero.cmd.fs.UsedFilesRequestI
finish() - Method in class omero.cmd.graphs.Chgrp2I
finish() - Method in class omero.cmd.graphs.ChgrpFacadeI: Deprecated.
finish() - Method in class omero.cmd.graphs.ChgrpI: Deprecated.
finish() - Method in class omero.cmd.graphs.Chmod2I
finish() - Method in class omero.cmd.graphs.ChmodFacadeI: Deprecated.
finish() - Method in class omero.cmd.graphs.ChmodI: Deprecated.
finish() - Method in class omero.cmd.graphs.Chown2I
finish() - Method in class omero.cmd.graphs.ChownFacadeI: Deprecated.
finish() - Method in class omero.cmd.graphs.ChownI: Deprecated.
finish() - Method in class omero.cmd.graphs.Delete2I
finish() - Method in class omero.cmd.graphs.DeleteFacadeI: Deprecated.
finish() - Method in class omero.cmd.graphs.DeleteI: Deprecated.
finish() - Method in class omero.cmd.graphs.DiskUsageI
finish() - Method in class omero.cmd.graphs.GraphSpecListI: Deprecated.
finish() - Method in class omero.cmd.graphs.SkipHeadI
finish() - Method in interface omero.cmd.IRequest: Method within the transaction boundaries after all processing has occurred.
finish() - Method in class omero.cmd.mail.SendEmailRequestI
finishCancelled() - Method in class ome.formats.importer.util.ErrorHandler: Action to take when finish cancelled
finishComplete() - Method in class ome.formats.importer.util.ErrorHandler: Action to take when finish completed
FINISHED - Static variable in interface ome.api.JobHandle
finished(Response, Status, Current) - Method in class omero.cmd.CmdCallbackI: Called when the command has completed.
finishWithErroredFiles() - Method in class ome.formats.importer.util.ErrorHandler: Action to take when finish completed but with some errors (For example, missing files)
firstIdOrNull(String) - Method in class omero.cmd.fs.OriginalMetadataRequestI: Use IQuery.projection(String, Parameters) to load the first long which matches the given query.
FIRSTNAME - 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_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.
flush() - Method in interface ome.api.local.LocalUpdate
flush(boolean) - Method in class ome.io.nio.FileBuffer: Flush the buffer, writing any pending content to the underlying storage device, optionally also the file's metadata.
flush() - Method in class ome.logic.UpdateImpl
flush() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
flushPreferences() - Method in class ome.formats.importer.util.IniFileLoader: Flush preferences to disk
FONT_BOLD - Static variable in class pojos.ShapeSettingsData: Set if font bold.
FONT_BOLD_ITALIC - Static variable in class pojos.ShapeSettingsData: Set if font bold.
FONT_ITALIC - Static variable in class pojos.ShapeSettingsData: Set if font italic.
FONT_REGULAR - Static variable in class pojos.ShapeSettingsData: Set if font bold.
ForceTransactionAttributeSource - Class in ome.tools.spring: Requires that all method calls have some other form of attribute source by throwing an exception if accessed;
ForceTransactionAttributeSource() - Constructor for class ome.tools.spring.ForceTransactionAttributeSource
forEachTile(TileLoopIteration, PixelBuffer, int, int) - Static method in class ome.io.nio.Utils: Iterates over every tile in a given pixel buffer based on the over arching dimensions and a requested maximum tile width and height.
forEachTile(TileLoopIteration, int, int, int, int, int, int, int) - Static method in class ome.io.nio.Utils: Iterates over every tile in a given pixel buffer based on the over arching dimensions and a requested maximum tile width and height.
forEachTile(int, int, TileLoopIteration) - Method in class omero.util.RPSTileLoop: Iterates over every tile in a given pixel based on the over arching dimensions and a requested maximum tile width and height.
forEachTile(int, int, int, int, int, int, int, TileLoopIteration) - Method in class omero.util.TileLoop: Iterates over every tile in a given pixel based on the over arching dimensions and a requested maximum tile width and height.
foreground(boolean, String[]) - Static method in class ome.services.fulltext.Main: Uses a PersistentEventLogLoader and cycles through all the remaining logs.
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
FrequencyI - Class in omero.model: Blitz wrapper around the Frequency class.
FrequencyI() - Constructor for class omero.model.FrequencyI
FrequencyI(double, UnitsFrequency) - Constructor for class omero.model.FrequencyI
FrequencyI(double, Unit<Frequency>) - Constructor for class omero.model.FrequencyI
FrequencyI(Frequency, Unit<Frequency>) - Constructor for class omero.model.FrequencyI: Copy constructor that converts the given Frequency based on the given ome-xml enum
FrequencyI(double, UnitsFrequency) - Constructor for class omero.model.FrequencyI: Copy constructor that converts the given Frequency based on the given ome.model enum
FrequencyI(Frequency, String) - Constructor for class omero.model.FrequencyI: Copy constructor that converts the given Frequency based on the given enum string.
FrequencyI(Frequency, UnitsFrequency) - Constructor for class omero.model.FrequencyI: Copy constructor that converts between units if possible.
FrequencyI(Frequency) - Constructor for class omero.model.FrequencyI: Convert a Bio-Formats Length to an OMERO Length.
from - Variable in class ome.services.blitz.util.ConvertToBlitzExceptionMessage
FROM - Static variable in class ome.services.mail.MapAnnotationSubethaListener
from(String, String) - Method in class ome.tools.hibernate.QueryBuilder
fromClass(Class) - Static method in class ome.services.blitz.measurements.Helper: Factory method to generate Helper instances from the Class of a given column.
fromLsid(String) - Static method in class ome.services.blitz.measurements.Helper: Factory method to generate Helper instances from the LSID of a given column.
fromObjectContainerStore(IObjectContainerStore, int, int) - Static method in class ome.formats.model.ChannelData: Retrieves channel data from an object container store.
fromPoints(String) - Method in class pojos.ShapeData: Parses out the type from the points string.
fromRType(RType) - Method in class omero.util.IceMapper: Uses the omero.rtypes hierarchy to properly convert any RType to its internal representation.
fromString(String) - Method in class ome.formats.importer.ImportConfig.AnnotationListValue
fromString(String) - Method in class ome.formats.importer.ImportConfig.BoolValue
fromString(String) - Method in class ome.formats.importer.ImportConfig.DoubleArrayValue
fromString(String) - Method in class ome.formats.importer.ImportConfig.FileValue
fromString(String) - Method in class ome.formats.importer.ImportConfig.IntValue
fromString(String) - Method in class ome.formats.importer.ImportConfig.LongValue
fromString(String) - Method in class ome.formats.importer.ImportConfig.StrValue
fromString(String) - Method in class ome.formats.importer.ImportConfig.Value
fsFile - Variable in class ome.services.blitz.repo.CheckedPath
FsFile - Class in ome.services.blitz.repo.path: An analog of File representing an FS repository file-path.
FsFile(Collection<String>) - Constructor for class ome.services.blitz.repo.path.FsFile: Construct an instance.
FsFile(String...) - Constructor for class ome.services.blitz.repo.path.FsFile: Construct an instance.
FsFile(FsFile, int) - Constructor for class ome.services.blitz.repo.path.FsFile: Construct an instance by trimming parent directories from an existing instance such that the depth does not exceed the given maximum.
FsFile(File) - Constructor for class ome.services.blitz.repo.path.FsFile: Construct an instance.
FsFile(String) - Constructor for class ome.services.blitz.repo.path.FsFile: Construct an instance.
fullImport(File, String) - Method in class ome.formats.OMEROImportFixture: Provides one complete import cycle.
fullname() - Method in class ome.services.scripts.RepoFile
FullText - Class in ome.services.search: Search based on Lucene's Query class.
FullText(SearchValues, String, String, String, String, String, Class<? extends Analyzer>) - Constructor for class ome.services.search.FullText: Constructs a new instance; Builds a Lucence query with the provided arguments and passes it on the Lucene parser
FullText(SearchValues, String, Class<? extends Analyzer>) - Constructor for class ome.services.search.FullText: Creates a new instance; Passes the query directly on to the Lucene parser.
FullTextAnalyzer - Class in ome.services.fulltext: Analyzer implementation based largely on SimpleAnalyzer, but with extensions for handling scientific and OS-type strings.
FullTextAnalyzer() - Constructor for class ome.services.fulltext.FullTextAnalyzer
fullTextBridge - Variable in class ome.logic.UpdateImpl
FullTextBridge - Class in ome.services.fulltext: Primary definition of what will be indexed via Hibernate Search.
FullTextBridge() - Constructor for class ome.services.fulltext.FullTextBridge: Since this constructor provides the instance with no way of parsing OriginalFile binaries, all files will be assumed to have blank content.
FullTextBridge(OriginalFilesService, Map<String, FileParser>) - Constructor for class ome.services.fulltext.FullTextBridge: Constructor which provides an empty set of custom bridges.
FullTextBridge(OriginalFilesService, Map<String, FileParser>, Class<FieldBridge>[]) - Constructor for class ome.services.fulltext.FullTextBridge: Main constructor.
FullTextIndexer - Class in ome.services.fulltext: Simple action which can be done in an asynchronous thread in order to index Hibernate entities.
FullTextIndexer(EventLogLoader) - Constructor for class ome.services.fulltext.FullTextIndexer
FullTextIndexer(EventLogLoader, Metrics) - Constructor for class ome.services.fulltext.FullTextIndexer
FullTextThread - Class in ome.services.fulltext: Library entry-point for indexing.
FullTextThread(SessionManager, Executor, FullTextIndexer, FullTextBridge) - Constructor for class ome.services.fulltext.FullTextThread: Uses default Principal for indexing
FullTextThread(SessionManager, Executor, FullTextIndexer, FullTextBridge, boolean) - Constructor for class ome.services.fulltext.FullTextThread: Uses default Principal for indexing
FullTextThread(SessionManager, Executor, FullTextIndexer, FullTextBridge, Principal) - Constructor for class ome.services.fulltext.FullTextThread: Main constructor.
FullTextThread(SessionManager, Executor, FullTextIndexer, FullTextBridge, Principal, boolean) - Constructor for class ome.services.fulltext.FullTextThread: Main constructor.

G

G_BAND - Static variable in class omeis.providers.re.RGBBuffer: Index of the green band in the image's data buffer.
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
generateThumbnails(ThumbnailGenerationJob) - Method in class ome.services.blitz.repo.ManagedImportRequestI
generateTiff_async(AMD_Exporter_generateTiff, Current) - Method in class ome.services.blitz.impl.ExporterI
generateXml(MetadataRetrieve) - Method in class ome.services.blitz.impl.ExporterI
generateXml_async(AMD_Exporter_generateXml, Current) - Method in class ome.services.blitz.impl.ExporterI: Generate XML and return the length
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.GroupContextMapper
get(String, DirContextAdapter) - Method in class ome.security.auth.PersonContextMapper
get() - Method in class ome.services.blitz.util.ResultHolder
get(Session, Class, long) - Method in class ome.services.fulltext.FullTextIndexer
get(int) - Method in class ome.services.graphs.GraphSteps: Deprecated.
get(Object) - Method in class ome.services.query.Definitions
get(String) - Method in class ome.services.query.Query: get the QueryParameter for this name argument.
get(PixelBuffer, int, int, int, int, int) - Method in class ome.services.roi.PixelData
get() - Method in class ome.services.sessions.SessionContext.Count: Return the current number of references which this session is aware of.
get(long) - Method in class ome.services.sharing.BlobShareStore
get(long) - Method in class ome.services.sharing.ShareStore
get(Future<T>) - Method in interface ome.services.util.Executor: Helper method to perform Future.get() and properly unwrap the exceptions.
get(Future<T>) - Method in class ome.services.util.Executor.Impl
get(int) - Method in class ome.util.mem.CopiableArray: Return the Copiable at the specified position.
get(int) - Method in class ome.util.mem.ReadOnlyByteArray: Reads the element at the index position within this slice.
get(Identity) - Method in class omero.util.ServantHolder
get(String[]) - Static method in class prefs: Returns either the given key=value pairs (or all if no argument is given).
get75thPercentile() - Method in class ome.system.metrics.DefaultSnapshot
get75thPercentile() - Method in interface ome.system.metrics.Snapshot
get95thPercentile() - Method in class ome.system.metrics.DefaultSnapshot
get95thPercentile() - Method in interface ome.system.metrics.Snapshot
get98thPercentile() - Method in class ome.system.metrics.DefaultSnapshot
get98thPercentile() - Method in interface ome.system.metrics.Snapshot
get999thPercentile() - Method in class ome.system.metrics.DefaultSnapshot
get999thPercentile() - Method in interface ome.system.metrics.Snapshot
get99thPercentile() - Method in class ome.system.metrics.DefaultSnapshot
get99thPercentile() - Method in interface ome.system.metrics.Snapshot
get_async(AMD_IQuery_get, String, long, Current) - Method in class ome.services.blitz.impl.QueryI
getA0() - Method in class omeis.providers.re.codomain.ContrastStretchingContext: Returns the slope of the first line.
getA1() - Method in class omeis.providers.re.codomain.ContrastStretchingContext: Returns the slope of the second line.
getA2() - Method in class omeis.providers.re.codomain.ContrastStretchingContext: Returns the slope of the third line.
getAbsolutePath() - Method in class ome.formats.importer.util.ErrorContainer: get path for file
getAbsolutePath() - Method in class pojos.FileData: Returns the absolute path.
getAbsolutePaths() - Method in class pojos.FilesetData: Returns the collections of absolute paths.
getAcquisitionData() - Method in class omero.sys.ParametersI
getAcquisitionDate() - Method in class pojos.ImageData: Returns the acquisition date.
getAction() - Method in class ome.services.mail.ObjectMailSender
getActionForStarting() - Method in class omero.cmd.graphs.Chgrp2I
getActionForStarting() - Method in class omero.cmd.graphs.Chmod2I
getActionForStarting() - Method in class omero.cmd.graphs.Chown2I
getActionForStarting() - Method in class omero.cmd.graphs.Delete2I
getActionForStarting() - Method in interface omero.cmd.graphs.WrappableRequest
getActiveConnections(long) - Method in interface ome.api.IShare: Gets actual active connections to share.
getActiveConnections(long) - Method in class ome.services.sharing.ShareBean
getActiveConnections_async(AMD_IShare_getActiveConnections, long, Current) - Method in class ome.services.blitz.impl.ShareI
getActualDeletes() - Method in class ome.services.delete.Deletion: Deprecated.
getAdapter() - Method in class omero.client
getAdapter() - Method in class omero.cmd.SessionI
getAdminService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
getAdminService() - Method in class ome.system.ServiceFactory
getAdminSession() - Method in interface ome.services.blitz.fire.Registry: Create a new AdminSessionPrx with the RegistryPrx.
getAdminSession() - Method in class ome.services.blitz.fire.Registry.Impl
getAgent(Current) - Method in class ome.services.blitz.fire.SessionManagerI
getAirPressure(UnitsPressure) - Method in class pojos.ImageAcquisitionData: Returns the air pressure in bar
getAirPressure() - Method in class pojos.ImageAcquisitionData: Deprecated.
Replaced by ImageAcquisitionData.getAirPressure(UnitsPressure)
getAll(String) - Method in class ome.security.auth.AttributeSet
getAllChecksumAlgorithms() - Static method in class ome.services.blitz.util.ChecksumAlgorithmMapper
getAllDatasets() - Method in interface ome.api.IAnalysis
getAllEnumerations(Class<T>) - Method in interface ome.api.IPixels: Retrieves the exhaustive list of enumerations for a given enumeration class.
getAllEnumerations(Class<T>) - Method in class ome.logic.PixelsImpl
getAllEnumerations_async(AMD_IPixels_getAllEnumerations, String, Current) - Method in class ome.services.blitz.impl.PixelsI
getAllForImage(long) - Method in interface ome.api.IAnalysis
getAllGuests(long) - Method in interface ome.api.IShare: Get the email addresses for all share guests.
getAllGuests(long) - Method in class ome.services.sharing.ShareBean
getAllGuests_async(AMD_IShare_getAllGuests, long, Current) - Method in class ome.services.blitz.impl.ShareI
getAllMembers(long) - Method in interface ome.api.IShare: Get all users who are a member of the share.
getAllMembers(long) - Method in class ome.services.sharing.ShareBean
getAllMembers_async(AMD_IShare_getAllMembers, long, Current) - Method in class ome.services.blitz.impl.ShareI
getAllPixels() - Method in class pojos.ImageData: Returns all the sets of pixels related to this image.
getAllSystemUsers(boolean) - Method in class ome.services.mail.MailSender
getAllUsers(long) - Method in interface ome.api.IShare: Get a single set containing the login names of the Experimenters as well email addresses for guests.
getAllUsers(long) - Method in class ome.services.sharing.ShareBean
getAllUsers_async(AMD_IShare_getAllUsers, long, Current) - Method in class ome.services.blitz.impl.ShareI
getAlpha() - Method in class 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
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(T) - Method in class ome.security.auth.OmeroModelContextMapper
getAttributeSet(T) - Method in class ome.security.auth.OmeroModelContextMapper
getAuthoritativeContainerCache() - Method in interface ome.formats.model.IObjectContainerStore: Returns the current authoritative LSID container cache.
getAuthoritativeContainerCache() - Method in class ome.formats.OMEROMetadataStoreClient
getAuthority() - Method in class ome.services.db.DatabaseIdentity
getAvailableFamilies() - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
getAvailableFamilies() - Method in interface omeis.providers.re.RenderingEngine: Returns the list of mapping families supported by the Rendering engine.
getAvailableFamilies_async(AMD_RenderingEngine_getAvailableFamilies, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
getAvailableModels() - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
getAvailableModels() - Method in interface omeis.providers.re.RenderingEngine: Returns the list of color models supported by the Rendering engine.
getAvailableModels_async(AMD_RenderingEngine_getAvailableModels, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
getAvailableTypes() - Method in interface ome.util.checksum.ChecksumProviderFactory
getAvailableTypes() - Method in class ome.util.checksum.ChecksumProviderFactoryImpl
getB0() - Method in class omeis.providers.re.codomain.ContrastStretchingContext: Returns the y-intercept of the first line.
getB1() - Method in class omeis.providers.re.codomain.ContrastStretchingContext: Returns the y-intercept of the second line.
getB2() - Method in class omeis.providers.re.codomain.ContrastStretchingContext: Returns the y-intercept of the third line.
getBaseType() - Method in class ome.tools.hibernate.SqlArray
getBaseTypeName() - Method in class ome.tools.hibernate.SqlArray
getBatchSize() - Method in interface ome.api.Search: Returns the current batch size.
getBatchSize() - Method in class ome.services.eventlogs.EventLogLoader
getBatchSize() - Method in class ome.services.SearchBean
getBatchSize_async(AMD_Search_getBatchSize, Current) - Method in class ome.services.blitz.impl.SearchI
getBeanHelper() - Method in class ome.logic.AbstractLevel1Service
getBeanHelper() - Method in class ome.logic.AbstractLevel2Service
getBeanHelper() - Method in class ome.services.AbstractStatefulBean
getBfReader(Pixels) - Method in class ome.io.nio.PixelsService: Short-cut in the FS case where we know that we are dealing with a FS-lite file, and want to retrieve the actual file as opposed to a pyramid or anything else.
getBioFormatsVersion() - Method in class ome.formats.importer.ImportConfig
getBit(byte[], int) - Method in class pojos.MaskData: Sets the bit value in a byte array at position bit to be the value value.
getBitDepth(PixelsType) - Method in interface ome.api.IPixels: Bit depth for a given pixel type.
getBitDepth(PixelsType) - Method in class ome.logic.PixelsImpl
getBitDepth_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() - Method in class ome.formats.importer.transfers.TransferState: (Not thread safe) Get a moderately large buffer for use in reading/writing data.
getBuffer(long) - Method in class ome.services.roi.PixelData
getByName(String, Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
getByPeriod_async(AMD_ITimeline_getByPeriod, List<String>, RTime, RTime, Parameters, boolean, Current) - Method in class ome.services.blitz.impl.TimelineI
getByteOrder() - Method in class ome.io.bioformats.BfPyramidPixelBuffer: Returns the current pixel byte order.
getBytesFailed() - Method in class ome.services.delete.files.AbstractFileDeletions
getByteWidth() - Method in interface ome.api.RawPixelsStore
getByteWidth() - Method in class ome.io.bioformats.BfPixelBuffer
getByteWidth() - Method in class ome.io.bioformats.BfPixelsWrapper
getByteWidth() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
getByteWidth() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
getByteWidth() - Method in interface ome.io.nio.PixelBuffer: Returns the byte width for the pixel buffer.
getByteWidth() - Method in class ome.io.nio.RomioPixelBuffer: Implemented as specified by PixelBuffer I/F.
getByteWidth() - Method in class ome.services.RawPixelsBean
getByteWidth_async(AMD_RawPixelsStore_getByteWidth, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
getByteWidth_async(AMD_RawPixelsStore_getByteWidth, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
getC() - Method in class pojos.ShapeData: Returns the channel.
getCalibratedMagnification() - Method in class pojos.ObjectiveData: Returns the objective's calibrated magnification factor.
getCallbackObject(String, String) - Method in class ome.services.sessions.SessionManagerImpl
getCallContext() - Method in class ome.security.basic.BasicEventContext
getCallContext() - Method in class ome.services.blitz.impl.commands.SaveI
getCallContext() - Method in class ome.services.blitz.repo.ManagedImportRequestI
getCallContext() - Method in class ome.services.blitz.repo.RawAccessRequestI
getCallContext() - Method in class omero.cmd.admin.CurrentSessionsRequestI
getCallContext() - Method in class omero.cmd.admin.ResetPasswordRequestI
getCallContext() - Method in class omero.cmd.admin.UpdateSessionTimeoutRequestI
getCallContext() - Method in class omero.cmd.basic.DoAllI
getCallContext() - Method in class omero.cmd.basic.ListRequestsI
getCallContext() - Method in class omero.cmd.basic.TimingI
getCallContext() - Method in class omero.cmd.fs.ManageImageBinariesI
getCallContext() - Method in class omero.cmd.fs.OriginalMetadataRequestI
getCallContext() - Method in class omero.cmd.fs.UsedFilesRequestI
getCallContext() - Method in class omero.cmd.graphs.Chgrp2I
getCallContext() - Method in class omero.cmd.graphs.ChgrpFacadeI: Deprecated.
getCallContext() - Method in class omero.cmd.graphs.ChgrpI: Deprecated.
getCallContext() - Method in class omero.cmd.graphs.Chmod2I
getCallContext() - Method in class omero.cmd.graphs.ChmodFacadeI: Deprecated.
getCallContext() - Method in class omero.cmd.graphs.ChmodI: Deprecated.
getCallContext() - Method in class omero.cmd.graphs.Chown2I
getCallContext() - Method in class omero.cmd.graphs.ChownFacadeI: Deprecated.
getCallContext() - Method in class omero.cmd.graphs.ChownI: Deprecated.
getCallContext() - Method in class omero.cmd.graphs.Delete2I
getCallContext() - Method in class omero.cmd.graphs.DeleteFacadeI: Deprecated.
getCallContext() - Method in class omero.cmd.graphs.DeleteI: Deprecated.
getCallContext() - Method in class omero.cmd.graphs.DiskUsageI
getCallContext() - Method in class omero.cmd.graphs.GraphSpecListI: Deprecated.
getCallContext() - Method in class omero.cmd.graphs.SkipHeadI
getCallContext() - Method in interface omero.cmd.IRequest: Returns the desired call context for this request.
getCallContext() - Method in class omero.cmd.mail.SendEmailRequestI
getCallContext() - Method in class omero.model.DetailsI
getCategory() - Method in class omero.client: Returns the category which should be used for all callbacks passed to the server.
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
getChannelEmissionWavelength(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
getChannelExcitationWavelength(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
getChannelFamily(int) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
getChannelFamily(int) - Method in interface omeis.providers.re.RenderingEngine: Returns the family associated to the specified channel.
getChannelFamily_async(AMD_RenderingEngine_getChannelFamily, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
getChannelFluor(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
getChannelID(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
getChannelIlluminationType(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
getChannelIndex() - Method in class ome.formats.model.ChannelData: Returns the index of the channel this channel data is for.
getChannelLabeling() - Method in class pojos.ChannelData: Returns the label of the channel.
getChannelLookupTable(int) - Method in class ome.services.RenderingBean
getChannelLookupTable(int) - Method in interface omeis.providers.re.RenderingEngine
getChannelLookupTable_async(AMD_RenderingEngine_getChannelLookupTable, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
getChannelName(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
getChannelNDFilter(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
getChannelNoiseReduction(int) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
getChannelNoiseReduction(int) - Method in interface omeis.providers.re.RenderingEngine: Returns true if the noise reduction algorithm used to map the pixels intensity values is turned on, false if the algorithm is turned off.
getChannelNoiseReduction_async(AMD_RenderingEngine_getChannelNoiseReduction, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
getChannelPinholeSize(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
getChannelPockelCellSetting(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
getChannelSamplesPerPixel(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
getChannelStats(int) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
getChannelStats(int) - Method in interface omeis.providers.re.RenderingEngine
getChannelStats_async(AMD_RenderingEngine_getChannelStats, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
getChannelWindowEnd(int) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
getChannelWindowEnd(int) - Method in interface omeis.providers.re.RenderingEngine: Returns the upper bound of the pixels intensity interval.
getChannelWindowEnd_async(AMD_RenderingEngine_getChannelWindowEnd, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
getChannelWindowStart(int) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
getChannelWindowStart(int) - Method in interface omeis.providers.re.RenderingEngine: Returns the lower bound of the pixels intensity interval.
getChannelWindowStart_async(AMD_RenderingEngine_getChannelWindowStart, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
getCheckDone() - Method in class ome.services.util.DBEnumCheck
getChecks(IObject, String) - Method in class ome.security.basic.GroupChmodStrategy
getChecks(IObject, String) - Method in interface ome.security.ChmodStrategy: Return all the checks necessary to validate the given object if it were to have its permissions.
getChecksum() - Method in class ome.formats.importer.transfers.TransferState: Get the digest string for the local file.
getChecksumAlgorithm() - Method in class ome.formats.importer.ImportContainer
getChecksumAlgorithm(String, Current) - Method in interface ome.services.blitz.repo.RepositoryDao: Retrieve the checksum algorithm of the given name.
getChecksumAlgorithm(String, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
getChecksumAlgorithm(String) - Static method in class ome.services.blitz.util.ChecksumAlgorithmMapper
getChecksumProvider() - Method in class ome.formats.importer.transfers.TransferState: Get the ChecksumProvider passed to the constructor.
getChecksumType(ChecksumAlgorithm) - Static method in class ome.services.blitz.util.ChecksumAlgorithmMapper
getChecksumType(ChecksumAlgorithm) - Static method in class ome.services.blitz.util.ChecksumAlgorithmMapper
getChildOptionsPolicy(GraphPolicy, Collection<ChildOptionI>, Set<GraphPolicy.Ability>) - Static method in class omero.cmd.graphs.ChildOptionsPolicy: Adjust an existing graph traversal policy so that child objects may be included or excluded regardless of if they are truly orphans.
getChildTransformer(Class) - Static method in class ome.services.query.Hierarchy
getClass(String) - Method in class ome.services.graphs.GraphState: Deprecated.
getClass(String) - Method in interface ome.services.graphs.GraphStep.Callback: Deprecated.
getClasses() - Method in interface ome.tools.hibernate.ExtendedMetadata
getClasses() - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
getClassForSimpleName(String) - Method in class ome.services.graphs.GraphPathBean
getCleanInstance() - Method in class ome.services.graphs.GraphPolicy: A stateful graph policy must override this method to provide a clone that has fresh state.
getClient() - Method in class ome.formats.importer.util.ClientKeepAlive
getClient() - Method in class omero.model.DetailsI
getClientConfigDefaults() - Method in interface ome.api.IConfig: reads the etc/omero.properties file and returns all the key/value pairs that are found there which match the prefix "omero.client".
getClientConfigDefaults() - Method in class ome.logic.ConfigImpl
getClientConfigDefaults_async(AMD_IConfig_getClientConfigDefaults, Current) - Method in class ome.services.blitz.impl.ConfigI
getClientConfigValues() - Method in interface ome.api.IConfig: retrieves configuration values like IConfig.getConfigValues(String) but only those with the prefix "omero.client".
getClientConfigValues() - Method in class ome.logic.ConfigImpl
getClientConfigValues_async(AMD_IConfig_getClientConfigValues, Current) - Method in class ome.services.blitz.impl.ConfigI
getClientContext() - Static method in class ome.system.OmeroContext: create (if necessary) and return the single default client OmeroContext.
getClientContext(Properties) - Static method in class ome.system.OmeroContext: initialize a new client OmeroContext (named OmeroContext.CLIENT_CONTEXT), using the OmeroContext.getContext(Properties, String) method.
getClientIds() - Method in class omero.util.ServantHolder
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
getCommunicationLink(String) - Method in class ome.formats.importer.util.HtmlMessenger: Creates a client to communicate.
getCommunicator() - Method in class ome.services.blitz.fire.Ring
getCommunicator() - Method in interface ome.services.blitz.redirect.Redirector.Context: Active communicator for use by the Redirector instance.
getCommunicator() - Method in class ome.services.blitz.repo.AbstractRepositoryI
getCommunicator() - Method in class ome.services.blitz.repo.InternalRepositoryConfig
getCommunicator() - Method in class ome.services.blitz.util.BlitzConfiguration
getCommunicator() - Method in class omero.client: Returns the Communicator for this instance or throws an exception if null.
getComponents() - Method in class ome.services.blitz.repo.path.FsFile: Get the path components of this instance.
getComponents() - Method in class pojos.MultiImageData: Returns the collection of images composing the file.
getCompressionLevel() - Method in interface ome.api.local.LocalCompress: Returns the current compression level for the service.
getCompressionLevel() - Method in class ome.logic.CompressImpl
getCompressionLevel() - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
getCompressionLevel() - Method in interface omeis.providers.re.RenderingEngine: Returns the current compression level for the service.
getCompressionLevel_async(AMD_RenderingEngine_getCompressionLevel, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
getConfig() - Method in class ome.formats.importer.OMEROWrapper
getConfigDefaults() - Method in interface ome.api.IConfig: reads the etc/omero.properties file and returns all the key/value pairs that are found there.
getConfigDefaults() - Method in class ome.logic.ConfigImpl
getConfigDefaults_async(AMD_IConfig_getConfigDefaults, Current) - Method in class ome.services.blitz.impl.ConfigI
getConfigService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
getConfigService() - Method in class ome.system.ServiceFactory
getConfigValue(String) - Method in interface ome.api.IConfig: retrieve a configuration value from the backend store.
getConfigValue(String) - Method in class ome.formats.OMEROMetadataStoreClient: Retrieves a configuration value from the IConfig service.
getConfigValue(String) - Method in class ome.logic.ConfigImpl: see IConfig.getConfigValue(String)
getConfigValue_async(AMD_IConfig_getConfigValue, String, Current) - Method in class ome.services.blitz.impl.ConfigI
getConfigValues(String) - Method in interface ome.api.IConfig: retrieves configuration values from the backend store which match the given regex.
getConfigValues(String) - Method in class ome.logic.ConfigImpl
getConfigValues_async(AMD_IConfig_getConfigValues, String, Current) - Method in class ome.services.blitz.impl.ConfigI
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
getConstraints() - Method in exception ome.services.graphs.GraphConstraintException: Deprecated.
getContainerCache() - Method in interface ome.formats.model.IObjectContainerStore: Returns the current container cache.
getContainerCache() - Method in class ome.formats.OMEROMetadataStoreClient
getContainers() - Method in class ome.formats.importer.ImportCandidates
getContainerService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
getContainerService() - Method in class ome.system.ServiceFactory
getContainerTypes() - Method in class ome.logic.TypesImpl
getContent() - Method in class pojos.AnnotationData: Returns the content of the annotation.
getContent() - Method in class pojos.BooleanAnnotationData: Returns the textual content of the annotation.
getContent() - Method in class pojos.DoubleAnnotationData: Returns the value.
getContent() - Method in class pojos.FileAnnotationData: Returns the original file.
getContent() - Method in class pojos.LongAnnotationData: Returns the rating value.
getContent() - Method in class pojos.MapAnnotationData
getContent() - Method in class pojos.RatingAnnotationData: Returns the rating value.
getContent() - Method in class pojos.TagAnnotationData: Returns the textual content of the annotation.
getContent() - Method in class pojos.TermAnnotationData: Returns the textual content of the annotation.
getContent() - Method in class pojos.TextualAnnotationData: Returns the textual content of the annotation.
getContent() - Method in class pojos.TimeAnnotationData: Returns the timestamp of the annotation.
getContent() - Method in class pojos.XMLAnnotationData: Returns the content of the annotation.
getContentAsString() - Method in class pojos.AnnotationData: Returns the content of the annotation as a String, which is parsed on a Class-by-Class basis.
getContentAsString() - Method in class pojos.BooleanAnnotationData: Returns the textual content of the annotation.
getContentAsString() - Method in class pojos.DoubleAnnotationData: Returns the value as a string.
getContentAsString() - Method in class pojos.FileAnnotationData: Returns the absolute path to the file
getContentAsString() - Method in class pojos.LongAnnotationData: Returns the value as a string.
getContentAsString() - Method in class pojos.MapAnnotationData
getContentAsString() - Method in class pojos.RatingAnnotationData: Returns the rating value as a string.
getContentAsString() - Method in class pojos.TagAnnotationData: Returns the textual content of the annotation.
getContentAsString() - Method in class pojos.TermAnnotationData: Returns the textual content of the annotation.
getContentAsString() - Method in class pojos.TextualAnnotationData: Returns the textual content of the annotation.
getContentAsString() - Method in class pojos.TimeAnnotationData: Returns the time as a string.
getContentAsString() - Method in class pojos.XMLAnnotationData: Returns the textual content of the annotation.
getContentMap(long) - Method in interface ome.api.IShare: Returns the contents of the share keyed by type.
getContentMap(long) - Method in class ome.services.sharing.ShareBean
getContentMap_async(AMD_IShare_getContentMap, long, Current) - Method in class ome.services.blitz.impl.ShareI
getContents(long) - Method in interface ome.api.IShare: Looks up all items belong to the share.
getContents(long) - Method in class ome.services.sharing.ShareBean
getContents_async(AMD_IShare_getContents, long, Current) - Method in class ome.services.blitz.impl.ShareI
getContentSize(long) - Method in interface ome.api.IShare: Returns the number of items in the share.
getContentSize(long) - Method in class ome.services.sharing.ShareBean
getContentSize_async(AMD_IShare_getContentSize, long, Current) - Method in class ome.services.blitz.impl.ShareI
getContentSubList(long, int, int) - Method in interface ome.api.IShare: Returns a range of items from the share.
getContentSubList(long, int, int) - Method in class ome.services.sharing.ShareBean
getContentSubList_async(AMD_IShare_getContentSubList, long, int, int, Current) - Method in class ome.services.blitz.impl.ShareI
getContext() - Method in class ome.security.basic.CurrentDetails
getContext() - Method in interface ome.services.util.Executor: Provides access to the context for Work-API consumers who need to publish events, etc.
getContext() - Method in class ome.services.util.Executor.Impl
getContext(Properties, String) - Static method in class ome.system.OmeroContext: initialize a new client OmeroContext using the Properties provided as values for property (e.g.
getContext() - Method in class ome.system.ServiceFactory: Deprecated.
getContrastMethod() - Method in class pojos.ChannelAcquisitionData: Returns the contrast method.
getContrastMethod() - Method in class pojos.ChannelData: Returns the contrast method.
getContrastMethodAsEnum() - Method in class pojos.ChannelData: Returns the contrast method enumeration value.
getControls() - Method in class ome.security.auth.GroupContextMapper
getControls() - Method in class ome.security.auth.PersonContextMapper
getCorrection() - Method in class 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: Deprecated.
getCount() - Method in interface ome.system.metrics.Counter
getCount() - Method in class ome.system.metrics.DefaultCounter
getCount() - Method in class ome.system.metrics.DefaultTimer
getCount() - Method in interface ome.system.metrics.Timer
getCountQuery(String) - Method in interface ome.tools.hibernate.ExtendedMetadata: Returns the query for obtaining the number of collection items to a particular instance.
getCountQuery(String) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl: Returns the query for obtaining the number of collection items to a particular instance.
getCreated() - Method in class pojos.DataObject: Returns the creation time of the object.
getCreationEvent(Current) - Method in class omero.model.DetailsI
getCurrent() - Method in class ome.services.blitz.util.FindServiceFactoryMessage
getCurrent() - Method in class ome.services.blitz.util.UnregisterServantMessage
getCurrentEventContext() - Method in interface ome.api.StatefulServiceInterface: Returns the current EventContext for this instance.
getCurrentEventContext() - Method in class ome.security.basic.CurrentDetails: Public view on the data contained here.
getCurrentEventContext() - Method in class ome.services.AbstractStatefulBean
getCurrentEventContext() - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
getCurrentEventContext() - Method in class ome.services.ThumbnailBean
getCurrentEventContext_async(AMD_StatefulServiceInterface_getCurrentEventContext, Current) - Method in class ome.services.blitz.impl.AbstractAmdServant
getCurrentEventContext_async(AMD_StatefulServiceInterface_getCurrentEventContext, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
getCurrentEventId() - Method in class ome.services.sessions.SessionContextImpl
getCurrentEventId() - Method in interface ome.system.EventContext
getCurrentEventId() - Method in class ome.system.SimpleEventContext
getCurrentEventType() - Method in class ome.services.sessions.SessionContextImpl
getCurrentEventType() - Method in interface ome.system.EventContext
getCurrentEventType() - Method in class ome.system.SimpleEventContext
getCurrentGroupId() - Method in class ome.services.sessions.SessionContextImpl
getCurrentGroupId() - Method in interface ome.system.EventContext
getCurrentGroupId() - Method in class ome.system.SimpleEventContext
getCurrentGroupName() - Method in class ome.services.sessions.SessionContextImpl
getCurrentGroupName() - Method in interface ome.system.EventContext
getCurrentGroupName() - Method in class ome.system.SimpleEventContext
getCurrentGroupPermissions() - Method in class ome.services.sessions.SessionContextImpl
getCurrentGroupPermissions() - Method in interface ome.system.EventContext
getCurrentGroupPermissions() - Method in class ome.system.SimpleEventContext
getCurrentId() - Method in class ome.services.eventlogs.PersistentEventLogLoader: Get current EventLog id.
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
getCurveCoefficient() - Method in class omeis.providers.re.quantum.QuantumStrategy: Returns the coefficient identifying a curve within a given family.
getCustomAnnotationList() - Method in class ome.formats.importer.ImportContainer: The list of custom, user specified, annotations to link to all images represented by this container.
getCustomImageNaming() - Method in class ome.formats.importer.ImportConfig
getCustomImageNaming() - Method in class ome.formats.importer.util.IniFileLoader
getCutIn(UnitsLength) - Method in class pojos.FilterData: Returns the cut in value or null.
getCutIn() - Method in class pojos.FilterData: Deprecated.
Replaced by FilterData.getCutIn(UnitsLength)
getCutInTolerance(UnitsLength) - Method in class pojos.FilterData: Returns the cut in tolerance value or null.
getCutInTolerance() - Method in class pojos.FilterData: Deprecated.
Replaced by FilterData.getCutInTolerance(UnitsLength)
getCutOut(UnitsLength) - Method in class pojos.FilterData: Returns the cut out value or null.
getCutOut() - Method in class pojos.FilterData: Deprecated.
Replaced by FilterData.getCutOut(UnitsLength)
getCutOutTolerance(UnitsLength) - Method in class pojos.FilterData: Returns the cut out tolerance value or null.
getCutOutTolerance() - Method in class pojos.FilterData: Deprecated.
Replaced by FilterData.getCutOutTolerance(UnitsLength)
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.
getDataset() - Method in class ome.formats.importer.util.TinyImportFixture: provides access to the created Dataset instance.
getDatasets(Project) - Method in class ome.formats.OMEROMetadataStoreClient
getDatasets() - Method in class pojos.ImageData: Returns the datasets containing this image.
getDatasets() - Method in class pojos.ProjectData: Returns the datasets contained in this project.
getDatasetsForProject(long) - Method in interface ome.api.IAnalysis
getDatasetsWithoutProjects() - Method in class ome.formats.OMEROMetadataStoreClient
getDataValue() - Method in class pojos.DoubleAnnotationData: Returns the value.
getDataValue() - Method in class pojos.LongAnnotationData: Returns the value.
getDate(Class) - Static method in class ome.system.Version: Parses the given class for its RevisionDate annotation.
getDebugLevel() - Method in class ome.formats.importer.ImportConfig
getDebugLevel() - Method in class ome.formats.importer.util.IniFileLoader: Returns the level of debugging which should be set on ImportConfig Any value lower than null will not call configureDebug.
getDefaultBatchSize() - Method in class ome.formats.OMEROMetadataStoreClient
getDefaultBlockSize() - Method in class ome.formats.OMEROMetadataStoreClient
getDefaultBlockSize() - Method in class omero.client: Returns the user configured setting for "omero.block_size" or DEFAULTBLOCKSIZE if none is set.
getDefaultBody() - Method in class ome.services.mail.MailSender
getDefaultCondition() - Method in class ome.security.basic.AllGroupsSecurityFilter
getDefaultCondition() - Method in class ome.security.basic.OneGroupSecurityFilter
getDefaultCondition() - Method in interface ome.security.SecurityFilter: Return the string to be used as the condition.
getDefaultCondition() - Method in class ome.security.SecurityFilterHolder
getDefaultContext() - Method in class ome.system.ServiceFactory: used when no context name is provided to the constructor.
getDefaultContext() - Method in class ome.tools.spring.InternalServiceFactory: returns null to prevent the lookup of any context, but rather wait on injection as a ApplicationContextAware
getDefaultContext() - Method in class ome.tools.spring.ManagedServiceFactory: returns null to prevent the lookup of any context, but rather wait on injection as a ApplicationContextAware
getDefaultGroup(long) - Method in interface ome.api.IAdmin: retrieve the default group for the given user id.
getDefaultGroup(long) - Method in class ome.logic.AdminImpl
getDefaultGroup() - Method in class pojos.ExperimenterData: Returns the default Group for this Experimenter
getDefaultGroup_async(AMD_IAdmin_getDefaultGroup, long, Current) - Method in class ome.services.blitz.impl.AdminI
getDefaultGroupLevel() - Method in class ome.formats.OMEROMetadataStoreClient: Deprecated.
getDefaultGroupName() - Method in class ome.formats.OMEROMetadataStoreClient: Retrieve the default group's name
getDefaultPixels() - Method in class pojos.ImageData: Returns the default set of pixels.
getDefaultSample() - Method in class pojos.PlateData: Returns the currently selected field or 0.
getDefaultScriptDir() - Static method in class ome.services.scripts.ScriptRepoHelper: Directory which will be used as the root of this repository if no directory is passed to a constructor.
getDefaultT() - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
getDefaultT() - Method in interface omeis.providers.re.RenderingEngine: Returns the default timepoint index.
getDefaultT_async(AMD_RenderingEngine_getDefaultT, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
getDefaultZ() - Method in class ome.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
getDeleteService() - Method in class ome.system.ServiceFactory
getDeletion() - Method in class omero.cmd.graphs.DeleteI: Deprecated.
getDescription(Current) - Method in class ome.services.blitz.repo.AbstractRepositoryI
getDescription(long) - Method in class ome.services.blitz.repo.AbstractRepositoryI
getDescription() - Method in class pojos.AnnotationData: Retrieves the description of the underlying Annotation instance.
getDescription() - Method in class pojos.DatasetData: Returns the description of the dataset.
getDescription() - Method in class pojos.FileAnnotationData: Returns the description of the annotation.
getDescription() - Method in class pojos.FileData: Returns the description of the file.
getDescription() - Method in class pojos.GroupData: Returns the description of the group.
getDescription() - Method in class pojos.ImageData: Returns the description of the image.
getDescription() - Method in class pojos.PlateAcquisitionData: Returns the description of the plate acquisition.
getDescription() - Method in class pojos.PlateData: Returns the description of the plate.
getDescription() - Method in class pojos.ProjectData: Returns the description of the project.
getDescription() - Method in class pojos.ScreenData: Returns the description of the screen.
getDescription() - Method in class pojos.XMLAnnotationData: Returns the description of the annotation.
getDetails(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(UnitsFrequency) - Method in class pojos.ChannelAcquisitionData: Returns the Read out rate set on the detector.
getDetectorSettingsReadOutRate() - Method in class pojos.ChannelAcquisitionData: Deprecated.
Replaced by ChannelAcquisitionData.getDetectorSettingsReadOutRate(UnitsFrequency)
getDetectorSettingsVoltage(UnitsElectricPotential) - Method in class pojos.ChannelAcquisitionData: Returns the voltage set on the detector.
getDetectorSettingsVoltage() - Method in class pojos.ChannelAcquisitionData: Deprecated.
Replaced by ChannelAcquisitionData.getDetectorSettingsVoltage(UnitsElectricPotential)
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.
getDirname() - Method in class ome.services.blitz.repo.CheckedPath: Assuming this is a directory, return relative path plus name with a final slash.
getDisabledSubsystems() - Method in class ome.security.basic.BasicEventContext
getDn(T) - Method in class ome.security.auth.OmeroModelContextMapper
getDnById(Long) - Method in class ome.security.auth.PasswordUtil
getDoThumbnails() - Method in class ome.formats.importer.ImportContainer: Retrieves whether or not we are performing thumbnail creation upon import completion.
getDoubleAnnotationCount() - Method in class ome.services.blitz.impl.OmeroMetadata
getDoubleAnnotationDescription(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getDoubleAnnotationID(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getDoubleAnnotationNamespace(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getDoubleAnnotationValue(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getEffectiveUID() - Method in class ome.security.basic.BasicSecuritySystem: Returns the Id of the currently logged in user.
getEffectiveUID() - Method in interface ome.security.SecuritySystem: Returns UID based on whether a share is active, etc.
getEffectiveUID() - Method in class ome.security.SecuritySystemHolder
getEffectiveUID() - Method in class ome.security.sharing.SharingSecuritySystem
getEmail() - Method in class ome.formats.importer.util.ErrorContainer
getEmail() - Method in class 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(UnitsLength) - Method in class pojos.ChannelData: Returns the emission wavelength of the channel.
getEmissionWavelength() - Method in class pojos.ChannelData: Deprecated.
Replaced by ChannelData.getEmissionWavelength(UnitsLength)
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
getError() - Method in class ome.services.delete.Deletion: Deprecated.
getEvent() - Method in class ome.security.basic.BasicEventContext
getEvent() - Method in class ome.security.basic.CurrentDetails
getEvent(Current) - Method in class ome.services.blitz.fire.SessionManagerI
getEvent() - Method in class ome.system.Login: simple getter for the event type passed into the constructor
getEventContext() - Method in interface ome.api.IAdmin: returns an implementation of EventContext loaded with the security for the current user and thread.
getEventContext() - Method in class ome.logic.AdminImpl
getEventContext(boolean) - Method in class ome.security.basic.BasicSecuritySystem
getEventContext() - Method in class ome.security.basic.BasicSecuritySystem
getEventContext() - Method in interface ome.security.SecuritySystem: Calls SecuritySystem.getEventContext(boolean) with a false as "refresh".
getEventContext(boolean) - Method in interface ome.security.SecuritySystem: If refresh is false, returns the current EventContext stored in the session.
getEventContext() - Method in class ome.security.SecuritySystemHolder
getEventContext(boolean) - Method in class ome.security.SecuritySystemHolder
getEventContext() - Method in class ome.security.sharing.SharingSecuritySystem
getEventContext(boolean) - Method in class ome.security.sharing.SharingSecuritySystem
getEventContext() - Method in class ome.services.blitz.impl.ServiceFactoryI: Doesn't take current into account
getEventContext(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI: Takes current into account
getEventContext(Current) - Method in interface ome.services.blitz.repo.RepositoryDao: Look up information for the current session as specified in the ctx field of the current.
getEventContext(Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
getEventContext(Principal) - Method in interface ome.services.sessions.SessionManager: Provides a partial EventContext for the current Session.
getEventContext(Principal) - Method in class ome.services.sessions.SessionManagerImpl
getEventContext() - Method in class omero.cmd.Helper: Provides an EventContext instance without reloading the session, via LocalAdmin.getEventContextQuiet().
getEventContext() - Method in class omero.model.DetailsI
getEventContext_async(AMD_IAdmin_getEventContext, Current) - Method in class ome.services.blitz.impl.AdminI
getEventContextQuiet() - Method in interface ome.api.local.LocalAdmin: Like IAdmin.getEventContext() but will not reload the context.
getEventContextQuiet() - Method in class ome.logic.AdminImpl
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(UnitsLength) - Method in class pojos.ChannelData: Returns the excitation wavelength of the channel.
getExcitationWavelength() - Method in class pojos.ChannelData: Deprecated.
Replaced by ChannelData.getExcitationWavelength(UnitsLength)
getExclude(int) - Method in class ome.services.graphs.AnnotationGraphSpec: Deprecated.

Returns the value from "...
getExecutor() - Method in class ome.services.mail.MailSender
getExecutor() - Method in class ome.services.scheduler.ThreadPool
getExecutor() - Method in class omero.cmd.SessionI
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.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
getFactory(String, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
getFailedFiles() - Method in exception ome.formats.importer.transfers.CleanupFailure
getFailedFilesCount() - Method in class ome.services.delete.files.FileDeleter
getFailureClass() - Method in exception ome.formats.enums.EnumerationException
getFailureClass() - Method in exception ome.formats.model.ModelException: Returns the class that was used during a failed instantiation.
getFamily(String) - Method in class omeis.providers.re.quantum.QuantumFactory: Helper method to retrieve a Family enumeration from the database.
getFamily() - Method in class omeis.providers.re.quantum.QuantumStrategy: Returns the mapping family.
getFeedbackUrl() - Method in class ome.formats.importer.ImportConfig
getFilament(int, int) - Method in class ome.formats.OMEROMetadataStoreClient
getFile() - Method in class ome.formats.importer.ImportContainer
getFile() - Method in class ome.formats.importer.transfers.TransferState: Return the target file passed to the constructor.
getFile(long, Current, String) - Method in interface ome.services.blitz.repo.RepositoryDao: Get an FsFile object based on its ID.
getFile(long, Current, String) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
getFile(ServiceFactory) - Method in class ome.services.scripts.ScriptFinder
getFileBuffer(OriginalFile, String) - Method in class ome.io.nio.OriginalFilesService: Returns FileBuffer based on OriginalFile path
getFileBuffer(String) - Method in class ome.services.blitz.repo.CheckedPath: Get a FileBuffer corresponding to this instance.
getFileFilter() - Method in class ome.services.scripts.ScriptFileType: A file-pattern (most likely of the form "*.EXT") which will be used to determine if a file is of this type.
getFileFormat() - Method in class ome.formats.importer.util.ErrorContainer: get the file format for import
getFileFormat() - Method in class pojos.FileAnnotationData: Returns the format of the uploaded file.
getFileId() - Method in interface ome.api.RawFileStore: Returns the current file id or null if none has been set.
getFileId() - Method in class ome.services.messages.DeleteLogMessage
getFileId() - Method in class ome.services.RawFileBean
getFileID() - Method in class pojos.FileAnnotationData: Returns the id of the file.
getFileId_async(AMD_RawFileStore_getFileId, Current) - Method in class ome.services.blitz.impl.RawFileStoreI
getFileIds() - Method in class ome.tools.RepositoryTask: This public method is used to return a list of file ids that require deletion from the disk repository.
getFileKind() - Method in class pojos.FileAnnotationData: Returns a user readable description of the file.
getFileName() - Method in class pojos.FileAnnotationData: Returns the name of the file.
getFilePath(OriginalFile, Current) - Method in class ome.services.blitz.repo.AbstractRepositoryI
getFilePath(OriginalFile, Current) - Method in class ome.services.blitz.repo.InternalRepositoryI
getFilePath(OriginalFile, Current) - Method in class ome.services.blitz.repo.LegacyRepositoryI
getFilePath(OriginalFile, Current) - Method in class ome.services.blitz.repo.ScriptRepositoryI
getFilePath(OriginalFile, Current) - Method in class ome.services.blitz.repo.TemporaryRepositoryI
getFilePath() - Method in class pojos.FileAnnotationData: Returns the absolute path to the file.
getFilePathRestrictions(String...) - Static method in enum ome.services.blitz.repo.path.FilePathRestrictionInstance: Get a set of rules by which local files may not be named on the file-system, formed by combining the rules of the given names with rules against control characters.
getFilePathRestrictions(FilePathRestrictionInstance...) - Static method in enum ome.services.blitz.repo.path.FilePathRestrictionInstance: Get a set of rules by which local files may not be named on the file-system, formed by combining the given rules identifiers with rules against control characters.
getFileRepo(OriginalFile) - Method in class ome.services.blitz.repo.AbstractRepositoryI
getFiles() - Method in class ome.formats.importer.util.ErrorContainer
getFileset() - Method in class ome.services.blitz.repo.ManagedImportProcessI
getFileset() - Method in interface ome.services.blitz.repo.ProcessContainer.Process
getFilesetId() - Method in class ome.services.delete.DeleteStep: Deprecated.
getFilesetId() - Method in class pojos.ImageData: Returns the ID of the fileset to which this image belongs.
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.
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: Deprecated.
Replaced by ShapeSettingsData.getFontSize(UnitsLength)
getFontSize(UnitsLength) - 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
getFsFileFromClientFile(File, int) - Method in class ome.services.blitz.repo.path.ClientFilePathTransformer: Given a client-local File, and a path component depth, returns the corresponding repository path.
getFsFileFromServerFile(File) - Method in class ome.services.blitz.repo.path.ServerFilePathTransformer: Given a server-local File, returns the corresponding repository path.
getFullFsPath() - Method in class ome.services.blitz.repo.CheckedPath: The full path of the entity to which this path corresponds.
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.
getGraphPathBean() - Method in class omero.cmd.graphs.GraphRequestFactory
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.BasicEventContext
getGroup() - Method in class ome.security.basic.CurrentDetails
getGroup(Current) - Method in class ome.services.blitz.fire.SessionManagerI
getGroup() - Method in class ome.services.blitz.repo.ManagedImportProcessI
getGroup() - Method in interface ome.services.blitz.repo.ProcessContainer.Process
getGroup() - Method in class ome.system.Login: simple getter for the group name passed into the constructor
getGroup() - Method in class ome.system.Principal
getGroup(Current) - Method in class omero.model.DetailsI
getGroup() - Method in class omero.sys.ParametersI: Returns the value of the group parameter.
getGroup_async(AMD_IAdmin_getGroup, long, Current) - Method in class ome.services.blitz.impl.AdminI
getGroupAttribute(String) - Method in class ome.security.auth.LdapConfig
getGroupFilter() - Method in class ome.security.auth.LdapConfig
getGroupId() - Method in class pojos.DataObject: Returns the id of the group.
getGroupId() - Method in class pojos.ExperimenterData: Overridden to return the id of the default group.
getGroupId() - Method in class pojos.GroupData: Overridden to return the id of the object.
getGroups() - Method in class pojos.ExperimenterData: Returns the groups the experimenter is a member of.
getGuestGroupId() - Method in class ome.system.Roles
getGuestGroupName() - Method in class ome.system.Roles
getGuestId() - Method in class ome.system.Roles
getGuestName() - Method in class ome.system.Roles
getHandle(Current) - Method in class ome.services.blitz.repo.ManagedImportProcessI
getHandler(Class<? extends IObject>) - Method in class ome.formats.enums.handler.EnumHandlerFactory: Returns an enumeration handler for a specific enumeration type.
getHandler(Class<? extends IObject>) - Method in class ome.formats.model.handler.ModelObjectHandlerFactory: Returns an enumeration handler for a specific enumeration type.
getHeight() - Method in class omeis.providers.re.data.RegionDef: Returns the height of the region.
getHeight() - Method in class pojos.MaskData: Returns the height of the mask.
getHeight() - Method in class pojos.RectangleData: Returns the height untransformed rectangle.
getHibernateClass(String) - Method in class ome.services.graphs.BaseGraphSpec: Deprecated.
getHibernateClass(String) - Method in interface ome.services.graphs.GraphSpec: Deprecated.

Return the Hibernate type (ome.model.*) for the given table.
getHibernateClass(String) - Method in interface ome.tools.hibernate.ExtendedMetadata: Given the name of a database table or alternatively the simple class name (non-fully qualified) of an IObject, this method returns the class which Hibernate will map that table to.
getHibernateClass(String) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
getHolder() - Method in class ome.services.blitz.util.UnregisterServantMessage
getHomeUrl() - Method in class ome.formats.importer.ImportConfig
getHomeUrl() - Method in class ome.formats.importer.util.IniFileLoader
getHost() - Method in class ome.system.Server: simple getter for the server host passed into the constructor
getHumidity() - Method in class pojos.ImageAcquisitionData: Returns the humidity level, this is a value in the interval [0, 1]
getHypercube(List<Integer>, List<Integer>, List<Integer>) - Method in interface ome.api.RawPixelsStore
getHypercube(List<Integer>, List<Integer>, List<Integer>) - Method in class ome.io.bioformats.BfPixelBuffer
getHypercube(List<Integer>, List<Integer>, List<Integer>, byte[]) - Method in class ome.io.bioformats.BfPixelsWrapper
getHypercube(List<Integer>, List<Integer>, List<Integer>) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
getHypercube(List<Integer>, List<Integer>, List<Integer>) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
getHypercube(List<Integer>, List<Integer>, List<Integer>) - Method in interface ome.io.nio.PixelBuffer: Retrieves a hypercube from this pixel buffer.
getHypercube(List<Integer>, List<Integer>, List<Integer>) - Method in class ome.io.nio.RomioPixelBuffer: Implemented as specified by PixelBuffer I/F.
getHypercube(List<Integer>, List<Integer>, List<Integer>) - Method in class ome.services.RawPixelsBean
getHypercube_async(AMD_RawPixelsStore_getHypercube, List<Integer>, List<Integer>, List<Integer>, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
getHypercube_async(AMD_RawPixelsStore_getHypercube, List<Integer>, List<Integer>, List<Integer>, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
getHypercubeDirect(List<Integer>, List<Integer>, List<Integer>, byte[]) - Method in class ome.io.bioformats.BfPixelBuffer
getHypercubeDirect(List<Integer>, List<Integer>, List<Integer>, byte[]) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
getHypercubeDirect(List<Integer>, List<Integer>, List<Integer>, byte[]) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
getHypercubeDirect(List<Integer>, List<Integer>, List<Integer>, byte[]) - Method in interface ome.io.nio.PixelBuffer: Retrieves a hypercube from the given pixels directly.
getHypercubeDirect(List<Integer>, List<Integer>, List<Integer>, byte[]) - Method in class ome.io.nio.RomioPixelBuffer: Implemented as specified by PixelBuffer I/F.
getHypercubeSize(List<Integer>, List<Integer>, List<Integer>) - Method in class ome.io.bioformats.BfPixelBuffer
getHypercubeSize(List<Integer>, List<Integer>, List<Integer>) - Method in class ome.io.bioformats.BfPixelsWrapper
getHypercubeSize(List<Integer>, List<Integer>, List<Integer>) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
getHypercubeSize(List<Integer>, List<Integer>, List<Integer>) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
getHypercubeSize(List<Integer>, List<Integer>, List<Integer>) - Method in interface ome.io.nio.PixelBuffer: Retrieves a the size of a hypercube from this pixel buffer.
getHypercubeSize(List<Integer>, List<Integer>, List<Integer>) - Method in class ome.io.nio.RomioPixelBuffer
getId() - Method in class ome.io.bioformats.BfPixelBuffer
getId() - Method in class ome.io.bioformats.BfPixelsWrapper
getId() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
getId() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
getId() - Method in interface ome.io.nio.PixelBuffer: Delegates to Pixels.getId().
getId() - Method in class ome.io.nio.RomioPixelBuffer: Implemented as specified by PixelBuffer I/F.
getId() - Method in class ome.services.blitz.repo.CheckedPath
getId() - Method in class ome.services.graphs.GraphEntry: Deprecated.
getId() - Method in class pojos.DataObject: Returns the database id of the IObject or -1 if null
getIdByOrder(int) - Method in class ome.services.export.ExporterIndex: Deprecated.

Returns the id of an object based on the order in which it was added.
getIdentifierProperty(String) - Method in class ome.services.graphs.GraphPathBean: Get the identifier property for the given class.
getIdentity(String) - Method in class omero.cmd.SessionI
getIdentity(String) - Method in class omero.util.ServantHolder: Constructs an Identity from the current session and from the given String which for stateless services are defined by the instance fields #adminKey, #configKey, etc. and for stateful services are UUIDs.
getIds() - Method in class ome.services.graphs.GraphStep: Deprecated.

Currently returns the ID array without copying therefore values should not be leaked to code outside of the ome.services.graphs hierarchy.
getIds() - Method in class ome.services.sessions.state.SessionCache: Since all methods which use SessionCache.getIds() will subsequently check for the existing session, we do not block here.
getIllumination() - Method in class 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(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getImage() - Method in class pojos.PixelsData: Returns the image linked to this pixels' set.
getImage() - Method in class pojos.ROIData: Returns the image for the ROI.
getImage() - Method in class pojos.WellSampleData: Returns the image related to that sample if any.
getImageAcquisitionDate(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getImageAndCount(Image[], long, UnloadedCollector) - Method in class ome.services.delete.DeleteBean: Uses the locally defined query to load an Image and calls DeleteBean.collect(UnloadedCollector, Image) in order to define a list of what will be deleted.
getImageAnnotationRef(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
getImageAnnotationRefCount(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getImageCount() - Method in class ome.services.blitz.impl.OmeroMetadata
getImageDescription(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getImageID(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getImageIds() - Method in class pojos.FilesetData: Returns the collection of images related to the file set.
getImageName(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getImageNames() - Method in class ome.formats.ImageNameMetadataStore: Retrieves the current map of Image names held.
getImageReader() - Method in class ome.formats.importer.OMEROWrapper: Return the base image reader
getImages(Class<T>, Set<Long>, Parameters) - Method in interface ome.api.IContainer: Retrieve a user's (or all users') images within any given container.
getImages(Class, Set, Parameters) - Method in class ome.logic.PojosImpl: Implemented as specified by the IContainer I/F
getImages() - Method in class pojos.DatasetData: Returns a set of images contained in the dataset.
getImages_async(AMD_IContainer_getImages, String, List<Long>, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI
getImagesByOptions(Parameters) - Method in interface ome.api.IContainer: Retrieve images by options.
getImagesByOptions(Parameters) - Method in class ome.logic.PojosImpl: Implemented as specified by the IContainer I/F
getImagesByOptions_async(AMD_IContainer_getImagesByOptions, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI
getImagesBySplitFilesets(Map<Class<? extends IObject>, List<Long>>, Parameters) - Method in interface ome.api.IContainer: Given a list of IDs of certain entity types, calculates which filesets are split such that a non-empty proper subset of their images are referenced, directly or indirectly, as being included.
getImagesBySplitFilesets(Map<Class<? extends IObject>, List<Long>>, Parameters) - Method in class ome.logic.PojosImpl: Implemented as specified by the IContainer I/F
getImagesBySplitFilesets_async(AMD_IContainer_getImagesBySplitFilesets, Map<String, List<Long>>, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI
getImagesForDataset(long) - Method in interface ome.api.IAnalysis
getImageSize(PlaneDef) - Method in class omeis.providers.re.Renderer: Returns the size, in bytes, of the RGBBuffer that would be rendered from the plane selected by pd.
getImagingEnvironment(int) - Method in class ome.formats.OMEROMetadataStoreClient
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.
getImportResponse() - Method in class ome.formats.importer.ImportLibrary.ImportCallback: Assumes that users have already waited on proper completion, i.e. that ImportLibrary.ImportCallback.onFinished(Response, Status, Current) has been called.
getImportSettings(Current) - Method in class ome.services.blitz.repo.ManagedImportProcessI
getImportTypes() - Method in class ome.logic.TypesImpl
getIndex() - Method in class ome.formats.importer.util.ErrorContainer: get the index for this error container
getIndex() - Method in class ome.services.fulltext.SimpleLuceneOptions
getIndex() - Method in class pojos.ChannelData: Returns the channel's index.
getIndex() - Method in class pojos.ImageData: Returns the index of the image within the multi-images file.
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.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
getIP(Current) - Method in class ome.services.blitz.fire.SessionManagerI
getIQuery() - Method in class ome.formats.OMEROMetadataStoreClient
getIsSPW() - Method in class ome.formats.importer.ImportContainer: Return true if this import container contains a Screen/Plate/Well image group.
getIterator() - Method in class pojos.ROIData: Returns the iterator of the collection of the map.
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
getKey() - Method in class ome.services.eventlogs.PersistentEventLogLoader
getKeySet() - Method in class ome.system.PreferenceContext
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(UnitsFrequency) - Method in class pojos.LightSourceData: Returns the repetition rate (Hz) if the laser is repetitive.
getLaserRepetitionRate() - Method in class pojos.LightSourceData: Deprecated.
Replaced by LightSourceData.getLaserRepetitionRate(UnitsFrequency)
getLaserTuneable() - Method in class pojos.LightSourceData: Returns the value of the tuneable field or null if no value set.
getLaserWavelength(UnitsLength) - Method in class pojos.LightSourceData: Returns the laser's wavelength.
getLaserWavelength() - Method in class pojos.LightSourceData: Deprecated.
Replaced by LightSourceData.getLaserWavelength(UnitsLength)
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
getLauncher() - Method in class ome.services.scripts.ScriptFileType: Return the name of the launcher (".
getLauncher(String) - Method in class ome.services.scripts.ScriptRepoHelper: Find an "omero.launcher..." property string for the given mimetype or return "" if none is found.
getLdapService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
getLdapService() - Method in class ome.system.ServiceFactory
getLeaderOfGroupIds(Experimenter) - Method in interface ome.api.IAdmin: Finds the ids for all groups for which the given Experimenter is owner/leader.
getLeaderOfGroupIds(Experimenter) - Method in class ome.logic.AdminImpl
getLeaderOfGroupIds_async(AMD_IAdmin_getLeaderOfGroupIds, Experimenter, Current) - Method in class ome.services.blitz.impl.AdminI
getLeaderOfGroupsList() - Method in class ome.security.basic.BasicEventContext
getLeaderOfGroupsList() - Method in class ome.services.sessions.SessionContextImpl
getLeaderOfGroupsList() - Method in interface ome.system.EventContext
getLeaderOfGroupsList() - Method in class ome.system.SimpleEventContext
getLeaders() - Method in class pojos.GroupData: Returns the experimenters contained in this group.
getLeaves() - Method in class omero.sys.ParametersI
getLength() - Method in class ome.formats.importer.transfers.TransferState: Return the length of the target file.
getLensNA() - Method in class 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.
getLightSettingsAttenuation() - Method in class pojos.ChannelAcquisitionData: Returns the attenuation of the light source, percent value between 0 and 1.
getLightSettingsWavelength(UnitsLength) - Method in class pojos.ChannelAcquisitionData: Returns the wavelength of the light source.
getLightSettingsWavelength() - Method in class pojos.ChannelAcquisitionData: Deprecated.
Replaced by ChannelAcquisitionData.getLightSettingsWavelength(UnitsLength)
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.
getLimit() - Method in class omero.sys.ParametersI: Returns the value of the limit parameter.
getLine(int, int) - Method in class ome.formats.OMEROMetadataStoreClient
getLine() - Method in class ome.services.blitz.repo.FileMaker
getLineCap() - Method in class pojos.ShapeSettingsData: Returns the shape of the end of the line..
getLinkedBy(String) - Method in class ome.services.graphs.GraphPathBean: Get the classes and properties that link to the given class.
getLinkedTo(String) - Method in class ome.services.graphs.GraphPathBean: Get the classes and properties to which the given class links.
getListAnnotation(int) - Method in class ome.formats.OMEROMetadataStoreClient
getLocalLocation(OriginalFile, OriginalFile) - Method in class ome.formats.importer.transfers.AbstractExecFileTransfer: Build a path of the form "root.path/root.name/file.path/file.name".
getLocationStats() - Method in class omeis.providers.re.metadata.StatsFactory: Returns the statistics.
getLockCandidateChecks(Class<? extends IObject>, boolean) - Method in interface ome.tools.hibernate.ExtendedMetadata: Rather than iterating over an IObject like ExtendedMetadata.getLockCandidates(IObject) this method returns type/field name pairs (like ExtendedMetadata.getLockChecks(Class)) to allow performing the queries manually.
getLockCandidateChecks(Class<? extends IObject>, boolean) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
getLockCandidateChecks(boolean) - Method in class ome.tools.hibernate.ExtendedMetadata.Locks
getLockCandidates() - Method in class ome.security.basic.BasicEventContext
getLockCandidates(IObject) - Method in interface ome.tools.hibernate.ExtendedMetadata: walks the IObject argument non-recursively and gathers all IObject instances which will be linked to by the creation or updating of the argument.
getLockCandidates(IObject) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl: walks the IObject argument non-recursively and gathers all IObject instances which will be linkd to by the creation or updating of the argument.
getLockCandidates(IObject) - Method in class ome.tools.hibernate.ExtendedMetadata.Locks
getLockChecks(Class<? extends IObject>) - Method in interface ome.tools.hibernate.ExtendedMetadata: returns all class/field name pairs which may possibly link to an object of type klass.
getLockChecks(Class<? extends IObject>) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl: returns all class/field name pairs which may possibly link to an object of type klass.
getLockingIds(Class<IObject>, long, Long) - Method in interface ome.api.local.LocalAdmin: Returns a map from Class (as string) to a count for all entities which point to the given IObject.
getLockingIds(IObject) - Method in class ome.logic.AdminImpl
getLockingIds(Class<IObject>, long, Long) - Method in class ome.logic.AdminImpl
getLogFile() - Method in class ome.formats.importer.ImportConfig
getLogFile() - Method in class ome.formats.importer.util.IniFileLoader
getLogFile() - Method in class ome.services.blitz.repo.ManagedImportLocationI: Return the server-side CheckedPath instance which can be used for writing a log file for a fileset.
getLogger() - Method in class ome.services.util.BeanHelper
getLogicalChannel() - Method in class ome.formats.model.ChannelData: Returns the logical channel for this channel data.
getLogs() - Method in class ome.security.basic.BasicEventContext
getLogs() - Method in class ome.security.basic.BasicSecuritySystem
getLogs() - Method in class ome.security.basic.CurrentDetails
getLogString(SelfConfigurableService) - Method in class ome.services.util.BeanHelper
getLongAnnotation(int) - Method in class ome.formats.OMEROMetadataStoreClient
getLongAnnotationCount() - Method in class ome.services.blitz.impl.OmeroMetadata
getLongAnnotationDescription(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getLongAnnotationID(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getLongAnnotationNamespace(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getLongAnnotationValue(int) - Method in class ome.services.blitz.impl.OmeroMetadata
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.
getMailUtil() - Method in class ome.services.mail.MailSender
getManagedServerContext() - Static method in class ome.system.OmeroContext: create (if necessary) and return the single default managed OmeroContext.
getManagerList(boolean) - Method in class ome.services.blitz.fire.Ring
getManagerList(boolean) - Method in interface ome.services.blitz.redirect.Redirector.Context: Return all known managers in the current cluster context, possibly filtering out the inactive ones.
getManufacturer() - Method in class 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.
getMapProperties(String) - Method in interface ome.tools.hibernate.ExtendedMetadata: Get the names of any String→RString map properties this class has, otherwise an empty set if none.
getMapProperties(String) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
getMarkerEnd() - Method in class pojos.ShapeSettingsData: Returns the marker end.
getMarkerStart() - Method in class pojos.ShapeSettingsData: Returns the marker start.
getMask(int, int) - Method in class ome.formats.OMEROMetadataStoreClient
getMask() - Method in class pojos.MaskData: Returns the mask as a byte array.
getMaskAsBinaryArray() - Method in class pojos.MaskData: Returns the mask image.
getMaskAsBufferedImage() - Method in class pojos.MaskData: Returns the mask image.
getMaskPoints() - Method in class pojos.PolygonData: Returns the points in the polygon.
getMaskPoints() - Method in class pojos.PolylineData: Returns the points in the Polyline.
getMatcher(String) - Method in class ome.services.graphs.GraphEntry: Deprecated.
getMax() - Method in class ome.system.metrics.DefaultSnapshot
getMax() - Method in interface ome.system.metrics.Snapshot
getMaximumFieldCount() - Method in class pojos.PlateAcquisitionData: Returns the maximum number of fields in any well.
getMaxPlaneHeight() - Method in class ome.io.nio.ConfiguredTileSizes
getMaxPlaneHeight() - Method in interface ome.io.nio.TileSizes
getMaxPlaneWidth() - Method in class ome.io.nio.ConfiguredTileSizes
getMaxPlaneWidth() - Method in interface ome.io.nio.TileSizes
getMean() - Method in class ome.system.metrics.DefaultSnapshot
getMean() - Method in interface ome.system.metrics.Snapshot
getMeasuredRois_async(AMD_IRoi_getMeasuredRois, long, long, RoiOptions, Current) - Method in class ome.services.blitz.impl.RoiI
getMeasuredRoisMap_async(AMD_IRoi_getMeasuredRoisMap, long, List<Long>, RoiOptions, Current) - Method in class ome.services.blitz.impl.RoiI
getMedian() - Method in class ome.system.metrics.DefaultSnapshot
getMedian() - Method in interface ome.system.metrics.Snapshot
getMedium() - Method in class pojos.ImageAcquisitionData: Returns the medium of the objective.
getMediumAsEnum() - Method in class pojos.ImageAcquisitionData: Returns the medium enumeration value.
getMemberCount(Set<Long>) - Method in interface ome.api.IShare: Returns a map from share id to the count of total members (including the owner).
getMemberCount(Set<Long>) - Method in class ome.services.sharing.ShareBean
getMemberCount_async(AMD_IShare_getMemberCount, List<Long>, Current) - Method in class ome.services.blitz.impl.ShareI
getMemberOfGroupIds(Experimenter) - Method in interface ome.api.IAdmin: Finds the ids for all groups for which the given Experimenter is a member.
getMemberOfGroupIds(Experimenter) - Method in class ome.logic.AdminImpl
getMemberOfGroupIds_async(AMD_IAdmin_getMemberOfGroupIds, Experimenter, Current) - Method in class ome.services.blitz.impl.AdminI
getMemberOfGroupsList() - Method in class ome.security.basic.BasicEventContext
getMemberOfGroupsList() - Method in class ome.services.sessions.SessionContextImpl
getMemberOfGroupsList() - Method in interface ome.system.EventContext
getMemberOfGroupsList() - Method in class ome.system.SimpleEventContext
getMemberShares(boolean) - Method in interface ome.api.IShare: Gets all shares where current Experimenter is a member.
getMemberShares(boolean) - Method in class ome.services.sharing.ShareBean
getMemberShares_async(AMD_IShare_getMemberShares, boolean, Current) - Method in class ome.services.blitz.impl.ShareI
getMemberSharesFor(Experimenter, boolean) - Method in interface ome.api.IShare: Gets all shares where given Experimenter is a member.
getMemberSharesFor(Experimenter, boolean) - Method in class ome.services.sharing.ShareBean
getMemberSharesFor_async(AMD_IShare_getMemberSharesFor, Experimenter, boolean, Current) - Method in class ome.services.blitz.impl.ShareI
getMembersOnly() - Method in class pojos.GroupData: Returns the list of experimenters that are not owners of the group.
getMemoizerDirectory() - Method in class ome.io.nio.PixelsService
getMemoizerWait() - Method in class ome.io.nio.PixelsService
getMessage() - Method in exception ome.io.nio.PixelBufferException
getMessageDigest() - Method in class ome.io.bioformats.BfPixelsWrapper
getMessages() - Method in class ome.services.messages.DeleteLogsMessage
getMetadata(long) - Method in class ome.services.ThumbnailCtx: Retrieves the Thumbnail object for a given Pixels ID.
getMetadata() - Method in class omeis.providers.re.Renderer: Returns the Pixels set the rendering engine is for.
getMetadataOptions() - Method in class ome.formats.importer.OMEROWrapper
getMetadataService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
getMetadataService() - Method in class ome.system.ServiceFactory
getMethod(String) - Method in class ome.services.blitz.util.IceMethodInvoker: For testing the cached method.
getMethodCount() - Method in class ome.services.messages.stats.MethodStatsMessage
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.
getMiddleRange(double) - Method in class omeis.providers.re.quantum.QuantumStrategy: Returns the range the values belongs to.
getMimetype() - Method in class ome.services.blitz.repo.CheckedPath: Get the mimetype for a file.
getMimetype() - Method in class ome.services.scripts.ScriptFileType: Returns the mimetype that must be set on an original file instance in order to be considered of this type.
getMin() - Method in class ome.system.metrics.DefaultSnapshot
getMin() - Method in interface ome.system.metrics.Snapshot
getMinimumDepth(Collection<File>) - Method in class ome.services.blitz.repo.path.ClientFilePathTransformer: Get the smallest path component depth that allows the given set of Files to be disambiguated.
getMode() - Method in class 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
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.AbstractSecurityFilter
getName() - Method in class ome.security.basic.BasicSecurityWiring: Lookup name.
getName() - Method in class ome.security.policy.BasePolicy
getName() - Method in class ome.security.policy.BinaryAccessPolicy
getName() - Method in interface ome.security.policy.Policy: Unique name for a class of restrictions that this Policy will enforce.
getName() - Method in interface ome.security.SecurityFilter: Name of this security filter.
getName() - Method in class ome.security.SecurityFilterHolder
getName() - Method in class ome.services.blitz.repo.CheckedPath: Get the last component of this path, the entity to which the path corresponds.
getName() - Method in class ome.services.graphs.BaseGraphSpec: Deprecated.
getName() - Method in class ome.services.graphs.GraphEntry: Deprecated.
getName(Matcher) - Method in class ome.services.graphs.GraphEntry: Deprecated.
getName() - Method in interface ome.services.graphs.GraphSpec: Deprecated.

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.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
getNewUserGroupOwner() - 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.
getNoStatsInfo() - Method in class ome.formats.importer.ImportContainer: Retrieves whether or not we disabling StatsInfo population.
getNumOfDirectories() - Method in class ome.formats.importer.ImportConfig
getNumOfDirectories() - Method in class ome.formats.importer.util.IniFileLoader
getObject(String, int) - Method in class ome.services.export.ExporterStepFactory: Deprecated.
getObject() - Method in interface ome.services.sessions.SessionCallback
getObject() - Method in class ome.services.sessions.SessionCallback.SimpleCloseCallback
getObject() - Method in class ome.services.sessions.state.CacheFactory
getObjectAdapter() - Method in class ome.services.blitz.repo.AbstractRepositoryI
getObjectAdapter() - Method in class ome.services.blitz.repo.InternalRepositoryConfig
getObjectByLSID(LSID) - Method in class ome.formats.OMEROMetadataStore: Retrieves an object from the internal object graph by LSID.
getObjectClass() - Method in class ome.services.mail.ObjectMailSender
getObjective(int, int) - Method in class ome.formats.OMEROMetadataStoreClient
getObjective() - Method in class pojos.ImageAcquisitionData: Returns the objective used to capture the image.
getObjective() - Method in class pojos.OTFData: Returns the associated objective.
getObjectives() - Method in class pojos.InstrumentData: Returns the collection of objectives.
getObjectiveSettings(int) - Method in class ome.formats.OMEROMetadataStoreClient
getObjectiveSettingsId() - Method in class pojos.ImageAcquisitionData: Returns the id of the Objective settings or -1 if not already linked to the image.
getObjectsRead() - Method in class ome.services.messages.stats.ObjectsReadStatsMessage
getObjectsWritten() - Method in class ome.services.messages.stats.ObjectsWrittenStatsMessage
getObjectType() - Method in class ome.security.basic.EventListenersFactoryBean: this FactoryBean produces a Map instance for use in LocalSessionFactoryBean.setEventListeners(Map)
getObjectType() - Method in class ome.services.delete.Deletion.Builder: Deprecated.
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.
getOmeroVersion() - Method in class ome.formats.importer.ImportConfig
getOp(Matcher) - Method in class ome.services.graphs.GraphEntry: Deprecated.
getOpString() - Method in class ome.services.graphs.GraphEntry: Deprecated.

Primarily used for passing back a string representation of the default operation to users for setting options.
getOptimisticFailureCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
getOptimizations() - Method in class omeis.providers.re.Renderer: Returns the optimizations that the renderer currently has enabled.
getOpts() - Method in class ome.services.graphs.GraphState: Deprecated.
getOrCreateParams(long, Current) - Method in class omero.grid.ParamsHelper: Get the script params for the file.
getOrder() - Method in class ome.io.nio.ReorderedPixelData: Returns the byte order of the backing buffer.
getOriginalEnumerations() - Method in interface ome.api.ITypes: Gets all original values.
getOriginalEnumerations() - Method in class ome.logic.TypesImpl
getOriginalEnumerations_async(AMD_ITypes_getOriginalEnumerations, Current) - Method in class ome.services.blitz.impl.TypesI
getOriginalFile() - Method in class ome.formats.importer.transfers.TransferState: Find original file as defined by the ID in the RawFileStorePrx regardless of group.
getOriginalFile(long, Current) - Method in interface ome.services.blitz.repo.RepositoryDao: Gets the original file instance for a given file ID.
getOriginalFile(long, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
getOriginalFilePath(AbstractFileSystemService, Pixels) - Method in interface ome.io.nio.FilePathResolver: Retrieves the original file path for a given set of pixels.
getOriginalFilePath(Pixels) - Method in class ome.io.nio.PixelsService: Retrieves the original file path for a given set of pixels.
getOriginalFilePath(AbstractFileSystemService, Pixels) - Method in class ome.services.OmeroFilePathResolver
getOriginalFiles(String, CheckedPath, Current) - Method in interface ome.services.blitz.repo.RepositoryDao: Return a non-null, possibly empty list of OriginalFile elements which are accessible to the given user at the given path.
getOriginalFiles(String, CheckedPath, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
getOriginalFiles(ServiceFactory, SqlAction, String, CheckedPath) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
getOriginalFileWithHasher(long, Current) - Method in interface ome.services.blitz.repo.RepositoryDao: Retrieve the original file of the given ID.
getOriginalFileWithHasher(long, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
getOriginalGlobalMax() - Method in class omeis.providers.re.quantum.QuantumStrategy: Returns the original maximum of all minima.
getOriginalGlobalMin() - Method in class omeis.providers.re.quantum.QuantumStrategy: Returns the original minimum of all minima.
getOriginalMimetype() - Method in class pojos.FileAnnotationData: Returns the format of the original file.
getOrphan() - Method in class omero.sys.ParametersI
getOSArch() - Method in class ome.formats.importer.util.ErrorContainer
getOSName() - Method in class ome.formats.importer.util.ErrorContainer
getOSVersion() - Method in class ome.formats.importer.util.ErrorContainer
getOTF() - Method in class pojos.ChannelAcquisitionData: Returns the OTF used for that channel.
getOTF() - Method in class pojos.InstrumentData: Returns the collection of OTFs.
getOutput(String, String) - Method in interface ome.api.ISession: Retrieves an entry from the session's output environment.
getOutput(String, String) - Method in class ome.services.sessions.SessionBean
getOutput(String, String) - Method in interface ome.services.sessions.SessionManager: Returns the output environment Object stored under the given key or null if none present.
getOutput(String, String) - Method in class ome.services.sessions.SessionManagerImpl
getOutput(String) - Method in class omero.client: Retrieves an item from the "output" shared (session) memory.
getOutput_async(AMD_ISession_getOutput, String, String, Current) - Method in class ome.services.blitz.impl.SessionI
getOutputKeys(String) - Method in interface ome.api.ISession: Retrieves all keys in the sesson's output environment.
getOutputKeys(String) - Method in class ome.services.sessions.SessionBean
getOutputKeys() - Method in class omero.client: Returns a list of keys for all items in the "output" shared (session) memory
getOutputKeys_async(AMD_ISession_getOutputKeys, String, Current) - Method in class ome.services.blitz.impl.SessionI
getOutputs(String) - Method in interface ome.api.ISession: Retrieves all outputs from the given session's input environment.
getOutputs(String) - Method in class ome.services.sessions.SessionBean
getOutputs_async(AMD_ISession_getOutputs, String, Current) - Method in class ome.services.blitz.impl.SessionI
getOverlays() - Method in class omeis.providers.re.Renderer: Returns the current set of overlays to be rendered.
getOwnedGroups() - Method in class ome.logic.LdapImpl.GroupLoader: Return the found owned groups for the given username.
getOwner() - Method in class ome.security.basic.BasicEventContext
getOwner() - Method in class ome.security.basic.CurrentDetails
getOwner(Current) - Method in class omero.model.DetailsI
getOwner() - Method in class pojos.DataObject: Returns the owner of the object.
getOwnShares(boolean) - Method in interface ome.api.IShare: Gets all owned shares for the current Experimenter
getOwnShares(boolean) - Method in class ome.services.sharing.ShareBean
getOwnShares_async(AMD_IShare_getOwnShares, boolean, Current) - Method in class ome.services.blitz.impl.ShareI
getParameterTypes() - Method in class ome.security.basic.AllGroupsSecurityFilter
getParameterTypes() - Method in class ome.security.basic.OneGroupSecurityFilter
getParameterTypes() - Method in interface ome.security.SecurityFilter: Return a mapping of the hibernate types for each of the parameters that the condition takes.
getParameterTypes() - Method in class ome.security.SecurityFilterHolder
getParams_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
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: Deprecated.
getPath() - Method in class pojos.FileData: Returns the (relative) path of the file.
getPath() - Method in class pojos.OTFData: Returns the path.
getPathFor(long) - Method in class ome.services.blitz.repo.path.MakeNextDirectory: Get the subdirectories to create for the given index, the first directories to be created corresponding to index == 0.
getPathFrom(FsFile) - Method in class ome.services.blitz.repo.path.FsFile: Find the relative path of this path from a given parent.
getPathIterator(AffineTransform) - Method in class ome.util.math.geom2D.EllipseArea: Required by the Shape I/F.
getPathIterator(AffineTransform, double) - Method in class ome.util.math.geom2D.EllipseArea: Required by the Shape I/F.
getPathIterator(AffineTransform) - Method in class ome.util.math.geom2D.RectangleArea: Required by the Shape I/F.
getPathIterator(AffineTransform, double) - Method in class ome.util.math.geom2D.RectangleArea: Required by the Shape I/F.
getPaths() - Method in class ome.formats.importer.ImportCandidates
getPathSanitizer() - Method in class ome.services.blitz.repo.path.ServerFilePathTransformer: Get the string transformer that is used to make file-path components safe across platforms.
getPathToFile() - Method in class pojos.ImageData: Returns the path to the file.
getPerm1(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.
getPermissionsForGroup(Long) - Method in class ome.security.basic.BasicEventContext: Never returns Permissions.DUMMY.
getPermissionsLevel() - Method in class pojos.PermissionData: Returns the permissions level.
getPhysicalMemory() - Static method in class ome.services.util.JvmSettingsCheck
getPinholeSize(UnitsLength) - Method in class pojos.ChannelData: Returns the pin hole size of the channel.
getPinholeSize() - Method in class pojos.ChannelData: Deprecated.
Replaced by ChannelData.getPinholeSize(UnitsLength)
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, ServiceFactory) - Method in class ome.services.pixeldata.PixelDataHandler
getPixels() - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
getPixels(long) - Method in class ome.services.ThumbnailCtx: Retrieves the Pixels object for a given Pixels ID.
getPixels() - Method in class omeis.providers.re.Renderer: Returns the object that allows to access the pixels raw data.
getPixels() - Method in interface omeis.providers.re.RenderingEngine: Returns the Pixels set the Rendering engine is for.
getPixels() - Method in class omero.util.RPSTileLoop: After saving the binary data, the update event of the Pixels instance will be updated and therefore need to be reloaded.
getPixels_async(AMD_RenderingEngine_getPixels, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
getPixelsBinDataBigEndian(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
getPixelsDimensionOrder(int) - Method in class ome.services.blitz.impl.OmeroMetadata
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
getPixelSizeX() - Method in class pojos.PixelsData: Deprecated.
Replaced by PixelsData.getPixelSizeX(UnitsLength)
getPixelSizeX(UnitsLength) - Method in class pojos.PixelsData: Returns the dimension of a pixel along the X-axis
getPixelSizeY() - Method in class pojos.PixelsData: Deprecated.
Replaced by PixelsData.getPixelSizeY(UnitsLength)
getPixelSizeY(UnitsLength) - Method in class pojos.PixelsData: Returns the dimension of a pixel along the Y-axis
getPixelSizeZ() - Method in class pojos.PixelsData: Deprecated.
Replaced by PixelsData.getPixelSizeZ(UnitsLength)
getPixelSizeZ(UnitsLength) - Method in class pojos.PixelsData: Returns the dimension of a pixel along the Z-axis
getPixelsPath() - Method in interface ome.api.RawPixelsStore: Returns the current Pixels path.
getPixelsPath(Long) - Method in class ome.io.nio.AbstractFileSystemService: Returns a numbered path relative to the root of this service, but is ignorant of FS and similar constructs.
getPixelsPath() - Method in class ome.services.RawPixelsBean
getPixelsPath_async(AMD_RawPixelsStore_getPixelsPath, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
getPixelsPath_async(AMD_RawPixelsStore_getPixelsPath, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
getPixelsPhysicalSizeX(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getPixelsPhysicalSizeY(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getPixelsPhysicalSizeZ(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getPixelsService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
getPixelsService() - Method in class ome.system.ServiceFactory
getPixelsSizeC(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getPixelsSizeT(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getPixelsSizeX(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getPixelsSizeY(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getPixelsSizeZ(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getPixelsTimeIncrement(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getPixelsType() - Method in class ome.io.bioformats.BfPixelsWrapper: cgb - created from the methods below?
getPixelsType(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getPixelsType() - Method in class omeis.providers.re.Renderer: Returns the pixels type.
getPixelsType() - Method in class pojos.OTFData: Returns the pixels type.
getPixelsTypeLowerBound(int) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
getPixelsTypeLowerBound(int) - Method in class omeis.providers.re.Renderer: Returns the minimum value for that channels depending on the pixels type and the original range (globalmax, globalmin)
getPixelsTypeLowerBound(int) - Method in interface omeis.providers.re.RenderingEngine: Returns the minimum value for that channels depending on the pixels type and the original range (globalmax, globalmin)
getPixelsTypeLowerBound_async(AMD_RenderingEngine_getPixelsTypeLowerBound, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
getPixelsTypeMax() - Method in class omeis.providers.re.quantum.QuantumStrategy: Returns the upper bound of the pixels range or 0 if the value couldn't be set.
getPixelsTypeMin() - Method in class omeis.providers.re.quantum.QuantumStrategy: Returns the lower bound of the pixels range or 0 if the value couldn't be set.
getPixelsTypeUpperBound(int) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
getPixelsTypeUpperBound(int) - Method in class omeis.providers.re.Renderer: Returns the maximum value for that channels depending on the pixels type and the original range (globalmax, globalmin)
getPixelsTypeUpperBound(int) - Method in interface omeis.providers.re.RenderingEngine: Returns the maximum value for that channels depending on the pixels type and the original range (globalmax, globalmin)
getPixelsTypeUpperBound_async(AMD_RenderingEngine_getPixelsTypeUpperBound, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
getPixelType() - Method in class pojos.PixelsData: Returns the pixels type.
getPixelValue(int, 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(int, int, int) - Method in class ome.services.RawPixelsBean
getPlane_async(AMD_RawPixelsStore_getPlane, int, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
getPlane_async(AMD_RawPixelsStore_getPlane, int, int, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
getPlaneCount(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getPlaneCount() - Method in class pojos.ROIData: Returns the number of planes occupied by the ROI.
getPlaneDeltaT(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
getPlaneDimsAsString(PlaneDef) - Method in class omeis.providers.re.Renderer: Returns a string with the dimensions of the specified plane.
getPlaneDirect(Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPixelBuffer
getPlaneDirect(Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
getPlaneDirect(Integer, Integer, Integer, byte[]) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
getPlaneDirect(Integer, Integer, Integer, byte[]) - Method in interface ome.io.nio.PixelBuffer: Retrieves a particular 2D image plane from this pixel buffer.
getPlaneDirect(Integer, Integer, Integer, byte[]) - Method in class ome.io.nio.RomioPixelBuffer: Implemented as specified by PixelBuffer I/F.
getPlaneExposureTime(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
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() - 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 Pockel 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(UnitsLength) - Method in class pojos.ImageAcquisitionData: Returns the x-coordinate in the frame microscope.
getPositionX() - Method in class pojos.ImageAcquisitionData: Deprecated.
Replaced by ImageAcquisitionData.getPositionX(UnitsLength)
getPositionX(UnitsLength) - Method in class pojos.WellSampleData: Returns the position X.
getPositionX() - Method in class pojos.WellSampleData: Deprecated.
Replaced by WellSampleData.getPositionX(UnitsLength)
getPositionY(UnitsLength) - Method in class pojos.ImageAcquisitionData: Returns the y-coordinate in the frame microscope.
getPositionY() - Method in class pojos.ImageAcquisitionData: Deprecated.
Replaced by ImageAcquisitionData.getPositionY(UnitsLength)
getPositionY(UnitsLength) - Method in class pojos.WellSampleData: Returns the position Y.
getPositionY() - Method in class pojos.WellSampleData: Deprecated.
Replaced by WellSampleData.getPositionY(UnitsLength)
getPositionZ(UnitsLength) - Method in class pojos.ImageAcquisitionData: Returns the z-coordinate in the frame microscope.
getPositionZ() - Method in class pojos.ImageAcquisitionData: Deprecated.
Replaced by ImageAcquisitionData.getPositionZ(UnitsLength)
getPower(UnitsPower) - Method in class pojos.LightSourceData: Returns the power of the light source.
getPower() - Method in class pojos.LightSourceData: Deprecated.
Replaced by LightSourceData.getPower(UnitsPower)
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.security.basic.BasicEventContext
getPrincipal() - Method in class ome.services.util.ExecutionThread
getPrincipal() - Method in class omero.cmd.SessionI
getProcess() - Method in class ome.services.scripts.ScriptFileType: Return the import name of the process class which will be used to invoke scripts of this type.
getProcess(String) - Method in class ome.services.scripts.ScriptRepoHelper: Find an "omero.process..." property string for the given mimetype or return "" if none is found.
getProcessedIds(String) - Method in class ome.services.graphs.GraphState: Deprecated.

Get the set of ids which were actually processed.
getProject(long) - Method in class ome.formats.OMEROMetadataStoreClient
getProjections(IObject) - Method in class ome.services.search.FullText
getProjectionService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
getProjectionService() - Method in class ome.system.ServiceFactory
getProjects() - Method in class ome.formats.OMEROMetadataStoreClient
getProjects() - Method in class pojos.DatasetData: Returns a set of projects containing the dataset.
getProjectsForDataset(long) - Method in interface ome.api.IAnalysis
getProjectsForUser(long) - Method in interface ome.api.IAnalysis
getProperties() - Method in class ome.security.auth.FilePasswordProvider
getProperties() - Method in class omero.client: Returns the active properties for this instance.
getProperty(String) - Method in class ome.system.OmeroContext
getProperty(String) - Method in class ome.system.PreferenceContext: Lookup method for getting access to the merged properties for this instance.
getProperty(String) - Method in class omero.client: Returns the property value for this key or the empty string if none.
getPropertyKind(String, String) - Method in class ome.services.graphs.GraphPathBean: Get what kind of property a specific class property is.
getPropertyMap() - Method in class omero.client: Returns all properties which are prefixed with "omero." or "Ice."
getPropertyMap(Properties) - Method in class omero.client: Returns all properties which are prefixed with "omero." or "Ice."
getProtocolDescription() - Method in class pojos.ScreenData: Returns the description of the protocol.
getProtocolIdentifier() - Method in class pojos.ScreenData: Returns the identifier of the protocol.
getProvider(ChecksumType) - Method in interface ome.util.checksum.ChecksumProviderFactory: Returns an implementation of ChecksumProvider depending on the specified ChecksumType.
getProvider(ChecksumType) - Method in class ome.util.checksum.ChecksumProviderFactoryImpl
getProxiedObject(T) - Static method in class ome.services.fulltext.BridgeHelper: Simpler wrapper to handle superclass proxy objects (e.g.
getProxy() - Method in class ome.services.blitz.impl.ScriptProcessI
getProxy(Current) - Method in class ome.services.blitz.repo.AbstractRepositoryI
getProxy() - Method in class ome.services.blitz.repo.ManagedImportProcessI
getProxy() - Method in interface ome.services.blitz.repo.ProcessContainer.Process
getProxy() - Method in class ome.services.blitz.util.RegisterServantMessage
getProxyOrNull(String, SessionControlPrx, Current) - Method in class ome.services.blitz.fire.Ring: Delegates to the Ring.redirector strategy configured for this instance.
getProxyOrNull(Redirector.Context, String, SessionControlPrx, Current) - Method in class ome.services.blitz.redirect.AbstractRedirector: Returns null early if the Current has already once been routed by a Redirector implementation, returns an existing session if it can be found, or returns a null.
getProxyOrNull(Redirector.Context, String, SessionControlPrx, Current) - Method in class ome.services.blitz.redirect.ConfigRedirector: Create or retrieve and returns a SessionPrx which the current method takes control of.
getProxyOrNull(Redirector.Context, String, SessionControlPrx, Current) - Method in class ome.services.blitz.redirect.NullRedirector: Always returns null
getProxyOrNull(Redirector.Context, String, SessionControlPrx, Current) - Method in interface ome.services.blitz.redirect.Redirector: Create or retrieve and returns a SessionPrx which the current method takes control of.
getProxyOrNull(Redirector.Context, String, SessionControlPrx, Current) - Method in class ome.services.blitz.redirect.ScaleRedirector
getQuantumDef() - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
getQuantumDef() - Method in interface omeis.providers.re.RenderingEngine: Returns the quantization object.
getQuantumDef_async(AMD_RenderingEngine_getQuantumDef, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
getQuantumManager() - Method in class omeis.providers.re.Renderer: Returns the object that manages and allows to retrieve the objects that are used to quantize wavelength data.
getQueries() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl: Get all executed query strings
getQueryCacheHitCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
getQueryCacheMissCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
getQueryCachePutCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
getQueryExecutionCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
getQueryExecutionMaxTime() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
getQueryExecutionMaxTimeQueryString() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
getQueryFactory() - Method in class ome.logic.AbstractLevel1Service
getQueryFactory() - Method in class ome.logic.AbstractLevel2Service
getQueryService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
getQueryService() - Method in class ome.services.mail.MailSender
getQueryService() - Method in class ome.system.ServiceFactory
getQueryStatistics(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl: Query statistics from query string (HQL or SQL)
getQueryString() - Method in class ome.services.mail.ObjectMailSender
getRadiusX() - Method in class pojos.EllipseData: Returns the radius along the X-axis.
getRadiusY() - Method in class pojos.EllipseData: Returns the radius along the Y-axis.
getRating() - Method in class pojos.RatingAnnotationData: Returns the rating value.
getRawFileStore(long, CheckedPath, String, Current) - Method in interface ome.services.blitz.repo.RepositoryDao: Create a RawFileBean (i.e. an implementation of RawFileStore which can be passed to RepoRawFileStore for performing internal functions.
getRawFileStore(long, CheckedPath, String, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
getReader() - Method in class ome.formats.importer.ImportContainer: Return the reader class name used for reading the contents of this import container.
getReader() - Method in interface ome.formats.model.IObjectContainerStore: Returns the current Bio-Formats reader that has been used to populate the container store.
getReader() - Method in class ome.formats.OMEROMetadataStoreClient
getReaderClass(Fileset, Current) - Method in class ome.services.blitz.repo.ManagedRepositoryI: Get the suggested BioFormats Reader for the given Fileset.
getReaderNames() - Static method in class ome.services.util.DBEnumCheck
getReaderType(String) - Method in class ome.formats.importer.ImportCandidates: Retrieve reader type for file specified in path
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 the "to" argument.
getRelativePath() - Method in class ome.services.blitz.repo.CheckedPath: Get the parent path of the entity to which this path corresponds.
getRenderingDef() - Method in class omeis.providers.re.Renderer: Returns the settings that define the transformation context.
getRenderingDefId() - Method in interface ome.api.ThumbnailStore: Return the id of the RenderingDef loaded in this instance.
getRenderingDefId() - Method in class ome.services.RenderingBean
getRenderingDefId() - Method in class ome.services.ThumbnailBean
getRenderingDefId() - Method in interface omeis.providers.re.RenderingEngine: Returns the id of the RederingDef loaded by either RenderingEngine.lookupRenderingDef(long) or RenderingEngine.loadRenderingDef(long).
getRenderingDefId_async(AMD_RenderingEngine_getRenderingDefId, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
getRenderingDefId_async(AMD_ThumbnailStore_getRenderingDefId, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
getRenderingSettings(long) - Method in interface ome.api.IRenderingSettings: Returns the default rendering settings for a given pixels for the current user.
getRenderingSettings(long) - Method in class ome.logic.RenderingSettingsImpl: Implemented as specified by the IRenderingSettings I/F
getRenderingSettings_async(AMD_IRenderingSettings_getRenderingSettings, long, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
getRenderingSettingsService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
getRenderingSettingsService() - Method in class ome.system.ServiceFactory
getRenderShapes() - Method in class omeis.providers.re.data.PlaneDef: Returns whether or not the shapes (masks) will be rendered.
getReorderedPixelOffset(int, int, int) - Static method in class ome.io.nio.ReorderedPixelData: Returns the re-ordered pixel offset.
getRepositoryInfoService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
getRepositoryInfoService() - Method in class ome.system.ServiceFactory
getRepositorySpace() - Method in class ome.formats.OMEROMetadataStoreClient
getRepoUuid() - Method in class ome.services.blitz.repo.AbstractRepositoryI
getRepoUuid() - Method in class ome.services.blitz.repo.PublicRepositoryI
getRequest(Class<R>) - Method in class omero.cmd.graphs.GraphRequestFactory: Construct a request.
getRequest(Current) - Method in class omero.cmd.HandleI
getRequests() - Method in class omero.cmd.graphs.Preprocessor: Deprecated.

Returns a copy of the requests field or an empty list if null.
getRequiredPermissions() - Method in interface ome.services.graphs.GraphTraversal.Processor
getRequiredPermissions() - Method in class omero.cmd.graphs.NullGraphTraversalProcessor
getResolutionDescriptions() - Method in interface ome.api.RawPixelsStore
getResolutionDescriptions() - Method in class ome.io.bioformats.BfPixelBuffer
getResolutionDescriptions() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
getResolutionDescriptions() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
getResolutionDescriptions() - Method in interface ome.io.nio.PixelBuffer: Return a list of lists each of which has sizeX, sizeY for the resolution level matching the index of the outer index.
getResolutionDescriptions() - Method in class ome.io.nio.RomioPixelBuffer
getResolutionDescriptions() - Method in class ome.services.RawPixelsBean
getResolutionDescriptions() - Method in class ome.services.RenderingBean
getResolutionDescriptions() - Method in class omeis.providers.re.Renderer: Returns the image's size information per resolution level.
getResolutionDescriptions() - Method in interface omeis.providers.re.RenderingEngine
getResolutionDescriptions_async(AMD_PyramidService_getResolutionDescriptions, Current) - Method in class ome.services.blitz.impl.AbstractPyramidServant
getResolutionDescriptions_async(AMD_PyramidService_getResolutionDescriptions, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
getResolutionLevel() - Method in interface ome.api.RawPixelsStore
getResolutionLevel() - Method in class ome.io.bioformats.BfPixelBuffer
getResolutionLevel() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
getResolutionLevel() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
getResolutionLevel() - Method in interface ome.io.nio.PixelBuffer: Retrieves the active resolution level.
getResolutionLevel() - Method in class ome.io.nio.RomioPixelBuffer
getResolutionLevel() - Method in class ome.services.RawPixelsBean
getResolutionLevel() - Method in class ome.services.RenderingBean
getResolutionLevel() - Method in class omeis.providers.re.Renderer: Retrieves the active resolution level.
getResolutionLevel() - Method in interface omeis.providers.re.RenderingEngine
getResolutionLevel_async(AMD_PyramidService_getResolutionLevel, Current) - Method in class ome.services.blitz.impl.AbstractPyramidServant
getResolutionLevel_async(AMD_PyramidService_getResolutionLevel, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
getResolutionLevels() - Method in interface ome.api.RawPixelsStore
getResolutionLevels() - Method in class ome.io.bioformats.BfPixelBuffer
getResolutionLevels() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
getResolutionLevels() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
getResolutionLevels() - Method in interface ome.io.nio.PixelBuffer: Retrieves the number of resolution levels that the backing pixels pyramid contains.
getResolutionLevels() - Method in class ome.io.nio.RomioPixelBuffer
getResolutionLevels() - Method in class ome.services.RawPixelsBean
getResolutionLevels() - Method in class ome.services.RenderingBean
getResolutionLevels() - Method in class omeis.providers.re.Renderer: Retrieves the number of resolution levels that the backing pixels pyramid contains.
getResolutionLevels() - Method in interface omeis.providers.re.RenderingEngine
getResolutionLevels_async(AMD_PyramidService_getResolutionLevels, Current) - Method in class ome.services.blitz.impl.AbstractPyramidServant
getResolutionLevels_async(AMD_PyramidService_getResolutionLevels, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
getResponse() - Method in class ome.services.blitz.impl.commands.SaveI
getResponse() - Method in class ome.services.blitz.repo.ManagedImportRequestI
getResponse() - Method in class ome.services.blitz.repo.RawAccessRequestI
getResponse() - Method in class omero.cmd.admin.CurrentSessionsRequestI
getResponse() - Method in class omero.cmd.admin.ResetPasswordRequestI
getResponse() - Method in class omero.cmd.admin.UpdateSessionTimeoutRequestI
getResponse() - Method in class omero.cmd.basic.DoAllI
getResponse() - Method in class omero.cmd.basic.ListRequestsI
getResponse() - Method in class omero.cmd.basic.TimingI
getResponse() - Method in class omero.cmd.CmdCallbackI: Returns possibly null Response value.
getResponse() - Method in class omero.cmd.fs.ManageImageBinariesI
getResponse() - Method in class omero.cmd.fs.OriginalMetadataRequestI
getResponse() - Method in class omero.cmd.fs.UsedFilesRequestI
getResponse() - Method in class omero.cmd.graphs.Chgrp2I
getResponse() - Method in class omero.cmd.graphs.ChgrpFacadeI: Deprecated.
getResponse() - Method in class omero.cmd.graphs.ChgrpI: Deprecated.
getResponse() - Method in class omero.cmd.graphs.Chmod2I
getResponse() - Method in class omero.cmd.graphs.ChmodFacadeI: Deprecated.
getResponse() - Method in class omero.cmd.graphs.ChmodI: Deprecated.
getResponse() - Method in class omero.cmd.graphs.Chown2I
getResponse() - Method in class omero.cmd.graphs.ChownFacadeI: Deprecated.
getResponse() - Method in class omero.cmd.graphs.ChownI: Deprecated.
getResponse() - Method in class omero.cmd.graphs.Delete2I
getResponse() - Method in class omero.cmd.graphs.DeleteFacadeI: Deprecated.
getResponse() - Method in class omero.cmd.graphs.DeleteI: Deprecated.
getResponse() - Method in class omero.cmd.graphs.DiskUsageI
getResponse() - Method in class omero.cmd.graphs.GraphSpecListI: Deprecated.
getResponse() - Method in class omero.cmd.graphs.SkipHeadI
getResponse(Current) - Method in class omero.cmd.HandleI
getResponse() - Method in class omero.cmd.Helper
getResponse() - Method in interface omero.cmd.IRequest: Returns the current response value.
getResponse() - Method in class omero.cmd.mail.SendEmailRequestI
getResponses() - Method in class ome.services.blitz.impl.ProcessorCallbackI: Return the number of times this instance has been called in a thread safe manner.
getResults(int, Current) - Method in class ome.services.blitz.impl.ScriptProcessI
getResults() - Method in class ome.services.delete.QueryConstraints
getResults(ProcessPrx, Current) - Method in class omero.grid.InteractiveProcessorI
getResultSet() - Method in class ome.tools.hibernate.SqlArray
getResultSet(Map<String, Class<?>>) - Method in class ome.tools.hibernate.SqlArray
getResultSet(long, int) - Method in class ome.tools.hibernate.SqlArray
getResultSet(long, int, Map<String, Class<?>>) - Method in class ome.tools.hibernate.SqlArray
getResultsString(Object, IdentityHashMap<Object, String>) - Static method in class ome.services.util.ServiceHandler: public for testing purposes.
getResultTypes() - Method in class ome.logic.TypesImpl
getRevision(Class) - Static method in class ome.system.Version: Parses the given class for its RevisionNumber annotation.
getRGBA(int) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
getRGBA(int) - Method in interface omeis.providers.re.RenderingEngine: Returns a 4D-array representing the color associated to the specified channel.
getRGBA_async(AMD_RenderingEngine_getRGBA, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
getRing() - Method in class ome.services.blitz.util.BlitzConfiguration
getROI() - Method in class 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
getRoles() - Method in class ome.services.mail.MailSender
getRoles() - Method in class ome.services.util.DBUserCheck
getRoot() - Method in class ome.formats.OMEROMetadataStoreClient
getRoot() - Method in class ome.services.blitz.impl.OmeroMetadata
getRoot() - Method in class ome.services.graphs.AbstractHierarchyGraphSpec: Deprecated.

Return the root class for this hierarchy.
getRoot() - Method in class ome.services.graphs.AnnotationGraphSpec: Deprecated.
getRoot() - Method in class ome.services.graphs.LightSourceGraphSpec: Deprecated.
getRootFile() - Method in class ome.formats.importer.transfers.TransferState: Find original file represented by the managed repository that import is taking place to.
getRootId() - Method in class ome.system.Roles
getRootName() - Method in class ome.system.Roles
getRouter(Communicator) - Static method in class omero.client: Acquires the default router, and throws an exception if it is not of type {Glacier2.RouterPrx}.
getRow(int, int, int, int) - Method in interface ome.api.RawPixelsStore
getRow(Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer
getRow(Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPixelsWrapper
getRow(Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
getRow(Integer, Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
getRow(Integer, Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer: Retrieves a particular row or scanline from this pixel buffer.
getRow(Integer, Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer: Implemented as specified by PixelBuffer I/F.
getRow(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() - 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
getScheduledDeletes() - Method in class ome.services.delete.Deletion: Deprecated.
getScore(IObject) - Method in class ome.services.search.FullText
getScreens() - Method in class ome.formats.OMEROMetadataStoreClient
getScreens() - Method in class pojos.PlateData: Returns a set of screens containing the plate.
getScriptDir() - Method in class ome.services.scripts.ScriptRepoHelper: Returns the actual root of this repository.
getScriptID_async(AMD_IScript_getScriptID, String, Current) - Method in class ome.services.blitz.impl.ScriptI: Get the id of the official script with given path.
getScriptRepository(Current) - Method in class ome.services.blitz.impl.SharedResourcesI
getScripts_async(AMD_IScript_getScripts, Current) - Method in class ome.services.blitz.impl.ScriptI: Get Scripts will return all the scripts by id and name available on the server.
getScriptService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
getScriptText_async(AMD_IScript_getScriptText, long, Current) - Method in class ome.services.blitz.impl.ScriptI: Return the script with the name to the user.
getScriptWithDetails_async(AMD_IScript_getScriptWithDetails, long, Current) - Method in class ome.services.blitz.impl.ScriptI: Return the script with the name to the user.
getSecondLevelCacheHitCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
getSecondLevelCacheMissCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
getSecondLevelCachePutCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
getSecondLevelCacheRegionNames() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl: Get all second-level cache region names
getSecondLevelCacheStatistics(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl: Second level cache statistics per region
getSecurityContexts(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
getSecurityRoles() - Method in interface ome.api.IAdmin: returns the active Roles in use by the server.
getSecurityRoles() - Method in class ome.logic.AdminImpl
getSecurityRoles() - Method in class ome.security.basic.BasicSecuritySystem
getSecurityRoles() - Method in interface ome.security.SecuritySystem
getSecurityRoles() - Method in class ome.security.SecuritySystemHolder
getSecurityRoles() - Method in class ome.security.sharing.SharingSecuritySystem
getSecurityRoles_async(AMD_IAdmin_getSecurityRoles, Current) - Method in class ome.services.blitz.impl.AdminI
getSecuritySystem() - Method in class ome.logic.AbstractLevel2Service
getSelectedFile() - Method in class ome.formats.importer.util.ErrorContainer
getSender() - Method in class ome.services.mail.MailUtil: Helper method that returns value of omero.mail.from.
getSerialNumber() - Method in class pojos.DetectorData: Returns the serial number of the detector.
getSerialNumber() - Method in class pojos.DichroicData: Returns the serial number.
getSerialNumber() - Method in class pojos.FilterData: Returns the serial number.
getSerialNumber() - Method in class pojos.FilterSetData: Returns the serial number.
getSerialNumber() - Method in class pojos.LightSourceData: Returns the serial number of the light source.
getSerialNumber() - Method in class pojos.ObjectiveData: Returns the serial number of the objective.
getSeries() - Method in class ome.io.bioformats.BfPixelBuffer: Retrieves the current series of the underlying Bio-Formats reader.
getSeries(Pixels) - Method in class ome.io.nio.PixelsService: Retrieves the series for a given set of pixels.
getSeries() - Method in class pojos.ImageData: Returns the series.
getServant(Identity) - Method in class ome.services.blitz.impl.ServiceFactoryI
getServant() - Method in class ome.services.blitz.util.RegisterServantMessage
getServantList() - Method in class omero.util.ServantHolder
getServerFileFromFsFile(FsFile) - Method in class ome.services.blitz.repo.path.ServerFilePathTransformer: Given a repository path, returns the corresponding server-local File.
getServerFileMimetype() - Method in class pojos.FileAnnotationData: Returns the file format as defined by the specification, corresponding to the file extension.
getServerPort() - Method in class ome.formats.importer.util.IniFileLoader
getServerTime() - Method in interface ome.api.IConfig: checks the current server for it's time.
getServerTime() - Method in class ome.logic.ConfigImpl: see IConfig.getServerTime()
getServerTime_async(AMD_IConfig_getServerTime, Current) - Method in class ome.services.blitz.impl.ConfigI
getService() - Method in interface ome.services.util.Executor: Returns the ExecutorService assigned to this instance.
getService() - Method in class ome.services.util.Executor.Impl
getServiceByClass(Class<T>) - Method in class ome.system.ServiceFactory: looks up services based on the current prefix and the class name of the service type.
getServiceCleanups() - Method in class ome.security.basic.BasicEventContext
getServiceFactory() - Method in class ome.formats.OMEROMetadataStoreClient: Returns the currently active service factory.
getServiceFactory(MethodInvocation) - Method in class ome.logic.HardWiredInterceptor
getServiceFactory(String, String) - Method in class ome.services.blitz.fire.SessionManagerI
getServiceFactory(Identity) - Method in class ome.services.blitz.fire.SessionManagerI
getServiceFactory() - Method in class ome.services.blitz.impl.RawFileStoreI
getServiceFactory() - Method in class ome.services.blitz.util.FindServiceFactoryMessage
getServiceFactory() - Method in class omero.client: Deprecated.
getServiceFactory() - Method in class omero.cmd.Helper
getServiceFactoryIdentity(Current) - Method in class ome.services.blitz.fire.SessionManagerI
getServiceInterface() - Method in class ome.logic.AdminImpl
getServiceInterface() - Method in class ome.logic.ConfigImpl
getServiceInterface() - Method in class ome.logic.LdapImpl
getServiceInterface() - Method in class ome.logic.MetadataImpl: Returns the Interface implemented by this class.
getServiceInterface() - Method in class ome.logic.PixelsImpl: Returns the interface this implementation is for.
getServiceInterface() - Method in class ome.logic.PojosImpl: Returns the Interface implemented by this class.
getServiceInterface() - Method in class ome.logic.QueryImpl
getServiceInterface() - Method in class ome.logic.RenderingSettingsImpl: Returns the interface this implementation is for.
getServiceInterface() - Method in class ome.logic.RepositoryInfoImpl
getServiceInterface() - Method in class ome.logic.TypesImpl
getServiceInterface() - Method in class ome.logic.UpdateImpl
getServiceInterface() - Method in class ome.services.delete.DeleteBean
getServiceInterface() - Method in class ome.services.JobBean
getServiceInterface() - Method in class ome.services.projection.ProjectionBean: Returns the interface this implementation is for.
getServiceInterface() - Method in class ome.services.RawFileBean
getServiceInterface() - Method in class ome.services.RawPixelsBean
getServiceInterface() - Method in class ome.services.RenderingBean: Returns the service corresponding to this class.
getServiceInterface() - Method in class ome.services.SearchBean
getServiceInterface() - Method in class ome.services.sessions.SessionBean
getServiceInterface() - Method in class ome.services.sharing.ShareBean
getServiceInterface() - Method in class ome.services.ThumbnailBean
getServiceInterface() - Method in interface ome.system.SelfConfigurableService
getServiceKey() - Method in class ome.services.blitz.util.ExpiredServantMessage
getSession(String) - Method in interface ome.api.ISession: Retrieves the session associated with this uuid, updating the last access time as well.
getSession(String) - Method in class ome.services.sessions.SessionBean
getSession() - Method in interface ome.services.sessions.SessionContext
getSession() - Method in class ome.services.sessions.SessionContextImpl
getSession() - Method in class ome.system.ServiceFactory
getSession() - Method in class ome.system.SessionInitializer
getSession() - Method in class ome.tools.hibernate.SessionFactory: Returns a session active for the current thread.
getSession() - Method in class omero.client: Returns the current active session or throws an exception if none has been created since the last client.closeSession()
getSession() - Method in class omero.cmd.Helper
getSession() - Method in class omero.model.DetailsI
getSession() - Method in class omero.util.RPSTileLoop
getSession() - Method in class omero.util.ServantHolder
getSession_async(AMD_ISession_getSession, String, Current) - Method in class ome.services.blitz.impl.SessionI
getSessionCloseCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
getSessionContext(String) - Method in class ome.services.sessions.state.SessionCache: Retrieve a session possibly raising either RemovedSessionException or SessionTimeoutException.
getSessionContext(String, boolean) - Method in class ome.services.sessions.state.SessionCache: Retrieve a session possibly raising either RemovedSessionException or SessionTimeoutException.
getSessionData() - Method in interface ome.services.sessions.SessionManager: Return all sessions that are active with associated possibly varing session data information.
getSessionData() - Method in class ome.services.sessions.SessionManagerImpl
getSessionData(String, boolean) - Method in class ome.services.sessions.state.SessionCache: Returns all the data contained in the internal implementation of this manger.
getSessionFactory() - Method in class ome.logic.AbstractLevel1Service: delegates to HibernateDaoSupport to get the current SessionFactory
getSessionId() - Method in class ome.services.messages.AbstractSessionMessage
getSessionId() - Method in class omero.client: Returns the UUID for the current session without making a remote call.
getSessionInitializer() - Method in class ome.system.ServiceFactory
getSessionOpenCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
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.
getShapeIds() - Method in class omeis.providers.re.data.PlaneDef: Returns whether or not the shapes (masks) will be rendered.
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).
getShareIfAccessible(long, boolean, long) - Method in class ome.services.sharing.ShareStore: Loads share and checks its owner and member data against the current context (owner/member/admin).
getShares(long, boolean, boolean) - Method in class ome.services.sharing.BlobShareStore
getShares(long, boolean, boolean) - Method in class ome.services.sharing.ShareStore
getShareService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
getShareService() - Method in class ome.system.ServiceFactory
getSharesOwnedBy(Experimenter, boolean) - Method in interface ome.api.IShare: Gets all shares owned by the given Experimenter.
getSharesOwnedBy(Experimenter, boolean) - Method in class ome.services.sharing.ShareBean
getSharesOwnedBy_async(AMD_IShare_getSharesOwnedBy, Experimenter, boolean, Current) - Method in class ome.services.blitz.impl.ShareI
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.
getSkipHeadPolicyPerform(GraphPolicy, SetMultimap<String, Long>) - Static method in class omero.cmd.graphs.SkipHeadPolicy: Adjust an existing graph traversal policy so that for specific model objects permissions are not checked.
getSkipHeadPolicySkip(GraphPolicy, GraphPathBean, Collection<String>, GraphPolicy.Action, SetMultimap<String, Long>) - Static method in class omero.cmd.graphs.SkipHeadPolicy: Adjust an existing graph traversal policy so that orphaned model objects will always or never be included, according to their type.
getSlice() - Method in class omeis.providers.re.data.PlaneDef: Returns an identifier to tell which kind of plane this object identifies.
getSnapshot() - Method in class ome.system.metrics.DefaultHistogram
getSnapshot() - Method in interface ome.system.metrics.Histogram
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
getSql() - Method in class omero.cmd.Helper
getSqlAction() - Method in class ome.services.util.Executor.SimpleWork
getSQLJoin(String, String, String, String) - Method in interface ome.tools.hibernate.ExtendedMetadata: provides the link between two tables similar to {link ExtendedMetadata.getRelationship(String, String).
getSQLJoin(String, String, String, String) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl: Note: this implementation does not yet take into account the mapping of joined subclasses like Job->UpdateJob.
getStack(int, int) - Method in interface ome.api.RawPixelsStore
getStack(Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer
getStack(Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPixelsWrapper
getStack(Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
getStack(Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
getStack(Integer, Integer) - Method in interface ome.io.nio.PixelBuffer: Retrieves the the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel buffer.
getStack(Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer: Implemented as specified by PixelBuffer I/F.
getStack(int, int) - Method in class ome.services.RawPixelsBean
getStack_async(AMD_RawPixelsStore_getStack, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
getStack_async(AMD_RawPixelsStore_getStack, int, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
getStackDirect(Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPixelBuffer
getStackDirect(Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
getStackDirect(Integer, Integer, byte[]) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
getStackDirect(Integer, Integer, byte[]) - Method in interface ome.io.nio.PixelBuffer: Retrieves the the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel buffer.
getStackDirect(Integer, Integer, byte[]) - Method in class ome.io.nio.RomioPixelBuffer: Implemented as specified by PixelBuffer I/F.
getStackOffset(int, int) - Method in interface ome.api.RawPixelsStore
getStackOffset(Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer
getStackOffset(Integer, Integer) - Method in class ome.io.bioformats.BfPixelsWrapper
getStackOffset(Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
getStackOffset(Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
getStackOffset(Integer, Integer) - Method in interface ome.io.nio.PixelBuffer: Retrieves the offset for the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel buffer.
getStackOffset(Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer: Implemented as specified by PixelBuffer I/F.
getStackOffset(int, int) - Method in class ome.services.RawPixelsBean
getStackOffset_async(AMD_RawPixelsStore_getStackOffset, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
getStackOffset_async(AMD_RawPixelsStore_getStackOffset, int, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
getStackSize() - Method in interface ome.api.RawPixelsStore
getStackSize() - Method in class ome.io.bioformats.BfPixelBuffer
getStackSize() - Method in class ome.io.bioformats.BfPixelsWrapper
getStackSize() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
getStackSize() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
getStackSize() - Method in interface ome.io.nio.PixelBuffer: Retrieves the in memory size of the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel buffer.
getStackSize() - Method in class ome.io.nio.RomioPixelBuffer: Implemented as specified by PixelBuffer I/F.
getStackSize() - Method in class ome.services.RawPixelsBean
getStackSize_async(AMD_RawPixelsStore_getStackSize, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
getStackSize_async(AMD_RawPixelsStore_getStackSize, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
getStackTrace(Throwable) - Static method in class ome.formats.importer.util.ErrorHandler: Return stack trace from throwable
getStageLabelId() - Method in class pojos.ImageAcquisitionData: Returns the id of the StageLabel or -1 if not already linked to the image.
getStart() - Method in class ome.services.delete.Deletion: Deprecated.
getStartFrom(Response) - Method in class omero.cmd.graphs.Chgrp2I
getStartFrom(Response) - Method in class omero.cmd.graphs.Chmod2I
getStartFrom(Response) - Method in class omero.cmd.graphs.Chown2I
getStartFrom(Response) - Method in class omero.cmd.graphs.Delete2I
getStartFrom(Response) - Method in interface omero.cmd.graphs.WrappableRequest: From the response of the head-skipping request, determine which model objects are the targets of the operation.
getStartTime() - Method in class omero.sys.ParametersI: Returns the value of the start time parameter.
getStartTime() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
getStartTime() - Method in class pojos.PlateAcquisitionData: Returns the time when the first image was collected.
getStartTime() - Method in class pojos.WellSampleData: Returns the time at which the field was acquired.
getStatefulServiceCount() - Method in class ome.services.blitz.impl.ServiceFactoryI: NB: Much of the logic here is similar to SessionI.doClose and should be pushed down.
getStatefulServiceCount() - Method in class omero.util.ServantHolder
getStatefulServices() - Method in class omero.client: Returns all active StatefulServiceInterface proxies.
getStaticDisableHistory() - Method in class ome.formats.importer.ImportConfig
getStaticDisableHistory() - Method in class ome.formats.importer.util.IniFileLoader
getStats() - Method in class ome.security.basic.BasicEventContext
getStats() - Method in class ome.security.basic.CurrentDetails
getStats(List<Long>) - Method in class ome.services.roi.GeomTool
getStats() - Method in class omeis.providers.re.Renderer: Returns a RenderingStats object that the rendering strategy can use to track performance.
getStats() - Method in class omeis.providers.re.RenderingStats: Returns a stats report ready to be written to the log file.
getStatus() - Method in class ome.formats.importer.util.ErrorContainer: return the error status
getStatus() - Method in class omero.cmd.CmdCallbackI: Returns possibly null Status value.
getStatus(Current) - Method in class omero.cmd.HandleI
getStatus() - Method in class omero.cmd.Helper
getStatus() - Method in class pojos.PlateData: Returns the status of the plate.
getStatus() - Method in class pojos.WellData: Returns the status of the well.
getStatusOrThrow() - Method in class omero.cmd.CmdCallbackI
getStdDev() - Method in class ome.system.metrics.DefaultSnapshot
getStdDev() - Method in interface ome.system.metrics.Snapshot
getStep(int) - Method in class ome.services.graphs.GraphState: Deprecated.
getSteps() - Method in class ome.services.delete.Deletion: Deprecated.
getSteps() - Method in class omero.cmd.Helper
getStop() - Method in class ome.services.delete.Deletion: Deprecated.
getStore() - Method in class ome.services.fulltext.SimpleLuceneOptions
getStrategy(QuantumDef, Pixels) - Method in class omeis.providers.re.quantum.QuantumFactory: Returns a strategy to carry out the quantization process whose context is defined by pd.
getStride() - Method in class omeis.providers.re.data.PlaneDef: Returns the stride.
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: Deprecated.
Replaced by ShapeSettingsData.getStrokeWidth(UnitsLength)
getStrokeWidth(UnitsLength) - Method in class pojos.ShapeSettingsData: Returns the stroke's width (or 1 px if it's not set or <= 0)
getSubclassesOf(String) - Method in class ome.services.graphs.GraphPathBean: Get the subclasses of the given class, if any.
getSubclassesOfReflexive(String) - Method in class ome.services.graphs.GraphPathBean: Get the name of this class and of its mapped subclasses.
getSubjectPrefix() - Method in class ome.services.mail.MailSender
getSubSpec() - Method in class ome.services.graphs.GraphEntry: Deprecated.
getSubtypeValue(int, int, Object) - Method in class ome.tools.hibernate.ExtendedMetadata.Locks: uses the ClassMetadata for this ExtendedMetadata.Locks tp retrieve the component value.
getSuccessfulTransactionCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
getSuperclassesOf(String) - Method in class ome.services.graphs.GraphPathBean: Get the superclasses of the given class, if any.
getSuperclassesOfReflexive(String) - Method in class ome.services.graphs.GraphPathBean: Get the name of this class and of its mapped superclasses.
getSuperSpec() - Method in class ome.services.graphs.BaseGraphSpec: Deprecated.
getSuperSpec() - Method in class ome.services.graphs.GraphEntry: Deprecated.
getSuperSpec() - Method in interface ome.services.graphs.GraphSpec: Deprecated.

Specification of where this GraphSpec is attached under another .
getSupportedMetadataLevels() - Method in class ome.formats.importer.OMEROWrapper
getSymbol(Current) - Method in class omero.model.ElectricPotentialI
getSymbol(Current) - Method in class omero.model.FrequencyI
getSymbol(Current) - Method in class omero.model.LengthI
getSymbol(Current) - Method in class omero.model.PowerI
getSymbol(Current) - Method in class omero.model.PressureI
getSymbol(Current) - Method in class omero.model.TemperatureI
getSymbol(Current) - Method in class omero.model.TimeI
getSystemGroupId() - Method in class ome.system.Roles
getSystemGroupName() - Method in class ome.system.Roles
getT() - Method in class omeis.providers.re.data.PlaneDef: Returns the timepoint.
getT() - Method in class pojos.ShapeData: Returns the time-point.
getTable() - Method in class ome.services.blitz.measurements.MeasurementStore
getTable() - Method in interface ome.services.blitz.measurements.OmeroMeasurementStore: Returns the Table proxy which is in use by this service.
getTable_async(AMD_IRoi_getTable, long, Current) - Method in class ome.services.blitz.impl.RoiI
getTagAnnotationCount() - Method in class ome.services.blitz.impl.OmeroMetadata
getTagAnnotationDescription(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getTagAnnotationID(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getTagAnnotationNamespace(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getTagAnnotationValue(int) - Method in class ome.services.blitz.impl.OmeroMetadata
getTagDescription() - Method in class pojos.TagAnnotationData: Returns the description of the tag.
getTagDescriptions() - Method in class pojos.TagAnnotationData: Returns the descriptions linked to that tag.
getTaggedObjectsCount(Set<Long>, Parameters) - Method in interface ome.api.IMetadata: Returns a map whose key is a tag's id and the value the number of Projects, Datasets, and Images linked to that tag.
getTaggedObjectsCount(Set<Long>, Parameters) - Method in class ome.logic.MetadataImpl: Implemented as specified by the IMetadata I/F
getTaggedObjectsCount_async(AMD_IMetadata_getTaggedObjectsCount, List<Long>, Parameters, Current) - Method in class ome.services.blitz.impl.MetadataI
getTags() - Method in class pojos.TagAnnotationData: Returns the collection of tags related to this tag.
getTagValue() - Method in class pojos.TagAnnotationData: Returns the text of the tag.
getTarget() - Method in class ome.formats.importer.ImportContainer
getTarget(Class<T>, long) - Method in class ome.formats.OMEROMetadataStoreClient: Helper method to retrieve an object from iQuery
getTarget() - Method in class ome.services.blitz.repo.ManagedImportLocationI: Return the server-side CheckedPath instance which can be passed to a Bio-Formats reader.
getTargetType(String) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl: Returns the IObject type which a given field points to.
getTempDir() - Method in class omero.util.TempFileManager: Returns the directory under which all temporary files and folders will be created.
gettempdir() - Static method in class omero.util.TempFileManager: Calls TempFileManager.getTempDir() on TempFileManager.manager.
getTemperature(UnitsTemperature) - Method in class pojos.ImageAcquisitionData: Returns the temperature in Celcius.
getTemperature() - Method in class pojos.ImageAcquisitionData: Deprecated.
Replaced by ImageAcquisitionData.getTemperature(UnitsTemperature)
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.
getThis() - Method in interface ome.services.util.Executor.StatefulWork
getThis(MethodInvocation) - Method in class ome.tools.hibernate.SessionHandler
getThumbnail(Integer, Integer) - Method in interface ome.api.ThumbnailStore: Retrieves a thumbnail for a pixels set using a given set of rendering settings (RenderingDef).
getThumbnail(Thumbnail) - Method in class ome.io.nio.ThumbnailService: Return byte array of Thumbnail
getThumbnail(Thumbnail, byte[]) - Method in class ome.io.nio.ThumbnailService: Return byte array of Thumbnail, providing byte array
getThumbnail(Integer, Integer) - Method in class ome.services.ThumbnailBean
getThumbnail_async(AMD_ThumbnailStore_getThumbnail, RInt, RInt, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
getThumbnailByLongestSide(Integer) - Method in interface ome.api.ThumbnailStore: Retrieves a thumbnail for a pixels set using a given set of rendering settings (RenderingDef).
getThumbnailByLongestSide(Integer) - Method in class ome.services.ThumbnailBean
getThumbnailByLongestSide_async(AMD_ThumbnailStore_getThumbnailByLongestSide, RInt, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
getThumbnailByLongestSideDirect(Integer) - Method in interface ome.api.ThumbnailStore: Retrieves a thumbnail for a pixels set using a given set of rendering settings (RenderingDef).
getThumbnailByLongestSideDirect(Integer) - Method in class ome.services.ThumbnailBean
getThumbnailByLongestSideDirect_async(AMD_ThumbnailStore_getThumbnailByLongestSideDirect, RInt, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
getThumbnailByLongestSideSet(Integer, Set<Long>) - Method in interface ome.api.ThumbnailStore: Retrieves a number of thumbnails for pixels sets using given sets of rendering settings (RenderingDef).
getThumbnailByLongestSideSet(Integer, Set<Long>) - Method in class ome.services.ThumbnailBean
getThumbnailByLongestSideSet_async(AMD_ThumbnailStore_getThumbnailByLongestSideSet, RInt, List<Long>, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
getThumbnailDirect(Integer, Integer) - Method in interface ome.api.ThumbnailStore: Retrieves a thumbnail for a pixels set using a given set of rendering settings (RenderingDef).
getThumbnailDirect(Integer, Integer) - Method in class ome.services.ThumbnailBean
getThumbnailDirect_async(AMD_ThumbnailStore_getThumbnailDirect, RInt, RInt, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
getThumbnailExists(Thumbnail) - Method in class ome.io.nio.ThumbnailService: Returns whether or not a thumbnail exists on disk.
getThumbnailForSectionByLongestSideDirect(int, int, Integer) - Method in interface ome.api.ThumbnailStore: Retrieves a thumbnail for a pixels set using a given set of rendering settings (RenderingDef) for a particular section.
getThumbnailForSectionByLongestSideDirect(int, int, Integer) - Method in class ome.services.ThumbnailBean
getThumbnailForSectionByLongestSideDirect_async(AMD_ThumbnailStore_getThumbnailForSectionByLongestSideDirect, int, int, RInt, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
getThumbnailForSectionDirect(int, int, Integer, Integer) - Method in interface ome.api.ThumbnailStore: Retrieves a thumbnail for a pixels set using a given set of rendering settings (RenderingDef) for a particular section.
getThumbnailForSectionDirect(int, int, Integer, Integer) - Method in class ome.services.ThumbnailBean
getThumbnailForSectionDirect_async(AMD_ThumbnailStore_getThumbnailForSectionDirect, int, int, RInt, RInt, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
getThumbnailIds() - Method in class ome.tools.RepositoryTask: This public method is used to return a list of thumbnail ids that require deletion from the disk repository.
getThumbnailLength(Thumbnail) - Method in class ome.io.nio.ThumbnailService: Returns length of Thumbnail on disk
getThumbnailOutputStream(Thumbnail) - Method in class ome.io.nio.ThumbnailService: Return FileOutputStream of Thumbnail
getThumbnailPath(Long) - Method in class ome.io.nio.AbstractFileSystemService: Returns a numbered path relative to the root of this service, but is ignorant of FS and similar constructs.
getThumbnailSet(Integer, Integer, Set<Long>) - Method in interface ome.api.ThumbnailStore: Retrieves a number of thumbnails for pixels sets using given sets of rendering settings (RenderingDef).
getThumbnailSet(Integer, Integer, Set<Long>) - Method in class ome.services.ThumbnailBean
getThumbnailSet_async(AMD_ThumbnailStore_getThumbnailSet, RInt, RInt, List<Long>, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
getTie(Identity) - Method in class ome.services.blitz.impl.ServiceFactoryI
getTile(int, int, int, int, int, int, int) - Method in interface ome.api.RawPixelsStore
getTile(Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer
getTile(int, int, int, int, int, int, int, byte[]) - Method in class ome.io.bioformats.BfPixelsWrapper
getTile(Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
getTile(Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
getTile(Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer: Retrieves a tile from this pixel buffer.
getTile(Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer
getTile(int, int, int, int, int, int, int) - Method in class ome.services.RawPixelsBean
getTile(int, int, int, int, int, int, int) - Method in class omero.util.RPSTileData
getTile(int, int, int, int, int, int, int) - Method in interface omero.util.TileData
getTile_async(AMD_RawPixelsStore_getTile, int, int, int, int, int, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
getTile_async(AMD_RawPixelsStore_getTile, int, int, int, int, int, int, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
getTileDirect(Integer, Integer, Integer, Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPixelBuffer
getTileDirect(Integer, Integer, Integer, Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
getTileDirect(Integer, Integer, Integer, Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
getTileDirect(Integer, Integer, Integer, Integer, Integer, Integer, Integer, byte[]) - Method in interface ome.io.nio.PixelBuffer: Retrieves a tile from this pixel buffer.
getTileDirect(Integer, Integer, Integer, Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.nio.RomioPixelBuffer
getTileHeight() - Method in class ome.io.nio.ConfiguredTileSizes
getTileHeight() - Method in interface ome.io.nio.TileSizes
getTileSize() - Method in interface ome.api.RawPixelsStore
getTileSize(Long) - Method in class ome.formats.OMEROMetadataStoreClient: Retrieves the suggested tile size for a pixels set.
getTileSize() - Method in class ome.io.bioformats.BfPixelBuffer
getTileSize() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
getTileSize() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
getTileSize() - Method in interface ome.io.nio.PixelBuffer: Retrieves the tile size for the pixel store.
getTileSize() - Method in class ome.io.nio.RomioPixelBuffer
getTileSize() - Method in class ome.services.RawPixelsBean
getTileSize() - Method in class ome.services.RenderingBean
getTileSize() - Method in class omeis.providers.re.Renderer: Retrieves the tile size for the pixel store.
getTileSize() - Method in interface omeis.providers.re.RenderingEngine
getTileSize_async(AMD_PyramidService_getTileSize, Current) - Method in class ome.services.blitz.impl.AbstractPyramidServant
getTileSize_async(AMD_PyramidService_getTileSize, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
getTileWidth() - Method in class ome.io.nio.ConfiguredTileSizes
getTileWidth() - Method in interface ome.io.nio.TileSizes
getTime() - Method in class 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() - 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
getTooSimilarFiles(Set<File>) - Method in class ome.services.blitz.repo.path.ClientFilePathTransformer: Get the files that are too similarly named.
getTopicManager() - Method in class ome.services.blitz.util.BlitzConfiguration
getTotalFoundCount() - Method in class ome.services.graphs.GraphState: Deprecated.

Return the total number of ids loaded into this instance.
getTotalProcessedCount() - Method in class ome.services.graphs.GraphState: Deprecated.

Return the total number of ids which were processed.
getTotalSize() - Method in interface ome.api.RawPixelsStore
getTotalSize() - Method in class ome.io.bioformats.BfPixelBuffer
getTotalSize() - Method in class ome.io.bioformats.BfPixelsWrapper
getTotalSize() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
getTotalSize() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
getTotalSize() - Method in interface ome.io.nio.PixelBuffer: Retrieves the in memory size of the entire pixel buffer.
getTotalSize() - Method in class ome.io.nio.RomioPixelBuffer: Implemented as specified by PixelBuffer I/F.
getTotalSize() - Method in class ome.services.RawPixelsBean
getTotalSize(IObject) - Method in class ome.services.search.FullText
getTotalSize_async(AMD_RawPixelsStore_getTotalSize, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
getTotalSize_async(AMD_RawPixelsStore_getTotalSize, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
getTransactionAttribute(Method, Class) - Method in class ome.services.sharing.ShareRestrictionTransactionAttributeSource
getTransactionAttribute(Method, Class) - Method in class ome.tools.spring.ForceTransactionAttributeSource
getTransactionCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
getTransform() - Method in class 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.
getTypes() - Method in class ome.security.policy.BasePolicy
getTypes() - Method in interface ome.security.policy.Policy: Each Policy should tell the PolicyService which types of IObject instances it cares about.
getTypes(ExtendedMetadata) - Method in class ome.services.graphs.AbstractHierarchyGraphSpec: Deprecated.

Returns all the types that are known for this hierarchy.
getTypes(ExtendedMetadata) - Method in class ome.services.graphs.AnnotationGraphSpec: Deprecated.
getTypes(ExtendedMetadata) - Method in class ome.services.graphs.LightSourceGraphSpec: Deprecated.
getTypesService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
getTypesService() - Method in class ome.system.ServiceFactory
getUIBounds() - Method in class ome.formats.importer.ImportConfig
getUIBounds() - Method in class ome.formats.importer.util.IniFileLoader
getUndeletedFiles() - Method in class ome.services.delete.Deletion: Deprecated.
getUndeletedFiles() - Method in class ome.services.delete.files.AbstractFileDeletions
getUndeletedFiles() - Method in class ome.services.delete.files.FileDeleter
getUnique() - Method in class omero.sys.ParametersI
getUnit(Current) - Method in class omero.model.ElectricPotentialI
getUnit(Current) - Method in class omero.model.FrequencyI
getUnit(Current) - Method in class omero.model.LengthI
getUnit(Current) - Method in class omero.model.PowerI
getUnit(Current) - Method in class omero.model.PressureI
getUnit(Current) - Method in class omero.model.TemperatureI
getUnit(Current) - Method in class omero.model.TimeI
getUntied(Identity) - Method in class omero.util.ServantHolder
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
getUploader() - Method in class ome.formats.importer.transfers.TransferState: Return the RawFileStorePrx instance for this index.
getUploader(String) - Method in class ome.formats.importer.transfers.TransferState: Return the RawFileStorePrx instance for this index setting the mode if not null.
getUploader(int, Current) - Method in class ome.services.blitz.repo.ManagedImportProcessI
getUploaderUrl() - Method in class ome.formats.importer.ImportConfig
getUploadOffset(int, Current) - Method in class ome.services.blitz.repo.ManagedImportProcessI
getUploadTimeLeft() - Method in class ome.formats.importer.transfers.TransferState
getUploadTimeLeft() - Method in class ome.formats.importer.util.ProportionalTimeEstimatorImpl
getUploadTimeLeft() - Method in interface ome.formats.importer.util.TimeEstimator: Return the estimated time left in milliseconds based on the calls to start and stop methods.
getUploadUrl() - Method in class ome.formats.importer.util.ErrorContainer
getUpperLimit() - Method in class omeis.providers.re.codomain.PlaneSlicingContext: Returns the constant level for bit-planes > planeSelected w.r.t the higher-order bits.
getUsageFraction() - Method in interface ome.api.IRepositoryInfo: This method returns a double of the used space divided by the free space.
getUsageFraction() - Method in class ome.logic.RepositoryInfoImpl: Deprecated.
getUsageFraction_async(AMD_IRepositoryInfo_getUsageFraction, Current) - Method in class ome.services.blitz.impl.RepositoryInfoI
getUsedFilePaths() - Method in class pojos.FilesetData: Returns the collection of file paths used for importing the files (in case of in-place imports these are the targets of the (sym)links)
getUsedFiles(String) - Method in class ome.formats.importer.ImportCandidates: Return string of files used by container item at path
getUsedFiles() - Method in class ome.formats.importer.ImportContainer: Return a list of file names that belong to this import container.
getUsedFilesTotalSize() - Method in class ome.formats.importer.ImportContainer: Returns the total size in bytes (based on File.length()) of all files in this import container.
getUsedSpaceInKilobytes() - Method in interface ome.api.IRepositoryInfo: This method returns the total space in bytes for this file system including nested subdirectories.
getUsedSpaceInKilobytes() - Method in class ome.logic.RepositoryInfoImpl: Deprecated.
getUsedSpaceInKilobytes_async(AMD_IRepositoryInfo_getUsedSpaceInKilobytes, Current) - Method in class ome.services.blitz.impl.RepositoryInfoI
getUseQuaqua() - Method in class ome.formats.importer.ImportConfig
getUseQuaqua() - Method in class ome.formats.importer.util.IniFileLoader
getUserAttribute(String) - Method in class ome.security.auth.LdapConfig
getUserDisableHistory() - Method in class ome.formats.importer.ImportConfig
getUserDisableHistory() - Method in class ome.formats.importer.util.IniFileLoader
getUserEmail(String) - Method in class ome.services.mail.MailSender
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
getUserInstitution(long, Current) - Method in interface ome.services.blitz.repo.RepositoryDao: Get the current user's institution.
getUserInstitution(long, ServiceFactory) - Method in interface ome.services.blitz.repo.RepositoryDao: Get the current user's institution.
getUserInstitution(long, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
getUserInstitution(long, ServiceFactory) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
getUserName() - Method in class pojos.ExperimenterData: Returns the last name of the experimenter.
getUserPasswordHash(Long) - Method in class ome.security.auth.PasswordUtil
getUserPixels() - Method in class ome.formats.importer.ImportContainer
getUserRoles(Experimenter) - Method in interface ome.api.local.LocalAdmin: Finds the group names for all groups for which the given Experimenter is a member.
getUserRoles(Experimenter) - Method in class ome.logic.AdminImpl
getUserRoles() - Method in interface ome.services.sessions.SessionContext
getUserRoles() - Method in class ome.services.sessions.SessionContextImpl
getUserRoles(String) - Method in interface ome.services.sessions.SessionManager
getUserRoles(String) - Method in class ome.services.sessions.SessionManagerImpl
getUserScripts_async(AMD_IScript_getUserScripts, List<IObject>, Current) - Method in class ome.services.blitz.impl.ScriptI
getUserSettingsDirectory() - Method in class ome.formats.importer.ImportConfig
getUserSettingsDirectory() - Method in class ome.formats.importer.util.IniFileLoader
getUserSpecifiedAnnotations() - Method in interface ome.formats.model.IObjectContainerStore: Returns the user specified annotations.
getUserSpecifiedAnnotations() - Method in class ome.formats.OMEROMetadataStoreClient
getUserSpecifiedDescription() - Method in class ome.formats.importer.ImportContainer: Retrieves the current custom image/plate description string.
getUserSpecifiedDescription() - Method in interface ome.formats.model.IObjectContainerStore: Returns the user specified image/plate description.
getUserSpecifiedDescription() - Method in class ome.formats.OMEROMetadataStoreClient
getUserSpecifiedImageName() - Method in class ome.formats.OMEROMetadataStoreClient
getUserSpecifiedName() - Method in class ome.formats.importer.ImportContainer: Retrieves the current custom image/plate name string.
getUserSpecifiedName() - Method in interface ome.formats.model.IObjectContainerStore: Returns the user specified image/plate name.
getUserSpecifiedName() - Method in class ome.formats.OMEROMetadataStoreClient
getUserSpecifiedPhysicalPixelSizes() - Method in interface ome.formats.model.IObjectContainerStore: Returns the user specified physical pixel sizes.
getUserSpecifiedPhysicalPixelSizes() - Method in class ome.formats.OMEROMetadataStoreClient
getUserSpecifiedTarget() - Method in interface ome.formats.model.IObjectContainerStore: Returns the user specified linkage target (usually a Dataset for Images and a Screen for Plates).
getUserSpecifiedTarget() - Method in class ome.formats.OMEROMetadataStoreClient
getUuid() - Method in class ome.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(double) - Method in class ome.system.metrics.DefaultSnapshot
getValue(double) - Method in interface ome.system.metrics.Snapshot
getValue(Current) - Method in class omero.model.ElectricPotentialI
getValue(Current) - Method in class omero.model.FrequencyI
getValue(Current) - Method in class omero.model.LengthI
getValue(Current) - Method in class omero.model.PowerI
getValue(Current) - Method in class omero.model.PressureI
getValue(Current) - Method in class omero.model.TemperatureI
getValue(Current) - Method in class omero.model.TimeI
getValue() - Method in class pojos.BooleanAnnotationData: Returns the text of this annotation.
getValues() - Method in class ome.system.metrics.DefaultSnapshot
getValues() - Method in interface ome.system.metrics.Snapshot
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(UnitsElectricPotential) - Method in class pojos.DetectorData: Returns the voltage of the detector.
getVoltage() - Method in class pojos.DetectorData: Deprecated.
Replaced by DetectorData.getVoltage(UnitsElectricPotential)
getWarmUpFactor() - Method in class ome.io.nio.SimpleBackOff
getWarning() - Method in class ome.services.delete.Deletion: Deprecated.
getWarning() - Method in class ome.services.delete.files.FileDeleter
getWavelength() - Method in exception omeis.providers.re.quantum.QuantizationException: Returns the index of the wavelength that couldn't be rendered.
getWellOriginX(UnitsLength) - Method in class pojos.PlateData: Returns the x-coordinate in 2D-space of the well.
getWellOriginX() - Method in class pojos.PlateData: Deprecated.
Replaced by PlateData.getWellOriginX(UnitsLength)
getWellOriginY(UnitsLength) - Method in class pojos.PlateData: Returns the y-coordinate in 2D-space of the well.
getWellOriginY() - Method in class pojos.PlateData: Deprecated.
Replaced by PlateData.getWellOriginY(UnitsLength)
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(UnitsLength) - Method in class pojos.ObjectiveData: Returns the working distance.
getWorkingDistance() - Method in class pojos.ObjectiveData: Deprecated.
Replaced by ObjectiveData.getWorkingDistance(UnitsLength)
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
GraphConstraintException - Exception in ome.services.graphs: Deprecated.
will be removed in OMERO 5.2, so use the new graphs implementation
GraphConstraintException(String, HashMultimap<String, Long>) - Constructor for exception ome.services.graphs.GraphConstraintException: Deprecated.
GraphEntry - Class in ome.services.graphs: Deprecated.
will be removed in OMERO 5.2, so use the new graphs implementation
GraphEntry(GraphSpec, String) - Constructor for class ome.services.graphs.GraphEntry: Deprecated.
GraphEntry(GraphSpec, String, GraphEntry) - Constructor for class ome.services.graphs.GraphEntry: Deprecated.
GraphException - Exception in ome.services.graphs: Exception which will be thrown by activities within GraphSpec implementations.
GraphException(String) - Constructor for exception ome.services.graphs.GraphException
graphException(GraphException, long, long) - Method in class omero.cmd.Helper: Deprecated.
GraphOpts - Class in ome.services.graphs: Deprecated.
will be removed in OMERO 5.3, so use the new graphs implementation
GraphOpts() - Constructor for class ome.services.graphs.GraphOpts: Deprecated.
GraphOpts.Op - Enum in ome.services.graphs: Deprecated.
GraphPathBean - Class in ome.services.graphs: The graph path bean holds the Hiberate object mapping and assists navigation thereof.
GraphPathBean() - Constructor for class ome.services.graphs.GraphPathBean
GraphPathReport - Class in ome.services.graphs: A standalone tool for producing a summary of the Hibernate object mapping for our Sphinx documentation.
GraphPathReport() - Constructor for class ome.services.graphs.GraphPathReport
GraphPolicy - Class in ome.services.graphs: A policy guides how to traverse the graph.
GraphPolicy() - Constructor for class ome.services.graphs.GraphPolicy
GraphPolicy.Ability - Enum in ome.services.graphs: Abilities that the user may have to operate upon model objects.
GraphPolicy.Action - Enum in ome.services.graphs: The action to take on an object instance.
GraphPolicy.Details - Class in ome.services.graphs: A tuple noting the state of a mapped object instance in the current graph traversal.
GraphPolicy.Orphan - Enum in ome.services.graphs: If an object instance has any GraphPolicy.Action.EXCLUDEd parents that would prevent it from being orphaned.
GraphPolicyRule - Class in ome.services.graphs: A graph policy rule specifies a component of a GraphPolicy.
GraphPolicyRule() - Constructor for class ome.services.graphs.GraphPolicyRule
GraphRequestFactory - Class in omero.cmd.graphs: Create request objects that are executed using the GraphPathBean.
GraphRequestFactory(ACLVoter, SystemTypes, GraphPathBean, Deletion, Map<Class<? extends Request>, List<GraphPolicyRule>>, List<String>, Set<String>, boolean) - Constructor for class omero.cmd.graphs.GraphRequestFactory: Construct a new graph request factory.
GraphSpec - Interface in ome.services.graphs: Deprecated.
will be removed in OMERO 5.2, so use the new graphs implementation
GraphSpecListI - Class in omero.cmd.graphs: Deprecated.
will be removed in OMERO 5.2, so use the new graphs implementation
GraphSpecListI(OmeroContext) - Constructor for class omero.cmd.graphs.GraphSpecListI: Deprecated.
GraphSpecPostProcessor - Class in ome.services.graphs: Deprecated.
will be removed in OMERO 5.2, so use the new graphs implementation
GraphSpecPostProcessor() - Constructor for class ome.services.graphs.GraphSpecPostProcessor: Deprecated.
GraphState - Class in ome.services.graphs: Deprecated.
will be removed in OMERO 5.2, so use the new graphs implementation
GraphState(EventContext, GraphStepFactory, SqlAction, Session, GraphSpec) - Constructor for class ome.services.graphs.GraphState: Deprecated.
GraphStep - Class in ome.services.graphs: Deprecated.
will be removed in OMERO 5.2, so use the new graphs implementation
GraphStep(ExtendedMetadata, int, List<GraphStep>, GraphSpec, GraphEntry, long[]) - Constructor for class ome.services.graphs.GraphStep: Deprecated.
GraphStep.Callback - Interface in ome.services.graphs: Deprecated.
GraphStepFactory - Interface in ome.services.graphs: Deprecated.
will be removed in OMERO 5.2, so use the new graphs implementation
GraphSteps - Class in ome.services.graphs: Deprecated.
will be removed in OMERO 5.2, so use the new graphs implementation
GraphSteps(List<GraphStep>) - Constructor for class ome.services.graphs.GraphSteps: Deprecated.
GraphTables - Class in ome.services.graphs: Deprecated.
will be removed in OMERO 5.2, so use the new graphs implementation
GraphTables() - Constructor for class ome.services.graphs.GraphTables: Deprecated.
GraphTraversal - Class in ome.services.graphs: An alternative implementation of model object graph traversal, relying on SELECTing in advance for making decisions, instead of rolling back to savepoints to recover from failed attempts to act.
GraphTraversal(Session, EventContext, ACLVoter, SystemTypes, GraphPathBean, SetMultimap<String, String>, GraphPolicy, GraphTraversal.Processor) - Constructor for class ome.services.graphs.GraphTraversal: Construct a new instance of a graph traversal manager.
GraphTraversal.Processor - Interface in ome.services.graphs: Executes the planned operation.
GraphUtil - Class in omero.cmd.graphs: Static utility methods for model graph operations.
GraphUtil() - Constructor for class omero.cmd.graphs.GraphUtil
graphValidation(Session) - Method in class ome.services.graphs.GraphStep: Deprecated.

Immediately we check that an object moved from GroupA to GroupB is no longer pointed at by any objects in GroupA via foreign key constraints.
GREEN_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_SUDO_NS - Static variable in class ome.services.sessions.SessionManagerImpl
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
GroupChmodStrategy - Class in ome.security.basic: ChmodStrategy which only permits modifying the permissions on groups.
GroupChmodStrategy(BasicACLVoter, SessionFactory, SqlAction, ExtendedMetadata) - Constructor for class ome.security.basic.GroupChmodStrategy
groupContext(Long, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl: Creates a copy of the Current.ctx map and if groupId is not null, sets the "omero.group" key to be a string version of the id.
GroupContextMapper - Class in ome.security.auth: Specialized OME ExperimenterGroup context mapper.
GroupContextMapper(LdapConfig, String) - Constructor for class ome.security.auth.GroupContextMapper
GroupContextMapper(LdapConfig, String, String) - Constructor for class ome.security.auth.GroupContextMapper
GroupData - Class in pojos: The data that makes up an OME Group along with the various members of the Group
GroupData() - Constructor for class pojos.GroupData: Creates a new instance.
GroupData(ExperimenterGroup) - Constructor for class pojos.GroupData: Creates a new instance.
groupId - Variable in class ome.services.graphs.GraphPolicy.Details: the ID of the object's ExperimenterGroup, or null if the object does not have a group
groupInfo(SqlAction) - Method in class ome.services.graphs.BaseGraphSpec: Deprecated.
groupInfo(SqlAction) - Method in interface ome.services.graphs.GraphSpec: Deprecated.

Like GraphSpec.load(Session) uses the current table and id information to look up information on the given target.
groupnameFilter(String) - Method in class ome.security.auth.LdapConfig
groupProxy(Long) - Method in interface ome.api.local.LocalAdmin: returns a possibly uninitialized proxy for the given group id.
groupProxy(String) - Method in interface ome.api.local.LocalAdmin: returns a possibly uninitialized proxy for the given group name.
groupProxy(Long) - Method in class ome.logic.AdminImpl
groupProxy(String) - Method in class ome.logic.AdminImpl
groupRestrictions(IObject) - Method in class ome.security.policy.BinaryAccessPolicy
groups(String, LdapConfig, LdapOperations, RoleProvider, AttributeSet) - Method in class ome.security.auth.AttributeNewUserGroupBean
groups(String, LdapConfig, LdapOperations, RoleProvider, AttributeSet) - Method in interface ome.security.auth.NewUserGroupBean
groups(String, LdapConfig, LdapOperations, RoleProvider, AttributeSet) - Method in class ome.security.auth.OrgUnitNewUserGroupBean
groups(String, LdapConfig, LdapOperations, RoleProvider, AttributeSet) - Method in class ome.security.auth.QueryNewUserGroupBean
groupsLed - Variable in class ome.services.sessions.SessionManager.CreationRequest
grp(RLong) - Method in class omero.sys.ParametersI: Sets the value of the group parameter.
GUEST - Static variable in class ome.system.Login: CopyOfLogin constant which has username and password values set to null and other values set to their default.
GUEST - Static variable in class pojos.GroupData: Identifies the Guest group.

H

handle(IObject) - Method in interface ome.formats.model.handler.ModelObjectHandler: Attempt to handle the model object of this type.
handle - Variable in class ome.services.blitz.repo.ManagedImportRequestI: Set by ManagedImportProcessI when verifyUpload has been called.
Handle - Class in ome.util.mem: Provides the basic machinery to share the same logical state across objects with different identities.
Handle(Copiable) - Constructor for class ome.util.mem.Handle: Subclasses use this constructor to specify the Body instance this handle will be paired up with.
handle - Variable in class omero.cmd.CmdCallbackI: Proxy passed to this instance on creation.
handle(int, int) - Method in interface omero.model.SmartShape.PointCallback
handleAnnotated(IAnnotated, Document, LuceneOptions) - Method in class ome.services.fulltext.bridges.TablesBridge: Responsible for iterating over any attached OMERO.tables and registering all appropriate row objects for later processing.
handleAnnotation(Annotation, TablesBridge.RowProcessor) - Method in class ome.services.fulltext.bridges.TablesBridge: Detects if the given annotation contains an OMERO.table and if so, passes it off for further processing.
handleCallbackException(Exception) - Method in class omero.cmd.SessionI: Reusable method for logging an exception that occurs on one-way communication with clients during callback notification.
handleContextRefreshedEvent(ContextRefreshedEvent) - Method in class ome.security.policy.DefaultPolicyService: Loads all Policy instances from the context, and uses them to initialize this PolicyService.
handleContextRefreshedEvent(ContextRefreshedEvent) - Method in class ome.services.blitz.util.CheckAllJobs
handleContextRefreshedEvent(ContextRefreshedEvent) - Method in class ome.services.graphs.GraphPathBean: The application context after refresh should contain a usable Hibernate session factory.
handleContextRefreshedEvent(ContextRefreshedEvent) - Method in class ome.services.mail.ServerUpMailSender
handleContextRefreshedEvent(ContextRefreshedEvent) - Method in class ome.services.scripts.ScriptRepoHelper: Loads all ScriptFileType instances from the context, and uses them to initialize all scripts in the repo.
handleContextRefreshedEvent(ContextRefreshedEvent) - Method in class ome.services.util.NamespaceCheck
handleContextRefreshedEvent(ContextRefreshedEvent) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl: Listener method which waits for a ContextRefreshedEvent and then extracts the SessionFactory from the ApplicationContext and pases it to ExtendedMetadata.Impl.setSessionFactory(SessionFactory).
handleContextRefreshedEvent(ContextRefreshedEvent) - Method in class ome.tools.spring.OnContextRefreshedEventListener
handleEventLog(FullTextSession, EventLog) - Method in class ome.services.fulltext.FullTextIndexer
handleEventLog(EventLog, Session, ServiceFactory) - Method in class ome.services.pixeldata.PixelDataHandler: Handles only single elements from the PersistentEventLogLoader in order to keep transactions short and safe.
handleException(Throwable) - Method in class ome.services.blitz.impl.ServiceFactoryI
handleException(Throwable, OmeroContext) - Method in class omero.util.IceMapper
HandleFactory - Class in omero.cmd: SPIOrthogonal interface hierarchy of types for working with the Request hierarchy.
HandleFactory(long) - Constructor for class omero.cmd.HandleFactory
handleFile(File, int, Collection) - Method in class ome.formats.importer.ImportCandidates: Handle a file import
handleHdf5(String, TablesBridge.RowProcessor) - Method in class ome.services.fulltext.bridges.TablesBridge: Process a single OMERO.tables file.
HandleI - Class in omero.cmd: Servant for the handle proxy from the Command API.
HandleI(int) - Constructor for class omero.cmd.HandleI: Create a HandleI in the State#CREATED state with the given cancel timeout in milliseconds.
HandleI.Cancel - Exception in omero.cmd: Signals that HandleI.run() has noticed that HandleI.state wants a cancellation or that the Request implementation wishes to stop execution.
HandleI.Cancel(String) - Constructor for exception omero.cmd.HandleI.Cancel
handleImage(Image, Document, LuceneOptions) - Method in class ome.services.fulltext.bridges.TablesBridge: Processes any annotations attached to the following types which contain this image: Plate, Dataset
handleInput(Class<?>, Object) - Method in class omero.util.IceMapper
handleLsid(IObject) - Method in class ome.services.blitz.impl.OmeroMetadata
handleMissingPyramid(Pixels, String) - Method in class ome.io.nio.PixelsService: If the outer loop should continue, this method returns successfully; otherwise it throws a MissingPyramidException.
handleMissingStatsInfo(Pixels) - Method in class ome.io.nio.PixelsService: If the outer loop should continue, this method returns successfully; otherwise it throws a MissingPyramidException.
handleOptions(int, String[]) - Method in class ome.services.graphs.AbstractHierarchyGraphSpec: Deprecated.

Called once per loop iteration throw rawOptions during AbstractHierarchyGraphSpec.initialize(long, String, Map)
handleOptions(int, String[]) - Method in class ome.services.graphs.AnnotationGraphSpec: Deprecated.
handleOptions(int, String[]) - Method in class ome.services.graphs.LightSourceGraphSpec: Deprecated.
handleOutput(Class, Object) - Method in class omero.util.IceMapper
handler - Variable in class ome.formats.importer.cli.CommandLineImporter: ErrorHandler which is also responsible for uploading files
handleRingShutdown(Redirector.Context, String) - Method in class ome.services.blitz.redirect.ConfigRedirector
handleRingShutdown(Redirector.Context, String) - Method in class ome.services.blitz.redirect.NullRedirector: Does nothing.
handleRingShutdown(Redirector.Context, String) - Method in interface ome.services.blitz.redirect.Redirector: Gives the Redirector a chance to remove the current Ring when it is being shutdown.
handleRingShutdown(Redirector.Context, String) - Method in class ome.services.blitz.redirect.ScaleRedirector: Nothing needs to be done on shutdown, since the Ring implementation will properly disable the Node table queried during the next call to Redirector.getProxyOrNull(Context, String, Glacier2.SessionControlPrx, Ice.Current)
handleServerError(Throwable, OmeroContext) - Method in class omero.util.IceMapper: wraps any non-ServerError returned by IceMapper.handleException(Throwable, OmeroContext) in an InternalException.
HardlinkFileTransfer - Class in ome.formats.importer.transfers: Local-only file transfer mechanism which makes use of hard-linking.
HardlinkFileTransfer() - Constructor for class ome.formats.importer.transfers.HardlinkFileTransfer
HardWiredInterceptor - Class in ome.logic: Extension point for interceptors which should be compiled in from third-party code.
HardWiredInterceptor() - Constructor for class ome.logic.HardWiredInterceptor
hasAlias(String) - Method in class ome.system.Preference
hasDectector() - Method in class pojos.ChannelAcquisitionData: Returns true if there is a detector for that channel, false otherwise.
hasEmissionData(ChannelData) - Static method in class ome.formats.model.ColorsFactory: Returns true if the channel has emission metadata, false otherwise.
hasEmissionData(LogicalChannel) - Static method in class omeis.providers.re.ColorsFactory: Returns true if the channel has emission metadata, false otherwise.
hasFilter() - Method in class pojos.ChannelAcquisitionData: Returns true if there is a filter set linked to the channel false otherwise.
hash - Variable in class ome.security.auth.ConfigurablePasswordProvider: Hash implementation to use for encoding passwords to check and changed passwords.
hash - Variable in class ome.services.blitz.repo.CheckedPath
hash() - Method in class ome.services.blitz.repo.CheckedPath
hash() - Method in class ome.services.scripts.RepoFile.FsFile
hash() - Method in class ome.services.scripts.RepoFile
hashCode() - Method in class ome.services.blitz.repo.CheckedPath: On Windows systems the calculation is not case-sensitive.
hashCode() - Method in class ome.services.blitz.repo.path.FsFile
hashCode() - Method in class ome.tools.FileSystem: Public hashcode implementation based on String hash() return
hashCode(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
hashCode() - Method in class ome.util.math.geom2D.Line: Overridden to reflect equality of abstract values (data object) as opposite to object identity.
hashCode() - Method in class ome.util.math.geom2D.PlanePoint: Overridden to reflect equality of abstract values (data object) as opposite to object identity.
hashCode() - Method in class ome.util.math.geom2D.Segment: Overridden to reflect equality of abstract values (data object) as opposite to object identity.
hashCode() - Method in class omeis.providers.re.data.PlaneDef: Overridden to reflect equality of abstract values (data object) as opposite to object identity.
hashCode() - Method in class omero.cmd.graphs.Preprocessor.GraphModifyTarget: Deprecated.
hashCode() - Method in class omero.model.ElectricPotentialI
hashCode() - Method in class omero.model.FrequencyI
hashCode() - Method in class omero.model.LengthI
hashCode() - Method in class omero.model.PowerI
hashCode() - Method in class omero.model.PressureI
hashCode() - Method in class omero.model.TemperatureI
hashCode() - Method in class omero.model.TimeI
hashCode() - Method in class pojos.ROICoordinate: Calculate the hashCode for the data, The hashcode is generated by bitshifting z by ZTBITSPLIT bits and adding t.
hasher() - Method in class ome.services.scripts.RepoFile.FsFile
hasher() - Method in class ome.services.scripts.RepoFile
hasIris() - Method in class pojos.ObjectiveData: Returns a boolean flag if the value has been set, null otherwise.
hasLightPath() - Method in class pojos.ChannelAcquisitionData: Returns true if there is a light path described for that channel, false otherwise.
hasMetadata(long) - Method in class ome.services.ThumbnailCtx: Whether or not thumbnail metadata is available for a given Pixels ID.
hasNext() - Method in interface ome.api.Search: Returns true if another call to Search.next() is valid.
hasNext() - Method in class ome.services.eventlogs.EventLogLoader: Tests for available objects.
hasNext() - Method in class ome.services.eventlogs.EventLogQueue: Checks if either any Entry instances are available or tries to load them if not.
hasNext() - Method in class ome.services.graphs.BaseGraphSpec.SubSpecIterator: Deprecated.
hasNext() - Method in class ome.services.SearchBean
hasNext_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: Deprecated.
hasSession() - Method in class ome.system.SessionInitializer
hasSettings(long) - Method in class ome.services.ThumbnailCtx: Whether or not settings are available for a given Pixels ID.
hasShapes - Variable in class ome.services.roi.GeomTool
hasStats() - Method in class pojos.ChannelData: Returns true if the channel has some channel information false otherwise.
hasSubtypes(int) - Method in class ome.tools.hibernate.ExtendedMetadata.Locks: returns true if this offset points to a field which is an embedded component.
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
helper - Variable in class ome.services.blitz.repo.RawAccessRequestI
helper - Variable in class omero.cmd.admin.CurrentSessionsRequestI
helper - Variable in class omero.cmd.admin.UpdateSessionTimeoutRequestI
Helper - Class in omero.cmd: Helper object for all omero.cmd implementations.
Helper(Request, Status, SqlAction, Session, ServiceFactory) - Constructor for class omero.cmd.Helper
HibernateUtils - Class in ome.tools.hibernate: contains methods for reloading unloaded entities and nulled collections as well as determining the index of certain properties in a dehydrated Hiberante array.
HibernateUtils() - Constructor for class ome.tools.hibernate.HibernateUtils
Hidden - Annotation Type in ome.annotations: annotation which specifies that a method parameter (e.g. a password) must be hidden from logging output.
Hierarchy - Class in ome.services.query: single-point of entry for walking of OME container hierarchies.
Hierarchy() - Constructor for class ome.services.query.Hierarchy
HierarchyNavigator - Class in ome.services.query: Query the database for relationships between model objects.
HierarchyNavigator(IQuery) - Constructor for class ome.services.query.HierarchyNavigator: Construct a new hierarchy navigator.
hierarchyNavigator - Variable in class omero.cmd.graphs.Preprocessor: Deprecated.
HierarchyNavigatorWrap<T,E> - Class in ome.services.query: Convenience class for creating versions of HierarchyNavigator with different model object representations.
HierarchyNavigatorWrap(IQuery) - Constructor for class ome.services.query.HierarchyNavigatorWrap
HierarchyTransformations - Class in ome.tools
HierarchyTransformations() - Constructor for class ome.tools.HierarchyTransformations
hints - Variable in class ome.services.SVGRasterizer: The transcoder hints.
histogram(Object, String) - Method in class ome.system.metrics.DefaultMetrics
Histogram - Interface in ome.system.metrics: Thin wrapper around Histogram
histogram(Object, String) - Method in interface ome.system.metrics.Metrics
histogram(Object, String) - Method in class ome.system.metrics.NullMetrics
holder - Variable in class ome.services.blitz.impl.AbstractAmdServant
holder - Variable in class omero.cmd.SessionI
hostname - Variable in class ome.formats.importer.ImportConfig
HqlQuery - Class in ome.services.search: 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, Map<String, String>) - Constructor for class ome.formats.importer.util.HtmlMessenger: Instantiate messenger
HtmlMessengerException - Exception in ome.formats.importer.util
HtmlMessengerException(String, Exception) - Constructor for exception ome.formats.importer.util.HtmlMessengerException: Creates a new instance.
HtmlMessengerException(String) - Constructor for exception ome.formats.importer.util.HtmlMessengerException: Creates a new instance.

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_exception(Exception) - Method in class ome.services.blitz.repo.PublicRepositoryI.AMD_submit
ice_postUnmarshal() - Method in class omero.model.PermissionsI: Called as Ice converts from a binary stream to a PermissionsI object.
ice_response(HandlePrx) - Method in class ome.services.blitz.repo.PublicRepositoryI.AMD_submit
IceMapper - Class in omero.util: Responsible for the mapping of ome.* types to omero.* types and back again.
IceMapper() - Constructor for class omero.util.IceMapper
IceMapper(IceMapper.ReturnMapping) - Constructor for class omero.util.IceMapper
IceMapper.ReturnMapping - Interface in omero.util
IceMethodInvoker - Class in ome.services.blitz.util: Method-cache primed either with an ServiceInterface instance or with a Class with generic type ServiceInterface.
IceMethodInvoker(ServiceInterface, OmeroContext) - Constructor for class ome.services.blitz.util.IceMethodInvoker: Create an IceMethodInvoker instance using the Class of the passed argument to call IceMethodInvoker#IceMethodInvoker(Class).
IceMethodInvoker(Class<S>, OmeroContext) - Constructor for class ome.services.blitz.util.IceMethodInvoker: Creates an IceMethodInvoker instance by using reflection on the Class argument.
IceUtil - Class in ome.services.util: Methods for working with Ice.
IceUtil() - Constructor for class ome.services.util.IceUtil
icMap - Variable in class ome.formats.importer.util.ErrorHandler: Host information about the file and its corresponding import candidate.
IConfig - Interface in ome.api: Access to server configuration.
IContainer - Interface in ome.api: Provides methods for dealing with the core "Pojos" of OME.
id - Variable in class ome.services.blitz.repo.CheckedPath
id - Variable in class ome.services.blitz.util.FindServiceFactoryMessage
id - Variable in class ome.services.graphs.BaseGraphSpec: Deprecated.

The id of the root type which will be processed.
id - Variable in class ome.services.graphs.GraphStep: Deprecated.

The actual id to be processed as opposed to GraphEntry.getId() which is the id of the root object.
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)
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: Deprecated.

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.
ignoreAnnotator(String, Object...) - Method in class ome.formats.OMEROMetadataStoreClient: For all cases of an annotator being ignore (WARN).
ignoreInsecure(String, Object...) - Method in class ome.formats.OMEROMetadataStoreClient: Called when saving a property to OMERO would result in a SecurityViolation (DEBUG).
ignoreMissing(String, Object...) - Method in class ome.formats.OMEROMetadataStoreClient: Called when a property is missing from the OMERO model (WARN).
ignoreUnknown - Variable in class ome.security.auth.ConfigurablePasswordProvider: If true, this implementation should return a null on #checkPassword(String, String) if the user is unknown, otherwise a Boolean.FALSE.
ignoreUnneeded(String, Object...) - Method in class ome.formats.OMEROMetadataStoreClient: Called when a property is not needed in OMERO since the data can be gotten elsewhere, as in directly from the file itself (DEBUG).
ignoreUnsupported(String, Object...) - Method in class ome.formats.OMEROMetadataStoreClient: Called when a property is not expected in a file to be imported.
IGraphModifyRequest - Interface in omero.cmd.graphs: Deprecated.
will be removed in OMERO 5.3, so use the new graphs implementation
IHandle - Interface in omero.cmd: SPIOrthogonal interface hierarchy of types for working with the Request hierarchy.
ILdap - Interface in ome.api: Administration interface providing access to admin-only functionality as well as JMX-based server access and selected user functions.
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.
imageID - Variable in class loci.ome.io.OMECredentials
ImageNameMetadataStore - Class in ome.formats: Stores all Image names consumed by the interface.
ImageNameMetadataStore() - Constructor for class ome.formats.ImageNameMetadataStore
ImagingEnvironment_AirPressure - Static variable in class ome.formats.model.UnitsFactory
ImagingEnvironment_Temperature - Static variable in class ome.formats.model.UnitsFactory
IMetadata - Interface in ome.api: Provides method to interact with acquisition metadata and annotations.
img - Variable in class ome.services.SVGRasterizer: The image that represents the SVG document.
IMPORT_LOG_MIMETYPE - Static variable in class ome.services.blitz.repo.PublicRepositoryI: media type for import logs
ImportCandidates - Class in ome.formats.importer: Utility class which given any File object will determine the correct number and members of a given import.
ImportCandidates(OMEROWrapper, String[], IObserver) - Constructor for class ome.formats.importer.ImportCandidates: 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, IniFileLoader, Properties) with user preferences, a local PreferenceContext, an IniFileLoader initialized with the given argument, and System.getProperties().
ImportConfig(Preferences, IniFileLoader, Properties) - Constructor for class ome.formats.importer.ImportConfig: Complete constructor.
ImportConfig.AnnotationListValue - Class in ome.formats.importer
ImportConfig.AnnotationListValue(String, ImportConfig, List<Annotation>) - Constructor for class ome.formats.importer.ImportConfig.AnnotationListValue
ImportConfig.BoolValue - Class in ome.formats.importer
ImportConfig.BoolValue(String, ImportConfig, boolean) - Constructor for class ome.formats.importer.ImportConfig.BoolValue
ImportConfig.DoubleArrayValue - Class in ome.formats.importer
ImportConfig.DoubleArrayValue(String, ImportConfig, Double[]) - Constructor for class ome.formats.importer.ImportConfig.DoubleArrayValue
ImportConfig.FileValue - Class in ome.formats.importer
ImportConfig.FileValue(String, ImportConfig) - Constructor for class ome.formats.importer.ImportConfig.FileValue
ImportConfig.IntValue - Class in ome.formats.importer
ImportConfig.IntValue(String, ImportConfig, int) - Constructor for class ome.formats.importer.ImportConfig.IntValue
ImportConfig.IntValue(String, ImportConfig, int, String) - Constructor for class ome.formats.importer.ImportConfig.IntValue
ImportConfig.LongValue - Class in ome.formats.importer
ImportConfig.LongValue(String, ImportConfig, Long) - Constructor for class ome.formats.importer.ImportConfig.LongValue
ImportConfig.PassValue - Class in ome.formats.importer
ImportConfig.PassValue(String, ImportConfig) - Constructor for class ome.formats.importer.ImportConfig.PassValue
ImportConfig.StrValue - Class in ome.formats.importer
ImportConfig.StrValue(String, ImportConfig) - Constructor for class ome.formats.importer.ImportConfig.StrValue
ImportConfig.StrValue(String, ImportConfig, String) - Constructor for class ome.formats.importer.ImportConfig.StrValue
ImportConfig.StrValue(String, ImportConfig, String, String) - Constructor for class ome.formats.importer.ImportConfig.StrValue
ImportConfig.Value<T> - Class in ome.formats.importer: Container which thread-safely makes a generic configuration value available, without requiring getters and setters.
ImportConfig.VersionInfo - Enum in ome.formats.importer: Keys for fileset version information entries.
ImportContainer - Class in ome.formats.importer
ImportContainer(File, IObject, Double[], String, String[], Boolean) - Constructor for class ome.formats.importer.ImportContainer
ImportContainer(ImportConfig, File, IObject, Double[], String, String[], Boolean) - Constructor for class ome.formats.importer.ImportContainer
ImportEvent - Class in ome.formats.importer: Simple event base-class used by IObservable and IObserver implementations.
ImportEvent() - Constructor for class ome.formats.importer.ImportEvent
ImportEvent.ADD - Class in ome.formats.importer
ImportEvent.ADD() - Constructor for class ome.formats.importer.ImportEvent.ADD
ImportEvent.BEGIN_POST_PROCESS - Class in ome.formats.importer
ImportEvent.BEGIN_POST_PROCESS(int, ImportContainer, IObject, Long, int, ImportSize) - Constructor for class ome.formats.importer.ImportEvent.BEGIN_POST_PROCESS
ImportEvent.BEGIN_SAVE_TO_DB - Class in ome.formats.importer
ImportEvent.BEGIN_SAVE_TO_DB(int, ImportContainer, IObject, Long, int, ImportSize) - Constructor for class ome.formats.importer.ImportEvent.BEGIN_SAVE_TO_DB
ImportEvent.COUNT_EVENT - Class in ome.formats.importer
ImportEvent.DATA_STORED - Class in ome.formats.importer
ImportEvent.DATA_STORED(int, ImportContainer, IObject, Long, int, ImportSize) - Constructor for class ome.formats.importer.ImportEvent.DATA_STORED
ImportEvent.DATASET_STORED - Class in ome.formats.importer
ImportEvent.DATASET_STORED(int, ImportContainer, IObject, Long, int, ImportSize, Integer, Integer) - Constructor for class ome.formats.importer.ImportEvent.DATASET_STORED
ImportEvent.DEBUG_SEND - Class in ome.formats.importer
ImportEvent.DEBUG_SEND(boolean, boolean) - Constructor for class ome.formats.importer.ImportEvent.DEBUG_SEND
ImportEvent.END_POST_PROCESS - Class in ome.formats.importer
ImportEvent.END_POST_PROCESS(int, ImportContainer, IObject, Long, int, ImportSize) - Constructor for class ome.formats.importer.ImportEvent.END_POST_PROCESS
ImportEvent.END_SAVE_TO_DB - Class in ome.formats.importer
ImportEvent.END_SAVE_TO_DB(int, ImportContainer, IObject, Long, int, ImportSize) - Constructor for class ome.formats.importer.ImportEvent.END_SAVE_TO_DB
ImportEvent.ERRORS_COMPLETE - Class in ome.formats.importer
ImportEvent.ERRORS_COMPLETE() - Constructor for class ome.formats.importer.ImportEvent.ERRORS_COMPLETE
ImportEvent.ERRORS_FAILED - Class in ome.formats.importer
ImportEvent.ERRORS_FAILED() - Constructor for class ome.formats.importer.ImportEvent.ERRORS_FAILED
ImportEvent.ERRORS_PENDING - Class in ome.formats.importer
ImportEvent.ERRORS_PENDING() - Constructor for class ome.formats.importer.ImportEvent.ERRORS_PENDING
ImportEvent.FILE_UPLOAD_BYTES - Class in ome.formats.importer
ImportEvent.FILE_UPLOAD_BYTES(String, int, int, Long, Long, Long, Exception) - Constructor for class ome.formats.importer.ImportEvent.FILE_UPLOAD_BYTES
ImportEvent.FILE_UPLOAD_CANCELLED - Class in ome.formats.importer
ImportEvent.FILE_UPLOAD_CANCELLED(String, int, int, Long, Long, Exception) - Constructor for class ome.formats.importer.ImportEvent.FILE_UPLOAD_CANCELLED
ImportEvent.FILE_UPLOAD_COMPLETE - Class in ome.formats.importer
ImportEvent.FILE_UPLOAD_COMPLETE(String, int, int, Long, Long, Exception) - Constructor for class ome.formats.importer.ImportEvent.FILE_UPLOAD_COMPLETE
ImportEvent.FILE_UPLOAD_ERROR - Class in ome.formats.importer
ImportEvent.FILE_UPLOAD_ERROR(String, int, int, Long, Long, Exception) - Constructor for class ome.formats.importer.ImportEvent.FILE_UPLOAD_ERROR
ImportEvent.FILE_UPLOAD_EVENT - Class in ome.formats.importer
ImportEvent.FILE_UPLOAD_FAILED - Class in ome.formats.importer
ImportEvent.FILE_UPLOAD_FAILED(String, int, int, Long, Long, Exception) - Constructor for class ome.formats.importer.ImportEvent.FILE_UPLOAD_FAILED
ImportEvent.FILE_UPLOAD_FINISHED - Class in ome.formats.importer
ImportEvent.FILE_UPLOAD_FINISHED(String, int, int, Long, Long, Exception) - Constructor for class ome.formats.importer.ImportEvent.FILE_UPLOAD_FINISHED
ImportEvent.FILE_UPLOAD_STARTED - Class in ome.formats.importer
ImportEvent.FILE_UPLOAD_STARTED(String, int, int, Long, Long, Exception) - Constructor for class ome.formats.importer.ImportEvent.FILE_UPLOAD_STARTED
ImportEvent.FILESET_EXCLUSION - Class in ome.formats.importer
ImportEvent.FILESET_EXCLUSION(String, int, int) - Constructor for class ome.formats.importer.ImportEvent.FILESET_EXCLUSION
ImportEvent.FILESET_UPLOAD_END - Class in ome.formats.importer
ImportEvent.FILESET_UPLOAD_END(String, int, int, Long, Long, String[], List<String>, Map<Integer, String>, Exception) - Constructor for class ome.formats.importer.ImportEvent.FILESET_UPLOAD_END
ImportEvent.FILESET_UPLOAD_PREPARATION - Class in ome.formats.importer
ImportEvent.FILESET_UPLOAD_PREPARATION(String, int, int, Long, Long, Exception) - Constructor for class ome.formats.importer.ImportEvent.FILESET_UPLOAD_PREPARATION
ImportEvent.FILESET_UPLOAD_START - Class in ome.formats.importer
ImportEvent.FILESET_UPLOAD_START(String, int, int, Long, Long, Exception) - Constructor for class ome.formats.importer.ImportEvent.FILESET_UPLOAD_START
ImportEvent.IMPORT_ARCHIVING - Class in ome.formats.importer
ImportEvent.IMPORT_ARCHIVING(int, ImportContainer, IObject, Long, int, ImportSize) - Constructor for class ome.formats.importer.ImportEvent.IMPORT_ARCHIVING
ImportEvent.IMPORT_DONE - Class in ome.formats.importer
ImportEvent.IMPORT_DONE(int, ImportContainer, IObject, Long, int, ImportSize, List<Pixels>, Fileset, List<IObject>) - Constructor for class ome.formats.importer.ImportEvent.IMPORT_DONE
ImportEvent.IMPORT_OVERLAYS - Class in ome.formats.importer
ImportEvent.IMPORT_OVERLAYS(int, ImportContainer, IObject, Long, int, ImportSize) - Constructor for class ome.formats.importer.ImportEvent.IMPORT_OVERLAYS
ImportEvent.IMPORT_PROCESSING - Class in ome.formats.importer
ImportEvent.IMPORT_PROCESSING(int, ImportContainer, IObject, Long, int, ImportSize) - Constructor for class ome.formats.importer.ImportEvent.IMPORT_PROCESSING
ImportEvent.IMPORT_STARTED - Class in ome.formats.importer
ImportEvent.IMPORT_STARTED(int, ImportContainer, IObject, Long, int, ImportSize, Integer, Integer, Long) - Constructor for class ome.formats.importer.ImportEvent.IMPORT_STARTED
ImportEvent.IMPORT_STEP - Class in ome.formats.importer
ImportEvent.IMPORT_STEP(int, int, int) - Constructor for class ome.formats.importer.ImportEvent.IMPORT_STEP
ImportEvent.IMPORT_SUMMARY - Class in ome.formats.importer
ImportEvent.IMPORT_SUMMARY(long, int) - Constructor for class ome.formats.importer.ImportEvent.IMPORT_SUMMARY
ImportEvent.LOADED_IMAGE - Class in ome.formats.importer
ImportEvent.LOADED_IMAGE(String, Integer, Integer, Integer) - Constructor for class ome.formats.importer.ImportEvent.LOADED_IMAGE
ImportEvent.LOADING_IMAGE - Class in ome.formats.importer
ImportEvent.LOADING_IMAGE(String, Integer, Integer, Integer) - Constructor for class ome.formats.importer.ImportEvent.LOADING_IMAGE
ImportEvent.LOGGED_IN - Class in ome.formats.importer
ImportEvent.LOGGED_IN() - Constructor for class ome.formats.importer.ImportEvent.LOGGED_IN
ImportEvent.LOGGED_OUT - Class in ome.formats.importer
ImportEvent.LOGGED_OUT() - Constructor for class ome.formats.importer.ImportEvent.LOGGED_OUT
ImportEvent.METADATA_IMPORTED - Class in ome.formats.importer
ImportEvent.METADATA_IMPORTED(int, ImportContainer, IObject, Long, int, ImportSize, Integer, Integer, Long) - Constructor for class ome.formats.importer.ImportEvent.METADATA_IMPORTED
ImportEvent.METADATA_PROCESSED - Class in ome.formats.importer
ImportEvent.METADATA_PROCESSED(int, ImportContainer, IObject, Long, int, ImportSize, Integer, Integer, Long) - Constructor for class ome.formats.importer.ImportEvent.METADATA_PROCESSED
ImportEvent.OBJECTS_RETURNED - Class in ome.formats.importer
ImportEvent.OBJECTS_RETURNED(int, ImportContainer, IObject, Long, int, ImportSize, Integer, Integer, Long) - Constructor for class ome.formats.importer.ImportEvent.OBJECTS_RETURNED
ImportEvent.PIXELDATA_PROCESSED - Class in ome.formats.importer
ImportEvent.PIXELDATA_PROCESSED(int, ImportContainer, IObject, Long, int, ImportSize, Integer, Integer, Long) - Constructor for class ome.formats.importer.ImportEvent.PIXELDATA_PROCESSED
ImportEvent.POST_UPLOAD_EVENT - Class in ome.formats.importer
ImportEvent.POST_UPLOAD_EVENT(int, ImportContainer, IObject, Long, int, ImportSize, Integer, Integer, Long) - Constructor for class ome.formats.importer.ImportEvent.POST_UPLOAD_EVENT
ImportEvent.PROGRESS_EVENT - Class in ome.formats.importer
ImportEvent.PROGRESS_EVENT(int, ImportContainer, IObject, Long, int, ImportSize, Integer, Integer) - Constructor for class ome.formats.importer.ImportEvent.PROGRESS_EVENT
ImportEvent.REIMPORT - Class in ome.formats.importer
ImportEvent.REIMPORT() - Constructor for class ome.formats.importer.ImportEvent.REIMPORT
ImportEvent.THUMBNAILS_GENERATED - Class in ome.formats.importer
ImportEvent.THUMBNAILS_GENERATED(int, ImportContainer, IObject, Long, int, ImportSize, Integer, Integer, Long) - Constructor for class ome.formats.importer.ImportEvent.THUMBNAILS_GENERATED
importFileset(Fileset, ImportSettings, Current) - Method in class ome.services.blitz.repo.ManagedRepositoryI: Return a template based directory path.
ImportFixture - Class in ome.formats.importer: test fixture for importing files without a GUI.
ImportFixture(OMEROMetadataStoreClient, OMEROWrapper) - Constructor for class ome.formats.importer.ImportFixture
importImage(ImportContainer, int, int, int) - Method in class ome.formats.importer.ImportLibrary: Perform an image import uploading files if necessary.
ImportLibrary - Class in ome.formats.importer: support class for the proper usage of OMEROMetadataStoreClient and FormatReader instances.
ImportLibrary(OMEROMetadataStoreClient, OMEROWrapper) - Constructor for class ome.formats.importer.ImportLibrary: The default implementation of FileTransfer performs a no-op and therefore need not have FileTransfer#afterTransfer(int, File[]) as with the ImportLibrary.ImportLibrary(OMEROMetadataStoreClient, OMEROWrapper, FileTransfer) constructor.
ImportLibrary(OMEROMetadataStoreClient, OMEROWrapper, FileTransfer) - Constructor for class ome.formats.importer.ImportLibrary: The library will not close the client instance.
ImportLibrary(OMEROMetadataStoreClient, OMEROWrapper, FileTransfer, int) - Constructor for class ome.formats.importer.ImportLibrary
ImportLibrary(OMEROMetadataStoreClient, OMEROWrapper, FileTransfer, List<FileExclusion>, int) - Constructor for class ome.formats.importer.ImportLibrary
ImportLibrary.ImportCallback - Class in ome.formats.importer
ImportLibrary.ImportCallback(ImportProcessPrx, HandlePrx, ImportContainer) - Constructor for class ome.formats.importer.ImportLibrary.ImportCallback
importMetadata(MetadataImportJob) - Method in class ome.services.blitz.repo.ManagedImportRequestI: Uses the OMEROMetadataStoreClient to save all metadata for the current image provided.
importPaths(List<String>, Current) - Method in class ome.services.blitz.repo.ManagedRepositoryI
ImportSize - Class in ome.formats.importer: Calculates the various dimensions of an image from a Pixels instance.
ImportSize(String, Pixels, String) - Constructor for class ome.formats.importer.ImportSize
importTime - Variable in class ome.formats.importer.ImportEvent.IMPORT_SUMMARY
in(PixelsType, String[]) - Static method in class omeis.providers.re.data.PlaneFactory: A static helper method to check if a type is one of the elements in an array.
inc() - Method in interface ome.system.metrics.Counter
inc() - Method in class ome.system.metrics.DefaultCounter
include(int) - Method in class ome.tools.hibernate.ExtendedMetadata.Locks: returns true if this offset points to a field which may contain an IObject instance
increment() - Method in class ome.services.sessions.SessionContext.Count: Increment the current reference count and return the new value atomically.
increment(int) - Method in class ome.services.sessions.stats.LongCounter
index - Variable in class ome.formats.importer.ImportEvent.COUNT_EVENT
index - Variable in class ome.formats.importer.ImportEvent.PROGRESS_EVENT
Index - Enum in ome.formats
index(IndexingJob) - Method in class ome.services.blitz.repo.ManagedImportRequestI
index(String, String[]) - Static method in class ome.tools.hibernate.HibernateUtils
indexAllEvents() - Static method in class ome.services.fulltext.Main
indexByClass(Set<String>) - Static method in class ome.services.fulltext.Main
indexer - Variable in class ome.services.fulltext.FullTextThread
indexFullDb() - Static method in class ome.services.fulltext.Main
indexObject(IObject) - Method in interface ome.api.IUpdate: Initiates full-text indexing for the given object.
indexObject(IObject) - Method in class ome.logic.UpdateImpl
indexObject_async(AMD_IUpdate_indexObject, IObject, Current) - Method in class ome.services.blitz.impl.UpdateI
info(String, Object...) - Method in class omero.cmd.Helper
IniFileLoader - Class in ome.formats.importer.util: This class loads in the default importer.ini file (or one specified from the command line when starting the app)
IniFileLoader(File) - Constructor for class ome.formats.importer.util.IniFileLoader: Load given file
init(String, boolean) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
init(ObjectAdapter, String) - Method in class ome.services.blitz.fire.Ring: Typically called from within BlitzConfiguration after the communicator and adapter have been properly setup.
init(Helper) - Method in class ome.services.blitz.impl.commands.SaveI
init(String) - Method in class ome.services.blitz.repo.FileMaker
init(Helper) - Method in class ome.services.blitz.repo.ManagedImportRequestI
init(Helper) - Method in class ome.services.blitz.repo.RawAccessRequestI
init() - Static method in class ome.services.fulltext.Main
init() - Method in class ome.services.sessions.SessionManagerImpl: Initialization method called by the Spring run-time to acquire an initial Session.
init() - Method in class ome.services.sharing.ShareStore: Calls ShareStore.doInit() within a transaction with a session available to all HibernateTemplate callbacks.
init(Helper) - Method in class omero.cmd.admin.CurrentSessionsRequestI
init(Helper) - Method in class omero.cmd.admin.ResetPasswordRequestI
init(Helper) - Method in class omero.cmd.admin.UpdateSessionTimeoutRequestI
init(Helper) - Method in class omero.cmd.basic.DoAllI
init(Helper) - Method in class omero.cmd.basic.ListRequestsI
init(Helper) - Method in class omero.cmd.basic.TimingI
init(Helper) - Method in class omero.cmd.fs.ManageImageBinariesI
init(Helper) - Method in class omero.cmd.fs.OriginalMetadataRequestI
init(Helper) - Method in class omero.cmd.fs.UsedFilesRequestI
init(Helper) - Method in class omero.cmd.graphs.Chgrp2I
init(Helper) - Method in class omero.cmd.graphs.ChgrpFacadeI: Deprecated.
init(Helper) - Method in class omero.cmd.graphs.ChgrpI: Deprecated.
init() - Method in class omero.cmd.graphs.ChildOptionI: Initialize this child option instance.
init(Helper) - Method in class omero.cmd.graphs.Chmod2I
init(Helper) - Method in class omero.cmd.graphs.ChmodFacadeI: Deprecated.
init(Helper) - Method in class omero.cmd.graphs.ChmodI: Deprecated.
init(Helper) - Method in class omero.cmd.graphs.Chown2I
init(Helper) - Method in class omero.cmd.graphs.ChownFacadeI: Deprecated.
init(Helper) - Method in class omero.cmd.graphs.ChownI: Deprecated.
init(Helper) - Method in class omero.cmd.graphs.Delete2I
init(Helper) - Method in class omero.cmd.graphs.DeleteFacadeI: Deprecated.
init(Helper) - Method in class omero.cmd.graphs.DeleteI: Deprecated.
init(Helper) - Method in class omero.cmd.graphs.DiskUsageI
init(Helper) - Method in class omero.cmd.graphs.GraphSpecListI: Deprecated.
init(Helper) - Method in class omero.cmd.graphs.SkipHeadI
init(Helper) - Method in interface omero.cmd.IRequest: Method called within the transaction boundaries before any processing occurs.
init(Helper) - Method in class omero.cmd.mail.SendEmailRequestI
initFile(String) - Method in class loci.ome.io.OmeroReader
initFile(String) - Method in class ome.services.formats.OmeroReader
INITIAL_DELAY - Static variable in class ome.logic.RepositoryInfoImpl: Time (2 minutes) between successive calls to RepositoryInfoImpl.sanityCheckRepository() needed to trigger an actual call to RepositoryInfoImpl.getUsageFraction()
INITIAL_FREE_PHYSICAL_MEMORY - Static variable in class ome.services.util.JvmSettingsCheck: FreePhysicalMemorySize value from the OperatingSystem JMX bean at startup.
initializationDone() - Method in class omero.cmd.CmdCallbackI: Subclasses which must perform their own initialization before CmdCallbackI.onFinished(Response, Status, Current) is called should call CmdCallbackI.initializationDone() once that setup is complete.
initialize(Object) - Method in interface ome.api.local.LocalQuery: Uses the Hibernate static method initialize to prepare an object for shipping over the wire.
initialize(ServiceFactoryPrx) - Method in class ome.formats.OMEROMetadataStoreClient: Initializes the MetadataStore with an already logged in, ready to go service factory.
initialize(client) - Method in class ome.formats.OMEROMetadataStoreClient: Initializes the MetadataStore with an already logged in, ready to go service factory.
initialize(String, String, String, int) - Method in class ome.formats.OMEROMetadataStoreClient: Initializes the MetadataStore taking string parameters to feed to the OMERO Blitz client object.
initialize(String, String, String, int, boolean) - Method in class ome.formats.OMEROMetadataStoreClient: Initializes the MetadataStore taking string parameters to feed to the OMERO Blitz client object.
initialize(String, String, String, int, Long, boolean) - Method in class ome.formats.OMEROMetadataStoreClient: Initializes the MetadataStore taking string parameters to feed to the OMERO Blitz client object.
initialize(String, int, String) - Method in class ome.formats.OMEROMetadataStoreClient: Initializes the MetadataStore by joining an existing session.
initialize(String, int, String, boolean) - Method in class ome.formats.OMEROMetadataStoreClient: Initializes the MetadataStore by joining an existing session.
initialize(ServiceFactoryPrx, List<Pixels>, List<Long>) - Method in class ome.formats.OverlayMetadataStore: Initializes the metadata store implementation.
initialize(Object) - Method in class ome.logic.QueryImpl
initialize(Session) - Method in class ome.services.blitz.impl.OmeroMetadata
initialize(String[], String[], Class[], Map<String, Object>) - Method in class ome.services.blitz.measurements.MeasurementStore
initialize(String[], String[], Class[], Map<String, Object>) - Method in interface ome.services.blitz.measurements.OmeroMeasurementStore
initialize(FileMaker, Long, String) - Method in class ome.services.blitz.repo.PublicRepositoryI: Called by the internal repository once initialization has taken place.
initialize() - Method in class ome.services.eventlogs.EventLogQueue: Do nothing.
initialize() - Method in class ome.services.eventlogs.PersistentEventLogLoader: Called when the configuration database does not contain a valid current_id.
initialize() - Method in class ome.services.fulltext.PersistentEventLogLoader: Called when the configuration database does not contain a valid current_id.
initialize(long, String, Map<String, String>) - Method in class ome.services.graphs.AbstractHierarchyGraphSpec: Deprecated.

In order to allow subclasses like the AnnotationGraphSpec to make use of this method, hooks have been added.
initialize(long, String, Map<String, String>) - Method in class ome.services.graphs.BaseGraphSpec: Deprecated.
initialize(long, String, Map<String, String>) - Method in class ome.services.graphs.GraphEntry: Deprecated.

Called during GraphSpec.initialize(long, String, Map) to give the entry a chance to modify its #op based on the options and to initialize subspecs.
initialize(long, String, Map<String, String>) - Method in interface ome.services.graphs.GraphSpec: Deprecated.

Called as each action is started.
initialize() - Method in class ome.services.pixeldata.PersistentEventLogLoader
initialize(Identity, IRequest, Map<String, String>) - Method in class omero.cmd.HandleI
initialize(Identity, IRequest, Map<String, String>) - Method in interface omero.cmd.IHandle: Must be called on all instances exactly once before processing.
initializeQuery(FullTextQuery) - Method in class ome.services.search.FullText: Allows settings offset and limit on the query.
initializeReader() - Method in class ome.io.bioformats.BfPyramidPixelBuffer: If the pyramid file exists (which the constructor guarantees) then we assume that even if a lock file is present, that it's no longer valid.
initializeRedirect(Redirector.Context, String) - Method in class ome.services.blitz.redirect.AbstractRedirector: Set the new redirect value if null, or if the uuid is null or empty, then the existing redirect will be removed.
initializeUserAttributes(MethodInvocation, ServiceFactory, Principal, AtomicBoolean) - Static method in class ome.logic.HardWiredInterceptor: Adds the given environment context objects to the ReflectiveMethodInvocation.getUserAttributes() Map for lookup in subclasses
initializeWriter(String, String, boolean, int, int) - Method in class ome.io.bioformats.BfPyramidPixelBuffer: Initializes the writer.
initialPoll() - Method in class omero.cmd.CmdCallbackI: Called at the end of construction to check a race condition.
initPixelsRange(Pixels) - Method in class omeis.providers.re.metadata.StatsFactory: Determines the minimum and maximum corresponding to the passed pixels.
inMemoryCache(String) - Method in interface ome.services.sessions.SessionManager: Returns after possibly creating an in-memory cache which can be used throughout the session.
inMemoryCache(String) - Method in class ome.services.sessions.SessionManagerImpl
inMemoryCache(String) - Method in class ome.services.sessions.state.SessionCache
InMemoryPlanarPixelBuffer - Class in ome.io.nio: Class implementation of the PixelBuffer interface for in memory planar pixel data.
InMemoryPlanarPixelBuffer(Pixels, byte[][][][]) - Constructor for class ome.io.nio.InMemoryPlanarPixelBuffer: Constructs an in memory pixel buffer based on a defined dimensionality.
INNER_JOIN - Static variable in class ome.services.query.Query: imported constant for ease of use
input - Variable in class ome.services.SVGRasterizer: The transcoder input.
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.
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, ScriptRepoHelper, Current) - Constructor for class omero.grid.InteractiveProcessorI
interceptor - Variable in class ome.security.basic.BasicSecuritySystem
internalDelete(IObject, UpdateFilter, Session) - Method in class ome.logic.UpdateImpl
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.
internalMkdir(CheckedPath) - Method in class ome.services.blitz.repo.RepositoryDaoImpl: This method should only be used by the register public method in order to guarantee that the DB is kept in sync with the file system.
internalMoveToCommonSpace(IObject) - Method in interface ome.api.local.LocalAdmin: Unconditionally move an object into the user group (usually id=1).
internalMoveToCommonSpace(IObject) - Method in class ome.logic.AdminImpl: Helpers which unconditionally moves the object to the common space.
InternalRepositoryConfig - Class in ome.services.blitz.repo: Simple configuration class which is created via repository.xml Spring configuration file after the OMERO.repository context is loaded.
InternalRepositoryConfig(String) - Constructor for class ome.services.blitz.repo.InternalRepositoryConfig
InternalRepositoryI - Class in ome.services.blitz.repo: Standalone repository service.
InternalRepositoryI(ObjectAdapter, Registry, Executor, Principal, String, PublicRepositoryI) - Constructor for class ome.services.blitz.repo.InternalRepositoryI
internalSave(IObject, ReloadFilter, Session) - Method in class ome.logic.UpdateImpl: Note if we use anything other than merge here, functionality from ome.tools.hibernate.MergeEventListener needs to be moved to UpdateFilter or to another event listener.
internalServantConfig(Object) - Method in class ome.services.blitz.impl.ServiceFactoryI
internalServantConfig(Object) - Method in class omero.cmd.SessionI
InternalServiceFactory - Class in ome.tools.spring: subclass of ome.system.ServiceFactory which retrieves unmanaged ("internal") service-instances.
InternalServiceFactory() - Constructor for class ome.tools.spring.InternalServiceFactory: default construtor
InternalServiceFactory(OmeroContext) - Constructor for class ome.tools.spring.InternalServiceFactory
internalSession - Variable in class ome.services.sessions.SessionManagerImpl: Internal SessionContext created during SessionManagerImpl.init() which is used for all method calls internal to the session manager (see execute* methods)
Intersection - Class in ome.services.search: Intersection SearchAction which combines two other search actions into one logical unit, e.g.
Intersection(SearchValues, SearchAction, SearchAction) - Constructor for class ome.services.search.Intersection
intersects(double, double, double, double) - Method in class ome.util.math.geom2D.EllipseArea: Required by the Shape I/F.
intersects(Rectangle2D) - Method in class ome.util.math.geom2D.EllipseArea: Required by the Shape I/F.
intersects(double, double, double, double) - Method in class ome.util.math.geom2D.RectangleArea: Required by the Shape I/F.
intersects(Rectangle2D) - Method in class ome.util.math.geom2D.RectangleArea: Required by the Shape I/F.
intervalEnd - Variable in class omeis.providers.re.codomain.CodomainMapContext: The upper bound of the codomain interval.
intervalStart - Variable in class omeis.providers.re.codomain.CodomainMapContext: The lower bound of the codomain interval.
InThreadThrottlingStrategy - Class in ome.services.throttling: Throttling implementation which uses the calling server Thread for execution.
InThreadThrottlingStrategy(CurrentDetails) - Constructor for class ome.services.throttling.InThreadThrottlingStrategy
invalidateConnection(long, Experimenter) - Method in interface ome.api.IShare: Makes the connection invalid for share for specifiec user.
invalidateConnection(long, Experimenter) - Method in class ome.services.sharing.ShareBean
invalidateConnection_async(AMD_IShare_invalidateConnection, long, Experimenter, Current) - Method in class ome.services.blitz.impl.ShareI
invalidateCurrentEventContext() - Method in class ome.security.basic.CurrentDetails: It suffices to set the Details to a new instance to make this context unusable.
invalidateEventContext() - Method in class ome.security.basic.BasicSecuritySystem
invalidateEventContext() - Method in interface ome.security.SecuritySystem: Clears the content of the EventContextso that the SecuritySystem will no longer return true for SecuritySystem.isReady().
invalidateEventContext() - Method in class ome.security.SecuritySystemHolder
invalidateEventContext() - Method in class ome.security.sharing.SharingSecuritySystem
InvalidQueryException - Exception in ome.util.search: Exception to indicate that the query string was invalid
InvalidQueryException() - Constructor for exception ome.util.search.InvalidQueryException
InvalidQueryException(String, Throwable) - Constructor for exception ome.util.search.InvalidQueryException
InvalidQueryException(String) - Constructor for exception ome.util.search.InvalidQueryException
InvalidQueryException(Throwable) - Constructor for exception ome.util.search.InvalidQueryException
invertPDI(Set<Image>, CBlock<T>) - Static method in class ome.tools.HierarchyTransformations
invoke(MethodInvocation) - Method in class ome.security.basic.BasicSecurityWiring: Wraps all OMERO invocations with login/logout semantics.
invoke(MethodInvocation) - Method in class ome.security.basic.EventHandler: invocation interceptor for prepairing this Thread for execution and subsequently reseting it.
invoke(MethodInvocation) - Method in class ome.security.basic.NullEventHandler
invoke(MethodInvocation) - Method in class ome.services.blitz.fire.AopContextInitializer
invoke(Object, Current, IceMapper, Object...) - Method in class ome.services.blitz.util.IceMethodInvoker: Calls the method named in Current.operation with the arguments provided mapped via the IceMapper instance.
invoke(MethodInvocation) - Method in class ome.services.util.ServiceHandler
invoke(MethodInvocation) - Method in class ome.tools.hibernate.EventMethodInterceptor
invoke(MethodInvocation) - Method in class ome.tools.hibernate.ProxyCleanupFilter.Interceptor
invoke(MethodInvocation) - Method in class ome.tools.hibernate.SessionFactory: Wraps all invocations to Session to prevent certain usages.
invoke(MethodInvocation) - Method in class ome.tools.hibernate.SessionHandler: delegates to HibernateInterceptor or manages sessions internally, based on the type of service.
invoke(MethodInvocation) - Method in class omero.cmd.CallContext
invoker - Variable in class ome.services.blitz.impl.AbstractAmdServant: If a service is provided, then an invoker will be created to cache all of its methods.
IObjectClassQuery - Class in ome.services.query: simple query subclass which uses the Parameters.CLASS parameter value to create a Criteria and then adds Expression instances based on all other parameter names.
IObjectClassQuery(Parameters) - Constructor for class ome.services.query.IObjectClassQuery
IObjectContainerStore - Interface in ome.formats.model: An object that handles the storage and manipulation of IObject containers and their references.
iObjectType - Variable in class ome.services.graphs.GraphStep: Deprecated.

Type of object which is being processed, using during GraphState#release(String) to send an EventLogMessage.
IObservable - Interface in ome.formats.importer
IObserver - Interface in ome.formats.importer
ip - Variable in class ome.services.sessions.SessionManager.CreationRequest
IPixels - Interface in ome.api: Metadata gateway for the RenderingEngine and clients.
iPixels - Variable in class ome.services.projection.ProjectionBean: Reference to the service used to retrieve the pixels metadata.
IProcessManager - Interface in ome.services.procs: Manages asynchronous processing logic for all Job instances created
IProjection - Interface in ome.api: Provides methods for performing projections of Pixels sets.
IQuery - Interface in ome.api: Provides methods for directly querying object graphs.
iQuery - Variable in class ome.logic.AbstractLevel2Service
iQuery - Variable in class ome.services.AbstractStatefulBean
iQuery - Variable in class ome.services.query.HierarchyNavigator: available query service
IQueryEnumProvider - Class in ome.formats.enums: An enumeration provider which uses IQuery and a cache to fulfill the contract of an EnumerationProvider.
IQueryEnumProvider(IQueryPrx) - Constructor for class ome.formats.enums.IQueryEnumProvider: Default IQuery based enumeration provider constructor.
IRenderingSettings - Interface in ome.api: Provides method to apply rendering settings to a collection of images.
IRepositoryInfo - Interface in ome.api: Provides methods for obtaining information for server repository disk space allocation.
IRequest - Interface in omero.cmd: SPI Orthogonal interface hierarchy of types for working with the Request hierarchy.
is_admin - Static variable in class ome.security.basic.AllGroupsSecurityFilter
is_adminorpi - Static variable in interface ome.security.SecurityFilter
is_nonprivate - Static variable in interface ome.security.SecurityFilter
IS_ROOT_USER - Variable in class ome.system.Roles
is_share - Static variable in interface ome.security.SecurityFilter
IS_SYSTEM_GROUP - Variable in class ome.system.Roles
IS_USER_GROUP - Variable in class ome.system.Roles
isAbstract - Variable in class ome.services.graphs.AbstractHierarchyGraphSpec: Deprecated.

Whether or not the type of types[i] is abstract.
isAcceptable(List<String>) - Method in class ome.services.blitz.repo.path.MakeNextDirectory: If the circumstances (filesystem, etc.) are such that it is okay to use the given subdirectories.
isAccepted(boolean, String, String, Current) - Method in class ome.services.blitz.impl.ProcessorCallbackI: Deprecated.
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() - Method in interface ome.services.procs.Process
isActive() - Method in class ome.services.procs.ProcessSkeleton
isActive(int) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
isActive(int) - Method in interface omeis.providers.re.RenderingEngine: Returns true if the channel is mapped, false otherwise.
isActive() - Method in class pojos.ExperimenterData: Returns true if the experimenter is active, false otherwise.
isActive_async(AMD_RenderingEngine_isActive, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
isAdjustedAfterReview(GraphPolicy.Details) - Method in class omero.cmd.graphs.BaseGraphPolicyAdjuster: An opportunity to adjust each model object after the graph policy reviews it.
isAdjustedBeforeReview(GraphPolicy.Details) - Method in class omero.cmd.graphs.BaseGraphPolicyAdjuster: An opportunity to adjust each model object before the graph policy reviews it.
isAdmin - Variable in class ome.system.SimpleEventContext
isAdminOrPi(EventContext) - Method in class ome.security.basic.AbstractSecurityFilter
isAllowLeadingWildcard() - Method in interface ome.api.Search: Returns the current leading-wildcard setting.
isAllowLeadingWildcard() - Method in class ome.services.SearchBean
isAllowLeadingWildcard_async(AMD_Search_isAllowLeadingWildcard, Current) - Method in class ome.services.blitz.impl.SearchI
isAlphalessRendering() - Method in class omeis.providers.re.Optimizations: Returns true if the alphaless rendering optimization is enabled, and false if it is not.
isArchived() - Method in class pojos.ImageData: Returns true if the image has been archived, false otherwise.
isAutoCloseEnabled() - Method in class ome.tools.hibernate.CurrentSessionContext
isBlockedFromAdjustment(GraphPolicy.Details) - Method in class omero.cmd.graphs.BaseGraphPolicyAdjuster: An opportunity to reverse any change to each model object after the graph policy reviews it.
IScale - Interface in ome.api: Provides methods for performing scaling (change of the image size through interpolation or other means) on BufferedImages.
isCancelled() - Method in class omero.cmd.CmdCallbackI: Returns whether Status::CANCELLED is contained in the flags variable of the Status instance.
isCaseSensitive() - Method in interface ome.api.Search: Returns the current case sensitivity setting.
isCaseSensitive() - Method in class ome.services.SearchBean
isCaseSensitive_async(AMD_Search_isCaseSensitive, Current) - Method in class ome.services.blitz.impl.SearchI
isCheckPermissions - Variable in class ome.services.graphs.GraphPolicy.Details: if the user's permissions for the object should be checked before the GraphTraversal.Processor acts upon it
isClientObject() - Method in class pojos.ShapeData: Returns true if the object one that has been created client side.
isClientSide() - Method in class pojos.ROIData: Returns true if the object a client-side object, false otherwise.
isCondition(String) - Method in class ome.services.graphs.GraphPolicy: Check if a condition has been set.
isCondition(String) - Method in class omero.cmd.graphs.BaseGraphPolicyAdjuster
IsConstant() - Method in class omeis.providers.re.codomain.PlaneSlicingContext: Returns the type of bit-planes mapping.
isCurrentUserAdmin() - Method in class ome.services.sessions.SessionContextImpl
isCurrentUserAdmin() - Method in interface ome.system.EventContext
isCurrentUserAdmin() - Method in class ome.system.SimpleEventContext
isDb() - Method in class ome.system.Preference
isDebugConsole() - Method in class ome.formats.importer.util.IniFileLoader
isDebugUI() - Method in class ome.formats.importer.util.IniFileLoader
isDetectorSettingsDirty() - Method in class pojos.ChannelAcquisitionData: Returns true if the detector settings has been updated, false otherwise.
isDirectory() - Method in class ome.services.blitz.repo.CheckedPath
isDirectory() - Method in class pojos.FileData: Returns true if the file is a directory, false otherwise.
isDirty() - Method in class pojos.DataObject: Returns true if setter value has modified the value of the stored IObject, false otherwise.
isDisabled(String) - Method in class ome.security.basic.BasicSecuritySystem
isDisabled(String) - Method in class ome.security.basic.CurrentDetails
isDisabled(String) - Method in interface ome.security.SecuritySystem: checks if the listed id is disabled for the current Thread.
isDisabled(String) - Method in class ome.security.SecuritySystemHolder
isDisabled(String) - Method in class ome.security.sharing.SharingSecuritySystem
isDisallow(int, Current) - Method in class omero.model.PermissionsI
isDiskSpaceChecking() - Method in class ome.services.RawFileBean: getter disk overflow checking
isDiskSpaceChecking() - Method in class ome.services.RawPixelsBean
isDiskSpaceChecking() - Method in class ome.services.ThumbnailBean
isEmpty() - Method in class ome.services.query.Definitions
isEmptyEventContext() - Method in class ome.security.sharing.SharingSecuritySystem
isEnabled() - Method in class ome.security.auth.LdapConfig
isEnabled() - Method in class ome.services.mail.MailSender
isEncryptedConnection() - Method in class ome.formats.OMEROMetadataStoreClient
isEndTime() - Method in class omero.sys.ParametersI: Returns true if the map contains the end time parameter, false otherwise.
isError(SqlAction.DeleteLog) - Method in class ome.services.messages.DeleteLogMessage
ISession - Interface in ome.api: Start here: Session creation service for OMERO.
isExceptionThrown() - Method in class ome.system.UpgradeCheck
isExperimenter() - Method in class omero.sys.ParametersI: Returns true if the filter contains and ownerId parameter, false otherwise.
isExtendedGraphCritical(Set<Long>) - Method in class ome.services.ThumbnailCtx: Whether or not we're extended graph critical for a given set of dimension pools.
isf - Variable in class ome.services.util.Executor.Impl
isFailure() - Method in class omero.cmd.CmdCallbackI: Returns whether Status::FAILURE is contained in the flags variable of the Status instance.
isFloat() - Method in interface ome.api.RawPixelsStore
isFloat() - Method in class ome.io.bioformats.BfPixelBuffer
isFloat() - Method in class ome.io.bioformats.BfPixelsWrapper
isFloat() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
isFloat() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
isFloat() - Method in interface ome.io.nio.PixelBuffer: Returns whether or not the pixel buffer has floating point pixels.
isFloat() - Method in class ome.io.nio.RomioPixelBuffer: Implemented as specified by PixelBuffer I/F.
isFloat() - Method in class ome.services.RawPixelsBean
isFloat_async(AMD_RawPixelsStore_isFloat, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
isFloat_async(AMD_RawPixelsStore_isFloat, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
isFontBold() - Method in class pojos.ShapeSettingsData: Returns true if it is bold, false otherwise.
isFontItalic() - Method in class pojos.ShapeSettingsData: Returns true if it is italic, false otherwise.
isForce() - Method in class ome.services.graphs.GraphOpts: Deprecated.
isFSImage() - Method in class pojos.ImageData: Returns true is the image has been imported the new import strategy known as FS import, false if imported using the previous import approach (data duplication).
isGranted(Permissions.Role, Permissions.Right) - Static method in class ome.security.basic.AllGroupsSecurityFilter
isGraphCritical(Details) - Method in class ome.security.basic.BasicSecuritySystem
isGraphCritical(Details) - Method in class ome.security.basic.CurrentDetails
isGraphCritical(Details) - Method in interface ome.security.SecuritySystem: Determines if the current security context has the possibility of corrupting consistent graphs.
isGraphCritical(Details) - Method in class ome.security.SecuritySystemHolder
isGraphCritical(Details) - Method in class ome.security.sharing.SharingSecuritySystem
isGraphsWrap() - Method in class omero.cmd.graphs.GraphRequestFactory
isGroup() - Method in class omero.sys.ParametersI: Returns true if the filter contains an groupId, false otherwise.
isGroupAnnotate(Current) - Method in class omero.model.PermissionsI
isGroupAnnotate() - Method in class pojos.PermissionData: Returns true if the group has annotate access i.e.
isGroupRead(Current) - Method in class omero.model.PermissionsI
isGroupRead() - Method in class pojos.PermissionData: Returns true if the group has read access i.e.
isGroupWrite(Current) - Method in class omero.model.PermissionsI
isGroupWrite() - Method in class pojos.PermissionData: Returns true if the group has write access i.e.
isHard() - Method in class ome.services.messages.stats.AbstractStatsMessage
IShare - Interface in ome.api: Provides method for sharing - collaboration process for images, datasets, projects.
isHidden() - Method in class pojos.FileData: Returns true if the file is hidden, false otherwise.
isIgnoreCaseLookup() - Method in interface ome.security.auth.RoleProvider
isIgnoreCaseLookup() - Method in class ome.security.auth.SimpleRoleProvider
isImagingEnvironmentDirty() - Method in class pojos.ImageAcquisitionData: Returns true if the StageLabel has been updated, false otherwise.
isImmutable(Object) - Method in class omero.util.IceMapper
isIncludeType(Class<? extends IObject>) - Method in class omero.cmd.graphs.ChildOptionI: Test if this child option adjusts graph traversal policy for the given child object class.
isInProgress() - Method in interface ome.api.ThumbnailStore: This returns the last available in progress state for a thumbnail.
isInProgress() - Method in class ome.services.ThumbnailBean
isInProgress_async(AMD_ThumbnailStore_isInProgress, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
isInRepo(long) - Method in class ome.services.scripts.ScriptRepoHelper
isInRepo(SqlAction, long) - Method in class ome.services.scripts.ScriptRepoHelper
isInSystemGroup(Long) - Method in class ome.security.SystemTypes
isInSystemGroup(Details) - Method in class ome.security.SystemTypes
isInUserGroup(Long) - Method in class ome.security.SystemTypes
isInUserGroup(Details) - Method in class ome.security.SystemTypes
isKeep() - Method in class ome.services.graphs.GraphEntry: Deprecated.
isLast(int) - Method in class omero.cmd.Helper: Returns true if this is the last step for the given request.
isLDAP() - Method in class pojos.ExperimenterData: Returns true if the user is connected via LDAP.
isLegalFsFile(FsFile) - Method in class ome.services.blitz.repo.path.ServerFilePathTransformer: Test if the given FsFile has been properly sanitized by the client.
isLeicaReader() - Method in class ome.formats.importer.OMEROWrapper
isLifetime() - Method in class pojos.ImageData: Returns true if the image is a lifetime image, false otherwise.
isLightSourceSettingsDirty() - Method in class pojos.ChannelAcquisitionData: Returns true if the light source settings has been updated, false otherwise.
isLinux() - Static method in class ome.services.blitz.util.CurrentPlatform
isLittleEndian() - Method in class ome.io.bioformats.BfPixelBuffer: Delegates to IFormatReader.isLittleEndian().
isLoaded() - Method in class pojos.DataObject: Returns true if the object is loaded, false otherwise.
isLockedByOthers() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
isMacOSX() - Static method in class ome.services.blitz.util.CurrentPlatform
isMemberOfGroup(long) - Method in class pojos.ExperimenterData: Checks if supplied group id matches any group to which the current experimenter belongs to.
isMergedBatches() - Method in interface ome.api.Search: Returns the current merged-batches setting.
isMergedBatches() - Method in class ome.services.SearchBean
isMergedBatches_async(AMD_Search_isMergedBatches, Current) - Method in class ome.services.blitz.impl.SearchI
isMinMaxSet() - Method in class ome.formats.importer.OMEROWrapper
isModified() - Method in class ome.services.AbstractStatefulBean
isModified() - Method in class ome.services.RawFileBean: Extends the check of the AbstractStatefulBean.modified flag performed by super with an additional check of the actual file size against the value stored in the database
isMovieFile() - Method in class pojos.FileAnnotationData: Returns true if it is a movie file.
isMutable() - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
isNoiseReduction() - Method in class omeis.providers.re.metadata.StatsFactory: Returns true if the flag is on, false otherwise.
isNonPrivate(EventContext) - Method in class ome.security.basic.AbstractSecurityFilter
isNull() - Method in class ome.services.graphs.GraphEntry: Deprecated.
isNullablePrimitive(Class<?>) - Static method in class omero.util.IceMapper
isObjectiveSettingsDirty() - Method in class pojos.ImageAcquisitionData: Returns true if the objective settings has been updated, false otherwise.
isOMERO - Variable in class loci.ome.io.OMECredentials
isOverrideKeep(int, QueryBuilder, String) - Method in class ome.services.graphs.AbstractHierarchyGraphSpec: Deprecated.

If BaseGraphSpec.overrideKeep() returns true for a subclass, then this method will likely want to (at least sometimes) return a true value.
isOverrideKeep(int, QueryBuilder, String) - Method in class ome.services.graphs.AnnotationGraphSpec: Deprecated.
isOverrideKeep(int, QueryBuilder, String) - Method in class ome.services.graphs.LightSourceGraphSpec: Deprecated.
isOwnerOrSupervisor(IObject) - Method in class ome.security.basic.BasicSecuritySystem: tests whether or not the current user is either the owner of this entity, or the superivsor of this entity, for example as root or as group owner.
isOwnerOrSupervisor(IObject) - Method in class ome.security.basic.CurrentDetails
isPagination() - Method in class omero.sys.ParametersI: Returns true if the filter contains a limit OR a offset, false otherwise.
isPasswordRequired(Long) - Method in class ome.security.auth.PasswordUtil: Returns a boolean based on the supplied user ID and system property setting.
isPixelsTypeSigned() - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
isPixelsTypeSigned() - Method in class omeis.providers.re.Renderer: Returns true if the pixels type is signed, false otherwise.
isPixelsTypeSigned() - Method in interface omeis.providers.re.RenderingEngine: Returns true if the pixels type is signed, false otherwise.
isPixelsTypeSigned_async(AMD_RenderingEngine_isPixelsTypeSigned, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
isPrefs() - Method in class ome.system.Preference
isPrimaryColorEnabled() - Method in class omeis.providers.re.Optimizations: Returns true if the primary color optimization is enabled, and false if it is not.
isPrimitive(Class<?>) - Method in class omero.util.IceMapper
isPropertyAccessible(String, String) - Method in class ome.services.graphs.GraphPathBean: Find if the given property can be accessed.
isProxyAccepted(boolean, String, ProcessorPrx, Current) - Method in class ome.services.blitz.impl.ProcessorCallbackI: Callback method called by the remote processor instance.
isReadOnly() - Method in class ome.services.sessions.SessionContextImpl
isReadOnly() - Method in interface ome.system.EventContext
isReadOnly - Variable in class ome.system.SimpleEventContext
isReadOnly() - Method in class ome.system.SimpleEventContext
isReadOnly() - Method in class pojos.ShapeData: Returns true if the object a read-only object, false otherwise.
isReady() - Method in class ome.security.basic.BasicSecuritySystem: implements SecuritySystem.isReady().
isReady() - Method in class ome.security.basic.CurrentDetails: Checks if the current Thread has non-null Experimenter, Event, and ExperimenterGroup, required for proper functioning of the security system.
isReady() - Method in interface ome.security.SecuritySystem: checks if this SecuritySystem instance is in a valid state.
isReady() - Method in class ome.security.SecuritySystemHolder
isReady() - Method in class ome.security.sharing.SharingSecuritySystem
isReap() - Method in class ome.services.graphs.GraphEntry: Deprecated.
isRestricted(IObject) - Method in class ome.security.policy.BasePolicy
isRestricted(IObject) - Method in class ome.security.policy.BinaryAccessPolicy
isRestricted(String, IObject) - Method in class ome.security.policy.DefaultPolicyService
isRestricted(IObject) - Method in interface ome.security.policy.Policy: Checks whether or not this instance would throw a SecurityViolation if the same instance were passed to Policy.checkRestriction(IObject).
isRestricted(String, IObject) - Method in interface ome.security.policy.PolicyService: Ask each configured Policy instance with the given name argument if it considers the restriction active for the given IObject argument.
isRestricted(String, Current) - Method in class omero.model.PermissionsI
isRetry() - Method in class ome.io.messages.MissingPyramidMessage
isReturnUnloaded() - Method in interface ome.api.Search: Returns the current return-unloaded setting.
isReturnUnloaded() - Method in class ome.services.SearchBean
isReturnUnloaded_async(AMD_Search_isReturnUnloaded, Current) - Method in class ome.services.blitz.impl.SearchI
isRoot - Variable in class ome.services.blitz.repo.CheckedPath
isRootUser(Experimenter) - Method in class ome.system.Roles
isSecure() - Method in class omero.client: Specifies whether or not this client was created via a call to client.createClient(boolean) with a boolean of false.
isSend(int) - Method in class ome.formats.importer.util.ErrorHandler: Check if files need sending at error container index
isShare(EventContext) - Method in class ome.security.basic.AbstractSecurityFilter
isSigned() - Method in interface ome.api.RawPixelsStore
isSigned() - Method in class ome.io.bioformats.BfPixelBuffer
isSigned() - Method in class ome.io.bioformats.BfPixelsWrapper
isSigned() - Method in class ome.io.bioformats.BfPyramidPixelBuffer
isSigned() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
isSigned() - Method in interface ome.io.nio.PixelBuffer: Returns whether or not the pixel buffer has signed pixels.
isSigned() - Method in class ome.io.nio.RomioPixelBuffer: Implemented as specified by PixelBuffer I/F.
isSigned() - Method in class ome.services.RawPixelsBean
isSigned_async(AMD_RawPixelsStore_isSigned, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
isSigned_async(AMD_RawPixelsStore_isSigned, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
isSingleton() - Method in class ome.security.basic.EventListenersFactoryBean: being a singleton implies that this FactoryBean will only ever create one instance.
isSoft() - Method in class ome.services.graphs.GraphEntry: Deprecated.
isSPWReader() - Method in class ome.formats.importer.OMEROWrapper
isStageLabelDirty() - Method in class pojos.ImageAcquisitionData: Returns true if the position has been updated, false otherwise.
isStartTime() - Method in class omero.sys.ParametersI: Returns true if the map contains the start time parameter, false otherwise.
isStatisticsEnabled() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl: Are statistics logged
isStopSet() - Method in class ome.services.eventlogs.EventLogLoader: Returns true if the stop flag has been set on this instance.
isSyncOnLogin() - Method in class ome.security.auth.LdapConfig
isSystemGroup(ExperimenterGroup) - Method in class ome.system.Roles
isSystemType(Class<? extends IObject>) - Method in class ome.security.basic.BasicSecuritySystem: classes which cannot be created by regular users.
isSystemType(Class<? extends IObject>) - Method in interface ome.security.SecuritySystem: checks if instances of the given type are "System-Types".
isSystemType(Class<? extends IObject>) - Method in class ome.security.SecuritySystemHolder
isSystemType(Class<? extends IObject>) - Method in class ome.security.sharing.SharingSecuritySystem
isSystemType(Class<?>) - Method in class ome.security.SystemTypes: classes which cannot be created by regular users.
isTargetNamespace(String) - Method in class omero.cmd.graphs.ChildOptionI: Test if this child option adjusts graph traversal policy for child objects that are annotations in the given namespace.
isThisType(String, boolean) - Method in class loci.ome.io.OmeroReader
isThisType(String, boolean) - Method in class ome.io.bioformats.OmeroPixelsPyramidReader
isThisType(String, boolean) - Method in class ome.services.formats.OmeroReader
isThisType(RandomAccessInputStream) - Method in class ome.services.formats.OmeroReader
isThreadSafe() - Method in class ome.services.messages.AbstractSessionMessage
isThreadSafe() - Method in class ome.util.messages.InternalMessage: Returns true if this message can safely be passed to another Thread.
isThumbnailCached(long) - Method in class ome.services.ThumbnailCtx: Checks to see if a thumbnail is in the on disk cache or not.
isTransient(Object) - Method in class ome.security.basic.OmeroInterceptor
isTypeSigned(PixelsType) - Static method in class omeis.providers.re.data.PlaneFactory: A static helper method to retrieve pixel byte signage.
isUnknown() - Static method in class ome.services.blitz.util.CurrentPlatform
isUnloaded(Object) - Static method in class ome.tools.hibernate.HibernateUtils
isUpgradeNeeded() - Method in class ome.formats.importer.ImportConfig: Check online to see if this is the current version
isUpgradeNeeded() - Method in class ome.system.UpgradeCheck
isUseProjections() - Method in interface ome.api.Search: Returns the current use-projection setting.
isUseProjections() - Method in class ome.services.SearchBean
isUseProjections_async(AMD_Search_isUseProjections, Current) - Method in class ome.services.blitz.impl.SearchI
isUserAnnotate(Current) - Method in class omero.model.PermissionsI
isUserGroup(ExperimenterGroup) - Method in class ome.system.Roles
isUserRead(Current) - Method in class omero.model.PermissionsI
isUserRead() - Method in class pojos.PermissionData: Returns true if the user has read access, false otherwise.
isUserWrite(Current) - Method in class omero.model.PermissionsI
isUserWrite() - Method in class pojos.PermissionData: Returns true if the user has write access, false otherwise.
isVisible() - Method in class pojos.ShapeData: Returns true if the shape is visible, false otherwise.
isVoid(Current) - Method in class ome.services.blitz.util.IceMethodInvoker: Checks for a void return type, which is needed to know what type of ice_response() method to invoke.
isVoid - Variable in class ome.services.throttling.Task
isVoid() - Method in class omero.util.IceMapper: Returns true only if the current mapping is the IceMapper.VOID mapping.
isWindows() - Method in class ome.formats.importer.transfers.AbstractFileTransfer: Uses os.name to determine whether or not this JVM is running under Windows.
isWindows() - Static method in class ome.services.blitz.util.CurrentPlatform
isWorldAnnotate(Current) - Method in class omero.model.PermissionsI
isWorldRead(Current) - Method in class omero.model.PermissionsI
isWorldRead() - Method in class pojos.PermissionData: Returns true if the world has read access, false otherwise.
isWorldWrite(Current) - Method in class omero.model.PermissionsI
isWorldWrite() - Method in class pojos.PermissionData: Returns true if the world has write access, false otherwise.
isWrapperArray(Class<?>) - Static method in class omero.util.IceMapper
isWrite() - Method in class ome.io.bioformats.BfPyramidPixelBuffer: Whether or not this instance is in writing-mode.
isXYPlanar() - Method in class omeis.providers.re.data.Plane2D: Returns true if the plane is an XY-plane, false otherwise.
iterate() - Method in class ome.services.scripts.ScriptRepoHelper
iterator() - Method in class ome.services.eventlogs.EventLogLoader
ITypes - Interface in ome.api: Access to reflective type information.
IUpdate - Interface in ome.api: Provides methods for directly updating object graphs.
iUpdate - Variable in class ome.logic.AbstractLevel2Service
iUpdate - Variable in class ome.services.AbstractStatefulBean

J

JavaImageScalingService - Class in ome.logic: Provides methods for scaling buffered images using Java Image Scaling.
JavaImageScalingService() - Constructor for class ome.logic.JavaImageScalingService
JdbcHashedPasswordProvider - Class in ome.security.auth: Central PasswordProvider which uses the "password" table in the central OMERO database.
JdbcHashedPasswordProvider(PasswordUtil) - Constructor for class ome.security.auth.JdbcHashedPasswordProvider
JdbcHashedPasswordProvider(PasswordUtil, boolean) - Constructor for class ome.security.auth.JdbcHashedPasswordProvider
JdbcPasswordProvider - Class in ome.security.auth: Central PasswordProvider which uses the "password" table in the central OMERO database.
JdbcPasswordProvider(PasswordUtil) - Constructor for class ome.security.auth.JdbcPasswordProvider
JdbcPasswordProvider(PasswordUtil, boolean) - Constructor for class ome.security.auth.JdbcPasswordProvider
JdbcPasswordProvider(PasswordUtil, boolean, boolean) - Constructor for class ome.security.auth.JdbcPasswordProvider
job(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: Deprecated.

Used to generate a join statement on the QueryBuilder making use of {@link ExtendedMetadata#getRelationship(String, String).
join(String) - Method in interface ome.services.sessions.SessionCallback
join(String) - Method in class ome.services.sessions.SessionCallback.SimpleCloseCallback
join(String, String, boolean, boolean) - Method in class ome.tools.hibernate.QueryBuilder
join(String...) - Static method in class prefs: Joins all the String arguments given into a single String (joined with " "), and returns that String as the first element of a new array.
joinChildren(Criteria, Class, int) - Static method in class ome.services.query.Hierarchy
joinDataset(QueryBuilder, String, String) - Method in class ome.services.graphs.BaseGraphSpec: Deprecated.
joinParents(Criteria, Class, int) - Static method in class ome.services.query.Hierarchy
joinPlate(QueryBuilder, String, String) - Method in class ome.services.graphs.BaseGraphSpec: Deprecated.
joinSession(String) - Method in class omero.client: Uses the given session uuid as name and password to rejoin a running session.
JvmSettingsCheck - Class in ome.services.util: Hook run by the context which prints out JVM-related information, primarily Java version, max heap size and available processors.
JvmSettingsCheck() - Constructor for class ome.services.util.JvmSettingsCheck

K

keepAlive(ServiceInterfacePrx, Current) - Method in class ome.services.blitz.impl.ServiceFactoryI: Currently ignoring the individual proxies
keepAllAlive(ServiceInterfacePrx[], Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
key - Variable in enum ome.formats.importer.ImportConfig.VersionInfo: the map key corresponding to this instance
key(String) - Method in class ome.security.auth.AttributeSet
key - Variable in class ome.services.eventlogs.PersistentEventLogLoader: Key used to look configuration value; 'name'
KeyAndTrustStoreConfiguration - Class in ome.security: Calls System.setProperty(String, String) for the "javax.net.ssl" properties needed to configure a trust store and a keystore for the Java process.
KeyAndTrustStoreConfiguration() - Constructor for class ome.security.KeyAndTrustStoreConfiguration
keys() - Method in class ome.services.sharing.BlobShareStore
keys() - Method in class ome.services.sharing.ShareStore
keys(String[]) - Static method in class prefs: 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.
Laser_RepetitionRate - Static variable in class ome.formats.model.UnitsFactory
Laser_Wavelength - Static variable in class ome.formats.model.UnitsFactory
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: Sets LdapConfig.syncOnLogin to false and LdapConfig.base to null.
LdapConfig(boolean, String, String, String, String, String, boolean) - Constructor for class ome.security.auth.LdapConfig: Sets LdapConfig.base to null.
LdapConfig(boolean, String, String, String, String, String, boolean, String) - Constructor for class ome.security.auth.LdapConfig: Sets LdapConfig.newUserGroupOwner to null.
LdapConfig(boolean, String, String, String, String, String, boolean, String, String) - Constructor for class ome.security.auth.LdapConfig: Base constructor which stores all LdapConfig.parse(String) and stores all values for later lookup.
LdapI - Class in ome.services.blitz.impl: Implementation of the ILdap service.
LdapI(ILdap, BlitzExecutor) - Constructor for class ome.services.blitz.impl.LdapI
LdapImpl - Class in ome.logic: Provides methods for administering user accounts, passwords, as well as methods which require special privileges.
LdapImpl(ContextSource, LdapOperations, Roles, LdapConfig, RoleProvider, SqlAction) - Constructor for class ome.logic.LdapImpl
LdapImpl.GroupLoader - Class in ome.logic: Data class which stores the state of the NewUserGroupBean and NewUserGroupOwnerBean operations.
LdapPasswordProvider - Class in ome.security.auth: LDAP PasswordProvider which can create users on request to synchronize with an LDAP directory.
LdapPasswordProvider(PasswordUtil, LdapImpl) - Constructor for class ome.security.auth.LdapPasswordProvider
LdapPasswordProvider(PasswordUtil, LdapImpl, boolean) - Constructor for class ome.security.auth.LdapPasswordProvider
LdapPasswordProvider431 - Class in ome.security.auth.providers: LDAP PasswordProvider which can create users on request to synchronize with an LDAP directory.
LdapPasswordProvider431(PasswordUtil, LdapImpl) - Constructor for class ome.security.auth.providers.LdapPasswordProvider431
LdapPasswordProvider431(PasswordUtil, LdapImpl, boolean) - Constructor for class ome.security.auth.providers.LdapPasswordProvider431
ldapUtil - Variable in class ome.logic.AdminImpl
ldapUtil - Variable in class ome.security.auth.LdapPasswordProvider
ldapUtil - Variable in class ome.security.auth.providers.LdapPasswordProvider431
leader_of_groups - Static variable in class ome.security.basic.AllGroupsSecurityFilter
leaderOfGroups - Variable in class ome.system.SimpleEventContext
leadingWildcard - Variable in class ome.services.search.SearchValues
leaves() - Method in class omero.sys.ParametersI: Sets the leaf parameter to true.
LEFT_JOIN - Static variable in class ome.services.query.Query: imported constant for ease of use
LegacyRepositoryI - Class in ome.services.blitz.repo: Repository which makes the ${omero.data.dir} directory available via the standard Repository API.
LegacyRepositoryI(ObjectAdapter, Registry, Executor, Principal, String, PublicRepositoryI) - Constructor for class ome.services.blitz.repo.LegacyRepositoryI
LegacyRepositoryI(ObjectAdapter, Registry, Executor, Principal, FileMaker, PublicRepositoryI) - Constructor for class ome.services.blitz.repo.LegacyRepositoryI
legacyUtil - Variable in class ome.security.auth.ConfigurablePasswordProvider: Possibly null PasswordUtil instance which will be used as a fallback for password checks if the ConfigurablePasswordProvider.util instance fails.
length() - Method in class ome.services.scripts.RepoFile.FsFile
length() - Method in class ome.services.scripts.RepoFile
length - Variable in class ome.util.mem.ReadOnlyByteArray: The length of the slice.
LengthI - Class in omero.model: Blitz wrapper around the Length class.
LengthI() - Constructor for class omero.model.LengthI
LengthI(double, UnitsLength) - Constructor for class omero.model.LengthI
LengthI(double, Unit<Length>) - Constructor for class omero.model.LengthI
LengthI(Length, Unit<Length>) - Constructor for class omero.model.LengthI: Copy constructor that converts the given Length based on the given ome-xml enum
LengthI(double, UnitsLength) - Constructor for class omero.model.LengthI: Copy constructor that converts the given Length based on the given ome.model enum
LengthI(Length, String) - Constructor for class omero.model.LengthI: Copy constructor that converts the given Length based on the given enum string.
LengthI(Length, UnitsLength) - Constructor for class omero.model.LengthI: Copy constructor that converts between units if possible.
LengthI(Length) - Constructor for class omero.model.LengthI: Convert a Bio-Formats Length to an OMERO Length.
LEVEL_FIVE - Static variable in class pojos.RatingAnnotationData: Indicates the object is rated with five stars.
LEVEL_FOUR - Static variable in class pojos.RatingAnnotationData: Indicates the object is rated with four stars.
LEVEL_ONE - Static variable in class pojos.RatingAnnotationData: Indicates the object is rated with one star.
LEVEL_THREE - Static variable in class pojos.RatingAnnotationData: Indicates the object is rated with three stars.
LEVEL_TWO - Static variable in class pojos.RatingAnnotationData: Indicates the object is rated with two stars.
LEVEL_ZERO - Static variable in class pojos.RatingAnnotationData: Indicates the object is not rated.
library - Variable in class ome.formats.importer.cli.CommandLineImporter: Base importer library, this is what we actually use to import.
lies(PlanePoint) - Method in class ome.util.math.geom2D.Line: Tells whether the specified point lies on this line.
lies(PlanePoint, boolean) - Method in class ome.util.math.geom2D.Line: Tells whether the specified point lies on this line and within the specified orientation.
lies(double, double) - Method in class ome.util.math.geom2D.Segment: Tells whether a specified point lies on this line.
LIGHT_EMITTING_DIODE - Static variable in class pojos.LightSourceData: Indicates that the light source is a light emitting diode.
LightPathData - Class in pojos: Object hosting a light path.
LightPathData(LightPath) - Constructor for class pojos.LightPathData: Creates a new instance.
LightSource_Power - Static variable in class ome.formats.model.UnitsFactory
LightSourceData - Class in pojos: Object hosting a light source: filament, arc, laser or light emitting diode
LightSourceData(LightSource) - Constructor for class pojos.LightSourceData: Creates a new instance.
LightSourceGraphSpec - Class in ome.services.graphs: Deprecated.
will be removed in OMERO 5.2, so use the new graphs implementation
LightSourceGraphSpec(List<String>) - Constructor for class ome.services.graphs.LightSourceGraphSpec: Deprecated.

Creates a new instance.
LightSourceSettings_Wavelength - Static variable in class ome.formats.model.UnitsFactory
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(String, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
list(List<Obj>) - Method in class ome.services.sharing.ShareBean
listActiveRestrictions(IObject) - Method in class ome.security.policy.DefaultPolicyService
listActiveRestrictions(IObject) - Method in interface ome.security.policy.PolicyService: Return all identifier strings as would be passed as the first argument to PolicyService.isRestricted(String, IObject) or PolicyService.checkRestriction(String, IObject) which considers itself active for the given argument.
listAllRestrictions() - Method in class ome.security.policy.DefaultPolicyService
listAllRestrictions() - Method in interface ome.security.policy.PolicyService: Return all configured identifier strings as would be passed as the first argument to PolicyService.isRestricted(String, IObject) or PolicyService.checkRestriction(String, IObject).
ListAsSQLArrayUserType<T> - Class in ome.tools.hibernate: Hibernate type to store Lists of primitives using SQL ARRAY.
ListAsSQLArrayUserType() - Constructor for class ome.tools.hibernate.ListAsSQLArrayUserType
ListAsSQLArrayUserType.ArrayFactory - Interface in ome.tools.hibernate
ListAsSQLArrayUserType.BOOLEAN - Class in ome.tools.hibernate: To use, define : hibernate.property type="ome.tools.hibernate.ListAsSQLArrayUserType$BOOLEAN" hibernate.column name="fieldName" sql-type="bool[]"
ListAsSQLArrayUserType.BOOLEAN() - Constructor for class ome.tools.hibernate.ListAsSQLArrayUserType.BOOLEAN
ListAsSQLArrayUserType.DATE - Class in ome.tools.hibernate: To use, define : hibernate.property type="ome.tools.hibernate.ListAsSQLArrayUserType$DATE" hibernate.column name="fieldName" sql-type="timestamp[]"
ListAsSQLArrayUserType.DATE() - Constructor for class ome.tools.hibernate.ListAsSQLArrayUserType.DATE
ListAsSQLArrayUserType.DOUBLE - Class in ome.tools.hibernate: To use, define : hibernate.property type="ome.tools.hibernate.ListAsSQLArrayUserType$DOUBLE" hibernate.column name="fieldName" sql-type="float8[]"
ListAsSQLArrayUserType.DOUBLE() - Constructor for class ome.tools.hibernate.ListAsSQLArrayUserType.DOUBLE
ListAsSQLArrayUserType.ENUM<E extends Enum<E>> - Class in ome.tools.hibernate: Warning, this one is special.
ListAsSQLArrayUserType.ENUM(E[]) - Constructor for class ome.tools.hibernate.ListAsSQLArrayUserType.ENUM
ListAsSQLArrayUserType.FLOAT - Class in ome.tools.hibernate: To use, define : hibernate.property type="ome.tools.hibernate.ListAsSQLArrayUserType$FLOAT" hibernate.column name="fieldName" sql-type="real[]"
ListAsSQLArrayUserType.FLOAT() - Constructor for class ome.tools.hibernate.ListAsSQLArrayUserType.FLOAT
ListAsSQLArrayUserType.INTEGER - Class in ome.tools.hibernate: To use, define : hibernate.property type="ome.tools.hibernate.ListAsSQLArrayUserType$INTEGER" hibernate.column name="fieldName" sql-type="int[]"
ListAsSQLArrayUserType.INTEGER() - Constructor for class ome.tools.hibernate.ListAsSQLArrayUserType.INTEGER
ListAsSQLArrayUserType.STRING - Class in ome.tools.hibernate: To use, define : hibernate.property type="ome.tools.hibernate.ListAsSQLArrayUserType$STRING" hibernate.column name="fieldName" sql-type="text[]"
ListAsSQLArrayUserType.STRING() - Constructor for class ome.tools.hibernate.ListAsSQLArrayUserType.STRING
ListAsSQLArrayUserType.STRING2 - Class in ome.tools.hibernate: To use, define : hibernate.property type="ome.tools.hibernate.ListAsSQLArrayUserType$STRING2" hibernate.column name="fieldName" sql-type="text[]" Added by Josh
ListAsSQLArrayUserType.STRING2() - Constructor for class ome.tools.hibernate.ListAsSQLArrayUserType.STRING2
listChecksumAlgorithms(Current) - Method in class ome.services.blitz.repo.ManagedRepositoryI
listFiles(String, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
listImports(Current) - Method in class ome.services.blitz.repo.ManagedRepositoryI
LISTOBJECTARRAY_TO_RTYPESEQSEQ - Static variable in class omero.util.IceMapper
listProcesses(Collection<Long>) - Method in class ome.services.blitz.repo.ProcessContainer
ListRequestsI - Class in omero.cmd.basic
ListRequestsI(OmeroContext) - Constructor for class omero.cmd.basic.ListRequestsI
ln(double, double, double, double) - Method in class ome.services.roi.GeomTool
load() - Method in class ome.formats.importer.ImportConfig.Value: Loads properties from various locations.
load(FileDeleter.Type) - Method in class ome.services.delete.files.FileDeleter: Lookup the ids which are scheduled for deletion.
load(FileDeleter.Type) - Method in class ome.services.delete.files.FileDeleterGraphState: Deprecated.

Lookup the ids which are scheduled for deletion from the GraphState.
load(List<Object[]>) - Method in class ome.services.eventlogs.EventLogQueue
load(Long, String, Long, String, Integer) - Method in class ome.services.eventlogs.EventLogQueue: Guarantees that the given arguments are available somewhere in the queue returning true if they were newly added.
load(Session) - Method in class ome.services.graphs.BaseGraphSpec: Deprecated.
load(Session) - Method in interface ome.services.graphs.GraphSpec: Deprecated.

Loads the object that this spec points to.
load() - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
load(long, boolean) - Method in class ome.services.scripts.ScriptRepoHelper
load(long, Session, SqlAction, boolean) - Method in class ome.services.scripts.ScriptRepoHelper
load() - Method in class ome.services.util.DBUserCheck
load() - Method in interface omeis.providers.re.RenderingEngine: Creates a instance of the rendering engine.
load() - Method in class omero.cmd.graphs.ChmodI: Deprecated.
load(String[]) - Static method in class prefs: Loads a profile from Properties files, or properly formatted System.in input if no files are given.
load_async(AMD_RenderingEngine_load, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
load_nowarn(String[]) - Static method in class prefs: Performs the same actions as prefs.load(String[]) but does not throw prefs.CONFLICT if a key already exists.
loadAll() - Method in class ome.formats.importer.ImportConfig: Loads all the values for which it makes sense to have a preferences values.
loadAll(boolean) - Method in class ome.services.scripts.ScriptRepoHelper: Walks all files in the repository (via ScriptRepoHelper.iterate() and adds them if not found in the database.
loadAllMetadata(long) - Method in class ome.services.ThumbnailCtx: Retrieves all thumbnail metadata available in the database for a given Pixels ID.
loadAndPrepareMetadata(Set<Long>, int) - Method in class ome.services.ThumbnailCtx: Bulk loads and prepares metadata for a group of pixels sets.
loadAndPrepareMetadata(Set<Long>, Dimension) - Method in class ome.services.ThumbnailCtx: Bulk loads and prepares metadata for a group of pixels sets.
loadAndPrepareMetadata(Set<Long>, Dimension, boolean) - Method in class ome.services.ThumbnailCtx: Bulk loads and prepares metadata for a group of pixels sets.
loadAndPrepareRenderingSettings(Set<Long>) - Method in class ome.services.ThumbnailCtx: Bulk loads a set of rendering settings for a group of pixels sets and prepares our internal data structures.
loadAndPrepareRenderingSettings(long, long) - Method in class ome.services.ThumbnailCtx: Loads and prepares a rendering settings for a Pixels ID and RenderingDef ID.
loadAnnotation(Set<Long>) - Method in interface ome.api.IMetadata: Loads the specified annotations.
loadAnnotation(Set<Long>) - Method in class ome.logic.MetadataImpl: Implemented as specified by the IMetadata I/F
loadAnnotation_async(AMD_IMetadata_loadAnnotation, List<Long>, Current) - Method in class ome.services.blitz.impl.MetadataI
loadAnnotations(Class<T>, Set<Long>, Set<String>, Set<Long>, Parameters) - Method in interface ome.api.IMetadata: Loads all the annotations of given types, that have been attached to the specified rootNodes for the specified annotatorIds.
loadAnnotations(Class<T>, Set<Long>, Set<String>, Set<Long>, Parameters) - Method in class ome.logic.MetadataImpl: Implemented as specified by the IMetadata I/F
loadAnnotations_async(AMD_IMetadata_loadAnnotations, String, List<Long>, List<String>, List<Long>, Parameters, Current) - Method in class ome.services.blitz.impl.MetadataI
loadAnnotationsUsedNotOwned(Class, long) - Method in interface ome.api.IMetadata: Loads the annotations of a given type used by the specified user but not owned by the user.
loadAnnotationsUsedNotOwned(Class, long) - Method in class ome.logic.MetadataImpl: Implemented as specified by the IMetadata I/F
loadAnnotationsUsedNotOwned_async(AMD_IMetadata_loadAnnotationsUsedNotOwned, String, long, Current) - Method in class ome.services.blitz.impl.MetadataI
loadChannelAcquisitionData(Set<Long>) - Method in interface ome.api.IMetadata: Loads the logical channels and the acquisition metadata related to them.
loadChannelAcquisitionData(Set<Long>) - Method in class ome.logic.MetadataImpl: Implemented as specified by the IMetadata I/F
loadChannelAcquisitionData_async(AMD_IMetadata_loadChannelAcquisitionData, List<Long>, Current) - Method in class ome.services.blitz.impl.MetadataI
loadCollection(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
loadContainerHierarchy(Class<T>, Set<Long>, Parameters) - Method in interface ome.api.IContainer: Retrieves hierarchy trees rooted by a given node (unless orphan is specified -- See below) This method also retrieves the Experimenters linked to the objects in the tree.
loadContainerHierarchy(Class, Set, Parameters) - Method in class ome.logic.PojosImpl: Implemented as specified by the IContainer I/F
loadContainerHierarchy_async(AMD_IContainer_loadContainerHierarchy, String, List<Long>, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI
loaded - Variable in class ome.services.blitz.fire.SessionManagerI
loadedObjects(int) - Method in class ome.services.sessions.stats.DelegatingStats
loadedObjects(int) - Method in class ome.services.sessions.stats.NullSessionStats
loadedObjects(int) - Method in interface ome.services.sessions.stats.SessionStats
loadedObjects(int) - Method in class ome.services.sessions.stats.SimpleSessionStats
loadEntity(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
loader - Variable in class ome.services.eventlogs.EventLogFailure
loader - Variable in class ome.services.fulltext.FullTextIndexer
loader - Variable in class ome.services.pixeldata.PixelDataHandler
loadEventContext(boolean) - Method in class ome.security.basic.BasicSecuritySystem
loadEventContext(boolean, boolean) - Method in class ome.security.basic.BasicSecuritySystem
loadEventContext(boolean) - Method in interface ome.security.SecuritySystem: Prepares the current EventContext instance with the current Principal.
loadEventContext(boolean) - Method in class ome.security.SecuritySystemHolder
loadEventContext(boolean) - Method in class ome.security.sharing.SharingSecuritySystem
loadFileAnnotation() - Method in class omero.cmd.fs.OriginalMetadataRequestI: Only called if OriginalMetadataRequestI.loadFileset() finds no Fileset.
loadFileset() - Method in class omero.cmd.fs.OriginalMetadataRequestI: Searches for a Fileset attached to this Image, and if present, uses Bio-Formats to parse the metadata into the OriginalMetadataResponse instance.
loadFilesets(List<Long>, Current) - Method in interface ome.services.blitz.repo.RepositoryDao: Load filesets by id.
loadFilesets(List<Long>, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
loadGui() - Method in class ome.formats.importer.ImportConfig: Loads gui specific values for which it makes sense to have a preferences values.
loadInstrument(long) - Method in interface ome.api.IMetadata: Loads the instrument and its components i.e. detectors, objectives, etc.
loadInstrument(long) - Method in class ome.logic.MetadataImpl: Implemented as specified by the IMetadata I/F
loadInstrument_async(AMD_IMetadata_loadInstrument, long, Current) - Method in class ome.services.blitz.impl.MetadataI
loadLdapGroups(String, DistinguishedName) - Method in class ome.logic.LdapImpl: Deprecated.
loadLogFile() - Method in class ome.formats.importer.ImportLibrary.ImportCallback
loadLogFiles(Class<? extends IObject>, Set<Long>) - Method in interface ome.api.IMetadata: Find the original file IDs for the import logs corresponding to the given Image or Fileset IDs.
loadLogFiles(Class<? extends IObject>, Set<Long>) - Method in class ome.logic.MetadataImpl
loadLogFiles_async(AMD_IMetadata_loadLogFiles, String, List<Long>, Current) - Method in class ome.services.blitz.impl.MetadataI
loadMeasuredRois(Session, long, long) - Method in class ome.services.blitz.impl.RoiI
loadMembers(ShareData) - Method in class ome.services.sharing.ShareBean
loadOriginalFile(RawFileStorePrx) - Method in class ome.formats.importer.ImportLibrary: Use RawFileStorePrx.getFileId() in order to load the OriginalFile that the service argument is acting on.
loadPermissions(Session) - Method in class ome.security.basic.BasicEventContext
loadPermissions(Session) - Method in class ome.security.basic.CurrentDetails: Checks the "groupPermissions" map in BasicEventContext which has been filled up by calls to BasicEventContext.setPermissionsForGroup(Long, Permissions) during BasicACLVoter.allowLoad(org.hibernate.Session, Class, Details, long).
loadRenderingDef(long) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
loadRenderingDef(long) - Method in interface omeis.providers.re.RenderingEngine: Loads a specific set of rendering settings that does not necessarily have to be linked to the given Pixels set.
loadRenderingDef_async(AMD_RenderingEngine_loadRenderingDef, long, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
loadRndSettings(long) - Method in interface ome.api.IPixels: Loads a specific set of rendering settings with the following objects pre-linked: renderingDef.quantization renderingDef.model renderingDef.waveRendering renderingDef.waveRendering.color renderingDef.waveRendering.family renderingDef.spatialDomainEnhancement
loadRndSettings(long) - Method in class ome.logic.PixelsImpl: Implemented as specified by the IPixels I/F.
loadRndSettings_async(AMD_IPixels_loadRndSettings, long, Current) - Method in class ome.services.blitz.impl.PixelsI
loadScripts(ServiceFactory, Parameters) - Method in class ome.services.scripts.ScriptFinder: Load all scripts that match the name, hash, and format for script
loadSpecifiedAnnotations(Class, Set<String>, Set<String>, Parameters) - Method in interface ome.api.IMetadata: Loads all the annotations of a given type.
loadSpecifiedAnnotations(Class, Set<String>, Set<String>, Parameters) - Method in class ome.logic.MetadataImpl: Implemented as specified by the IMetadata I/F
loadSpecifiedAnnotations_async(AMD_IMetadata_loadSpecifiedAnnotations, String, List<String>, List<String>, Parameters, Current) - Method in class ome.services.blitz.impl.MetadataI
loadSpecifiedAnnotationsLinkedTo(Class, Set<String>, Set<String>, Class, Set<Long>, Parameters) - Method in interface ome.api.IMetadata: Loads the annotations of a given type linked to the specified objects.
loadSpecifiedAnnotationsLinkedTo(Class, Set<String>, Set<String>, Class, Set<Long>, Parameters) - Method in class ome.logic.MetadataImpl: Implemented as specified by the IMetadata I/F
loadSpecifiedAnnotationsLinkedTo_async(AMD_IMetadata_loadSpecifiedAnnotationsLinkedTo, String, List<String>, List<String>, String, List<Long>, Parameters, Current) - Method in class ome.services.blitz.impl.MetadataI
loadTagContent(Set<Long>, Parameters) - Method in interface ome.api.IMetadata: Loads the Tag Set if the id is specified otherwise loads all the Tag Set.
loadTagContent(Set<Long>, Parameters) - Method in class ome.logic.MetadataImpl: Implemented as specified by the IMetadata I/F
loadTagContent_async(AMD_IMetadata_loadTagContent, List<Long>, Parameters, Current) - Method in class ome.services.blitz.impl.MetadataI
loadTagSets(Parameters) - Method in interface ome.api.IMetadata: Loads all the tag Sets.
loadTagSets(Parameters) - Method in class ome.logic.MetadataImpl: Implemented as specified by the IMetadata I/F
loadTagSets_async(AMD_IMetadata_loadTagSets, Parameters, Current) - Method in class ome.services.blitz.impl.MetadataI
local(AbstractRepositoryI, PublicRepositoryI, Current) - Method in class ome.services.blitz.repo.RawAccessRequestI: Method called locally to the repository during RawAccessRequestI.rawAccess().
LocalAdmin - Interface in ome.api.local: Provides local (internal) extensions for administration
LocalCompress - Interface in ome.api.local: Provides methods for performing scaling (change of the image size through interpolation or other means) on BufferedImages.
LocalConfig - Interface in ome.api.local: Provides local (internal) extensions for configuration.
LocalQuery - Interface in ome.api.local: Provides local (internal) extensions for querying
localQuery - Variable in class ome.logic.UpdateImpl
LocalShare - Interface in ome.api.local: Provides local (internal) extensions for shares
LocalUpdate - Interface in ome.api.local: Provides local (internal) extensions for updating
loci.ome.io - package loci.ome.io: OME I/O: a library for OME database import, upload and download.
loci.ome.io.services - package loci.ome.io.services
log - Variable in class ome.formats.importer.exclusions.AbstractFileExclusion
log - Variable in class ome.formats.importer.transfers.AbstractFileTransfer
log - Variable in class ome.formats.importer.util.ErrorHandler
log - Variable in class ome.security.auth.ConfigurablePasswordProvider
log - Variable in class ome.security.basic.AbstractSecurityFilter
log(String) - Method in class ome.security.basic.OmeroInterceptor
log - Variable in class ome.services.blitz.impl.AbstractAmdServant
log - Variable in class ome.services.blitz.redirect.AbstractRedirector
log - Static variable in class ome.services.delete.DeleteBean
log - Variable in class ome.services.eventlogs.EventLogFailure
log - Variable in class ome.services.eventlogs.EventLogLoader
log - Variable in class ome.services.fulltext.BridgeHelper
log(String) - Method in class ome.services.graphs.GraphEntry: Deprecated.

Similar to GraphEntry.toString() but used to
log - Variable in class ome.services.mail.MailSender
log - Variable in class ome.services.roi.GeomTool
log - Variable in class ome.services.roi.PixelData
log - Variable in class ome.services.scripts.ScriptFinder
log - Variable in class ome.services.scripts.ScriptRepoHelper
log - Static variable in class ome.services.sharing.ShareBean
log - Variable in class ome.services.sharing.ShareStore
log - Variable in class ome.services.throttling.AbstractThrottlingStrategy
log - Static variable in class ome.services.util.DBEnumCheck
log - Static variable in class ome.services.util.DBPatchCheck
log - Static variable in class ome.services.util.DBUserCheck
log - Static variable in class ome.services.util.JvmSettingsCheck
log - Static variable in class ome.services.util.NamespaceCheck
log - Static variable in class ome.services.util.ServerDirectoryCheck
log - Static variable in class ome.services.util.ServerVersionCheck
log(String) - Method in class ome.tools.hibernate.EventMethodInterceptor
log - Variable in class omero.util.ObjectFactoryRegistry
LOG_FILE_NS - Static variable in class pojos.FileAnnotationData: The name space used to indicate that the FileAnnotation is an import log file.
LOGARITHMIC - Static variable in class omeis.providers.re.quantum.QuantumFactory: Flag to select a logarithmic map for the quantization process.
LogarithmicMap - Class in omeis.providers.re.quantum: This class implements the QuantumMap interface.
LogarithmicMap() - Constructor for class omeis.providers.re.quantum.LogarithmicMap
LOGFILE - Static variable in class ome.formats.importer.util.IniFileLoader: Public in order to configure LogAppenderProxy, but then the value might as well be configured in the log4j.properties file
logFile - Variable in class ome.services.blitz.repo.ManagedImportLocationI
logFileId - Variable in class ome.formats.importer.ImportEvent.POST_UPLOAD_EVENT
logger() - Method in class ome.services.fulltext.BridgeHelper
LOGGER - Static variable in class ome.services.util.DBUnicodeUnitsCheck
LoggingImportMonitor - Class in ome.formats.importer.cli: Basic import process monitor that writes information to the log.
LoggingImportMonitor() - Constructor for class ome.formats.importer.cli.LoggingImportMonitor
login(Principal) - Method in class ome.security.basic.BasicSecuritySystem
login(Principal) - Method in class ome.security.basic.CurrentDetails
login(BasicEventContext) - Method in class ome.security.basic.CurrentDetails: Login method which can be used by the security system to replace the existing BasicEventContext.
login(Principal) - Method in interface ome.security.basic.PrincipalHolder: Add a new principal context to the stack.
login(BasicEventContext) - Method in interface ome.security.basic.PrincipalHolder: Allow logging in directly with an event context.
login(Principal) - Method in interface ome.security.SecuritySystem: stores this Principal instance in the current thread context for authenticating and authorizing all actions.
login(Principal) - Method in class ome.security.SecuritySystemHolder
login(Principal) - Method in class ome.security.sharing.SharingSecuritySystem
Login - Class in ome.system: Provides simplified handling of login properties when creating a ServiceFactory.
Login(String, String) - Constructor for class ome.system.Login: standard constructor which leaves OMERO_GROUP and OMERO_EVENT null.
Login(String, String, String, String) - Constructor for class ome.system.Login: extended constructor.
loginAttempt(String, Boolean) - Method in class ome.security.auth.ConfigurablePasswordProvider
LoginAttemptListener - Class in ome.security.auth: Listens for any LoginAttemptMessage.
LoginAttemptListener(int, long) - Constructor for class ome.security.auth.LoginAttemptListener
LoginAttemptMessage - Class in ome.services.messages: Published when any check is performed against a password.
LoginAttemptMessage(Object, String, Boolean) - Constructor for class ome.services.messages.LoginAttemptMessage
logout() - Method in class ome.formats.OMEROMetadataStoreClient: Destroys the sessionFactory and closes the client.
logout() - Method in class ome.security.basic.BasicSecuritySystem
logout() - Method in class ome.security.basic.CurrentDetails
logout() - Method in interface ome.security.basic.PrincipalHolder: Pop the last created principal context and return the number of active contexts remaining.
logout() - Method in interface ome.security.SecuritySystem: clears the top Principal instance from the current thread context.
logout() - Method in class ome.security.SecuritySystemHolder
logout() - Method in class ome.security.sharing.SharingSecuritySystem
logPhase(String) - Method in class ome.services.graphs.GraphStep: Deprecated.
logResults(int) - Method in class ome.services.graphs.GraphStep: Deprecated.
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
lookup() - Method in class ome.services.eventlogs.EventLogQueue
lookup(long) - Method in class ome.services.procs.ProcessorSkeleton
lookup(String, Parameters) - Method in class ome.services.query.ClassQuerySource
lookup(String, Parameters) - Method in class ome.services.query.NullQuerySource
lookup(String, Parameters) - Method in class ome.services.query.QueryFactory
lookup(String, Parameters) - Method in class ome.services.query.QuerySource: map the queryID argument to some Query instance (including null).
lookup(String, Parameters) - Method in class ome.services.query.StringQuerySource
lookup(String, ApplicationContext) - Method in class ome.system.OmeroContext.Locator: uses ContextSingletonBeanFactoryLocator.createDefinition(java.lang.String, java.lang.String) and ContextSingletonBeanFactoryLocator.initializeDefinition(org.springframework.beans.factory.BeanFactory) to create a new context from a given definition.
lookupClusterNodes() - Method in class ome.services.blitz.fire.Registry.Impl
lookupClusterNodes() - Method in interface ome.services.blitz.fire.Registry: Returns all found cluster nodes or null if something goes wrong during lookup (null QueryPrx for example)
lookupExperimenter(String) - Method in interface ome.api.IAdmin: look up an Experimenter and all related groups by name.
lookupExperimenter(String) - Method in class ome.logic.AdminImpl
lookupExperimenter_async(AMD_IAdmin_lookupExperimenter, String, Current) - Method in class ome.services.blitz.impl.AdminI
lookupExperimenters() - Method in interface ome.api.IAdmin: Looks up all experimenters present and all related groups.
lookupExperimenters() - Method in class ome.logic.AdminImpl
lookupExperimenters_async(AMD_IAdmin_lookupExperimenters, Current) - Method in class ome.services.blitz.impl.AdminI
lookupGroup(String) - Method in interface ome.api.IAdmin: look up an ExperimenterGroup and all contained users by name.
lookupGroup(String) - Method in class ome.logic.AdminImpl
lookupGroup_async(AMD_IAdmin_lookupGroup, String, Current) - Method in class ome.services.blitz.impl.AdminI
lookupGroups() - Method in interface ome.api.IAdmin: Looks up all groups present and all related experimenters.
lookupGroups() - Method in class ome.logic.AdminImpl
lookupGroups_async(AMD_IAdmin_lookupGroups, Current) - Method in class ome.services.blitz.impl.AdminI
lookupLdapAuthExperimenter(long) - Method in interface ome.api.IAdmin: Looks up experimenters who uses LDAP authentication (has set dn on password table).
lookupLdapAuthExperimenter(long) - Method in class ome.logic.AdminImpl
lookupLdapAuthExperimenter(Long) - Method in class ome.logic.LdapImpl: Queries the LDAP server and returns the DN for the specified OMERO user ID.
lookupLdapAuthExperimenter_async(AMD_IAdmin_lookupLdapAuthExperimenter, long, Current) - Method in class ome.services.blitz.impl.AdminI
lookupLdapAuthExperimenters() - Method in interface ome.api.IAdmin: Looks up all id of experimenters who uses LDAP authentication (has set dn on password table).
lookupLdapAuthExperimenters() - Method in class ome.logic.AdminImpl
lookupLdapAuthExperimenters() - Method in class ome.logic.LdapImpl: Queries the LDAP server and returns the DN for all OMERO users that have the ldap flag enabled.
lookupLdapAuthExperimenters_async(AMD_IAdmin_lookupLdapAuthExperimenters, Current) - Method in class ome.services.blitz.impl.AdminI
lookupManagedRepository() - Method in class ome.formats.importer.ImportLibrary: Retrieves the first managed repository from the list of current active repositories.
lookupMonitorServers() - Method in class ome.services.blitz.fire.Registry.Impl
lookupMonitorServers() - Method in interface ome.services.blitz.fire.Registry
lookupPixels(long) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
lookupPixels(long) - Method in interface omeis.providers.re.RenderingEngine: Loads the Pixels set this Rendering Engine is for.
lookupPixels_async(AMD_RenderingEngine_lookupPixels, long, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
lookupProcessors() - Method in class ome.services.blitz.fire.Registry.Impl
lookupProcessors() - Method in interface ome.services.blitz.fire.Registry
lookupRenderingDef(long) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
lookupRenderingDef(long) - Method in interface omeis.providers.re.RenderingEngine: Loads the rendering settings associated to the specified pixels set.
lookupRenderingDef_async(AMD_RenderingEngine_lookupRenderingDef, long, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
lookupRepositories() - Method in class ome.services.blitz.fire.Registry.Impl
lookupRepositories() - Method in interface ome.services.blitz.fire.Registry
lookupSymbol(UnitsElectricPotential) - Static method in class omero.model.ElectricPotentialI
lookupSymbol(UnitsFrequency) - Static method in class omero.model.FrequencyI
lookupSymbol(UnitsLength) - Static method in class omero.model.LengthI
lookupSymbol(UnitsPower) - Static method in class omero.model.PowerI
lookupSymbol(UnitsPressure) - Static method in class omero.model.PressureI
lookupSymbol(UnitsTemperature) - Static method in class omero.model.TemperatureI
lookupSymbol(UnitsTime) - Static method in class omero.model.TimeI
lookupTables() - Method in class ome.services.blitz.fire.Registry.Impl
lookupTables() - Method in interface ome.services.blitz.fire.Registry
loop(int, long) - Method in class omero.cmd.CmdCallbackI: Calls block(long) "loops" number of times with the "ms" argument.
loop - Variable in class omero.util.RPSTileData
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
LuceneQueryBuilder - Class in ome.util.search: Utility class for building lucene queries

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

will be transformed to this lucene expression:
name:a description:a name:f description:f ((name:b description:b) AND (name:c description:c) AND (name:d description:d))
LuceneQueryBuilder() - Constructor for class ome.util.search.LuceneQueryBuilder

M

mailSender - Variable in class ome.logic.AdminImpl
MailSender - Class in ome.services.mail: Basic bean with setter injection that can be used as a base class for other senders.
MailSender() - Constructor for class ome.services.mail.MailSender
mailSender - Variable in class ome.services.mail.MailUtil
MailUtil - Class in ome.services.mail: Methods for dealing with the preparation of JavaMail MIME messages.
MailUtil(String, JavaMailSender) - Constructor for class ome.services.mail.MailUtil
mailUtil - Variable in class ome.services.sharing.ShareBean
main(String[]) - Static method in class loci.ome.io.OmeroReader: A simple command line tool for downloading images from OMERO.
main(String[]) - Static method in class ome.formats.importer.cli.CommandLineImporter: Command line application entry point which parses CLI arguments and passes them into the importer.
main(String[]) - Static method in class ome.security.auth.PasswordUtil: Main method which takes exactly one argument, passes it to PasswordUtil.preparePassword(String) and prints the results on System.out.
main(String[]) - Static method in class ome.services.blitz.Entry: Entry point to the server.
main(String[]) - Static method in class ome.services.blitz.Status: Uses the passed args to create an Communicator.
Main - Class in ome.services.fulltext: Commandline entry-point for various full text actions.
Main() - Constructor for class ome.services.fulltext.Main
main(String[]) - Static method in class ome.services.fulltext.Main
main(String[]) - Static method in class ome.services.graphs.GraphPathReport: Generate a Sphinx report of OMERO Hibernate entities.
main(String[]) - Static method in class ome.services.sharing.BlobShareStore
main(String[]) - Static method in class ome.services.util.JvmSettingsCheck
main(String[]) - Static method in class ome.tools.FileSystem
main(String[]) - Static method in class omero.cmd.fs.OriginalMetadataRequestI
main(String[]) - Static method in class omero.util.TempFileManager: Command-line interface to the global TempFileManager instance ( #manger).
main(String[]) - Static method in class prefs: Entry point to the prefs command line too.
makeAdjustedCurrent(Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
makeCheckedDirs(LinkedList<CheckedPath>, boolean, Session, ServiceFactory, SqlAction, EventContext) - Method in class ome.services.blitz.repo.ManagedRepositoryI: Checks for the top-level user directory restriction before calling PublicRepositoryI#makeCheckedDirs(LinkedList, boolean, Current)
makeCheckedDirs(LinkedList<CheckedPath>, boolean, Session, ServiceFactory, SqlAction, EventContext) - Method in class ome.services.blitz.repo.PublicRepositoryI: Internal method to be used by subclasses to perform any extra checks on the listed of CheckedPath instances before allowing the creation of directories.
makeDir(String, boolean, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI: Create a nested path in the repository.
makeDir(CheckedPath, boolean, Session, ServiceFactory, SqlAction, EventContext) - Method in class ome.services.blitz.repo.PublicRepositoryI
makeDirs(PublicRepositoryI, List<CheckedPath>, boolean, Current) - Method in interface ome.services.blitz.repo.RepositoryDao: Create a number of directories in a single transaction, using the PublicRepositoryI instance as a callback for implementation specific logic.
makeDirs(PublicRepositoryI, List<CheckedPath>, boolean, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
makeElectricPotential(double, Unit<ElectricPotential>) - Static method in class ome.formats.model.UnitsFactory
makeElectricPotential(double, UnitsElectricPotential) - Static method in class ome.formats.model.UnitsFactory
makeElectricPotentialUnitXML(String) - Static method in class ome.formats.model.UnitsFactory
makeElectricPotentialXML(double, String) - Static method in class ome.formats.model.UnitsFactory
makeFactory(client) - Static method in class omero.model.DetailsI
makeFactory(client) - Static method in class omero.model.ElectricPotentialI
makeFactory(client) - Static method in class omero.model.FrequencyI
makeFactory(client) - Static method in class omero.model.LengthI
makeFactory(client) - Static method in class omero.model.PowerI
makeFactory(client) - Static method in class omero.model.PressureI
makeFactory(client) - Static method in class omero.model.TemperatureI
makeFactory(client) - Static method in class omero.model.TimeI
makeFrequency(double, Unit<Frequency>) - Static method in class ome.formats.model.UnitsFactory
makeFrequency(double, UnitsFrequency) - Static method in class ome.formats.model.UnitsFactory
makeFrequencyUnitXML(String) - Static method in class ome.formats.model.UnitsFactory
makeFrequencyXML(double, String) - Static method in class ome.formats.model.UnitsFactory
makeLength(double, Unit<Length>) - Static method in class ome.formats.model.UnitsFactory
makeLength(double, UnitsLength) - Static method in class ome.formats.model.UnitsFactory
makeLengthUnitXML(String) - Static method in class ome.formats.model.UnitsFactory
makeLengthXML(double, String) - Static method in class ome.formats.model.UnitsFactory
makeNew(int) - Method in class ome.util.mem.CopiableArray: Creates a new array of the speficied size.
MakeNextDirectory - Class in ome.services.blitz.repo.path: Abstracts a pattern for using repository template path directories in {@link ManagedRepositoryI.TemplateDirectoryCreator): pinpoint the next directory to use, then try to use it while watching for conflicts from other similar threads.
MakeNextDirectory() - Constructor for class ome.services.blitz.repo.path.MakeNextDirectory
MakePathComponentSafe - Class in ome.services.blitz.repo.path
MakePathComponentSafe(FilePathRestrictions...) - Constructor for class ome.services.blitz.repo.path.MakePathComponentSafe
makePower(double, Unit<Power>) - Static method in class ome.formats.model.UnitsFactory
makePower(double, UnitsPower) - Static method in class ome.formats.model.UnitsFactory
makePowerUnitXML(String) - Static method in class ome.formats.model.UnitsFactory
makePowerXML(double, String) - Static method in class ome.formats.model.UnitsFactory
makePressure(double, Unit<Pressure>) - Static method in class ome.formats.model.UnitsFactory
makePressure(double, UnitsPressure) - Static method in class ome.formats.model.UnitsFactory
makePressureUnitXML(String) - Static method in class ome.formats.model.UnitsFactory
makePressureXML(double, String) - Static method in class ome.formats.model.UnitsFactory
makePyramid(Pixels) - Method in class ome.io.nio.PixelsService: Creates a pixels pyramid for a given set of pixels.
makeTemperature(double, Unit<Temperature>) - Static method in class ome.formats.model.UnitsFactory
makeTemperature(double, UnitsTemperature) - Static method in class ome.formats.model.UnitsFactory
makeTemperatureUnitXML(String) - Static method in class ome.formats.model.UnitsFactory
makeTemperatureXML(double, String) - Static method in class ome.formats.model.UnitsFactory
makeTime(double, Unit<Time>) - Static method in class ome.formats.model.UnitsFactory
makeTime(double, UnitsTime) - Static method in class ome.formats.model.UnitsFactory
makeTimeUnitXML(String) - Static method in class ome.formats.model.UnitsFactory
makeTimeXML(double, String) - Static method in class ome.formats.model.UnitsFactory
makeXMLQuantity(double, String) - Static method in class omero.model.ElectricPotentialI
makeXMLQuantity(double, String) - Static method in class omero.model.FrequencyI
makeXMLQuantity(double, String) - Static method in class omero.model.LengthI
makeXMLQuantity(double, String) - Static method in class omero.model.PowerI
makeXMLQuantity(double, String) - Static method in class omero.model.PressureI
makeXMLQuantity(double, String) - Static method in class omero.model.TemperatureI
makeXMLQuantity(double, String) - Static method in class omero.model.TimeI
makeXMLUnit(String) - Static method in class omero.model.ElectricPotentialI
makeXMLUnit(String) - Static method in class omero.model.FrequencyI
makeXMLUnit(String) - Static method in class omero.model.LengthI
makeXMLUnit(String) - Static method in class omero.model.PowerI
makeXMLUnit(String) - Static method in class omero.model.PressureI
makeXMLUnit(String) - Static method in class omero.model.TemperatureI
makeXMLUnit(String) - Static method in class omero.model.TimeI
MANAGED_CONTEXT - Static variable in class ome.system.OmeroContext: identifier for an OmeroContext configured in classpath*:beanRefContext.xml for use by server-side processes.
managedEvent(boolean, IObject, Details, Details, Details) - Method in class ome.security.basic.OmeroInterceptor
managedExternalInfo(boolean, IObject, Details, Details, Details) - Method in class ome.security.basic.OmeroInterceptor: responsible for guaranteeing that external info is not modified by any users, including rot.
managedGroup(boolean, IObject, Details, Details, Details, BasicEventContext) - Method in class ome.security.basic.OmeroInterceptor
ManagedImportLocationI - Class in ome.services.blitz.repo: Server-side implementation of ImportLocation for also storing the CheckedPath instances for each used file.
ManagedImportLocationI() - Constructor for class ome.services.blitz.repo.ManagedImportLocationI
ManagedImportProcessI - Class in ome.services.blitz.repo: Represents a single import within a defined-session all running server-side.
ManagedImportProcessI(ManagedRepositoryI, Fileset, ImportLocation, ImportSettings, Current) - Constructor for class ome.services.blitz.repo.ManagedImportProcessI: Create and register a servant for servicing the import process within a managed repository.
ManagedImportRequestI - Class in ome.services.blitz.repo: Wrapper around FilesetJobLink instances which need to be handled on the server-side.
ManagedImportRequestI(Registry, TileSizes, RepositoryDao, OMEROWrapper, String) - Constructor for class ome.services.blitz.repo.ManagedImportRequestI
managedOwner(boolean, IObject, Details, Details, Details, BasicEventContext) - Method in class ome.security.basic.OmeroInterceptor
ManagedRepositoryI - Class in ome.services.blitz.repo: Extension of the PublicRepository API which only manages files under ${omero.data.dir}/ManagedRepository.
ManagedRepositoryI(String, RepositoryDao) - Constructor for class ome.services.blitz.repo.ManagedRepositoryI: Creates a ProcessContainer internally that will not be managed by background threads.
ManagedRepositoryI(String, RepositoryDao, ProcessContainer, ChecksumProviderFactory, String, String, String, Roles) - Constructor for class ome.services.blitz.repo.ManagedRepositoryI
ManagedServiceFactory - Class in ome.tools.spring: subclass of ome.system.ServiceFactory which retrieves managed service-instances.
ManagedServiceFactory() - Constructor for class ome.tools.spring.ManagedServiceFactory
ManageImageBinariesI - Class in omero.cmd.fs: Workflow for converting attached original images into OMERO5+ filesets.
ManageImageBinariesI(PixelsService, ACLVoter) - Constructor for class omero.cmd.fs.ManageImageBinariesI
manager - Variable in class ome.services.util.ExecutionThread
manager - Variable in class omero.cmd.admin.CurrentSessionsRequestI
manager - Variable in class omero.cmd.admin.UpdateSessionTimeoutRequestI
managerOrNull() - Method in class ome.services.blitz.fire.TopicManager.Impl
ManualFlushHibernateTemplate - Class in ome.tools.spring
ManualFlushHibernateTemplate() - Constructor for class ome.tools.spring.ManualFlushHibernateTemplate
map() - Method in class ome.formats.importer.ImportConfig
map(List<String>) - Method in class ome.services.blitz.impl.MetadataI
map(String) - Method in class ome.services.blitz.impl.MetadataI
map(Map<String, List<Long>>) - Method in class ome.services.sharing.ShareBean
map() - Method in class omero.sys.ParametersI: Deprecated.
map(Filterable[]) - Method in class omero.util.IceMapper
MapAnnotationData - Class in pojos
MapAnnotationData(MapAnnotation) - Constructor for class pojos.MapAnnotationData
MapAnnotationData() - Constructor for class pojos.MapAnnotationData
MapAnnotationSubethaListener - Class in ome.services.mail: Basic SimpleMessageListener which stores all received emails as MapAnnotation instances belong to root with the namespace MapAnnotationSubethaListener.NAMESPACE.
MapAnnotationSubethaListener(Executor, Principal) - Constructor for class ome.services.mail.MapAnnotationSubethaListener
MapAnnotationSubethaListener(Executor, String) - Constructor for class ome.services.mail.MapAnnotationSubethaListener
mapFlexServer(String, String) - Method in class ome.formats.importer.util.IniFileLoader: Append keep to server map
mapFromAttributes(Attributes) - Method in class ome.security.auth.GroupAttributeMapper
mapFromContext(Object) - Method in class ome.security.auth.GroupContextMapper
mapFromContext(Object) - Method in class ome.security.auth.OmeroModelContextMapper
mapFromContext(Object) - Method in class ome.security.auth.PersonContextMapper
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
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.
markModified() - Method in class ome.services.blitz.repo.CheckedPath: Mark this existing file as having been modified at the present moment.
MaskData - Class in pojos: Represents an Mask in the Euclidean space R².
MaskData(Shape) - Constructor for class pojos.MaskData: Creates a new instance.
MaskData() - Constructor for class pojos.MaskData: Creates a new instance of MaskData.
MaskData(double, double, double, double, byte[]) - Constructor for class pojos.MaskData: Creates a new instance of the MaskData.
matches(Class, Class) - Static method in class ome.services.blitz.util.ApiConsistencyCheck: Defines what Class types match.
matches(String, String) - Method in class ome.services.messages.EventLogsMessage
matches(File) - Method in class ome.services.scripts.RepoFile
MAX - Static variable in class omeis.providers.re.quantum.QuantumStrategy: Maximum value (255) allowed for the upper bound of the codomain interval.
MAX_CHANNELS - Static variable in class omeis.providers.re.Renderer: The maximum number of channels.
maxFileSize - Variable in class ome.services.fulltext.FileParser
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
mayHaveMapProperties(Class<? extends IObject>) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
mayHaveMapProperties(Class<? extends IObject>) - Method in interface ome.tools.hibernate.ExtendedMetadata: Check if an object of this class may have map properties.
MD5ChecksumProviderImpl - Class in ome.util.checksum: An implementation of the ChecksumProvider interface using MD5 as the message digest algorithm.
MD5ChecksumProviderImpl() - Constructor for class ome.util.checksum.MD5ChecksumProviderImpl
MEAN_INTENSITY - Static variable in interface ome.api.IProjection: Mean intensity projection
MEASUREMENT_NS - Static variable in class pojos.FileAnnotationData: The name space used to indicate that the FileAnnotation is a Measurement file.
MeasurementStore - Class in ome.services.blitz.measurements: Parser API implementation for storing result measurements from SPW companion files as ROIs and OMERO.tables.
MeasurementStore(LocalUpdate, TablePrx) - Constructor for class ome.services.blitz.measurements.MeasurementStore
member_of_groups - Static variable in class ome.security.basic.AllGroupsSecurityFilter
memberOfGroups - Variable in class ome.system.SimpleEventContext
MEMOIZER_WAIT - Static variable in class ome.io.nio.PixelsService: Default of 100 ms for PixelsService.memoizerWait
memoizerDirectory - Variable in class ome.io.nio.PixelsService: Location where cached data from the Memoizer should be stored.
memoizerWait - Variable in class ome.io.nio.PixelsService: Time in ms. which setId must take before a file is memoized
MERGE_EVENT - Static variable in class ome.security.basic.MergeEventListener
mergedBatches - Variable in class ome.services.search.SearchValues
MergeEventListener - Class in ome.security.basic: responsible for responding to merge events. in particular in load/re-loading certain types to make use by clients easier.
MergeEventListener(CurrentDetails, TokenHolder) - Constructor for class ome.security.basic.MergeEventListener: main constructor.
message - Variable in exception ome.io.nio.PixelBufferException
message - Variable in 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
Metrics - Interface in ome.system.metrics: Thin-interface around com.codahale.metrics.Metrics.
MIDDLENAME - Static variable in class pojos.ExperimenterData: Identifies the Experimenter#MIDDLENAME field.
mime - Variable in class ome.services.blitz.repo.CheckedPath
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
MissingStatsInfoMessage - Class in ome.io.messages: Published when an request is made for a pixels pyramid when the file does not yet contain channel statistics.
MissingStatsInfoMessage(Object, long) - Constructor for class ome.io.messages.MissingStatsInfoMessage
mkdir() - Method in class ome.services.blitz.repo.CheckedPath: Create this directory on the underlying filesystem.
mkdirs() - Method in class ome.services.blitz.repo.CheckedPath: Create this directory, and parents if necessary, on the underlying filesystem.
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.
ModelObjectSequencer - Class in ome.services.graphs: OMERO model objects sometimes must be processed in a specific order.
ModelObjectSequencer() - Constructor for class ome.services.graphs.ModelObjectSequencer
ModelProcessor - Interface in ome.formats.model: An object which performs post-processing on an IObjectContainerStore.
modificationCheck() - Method in class ome.services.scripts.ScriptRepoHelper: Checks if
modified - Variable in class ome.services.AbstractStatefulBean: True if any write operation took place on this bean.
modified() - Method in class ome.services.AbstractStatefulBean
modifiedStart - Variable in class ome.services.search.SearchValues
modifiedStop - Variable in class ome.services.search.SearchValues
MODULO_NS - Static variable in class pojos.XMLAnnotationData: The name space used to identify modulo concept.
more() - Method in class ome.services.eventlogs.AllEntitiesPseudoLogLoader: Returns the number of classes which are still unprocessed as a proxy for how much is left to process.
more() - Method in class ome.services.eventlogs.AllEventsLogLoader
more() - Method in class ome.services.eventlogs.EventLogLoader: Should return an estimate of how many more EventLog instances are available for processing.
more() - Method in class ome.services.eventlogs.EventLogQueue: In general, EventLogQueue will intend to use much larger batch sizes, and so further loops should likely not be attempted.
more() - Method in class ome.services.eventlogs.PersistentEventLogLoader
MoveFileTransfer - Class in ome.formats.importer.transfers: Local-only file transfer mechanism which makes use of hard-linking followed by the deletion of the original source file.
MoveFileTransfer() - Constructor for class ome.formats.importer.transfers.MoveFileTransfer
moveToCommonSpace(IObject...) - Method in interface ome.api.IAdmin: Moves the given objects into the "user" group to make them visible and linkable from all security contexts.
moveToCommonSpace(IObject...) - Method in class ome.logic.AdminImpl
moveToCommonSpace_async(AMD_IAdmin_moveToCommonSpace, List<IObject>, Current) - Method in class ome.services.blitz.impl.AdminI
MOVIE_MPEG_NS - Static variable in interface ome.api.IMetadata: The name space used to indicate that the FileAnnotation is an MPEG file.
MOVIE_NS - Static variable in class pojos.FileAnnotationData: The name space used to indicate that the FileAnnotation is a movie.
MOVIE_QT_NS - Static variable in interface ome.api.IMetadata: The name space used to indicate that the FileAnnotation is an QT file.
MOVIE_WMV_NS - Static variable in interface ome.api.IMetadata: The name space used to indicate that the FileAnnotation is an WMV file.
MS_EXCEL - Static variable in class pojos.FileAnnotationData: Identifies the Excel file formats.
MS_POWER_POINT - Static variable in class pojos.FileAnnotationData: Identifies the Power point file formats.
MS_POWER_POINT_SHOW - Static variable in class pojos.FileAnnotationData: Identifies the Power point file formats.
MS_POWER_POINT_X - Static variable in class pojos.FileAnnotationData: Identifies the Power point file formats.
MS_WORD - Static variable in class pojos.FileAnnotationData: Identifies the Word file formats.
MS_WORD_X - Static variable in class pojos.FileAnnotationData: Identifies the Word file formats.
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.
Murmur128ChecksumProviderImpl - Class in ome.util.checksum: An implementation of the ChecksumProvider interface using Murmur3_128 as the hash algorithm.
Murmur128ChecksumProviderImpl() - Constructor for class ome.util.checksum.Murmur128ChecksumProviderImpl
Murmur32ChecksumProviderImpl - Class in ome.util.checksum: An implementation of the ChecksumProvider interface using Murmur3_32 as the hash algorithm.
Murmur32ChecksumProviderImpl() - Constructor for class ome.util.checksum.Murmur32ChecksumProviderImpl
mustEdit() - Method in class ome.services.blitz.repo.CheckedPath
mustExist() - Method in class ome.services.blitz.repo.CheckedPath: Checks for existence of the original path, throwing an exception if not present.
mutex - Variable in class ome.system.SessionInitializer
MySeqGenerator - Class in ome.tools.hibernate: http://www.hibernate.org/296.html
MySeqGenerator() - Constructor for class ome.tools.hibernate.MySeqGenerator

N

NAME - Static variable in class ome.security.policy.BinaryAccessPolicy: This string can also be found in the Constants.ice file in the blitz package.
name - Variable in enum ome.services.blitz.repo.path.FilePathRestrictionInstance
name - Variable in class ome.services.query.QueryParameterDef: name of this parameter.
name - Variable in class ome.services.scripts.RepoFile.FsFile
name - Variable in class ome.system.Principal
NAME - 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
NAMESPACE - Static variable in class ome.services.mail.MapAnnotationSubethaListener
NamespaceCheck - Class in ome.services.util: Hook run by the context.
NamespaceCheck(Executor, String, Roles) - Constructor for class ome.services.util.NamespaceCheck
neededRight(Class<?>, Class<?>) - Method in class ome.security.basic.OmeroInterceptor: The default right need for a linkage is WRITE If however, this is only an annotation or only a viewing, then less permission is needed.
needsInit() - Method in class ome.services.blitz.repo.FileMaker
needsSanityCheck() - Method in class ome.logic.RepositoryInfoImpl: Calculates based on the cached usage and the elapsed time whether or not a real RepositoryInfoImpl.sanityCheckRepository() should be calculated.
newBlueColor() - Static method in class ome.formats.model.ColorsFactory: Creates a new Blue Color object.
newBlueColor() - Static method in class omeis.providers.re.ColorsFactory: Creates a new Blue Color object.
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.
newOMEROReader() - Method in interface loci.ome.io.services.OMEReaderWriterService: Creates a new OMERO IFormatReader implementation.
newOMEROReader() - Method in class loci.ome.io.services.OMEReaderWriterServiceImpl
newOMEROWriter() - Method in class loci.ome.io.services.OMEReaderWriterServiceImpl
newRedColor() - Static method in class ome.formats.model.ColorsFactory: Creates a new Red Color object.
newRedColor() - Static method in class omeis.providers.re.ColorsFactory: Creates a new Red Color object.
newTable(long, String, Current) - Method in class ome.services.blitz.impl.SharedResourcesI
newTransientDetails(IObject) - Method in class ome.security.basic.BasicSecuritySystem
newTransientDetails(IObject) - Method in class ome.security.basic.OmeroInterceptor
newTransientDetails(IObject, Details) - Method in class ome.security.basic.OmeroInterceptor: Like OmeroInterceptor.newTransientDetails(IObject) but allows passing in a newDetails object with possibly pre-set values.
newTransientDetails(IObject) - Method in interface ome.security.SecuritySystem: creates a new secure details for transient entities.
newTransientDetails(IObject) - Method in class ome.security.SecuritySystemHolder
newTransientDetails(IObject) - Method in class ome.security.sharing.SharingSecuritySystem
NewUserGroupBean - Interface in ome.security.auth: Strategy for finding the appropriate groups for a given user in LDAP.
NewUserGroupOwnerBean - Interface in ome.security.auth: Strategy for finding the appropriate group owners for a given user in LDAP.
newWhiteColor() - Static method in class ome.formats.model.ColorsFactory: Creates a new White Color object.
newWhiteColor() - Static method in class omeis.providers.re.ColorsFactory: Creates a new White Color object.
next() - Method in interface ome.api.Search: Returns the next entity from the current query.
next() - Method in class ome.services.eventlogs.EventLogLoader: Returns the current EventLogLoader.log instance which may be loaded by a call to EventLogLoader.hasNext() if necessary.
next() - Method in class ome.services.eventlogs.EventLogQueue: Return a wrapped version of Data#next() which could possibly be null.
next() - Method in class ome.services.graphs.BaseGraphSpec.SubSpecIterator: Deprecated.
next() - Method in class ome.services.SearchBean
next_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.
noStatsInfo - Variable in class ome.formats.importer.ImportConfig
not() - Method in interface ome.api.Search: Applies the next by* method to the previous by* method, so that a call Search.hasNext(), Search.next(), or Search.results() sees only the intersection of the two calls.
not() - Method in class ome.services.SearchBean
not_async(AMD_Search_not, Current) - Method in class ome.services.blitz.impl.SearchI
notAnnotatedBy(Details) - Method in interface ome.api.Search: Restricts entities by who has not annotated them with an Annotation matching the other filters.
notAnnotatedBy - Variable in class ome.services.search.SearchValues
notAnnotatedBy(Details) - Method in class ome.services.SearchBean
notAnnotatedBy_async(AMD_Search_notAnnotatedBy, Details, Current) - Method in class ome.services.blitz.impl.SearchI
noteDetails(Session, IObject, String, long) - Method in class ome.services.graphs.GraphPolicy: Any model object about which policy may be asked is first passed to #noteDetails(IObject, String, long) before #review(Map, Details, Map, Set).
noteDetails(Session, IObject, String, long) - Method in class omero.cmd.graphs.BaseGraphPolicyAdjuster
notifications(String) - Method in class ome.services.sessions.SessionManagerImpl
notifyCallbacks() - Method in class omero.cmd.HandleI: Calls the proper notification on all callbacks based on the current HandleI.state.
notifyElementEvicted(Ehcache, Element) - Method in class ome.services.sessions.state.CacheListener
notifyElementExpired(Ehcache, Element) - Method in class ome.services.sessions.state.CacheListener
notifyElementPut(Ehcache, Element) - Method in class ome.services.sessions.state.CacheListener
notifyElementRemoved(Ehcache, Element) - Method in class ome.services.sessions.state.CacheListener
notifyElementUpdated(Ehcache, Element) - Method in class ome.services.sessions.state.CacheListener
notifyMembersOfShare(long, String, String, boolean) - Method in interface ome.api.IShare: Notify via email selected members of share.
notifyMembersOfShare(long, String, String, boolean) - Method in class ome.services.sharing.ShareBean
notifyMembersOfShare_async(AMD_IShare_notifyMembersOfShare, long, String, String, boolean, Current) - Method in class ome.services.blitz.impl.ShareI
notifyObservers(ImportEvent) - Method in class ome.formats.importer.ImportLibrary
notifyObservers(ImportEvent) - Method in interface ome.formats.importer.IObservable: Notify observers of event
notifyObservers(ImportEvent) - Method in class ome.formats.importer.util.ClientKeepAlive
notifyObservers(ImportEvent) - Method in class ome.formats.importer.util.ErrorHandler
notifyObservers(ImportEvent) - Method in class ome.formats.importer.util.FileUploader
notifyRemoveAll(Ehcache) - Method in class ome.services.sessions.state.CacheListener
NotNull - Annotation Type in ome.annotations: annotation used for determining the types of a Set
notNull(String[]) - Static method in class prefs: Returns an empty array if the argument is null.
notNullOrLikeOrEqual(QueryBuilder, String, Class, Object, boolean, boolean) - Static method in class ome.services.search.SearchAction
notNullOrLikeOrEqual(String, Class, Object, boolean, boolean) - Static method in class ome.services.search.SearchAction
notOwnedBy(Details) - Method in interface ome.api.Search: Uses the Details.getOwner() and Details.getGroup() information to restrict the entities which will be returned.
notOwnedBy - Variable in class ome.services.search.SearchValues
notOwnedBy(Details) - Method in class ome.services.SearchBean
notOwnedBy_async(AMD_Search_notOwnedBy, Details, Current) - Method in class ome.services.blitz.impl.SearchI
noUnique() - Method in class omero.sys.ParametersI
NS_CLIENT_CREATED - Static variable in class pojos.MapAnnotationData: The name space used to identify MapAnnotations created be the user
NS_COMMENT - Static variable in class ome.services.sharing.ShareBean
NS_ENABLED - Static variable in class ome.services.sharing.ShareBean
NS_IMPORTER_ARCHIVED - Static variable in interface ome.api.IMetadata: The name space indicating that the Boolean annotation indicated if an archived image is imported with the image.
NS_INSIGHT_RATING - Static variable in interface ome.api.IMetadata: The name space indicating that the Long annotation is a rating annotation i.e. an integer in the interval [0, 5].
NS_INSIGHT_TAG_SET - Static variable in interface ome.api.IMetadata: The name space indicating that the tag is used a tag set.
nsExcludes - Static variable in class ome.services.graphs.AnnotationGraphSpec: Deprecated.

Collection of namespace values (defined as AnnotationGraphSpec.nsIncludes) which will be omitted from processing by default.
NSEXPERIMENTERPHOTO - Static variable in class ome.logic.AdminImpl
nsIncludes - Static variable in class ome.services.graphs.AnnotationGraphSpec: Deprecated.

Collection of namespace values (or LIKE values if they contain '%' or '?')
NULL_PLANE_SIZE - Static variable in class ome.io.nio.PixelsService: Null plane size constant.
NULL_RENDERER - Static variable in class ome.services.RenderingBean: Message if the rendering engine is not ready.
nullDetails() - Method in class pojos.DataObject: Returns true if the details are null otherwise false otherwise.
NullEventHandler - Class in ome.security.basic: Provides only the bare minimum of functionality to allow methods to succeed.
NullEventHandler(SecuritySystem, SessionFactory) - Constructor for class ome.security.basic.NullEventHandler
NullGraphTraversalProcessor - Class in omero.cmd.graphs: A GraphTraversal.Processor that does nothing whatsoever.
NullGraphTraversalProcessor(Set<GraphPolicy.Ability>) - Constructor for class omero.cmd.graphs.NullGraphTraversalProcessor: Construct a GraphTraversal.Processor that does nothing whatsoever.
NullMetrics - Class in ome.system.metrics: No-op version of Metrics
NullMetrics() - Constructor for class ome.system.metrics.NullMetrics
nullPlane - Static variable in class ome.io.nio.PixelsService: Null plane byte array.
nullProperties(String, String, Collection<Long>) - Method in interface ome.services.graphs.GraphTraversal.Processor: Null the given property of the indicated instances.
nullProperties(String, String, Collection<Long>) - Method in class omero.cmd.graphs.BaseGraphTraversalProcessor
nullProperties(String, String, Collection<Long>) - Method in class omero.cmd.graphs.NullGraphTraversalProcessor
NullQuerySource - Class in ome.services.query: always returns null for any id.
NullQuerySource() - Constructor for class ome.services.query.NullQuerySource
NullRedirector - Class in ome.services.blitz.redirect: Redirector implementation to effectively disable redirects.
NullRedirector() - Constructor for class ome.services.blitz.redirect.NullRedirector
nullSafe(Integer) - Method in class pojos.DataObject
nullSafe(RInt) - Method in class pojos.DataObject
nullSafe(Long) - Method in class pojos.DataObject
nullSafe(Double) - Method in class pojos.DataObject
nullSafe(Float) - Method in class pojos.DataObject
nullSafe(RFloat) - Method in class pojos.DataObject
nullSafe(RDouble) - Method in class pojos.DataObject
nullSafe(Length) - Method in class pojos.DataObject
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
numThreads - Variable in class ome.services.pixeldata.PersistentEventLogLoader

O

OBJECT_TO_RTYPE - Static variable in class omero.util.IceMapper
OBJECTARRAY_TO_RTYPESEQ - Static variable in class omero.util.IceMapper
ObjectFactoryRegistry - Class in omero.util: SPI type picked up from the Spring configuration and given a chance to register all its ObjectFactory instances with the Communicator.
ObjectFactoryRegistry() - Constructor for class omero.util.ObjectFactoryRegistry
ObjectFactoryRegistry.ObjectFactory - Class in omero.util
ObjectFactoryRegistry.ObjectFactory(String) - Constructor for class omero.util.ObjectFactoryRegistry.ObjectFactory
Objective_WorkingDistance - Static variable in class ome.formats.model.UnitsFactory
ObjectiveData - Class in pojos: Hosts an objective used to capture an image.
ObjectiveData(Objective) - Constructor for class pojos.ObjectiveData: Creates a new instance.
ObjectMailSender - Class in ome.services.mail: When an EventLogMessage of the specified type and kind is received, an email is sent to all users which are returned by a given query.
ObjectMailSender() - Constructor for class ome.services.mail.ObjectMailSender
objects - Variable in class ome.formats.importer.ImportEvent.IMPORT_DONE
objects - Variable in class ome.services.messages.ReindexMessage
ObjectsReadCounter - Class in ome.services.sessions.stats: Counter for all the objects read in a session.
ObjectsReadCounter(int) - Constructor for class ome.services.sessions.stats.ObjectsReadCounter
objectsReadHardLimit - Variable in class ome.services.sessions.stats.CounterFactory
ObjectsReadStatsMessage - Class in ome.services.messages.stats: Published when some limit in user/group/session activity has been reached.
ObjectsReadStatsMessage(Object, long) - Constructor for class ome.services.messages.stats.ObjectsReadStatsMessage
ObjectsWrittenCounter - Class in ome.services.sessions.stats: Counter for all the objects read in a session.
ObjectsWrittenCounter(int) - Constructor for class ome.services.sessions.stats.ObjectsWrittenCounter
objectsWrittenHardLimit - Variable in class ome.services.sessions.stats.CounterFactory
ObjectsWrittenStatsMessage - Class in ome.services.messages.stats
ObjectsWrittenStatsMessage(Object, long) - Constructor for class ome.services.messages.stats.ObjectsWrittenStatsMessage
observers - Variable in class ome.formats.importer.util.ErrorHandler
obtainProxy(String, Redirector.Context, String, SessionControlPrx, Current) - Method in class ome.services.blitz.redirect.AbstractRedirector
obToImageCache - Variable in class ome.services.sharing.BlobShareStore
offset - Variable in class ome.util.mem.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.cli - package ome.formats.importer.cli
ome.formats.importer.exclusions - package ome.formats.importer.exclusions: mechanism for determing which potential filesets should be excluded from import.
ome.formats.importer.transfers - package ome.formats.importer.transfers: mechanism for shipping client-side files to the server-side.
ome.formats.importer.util - package ome.formats.importer.util
ome.formats.model - package ome.formats.model
ome.formats.model.handler - package ome.formats.model.handler
ome.io.bioformats - package ome.io.bioformats
ome.io.messages - package ome.io.messages
ome.io.nio - package ome.io.nio: New Input/Output handling for the OMERO server This includes interfaces/classes for the input and output handling of data within the OMERO server.
ome.logic - package ome.logic: The central repository of implementations which will be accessible through this server.
ome.security - package ome.security: JBoss and OMERO security handling This includes classes that provide security for the execution and usage of the OMERO server on a JBoss platform.
ome.security.auth - package ome.security.auth
ome.security.auth.providers - package ome.security.auth.providers
ome.security.basic - package ome.security.basic: Basic OMERO security contextual classes Basic classes that provide security context objects necessary to secure the implementation of the OMERO server on a JBoss platform.
ome.security.policy - package ome.security.policy: Extensible service and security policies which can influence whether a user, group, or other agent can perform a certain action.
ome.security.sharing - package ome.security.sharing
ome.services - package ome.services: Base services package for OMERO API services This includes classes that implement OMERO API services described as interfaces in the OMERO Common component.
ome.services.blitz - package ome.services.blitz
ome.services.blitz.fire - package ome.services.blitz.fire
ome.services.blitz.impl - package ome.services.blitz.impl
ome.services.blitz.impl.commands - package ome.services.blitz.impl.commands
ome.services.blitz.measurements - package ome.services.blitz.measurements
ome.services.blitz.redirect - package ome.services.blitz.redirect
ome.services.blitz.repo - package ome.services.blitz.repo
ome.services.blitz.repo.path - package ome.services.blitz.repo.path
ome.services.blitz.util - package ome.services.blitz.util
ome.services.chgrp - package ome.services.chgrp
ome.services.chown - package ome.services.chown
ome.services.db - package ome.services.db
ome.services.delete - package ome.services.delete: Implementations of the ome.api.IDelete service.
ome.services.delete.files - package ome.services.delete.files
ome.services.eventlogs - package ome.services.eventlogs
ome.services.export - package ome.services.export: Helpers for implementing the necessary interfaces from Bio-Formats for mapping OMERO objects (ome.model.*) to OME-XML and OME-TIFF
ome.services.formats - package ome.services.formats
ome.services.fulltext - package ome.services.fulltext: All necessary classes for background indexing of metadata and attached binary files.
ome.services.fulltext.bridges - package ome.services.fulltext.bridges: Custom FieldBridge implementations which can be configured to be run on each indexing activity.
ome.services.graphs - package ome.services.graphs: Server classes for handling complicated graphs of model objects.
ome.services.mail - package ome.services.mail: General mail services.
ome.services.messages - package ome.services.messages: Message implementations used throughout the server for internal communication.
ome.services.messages.stats - package ome.services.messages.stats
ome.services.pixeldata - package ome.services.pixeldata
ome.services.procs - package ome.services.procs: Internal process and process management This includes interfaces and classes that provide thread process management for internal processes critical to the operation of the OMERO server.
ome.services.procs.scripts - package ome.services.procs.scripts: Script processor infrastructure.
ome.services.projection - package ome.services.projection
ome.services.query - package ome.services.query: facilitates the creation of Hibernate Queries and Criteria.
ome.services.roi - package ome.services.roi
ome.services.scheduler - package ome.services.scheduler
ome.services.scripts - package ome.services.scripts
ome.services.search - package ome.services.search: Internal search implementation classes.
ome.services.sessions - package ome.services.sessions
ome.services.sessions.events - package ome.services.sessions.events
ome.services.sessions.state - package ome.services.sessions.state
ome.services.sessions.stats - package ome.services.sessions.stats
ome.services.sharing - package ome.services.sharing: ome.api.IShare support infrastructure.
ome.services.throttling - package ome.services.throttling
ome.services.util - package ome.services.util: Helper classes to support OMERO service beans Instead of abstract classes, IOC methods and dependency injection is used to provide service interception for the Service (binary) bean classes.
ome.system - package ome.system: Provides the necessary container structure for the entire Omero system.
ome.system.metrics - package ome.system.metrics: General metrics registry for use by all server-side components.
ome.tools - package ome.tools: OMERO Server Utility and Spring/Hibernate Tools Classes/Interfaces that implement File, Hibernate, Spring, Annotation, Hierarchy, etc. method mechanics for the OMERO server Related Documentation For more information, please see: TODO
ome.tools.hibernate - package ome.tools.hibernate: Hibernate specific tools for the OMERO Server Classes/Interfaces that implement Hibernate method mechanics for the OMERO server Related Documentation For more information, please see: TODO
ome.tools.lsid - package ome.tools.lsid: Life Science Identifier (LSID) tools Classes/Interfaces that manage conversions and creation of LSID unique identifiers Related Documentation For more information, please see: TODO
ome.tools.spring - package ome.tools.spring: OMERO Server tools specific to Spring Classes/Interfaces that implement AOP, Post-processing injection, session flushing, and factory management.
ome.util.checksum - package ome.util.checksum
ome.util.logback - package ome.util.logback
ome.util.math.geom2D - package ome.util.math.geom2D: Plane geometry data structures for OMERO This includes a several implementations of various two dimensional simple geometry classes to represent these structures within the OMERO system.
ome.util.mem - package ome.util.mem: Dynamic object instance and state management for OMERO This includes various implementations of copy and clonable operations.
ome.util.messages - package ome.util.messages: Messages package for specialized exception handling for OMERO.
ome.util.search - package ome.util.search
OMECredentials - Class in loci.ome.io: Stores credentials for logging into an OME/OMERO server.
OMECredentials(String, String, String) - Constructor for class loci.ome.io.OMECredentials
OMECredentials(String) - Constructor for class loci.ome.io.OMECredentials: Get credentials from a string.
omeis.providers.re - package omeis.providers.re: Red-Green-Blue (RGB) data structures and Image Rendering Service This package provides basic data structures to represent an RGB pixel set and provide a service for the rendering of this pixel set.
omeis.providers.re.codomain - package omeis.providers.re.codomain: Provides codomain pixel set data structures for Maps and Contexts.
omeis.providers.re.data - package omeis.providers.re.data: Provides classes needed to define XY planes within a dynamic 3D context.
omeis.providers.re.metadata - package omeis.providers.re.metadata
omeis.providers.re.quantum - package omeis.providers.re.quantum
OMENAME - Static variable in class pojos.ExperimenterData: Identifies the Experimenter#OMENAME field.
OMEReaderWriterService - Interface in loci.ome.io.services
OMEReaderWriterServiceImpl - Class in loci.ome.io.services
OMEReaderWriterServiceImpl() - Constructor for class loci.ome.io.services.OMEReaderWriterServiceImpl
omero - package omero
omero.cmd - package omero.cmd
omero.cmd.admin - package omero.cmd.admin
omero.cmd.basic - package omero.cmd.basic
omero.cmd.fs - package omero.cmd.fs
omero.cmd.graphs - package omero.cmd.graphs
omero.cmd.mail - package omero.cmd.mail
omero.grid - package omero.grid
omero.model - package omero.model
omero.sys - package omero.sys
omero.util - package omero.util
OMERO_EMISSION_FILTER_SUFFIX - Static variable in class ome.formats.OMEROMetadataStoreClient: Emission filter LSID suffix.
OMERO_EVENT - Static variable in class ome.system.Login: Java property name for use in configuration of client login.
OMERO_EXCITATION_FILTER_SUFFIX - Static variable in class ome.formats.OMEROMetadataStoreClient: Excitation filter LSID suffix.
OMERO_GROUP - Static variable in class ome.system.Login: Java property name for use in configuration of client login.
OMERO_HOST - Static variable in class ome.system.Server: Java property name for use in configuration of the client connection.
OMERO_PASS - Static variable in class ome.system.Login: Java property name for use in configuration of client login.
OMERO_PORT - Static variable in class ome.system.Server: Java property name for use in configuration of the client connection.
OMERO_TABLE - Variable in class ome.services.fulltext.bridges.TablesBridge: Mimetype set on OriginalFile.mimetype (or in previous version, OriginalFile.format.value).
OMERO_USER - Static variable in class ome.system.Login: Java property name for use in configuration of client login.
omeroClass(String, boolean) - Static method in class omero.util.IceMapper
OmeroContext - Class in ome.system: Provides static access for the creation of singleton and non-singleton application contexts.
OmeroContext(String) - Constructor for class ome.system.OmeroContext
OmeroContext(String[]) - Constructor for class ome.system.OmeroContext
OmeroContext(String[], boolean) - Constructor for class ome.system.OmeroContext
OmeroContext(String[], ApplicationContext) - Constructor for class ome.system.OmeroContext
OmeroContext(String[], boolean, ApplicationContext) - Constructor for class ome.system.OmeroContext
OmeroContext.Locator - Class in ome.system: provides access to the protected methods of ContextSingletonBeanFactoryLocator which cannot be used externally.
OmeroContext.Locator() - Constructor for class ome.system.OmeroContext.Locator
omeroDataDir - Variable in class ome.services.blitz.impl.MetadataStoreI
omeroDataDir - Variable in class ome.services.OmeroFilePathResolver: The server's OMERO data directory.
OmeroFilePathResolver - Class in ome.services: OMERO server based resolver for file paths.
OmeroFilePathResolver(SqlAction, String) - Constructor for class ome.services.OmeroFilePathResolver: Constructor.
OMEROImportFixture - Class in ome.formats: test fixture for importing files without a GUI.
OMEROImportFixture(OMEROMetadataStoreClient, OMEROWrapper) - Constructor for class ome.formats.OMEROImportFixture
OmeroInterceptor - Class in ome.security.basic: implements Interceptor for controlling various aspects of the Hibernate runtime.
OmeroInterceptor(Roles, SystemTypes, ExtendedMetadata, CurrentDetails, TokenHolder, SessionStats) - Constructor for class ome.security.basic.OmeroInterceptor
OmeroMeasurementStore - Interface in ome.services.blitz.measurements: Sub-interface of MeasurementStore with extended life-cycle methods for handling exceptions during saving the measurements to multiple stores.
OmeroMetadata - Class in ome.services.blitz.impl: An implementation for MetadataStore and MetadataRetrieve that knows how to read and write the OMERO object model.
OmeroMetadata(DatabaseIdentity) - Constructor for class ome.services.blitz.impl.OmeroMetadata
OMEROMetadataStore - Class in ome.formats: An OMERO metadata store.
OMEROMetadataStore() - Constructor for class ome.formats.OMEROMetadataStore: Empty constructor for testing purposes.
OMEROMetadataStore(ServiceFactory, SqlAction) - Constructor for class ome.formats.OMEROMetadataStore: Creates a new instance.
OMEROMetadataStoreClient - Class in ome.formats: Client side implementation of the Bio-Formats MetadataStore.
OMEROMetadataStoreClient() - Constructor for class ome.formats.OMEROMetadataStoreClient
OMEROMetadataStoreClientRoot - Class in ome.formats: MetadataRoot implementation for the client side implementation of the Bio-Formats MetadataStore.
OMEROMetadataStoreClientRoot() - Constructor for class ome.formats.OMEROMetadataStoreClientRoot: Default constructor.
OMEROMetadataStoreClientRoot(List<Pixels>) - Constructor for class ome.formats.OMEROMetadataStoreClientRoot: Copy constructor.
OmeroModelContextMapper - Class in ome.security.auth: Parent class for any OMERO model-to-LDAP mappers.
OmeroModelContextMapper(LdapConfig, String, String) - Constructor for class ome.security.auth.OmeroModelContextMapper
OmeroPixelsPyramidReader - Class in ome.io.bioformats: File format reader for OMERO pixels pyramid files.
OmeroPixelsPyramidReader() - Constructor for class ome.io.bioformats.OmeroPixelsPyramidReader
OmeroPixelsPyramidWriter - Class in ome.io.bioformats: File format writer for OMERO pixels pyramid files.
OmeroPixelsPyramidWriter() - Constructor for class ome.io.bioformats.OmeroPixelsPyramidWriter
OmeroReader - Class in loci.ome.io: Implementation of IFormatReader for use in export from an OMERO Beta 4.2.x database.
OmeroReader() - Constructor for class loci.ome.io.OmeroReader
OmeroReader - Class in ome.services.formats: Implementation of IFormatReader for use in export.
OmeroReader(RawPixelsStore, Pixels) - Constructor for class ome.services.formats.OmeroReader
OmeroReader(RawPixelsStorePrx, Pixels) - Constructor for class ome.services.formats.OmeroReader
OMEROWrapper - Class in ome.formats.importer
OMEROWrapper(ImportConfig) - Constructor for class ome.formats.importer.OMEROWrapper: Wrapper for bio-formats
OMEROWrapper(ImportConfig, long, File) - Constructor for class ome.formats.importer.OMEROWrapper
OMEXMLModelComparator - Class in ome.formats: This comparator takes into account the OME-XML data model hierarchy and uses that to define equivalence.
OMEXMLModelComparator() - Constructor for class ome.formats.OMEXMLModelComparator
onAddError(ErrorContainer, String) - Method in class ome.formats.importer.util.ErrorHandler: Action to take on adding an error to container
onApplicationEvent(LoginAttemptMessage) - Method in class ome.security.auth.LoginAttemptListener
onApplicationEvent(EventLogMessage) - Method in class ome.security.basic.BasicSecuritySystem
onApplicationEvent(ContextMessage) - Method in class ome.security.basic.EventHandler: If a ContextMessage is received, then we either need to add a ContextMessage.Push login to the stack or ContextMessage.Pop remove one.
onApplicationEvent(InternalMessage) - Method in class ome.services.blitz.fire.SessionManagerI
onApplicationEvent(ApplicationEvent) - Method in class ome.services.blitz.fire.TopicManager.Impl
onApplicationEvent(InternalMessage) - Method in class ome.services.blitz.repo.AbstractRepositoryI
onApplicationEvent(UserSignalMessage) - Method in class ome.services.db.SelfCorrectingDataSource: Handles the USR1 posix signal by calling close on the underlying data source via reflection.
onApplicationEvent(ApplicationEvent) - Method in class ome.services.eventlogs.EventLogLoader
onApplicationEvent(ApplicationEvent) - Method in class ome.services.eventlogs.EventLogQueue
onApplicationEvent(ApplicationEvent) - Method in class ome.services.fulltext.ParserSession
onApplicationEvent(ApplicationEvent) - Method in class ome.services.fulltext.PersistentEventLogLoader
onApplicationEvent(LoginAttemptMessage) - Method in class ome.services.mail.FailedLoginMailSender
onApplicationEvent(EventLogsMessage) - Method in class ome.services.mail.ObjectMailSender
onApplicationEvent(ShutdownMessage) - Method in class ome.services.mail.ServerDownMailSender
onApplicationEvent(MissingPyramidMessage) - Method in class ome.services.pixeldata.PixelDataThread: Called in the main server (Blitz-0) in order to create a PIXELDATA EventLog which will get processed by PixelData-0.
onApplicationEvent(ContextRefreshedEvent) - Method in class ome.services.scheduler.SchedulerFactoryBean
onApplicationEvent(ApplicationEvent) - Method in class ome.services.sessions.SessionManagerImpl
onApplicationEvent(ApplicationEvent) - Method in class ome.services.throttling.AbstractThrottlingStrategy
onApplicationEvent(ApplicationEvent) - Method in class ome.services.util.ServiceHandler
onApplicationEvent(ContextRefreshedEvent) - Method in class ome.tools.spring.OnContextRefreshedEventListener
onBoundaries(double, double) - Method in class ome.util.math.geom2D.EllipseArea: Implemented as specified by the PlaneArea I/F.
onBoundaries(double, double) - Method in interface ome.util.math.geom2D.PlaneArea: Controls if a specified point is on the boundary of the PlaneArea.
onBoundaries(double, double) - Method in class ome.util.math.geom2D.RectangleArea: Implemented as specified by the PlaneArea I/F.
onCancel() - Method in class ome.formats.importer.util.ErrorHandler: action to take on cancel
onCollectionRecreate(Object, Serializable) - Method in class ome.security.basic.OmeroInterceptor
onCollectionRemove(Object, Serializable) - Method in class ome.security.basic.OmeroInterceptor
onCollectionUpdate(Object, Serializable) - Method in class ome.security.basic.OmeroInterceptor
OnContextRefreshedEventListener - Class in ome.tools.spring: ApplicationListener which only listens for ContextRefreshedEvent and only responds to the first one.
OnContextRefreshedEventListener() - Constructor for class ome.tools.spring.OnContextRefreshedEventListener
OnContextRefreshedEventListener(boolean, int) - Constructor for class ome.tools.spring.OnContextRefreshedEventListener
onDelete(Object, Serializable, Object[], String[], Type[]) - Method in class ome.security.basic.OmeroInterceptor: default logic
onDiskCache(String) - Method in interface ome.services.sessions.SessionManager: Returns after possibly creating an on-disk cache which can be used throughout the session.
onDiskCache(String) - Method in class ome.services.sessions.SessionManagerImpl
onDiskCache(String) - Method in class ome.services.sessions.state.SessionCache
onegroup - Variable in class ome.security.SecurityFilterHolder
OneGroupSecurityFilter - Class in ome.security.basic: overrides FilterDefinitionFactoryBean in order to construct our security filter in code and not in XML.
OneGroupSecurityFilter() - Constructor for class ome.security.basic.OneGroupSecurityFilter: default constructor which calls all the necessary setters for this FactoryBean.
OneGroupSecurityFilter(Roles) - Constructor for class ome.security.basic.OneGroupSecurityFilter
onException(Exception) - Method in class ome.formats.importer.util.ErrorHandler: Action to take on exception
onExecutionException(ExecutionException) - Method in class ome.services.pixeldata.PixelDataThread: Basic handling just logs at ERROR level.
onFinished(Response, Status, Current) - Method in class ome.formats.importer.ImportLibrary.ImportCallback: Overridden to handle the end of the process.
onFinished(Response, Status, Current) - Method in class omero.cmd.CmdCallbackI: Method intended to be overridden by subclasses.
onFinishedDone() - Method in class omero.cmd.CmdCallbackI
onFlushDirty(Object, Serializable, Object[], Object[], String[], Type[]) - Method in class ome.security.basic.OmeroInterceptor: calls back to BasicSecuritySystem.checkManagedDetails(IObject, Details) for properly setting Details.
onHeartbeat(Runnable) - Method in class omero.client
onLoad(Object, Serializable, Object[], String[], Type[]) - Method in class ome.security.basic.OmeroInterceptor: default logic.
onlyAnnotatedBetween(Timestamp, Timestamp) - Method in interface ome.api.Search: Restricts entities by the time in which any annotation (which matches the other filters) was added them.
onlyAnnotatedBetween(Timestamp, Timestamp) - Method in class ome.services.SearchBean
onlyAnnotatedBetween_async(AMD_Search_onlyAnnotatedBetween, RTime, RTime, Current) - Method in class ome.services.blitz.impl.SearchI
onlyAnnotatedBy(Details) - Method in interface ome.api.Search: Restricts entities by who has annotated them with an Annotation matching the other filters.
onlyAnnotatedBy(Details) - Method in class ome.services.SearchBean
onlyAnnotatedBy_async(AMD_Search_onlyAnnotatedBy, Details, Current) - Method in class ome.services.blitz.impl.SearchI
onlyAnnotatedWith(Class...) - Method in interface ome.api.Search: Restricts entities to having an Annotation of all the given types.
onlyAnnotatedWith - Variable in class ome.services.search.SearchValues
onlyAnnotatedWith(Class...) - Method in class ome.services.SearchBean
onlyAnnotatedWith_async(AMD_Search_onlyAnnotatedWith, List<String>, Current) - Method in class ome.services.blitz.impl.SearchI
onlyCreatedBetween(Timestamp, Timestamp) - Method in interface ome.api.Search: Restricts the time between which an entity may have been created.
onlyCreatedBetween(Timestamp, Timestamp) - Method in class ome.services.SearchBean
onlyCreatedBetween_async(AMD_Search_onlyCreatedBetween, RTime, RTime, Current) - Method in class ome.services.blitz.impl.SearchI
onlyIds(Long...) - Method in interface ome.api.Search: Restricts the set of ids which will be checked.
onlyIds - Variable in class ome.services.search.SearchValues
onlyIds(Long...) - Method in class ome.services.SearchBean
onlyIds_async(AMD_Search_onlyIds, List<Long>, Current) - Method in class ome.services.blitz.impl.SearchI
onlyModifiedBetween(Timestamp, Timestamp) - Method in interface ome.api.Search: Restricts the time between which an entity may have last been modified.
onlyModifiedBetween(Timestamp, Timestamp) - Method in class ome.services.SearchBean
onlyModifiedBetween_async(AMD_Search_onlyModifiedBetween, RTime, RTime, Current) - Method in class ome.services.blitz.impl.SearchI
onlyOwnedBy(Details) - Method in interface ome.api.Search: Uses the Details.getOwner() and Details.getGroup() information to restrict the entities which will be returned.
onlyOwnedBy(Details) - Method in class ome.services.SearchBean
onlyOwnedBy_async(AMD_Search_onlyOwnedBy, Details, Current) - Method in class ome.services.blitz.impl.SearchI
onlyPermissionsChanged(Details, Details) - Static method in class ome.tools.hibernate.HibernateUtils
onlyType(Class<T>) - Method in interface ome.api.Search: Restricts the search to a single type.
onlyType(Class<T>) - Method in class ome.services.SearchBean
onlyType_async(AMD_Search_onlyType, String, Current) - Method in class ome.services.blitz.impl.SearchI
onlyTypes(Class<T>...) - Method in interface ome.api.Search: Restricts searches to a set of types.
onlyTypes - Variable in class ome.services.search.SearchValues
onlyTypes(Class<T>...) - Method in class ome.services.SearchBean
onlyTypes_async(AMD_Search_onlyTypes, List<String>, Current) - Method in class ome.services.blitz.impl.SearchI
onMerge(MergeEvent) - Method in class ome.security.basic.MergeEventListener
onMerge(MergeEvent, Map) - Method in class ome.security.basic.MergeEventListener
onNotSending(int, String) - Method in class ome.formats.importer.util.ErrorHandler
onPostDelete(PostDeleteEvent) - Method in class ome.security.ACLEventListener: unused
onPostDelete(PostDeleteEvent) - Method in class ome.security.basic.EventLogListener
onPostInsert(PostInsertEvent) - Method in class ome.security.ACLEventListener: unused
onPostInsert(PostInsertEvent) - Method in class ome.security.basic.EventLogListener
onPostLoad(PostLoadEvent) - Method in class ome.security.ACLEventListener: catches all load events after the fact, and tests the current users permissions to read that object.
onPostProcess(List<GraphStep>) - Method in class ome.services.graphs.AbstractStepFactory: Deprecated.
onPostUpdate(PostUpdateEvent) - Method in class ome.security.ACLEventListener: unused
onPostUpdate(PostUpdateEvent) - Method in class ome.security.basic.EventLogListener
onPreDelete(PreDeleteEvent) - Method in class ome.security.ACLEventListener
onPreInsert(PreInsertEvent) - Method in class ome.security.ACLEventListener
onPreLoad(PreLoadEvent) - Method in class ome.security.ACLEventListener: unused
onPrepareStatement(String) - Method in class ome.security.basic.OmeroInterceptor
onPreUpdate(PreUpdateEvent) - Method in class ome.security.ACLEventListener
onPreUpdate(PreUpdateEvent) - Method in class ome.security.basic.UpdateEventListener: updates the update event field of an IObject instance.
onRefresh() - Method in class ome.system.OmeroContext
onRefresh(RefreshEvent) - Method in class ome.tools.hibernate.ReloadingRefreshEventListener
onRefresh(RefreshEvent, Map) - Method in class ome.tools.hibernate.ReloadingRefreshEventListener
onRelease(Class<IObject>, Set<Long>) - Method in class ome.services.chgrp.ChgrpStep: Deprecated.
onRelease(Class<IObject>, Set<Long>) - Method in class ome.services.chown.ChownStep: Deprecated.
onRelease(Class<IObject>, Set<Long>) - Method in class ome.services.delete.DeleteStep: Deprecated.
onRelease(Class<IObject>, Set<Long>) - Method in class ome.services.export.ExporterStep: Deprecated.
onRelease(Class<IObject>, Set<Long>) - Method in class ome.services.graphs.GraphStep: Deprecated.
onSave(Object, Serializable, Object[], String[], Type[]) - Method in class ome.security.basic.OmeroInterceptor: 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.cli.ErrorHandler
onUpdate(IObservable, ImportEvent) - Method in class ome.formats.importer.util.ErrorHandler: abstract on update method
onWindowChange() - Method in class omeis.providers.re.quantum.BinaryMaskQuantizer
onWindowChange() - Method in class omeis.providers.re.quantum.Quantization_32_bit: The input window size changed, re-map the values.
onWindowChange() - Method in class omeis.providers.re.quantum.Quantization_8_16_bit: The input window size changed, rebuild the LUT.
onWindowChange() - Method in class omeis.providers.re.quantum.Quantization_float: The input window size changed, re-map the values.
onWindowChange() - Method in class omeis.providers.re.quantum.QuantumStrategy: Notifies when the input interval has changed or the mapping strategy has changed.
openBytes(int, byte[], int, int, int, int) - Method in class loci.ome.io.OmeroReader
openBytes(int, byte[], int, int, int, int) - Method in class ome.services.formats.OmeroReader
openPlane2D(String, int, byte[]) - Method in class ome.formats.importer.OMEROWrapper: Obtains an object which represents a given sub-image of a plane within the file.
openPlane2D(String, int, byte[], int, int, int, int) - Method in class ome.formats.importer.OMEROWrapper: Obtains an object which represents a given sub-image of a plane within the file.
openSession() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
openTable(OriginalFile, Current) - Method in class ome.services.blitz.impl.SharedResourcesI
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.
optionallyNullField(Session, Long) - Method in class ome.services.graphs.GraphStep: Deprecated.
optionalNullBuilder() - Method in class ome.services.graphs.GraphStep: Deprecated.
options - Variable in class ome.services.graphs.BaseGraphSpec: Deprecated.

Options passed to the #initialize(long, Map) method, which may be used during GraphState.execute(int) to alter behavior.
optSource - Variable in class ome.services.graphs.AbstractHierarchyGraphSpec: Deprecated.

Key from the options map which was the source of the rawOption value of the same index.
or() - Method in interface ome.api.Search: Applies the next by* method to the previous by* method, so that a call Search.hasNext(), Search.next(), or Search.results() sees only the union of the two calls.
or() - Method in class ome.services.SearchBean
or(String) - Method in class ome.tools.hibernate.QueryBuilder: Appends "or" plus your string unless this is the first where-spec in which case it is simply appended.
or_async(AMD_Search_or, Current) - Method in class ome.services.blitz.impl.SearchI
order(String, boolean) - Method in class ome.tools.hibernate.QueryBuilder
orderBy - Variable in class ome.services.search.SearchValues
orderByAscending(String) - Static method in class ome.services.search.SearchAction
orderByPath(String) - Static method in class ome.services.search.SearchAction
org.hibernate.stat - package org.hibernate.stat
OrgUnitNewUserGroupBean - Class in ome.security.auth: Handles the ":ou:" specifier from etc/omero.properties by adding the user to a group named by the final organizational unit.
OrgUnitNewUserGroupBean(DistinguishedName) - Constructor for class ome.security.auth.OrgUnitNewUserGroupBean
origin - Variable in class ome.util.math.geom2D.Line: The origin point of the line.
ORIGINAL_METADATA_NAME - Static variable in class pojos.FileAnnotationData: The default name for the original metadata file.
OriginalFileDeletions - Class in ome.services.delete.files: Deletes all repository files immediately.
OriginalFileDeletions(AbstractFileSystemService, Set<Long>, OmeroContext) - Constructor for class ome.services.delete.files.OriginalFileDeletions
OriginalFilesService - Class in ome.io.nio: Raw file service which provides access to FileBuffers.
OriginalFilesService(String) - Constructor for class ome.io.nio.OriginalFilesService: Constructor
OriginalMetadataRequestI - Class in omero.cmd.fs: Original metadata loader, handling both pre-FS and post-FS data.
OriginalMetadataRequestI(PixelsService) - Constructor for class omero.cmd.fs.OriginalMetadataRequestI
originalSize - Variable in class ome.services.graphs.AbstractStepFactory: Deprecated.
originX1 - Variable in class ome.util.math.geom2D.Segment: The origin of the segment's first element.
originX2 - Variable in class ome.util.math.geom2D.Segment: The origin of the segment's first element.
orphan - Variable in class ome.services.graphs.GraphPolicy.Details: the current orphan state of the object, may be mutated by Policy#review(Map, Details, Map, Set); applies only if GraphPolicy.Details.action is GraphPolicy.Action.EXCLUDE
orphan() - Method in class omero.sys.ParametersI: Sets the orphan parameter to true.
osf - Variable in class ome.logic.AdminImpl
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: Deprecated.

Returns true to prevent skipping of the entire subspec if there were any "excludes" passed in with the options.
overrideKeep() - Method in class ome.services.graphs.BaseGraphSpec: Deprecated.

Always returns false.
overrideKeep() - Method in interface ome.services.graphs.GraphSpec: Deprecated.

For some GraphSpec type/option combinations, a "KEEP" setting may need to be overridden.
overrideKeep() - Method in class ome.services.graphs.LightSourceGraphSpec: Deprecated.
overrides() - Method in class ome.security.basic.EventListenersFactoryBean
own(String) - Method in class ome.services.db.DatabaseIdentity
ownedBy - Variable in class ome.services.search.SearchValues
ownerId - Variable in class ome.services.graphs.GraphPolicy.Details: the ID of the object's Experimenter, or null if the object does not have an owner
ownerOfGroups(String, LdapConfig, LdapOperations, RoleProvider, AttributeSet) - Method in interface ome.security.auth.NewUserGroupOwnerBean
ownerOfGroups(String, LdapConfig, LdapOperations, RoleProvider, AttributeSet) - Method in class ome.security.auth.QueryNewUserGroupBean
ownerOrGroup(Class, Criteria) - Method in class ome.services.search.SearchAction
ownerOrGroup(Class, QueryBuilder, String) - Method in class ome.services.search.SearchAction
ownerOrGroupFilters(Session, String[], String[]) - Method in class ome.services.query.Query: standard filter used by many subclasses which uses the PojoOptions#isExperimenter() and PojoOptions#isGroup() booleans to see if a filter should be turned on.
ownParts() - Method in class ome.services.graphs.GraphEntry: Deprecated.

Returns the size of GraphEntry.parts and GraphEntry.path combined.

P

page(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(int, Object) - Method in class ome.tools.hibernate.QueryBuilder
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() - Method in class omero.cmd.graphs.ChmodI: Deprecated.
params(String...) - Method in class omero.cmd.Helper: Converts pairs of values from the varargs list into a map.
params(Current) - Method in class omero.grid.InteractiveProcessorI
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() - Method in class ome.services.blitz.repo.CheckedPath: Returns a new CheckedPath using File.getParent() and passing in all other values.
parent - Variable in class ome.services.graphs.GraphStep: Deprecated.

Final member of GraphStep.stack which is the direct ancestor of this step.
parse(String[]) - Static method in class ome.logic.HardWiredInterceptor: Produces a List of instantiated interceptors from a list of HardWiredInterceptor subclass names.
parse(String) - Method in class ome.security.auth.LdapConfig
parse(OriginalFile, OriginalFilesService, Map<String, FileParser>) - Method in class ome.services.fulltext.BridgeHelper: Attempts to parse the given OriginalFile.
parse(File) - Method in class ome.services.fulltext.FileParser: Uses FileParser.doParse(File) to create manageable chunks of a file for indexing.
parse(String[], String[], String[]) - Static method in class ome.services.search.SomeMustNone
parse(ShareData) - Method in class ome.services.sharing.ShareStore
parse(long, byte[]) - Method in class ome.services.sharing.ShareStore
parseAndSetInt(InitializationData, String, int) - Method in class omero.client
parseAwtPath(String) - Static method in class omero.model.SmartShape.Util
parseData(String, int, ImportSize) - Method in class ome.services.blitz.repo.ManagedImportRequestI: Parse the binary data to generate min/max values and allow an md to be calculated.
parseField(String) - Static method in class ome.tools.lsid.LsidUtils: takes a field identifier as code-generated in each IObject class and produces a back-end useable name.
parseFilter(Criteria, Filter) - Method in class ome.logic.QueryImpl: responsible for applying the information provided in a Filter to a org.hibernate.Critieria instance.
parseFlexMaps(Preferences) - Method in class ome.formats.importer.util.IniFileLoader: Parse Flex reader server maps
parseOriginalMetadataTxt(File) - Method in class omero.cmd.fs.OriginalMetadataRequestI: Read the given INI-style file and populate the maps with the properties from the corresponding sections.
parsePoints(String) - Static method in class loci.ome.io.OmeroReader: Parse Points String obtained from convertPoints and extract Coordinates as String
parsePoints(String) - Static method in class omero.model.SmartShape.Util
parsePointsToIntegerList(String) - Method in class pojos.ShapeData: Parses the points list from the string to a list of integer objects.
parsePointsToPath(String, boolean) - Static method in class omero.model.SmartShape.Util
parsePointsToPoint2DList(String) - Method in class pojos.ShapeData: Parses the points list from the string to a list of point2d objects.
parseResults(String[], GraphEntry, List<List<Long>>) - Method in class ome.services.graphs.BaseGraphSpec: Deprecated.
ParserOpenFileMessage - Class in ome.services.messages: A trivial copy of RegisterServiceCleanupMessage with a different name so that we can catch files opened during search indexing and close them at the end of parsing.
ParserOpenFileMessage(Object, Object) - Constructor for class ome.services.messages.ParserOpenFileMessage
parsers - Variable in class ome.services.fulltext.FullTextBridge
parserSession - Variable in class ome.services.fulltext.FullTextIndexer
ParserSession - Class in ome.services.fulltext: Provides a session for file parsing by the search indexer
ParserSession() - Constructor for class ome.services.fulltext.ParserSession
parseRules(GraphPathBean, Collection<GraphPolicyRule>) - Static method in class ome.services.graphs.GraphPolicyRule: Convert the text-based rules as specified in the configuration metadata into a policy applicable in model object graph traversal.
parseStream(InputStream) - Method in class ome.services.mail.MapAnnotationSubethaListener
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(Session, Details, EventContext) - Method in class ome.security.basic.AllGroupsSecurityFilter: tests that the Details argument passes the security test that this filter defines.
passesFilter(Session, Details, EventContext) - Method in class ome.security.basic.OneGroupSecurityFilter: tests that the Details argument passes the security test that this filter defines.
passesFilter(Session, Details, EventContext) - Method in interface ome.security.SecurityFilter: tests that the Details argument passes the security test that this filter defines.
passesFilter(Session, Details, EventContext) - Method in class ome.security.SecurityFilterHolder
passivate() - Method in interface ome.api.StatefulServiceInterface: Perform whatever passivation is possible or throw an exception.
passivate() - Method in class ome.services.JobBean: Does nothing.
passivate() - Method in class ome.services.RawFileBean
passivate() - Method in class ome.services.RawPixelsBean
passivate() - Method in class ome.services.RenderingBean
passivate() - Method in class ome.services.SearchBean
passivate() - Method in class ome.services.ThumbnailBean
passivate_async(AMD_StatefulServiceInterface_passivate, Current) - Method in class ome.services.blitz.impl.AbstractAmdServant
passivate_async(AMD_StatefulServiceInterface_passivate, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
passivationNotAllowed() - Method in class ome.services.util.BeanHelper
password - Variable in class loci.ome.io.OMECredentials
password - Variable in class ome.formats.importer.ImportConfig
PasswordChangeException - Exception in ome.security.auth: Caught exception thrown from PasswordProvider.changePassword(String, String) to allow read-only implementations to refuse an action.
PasswordChangeException(String) - Constructor for exception ome.security.auth.PasswordChangeException
passwordDigest(String) - Method in class ome.security.auth.PasswordUtil: Creates an MD5 hash of the given clear text and base64 encodes it.
passwordDigest(Long, String, boolean) - Method in class ome.security.auth.PasswordUtil
passwordProvider - Variable in class ome.logic.AdminImpl
PasswordProvider - Interface in ome.security.auth: Authentication interface responsible for checking and changing passwords.
PasswordProviders - Class in ome.security.auth: Composite class which delegates to each of the configured providers in turn.
PasswordProviders(PasswordProvider...) - Constructor for class ome.security.auth.PasswordProviders
PasswordProviders(AtomicBoolean, PasswordProvider...) - Constructor for class ome.security.auth.PasswordProviders
passwordUtil - Variable in class ome.logic.AdminImpl
PasswordUtil - Class in ome.security.auth: Static methods for dealing with password hashes and the "password" table.
PasswordUtil(SqlAction) - Constructor for class ome.security.auth.PasswordUtil
PasswordUtil(SqlAction, boolean) - Constructor for class ome.security.auth.PasswordUtil
PasswordUtil(SqlAction, Charset) - Constructor for class ome.security.auth.PasswordUtil
PasswordUtil(SqlAction, boolean, Charset) - Constructor for class ome.security.auth.PasswordUtil
PasswordUtil(SqlAction, Roles, boolean) - Constructor for class ome.security.auth.PasswordUtil
PasswordUtil(SqlAction, Roles, boolean, Charset) - Constructor for class ome.security.auth.PasswordUtil
PasswordUtil.METHOD - Enum in ome.security.auth
PasswordUtility - Interface in ome.security.auth: Extension interface to PasswordProvider for methods which may or may not be available from a provider implementation.
path(String) - Method in class ome.services.graphs.GraphEntry: Deprecated.
path - Variable in class ome.services.scripts.RepoFile.FsFile
pathMsg - Variable in class ome.services.graphs.GraphStep: Deprecated.

String representation of the path to this GraphEntry used for logging.
PDF - Static variable in class pojos.FileAnnotationData: Identifies the PDF file formats.
PdfParser - Class in ome.services.fulltext: FileParser for "application/pdf" files using PDFBox.
PdfParser() - Constructor for class ome.services.fulltext.PdfParser
perform(int, boolean) - Method in class ome.services.graphs.GraphState: Deprecated.
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
permissions - Variable in class ome.services.graphs.GraphPolicy.Details: the current permissions on the object
PERMISSIONS_GROUP_READ - Static variable in class pojos.GroupData: Indicates that the group is Group i.e.
PERMISSIONS_GROUP_READ_LINK - Static variable in class pojos.GroupData: Indicates that the group is Group i.e.
PERMISSIONS_GROUP_READ_LINK_SHORT_TEXT - Static variable in class pojos.GroupData: Indicates that the group is Group i.e.
PERMISSIONS_GROUP_READ_LINK_TEXT - Static variable in class pojos.GroupData: Indicates that the group is Group i.e.
PERMISSIONS_GROUP_READ_SHORT_TEXT - Static variable in class pojos.GroupData: Indicates that the group is Group i.e.
PERMISSIONS_GROUP_READ_TEXT - Static variable in class pojos.GroupData: Indicates that the group is Group i.e.
PERMISSIONS_GROUP_READ_WRITE - Static variable in class pojos.GroupData: Indicates that the group is Group i.e.
PERMISSIONS_GROUP_READ_WRITE_SHORT_TEXT - Static variable in class pojos.GroupData: Indicates that the group is Group i.e.
PERMISSIONS_GROUP_READ_WRITE_TEXT - Static variable in class pojos.GroupData: Indicates that the group is Group i.e.
PERMISSIONS_PRIVATE - Static variable in class pojos.GroupData: Indicates that the group is Private i.e.
PERMISSIONS_PRIVATE_TEXT - Static variable in class pojos.GroupData: Indicates that the group is Private i.e.
PERMISSIONS_PUBLIC_READ - Static variable in class pojos.GroupData: Indicates that the group is Public i.e.
PERMISSIONS_PUBLIC_READ_TEXT - Static variable in class pojos.GroupData: Indicates that the group is Public i.e.
PERMISSIONS_PUBLIC_READ_WRITE - Static variable in class pojos.GroupData: Indicates that the group is Public i.e.
PERMISSIONS_PUBLIC_READ_WRITE_TEXT - Static variable in class pojos.GroupData: Indicates that the group is Public i.e.
permissionsClause(EventContext, QueryBuilder, boolean) - Method in class ome.services.graphs.BaseGraphSpec: Deprecated.

Appends a clause to the QueryBuilder based on the current user.
PermissionsI - Class in omero.model: Blitz wrapper around the Permissions class.
PermissionsI() - Constructor for class omero.model.PermissionsI
PermissionsI(String) - Constructor for class omero.model.PermissionsI
PermissionsI(PermissionsI) - Constructor for class omero.model.PermissionsI
PermissionsI(Permissions) - Constructor for class omero.model.PermissionsI
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, int) - Constructor for class ome.services.pixeldata.PersistentEventLogLoader
persistLogFile(OriginalFile, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI: Deprecated.
PersonContextMapper - Class in ome.security.auth: Specialized OME Experimenter context mapper.
PersonContextMapper(LdapConfig, String) - Constructor for class ome.security.auth.PersonContextMapper
PersonContextMapper(LdapConfig, String, String) - Constructor for class ome.security.auth.PersonContextMapper
PerThreadStats - Class in ome.services.sessions.stats: Delegates to a SessionStats which is acquired on every method invocation.
PerThreadStats(CurrentDetails) - Constructor for class ome.services.sessions.stats.PerThreadStats
PHOTOMETRIC_MONOCHROME - Static variable in class omeis.providers.re.Renderer: Identifies the type used to store photometric interpretation values.
pid() - Method in class omero.util.TempFileManager: Returns some representation of the current process's id
ping() - Method in class ome.formats.OMEROMetadataStoreClient: Pings all registered OMERO Blitz proxies.
ping() - Method in class ome.services.blitz.repo.ManagedImportProcessI
ping() - Method in interface ome.services.blitz.repo.ProcessContainer.Process
pingAll() - Method in class ome.services.blitz.repo.ProcessContainer: Called periodically by quartz to keep the sessions alive.
PixelBuffer - Interface in ome.io.nio: This interface declares the I/O responsibilities of a buffer, file or otherwise, that contains a 5-dimensional Pixel array (XYZCT).
PixelBufferException - Exception in ome.io.nio
PixelBufferException(String) - Constructor for exception ome.io.nio.PixelBufferException
pixelData(PixelDataJob) - Method in class ome.services.blitz.repo.ManagedImportRequestI
PixelData - Class in ome.services.roi: Strategy for loading and optionally caching pixel data.
PixelData(PixelsService, IPixels) - Constructor for class ome.services.roi.PixelData
PixelDataHandler - Class in ome.services.pixeldata: Simple action which can be done in an asynchronous thread in order to process PIXELDATA event logs.
PixelDataHandler(EventLogLoader, PixelsService) - Constructor for class ome.services.pixeldata.PixelDataHandler
PixelDataThread - Class in ome.services.pixeldata
PixelDataThread(SessionManager, Executor, PixelDataHandler, String) - Constructor for class ome.services.pixeldata.PixelDataThread: Uses default Principal for processing
PixelDataThread(SessionManager, Executor, PixelDataHandler, String, int) - Constructor for class ome.services.pixeldata.PixelDataThread: Uses default Principal for processing and a NullMetrics instance.
PixelDataThread(SessionManager, Executor, PixelDataHandler, Principal, String, int) - Constructor for class ome.services.pixeldata.PixelDataThread: Calculates PixelDataThread.performProcessing based on the existence of the "pixelDataTrigger" and passes all parameters to the main ctor passing a NullMetrics as necessary.
PixelDataThread(SessionManager, Executor, PixelDataHandler, String, int, Metrics) - Constructor for class ome.services.pixeldata.PixelDataThread: Calculates PixelDataThread.performProcessing based on the existence of the "pixelDataTrigger" and passes all parameters to the main ctor.
PixelDataThread(SessionManager, Executor, PixelDataHandler, Principal, String, int, Metrics) - Constructor for class ome.services.pixeldata.PixelDataThread: Calculates PixelDataThread.performProcessing based on the existence of the "pixelDataTrigger" and passes all parameters to the main ctor.
PixelDataThread(boolean, SessionManager, Executor, PixelDataHandler, Principal, String, int) - Constructor for class ome.services.pixeldata.PixelDataThread: Calls main constructor with NullMetrics.
PixelDataThread(boolean, SessionManager, Executor, PixelDataHandler, Principal, String, int, Metrics) - Constructor for class ome.services.pixeldata.PixelDataThread: Main constructor.
pixels - Variable in class ome.formats.importer.ImportEvent.IMPORT_DONE
pixels - Variable in class ome.formats.importer.ImportSize
pixels(String, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
pixels - Variable in class omeis.providers.re.quantum.QuantumStrategy: The pixels this strategy is for.
pixels - Variable in class omero.util.RPSTileLoop: Instance will be replaced on RawPixelsStorePrx.save()
PIXELS - Static variable in class pojos.ImageData: Identifies the Image#PIXELS field.
PIXELS_PATH - Static variable in class ome.io.nio.AbstractFileSystemService
Pixels_PhysicalSizeX - Static variable in class ome.formats.model.UnitsFactory
Pixels_PhysicalSizeY - Static variable in class ome.formats.model.UnitsFactory
Pixels_PhysicalSizeZ - Static variable in class ome.formats.model.UnitsFactory
Pixels_TimeIncrement - Static variable in class ome.formats.model.UnitsFactory
pixelsData - Variable in class ome.logic.RenderingSettingsImpl: Reference to the service used to retrieve the pixels data.
PixelsData - Class in pojos: The data that makes up an OME Pixels object along with a back pointer to the Image that owns this Pixels.
PixelsData() - Constructor for class pojos.PixelsData: Creates a new instance.
PixelsData(Pixels) - Constructor for class pojos.PixelsData: Creates a new instance.
PixelsFileDeletions - Class in ome.services.delete.files: Registers the given file paths as well as other Pixel-related files like Pyramids for later deletion via #deleteLocal(java.util.Map).
PixelsFileDeletions(AbstractFileSystemService, Set<Long>) - Constructor for class ome.services.delete.files.PixelsFileDeletions
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, IQuery) - Constructor for class ome.io.nio.PixelsService: Constructor.
PixelsService(String, long, FilePathResolver, BackOff, TileSizes, IQuery) - Constructor for class ome.io.nio.PixelsService: Call #PixelsService(String, File, long, FilePathResolver, BackOff, TileSizes) with PixelsService.MEMOIZER_WAIT.
PixelsService(String, File, FilePathResolver, BackOff, TileSizes, IQuery) - Constructor for class ome.io.nio.PixelsService: Call #PixelsService(String, File, long, FilePathResolver, BackOff, TileSizes) with PixelsService.MEMOIZER_WAIT.
PixelsService(String, File, long, FilePathResolver, BackOff, TileSizes, IQuery) - Constructor for class ome.io.nio.PixelsService
pixelsService - Variable in class ome.services.pixeldata.PixelDataHandler
pixelsService - Variable in class ome.services.projection.ProjectionBean: Reference to the service used to retrieve the pixels data.
pixId - Variable in class ome.formats.importer.ImportEvent.PROGRESS_EVENT
pixToImageCache - Variable in class ome.services.sharing.BlobShareStore
Plane2D - Class in omeis.providers.re.data
Plane2D(PlaneDef, Pixels, PixelData) - Constructor for class omeis.providers.re.data.Plane2D: Constructor that sub-classes must call.
Plane_DeltaT - Static variable in class ome.formats.model.UnitsFactory
Plane_ExposureTime - Static variable in class ome.formats.model.UnitsFactory
Plane_PositionX - Static variable in class ome.formats.model.UnitsFactory
Plane_PositionY - Static variable in class ome.formats.model.UnitsFactory
Plane_PositionZ - Static variable in class ome.formats.model.UnitsFactory
PlaneArea - Interface in ome.util.math.geom2D: Interface that all areas of the Euclidean space R² must implement.
planeDef - Variable in class omeis.providers.re.data.Plane2D: The type of plane.
PlaneDef - Class in omeis.providers.re.data: Identifies a 2D-plane in the XYZ moving frame of the 3D stack.
PlaneDef(int, int) - Constructor for class omeis.providers.re.data.PlaneDef: Creates a new instance.
PlaneFactory - Class in omeis.providers.re.data: Encapsulates access to the image raw data.
PlaneFactory() - Constructor for class omeis.providers.re.data.PlaneFactory
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.
planOperation(Session, SetMultimap<String, Long>, boolean) - Method in class ome.services.graphs.GraphTraversal: Traverse model object graph to determine steps for the proposed operation.
planOperation(Session, Collection<? extends IObject>, boolean) - Method in class ome.services.graphs.GraphTraversal: Traverse model object graph to determine steps for the proposed operation.
PLATE_LINKS - Static variable in class pojos.ScreenData: Identifies the Screen#PLATELINKS field.
Plate_WellOriginX - Static variable in class ome.formats.model.UnitsFactory
Plate_WellOriginY - Static variable in class ome.formats.model.UnitsFactory
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.
PLATEIMAGES_QUERY - Static variable in class ome.services.delete.DeleteBean
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
Policy - Interface in ome.security.policy: Strategy to permit the flexible restriction of certain actions throughout OMERO.
policyService - Variable in class ome.security.basic.BasicACLVoter
policyService - Variable in class ome.security.basic.BasicSecuritySystem
PolicyService - Interface in ome.security.policy: Internal service containing a number of configured Policy instances.
poll(Current) - Method in class ome.services.blitz.impl.ScriptProcessI
poll() - Method in class omero.cmd.CmdCallbackI: Calls HandlePrx.getResponse() in order to check for a non-null value.
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: Deprecated.
pop() - Method in class ome.services.graphs.GraphOpts: Deprecated.
pop(GraphOpts) - Method in class ome.services.graphs.GraphStep: Deprecated.
pop() - Method in class ome.services.pixeldata.PersistentEventLogLoader
pop(List<IObject>) - Method in class ome.services.SearchBean: Wrapper method which should be called on all results for the user.
pop(String[]) - Static method in class prefs: Creates a new subarray from the argument, effectively popping off the first element.
popRoi - Variable in class ome.services.blitz.impl.MetadataStoreI
populateMinMax(double[][][]) - Method in class ome.formats.OMEROMetadataStore: Synchronize the minimum and maximum intensity values with those specified by the client and save them in the DB.
populateMinMax() - Method in class ome.formats.OMEROMetadataStoreClient: Sends all the minimums and maximums for all images processed so far to the server.
populateMinMax_async(AMD_MetadataStore_populateMinMax, double[][][], Current) - Method in class ome.services.blitz.impl.MetadataStoreI
PopulateRoiJob - Class in ome.services.roi: Start-up task which guarantees that lib/python/populateroi.py is added as a script to the server.
PopulateRoiJob(Roles, String, Executor) - Constructor for class ome.services.roi.PopulateRoiJob
PopulateRoiJob(Roles, String, Executor, File) - Constructor for class ome.services.roi.PopulateRoiJob
PopulateRoiJob(Roles, Principal, Executor, File) - Constructor for class ome.services.roi.PopulateRoiJob
port - Variable in class loci.ome.io.OMECredentials
port - Variable in class ome.formats.importer.ImportConfig
postClose(Current) - Method in class ome.services.blitz.impl.AbstractCloseableAmdServant: Should not throw any exceptions which should be detected by clients since it is called in a finally block after the client thread has been released.
postClose(Current) - Method in class ome.services.blitz.impl.AbstractPyramidServant
postClose(Current) - Method in class ome.services.blitz.impl.ExporterI
postClose(Current) - Method in class ome.services.blitz.impl.JobHandleI
postClose(Current) - Method in class ome.services.blitz.impl.MetadataStoreI
postClose(Current) - Method in class ome.services.blitz.impl.RawFileStoreI
postClose(Current) - Method in class ome.services.blitz.impl.SearchI
postClose(Current) - Method in class ome.services.blitz.impl.SharedResourcesI
postClose(Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
postClose(Current) - Method in class ome.services.blitz.repo.ManagedImportProcessI
postClose(Current) - Method in class ome.services.blitz.repo.RepoRawFileStoreI
postFlush(Iterator) - Method in class ome.security.basic.OmeroInterceptor
postProcess() - Method in class ome.formats.OMEROMetadataStoreClient: Post processes the internal structure of the client side MetadataStore.
postProcess() - Method in class ome.io.bioformats.OmeroPixelsPyramidWriter: Performs re-compression post processing on the pixel pyramid.
postProcess(IObject) - Method in interface ome.security.ACLVoter: Gives the ACLVoter instance a chance to act on the IObject after the transaction but before finishing the AOP stack.
postProcess(IObject) - Method in class ome.security.basic.BasicACLVoter
postProcess(IObject) - Method in class ome.security.CompositeACLVoter
postProcess(IObject) - Method in class ome.security.sharing.SharingACLVoter
postProcess(List<GraphStep>) - Method in class ome.services.export.ExporterStepFactory: Deprecated.
postProcess(List<GraphStep>) - Method in class ome.services.graphs.AbstractStepFactory: Deprecated.
postProcess(ListableBeanFactory) - Method in class ome.services.graphs.BaseGraphSpec: Deprecated.
postProcess(ListableBeanFactory) - Method in class ome.services.graphs.GraphEntry: Deprecated.

Load the spec which has the same name as this entry, but do not load the spec if the name matches GraphEntry.name.
postProcess(ListableBeanFactory) - Method in interface ome.services.graphs.GraphSpec: Deprecated.

Gives all specs a chance to reference subspecs.
postProcess(List<GraphStep>) - Method in interface ome.services.graphs.GraphStepFactory: Deprecated.

Gives the GraphStepFactory a chance to add pre or post-steps for validation and similar activities.
postProcess_async(AMD_MetadataStore_postProcess, Current) - Method in class ome.services.blitz.impl.MetadataStoreI: Called after some number of Passes the #savedPixels to a background processor for further work.
postProcessAfterInitialization(Object, String) - Method in class ome.services.blitz.util.ApiConsistencyCheck
postProcessAfterInitialization(Object, String) - Method in class ome.services.graphs.GraphSpecPostProcessor: Deprecated.
postProcessBeanFactory(ConfigurableListableBeanFactory) - Method in class ome.system.PreferenceContext
postProcessBeforeInitialization(Object, String) - Method in class ome.services.blitz.util.ApiConsistencyCheck: No-op
postProcessBeforeInitialization(Object, String) - Method in class ome.services.graphs.GraphSpecPostProcessor: Deprecated.
postProcessOptions() - Method in class ome.services.graphs.AbstractHierarchyGraphSpec: Deprecated.

If any options exist, this method will be called to finalize any of the processing done by AbstractHierarchyGraphSpec.handleOptions(int, String[]).
postProcessOptions() - Method in class ome.services.graphs.AnnotationGraphSpec: Deprecated.
postProcessOptions() - Method in class ome.services.graphs.LightSourceGraphSpec: Deprecated.
PowerI - Class in omero.model: Blitz wrapper around the Power class.
PowerI() - Constructor for class omero.model.PowerI
PowerI(double, UnitsPower) - Constructor for class omero.model.PowerI
PowerI(double, Unit<Power>) - Constructor for class omero.model.PowerI
PowerI(Power, Unit<Power>) - Constructor for class omero.model.PowerI: Copy constructor that converts the given Power based on the given ome-xml enum
PowerI(double, UnitsPower) - Constructor for class omero.model.PowerI: Copy constructor that converts the given Power based on the given ome.model enum
PowerI(Power, String) - Constructor for class omero.model.PowerI: Copy constructor that converts the given Power based on the given enum string.
PowerI(Power, UnitsPower) - Constructor for class omero.model.PowerI: Copy constructor that converts between units if possible.
PowerI(Power) - Constructor for class omero.model.PowerI: Convert a Bio-Formats Length to an OMERO Length.
preClose(Current) - Method in class ome.services.blitz.impl.AbstractCloseableAmdServant
preClose(Current) - Method in class ome.services.blitz.impl.AbstractPyramidServant
preClose(Current) - Method in class ome.services.blitz.impl.ExporterI
preClose(Current) - Method in class ome.services.blitz.impl.JobHandleI
preClose(Current) - Method in class ome.services.blitz.impl.MetadataStoreI
preClose(Current) - Method in class ome.services.blitz.impl.RawFileStoreI
preClose(Current) - Method in class ome.services.blitz.impl.SearchI
preClose(Current) - Method in class ome.services.blitz.impl.SharedResourcesI
preClose(Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
preClose(Current) - Method in class ome.services.blitz.repo.ManagedImportProcessI
preClose(Current) - Method in class ome.services.blitz.repo.RepoRawFileStoreI
Preference - Class in ome.system: Definition of a server configuration variable ("preference") along with its mutability, visibility, aliases and other important information.
Preference() - Constructor for class ome.system.Preference: By default, configures this instance for PropertyPlaceholderConfigurer.SYSTEM_PROPERTIES_MODE_OVERRIDE as well as ignoring unfound resources.
Preference(String, boolean, Preference.Visibility, String[]) - Constructor for class ome.system.Preference
Preference.Visibility - Enum in ome.system
PreferenceContext - Class in ome.system: Central configuration for OMERO properties from (in order): Any injected Properties instances Java System.getProperties() Any configured property files As of OMERO 4.2, server configurations are not stored in Java's Preferences API but in an IceGrid xml file under etc/grid of the server installation.
PreferenceContext() - Constructor for class ome.system.PreferenceContext: By default, configures this instance for PropertyPlaceholderConfigurer.SYSTEM_PROPERTIES_MODE_OVERRIDE as well as ignoring unfound resources.
preFlush(Iterator) - Method in class ome.security.basic.OmeroInterceptor
prefs - Class in <Unnamed>: Command-line (and static) utility for working with the omero.prefs Preferences node in order to store Java properties-file like values on a user basis.
prefs() - Constructor for class prefs
prepare(Set<Long>) - Method in interface ome.api.RawPixelsStore: Prepares the stateful service with a cache of loaded Pixels objects.
prepare(Map<Integer, Image>) - Method in class ome.formats.OMEROMetadataStoreClient: Prepares the metadata store using existing metadata that has been pre-registered by OMERO.fs.
prepare(Set<Long>) - Method in class ome.services.RawPixelsBean
prepare_async(AMD_RawPixelsStore_prepare, List<Long>, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
prepare_async(AMD_RawPixelsStore_prepare, List<Long>, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
prepareLookups(String, String, Collection<Long>) - Method in class ome.services.query.HierarchyNavigator: Batch bulk database queries to prime the cache for HierarchyNavigator.doLookup(String, String, Long).
prepareLookups(T, Collection<E>) - Method in class ome.services.query.HierarchyNavigatorWrap: Batch bulk database queries to prime the cache for HierarchyNavigatorWrap.doLookup(Object, Object).
preparePassword(String) - Method in class ome.security.auth.PasswordUtil
preparePassword(Long, String, boolean) - Method in class ome.security.auth.PasswordUtil
preparePixelsStore(List<Long>) - Method in class ome.formats.OMEROMetadataStoreClient: Prepares the server side RawPixelsStore.
prepareReload() - Method in class ome.services.sessions.SessionManagerImpl
prepareSaltedPassword(Long, String) - Method in class ome.security.auth.PasswordUtil
prepareStatement() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
Preprocessor - Class in omero.cmd.graphs: Deprecated.
will be removed in OMERO 5.2, so use the new graphs implementation
Preprocessor(List<Request>, Helper) - Constructor for class omero.cmd.graphs.Preprocessor: Deprecated.
Preprocessor(List<Request>, HierarchyNavigatorWrap<Preprocessor.TargetType, Preprocessor.GraphModifyTarget>) - Constructor for class omero.cmd.graphs.Preprocessor: Deprecated.
Preprocessor.GraphModifyTarget - Class in omero.cmd.graphs: Deprecated.

A tuple of target type and target ID.
Preprocessor.GraphModifyTarget(Preprocessor.TargetType, long) - Constructor for class omero.cmd.graphs.Preprocessor.GraphModifyTarget: Deprecated.

Construct a target type-ID tuple.
Preprocessor.TargetType - Enum in omero.cmd.graphs: Deprecated.

The types of target for which we care about adjusting graph operation requests.
PressureI - Class in omero.model: Blitz wrapper around the Pressure class.
PressureI() - Constructor for class omero.model.PressureI
PressureI(double, UnitsPressure) - Constructor for class omero.model.PressureI
PressureI(double, Unit<Pressure>) - Constructor for class omero.model.PressureI
PressureI(Pressure, Unit<Pressure>) - Constructor for class omero.model.PressureI: Copy constructor that converts the given Pressure based on the given ome-xml enum
PressureI(double, UnitsPressure) - Constructor for class omero.model.PressureI: Copy constructor that converts the given Pressure based on the given ome.model enum
PressureI(Pressure, String) - Constructor for class omero.model.PressureI: Copy constructor that converts the given Pressure based on the given enum string.
PressureI(Pressure, UnitsPressure) - Constructor for class omero.model.PressureI: Copy constructor that converts between units if possible.
PressureI(Pressure) - Constructor for class omero.model.PressureI: Convert a Bio-Formats Length to an OMERO Length.
previewImageDelete(long, boolean) - Method in interface ome.api.IDelete: Returns all entities which would be deleted by a call to IDelete.deleteImage(long, boolean).
previewImageDelete(long, boolean) - Method in class ome.services.delete.DeleteBean: This uses DeleteBean.IMAGE_QUERY to load all the subordinate metadata of the Image which will be deleted.
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.blitz.repo.RepositoryDaoImpl
principal - Variable in class ome.services.sessions.SessionManager.CreationRequest
principal - Variable in class ome.services.util.ExecutionThread
principal() - Method in class ome.services.util.Executor.Impl
principal() - Method in interface ome.services.util.Executor: Returns a Principal representing your current session or null, if none is active.
Principal - Class in ome.system: implementation of Principal.
Principal(String) - Constructor for class ome.system.Principal: Creates a Principal with null group and event type.
Principal(String, String, String) - Constructor for class ome.system.Principal
principal - Variable in class ome.system.SessionInitializer: Principal given by the user
principal - Variable in class omero.cmd.SessionI
principalHolder - Variable in class ome.security.basic.BasicSecurityWiring
PrincipalHolder - Interface in ome.security.basic: Stack of active Principal instances.
principalHolder - Variable in class ome.services.sessions.SessionManagerImpl
principalHolder - Variable in class ome.services.util.Executor.Impl
print() - Method in class ome.formats.importer.ImportCandidates: Prints the "standard" representation of the groups, which is parsed by other software layers.
print(String[]) - Static method in class prefs: Prints the arg array and returns an empty array (for exit purposes)
printDebug(String[]) - Static method in class prefs: Delegates to prefs.printErr(String[]) iff prefs.DEBUG is true.
printErr(String[]) - Static method in class prefs: Prints the arg array and returns the input array (for exit purposes)
printLine() - Method in class ome.formats.importer.transfers.AbstractExecFileTransfer
printLine() - Method in class ome.formats.importer.transfers.AbstractFileTransfer
process(IObjectContainerStore) - Method in class ome.formats.model.ChannelProcessor: Processes the OMERO client side metadata store.
process(IObjectContainerStore) - Method in class ome.formats.model.InstrumentProcessor: Processes the OMERO client side metadata store.
process(IObjectContainerStore) - Method in interface ome.formats.model.ModelProcessor: Processes the an IObjectContainerStore.
process(IObjectContainerStore) - Method in class ome.formats.model.PixelsProcessor: Processes the OMERO client side metadata store.
process(IObjectContainerStore) - Method in class ome.formats.model.PlaneInfoProcessor: Processes the OMERO client side metadata store.
process(IObjectContainerStore) - Method in class ome.formats.model.ReferenceProcessor
process(IObjectContainerStore) - Method in class ome.formats.model.ShapeProcessor: Processes the OMERO client side metadata store.
process(IObjectContainerStore) - Method in class ome.formats.model.TargetProcessor: Processes the OMERO client side metadata store.
process(IObjectContainerStore) - Method in class ome.formats.model.WellProcessor: Processes the OMERO client side metadata store.
process(Long, ServiceFactory, Session) - Method in class ome.services.pixeldata.PixelDataHandler: Here we assume that our log loader will only return us the proper types, since we are using the specific type defined in this package.
Process - Interface in ome.services.procs
process(long) - Method in interface ome.services.procs.Processor
process(long) - Method in class ome.services.procs.ProcessorSkeleton
process(Job) - Method in class ome.services.procs.ProcessorSkeleton
process() - Method in class omero.cmd.graphs.Preprocessor: Deprecated.

Preprocess the list of requests.
process - Variable in class omero.grid.ProcessCallbackI: Proxy passed to this instance on creation.
ProcessCallback - Interface in ome.services.procs
ProcessCallbackI - Class in omero.grid
ProcessCallbackI(client, ProcessPrx) - Constructor for class omero.grid.ProcessCallbackI
ProcessCallbackI(client, ProcessPrx, boolean) - Constructor for class omero.grid.ProcessCallbackI
ProcessCallbackI(ObjectAdapter, String, ProcessPrx) - Constructor for class omero.grid.ProcessCallbackI
ProcessCallbackI(ObjectAdapter, String, ProcessPrx, boolean) - Constructor for class omero.grid.ProcessCallbackI
ProcessCallbackI.Action - Enum in omero.grid
processCancelled(Process) - Method in class ome.services.JobBean
processCancelled(Process) - Method in interface ome.services.procs.ProcessCallback
processCancelled(boolean, Current) - Method in class omero.grid.ProcessCallbackI
ProcessContainer - Class in ome.services.blitz.repo: Helper class for holding the individual ManagedImportProcessI instances created by ManagedRepositoryI.
ProcessContainer() - Constructor for class ome.services.blitz.repo.ProcessContainer
ProcessContainer.Process - Interface in ome.services.blitz.repo
processFinished(Process) - Method in class ome.services.JobBean
processFinished(Process) - Method in interface ome.services.procs.ProcessCallback
processFinished(int, Current) - Method in class omero.grid.ProcessCallbackI
processInstances(String, Collection<Long>) - Method in interface ome.services.graphs.GraphTraversal.Processor: Process the given instances.
processInstances(String, Collection<Long>) - Method in class omero.cmd.graphs.NullGraphTraversalProcessor
processKilled(boolean, Current) - Method in class omero.grid.ProcessCallbackI
ProcessManager - Class in ome.services.procs
ProcessManager(SessionManager, SecuritySystem, Executor, Processor...) - Constructor for class ome.services.procs.ProcessManager: main constructor which takes a non-null array of Processor instances as its only argument.
ProcessManager.Work - Class in ome.services.procs: Task performed by the ProcessManager on each invocation of ExecutionThread.run().
ProcessManager.Work(SecuritySystem, Processor...) - Constructor for class ome.services.procs.ProcessManager.Work
processor() - Method in interface ome.services.procs.Process
Processor - Interface in ome.services.procs
processor() - Method in class ome.services.procs.ProcessSkeleton
ProcessorCallbackI - Class in ome.services.blitz.impl: Callback used to lookup active processors via IceStorm.
ProcessorCallbackI(ServiceFactoryI) - Constructor for class ome.services.blitz.impl.ProcessorCallbackI: Simplified constructor used to see if any usermode processor is active for either the current group or the current user.
ProcessorCallbackI(ServiceFactoryI, ResultHolder<ProcessorPrx>, Job) - Constructor for class ome.services.blitz.impl.ProcessorCallbackI: Primary constructor.
processors - Variable in class ome.services.procs.ProcessManager.Work: processors available for processing.
ProcessorSkeleton - Class in ome.services.procs
ProcessorSkeleton() - Constructor for class ome.services.procs.ProcessorSkeleton
ProcessSkeleton - Class in ome.services.procs
ProcessSkeleton(Processor) - Constructor for class ome.services.procs.ProcessSkeleton
processTargets() - Method in class ome.services.graphs.GraphTraversal: Process the targeted model objects.
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
ProportionalTimeEstimatorImpl - Class in ome.formats.importer.util: Class implementing the TimeEstimator interface.
ProportionalTimeEstimatorImpl(long) - Constructor for class ome.formats.importer.util.ProportionalTimeEstimatorImpl: Creates a new object of this class with a defined internal buffer size.
proxy() - Method in class ome.services.blitz.impl.ServiceFactoryI
ProxyCleanupFilter - Class in ome.tools.hibernate: removes all proxies from a return graph to prevent ClassCastExceptions and Session Closed exceptions.
ProxyCleanupFilter() - Constructor for class ome.tools.hibernate.ProxyCleanupFilter: Passes null to ProxyCleanupFilter#ProxyCleanupFilter(CurrentDetails) such that all restricted objects will be unloaded.
ProxyCleanupFilter(ACLVoter, CurrentDetails) - Constructor for class ome.tools.hibernate.ProxyCleanupFilter: Constructor take a CurrentDetails object in order to check the security restrictions on certain objects.
ProxyCleanupFilter.Interceptor - Class in ome.tools.hibernate: wraps a filter for each invocation
ProxyCleanupFilter.Interceptor(ACLVoter, SessionHandler, CurrentDetails) - Constructor for class ome.tools.hibernate.ProxyCleanupFilter.Interceptor
proxyForSession(Redirector.Context, String) - Method in class ome.services.blitz.redirect.AbstractRedirector
proxyNames - Variable in class ome.services.util.Executor.Impl
ProxySafeFilter - Class in ome.tools.hibernate: extension to ContextFilter to check for uninitialized Hibernate proxies before stepping into an entity or collection.
ProxySafeFilter() - Constructor for class ome.tools.hibernate.ProxySafeFilter
pt(double, double) - Method in class ome.services.roi.GeomTool
PublicRepositoryI - Class in ome.services.blitz.repo: An implementation of the PublicRepository interface.
PublicRepositoryI(RepositoryDao, ChecksumProviderFactory, String, String) - Constructor for class ome.services.blitz.repo.PublicRepositoryI
PublicRepositoryI.AMD_submit - Class in ome.services.blitz.repo
PublicRepositoryI.AMD_submit() - Constructor for class ome.services.blitz.repo.PublicRepositoryI.AMD_submit
publish(EventLogMessage) - Method in class ome.services.chgrp.ChgrpStep: Deprecated.
publisher - Variable in class ome.services.fulltext.BridgeHelper
publisher - Variable in class ome.services.sessions.stats.CounterFactory
publisherOrNull(String) - Method in class ome.services.blitz.fire.TopicManager.Impl
publishEvent(ApplicationEvent) - Method in class ome.system.OmeroContext
publishMessage(InternalMessage) - Method in class ome.services.blitz.repo.PublicRepositoryI
publishMessage(InternalMessage) - Method in class ome.system.OmeroContext: Convenience method around OmeroContext.publishEvent(org.springframework.context.ApplicationEvent) which catches all MessageException and unwraps the contained Throwable instance and rethrows.
purgeNode(String) - Method in class ome.services.blitz.fire.Ring
push(GraphOpts, EventContext) - Method in class ome.services.graphs.GraphEntry: Deprecated.
push(GraphOpts.Op, boolean, EventContext) - Method in class ome.services.graphs.GraphOpts: Deprecated.

Adds the given operation to the current list if the user has permissions to do so.
push(GraphOpts) - Method in class ome.services.graphs.GraphStep: Deprecated.
put(File, Dataset) - Method in class ome.formats.importer.ImportFixture
put(String, String) - Method in class ome.security.auth.AttributeSet
put(Callback) - Method in class ome.services.throttling.Queue
put(Identity, Object) - Method in class omero.util.ServantHolder
putAll(Map<File, Dataset>) - Method in class ome.formats.importer.ImportFixture
putBytes(byte[]) - Method in class ome.util.checksum.AbstractChecksumProvider
putBytes(byte[], int, int) - Method in class ome.util.checksum.AbstractChecksumProvider
putBytes(ByteBuffer) - Method in class ome.util.checksum.AbstractChecksumProvider
putBytes(byte[]) - Method in interface ome.util.checksum.ChecksumProvider: Updates the internal checksum value with data from a byte array.
putBytes(byte[], int, int) - Method in interface ome.util.checksum.ChecksumProvider: Updates the internal checksum value with data from a chunk of a byte array.
putBytes(ByteBuffer) - Method in interface ome.util.checksum.ChecksumProvider: Updates the internal checksum value with data from a byte buffer.
putBytes(byte[]) - Method in class ome.util.checksum.FileSizeChecksumProviderImpl
putBytes(byte[], int, int) - Method in class ome.util.checksum.FileSizeChecksumProviderImpl
putBytes(ByteBuffer) - Method in class ome.util.checksum.FileSizeChecksumProviderImpl
putFile(String) - Method in class ome.util.checksum.AbstractChecksumProvider
putFile(String) - Method in interface ome.util.checksum.ChecksumProvider: Updates the internal checksum value with data from a file identified by a path.
putFile(String) - Method in class ome.util.checksum.FileSizeChecksumProviderImpl
putSession(String, SessionContext) - Method in class ome.services.sessions.state.SessionCache: Puts a session blindly into the context.
putStatus(MethodInvocation, SessionStatus) - Method in class ome.tools.hibernate.SessionHandler
PYR_LOCK_EXT - Static variable in class ome.io.bioformats.BfPyramidPixelBuffer
PYRAMID_SUFFIX - Static variable in class ome.io.nio.PixelsService: Suffix for an the image pyramid of a given pixels set.

Q

qaBaseURL - Variable in class ome.formats.importer.ImportConfig
qDef - Variable in class omeis.providers.re.quantum.QuantumStrategy: Reference to a quantumDef object.
Quantization_32_bit - Class in omeis.providers.re.quantum: Quantization process.
Quantization_32_bit(QuantumDef, Pixels) - Constructor for class omeis.providers.re.quantum.Quantization_32_bit: Creates a new strategy.
Quantization_8_16_bit - Class in omeis.providers.re.quantum: Quantization process.
Quantization_8_16_bit(QuantumDef, Pixels) - Constructor for class omeis.providers.re.quantum.Quantization_8_16_bit: Creates a new strategy.
Quantization_float - Class in omeis.providers.re.quantum: Quantization process.
Quantization_float(QuantumDef, Pixels) - Constructor for class omeis.providers.re.quantum.Quantization_float: Creates a new strategy.
QuantizationException - Exception in omeis.providers.re.quantum: This exception is thrown during the quantization process if something goes wrong.
QuantizationException() - Constructor for exception omeis.providers.re.quantum.QuantizationException: Creates a new exception.
QuantizationException(String) - Constructor for exception omeis.providers.re.quantum.QuantizationException: Constructs a new exception with the specified detail message.
QuantizationException(Throwable) - Constructor for exception omeis.providers.re.quantum.QuantizationException: Constructs a new exception with the specified cause.
QuantizationException(String, Throwable) - Constructor for exception omeis.providers.re.quantum.QuantizationException: Constructs a new exception with the specified detail message and cause.
quantize(double) - Method in class omeis.providers.re.quantum.BinaryMaskQuantizer: Implemented as specified in QuantumStrategy.
quantize(double) - Method in class omeis.providers.re.quantum.Quantization_32_bit: Implemented as specified in QuantumStrategy.
quantize(double) - Method in class omeis.providers.re.quantum.Quantization_8_16_bit: Implemented as specified in QuantumStrategy.
quantize(double) - Method in class omeis.providers.re.quantum.Quantization_float: Implemented as specified in QuantumStrategy.
quantize(double) - Method in class omeis.providers.re.quantum.QuantumStrategy: Maps a value from [windowStart, windowEnd] to a value in the codomain interval.
QuantumFactory - Class in omeis.providers.re.quantum: Factory to create objects to carry out quantization for a given context.
QuantumFactory(List<Family>) - Constructor for class omeis.providers.re.quantum.QuantumFactory: Default constructor.
QuantumMap - Interface in omeis.providers.re.quantum: Provides methods to map value.
QuantumStrategy - Class in omeis.providers.re.quantum: Subclasses Work on explicit pixel types.
QuantumStrategy(QuantumDef, Pixels) - Constructor for class omeis.providers.re.quantum.QuantumStrategy: Creates a new instance.
query() - Method in class ome.services.eventlogs.AllEntitiesPseudoLogLoader
query() - Method in class ome.services.eventlogs.AllEventsLogLoader
query - Variable in class ome.services.eventlogs.EventLogLoader: Query string to be kept in sync with EventLogLoader.excludes.
query() - Method in class ome.services.eventlogs.EventLogLoader
query() - Method in class ome.services.eventlogs.EventLogQueue
query() - Method in class ome.services.eventlogs.PersistentEventLogLoader
query() - Method in class ome.services.pixeldata.PersistentEventLogLoader: Uses data from the PersistentEventLogLoader.dataPerUser "queue" to allow new requests to be processed even if one user adds a large number of PIXELDATA events.
Query<T> - Class in ome.services.query: base Query type to facilitate the creation of ORM queries.
Query(Definitions, Parameters) - Constructor for class ome.services.query.Query: main constructor used by subclasses.
query(Session) - Method in class ome.tools.hibernate.QueryBuilder
query - Variable in class omero.cmd.admin.UpdateSessionTimeoutRequestI
queryBackupIds(Session, int, GraphEntry, QueryBuilder) - Method in class ome.services.graphs.AbstractHierarchyGraphSpec: Deprecated.
queryBackupIds(Session, int, GraphEntry, QueryBuilder) - Method in class ome.services.graphs.BaseGraphSpec: Deprecated.
queryBackupIds(Session, int, GraphEntry, QueryBuilder) - Method in interface ome.services.graphs.GraphSpec: Deprecated.

If a given path is processed before its sub-path, this points to a one-to-one relationship.
QueryBuilder - Class in ome.tools.hibernate: Very thin wrapper around a StringBuilder to generate HQL queries.
QueryBuilder() - Constructor for class ome.tools.hibernate.QueryBuilder
QueryBuilder(boolean) - Constructor for class ome.tools.hibernate.QueryBuilder: Whether Session.createSQLQuery(String) should be used or not during QueryBuilder.__query(Session, boolean)
QueryBuilder(int) - Constructor for class ome.tools.hibernate.QueryBuilder
queryCacheHit(String, String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
queryCacheMiss(String, String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
queryCachePut(String, String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
QueryConstraints - Class in ome.services.delete: AdminAction which queries all datasets and annotations belonging to the given Image
QueryConstraints(LocalAdmin, LocalQuery, long, boolean) - Constructor for class ome.services.delete.QueryConstraints
QueryException - Exception in ome.services.query: something failed in looking up a query
QueryException(String) - Constructor for exception ome.services.query.QueryException
queryExecuted(String, int, long) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
queryFactory - Variable in class ome.logic.AbstractLevel1Service
queryFactory - Variable in class ome.logic.AbstractLevel2Service
QueryFactory - Class in ome.services.query: query locator which is configured by Spring.
QueryFactory(QuerySource...) - Constructor for class ome.services.query.QueryFactory: main constructor which takes a non-null array of query sources as its only argument.
QueryI - Class in ome.services.blitz.impl: Implementation of the IQuery service.
QueryI(IQuery, BlitzExecutor) - Constructor for class ome.services.blitz.impl.QueryI
QueryImpl - Class in ome.logic: Provides methods for directly querying object graphs.
QueryImpl() - Constructor for class ome.logic.QueryImpl
QueryNewUserGroupBean - Class in ome.security.auth: Handles the ":query:" specifier from etc/omero.properties.
QueryNewUserGroupBean(String) - Constructor for class ome.security.auth.QueryNewUserGroupBean
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.
queryService - Variable in class ome.services.eventlogs.EventLogLoader
QuerySource - Class in ome.services.query: contract for any source of queries.
QuerySource() - Constructor for class ome.services.query.QuerySource
queryString() - Method in class ome.tools.hibernate.QueryBuilder: Returns the current query as a String.
queryWithoutFilter(Session) - Method in class ome.tools.hibernate.QueryBuilder
Queue - Class in ome.services.throttling: Manages AMD-based method dispatches from blitz
Queue(OmeroContext) - Constructor for class ome.services.throttling.Queue
QUEUED - Static variable in interface ome.api.JobHandle

R

R_BAND - Static variable in class omeis.providers.re.RGBBuffer: Index of the red band in the image's data buffer.
random(int) - Method in class ome.services.roi.GeomTool
randomize(Random) - Method in class omero.model.SmartEllipseI
randomize(Random) - Method in class omero.model.SmartLineI
randomize(Random) - Method in class omero.model.SmartMaskI
randomize(Random) - Method in class omero.model.SmartPathI
randomize(Random) - Method in class omero.model.SmartPointI
randomize(Random) - Method in class omero.model.SmartPolygonI
randomize(Random) - Method in class omero.model.SmartPolylineI
randomize(Random) - Method in class omero.model.SmartRectI
randomize(Random) - Method in interface omero.model.SmartShape: Initializes this shape with completely random data.
randomize(Random) - Method in class omero.model.SmartTextI
rarray(RType...) - Static method in class omero.rtypes
rarray(Collection<RType>) - Static method in class omero.rtypes
RatingAnnotationData - Class in pojos: Annotation used to rate an object.
RatingAnnotationData() - Constructor for class pojos.RatingAnnotationData: Creates a new instance of value LEVEL_ZERO.
RatingAnnotationData(int) - Constructor for class pojos.RatingAnnotationData: Creates a new instance.
RatingAnnotationData(LongAnnotation) - Constructor for class pojos.RatingAnnotationData: Creates a new instance.
rawAccess(RawAccessRequest, Current) - Method in class ome.services.blitz.repo.AbstractRepositoryI
rawAccess() - Method in class ome.services.blitz.repo.RawAccessRequestI
RawAccessRequestI - Class in ome.services.blitz.repo: Command request for accessing a repository directly.
RawAccessRequestI(Registry) - Constructor for class ome.services.blitz.repo.RawAccessRequestI
RawFileBean - Class in ome.services: Raw file gateway which provides access to the OMERO file repository.
RawFileBean() - Constructor for class ome.services.RawFileBean: default constructor
RawFileBean(boolean) - Constructor for class ome.services.RawFileBean: overridden to allow Spring to set boolean
RawFileStore - Interface in ome.api: Raw file gateway which provides access to the OMERO file repository.
RawFileStoreI - Class in ome.services.blitz.impl: Implementation of the RawFileStore service.
RawFileStoreI(RawFileStore, BlitzExecutor) - Constructor for class ome.services.blitz.impl.RawFileStoreI
rawOption - Variable in class ome.services.graphs.AbstractHierarchyGraphSpec: Deprecated.

Original string contained in the options Map before parsing.
RawPixelsBean - Class in ome.services: Implementation of the RawPixelsStore stateful service.
RawPixelsBean() - Constructor for class ome.services.RawPixelsBean: default constructor
RawPixelsBean(boolean, String) - Constructor for class ome.services.RawPixelsBean: overridden to allow Spring to set boolean
RawPixelsStore - Interface in ome.api: Binary data provider.
RawPixelsStoreI - Class in ome.services.blitz.impl: Implementation of the RawPixelsStore service.
RawPixelsStoreI(RawPixelsStore, BlitzExecutor) - Constructor for class ome.services.blitz.impl.RawPixelsStoreI
rbool(boolean) - Static method in class omero.rtypes
rclass(String) - Static method in class omero.rtypes
rdouble(double) - Static method in class omero.rtypes
read(long, int) - Method in interface ome.api.RawFileStore: Delegates to FileBuffer
read(ByteBuffer) - Method in class ome.io.nio.FileBuffer: Delegates to FileChannel
read(ByteBuffer, long) - Method in class ome.io.nio.FileBuffer: Delegates to FileChannel
read(long, int) - Method in class ome.services.RawFileBean
read(String) - Method in class ome.services.scripts.ScriptRepoHelper
read_async(AMD_Exporter_read, long, int, Current) - Method in class ome.services.blitz.impl.ExporterI
read_async(AMD_RawFileStore_read, long, int, Current) - Method in class ome.services.blitz.impl.RawFileStoreI
read_async(AMD_RawFileStore_read, long, int, Current) - Method in class ome.services.blitz.repo.RepoRawFileStoreI
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.
reapSession(String) - Method in class ome.services.blitz.fire.SessionManagerI: Destroys all the ServiceFactoryI instances based on the given sessionId.
recompressSeries(TiffReader, int) - Method in class ome.io.bioformats.OmeroPixelsPyramidWriter: Re-compresses a source series, that is JPEG 2000 compressed, via its resolution level.
recreateCollection(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
rect(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(String, CheckedPath, String, Current) - Method in interface ome.services.blitz.repo.RepositoryDao: Register an OriginalFile object
register(String, CheckedPath, String, ServiceFactory, SqlAction) - Method in interface ome.services.blitz.repo.RepositoryDao: Like {@link #register(String, CheckedPath, String, Ice.Current) but does not create a new transaction.
register(String, CheckedPath, String, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
register(String, CheckedPath, String, ServiceFactory, SqlAction) - Method in class ome.services.blitz.repo.RepositoryDaoImpl: Returned original file object is "live" within the Hibernate session.
register(Logger, Communicator, boolean) - Method in class omero.util.ObjectFactoryRegistry.ObjectFactory
registerAll(Ehcache, CacheEventListener...) - Method in class ome.services.sessions.state.CacheFactory
registerCallback(ProcessCallbackPrx, Current) - Method in class ome.services.blitz.impl.ScriptProcessI
registerCallback(RawFileStorePrx, int) - Method in class ome.services.blitz.repo.ManagedImportProcessI
registerCallback(ProcessCallback) - Method in interface ome.services.procs.Process
registerCallback(ProcessCallback) - Method in class ome.services.procs.ProcessSkeleton
registerProxy(Current) - Method in class ome.services.blitz.repo.ManagedImportProcessI: Adds this instance to the current session so that clients can communicate with it.
registerServant(Identity, Object) - Method in class omero.cmd.SessionI: Registers the servant with the adapter (or throws an exception if one is already registered) as well as configures the servant in any post-Spring way necessary, based on the type of the servant.
RegisterServantMessage - Class in ome.services.blitz.util: InternalMessage raised when a servant should be registered for clean.
RegisterServantMessage(Object, Object, Current) - Constructor for class ome.services.blitz.util.RegisterServantMessage
RegisterServantMessage(Object, Object, String, Current) - Constructor for class ome.services.blitz.util.RegisterServantMessage
RegisterServiceCleanupMessage - Class in ome.services.messages: Published when some resource must be cleaned up after method execution.
RegisterServiceCleanupMessage(Object, Object) - Constructor for class ome.services.messages.RegisterServiceCleanupMessage
registerTrigger(String, Trigger) - Method in class ome.services.scheduler.SchedulerFactoryBean: Registers a JobDetailAwareTrigger.
Registry - Interface in ome.services.blitz.fire: Helper class which makes the RegistryPrx available within OmeroBlitz.
registry - Variable in class ome.services.blitz.fire.SessionManagerI
Registry.Impl - Class in ome.services.blitz.fire
Registry.Impl(Communicator) - Constructor for class ome.services.blitz.fire.Registry.Impl
reindex(T) - Method in class ome.services.fulltext.BridgeHelper: Publishes a ReindexMessage which will get processed asynchronously.
reindexAll(List<T>) - Method in class ome.services.fulltext.BridgeHelper: Publishes a ReindexMessage which will get processed asynchronously.
ReindexMessage<T extends 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
relativeDN(String) - Method in class ome.security.auth.LdapConfig: Calculate the relative DN based on the current base.
release(String, int) - Method in class ome.services.graphs.GraphState: Deprecated.
release(String, int) - Method in interface ome.services.graphs.GraphStep.Callback: Deprecated.
release(GraphStep.Callback) - Method in class ome.services.graphs.GraphStep: Deprecated.
releaseDate - Static variable in class ome.formats.importer.Version: The data of the last release date.
releaseLock(String) - Method in class omero.util.ServantHolder: Releases the given lock if found, otherwise throws an InternalException
reload(String) - Method in interface ome.services.sessions.SessionManager: Similar to SessionManager.getEventContext(Principal) but uses the internal reload logic to get a fresh representation of the context.
reload(String) - Method in class ome.services.sessions.SessionManagerImpl
reload(SessionContext) - Method in class ome.services.sessions.SessionManagerImpl: Will be called in a synchronized block by SessionCache in order to allow for an update.
reload(String) - Method in class ome.services.sessions.state.SessionCache: Provides the reloading logic of the SessionCache for the SessionManagerImpl to use.
reload(SessionContext) - Method in interface ome.services.sessions.state.SessionCache.StaleCacheListener: Method called for every active session in the cache.
ReloadFilter - Class in ome.tools.hibernate: UpdateFilter subclass specialized for use with the Session.save(Object) (as opposed to Session.merge(Object)) method.
ReloadFilter(Session) - Constructor for class ome.tools.hibernate.ReloadFilter
ReloadingRefreshEventListener - Class in ome.tools.hibernate: responsible for responding to RefreshEvent. in particular in reloading the unloaded entities.
ReloadingRefreshEventListener() - Constructor for class ome.tools.hibernate.ReloadingRefreshEventListener
remove() - Method in interface ome.api.Search: Unsupported operation.
remove() - Method in class ome.services.eventlogs.EventBacklog: Removes and returns the next EventLog instance or null if none is present.
remove() - Method in class ome.services.eventlogs.EventLogLoader
remove() - Method in class ome.services.graphs.BaseGraphSpec.SubSpecIterator: Deprecated.
remove() - Method in class ome.services.SearchBean
remove() - Method in class omeis.providers.re.codomain.CodomainChain: Removes all CodomainMapContexts except the identity and resets the interval.
remove(CodomainMapContext) - Method in class omeis.providers.re.codomain.CodomainChain: Removes a map context from the chain.
remove(Resources.Entry) - Method in class omero.util.Resources
remove(Identity) - Method in class omero.util.ServantHolder
remove_async(AMD_Search_remove, Current) - Method in class ome.services.blitz.impl.SearchI
remove_path(File) - Static method in class omero.util.TempFileManager: 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
removeCallback(CmdCallbackPrx, Current) - Method in class omero.cmd.HandleI
removeClientId(String) - Method in class omero.util.ServantHolder
removeCodomainMap(CodomainMapContext) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
removeCodomainMap(CodomainMapContext) - Method in interface omeis.providers.re.RenderingEngine: Removes the specified context from the chain.
removeCodomainMap_async(AMD_RenderingEngine_removeCodomainMap, CodomainMapContext, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
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 an experimenter from the given groups.
removeGroups(Experimenter, ExperimenterGroup...) - Method in class ome.logic.AdminImpl
removeGroups(Experimenter, ExperimenterGroup...) - Method in interface ome.security.auth.RoleProvider
removeGroups(Experimenter, ExperimenterGroup...) - Method in class ome.security.auth.SimpleRoleProvider
removeGroups_async(AMD_IAdmin_removeGroups, Experimenter, List<ExperimenterGroup>, Current) - Method in class ome.services.blitz.impl.AdminI
removeGuest(long, String) - Method in interface ome.api.IShare: Removes guest email address from share.
removeGuest(long, String) - Method in class ome.services.sharing.ShareBean
removeGuest_async(AMD_IShare_removeGuest, long, String, Current) - Method in class ome.services.blitz.impl.ShareI
removeGuests(long, String...) - Method in interface ome.api.IShare: Removes guest email addresses from the share.
removeGuests(long, String...) - Method in class ome.services.sharing.ShareBean
removeGuests_async(AMD_IShare_removeGuests, long, List<String>, Current) - Method in class ome.services.blitz.impl.ShareI
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
removeProcess(ProcessContainer.Process) - Method in class ome.services.blitz.repo.ProcessContainer
removeProcessor(ProcessorPrx, Current) - Method in class ome.services.blitz.impl.SharedResourcesI
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.
removeStatus(MethodInvocation) - Method in class ome.tools.hibernate.SessionHandler
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.
render(PlaneDef) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
render(PlaneDef) - Method in class omeis.providers.re.Renderer: Renders the data selected by pd according to the current rendering settings.
render(PlaneDef) - Method in interface omeis.providers.re.RenderingEngine: Renders the data selected by pd according to the current rendering settings.
render_async(AMD_RenderingEngine_render, PlaneDef, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
renderAsPackedInt(PlaneDef) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
renderAsPackedInt(PlaneDef, PixelBuffer) - Method in class omeis.providers.re.Renderer: Renders the data selected by pd according to the current rendering settings.
renderAsPackedInt(PlaneDef) - Method in interface omeis.providers.re.RenderingEngine: Renders the data selected by pd according to the current rendering settings.
renderAsPackedInt_async(AMD_RenderingEngine_renderAsPackedInt, PlaneDef, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
renderCompressed(PlaneDef) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
renderCompressed(PlaneDef) - Method in interface omeis.providers.re.RenderingEngine: Renders the data selected by pd according to the current rendering settings and compresses the resulting RGBA composite image.
renderCompressed_async(AMD_RenderingEngine_renderCompressed, PlaneDef, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
Renderer - Class in omeis.providers.re: Transforms raw image data into an RGB image that can be displayed on screen.
Renderer(QuantumFactory, List<RenderingModel>, Pixels, RenderingDef, PixelBuffer) - Constructor for class omeis.providers.re.Renderer: Creates a new instance to render the specified pixels set and get this new instance ready for rendering.
RENDERING_DEF_QUERY_PREFIX - Static variable in class ome.logic.PixelsImpl: Standard rendering definition HQL query prefix
RenderingBean - Class in ome.services: Provides the RenderingEngine service.
RenderingBean(PixelsService, LocalCompress, Executor, SecuritySystem) - Constructor for class ome.services.RenderingBean: Compression service Bean injector.
RenderingDefGraphSpec - Class in ome.services.graphs: Deprecated.
will be removed in OMERO 5.2, so use the new graphs implementation
RenderingDefGraphSpec(List<String>) - Constructor for class ome.services.graphs.RenderingDefGraphSpec: Deprecated.

Creates a new instance.
RenderingEngine - Interface in omeis.providers.re: Defines a service to render a given pixels set.
RenderingEngineI - Class in ome.services.blitz.impl: Implementation of the RenderingEngine service.
RenderingEngineI(RenderingEngine, BlitzExecutor) - Constructor for class ome.services.blitz.impl.RenderingEngineI
RenderingSettingsI - Class in ome.services.blitz.impl: Implementation of the IRenderingSettings service.
RenderingSettingsI(IRenderingSettings, BlitzExecutor) - Constructor for class ome.services.blitz.impl.RenderingSettingsI
RenderingSettingsImpl - Class in ome.logic: Implementation of the IRenderingSettings I/F.
RenderingSettingsImpl() - Constructor for class ome.logic.RenderingSettingsImpl
RenderingStats - Class in omeis.providers.re: Exposes methods to time the various steps in the rendering process and provides a stats report.
RenderingStats(Renderer, PlaneDef) - Constructor for class omeis.providers.re.RenderingStats: Creates a new instance.
RenderingTask - Interface in omeis.providers.re: This interface represents a rendering operation task.
renderProjectedAsPackedInt(int, int, int, int, int) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
renderProjectedAsPackedInt(int, int, int, int, int) - Method in interface omeis.providers.re.RenderingEngine: Performs a projection through selected optical sections of a particular timepoint with the currently active channels and renders the data for display.
renderProjectedAsPackedInt_async(AMD_RenderingEngine_renderProjectedAsPackedInt, ProjectionType, int, int, int, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
renderProjectedCompressed(int, int, int, int, int) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
renderProjectedCompressed(int, int, int, int, int) - Method in interface omeis.providers.re.RenderingEngine: Performs a projection through selected optical sections of a particular timepoint with the currently active channels, renders the data for display and compresses the resulting RGBA composite image.
renderProjectedCompressed_async(AMD_RenderingEngine_renderProjectedCompressed, ProjectionType, int, int, int, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
ReorderedPixelData - Class in ome.io.nio: Represents a block of pixel data that needs to be re-ordered in accordance with a DeltaVision file.
ReorderedPixelData(String, ByteBuffer, int) - Constructor for class ome.io.nio.ReorderedPixelData: Default constructor.
replace(Object, Object, Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
repo - Variable in class ome.services.blitz.repo.RawAccessRequestI
repo - Variable in class ome.services.pixeldata.PersistentEventLogLoader
RepoFile - Class in ome.services.scripts: File type wrapper for paths which are intended for being stored in the database as a part of this repository.
RepoFile(File, String) - Constructor for class ome.services.scripts.RepoFile: Assumes that path is relative under root, and constructs a new File and calls RepoFile.RepoFile(File, File)
RepoFile(File, File) - Constructor for class ome.services.scripts.RepoFile: Both root and file are absolute paths to files.
RepoFile.FsFile - Class in ome.services.scripts: File type wrapper for actual OS files.
RepoRawFileStoreI - Class in ome.services.blitz.repo: An implementation of the RepoRawFileStore interface
RepoRawFileStoreI(BlitzExecutor, RawFileStore, Current) - Constructor for class ome.services.blitz.repo.RepoRawFileStoreI
reportForgottenPassword(String, String) - Method in interface ome.api.IAdmin: Deprecated.
reportForgottenPassword(String, String) - Method in class ome.logic.AdminImpl
reportForgottenPassword_async(AMD_IAdmin_reportForgottenPassword, String, String, Current) - Method in class ome.services.blitz.impl.AdminI
reportingLoops - Variable in class ome.services.fulltext.FullTextIndexer: Frequency with which the percentage done should be calculated.
repositories(Current) - Method in class ome.services.blitz.impl.SharedResourcesI
repositoryDao - Variable in class ome.services.blitz.repo.PublicRepositoryI
RepositoryDao - Interface in ome.services.blitz.repo
RepositoryDaoImpl - Class in ome.services.blitz.repo: DAO class for encapsulating operations related to resource access inside the repository.
RepositoryDaoImpl(Principal, Roles, Executor, Executor) - Constructor for class ome.services.blitz.repo.RepositoryDaoImpl: Primary constructor which takes all final fields.
RepositoryDaoImpl(Principal, Executor) - Constructor for class ome.services.blitz.repo.RepositoryDaoImpl: Previous constructor which should no longer be used.
RepositoryInfoI - Class in ome.services.blitz.impl: Implementation of the IRepositoryInfo service.
RepositoryInfoI(IRepositoryInfo, BlitzExecutor) - Constructor for class ome.services.blitz.impl.RepositoryInfoI
RepositoryInfoImpl - Class in ome.logic: Class implementation of the IRepositoryInfo service interface.
RepositoryInfoImpl() - Constructor for class ome.logic.RepositoryInfoImpl
RepositoryTask - Class in ome.tools: Class implementation of various mechanised tasks, database queries, file I/O, etc.
RepositoryTask(SqlAction) - Constructor for class ome.tools.RepositoryTask: Constructor
reps - Variable in class ome.services.fulltext.FullTextIndexer
reps - Variable in class ome.services.pixeldata.PixelDataHandler
requestFromUser() - Method in class ome.formats.importer.ImportConfig: if can't log in request needed information
requestHeartBeats() - Method in class ome.services.blitz.fire.SessionManagerI: Destroys all the ServiceFactoryI instances based on the given sessionId.
RequestObjectFactoryRegistry - Class in ome.services.blitz.impl.commands: Types which rely on the omero.model and omero.api objects rather than just the omero.cmd types.
RequestObjectFactoryRegistry() - Constructor for class ome.services.blitz.impl.commands.RequestObjectFactoryRegistry
RequestObjectFactoryRegistry - Class in ome.services.blitz.repo: Requests which are handled by the repository servants.
RequestObjectFactoryRegistry(Registry, TileSizes, RepositoryDao, Ring, PixelsService) - Constructor for class ome.services.blitz.repo.RequestObjectFactoryRegistry
RequestObjectFactoryRegistry - Class in omero.cmd: SPI type picked up from the Spring configuration and given a chance to register all its ObjectFactory instances with the Communicator.
RequestObjectFactoryRegistry(ExtendedMetadata, ACLVoter, Roles, PixelsService, ThumbnailService, MailUtil, PasswordUtil, SecuritySystem, PasswordProvider, GraphRequestFactory) - Constructor for class omero.cmd.RequestObjectFactoryRegistry
requests - Variable in class omero.cmd.graphs.Preprocessor: Deprecated.
requestToString(Request) - Method in class omero.cmd.graphs.Preprocessor: Deprecated.

Convert a single request to a pretty string.
REQUEUED - Static variable in interface ome.api.JobHandle
requiresCompanion(String) - Static method in class ome.services.util.DBEnumCheck
requiresPixelsPyramid() - Method in interface ome.api.RawPixelsStore
requiresPixelsPyramid(Pixels) - Method in class ome.io.nio.PixelsService: Returns true if a pyramid should be used for the given Pixels.
requiresPixelsPyramid() - Method in class ome.services.RawPixelsBean
requiresPixelsPyramid() - Method in class ome.services.RenderingBean
requiresPixelsPyramid() - Method in interface omeis.providers.re.RenderingEngine
requiresPixelsPyramid_async(AMD_PyramidService_requiresPixelsPyramid, Current) - Method in class ome.services.blitz.impl.AbstractPyramidServant
requiresPixelsPyramid_async(AMD_PyramidService_requiresPixelsPyramid, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
reset(String[]) - Static method in class ome.services.fulltext.Main: Can be used to reset the value that the PersistentEventLogLoader would read if started now.
resetDefaults(RenderingDef, Pixels) - Method in interface ome.api.IRenderingSettings: Resets the given rendering settings to those that are specified by the rendering engine intelligent pretty good image (PG) logic for the pixels set linked to that set of rendering settings.
resetDefaults() - Method in interface ome.api.Search: Resets all settings (non-query state) to the original default values, as if the instance had just be created.
resetDefaults() - Method in interface ome.api.ThumbnailStore: Resets the rendering definition for the active pixels set to its default settings.
resetDefaults(RenderingDef, Pixels) - Method in class ome.logic.RenderingSettingsImpl: Implemented as specified by the IRenderingSettings I/F
resetDefaults() - Method in class ome.services.SearchBean
resetDefaults() - Method in class ome.services.ThumbnailBean
resetDefaults_async(AMD_IRenderingSettings_resetDefaults, RenderingDef, Pixels, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
resetDefaults_async(AMD_Search_resetDefaults, Current) - Method in class ome.services.blitz.impl.SearchI
resetDefaults_async(AMD_ThumbnailStore_resetDefaults, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
resetDefaultsAndGenerateThumbnails(List<Long>, List<Long>) - Method in class ome.formats.OMEROMetadataStoreClient: Resets the defaults and generates thumbnails for a given set of Pixels IDs.
resetDefaultsByOwnerInSet(Class<T>, Set<Long>) - Method in interface ome.api.IRenderingSettings: Resets the rendering settings of a given group of containers based on the owner's (essentially a copy).
resetDefaultsByOwnerInSet(Class<T>, Set<Long>) - Method in class ome.logic.RenderingSettingsImpl: Implemented as specified by the IRenderingSettings I/F.
resetDefaultsByOwnerInSet_async(AMD_IRenderingSettings_resetDefaultsByOwnerInSet, String, List<Long>, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
resetDefaultSettings(boolean) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
resetDefaultSettings(boolean) - Method in interface omeis.providers.re.RenderingEngine: Resets the default settings i.e. the default values internal to the Rendering engine.
resetDefaultSettings_async(AMD_RenderingEngine_resetDefaultSettings, boolean, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
resetDefaultsForPixels(long) - Method in interface ome.api.IRenderingSettings: Resets a Pixels' default rendering settings back to those that are specified by the rendering engine intelligent pretty good image (PG) logic.
resetDefaultsForPixels(long) - Method in class ome.logic.RenderingSettingsImpl: Implemented as specified by the IRenderingSettings I/F.
resetDefaultsForPixels_async(AMD_IRenderingSettings_resetDefaultsForPixels, long, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
resetDefaultsInDataset(long) - Method in interface ome.api.IRenderingSettings: Resets a dataset's rendering settings back to those that are specified by the rendering engine intelligent pretty good image (PG) logic.
resetDefaultsInDataset(long) - Method in class ome.logic.RenderingSettingsImpl: Implemented as specified by the IRenderingSettings I/F.
resetDefaultsInDataset_async(AMD_IRenderingSettings_resetDefaultsInDataset, long, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
resetDefaultsInImage(long) - Method in interface ome.api.IRenderingSettings: Resets an image's default rendering settings back to those that are specified by the rendering engine intelligent pretty good image (PG) logic.
resetDefaultsInImage(long) - Method in class ome.logic.RenderingSettingsImpl: Implemented as specified by the IRenderingSettings I/F.
resetDefaultsInImage_async(AMD_IRenderingSettings_resetDefaultsInImage, long, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
resetDefaultsInSet(Class<T>, Set<Long>) - Method in interface ome.api.IRenderingSettings: Resets a rendering settings back to one or many containers that are specified by the rendering engine intelligent pretty good image (PG) logic.
resetDefaultsInSet(Class<T>, Set<Long>) - Method in class ome.logic.RenderingSettingsImpl: Implemented as specified by the IRenderingSettings I/F.
resetDefaultsInSet_async(AMD_IRenderingSettings_resetDefaultsInSet, String, List<Long>, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
resetDefaultsNoSave(RenderingDef, Pixels) - Method in interface ome.api.IRenderingSettings: Resets the given rendering settings to those that are specified by the rendering engine intelligent pretty good image (PG) logic for the pixels set linked to that set of rendering settings.
resetDefaultsNoSave(RenderingDef, Pixels) - Method in class ome.logic.RenderingSettingsImpl: Implemented as specified by the IRenderingSettings I/F
resetDefaultsNoSave_async(AMD_IRenderingSettings_resetDefaultsNoSave, RenderingDef, Pixels, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
resetDetails(IObject, Object[], Object[], int, Details) - Method in class ome.security.basic.OmeroInterceptor: asks BasicSecuritySystem to create a new managed Details based on the previous state of this entity.
resetEnumerations(Class<T>) - Method in interface ome.api.ITypes
resetEnumerations(Class<T>) - Method in class ome.logic.TypesImpl
resetEnumerations_async(AMD_ITypes_resetEnumerations, String, Current) - Method in class ome.services.blitz.impl.TypesI
resetMinMaxInSet(Class<T>, Set<Long>) - Method in interface ome.api.IRenderingSettings: Resets a the channel windows for one or many containers back to their global minimum and global maximum for the channel.
resetMinMaxInSet(Class<T>, Set<Long>) - Method in class ome.logic.RenderingSettingsImpl: Implemented as specified by the IRenderingSettings I/F.
resetMinMaxInSet_async(AMD_IRenderingSettings_resetMinMaxInSet, String, List<Long>, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
ResetPasswordRequestI - Class in omero.cmd.admin: Callback interface allowing to reset password for the given user.
ResetPasswordRequestI(MailUtil, PasswordUtil, SecuritySystem, PasswordProvider) - Constructor for class omero.cmd.admin.ResetPasswordRequestI
resetReadFilter(Session) - Method in interface ome.api.local.LocalShare
resetReadFilter(Session) - Method in class ome.services.sharing.ShareBean
RESOLUTION_DESCRIPTIONS - Static variable in class ome.services.blitz.impl.AbstractPyramidServant: This is a fairly brittle mapping from the List> created by the PixelBuffers to the List which is remotely provided by Blitz.
resolveAlias(String) - Method in class ome.system.PreferenceContext
resolveConfigFile(String) - Method in class ome.services.blitz.util.BlitzConfiguration: Resolve the given config file to a concrete location, possibly throwing an exception if stored in a jar.
resolver - Variable in class ome.io.nio.PixelsService: Resolver of archived original file paths for pixels sets.
resource - Variable in class ome.services.messages.ParserOpenFileMessage
resource - Variable in class ome.services.messages.RegisterServiceCleanupMessage
Resources - Class in omero.util: Container class for storing resources which should be cleaned up on close and periodically checked.
Resources() - Constructor for class omero.util.Resources: As Resources.Resources(int) but specifies a 60 second sleep period between task execution.
Resources(int) - Constructor for class omero.util.Resources: As Resources#Resources(int, ExecutorService) but uses a Executors.newSingleThreadExecutor().
Resources(int, ScheduledExecutorService) - Constructor for class omero.util.Resources
Resources.Entry - Interface in omero.util: Interface to be implemented by any object which wants to be managed by the Resources class.
response - Variable in class ome.services.throttling.Task
response(Object, OmeroContext) - Method in class ome.services.throttling.Task: Calls the response method
responseRunning(List<Long>, Current) - Method in class ome.services.blitz.impl.ProcessorCallbackI: Callback method which should not be called for this instance.
restartIfNeeded() - Method in class ome.services.scheduler.SchedulerFactoryBean: Similar to the SchedulerFactoryBean.isRunning() method, but properly handles the situation where the Scheduler has been completely shutdown and therefore must be replaced.
restrictions(IObject) - Method in interface ome.security.ACLVoter: Provide the active restrictions for this IObject.
restrictions(IObject) - Method in class ome.security.basic.BasicACLVoter
restrictions(IObject) - Method in class ome.security.CompositeACLVoter
restrictions(IObject) - Method in class ome.security.sharing.SharingACLVoter
RESUBMITTED - Static variable in interface ome.api.JobHandle
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
retrieveRndSettings(long) - Method in interface ome.api.IPixels: Retrieves the rendering settings for a given pixels set and the currently logged in user.
retrieveRndSettings(long) - Method in class ome.logic.PixelsImpl: Implemented as specified by the IPixels I/F.
retrieveRndSettings_async(AMD_IPixels_retrieveRndSettings, long, Current) - Method in class ome.services.blitz.impl.PixelsI
retrieveRndSettingsFor(long, long) - Method in interface ome.api.IPixels: Retrieves the rendering settings for a given pixels set and the passed user with the following objects pre-linked: renderingDef.quantization renderingDef.model renderingDef.waveRendering renderingDef.waveRendering.color renderingDef.waveRendering.family renderingDef.spatialDomainEnhancement
retrieveRndSettingsFor(long, long) - Method in class ome.logic.PixelsImpl: Implemented as specified by the IPixels I/F.
retrieveRndSettingsFor_async(AMD_IPixels_retrieveRndSettingsFor, long, long, Current) - Method in class ome.services.blitz.impl.PixelsI
returnedClass() - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
returnSeen(Object) - Method in class ome.tools.hibernate.UpdateFilter
returnUnloaded - Variable in class ome.services.search.SearchValues
reusedSession - Variable in class omero.cmd.SessionI
reverse(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
reverseNamedList(List<NamedValue>) - Static method in class omero.util.IceMapper
reverseStringStringMap(Map<String, RString>) - Static method in class omero.util.IceMapper: Reverse a String→String map's values from RStrings.
review(Map<String, Set<GraphPolicy.Details>>, GraphPolicy.Details, Map<String, Set<GraphPolicy.Details>>, Set<String>, boolean) - Method in class ome.services.graphs.GraphPolicy: The action to take about the link between the mapped objects.
review(Map<String, Set<GraphPolicy.Details>>, GraphPolicy.Details, Map<String, Set<GraphPolicy.Details>>, Set<String>, boolean) - Method in class omero.cmd.graphs.BaseGraphPolicyAdjuster
revision - Static variable in class ome.formats.importer.Version: The repository revision.
RevisionDate - Annotation Type in ome.annotations: annotation used for tracking source code changes.
revisionDate - Static variable in class ome.formats.importer.Version: The data of the last repository revision.
RevisionNumber - Annotation Type in ome.annotations: annotation used for tracking source code changes.
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.RoiTypesObjectFactoryRegistry - Class in ome.services.roi
RoiTypes.RoiTypesObjectFactoryRegistry() - Constructor for class ome.services.roi.RoiTypes.RoiTypesObjectFactoryRegistry
roleProvider - Variable in class ome.logic.AdminImpl
RoleProvider - Interface in ome.security.auth: Provides user and group creation, deletion, and modification for use by services.
roles - Variable in class ome.security.basic.AbstractSecurityFilter
roles - Variable in class ome.security.basic.BasicACLVoter
roles - Variable in class ome.security.basic.BasicSecuritySystem
roles - Variable in class ome.services.blitz.repo.RepositoryDaoImpl
roles - Variable in class ome.services.sessions.SessionManagerImpl
Roles - Class in ome.system: encapsulates the naming scheme for critical system groups and accounts.
Roles() - Constructor for class ome.system.Roles: default constructor which assigns hard-coded values to all roles
Roles(long, String, long, String, long, String, long, String, long, String) - Constructor for class ome.system.Roles: constructor which allows full specification of all roles
RolesAllowed - Annotation Type in ome.annotations: Security annotation which specifies a list of user roles which will be permitted to execute this method.
rollback(EventLog) - Method in class ome.services.eventlogs.EventLogLoader
rollback(String, int) - Method in class ome.services.graphs.GraphState: Deprecated.
rollback(String, int) - Method in interface ome.services.graphs.GraphStep.Callback: Deprecated.
rollback(GraphStep.Callback) - Method in class ome.services.graphs.GraphStep: Deprecated.
rollbackOnly() - Method in class ome.services.graphs.GraphStep: Deprecated.
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(Object) - Static method in class omero.rtypes: Attempts to dispatch to the other omero.rtypes.* static methods to create a proper RType subclass by checking the type of the input.
RTYPEDICT - Static variable in class omero.util.IceMapper
RTypeMapper - Class in omero.util: Extension of IceMapper which guarantees that RCollection and RMap instances are properly created.
RTypeMapper(IceMapper.ReturnMapping) - Constructor for class omero.util.RTypeMapper
rtypes - Class in omero: Abstract class similar to Arrays or Collections which is responsible for creating RTypes from static factory methods.
rtypes() - Constructor for class omero.rtypes
rtypes.Conversion - Interface in omero: SPI-style interface which helps the omero server to properly convert omero.RType objects into Java-native objects for use in Hibernate.
rtypes.RTypeObjectFactoryRegistry - Class in omero
rtypes.RTypeObjectFactoryRegistry() - Constructor for class omero.rtypes.RTypeObjectFactoryRegistry
rules - Variable in class ome.services.blitz.repo.path.FilePathNamingValidator
rules - Variable in class ome.services.blitz.repo.path.MakePathComponentSafe
run() - Method in class ome.formats.importer.util.ClientKeepAlive
run(int, int, int, int, int, int, int, int) - Method in interface ome.io.nio.TileLoopIteration: Invoke a single loop iteration.
run() - Method in class ome.services.blitz.Status
run() - Method in class ome.services.blitz.util.CheckAllJobs
run() - Method in class ome.services.delete.files.FileDeleter
run() - Method in interface ome.services.procs.IProcessManager: Runs the processing phase as root.
run(OmeroContext) - Method in class ome.services.throttling.Adapter
run(OmeroContext) - Method in class ome.services.throttling.Callback
run(OmeroContext) - Method in class ome.services.throttling.Callback2
run() - Method in class ome.services.throttling.Slot
run(OmeroContext) - Method in class ome.services.throttling.Task
run() - Method in class ome.services.util.ExecutionThread: Initializes the Session for this Thread if necessary, then calls ExecutionThread.doRun().
run() - Method in class ome.services.util.ServerDirectoryCheck: Synchronizes the ${omero.data.dir}/Server directory by creating a directory for any user who does not have one.
run() - Method in class ome.system.UpgradeCheck: If the UpgradeCheck.url has been set to null or the empty string, then no upgrade check will be performed (silently).
run() - Method in class omero.cmd.HandleI: NB: only executes if HandleI.state is State#CREATED.
run(TileData, int, int, int, int, int, int, int, int) - Method in interface omero.util.TileLoopIteration: Invoke a single loop iteration.
runAsAdmin() - Method in interface ome.security.AdminAction: executes with special privilegs within the SecuritySystem.
runAsAdmin(AdminAction) - Method in class ome.security.basic.BasicSecuritySystem: Calls BasicSecuritySystem.runAsAdmin(AdminAction) with a null-group id.
runAsAdmin(ExperimenterGroup, AdminAction) - Method in class ome.security.basic.BasicSecuritySystem: merge event is disabled for BasicSecuritySystem.runAsAdmin(AdminAction) because passing detached (client-side) entities to this method is particularly dangerous.
runAsAdmin(ExperimenterGroup, AdminAction) - Method in interface ome.security.SecuritySystem: Allows actions to be performed with the EventContext.isCurrentUserAdmin() flag enabled but without changing the value of EventContext.getCurrentUserId(), so that ownerships are properly handled.
runAsAdmin(AdminAction) - Method in interface ome.security.SecuritySystem: Calls SecuritySystem.runAsAdmin(ExperimenterGroup, AdminAction) with a null group.
runAsAdmin(AdminAction) - Method in class ome.security.SecuritySystemHolder
runAsAdmin(ExperimenterGroup, AdminAction) - Method in class ome.security.SecuritySystemHolder
runAsAdmin(ExperimenterGroup, AdminAction) - Method in class ome.security.sharing.SharingSecuritySystem
runAsAdmin(AdminAction) - Method in class ome.security.sharing.SharingSecuritySystem
runAsAdmin() - Method in class ome.services.delete.QueryConstraints
runnableCall(Current, Task) - Method in class ome.services.blitz.impl.AbstractAmdServant
runnableCall(Current, Task) - Method in interface ome.services.blitz.util.BlitzExecutor
runnableCall(Current, Task) - Method in class ome.services.throttling.InThreadThrottlingStrategy
runnableCall(Current, Task) - Method in class ome.services.throttling.SerialThrottlingStrategy
RUNNING - Static variable in interface ome.api.JobHandle
runningProcess(long) - Method in interface ome.services.procs.IProcessManager: Returns a running Process for the id or null.
runningProcess(long) - Method in class ome.services.procs.ProcessManager
runQuery(String[], GraphEntry, Query, Session) - Method in class ome.services.graphs.BaseGraphSpec: Deprecated.
runScript_async(AMD_IScript_runScript, long, Map<String, RType>, RInt, Current) - Method in class ome.services.blitz.impl.ScriptI

S

safeCharacter - Variable in class ome.services.blitz.repo.path.FilePathRestrictions
safeCharacters - Variable in class ome.services.blitz.repo.path.FilePathRestrictions
safeLongToInteger(Long) - Static method in class ome.io.nio.RomioPixelBuffer: Converts a Long value to an Integer safely.
safeRunnableCall(Current, Object, boolean, Callable<R>) - Method in class ome.services.blitz.impl.AbstractAmdServant
safeRunnableCall(Current, Object, boolean, Callable<R>) - Method in interface ome.services.blitz.util.BlitzExecutor
safeRunnableCall(Current, Object, boolean, Callable<R>) - Method in class ome.services.throttling.InThreadThrottlingStrategy
safeRunnableCall(Current, Object, boolean, Callable<R>) - Method in class ome.services.throttling.SerialThrottlingStrategy
salt - Variable in class ome.security.auth.ConfigurablePasswordProvider: Whether or not salting based on the user ID should be attempted.
saltedPasswordDigest(Long, String) - Method in class ome.security.auth.PasswordUtil: Creates an MD5 hash of the given clear text and base64 encodes it.
sanityCheckPixels(Pixels, Pixels) - Method in interface ome.api.IRenderingSettings: Checks if the specified sets of pixels are compatible.
sanityCheckPixels(Pixels, Pixels) - Method in class ome.logic.RenderingSettingsImpl: Implemented as specified by the IRenderingSettings I/F
sanityCheckPixels_async(AMD_IRenderingSettings_sanityCheckPixels, Pixels, Pixels, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
sanityCheckRepository() - Method in interface ome.api.IRepositoryInfo: Checks that image data repository has not exceeded 95% disk space use level.
sanityCheckRepository() - Method in class ome.logic.RepositoryInfoImpl
sanityCheckRepository_async(AMD_IRepositoryInfo_sanityCheckRepository, Current) - Method in class ome.services.blitz.impl.RepositoryInfoI
save() - Method in interface ome.api.RawFileStore: Saves the OriginalFile associated with the service if it has been modified.
save() - Method in interface ome.api.RawPixelsStore
save() - Method in class ome.formats.importer.transfers.TransferState: Calls RawFileStorePrx.save() and stores the resultant OriginalFile for future inspection along with the local checksum.
save() - Method in class ome.services.blitz.measurements.MeasurementStore
save() - Method in interface ome.services.blitz.measurements.OmeroMeasurementStore
save() - Method in class ome.services.RawFileBean
save() - Method in class ome.services.RawPixelsBean
save_async(AMD_RawFileStore_save, Current) - Method in class ome.services.blitz.impl.RawFileStoreI
save_async(AMD_RawPixelsStore_save, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
save_async(AMD_RawPixelsStore_save, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
SAVE_EVENT - Static variable in class ome.security.basic.SaveEventListener
saveAll() - Method in class ome.formats.importer.ImportConfig
saveAndReturnArray(IObject[]) - Method in interface ome.api.IUpdate
saveAndReturnArray(IObject[]) - Method in class ome.logic.UpdateImpl
saveAndReturnArray_async(AMD_IUpdate_saveAndReturnArray, List<IObject>, Current) - Method in class ome.services.blitz.impl.UpdateI
saveAndReturnIds(IObject[]) - Method in interface ome.api.IUpdate: Logic differs from other methods.
saveAndReturnIds(IObject[]) - Method in class ome.logic.UpdateImpl
saveAndReturnIds_async(AMD_IUpdate_saveAndReturnIds, List<IObject>, Current) - Method in class ome.services.blitz.impl.UpdateI
saveAndReturnObject(T) - Method in interface ome.api.IUpdate
saveAndReturnObject(IObject) - Method in class ome.logic.UpdateImpl
saveAndReturnObject_async(AMD_IUpdate_saveAndReturnObject, IObject, Current) - Method in class ome.services.blitz.impl.UpdateI
saveArray(IObject[]) - Method in interface ome.api.IUpdate
saveArray(IObject[]) - Method in class ome.logic.UpdateImpl
saveArray_async(AMD_IUpdate_saveArray, List<IObject>, Current) - Method in class ome.services.blitz.impl.UpdateI
saveAsNewSettings() - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
saveAsNewSettings() - Method in interface omeis.providers.re.RenderingEngine: Saves the current rendering settings in the database as a new RenderingDef and loads the object into the current RenderingEngine.
saveAsNewSettings_async(AMD_RenderingEngine_saveAsNewSettings, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
saveCollection(Collection<IObject>) - Method in interface ome.api.IUpdate
saveCollection(Collection) - Method in class ome.logic.UpdateImpl
saveCollection_async(AMD_IUpdate_saveCollection, List<IObject>, Current) - Method in class ome.services.blitz.impl.UpdateI
saveCurrentSettings() - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
saveCurrentSettings() - Method in interface omeis.providers.re.RenderingEngine: Saves the current rendering settings in the database.
saveCurrentSettings_async(AMD_RenderingEngine_saveCurrentSettings, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
savedDataset - Variable in class ome.formats.importer.ImportConfig
savedDirectory - Variable in class ome.formats.importer.ImportConfig
savedImagesNotInPlates - Variable in class ome.services.blitz.impl.MetadataStoreI
savedPlates - Variable in class ome.services.blitz.impl.MetadataStoreI
savedProject - Variable in class ome.formats.importer.ImportConfig
savedScreen - Variable in class ome.formats.importer.ImportConfig
SaveEventListener - Class in ome.security.basic: event listener which will only handle newly created (transient) objects in a given graph.
SaveEventListener(CurrentDetails, TokenHolder) - Constructor for class ome.security.basic.SaveEventListener: main constructor.
saveFileset(String, Fileset, ChecksumAlgorithm, List<CheckedPath>, Current) - Method in interface ome.services.blitz.repo.RepositoryDao: Fill the various fields of the Fileset and then save the entire instance into the database.
saveFileset(String, Fileset, ChecksumAlgorithm, List<CheckedPath>, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
saveGui() - Method in class ome.formats.importer.ImportConfig: Saves gui specific values for which it makes sense to have a preferences values.
SaveI - Class in ome.services.blitz.impl.commands: Permits saving a single IObject instance.
SaveI() - Constructor for class ome.services.blitz.impl.commands.SaveI
saveJob(T, Current) - Method in interface ome.services.blitz.repo.RepositoryDao: Create a job from an instance provided by either the client or the server.
saveJob(Job, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
saveObject(IObject) - Method in interface ome.api.IUpdate
saveObject(IObject) - Method in class ome.logic.UpdateImpl
saveObject(IObject, Current) - Method in interface ome.services.blitz.repo.RepositoryDao: Save the given model object.
saveObject(IObject, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
saveObject_async(AMD_IUpdate_saveObject, IObject, Current) - Method in class ome.services.blitz.impl.UpdateI
saveOmeroRoiToMetadataStore(List<Roi>, MetadataStore) - Static method in class loci.ome.io.OmeroReader: Converts omero.model.Roi to ome.xml.model.* and updates the MetadataStore
savepoint(String) - Method in class ome.services.graphs.GraphState: Deprecated.
savepoint(String) - Method in interface ome.services.graphs.GraphStep.Callback: Deprecated.
savepoint(GraphStep.Callback) - Method in class ome.services.graphs.GraphStep: Deprecated.
saveRndSettings(RenderingDef) - Method in interface ome.api.IPixels: Saves the specified rendering settings.
saveRndSettings(RenderingDef) - Method in class ome.logic.PixelsImpl
saveRndSettings_async(AMD_IPixels_saveRndSettings, RenderingDef, Current) - Method in class ome.services.blitz.impl.PixelsI
saveToDB(FilesetJobLink) - Method in class ome.formats.OMEROMetadataStore: Saves the current object graph to the database.
saveToDB(FilesetJobLink) - Method in class ome.formats.OMEROMetadataStoreClient: Updates the server side MetadataStore with a list of our objects and references and saves them into the database.
saveToDB_async(AMD_MetadataStore_saveToDB, FilesetJobLink, Current) - Method in class ome.services.blitz.impl.MetadataStoreI
scalar(double) - Method in class ome.util.math.geom2D.PlanePoint: Multiplies this vector by the specified scalar.
scale(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(ScriptJob) - Method in class ome.services.blitz.repo.ManagedImportRequestI
SCRIPT_REPO - Static variable in class ome.services.scripts.ScriptRepoHelper: Id used by all script repositories.
ScriptFileType - Class in ome.services.scripts: Definition of the script types that will be accepted by the server.
ScriptFileType(String, String) - Constructor for class ome.services.scripts.ScriptFileType
ScriptFileType(String, String, String, String) - Constructor for class ome.services.scripts.ScriptFileType
ScriptFinder - Class in ome.services.scripts: Looks up an official script based on path for internal use.
ScriptFinder(Roles, String, Executor, File) - Constructor for class ome.services.scripts.ScriptFinder
ScriptFinder(Roles, Principal, Executor, File) - Constructor for class ome.services.scripts.ScriptFinder
ScriptI - Class in ome.services.blitz.impl: implementation of the IScript service interface.
ScriptI(BlitzExecutor, ScriptRepoHelper, ChecksumProviderFactory) - 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, _InteractiveProcessorOperations, ProcessPrx) - Constructor for class ome.services.blitz.impl.ScriptProcessI
ScriptProcessor - Class in ome.services.procs.scripts
ScriptProcessor() - Constructor for class ome.services.procs.scripts.ScriptProcessor
ScriptRepoHelper - Class in ome.services.scripts: Strategy used by the ScriptRepository for registering, loading, and saving files.
ScriptRepoHelper(Executor, String, Roles) - Constructor for class ome.services.scripts.ScriptRepoHelper
ScriptRepoHelper(File, Executor, Principal, Roles) - Constructor for class ome.services.scripts.ScriptRepoHelper
ScriptRepoHelper(String, File, Executor, Principal, Roles) - Constructor for class ome.services.scripts.ScriptRepoHelper
ScriptRepositoryI - Class in ome.services.blitz.repo: Repository which makes the included script files available to users.
ScriptRepositoryI(ObjectAdapter, Registry, Executor, Principal, ScriptRepoHelper, PublicRepositoryI) - Constructor for class ome.services.blitz.repo.ScriptRepositoryI
scripts - Variable in class ome.services.blitz.impl.ScriptI
Search - Interface in ome.api: Central search interface, allowing Web2.0 style queries.
SearchAction - Class in ome.services.search: Serializable action used by SearchBean to generate results lazily.
SearchAction(SearchValues) - Constructor for class ome.services.search.SearchAction
searchAll() - Method in interface ome.api.ILdap: Searches all Experimenter list on LDAP for attribute objectClass = person.
searchAll() - Method in class ome.logic.LdapImpl
searchAll_async(AMD_ILdap_searchAll, Current) - Method in class ome.services.blitz.impl.LdapI
SearchBean - Class in ome.services: Implements the Search interface.
SearchBean(Executor, Class<? extends Analyzer>) - Constructor for class ome.services.SearchBean
SearchBean() - Constructor for class ome.services.SearchBean: Empty constructor required by EJB and self configuration.
searchByAttribute(String, String, String) - Method in interface ome.api.ILdap: Searches all Experimenter in LDAP for specified attribute
searchByAttribute(String, String, String) - Method in class ome.logic.LdapImpl
searchByAttribute_async(AMD_ILdap_searchByAttribute, String, String, String, Current) - Method in class ome.services.blitz.impl.LdapI
searchByAttributes(String, String[], String[]) - Method in interface ome.api.ILdap: Searches all Experimenter in LDAP for specified attributes.
searchByAttributes(String, String[], String[]) - Method in class ome.logic.LdapImpl
searchByAttributes_async(AMD_ILdap_searchByAttributes, String, List<String>, List<String>, Current) - Method in class ome.services.blitz.impl.LdapI
searchByDN(String) - Method in interface ome.api.ILdap: Searches one Experimenter in LDAP for specified Distinguished Name - String
searchByDN(String) - Method in class ome.logic.LdapImpl
searchByDN_async(AMD_ILdap_searchByDN, String, Current) - Method in class ome.services.blitz.impl.LdapI
searchDnInGroups(String, String) - Method in interface ome.api.ILdap: Searches Distinguished Name - String in groups
searchDnInGroups(String, String) - Method in class ome.logic.LdapImpl
searchDnInGroups_async(AMD_ILdap_searchDnInGroups, String, String, Current) - Method in class ome.services.blitz.impl.LdapI
SearchI - Class in ome.services.blitz.impl: Implementation of the Search service.
SearchI(Search, BlitzExecutor) - Constructor for class ome.services.blitz.impl.SearchI
SearchValues - Class in ome.services.search: Values used by SearchBean to store user requests.
SearchValues() - Constructor for class ome.services.search.SearchValues
sec - Variable in class ome.logic.AbstractLevel2Service
sec - Variable in class ome.security.auth.SimpleRoleProvider
sec - Variable in class ome.services.AbstractStatefulBean
sec - Variable in class ome.services.procs.ProcessManager.Work: SecuritySystem in order to perform a secure save on the Job instance.
secondLevelCacheHit(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
secondLevelCacheMiss(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
secondLevelCachePut(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
secSys - Variable in class ome.security.basic.EventHandler
SecureAction - Interface in ome.security: action for passing to SecuritySystem#doAction(IObject, SecureAction).
SecureMerge - Class in ome.tools.hibernate: Helper originally from SimpleRoleProvider for merging admin objects.
SecureMerge(Session) - Constructor for class ome.tools.hibernate.SecureMerge
SecureMerge(Session, boolean) - Constructor for class ome.tools.hibernate.SecureMerge
security - Variable in class omero.cmd.admin.UpdateSessionTimeoutRequestI
securityFilter - Variable in class ome.security.basic.BasicACLVoter
SecurityFilter - Interface in ome.security: Base filter interface ...
SecurityFilterHolder - Class in ome.security: Security dispatcher holding each currently active SecurityFilter instance and allowing dispatching between them.
SecurityFilterHolder(CurrentDetails, OneGroupSecurityFilter, AllGroupsSecurityFilter) - Constructor for class ome.security.SecurityFilterHolder
SecuritySystem - Interface in ome.security: central security interface.
securitySystem - Variable in class ome.services.blitz.fire.SessionManagerI
SecuritySystemHolder - Class in ome.security: Security dispatcher holding each currently active SecuritySystem instance and allowing dispatching between them.
SecuritySystemHolder(BasicSecuritySystem, SharingSecuritySystem) - Constructor for class ome.security.SecuritySystemHolder
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, SessionCache) - Static method in class ome.security.basic.BasicSecuritySystem: Simplified factory method which generates all the security primitives internally.
selfConfigure() - Method in class ome.services.AbstractStatefulBean
selfConfigure() - Method in interface ome.system.SelfConfigurableService
SelfCorrectingDataSource - Class in ome.services.db: DataSource delegate which wraps the
SelfCorrectingDataSource(DataSource, long) - Constructor for class ome.services.db.SelfCorrectingDataSource
SelfCorrectingDataSource(DataSource, long, int, long) - Constructor for class ome.services.db.SelfCorrectingDataSource
sendBlind(Set<String>, String) - Method in class ome.services.mail.MailSender
sendBlind(Set<String>, String, String) - Method in class ome.services.mail.MailSender
sendEmail(String, String, String, String, boolean, List<String>, List<String>) - Method in class ome.services.mail.MailUtil: Main method which takes typical email fields as arguments, to prepare and populate the given new MimeMessage instance and send.
sendEmail(String, String, String, boolean, List<String>, List<String>) - Method in class ome.services.mail.MailUtil: Overloaded method which takes typical email fields as arguments, to prepare and populate the given new MimeMessage instance and send.
sendEmail(Collection<EventLog>) - Method in class ome.services.mail.ObjectMailSender
SendEmailRequestI - Class in omero.cmd.mail: Callback interface allowing to send email using JavaMailSender, supporting MIME messages through preparation callbacks.
SendEmailRequestI(MailUtil) - Constructor for class omero.cmd.mail.SendEmailRequestI
sender - Variable in class ome.services.mail.MailUtil
sender - Variable in class ome.services.mail.ServerUpMailSender
sendErrors() - Method in class ome.formats.importer.util.ErrorHandler: Send existing errors in ErrorContainer array to server
sendFiles - Variable in class ome.formats.importer.ImportConfig
sendFiles - Variable in class ome.formats.importer.ImportEvent.DEBUG_SEND
sendFiles - Variable in class ome.formats.importer.util.ErrorHandler
sendLogFile - Variable in class ome.formats.importer.ImportConfig
sendLogs - Variable in class ome.formats.importer.ImportEvent.DEBUG_SEND
sendLogs - Variable in class ome.formats.importer.util.ErrorHandler
sendReport - Variable in class ome.formats.importer.ImportConfig
separatorChar - Static variable in class ome.services.blitz.repo.path.FsFile: the separator character for delimiting repository path components
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 omero.util: Manager for all active servants in a single session.
ServantHolder(String) - Constructor for class omero.util.ServantHolder
ServantHolder(String, int) - Constructor for class omero.util.ServantHolder
servantsPerSession - Variable in class ome.services.blitz.fire.SessionManagerI
server - Variable in class loci.ome.io.OMECredentials
Server - Class in ome.system: Provides simplified handling of server properties when creating a ServiceFactory.
Server(String) - Constructor for class ome.system.Server: standard constructor which users Server.DEFAULT_PORT.
Server(String, int) - Constructor for class ome.system.Server: extended constructor.
SERVER_NAME_SEPARATOR - Static variable in class ome.formats.importer.ImportConfig: Delimiter used to encode multiple servers in one preferences value.
ServerDirectoryCheck - Class in ome.services.util: Hook run by the context at startup to create needed directories for the server.
ServerDirectoryCheck(String) - Constructor for class ome.services.util.ServerDirectoryCheck
ServerDownMailSender - Class in ome.services.mail: Send an email to all members of the system group when the server is shutting down.
ServerDownMailSender() - Constructor for class ome.services.mail.ServerDownMailSender
ServerFilePathTransformer - Class in ome.services.blitz.repo.path: Transform between repository FsFile path and server-local File.
ServerFilePathTransformer() - Constructor for class ome.services.blitz.repo.path.ServerFilePathTransformer
serverPaths - Variable in class ome.services.blitz.repo.PublicRepositoryI
ServerUpMailSender - Class in ome.services.mail: Announces to all members of the system group that the server has come up.
ServerUpMailSender(MailSender) - Constructor for class ome.services.mail.ServerUpMailSender
ServerVersionCheck - Class in ome.services.util: Hook run by the context.
ServerVersionCheck(String) - Constructor for class ome.services.util.ServerVersionCheck
service - Variable in class ome.services.blitz.impl.AbstractAmdServant: If there is no undering ome.* service, then this value can be null.
service - Variable in class ome.services.util.Executor.Impl
ServiceFactory - Class in ome.system: Entry point for all client calls.
ServiceFactory() - Constructor for class ome.system.ServiceFactory: default constructor which obtains the global static client context from OmeroContext.
ServiceFactory(Login) - Constructor for class ome.system.ServiceFactory: constructor which obtains a new (non-static) client context, passing in the Properties representation of the Login for configuration.
ServiceFactory(Server) - Constructor for class ome.system.ServiceFactory: constructor which obtains a new (non-static) client context, passing in the Properties representation of the Server for configuration.
ServiceFactory(Server, Login) - Constructor for class ome.system.ServiceFactory: constructor which obtains a new (non-static) client context, passing in the Properties representation of both the Server and the Login for configuration.
ServiceFactory(Properties) - Constructor for class ome.system.ServiceFactory: constructor which obtains a new client context, passing in the provided properties for configuration.
ServiceFactory(OmeroContext) - Constructor for class ome.system.ServiceFactory: constructor which uses the provided OmeroContext for all loookups.
ServiceFactory(String) - Constructor for class ome.system.ServiceFactory: constructor which finds the global static OmeroContext with the given name.
ServiceFactoryAware - Interface in ome.services.blitz.util: Servant which is aware of the ServiceFactoryI-instance which it belongs to and will have it injected on instantiation.
ServiceFactoryI - Class in ome.services.blitz.impl: Responsible for maintaining all servants for a single session.
ServiceFactoryI(Current, ServantHolder, SessionControlPrx, OmeroContext, SessionManager, Executor, Principal, List<HardWiredInterceptor>, TopicManager, Registry) - Constructor for class ome.services.blitz.impl.ServiceFactoryI
ServiceFactoryI(boolean, Current, ServantHolder, SessionControlPrx, OmeroContext, SessionManager, Executor, Principal, List<HardWiredInterceptor>, TopicManager, Registry, String) - Constructor for class ome.services.blitz.impl.ServiceFactoryI
ServiceHandler - Class in ome.services.util
ServiceHandler(CurrentDetails) - Constructor for class ome.services.util.ServiceHandler
ServiceHandler(CurrentDetails, long, long) - Constructor for class ome.services.util.ServiceHandler
ServiceInterface - Interface in ome.api: Marker interface representing an OMERO API Interface.
session - Variable in class ome.system.SessionInitializer
session - Variable in class omero.cmd.graphs.BaseGraphTraversalProcessor
session - Variable in class omero.model.DetailsI
session - Variable in class omero.util.RPSTileLoop
SessionAware - Interface in omero.cmd: Servant which is aware of the SessionI-instance which it belongs to and will have it injected on instantiation.
SessionBean - Class in ome.services.sessions: Implementation of ISession.
SessionBean(SessionManager, Executor, CurrentDetails) - Constructor for class ome.services.sessions.SessionBean
SessionCache - Class in ome.services.sessions.state: Synchronized and lockable state for the SessionManager.
SessionCache() - Constructor for class ome.services.sessions.state.SessionCache
SessionCache.StaleCacheListener - Interface in ome.services.sessions.state: Observer pattern used to refresh sessions in doUpdate.
SessionCallback - Interface in ome.services.sessions
SessionCallback.SimpleCloseCallback - Class in ome.services.sessions: Assumes that only close() will be called.
SessionCallback.SimpleCloseCallback() - Constructor for class ome.services.sessions.SessionCallback.SimpleCloseCallback
SessionContext - 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
SessionI - Class in omero.cmd
SessionI(boolean, Current, ServantHolder, SessionControlPrx, OmeroContext, SessionManager, Executor, Principal, String) - Constructor for class omero.cmd.SessionI
sessionId(String, String) - Static method in class omero.cmd.SessionI: Definition of session ids: "session-/"
sessionId() - Method in class omero.cmd.SessionI: Returns the Identity for this instance as defined by SessionI.sessionId(String, String)
sessionInit() - Method in class ome.services.util.ExecutionThread
SessionInitializer - Class in ome.system: Manages the creation of a single Session created via the injected ISession service.
SessionInitializer() - Constructor for class ome.system.SessionInitializer
sessionKey - Variable in class ome.formats.importer.ImportConfig
sessionManager - Variable in class ome.logic.UpdateImpl
sessionManager - Variable in class ome.security.basic.BasicSecuritySystem
sessionManager - Variable in class ome.services.blitz.fire.SessionManagerI
SessionManager - Interface in ome.services.sessions: Responsible for holding onto Session instances for optimized login.
sessionManager - Variable in class ome.services.sharing.ShareBean
sessionManager - Variable in class omero.cmd.SessionI
SessionManager.CreationRequest - Class in ome.services.sessions: Extensible data object which can be passed to create* methods to stop the explosion of different methods.
SessionManager.CreationRequest() - Constructor for class ome.services.sessions.SessionManager.CreationRequest
SessionManagerI - Class in ome.services.blitz.fire: Central login logic for all OMERO.blitz clients.
SessionManagerI(Ring, ObjectAdapter, SecuritySystem, SessionManager, Executor, TopicManager, Registry, int) - Constructor for class ome.services.blitz.fire.SessionManagerI
SessionManagerImpl - Class in ome.services.sessions: Is for ISession a cache and will be kept there in sync?
SessionManagerImpl() - Constructor for class ome.services.sessions.SessionManagerImpl
sessions - Variable in class ome.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
sessionToHolder - Variable in class ome.services.blitz.fire.SessionManagerI: An internal mapping to all ServiceFactoryI instances for a given session since there is no method on ObjectAdapter to retrieve all servants.
set(T) - Method in class ome.formats.importer.ImportConfig.Value: Sets the in-memory value, which will get persisted on ImportConfig.Value.store() when ImportConfig.saveAll() is called.
set(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
setAction(String) - Method in class ome.services.mail.ObjectMailSender
setActive(long, boolean) - Method in interface ome.api.IShare
setActive(int, boolean) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
setActive(long, boolean) - Method in class ome.services.sharing.ShareBean
setActive(int, boolean) - Method in class omeis.providers.re.Renderer: Makes a particular channel active or inactive.
setActive(int, boolean) - Method in interface omeis.providers.re.RenderingEngine: Maps the specified channel if true, unmaps the channel otherwise.
setActive_async(AMD_RenderingEngine_setActive, int, boolean, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
setActive_async(AMD_IShare_setActive, long, boolean, Current) - Method in class ome.services.blitz.impl.ShareI
setAdmin(boolean) - Method in class ome.security.basic.BasicEventContext
setAdminService(IAdmin) - Method in class ome.services.RawFileBean
setAgent(String) - Method in class omero.client: Sets the user agent string for this client.
setAirPressure(Pressure) - Method in class pojos.ImageAcquisitionData: Sets the air pressure.
setAirPressure(double) - Method in class pojos.ImageAcquisitionData: Deprecated.
Replaced by ImageAcquisitionData.setAirPressure(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.security.basic.GroupChmodStrategy
setApplicationContext(ApplicationContext) - Method in class ome.services.blitz.fire.SessionManagerI
setApplicationContext(ApplicationContext) - Method in class ome.services.blitz.impl.AbstractAmdServant: Creates an IceMethodInvoker for this instance if AbstractAmdServant.service is non-null.
setApplicationContext(ApplicationContext) - Method in class ome.services.blitz.impl.commands.RequestObjectFactoryRegistry
setApplicationContext(ApplicationContext) - Method in class ome.services.blitz.repo.PublicRepositoryI
setApplicationContext(ApplicationContext) - Method in class ome.services.blitz.repo.RequestObjectFactoryRegistry
setApplicationContext(ApplicationContext) - Method in class ome.services.delete.Deletion.Builder: Deprecated.
setApplicationContext(ApplicationContext) - Method in class ome.services.fulltext.FileParser
setApplicationContext(ApplicationContext) - Method in class ome.services.fulltext.FullTextIndexer
setApplicationContext(ApplicationContext) - Method in class ome.services.graphs.GraphSpecPostProcessor: Deprecated.
setApplicationContext(ApplicationContext) - Method in class ome.services.scheduler.SchedulerFactoryBean
setApplicationContext(ApplicationContext) - Method in class ome.services.sessions.SessionManagerImpl
setApplicationContext(ApplicationContext) - Method in class ome.services.sessions.state.CacheFactory
setApplicationContext(ApplicationContext) - Method in class ome.services.sessions.state.SessionCache: Context injector.
setApplicationContext(ApplicationContext) - Method in class ome.services.sharing.BlobShareStore: Because there is a cyclic dependency (SF->ACLVoter->BlobStore->SF), we have to lazy-load the session factory via the context.
setApplicationContext(ApplicationContext) - Method in class ome.services.throttling.AbstractThrottlingStrategy
setApplicationContext(ApplicationContext) - Method in class ome.services.util.Executor.Impl
setApplicationContext(ApplicationContext) - Method in class ome.tools.hibernate.SessionHandler
setApplicationContext(ApplicationContext) - Method in class ome.tools.spring.InternalServiceFactory: simple injector for the ApplicationContext
setApplicationContext(ApplicationContext) - Method in class ome.tools.spring.ManagedServiceFactory: simple injector for the ApplicationContext
setApplicationContext(ApplicationContext) - Method in class ome.tools.spring.OnContextRefreshedEventListener
setApplicationContext(ApplicationContext) - Method in class omero.cmd.RequestObjectFactoryRegistry
setApplicationEventPublisher(ApplicationEventPublisher) - Method in class ome.io.nio.PixelsService
setApplicationEventPublisher(ApplicationEventPublisher) - Method in class ome.services.fulltext.BridgeHelper
setApplicationEventPublisher(ApplicationEventPublisher) - Method in class ome.services.fulltext.bridges.TablesBridge
setApplicationEventPublisher(ApplicationEventPublisher) - Method in class ome.services.sessions.stats.CounterFactory
setApplicationEventPublisher(ApplicationEventPublisher) - Method in class ome.services.sessions.stats.LongCounter
setAppVersion(String) - Method in class ome.formats.importer.util.ErrorContainer
setArcAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setArcID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setArcLotNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setArcManufacturer(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setArcModel(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setArcPower(Power, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setArcSerialNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setArcType(ArcType, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setArgument(Map<String, Boolean>, String) - Static method in class ome.formats.importer.cli.CommandLineImporter: Set a conflicting argument and return the usage if the key is already set
setBackgroundColor(Paint) - Method in class ome.services.SVGRasterizer: Sets the Paint to use for the background of the image.
setBaseDirFile(File) - Method in class ome.services.blitz.repo.path.ServerFilePathTransformer: Set the repository root directory, to which FsFile instances are considered to be relative.
setBatchSize(int) - Method in interface ome.api.Search: Sets the maximum number of results that will be returned by one call to Search.results().
setBatchSize(int) - Method in class ome.services.eventlogs.EventLogLoader: Set the number of EventLog instances will be loaded in a single run.
setBatchSize(int) - Method in class ome.services.SearchBean
setBatchSize_async(AMD_Search_setBatchSize, int, Current) - Method in class ome.services.blitz.impl.SearchI
setBeanFactory(BeanFactory) - Method in class ome.services.messages.GlobalMulticaster
setBeanName(String) - Method in class ome.services.graphs.BaseGraphSpec: Deprecated.
setBeanName(String) - Method in class ome.system.Preference: Setter injector
setBeginsWith(Collection<String>) - Method in class ome.system.metrics.DefaultMetrics
setBinaryFileFileName(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setBinaryFileMIMEType(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setBinaryFileSize(NonNegativeLong, int) - Method in class ome.formats.OMEROMetadataStoreClient
setBinaryOnlyMetadataFile(String) - Method in class ome.formats.OMEROMetadataStoreClient
setBinaryOnlyUUID(String) - Method in class ome.formats.OMEROMetadataStoreClient
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
setBooleanAnnotationAnnotator(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setBooleanAnnotationDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setBooleanAnnotationID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setBooleanAnnotationNamespace(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setBooleanAnnotationValue(Boolean, int) - Method in class ome.formats.OMEROMetadataStoreClient
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
setCallback(RepoRawFileStoreI.Callback) - Method in class ome.services.blitz.repo.RepoRawFileStoreI
setCallContext(Map<String, String>) - Method in class ome.security.basic.BasicEventContext
setCaseSentivice(boolean) - Method in interface ome.api.Search: Sets the case sensitivity on all queries where case-sensitivity is supported.
setCaseSentivice(boolean) - Method in class ome.services.SearchBean
setCaseSentivice_async(AMD_Search_setCaseSentivice, boolean, Current) - Method in class ome.services.blitz.impl.SearchI
setChanges(String) - Method in class ome.services.graphs.GraphPolicyRule
setChannelAcquisitionMode(AcquisitionMode, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setChannelAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setChannelColor(Color, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setChannelContrastMethod(ContrastMethod, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setChannelEmissionWavelength(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setChannelExcitationWavelength(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient: (non-Javadoc)
setChannelFilterSetRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setChannelFluor(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setChannelGlobalMinMax(long, int, double, double) - Method in interface ome.api.IPixels: Sets the channel global (all 2D optical sections corresponding to a particular channel) minimum and maximum for a Pixels set.
setChannelGlobalMinMax(int, double, double, int) - Method in class ome.formats.OMEROMetadataStoreClient
setChannelGlobalMinMax(long, int, double, double) - Method in class ome.logic.PixelsImpl
setChannelGlobalMinMax_async(AMD_IPixels_setChannelGlobalMinMax, long, int, double, double, Current) - Method in class ome.services.blitz.impl.PixelsI
setChannelID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setChannelIlluminationType(IlluminationType, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setChannelLightSourceSettingsAttenuation(PercentFraction, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setChannelLightSourceSettingsID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setChannelLightSourceSettingsWavelength(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setChannelLookupTable(int, String) - Method in class ome.services.RenderingBean
setChannelLookupTable(int, String) - Method in interface omeis.providers.re.RenderingEngine
setChannelLookupTable_async(AMD_RenderingEngine_setChannelLookupTable, int, String, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
setChannelName(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setChannelNDFilter(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setChannelPinholeSize(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setChannelPockelCellSetting(Integer, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setChannelSamplesPerPixel(PositiveInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setChannelWindow(int, double, double) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
setChannelWindow(int, double, double) - Method in class omeis.providers.re.Renderer: Sets the pixels intensity interval for the specified channel.
setChannelWindow(int, double, double) - Method in interface omeis.providers.re.RenderingEngine: Returns the pixels intensity interval.
setChannelWindow_async(AMD_RenderingEngine_setChannelWindow, int, double, double, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
setChecksumAlgorithm(String) - Method in class ome.formats.importer.ImportContainer
setChecksumAlgorithm(ChecksumAlgorithm, List<Long>, Current) - Method in class ome.services.blitz.repo.ManagedRepositoryI
setChecksumProviderFactory(ChecksumProviderFactory) - Method in class ome.services.RawFileBean: ChecksumProviderFactory Bean injector
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
setComment(String) - Method in class ome.formats.importer.util.ErrorContainer
setCommentAnnotationAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setCommentAnnotationAnnotator(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setCommentAnnotationDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setCommentAnnotationID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setCommentAnnotationNamespace(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setCommentAnnotationValue(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setCommentType(String) - Method in class ome.formats.importer.util.ErrorContainer
setComponents(List<ImageData>) - Method in class pojos.MultiImageData: Sets the images composing the file.
setCompressionLevel(float) - Method in interface ome.api.local.LocalCompress: Sets the current compression level for the service.
setCompressionLevel(float) - Method in class ome.logic.CompressImpl
setCompressionLevel(float) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
setCompressionLevel(float) - Method in interface omeis.providers.re.RenderingEngine: Sets the current compression level for the service.
setCompressionLevel_async(AMD_RenderingEngine_setCompressionLevel, float, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
setCompressionService(LocalCompress) - Method in class ome.services.ThumbnailBean: Compression service Bean injector.
setCondition(String) - Method in class ome.services.graphs.GraphPolicy: Set a named condition,
setCondition(String) - Method in class omero.cmd.graphs.BaseGraphPolicyAdjuster
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.
setContactSystem(boolean) - Method in class ome.services.mail.FailedLoginMailSender
setContactUser(boolean) - Method in class ome.services.mail.FailedLoginMailSender
setContent(Object) - Method in class pojos.AnnotationData: Sets the annotation value.
setContent(Object) - Method in class pojos.BooleanAnnotationData: Sets the text annotation.
setContent(Object) - Method in class pojos.DoubleAnnotationData: Sets the text annotation.
setContent(Object) - Method in class pojos.FileAnnotationData: Sets the text annotation.
setContent(Object) - Method in class pojos.LongAnnotationData: Sets the text annotation.
setContent(Object) - Method in class pojos.MapAnnotationData
setContent(Object) - Method in class pojos.RatingAnnotationData: Sets the text annotation.
setContent(Object) - Method in class pojos.TagAnnotationData: Sets the text annotation.
setContent(Object) - Method in class pojos.TermAnnotationData: Sets the text annotation.
setContent(Object) - Method in class pojos.TextualAnnotationData: Sets the text annotation.
setContent(Object) - Method in class pojos.TimeAnnotationData: Sets the time annotation.
setContent(Object) - Method in class pojos.XMLAnnotationData: Sets the annotation.
setContext(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.
setCurrentGroup(long) - Method in class ome.formats.OMEROMetadataStoreClient: Changes the default group of the currently logged in user.
setCurrentId(long) - Method in class ome.services.eventlogs.PersistentEventLogLoader
setCurrentLogFile(String, String) - Method in class ome.formats.OMEROMetadataStoreClient
setCustomAnnotationList(List<Annotation>) - Method in class ome.formats.importer.ImportContainer: Sets the list of custom, user specified, annotations to link to all images represented by this container.
setCustomImageNaming(boolean) - Method in class ome.formats.importer.ImportConfig
setCustomImageNaming(boolean) - Method in class ome.formats.importer.util.IniFileLoader
setDatabaseIdentity(DatabaseIdentity) - Method in class ome.logic.ConfigImpl
setDatadir(String) - Method in class ome.logic.RepositoryInfoImpl: Bean injection setter for data repository directory
setDataObjects(Set<DataObject>) - Method in class pojos.TagAnnotationData: Sets the collection of data objects related to that tag.
setDatasetAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setDatasetDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setDatasetExperimenterGroupRef(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setDatasetExperimenterRef(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setDatasetID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setDatasetImageRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setDatasetName(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setDatasets(Set) - Method in class pojos.ImageData: Sets the datasets containing the image.
setDatasets(Set<DatasetData>) - Method in class pojos.ProjectData: Sets the datasets contained in this project.
setDataValue(double) - Method in class pojos.DoubleAnnotationData: Sets the rating value.
setDataValue(long) - Method in class pojos.LongAnnotationData: Sets the rating value.
setDb(boolean) - Method in class ome.system.Preference: Setter injector
setDebug(boolean) - Method in class ome.tools.hibernate.EventMethodInterceptor
setDebugAll(boolean) - Method in class ome.security.basic.EventListenersFactoryBean: for setter injection
setDebugLevel(int) - Method in class ome.formats.importer.ImportConfig
setDebugLevel(int) - Method in class ome.formats.importer.util.IniFileLoader: Set debug level for application
setDefaultBody(String) - Method in class ome.services.mail.MailSender
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(int) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
setDefaultT(int) - Method in class omeis.providers.re.Renderer: Sets the default timepoint index.
setDefaultT(int) - Method in interface omeis.providers.re.RenderingEngine: Sets the default timepoint index.
setDefaultT_async(AMD_RenderingEngine_setDefaultT, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
setDefaultTimeToIdle(long) - Method in class ome.services.sessions.SessionManagerImpl
setDefaultTimeToLive(long) - Method in class ome.services.sessions.SessionManagerImpl
setDefaultZ(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
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.AnnotationData: Sets the description of the underlying Annotation instance.
setDescription(String) - Method in class pojos.DatasetData: Sets the description of the dataset.
setDescription(String) - Method in class pojos.FileAnnotationData: Sets the description of the annotation.
setDescription(String) - Method in class pojos.FileData: Sets the description.
setDescription(String) - Method in class pojos.GroupData: Sets the name of the group.
setDescription(String) - Method in class pojos.ImageData: Sets the description of the image.
setDescription(String) - Method in class pojos.PlateAcquisitionData: Sets the name of the acquisition.
setDescription(String) - Method in class pojos.PlateData: Sets the description of the plate.
setDescription(String) - Method in class pojos.ProjectData: Sets the description of the project.
setDescription(String) - Method in class pojos.ScreenData: Sets the description of the screen.
setDescription(String) - Method in class pojos.XMLAnnotationData: Sets the description of the annotation.
setDescription_async(AMD_IShare_setDescription, long, String, Current) - Method in class ome.services.blitz.impl.ShareI
setDetach(boolean, Current) - Method in class omero.grid.InteractiveProcessorI
setDetectorAmplificationGain(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setDetectorAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setDetectorGain(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setDetectorID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setDetectorLotNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setDetectorManufacturer(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setDetectorModel(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setDetectorOffset(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setDetectorSerialNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setDetectorSettingBinning(Binning) - Method in class pojos.ChannelAcquisitionData: Sets the detector's binning.
setDetectorSettingOffset(double) - Method in class pojos.ChannelAcquisitionData: Sets the detector's setting offset.
setDetectorSettingsBinning(Binning, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setDetectorSettingsGain(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setDetectorSettingsGain(double) - Method in class pojos.ChannelAcquisitionData: Sets the detector setting's gain.
setDetectorSettingsID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setDetectorSettingsIntegration(PositiveInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setDetectorSettingsOffset(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setDetectorSettingsReadOutRate(Frequency, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setDetectorSettingsReadOutRate(Frequency) - Method in class pojos.ChannelAcquisitionData: Sets the detector setting's read out rate.
setDetectorSettingsReadOutRate(double) - Method in class pojos.ChannelAcquisitionData: Deprecated.
Replaced by ChannelAcquisitionData.setDetectorSettingsReadOutRate(Frequency)
setDetectorSettingsVoltage(ElectricPotential, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setDetectorSettingsVoltage(ElectricPotential) - Method in class pojos.ChannelAcquisitionData: Sets the detector setting's voltage.
setDetectorSettingsVoltage(double) - Method in class pojos.ChannelAcquisitionData: Deprecated.
Replaced by ChannelAcquisitionData.setDetectorSettingsVoltage(ElectricPotential)
setDetectorSettingsZoom(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setDetectorType(DetectorType, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setDetectorVoltage(ElectricPotential, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setDetectorZoom(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setDichroicAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setDichroicID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setDichroicLotNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setDichroicManufacturer(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setDichroicModel(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setDichroicSerialNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setDirty(boolean) - Method in class pojos.DataObject: Sets to true if the value has been modified, otherwise.
setDirty(boolean) - Method in class pojos.ShapeData: Sets to true if the figure been changed from the server side version, false otherwise.
setDisabledSubsystems(Set<String>) - Method in class ome.security.basic.BasicEventContext
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: Deprecated.
As of release 5.1, relevant model objects have the "ldap" property added to their state.
setDN(Long, String) - Method in class ome.logic.LdapImpl: Deprecated.
setDN_async(AMD_ILdap_setDN, RLong, String, Current) - Method in class ome.services.blitz.impl.LdapI
setDoThumbnails(boolean) - Method in class ome.formats.importer.ImportContainer: Sets whether or not we are performing thumbnail creation upon import completion.
setDoubleAnnotationAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setDoubleAnnotationAnnotator(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setDoubleAnnotationDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setDoubleAnnotationID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setDoubleAnnotationNamespace(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setDoubleAnnotationValue(Double, int) - Method in class ome.formats.OMEROMetadataStoreClient
setDryRun(boolean) - Method in class ome.services.fulltext.FullTextIndexer
setEllipseAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setEllipseFillColor(Color, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setEllipseFillRule(FillRule, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setEllipseFontFamily(FontFamily, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setEllipseFontSize(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setEllipseFontStyle(FontStyle, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setEllipseID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setEllipseLineCap(LineCap, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setEllipseLocked(Boolean, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setEllipseRadiusX(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setEllipseRadiusY(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setEllipseStrokeColor(Color, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setEllipseStrokeDashArray(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setEllipseStrokeWidth(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setEllipseText(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setEllipseTheC(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setEllipseTheT(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setEllipseTheZ(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setEllipseTransform(AffineTransform, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setEllipseVisible(Boolean, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setEllipseX(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setEllipseY(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setEmail(String) - Method in class ome.formats.importer.util.ErrorContainer
setEmail(String) - Method in class pojos.ExperimenterData: Sets the e-mail of the experimenter.
setEmissionWavelength(Length) - Method in class pojos.ChannelData: Sets the emission wavelength.
setEmissionWavelength(double) - Method in class pojos.ChannelData: Deprecated.
Replaced by ChannelData.setEmissionWavelength(Length)
setEnabled(boolean) - Method in class ome.services.mail.MailSender
setEncrypted(boolean) - Method in class loci.ome.io.OmeroReader
setEncryptedConnection(boolean) - Method in class ome.formats.OMEROMetadataStoreClient
setEnumerationProvider(EnumerationProvider) - Method in class ome.formats.OMEROMetadataStoreClient: Sets the active enumeration provider.
setError(Throwable) - Method in class ome.formats.importer.util.ErrorContainer
setError(String) - Method in class ome.services.graphs.GraphPolicyRule
setEvent(Event) - Method in class ome.security.basic.BasicEventContext
setEventContext(EventContext) - Method in class ome.services.graphs.GraphStep: Deprecated.
setExcitationWavelength(Length) - Method in class pojos.ChannelData: Sets the excitation wavelength.
setExcitationWavelength(double) - Method in class pojos.ChannelData: Deprecated.
Replaced by ChannelData.setExcitationWavelength(Length)
setExcludes(String[]) - Method in class ome.services.eventlogs.EventLogLoader: Spring injector
setExecutor(Executor) - Method in class ome.logic.UpdateImpl
setExecutor(Executor) - Method in class ome.services.mail.MailSender
setExecutor(Executor) - Method in class ome.services.SearchBean: Injector used by Spring, currently, since SelfConfigurableService.selfConfigure() requires it.
setExecutor(Executor) - Method in class ome.services.sessions.SessionManagerImpl
setExperimentDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setExperimenterAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setExperimenterEmail(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setExperimenterFirstName(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setExperimenterGroupAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setExperimenterGroupDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setExperimenterGroupExperimenterRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setExperimenterGroupID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setExperimenterGroupLeader(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setExperimenterGroupName(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setExperimenterID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setExperimenterInstitution(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setExperimenterLastName(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setExperimenterMiddleName(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setExperimenters(Set<ExperimenterData>) - Method in class pojos.GroupData: Sets the experimenters contained in this group.
setExperimenterUserName(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setExperimentExperimenterRef(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setExperimentID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setExperimentType(ExperimentType, int) - Method in class ome.formats.OMEROMetadataStoreClient
setExpiration(long, Timestamp) - Method in interface ome.api.IShare
setExpiration(long, Timestamp) - Method in class ome.services.sharing.ShareBean
setExpiration_async(AMD_IShare_setExpiration, long, RTime, Current) - Method in class ome.services.blitz.impl.ShareI
setExtendedMetadata(ExtendedMetadata) - Method in class ome.logic.AbstractLevel2Service
setExtendedMetadata(ExtendedMetadata) - Method in class ome.services.graphs.AbstractHierarchyGraphSpec: Deprecated.

Performs sanity checks on the entries found in ExtendedMetadata.
setExtendedMetadata(ExtendedMetadata) - Method in class ome.services.graphs.BaseGraphSpec: Deprecated.
setExtent(double, double) - Method in class omeis.providers.re.quantum.QuantumStrategy: Sets the maximum range of the input window.
setExternalDescription(String) - Method in class 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
setFastShutdown(boolean) - Method in class omero.client: Sets the client.fastShutdown flag.
setFilamentAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setFilamentID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setFilamentLotNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setFilamentManufacturer(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setFilamentModel(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setFilamentPower(Power, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setFilamentSerialNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setFilamentType(FilamentType, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setFile(File) - Method in class ome.formats.OMEROImportFixture
setFileAnnotationAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setFileAnnotationAnnotator(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setFileAnnotationDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setFileAnnotationID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setFileAnnotationNamespace(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setFileId(long) - Method in interface ome.api.RawFileStore: This method manages the state of the service.
setFileId(long) - Method in class ome.services.RawFileBean
setFileId_async(AMD_RawFileStore_setFileId, long, Current) - Method in class ome.services.blitz.impl.RawFileStoreI
setFileId_async(AMD_RawFileStore_setFileId, long, Current) - Method in class ome.services.blitz.repo.RepoRawFileStoreI
setFileIdWithBuffer(long, FileBuffer) - Method in class ome.services.RawFileBean
setFilePathResolver(FilePathResolver) - Method in class ome.io.nio.PixelsService
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 color.
setFillRule(String) - Method in class pojos.ShapeSettingsData: Set the fill rule.
setFilterAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setFilterFilterWheel(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setFilterID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setFilterLotNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setFilterManufacturer(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setFilterModel(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setFilterSerialNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
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: Deprecated.
Replaced by ShapeSettingsData.setFontSize(Length)
setFontSize(Length) - 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
setGenericExcitationSourceAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setGenericExcitationSourceID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setGenericExcitationSourceLotNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setGenericExcitationSourceManufacturer(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setGenericExcitationSourceMap(List<MapPair>, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setGenericExcitationSourceModel(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setGenericExcitationSourcePower(Power, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setGenericExcitationSourceSerialNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setGraphiteAddress(String) - Method in class ome.system.metrics.DefaultMetrics
setGreen(Integer) - Method in class pojos.WellData: Sets the green component of the color associated to the well.
setGreenValue(int, int) - Method in class omeis.providers.re.RGBAIntBuffer: Sets the Green value for a particular pixel index.
setGreenValue(int, int) - Method in class omeis.providers.re.RGBBuffer: Sets the Green value for a particular pixel index.
setGreenValue(int, int) - Method in class omeis.providers.re.RGBIntBuffer: Sets the Green value for a particular pixel index.
setGroup(Long) - Method in class ome.formats.OMEROMetadataStoreClient: Sets the id which will be used by OMEROMetadataStoreClient.initializeServices(boolean) to set the call context for all services.
setGroup(ExperimenterGroup, Permissions) - Method in class ome.security.basic.BasicEventContext
setGroup(long) - Method in class ome.services.chgrp.ChgrpStepFactory: Deprecated.

Set the group id which will be passed to all new ChgrpStep instances.
setGroup(long) - Method in class ome.services.chown.ChownStepFactory: Deprecated.

Set the group id which will be passed to all new ChownStep instances.
setGroup(ExperimenterGroup, Current) - Method in class omero.model.DetailsI
setGroupAnnotate(boolean, Current) - Method in class omero.model.PermissionsI
setGroupAnnotate(boolean) - Method in class pojos.PermissionData: Sets to true if the group has annotate access, false otherwise.
setGroupID(Long) - Method in class loci.ome.io.OmeroReader
setGroupName(String) - Method in class loci.ome.io.OmeroReader
setGroupOwner(ExperimenterGroup, Experimenter) - Method in interface ome.api.IAdmin: adds the user to the owner list for this group.
setGroupOwner(ExperimenterGroup, Experimenter) - Method in class ome.logic.AdminImpl
setGroupOwner(Experimenter, ExperimenterGroup, boolean) - Method in interface ome.security.auth.RoleProvider
setGroupOwner(Experimenter, ExperimenterGroup, boolean) - Method in class ome.security.auth.SimpleRoleProvider
setGroupOwner_async(AMD_IAdmin_setGroupOwner, ExperimenterGroup, Experimenter, Current) - Method in class ome.services.blitz.impl.AdminI
setGroupPermissions(Permissions) - Method in class ome.system.SimpleEventContext
setGroupRead(boolean, Current) - Method in class omero.model.PermissionsI
setGroupRead(boolean) - Method in class pojos.PermissionData: Sets to true if the group has read access, false otherwise.
setGroups(List<GroupData>) - Method in class pojos.ExperimenterData: Sets the groups the experimenter is a member of.
setGroupWrite(boolean, Current) - Method in class omero.model.PermissionsI
setGroupWrite(boolean) - Method in class pojos.PermissionData: Sets to true if the group has write access, false otherwise.
setHeight(int) - Method in class omeis.providers.re.data.RegionDef: Sets the height of the region.
setHeight(double) - Method in class pojos.MaskData: Sets the height of an untransformed mask.
setHeight(double) - Method in class pojos.RectangleData: Sets the height of an untransformed rectangle.
setHolder(ServantHolder) - Method in class ome.services.blitz.impl.AbstractAmdServant: Sets the ServantHolder for the current session so that on #close_async(AMD_StatefulServiceInterface_close, Current) it will be possible to cleanup the resources.
setHumidity(double) - Method in class pojos.ImageAcquisitionData: Sets the humidity.
setIceCommunicator(Communicator) - Method in class omero.util.ObjectFactoryRegistry
setIContainer(IContainer) - Method in class ome.logic.MetadataImpl: IContainer bean injector.
setId(String) - Method in class ome.io.bioformats.OmeroPixelsPyramidReader
setId(String) - Method in class ome.io.bioformats.OmeroPixelsPyramidWriter
setId(Long) - Method in class ome.services.blitz.repo.CheckedPath
setId(long) - Method in class pojos.DataObject: Sets the database id.
setIdOnly() - Method in class ome.services.SearchBean
setIllumination(Illumination) - Method in class 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.
setImageAcquisitionDate(Timestamp, int) - Method in class ome.formats.OMEROMetadataStoreClient
setImageAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setImageDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setImageExperimenterGroupRef(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setImageExperimenterRef(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setImageExperimentRef(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setImageHeight(float) - Method in class ome.services.SVGRasterizer: Sets the height of the image to rasterize.
setImageID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setImageInstrumentRef(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
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
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(Pressure, int) - Method in class ome.formats.OMEROMetadataStoreClient
setImagingEnvironmentCO2Percent(PercentFraction, int) - Method in class ome.formats.OMEROMetadataStoreClient
setImagingEnvironmentHumidity(PercentFraction, int) - Method in class ome.formats.OMEROMetadataStoreClient
setImagingEnvironmentMap(List<MapPair>, int) - Method in class ome.formats.OMEROMetadataStoreClient
setImagingEnvironmentTemperature(Temperature, int) - Method in class ome.formats.OMEROMetadataStoreClient
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.
setInstrumentAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
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.
setIP(String) - Method in class omero.client: Sets the user ip string for this client.
setIPixels(IPixels) - Method in class ome.services.projection.ProjectionBean: IPixels bean injector.
setIPixels(IPixels) - Method in class ome.services.ThumbnailBean: Pixels service Bean injector.
setIRepositoryInfo(IRepositoryInfo) - Method in class ome.services.RawFileBean: Disk Space Usage service Bean injector
setIRepositoryInfo(IRepositoryInfo) - Method in class ome.services.RawPixelsBean: Disk Space Usage service Bean injector
setIRepositoryInfo(IRepositoryInfo) - Method in class ome.services.ThumbnailBean: Disk Space Usage service Bean injector
setIsSPW(Boolean) - Method in class ome.formats.importer.ImportContainer: Set true if the import container is filled in with a Screen/Plate/Well image structure.
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.
setLabelAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLabelFillColor(Color, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLabelFillRule(FillRule, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLabelFontFamily(FontFamily, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLabelFontSize(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLabelFontStyle(FontStyle, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLabelID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLabelLineCap(LineCap, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLabelLocked(Boolean, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLabelName(String) - Method in class pojos.ImageAcquisitionData: Sets the name of the stage label.
setLabelStrokeColor(Color, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLabelStrokeDashArray(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLabelStrokeWidth(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLabelText(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLabelTheC(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLabelTheT(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLabelTheZ(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLabelTransform(AffineTransform, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLabelVisible(Boolean, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLabelX(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLabelY(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLanguages(String) - Method in class ome.services.SVGRasterizer: Sets the preferred language to use.
setLaserAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLaserFrequencyMultiplication(PositiveInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLaserID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLaserLaserMedium(LaserMedium, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLaserLotNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLaserManufacturer(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLaserModel(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLaserPockelCell(Boolean, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLaserPower(Power, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLaserPulse(Pulse, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLaserPump(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLaserRepetitionRate(Frequency, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLaserSerialNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLaserTuneable(Boolean, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLaserType(LaserType, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLaserWavelength(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLastName(String) - Method in class pojos.ExperimenterData: Sets the last name of the experimenter.
setLeaderOfGroups(List<Long>) - Method in class ome.security.basic.BasicEventContext
setLegacyUtil(PasswordUtil) - Method in class ome.security.auth.ConfigurablePasswordProvider
setLightEmittingDiodeAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLightEmittingDiodeID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLightEmittingDiodeLotNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLightEmittingDiodeManufacturer(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLightEmittingDiodeModel(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLightEmittingDiodePower(Power, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLightEmittingDiodeSerialNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLightPathAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLightPathDichroicRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLightPathEmissionFilterRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLightPathExcitationFilterRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLightSettingsAttenuation(double) - Method in class pojos.ChannelAcquisitionData: Sets the attenuation of the light settings.
setLightSettingsWavelength(Length) - Method in class pojos.ChannelAcquisitionData: Sets the wavelength of the light source.
setLightSettingsWavelength(double) - Method in class pojos.ChannelAcquisitionData: Deprecated.
Replaced by ChannelAcquisitionData.setLightSettingsWavelength(Length)
setLightSource(LightSourceData) - Method in class pojos.ChannelAcquisitionData: Sets the light source associated to the settings.
setLimits(int, int) - Method in class omeis.providers.re.codomain.PlaneSlicingContext: Set the limits.
setLineAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLineCap(int) - Method in class pojos.ShapeSettingsData: Sets the line cap.
setLineFillColor(Color, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLineFillRule(FillRule, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLineFontFamily(FontFamily, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLineFontSize(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLineFontStyle(FontStyle, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLineID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLineLineCap(LineCap, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLineLocked(Boolean, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLineMarkerEnd(Marker, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLineMarkerStart(Marker, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLineStrokeColor(Color, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLineStrokeDashArray(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLineStrokeWidth(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLineText(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLineTheC(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLineTheT(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLineTheZ(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLineTransform(AffineTransform, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLineVisible(Boolean, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLineX1(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLineX2(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLineY1(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLineY2(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setListAnnotationAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setListAnnotationAnnotator(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setListAnnotationDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setListAnnotationID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setListAnnotationNamespace(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLockCandidates(Set<IObject>) - Method in class ome.security.basic.BasicEventContext
setLogs(List<EventLog>) - Method in class ome.security.basic.BasicEventContext
setLongAnnotationAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLongAnnotationAnnotator(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLongAnnotationDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLongAnnotationID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLongAnnotationNamespace(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setLongAnnotationValue(Long, int) - Method in class ome.formats.OMEROMetadataStoreClient
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.
setMailUtil(MailUtil) - Method in class ome.services.mail.MailSender
setMap(QuantumMap) - Method in class omeis.providers.re.quantum.QuantumStrategy: Sets the quantum map.
setMapAnnotationAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setMapAnnotationAnnotator(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setMapAnnotationDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setMapAnnotationID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setMapAnnotationNamespace(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setMapAnnotationValue(List<MapPair>, int) - Method in class ome.formats.OMEROMetadataStoreClient
setMapping(Family, double, boolean) - Method in class omeis.providers.re.quantum.QuantumStrategy: Sets the selected family, the curve coefficient and the noise reduction flag.
setMarkerEnd(String) - Method in class pojos.ShapeSettingsData: Returns the marker end.
setMarkerStart(String) - Method in class pojos.ShapeSettingsData: Returns the marker start.
setMask(byte[]) - Method in class pojos.MaskData: Sets the mask image.
setMask(BufferedImage) - Method in class pojos.MaskData: Sets the mask from the bufferedImage.
setMaskAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setMaskBinData(byte[], int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setMaskBinData(byte[], int, int) - Method in class ome.formats.OverlayMetadataStore
setMaskFillColor(Color, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setMaskFillRule(FillRule, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setMaskFontFamily(FontFamily, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setMaskFontSize(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setMaskFontStyle(FontStyle, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setMaskHeight(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setMaskHeight(Double, int, int) - Method in class ome.formats.OverlayMetadataStore
setMaskID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setMaskLineCap(LineCap, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setMaskLocked(Boolean, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setMaskStrokeColor(Color, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setMaskStrokeColor(Color, int, int) - Method in class ome.formats.OverlayMetadataStore
setMaskStrokeDashArray(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setMaskStrokeWidth(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setMaskText(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setMaskTheC(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setMaskTheT(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setMaskTheZ(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setMaskTransform(AffineTransform, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setMaskVisible(Boolean, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setMaskWidth(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setMaskWidth(Double, int, int) - Method in class ome.formats.OverlayMetadataStore
setMaskX(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setMaskX(Double, int, int) - Method in class ome.formats.OverlayMetadataStore
setMaskY(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setMaskY(Double, int, int) - Method in class ome.formats.OverlayMetadataStore
setMatches(String) - Method in class ome.services.graphs.GraphPolicyRule
setMaxClauseCount(Integer) - Method in class ome.services.SearchBean: Injector used by Spring.
setMaxFileSize(Long) - Method in class ome.services.fulltext.FileParser
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.
setMemberOfGroups(List<Long>) - Method in class ome.security.basic.BasicEventContext
setMergedBatches(boolean) - Method in interface ome.api.Search: Set whether or not results from two separate queries can be returned in the same call to Search.results().
setMergedBatches(boolean) - Method in class ome.services.SearchBean
setMergedBatches_async(AMD_Search_setMergedBatches, boolean, Current) - Method in class ome.services.blitz.impl.SearchI
setMessage(String) - Method in interface ome.api.JobHandle: Sets the job's message string, and returns the previous value.
setMessage(String, Current) - Method in class ome.services.blitz.impl.ScriptProcessI
setMessage(String) - Method in class ome.services.JobBean
setMessage_async(AMD_JobHandle_setMessage, String, Current) - Method in class ome.services.blitz.impl.JobHandleI
setMetadataOptions(MetadataOptions) - Method in class ome.formats.importer.OMEROWrapper
setMethodHardLimit(int) - Method in class ome.services.sessions.stats.CounterFactory
setMethodSecurity(MethodSecurity) - Method in class ome.security.basic.BasicSecurityWiring: Setter injection.
setMetrics(Metrics) - Method in class ome.io.nio.PixelsService
setMicrobeamManipulationDescription(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setMicrobeamManipulationExperimenterRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setMicrobeamManipulationID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setMicrobeamManipulationLightSourceSettingsAttenuation(PercentFraction, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setMicrobeamManipulationLightSourceSettingsID(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setMicrobeamManipulationLightSourceSettingsWavelength(Length, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setMicrobeamManipulationROIRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setMicrobeamManipulationType(MicrobeamManipulationType, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
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.
setMimetype(OriginalFile) - Method in class ome.services.scripts.ScriptFileType: Sets the mimetype on the given OriginalFile if the name field matches the wildcard pattern for this instance.
setMimetype(OriginalFile) - Method in class ome.services.scripts.ScriptRepoHelper
setMode(AcquisitionMode) - Method in class 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
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.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.
setNoStatsInfo(boolean) - Method in class ome.formats.importer.ImportContainer: Sets whether or not we disabling StatsInfo population.
setNumOfDirectories(int) - Method in class ome.formats.importer.ImportConfig
setNumOfDirectories(int) - Method in class ome.formats.importer.util.IniFileLoader
setObjectClass(Class<IObject>) - Method in class ome.services.mail.ObjectMailSender
setObjectiveAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setObjectiveCalibratedMagnification(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setObjectiveCorrection(Correction, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setObjectiveID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setObjectiveImmersion(Immersion, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setObjectiveIris(Boolean, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setObjectiveLensNA(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setObjectiveLotNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setObjectiveManufacturer(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setObjectiveModel(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setObjectiveNominalMagnification(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setObjectiveSerialNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setObjectiveSettingsCorrectionCollar(Double, int) - Method in class ome.formats.OMEROMetadataStoreClient
setObjectiveSettingsID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setObjectiveSettingsMedium(Medium, int) - Method in class ome.formats.OMEROMetadataStoreClient
setObjectiveSettingsRefractiveIndex(Double, int) - Method in class ome.formats.OMEROMetadataStoreClient
setObjectiveWorkingDistance(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setObjectsReadHardLimit(int) - Method in class ome.services.sessions.stats.CounterFactory
setObjectsWrittenHardLimit(int) - Method in class ome.services.sessions.stats.CounterFactory
setOffset(int, long) - Method in class ome.services.blitz.repo.ManagedImportProcessI
setOnAllUsers(boolean) - Method in class ome.services.mail.FailedLoginMailSender
setOnSpecificUsers(Set<String>) - Method in class ome.services.mail.FailedLoginMailSender
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
setOutput(String, String, Object) - Method in interface ome.api.ISession: Places an entry in the given session's output environment.
setOutput(String, String, Object) - Method in class ome.services.sessions.SessionBean
setOutput(String, String, Object) - Method in interface ome.services.sessions.SessionManager: Places the argument in the output environment under the given key, possibly initializing the Map Throws an exception if there is no Session with the given identifier.
setOutput(String, String, Object) - Method in class ome.services.sessions.SessionManagerImpl
setOutput(String, RType) - Method in class omero.client: Sets an item in the "output" shared (session) memory under the given name.
setOutput_async(AMD_ISession_setOutput, String, String, RType, Current) - Method in class ome.services.blitz.impl.SessionI
setOverlays(Map<byte[], Integer>) - Method in class ome.services.RenderingBean: Deprecated.
As of release 5.1.0, replaced by PlaneDef.setShapeIds(List).
setOverlays(Map<byte[], Integer>) - Method in class omeis.providers.re.Renderer: Sets a map of overlays to be rendered.
setOverlays(Map<byte[], Integer>) - Method in interface omeis.providers.re.RenderingEngine: Informs the rendering engine that it should render a set of overlays on each rendered frame.
setOverlays_async(AMD_RenderingEngine_setOverlays, RLong, RLong, Map<Long, Integer>, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
setOwner(Experimenter) - Method in class ome.security.basic.BasicEventContext
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.
setPassword(String) - Method in class loci.ome.io.OmeroReader
setPathSanitizer(Function<String, String>) - Method in class ome.services.blitz.repo.path.ServerFilePathTransformer: Set the string transformer that is used to make file-path components safe across platforms.
setPathToFile(String) - Method in class pojos.ImageData: Sets the path to the file.
setPerm1(long, Current) - Method in class omero.model.PermissionsI
setPerm1(Long) - Method in class omero.model.PermissionsI
setPermissions(Permissions, Current) - Method in class omero.model.DetailsI
setPermissionsForGroup(Long, Permissions) - Method in class ome.security.basic.BasicEventContext: Called during BasicACLVoter.allowLoad(org.hibernate.Session, Class, ome.model.internal.Details, long) to track groups that will need resolving later.
setPermissionsVerifier(String, int) - Method in class ome.services.blitz.Router
setPinholeSize(Length) - Method in class pojos.ChannelData: Sets the pinhole size.
setPinholeSize(double) - Method in class pojos.ChannelData: Deprecated.
Replaced by ChannelData.setPinholeSize(Length)
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.
setPixelsBigEndian(Boolean, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPixelsBinDataBigEndian(Boolean, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPixelsData(PixelsService) - Method in class ome.logic.RenderingSettingsImpl: Sets injector.
setPixelsData(PixelsService) - Method in class ome.services.RawPixelsBean
setPixelsDimensionOrder(DimensionOrder, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPixelsFile(long, String, String) - Method in class ome.formats.OMEROMetadataStoreClient: Sets the path, name and repo in the pixels table.
setPixelsFile_async(AMD_MetadataStore_setPixelsFile, long, String, String, Current) - Method in class ome.services.blitz.impl.MetadataStoreI
setPixelsId(long, boolean) - Method in interface ome.api.RawPixelsStore: Initializes the stateful service for a given Pixels set.
setPixelsId(long) - Method in interface ome.api.ThumbnailStore: This method manages the state of the service; it must be invoked before using any other methods.
setPixelsID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPixelsId(long, boolean) - Method in class ome.services.RawPixelsBean
setPixelsId(long) - Method in class ome.services.ThumbnailBean
setPixelsId_async(AMD_RawPixelsStore_setPixelsId, long, boolean, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
setPixelsId_async(AMD_ThumbnailStore_setPixelsId, long, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
setPixelsId_async(AMD_RawPixelsStore_setPixelsId, long, boolean, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
setPixelsInterleaved(Boolean, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPixelSizeX(double) - Method in class pojos.PixelsData: Deprecated.
Replaced by PixelsData.setPixelSizeX(Length)
setPixelSizeX(Length) - Method in class pojos.PixelsData: Sets the dimension of a pixel along the X-axis
setPixelSizeY(double) - Method in class pojos.PixelsData: Deprecated.
Replaced by PixelsData.setPixelSizeY(Length)
setPixelSizeY(Length) - Method in class pojos.PixelsData: Sets the dimension of a pixel along the Y-axis
setPixelSizeZ(double) - Method in class pojos.PixelsData: Deprecated.
Replaced by PixelsData.setPixelSizeZ(Length)
setPixelSizeZ(Length) - Method in class pojos.PixelsData: Sets the dimension of a pixel along the Z-axis
setPixelsMetadata(IPixels) - Method in class ome.logic.RenderingSettingsImpl: Sets injector.
setPixelsMetadata(IPixels) - Method in class ome.services.RawPixelsBean
setPixelsPhysicalSizeX(Length, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPixelsPhysicalSizeY(Length, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPixelsPhysicalSizeZ(Length, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPixelsService(PixelsService) - Method in class ome.logic.RepositoryInfoImpl: Bean injection setter for ROMIO pixels service
setPixelsService(PixelsService) - Method in class ome.services.projection.ProjectionBean: PixelsService bean injector.
setPixelsSignificantBits(PositiveInteger, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPixelsSizeC(PositiveInteger, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPixelsSizeT(PositiveInteger, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPixelsSizeX(PositiveInteger, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPixelsSizeY(PositiveInteger, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPixelsSizeZ(PositiveInteger, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPixelsTimeIncrement(Time, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPixelsType(PixelType, int) - Method in class ome.formats.OMEROMetadataStoreClient
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(byte[], int, int, int) - Method in class ome.services.RawPixelsBean
setPlane_async(AMD_RawPixelsStore_setPlane, byte[], int, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
setPlane_async(AMD_RawPixelsStore_setPlane, byte[], int, int, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
setPlaneAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPlaneDeltaT(Time, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPlaneExposureTime(Time, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPlaneHashSHA1(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPlanePositionX(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPlanePositionY(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPlanePositionZ(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
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(Timestamp, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPlateAcquisitionID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPlateAcquisitionMaximumFieldCount(PositiveInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPlateAcquisitionName(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPlateAcquisitionStartTime(Timestamp, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPlateAcquisitionWellSampleRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPlateAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPlateColumnNamingConvention(NamingConvention, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPlateColumns(PositiveInteger, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPlateDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPlateExternalIdentifier(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPlateFieldIndex(NonNegativeInteger, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPlateID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPlateName(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPlateRowNamingConvention(NamingConvention, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPlateRows(PositiveInteger, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPlates(Set<PlateData>) - Method in class pojos.ScreenData: Sets the plates contained in this screen.
setPlateStatus(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPlateWellOriginX(Length, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPlateWellOriginY(Length, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPockelCell(int) - Method in class pojos.ChannelData: Sets the pockel cell.
setPointAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPointFillColor(Color, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPointFillRule(FillRule, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPointFontFamily(FontFamily, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPointFontSize(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPointFontStyle(FontStyle, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPointID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPointLineCap(LineCap, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPointLocked(Boolean, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPoints(List<Point2D.Double>, List<Point2D.Double>, List<Point2D.Double>, List<Integer>) - Method in class pojos.PolygonData: Sets the points in the polygon.
setPoints(List<Point2D.Double>, List<Point2D.Double>, List<Point2D.Double>, List<Integer>) - Method in class pojos.PolylineData: Sets the points in the polyline.
setPointStrokeColor(Color, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPointStrokeDashArray(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPointStrokeWidth(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPointText(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPointTheC(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPointTheT(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPointTheZ(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPointTransform(AffineTransform, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPointVisible(Boolean, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPointX(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPointY(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPolygonAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPolygonFillColor(Color, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPolygonFillRule(FillRule, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPolygonFontFamily(FontFamily, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPolygonFontSize(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPolygonFontStyle(FontStyle, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPolygonID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPolygonLineCap(LineCap, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPolygonLocked(Boolean, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPolygonPoints(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPolygonStrokeColor(Color, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPolygonStrokeDashArray(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPolygonStrokeWidth(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPolygonText(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPolygonTheC(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPolygonTheT(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPolygonTheZ(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPolygonTransform(AffineTransform, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPolygonVisible(Boolean, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPolylineAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPolylineFillColor(Color, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPolylineFillRule(FillRule, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPolylineFontFamily(FontFamily, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPolylineFontSize(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPolylineFontStyle(FontStyle, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPolylineID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPolylineLineCap(LineCap, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPolylineLocked(Boolean, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPolylineMarkerEnd(Marker, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPolylineMarkerStart(Marker, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPolylinePoints(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPolylineStrokeColor(Color, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPolylineStrokeDashArray(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPolylineStrokeWidth(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPolylineText(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPolylineTheC(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPolylineTheT(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPolylineTheZ(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPolylineTransform(AffineTransform, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPolylineVisible(Boolean, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setPort(int) - Method in class loci.ome.io.OmeroReader
setPositionX(Length) - Method in class pojos.ImageAcquisitionData: Sets the x-position.
setPositionX(double) - Method in class pojos.ImageAcquisitionData: Deprecated.
Replaced by ImageAcquisitionData.setPositionX(Length)
setPositionY(Length) - Method in class pojos.ImageAcquisitionData: Sets the y-position.
setPositionY(double) - Method in class pojos.ImageAcquisitionData: Deprecated.
Replaced by ImageAcquisitionData.setPositionY(Length)
setPositionZ(Length) - Method in class pojos.ImageAcquisitionData: Sets the z-position.
setPositionZ(double) - Method in class pojos.ImageAcquisitionData: Deprecated.
Replaced by ImageAcquisitionData.setPositionZ(Length)
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
setProjectDatasetRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setProjectDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setProjectExperimenterGroupRef(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setProjectExperimenterRef(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setProjectID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
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.
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
setQuantumStrategy(int) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
setQuantumStrategy(int) - Method in class omeis.providers.re.Renderer: Sets the bit resolution.
setQuantumStrategy(int) - Method in interface omeis.providers.re.RenderingEngine: Sets the quantization strategy.
setQuantumStrategy_async(AMD_RenderingEngine_setQuantumStrategy, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
setQuery(Query) - Method in class ome.services.query.Query: provide this Query instance with a Query to be used for retrieving data.
setQueryFactory(QueryFactory) - Method in class ome.logic.AbstractLevel1Service
setQueryFactory(QueryFactory) - Method in class ome.logic.AbstractLevel2Service
setQueryService(LocalQuery) - Method in class ome.logic.AbstractLevel2Service
setQueryService(LocalQuery) - Method in class ome.logic.UpdateImpl
setQueryService(LocalQuery) - Method in class ome.services.AbstractStatefulBean: Query service Bean injector.
setQueryService(IQuery) - Method in class ome.services.eventlogs.EventLogLoader: Spring injector
setQueryService(IQuery) - Method in class ome.services.mail.MailSender
setQueryService(IQuery) - Method in class ome.services.procs.ProcessorSkeleton
setQueryString(String) - Method in class ome.services.mail.ObjectMailSender
setRadiusX(double) - Method in class pojos.EllipseData: Sets the radius along the X-axis.
setRadiusY(double) - Method in class pojos.EllipseData: Sets the radius along the Y-axis.
setRating(int) - Method in class pojos.RatingAnnotationData: Sets the rating value.
setReader(String) - Method in class ome.formats.importer.ImportContainer: Sets the reader class name used for reading the contents of this import container.
setReader(IFormatReader) - Method in interface ome.formats.model.IObjectContainerStore: Sets the Bio-Formats reader that will be used to populate the container store.
setReader(IFormatReader) - Method in class ome.formats.OMEROMetadataStoreClient
setReaderType(String) - Method in class ome.formats.importer.util.ErrorContainer: set file format for import
setReadOnly(boolean) - Method in class ome.security.basic.BasicEventContext
setReadOnly(boolean) - Method in class ome.services.sessions.SessionManagerImpl
setReadOnly(boolean) - Method in class pojos.ShapeData: Sets to true if the object is a read-only object, false otherwise.
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.
setRectangleAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setRectangleFillColor(Color, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setRectangleFillRule(FillRule, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setRectangleFontFamily(FontFamily, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setRectangleFontSize(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setRectangleFontStyle(FontStyle, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setRectangleHeight(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setRectangleID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setRectangleLineCap(LineCap, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setRectangleLocked(Boolean, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setRectangleStrokeColor(Color, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setRectangleStrokeDashArray(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setRectangleStrokeWidth(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setRectangleText(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setRectangleTheC(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setRectangleTheT(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setRectangleTheZ(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setRectangleTransform(AffineTransform, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setRectangleVisible(Boolean, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setRectangleWidth(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setRectangleX(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setRectangleY(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setRed(Integer) - Method in class 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) - Method in class ome.services.ThumbnailBean
setRenderingDefId_async(AMD_ThumbnailStore_setRenderingDefId, long, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
setRenderShapes(boolean) - Method in class omeis.providers.re.data.PlaneDef: Sets whether or not to render the shapes (masks).
setRepetitions(int) - Method in class ome.services.fulltext.FullTextIndexer: Spring injector.
setRepetitions(int) - Method in class ome.services.pixeldata.PixelDataHandler: Spring injector.
setReportingLoops(int) - Method in class ome.services.fulltext.FullTextIndexer
setRepositoryPath(String) - Method in class pojos.FileData: Sets the path to the parent.
setResolutionLevel(int) - Method in interface ome.api.RawPixelsStore
setResolutionLevel(int) - Method in class ome.io.bioformats.BfPixelBuffer
setResolutionLevel(int) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
setResolutionLevel(IFD) - Method in class ome.io.bioformats.OmeroPixelsPyramidReader
setResolutionLevel(int) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
setResolutionLevel(int) - Method in interface ome.io.nio.PixelBuffer: Sets the active resolution level.
setResolutionLevel(int) - Method in class ome.io.nio.RomioPixelBuffer
setResolutionLevel(int) - Method in class ome.services.RawPixelsBean
setResolutionLevel(int) - Method in class ome.services.RenderingBean
setResolutionLevel(int) - Method in class omeis.providers.re.Renderer: Sets the active resolution level.
setResolutionLevel(int) - Method in interface omeis.providers.re.RenderingEngine
setResolutionLevel_async(AMD_PyramidService_setResolutionLevel, int, Current) - Method in class ome.services.blitz.impl.AbstractPyramidServant
setResolutionLevel_async(AMD_PyramidService_setResolutionLevel, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
setResponseIfNull(Response) - Method in class omero.cmd.Helper: Set the response if there is not currently run, in which case true is returned.
setRetry() - Method in class ome.io.messages.MissingPyramidMessage
setReturnUnloaded(boolean) - Method in interface ome.api.Search: Determines if all results should be returned as unloaded objects.
setReturnUnloaded(boolean) - Method in class ome.services.SearchBean
setReturnUnloaded_async(AMD_Search_setReturnUnloaded, boolean, Current) - Method in class ome.services.blitz.impl.SearchI
setRGBA(int, int, int, int, int) - Method in class ome.services.RenderingBean: Implemented as specified by the RenderingEngine interface.
setRGBA(int, int, int, int, int) - Method in class omeis.providers.re.Renderer: Sets the color associated to the specified channel.
setRGBA(int, int, int, int, int) - Method in interface omeis.providers.re.RenderingEngine: Sets the four components composing the color associated to the specified channel.
setRGBA_async(AMD_RenderingEngine_setRGBA, int, int, int, int, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
setRightsRightsHeld(String) - Method in class ome.formats.OMEROMetadataStoreClient
setRightsRightsHolder(String) - Method in class ome.formats.OMEROMetadataStoreClient
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.mail.MailSender
setRoles(Roles) - Method in class ome.services.sessions.SessionManagerImpl
setRoot(MetadataRoot) - Method in class ome.formats.OMEROMetadataStoreClient
setRow(byte[], int, int, int, int) - Method in interface ome.api.RawPixelsStore
setRow(ByteBuffer, Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer
setRow(ByteBuffer, Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
setRow(ByteBuffer, Integer, Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
setRow(ByteBuffer, Integer, Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer: Sets a particular row or scanline in this pixel buffer.
setRow(ByteBuffer, Integer, Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer: Implemented as specified by PixelBuffer I/F.
setRow(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.
setServer(String) - Method in class loci.ome.io.OmeroReader
setServerEndpoints(String, int) - Method in class ome.services.blitz.Router
setServiceCleanups(Set<RegisterServiceCleanupMessage>) - Method in class ome.security.basic.BasicEventContext
setServiceFactory(ServiceFactoryI) - Method in class ome.services.blitz.impl.ExporterI
setServiceFactory(ServiceFactoryI) - Method in class ome.services.blitz.impl.MetadataStoreI
setServiceFactory(ServiceFactoryI) - Method in class ome.services.blitz.impl.RawFileStoreI
setServiceFactory(ServiceFactoryI) - Method in class ome.services.blitz.impl.RenderingEngineI
setServiceFactory(ServiceFactoryI) - Method in class ome.services.blitz.impl.RoiI
setServiceFactory(ServiceFactoryI) - Method in class ome.services.blitz.impl.ScriptI
setServiceFactory(ServiceFactoryI) - Method in class ome.services.blitz.impl.SharedResourcesI
setServiceFactory(ServiceFactoryI) - Method in class ome.services.blitz.impl.TimelineI
setServiceFactory(ServiceFactoryI) - Method in class ome.services.blitz.repo.ManagedImportProcessI
setServiceFactory(Identity, ServiceFactoryI) - Method in class ome.services.blitz.util.FindServiceFactoryMessage: Store the information.
setServiceFactory(Identity, ServiceFactoryI) - Method in class ome.services.blitz.util.RegisterServantMessage
setServiceFactory(ServiceFactoryI) - Method in interface ome.services.blitz.util.ServiceFactoryAware
setSession(Session) - Method in class ome.system.ServiceFactory
setSession(Session) - Method in class ome.system.SessionInitializer
setSession(SessionI) - Method in class omero.cmd.HandleI
setSession(SessionI) - Method in interface omero.cmd.SessionAware
setSessionCache(SessionCache) - Method in class ome.services.sessions.SessionManagerImpl
setSessionFactory(SessionFactory) - Method in class ome.logic.AbstractLevel1Service: delegates to HibernateDaoSupport.
setSessionFactory(SessionFactory) - Method in class ome.logic.TypesImpl: injector for usage by the container.
setSessionFactory(SessionFactory) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl: Initializes the metadata needed by this instance.
setSessionID(String) - Method in class loci.ome.io.OmeroReader
setSessionManager(SessionManager) - Method in class ome.logic.UpdateImpl
setSessionManager(SessionManager) - Method in class ome.security.basic.BasicMethodSecurity
setSessionManager(SessionManager) - Method in class ome.services.blitz.impl.TimelineI
setSessionManager(String, int) - Method in class ome.services.blitz.Router
setSessionService(ISession) - Method in class ome.system.SessionInitializer
setSettingsService(IRenderingSettings) - Method in class ome.services.ThumbnailBean: Rendering settings service Bean injector.
setShapeIds(List<Long>) - Method in class omeis.providers.re.data.PlaneDef: Sets whether or not to render the shapes (masks).
setShapeSettings(Shape) - Method in class pojos.ShapeData: Set the settings associated to the shape.
setShareId(Long) - Method in class ome.security.basic.BasicEventContext
setShareId(Long) - Method in interface ome.services.sessions.SessionContext: The Share id is the only mutable bit in the SessionContext.
setShareId(Long) - Method in class ome.services.sessions.SessionContextImpl
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.
setSlf4jMinutes(int) - Method in class ome.system.metrics.DefaultMetrics
setSqlAction(SqlAction) - Method in class ome.logic.ConfigImpl: SqlAction setter for dependency injection.
setSqlAction(SqlAction) - Method in class ome.logic.RepositoryInfoImpl: Bean injection setter for SQL operations
setSqlAction(SqlAction) - Method in class ome.services.eventlogs.PersistentEventLogLoader
setSqlAction(SqlAction) - Method in class ome.services.fulltext.FullTextIndexer: Since these instances are used repeatedly, we need to check for already set SqlAction
setSqlAction(SqlAction) - Method in class ome.services.pixeldata.PixelDataHandler: Since these instances are used repeatedly, we need to check for already set SqlAction
setSqlAction(SqlAction) - Method in class ome.services.RawPixelsBean: SQL action Bean injector
setSqlAction(SqlAction) - Method in class ome.services.sharing.BlobShareStore
setSqlAction(SqlAction) - Method in class ome.services.util.Executor.SimpleWork
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(Length, int) - Method in class ome.formats.OMEROMetadataStoreClient
setStageLabelY(Length, int) - Method in class ome.formats.OMEROMetadataStoreClient
setStageLabelZ(Length, int) - Method in class ome.formats.OMEROMetadataStoreClient
setStaleCacheListener(SessionCache.StaleCacheListener) - Method in class ome.services.sessions.state.SessionCache
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
setSteps(int) - Method in class omero.cmd.Helper
setStop(boolean) - Method in class ome.services.eventlogs.EventLogLoader: Called by controlling objects (a worker thread) in order to free up the thread.
setStride(int) - Method in class omeis.providers.re.data.PlaneDef: Returns the stride.
setStroke(Color) - Method in class pojos.ShapeSettingsData: Set the stroke color.
setStrokeDashArray(double[]) - Method in class pojos.ShapeSettingsData: Set the stroke dashes.
setStrokeWidth(Double) - Method in class pojos.ShapeSettingsData: Deprecated.
Replaced by ShapeSettingsData.setStrokeWidth(Length)
setStrokeWidth(Length) - Method in class pojos.ShapeSettingsData: Set the stroke width.
setSubjectPrefix(String) - Method in class ome.services.mail.MailSender
setT(int) - Method in class pojos.ShapeData: Sets the time-point.
setTagAnnotationAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setTagAnnotationAnnotator(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setTagAnnotationDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setTagAnnotationID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setTagAnnotationNamespace(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setTagAnnotationValue(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setTagDescription(String) - Method in class pojos.TagAnnotationData: Sets the description of the tag.
setTagDescriptions(List<TextualAnnotationData>) - Method in class pojos.TagAnnotationData: Sets the tag's descriptions.
setTagValue(String) - Method in class pojos.TagAnnotationData: Sets the value of the tag.
setTarget(IObject) - Method in class ome.formats.importer.ImportContainer
setTemperature(Temperature) - Method in class pojos.ImageAcquisitionData: Sets the temperature.
setTemperature(double) - Method in class pojos.ImageAcquisitionData: Deprecated.
Replaced by ImageAcquisitionData.setTemperature(Temperature)
setTerm(String) - Method in class pojos.TermAnnotationData: Sets the term.
setTermAnnotationAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setTermAnnotationAnnotator(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setTermAnnotationDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setTermAnnotationID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setTermAnnotationNamespace(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setTermAnnotationValue(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setTermDescription(String) - Method in class pojos.TermAnnotationData: Sets the description of the tag.
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.
setThumbnailService(ThumbnailService) - Method in class ome.logic.RepositoryInfoImpl: Bean injection setter for ROMIO thumbnail service
setTie(TieBase) - Method in class ome.services.blitz.impl.RawFileStoreI
setTie(TieBase) - Method in interface omero.util.TieAware
setTiffDataFirstC(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setTiffDataFirstT(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setTiffDataFirstZ(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setTiffDataIFD(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setTiffDataPlaneCount(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setTile(byte[], int, int, int, int, int, int, int) - Method in interface ome.api.RawPixelsStore
setTile(Long, byte[], int, int, int, int, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient: Writes a tile of pixels to the server.
setTile(byte[], Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer
setTile(byte[], Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
setTile(byte[], Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
setTile(byte[], Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer: Sets a tile in this pixel buffer.
setTile(byte[], Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer
setTile(byte[], int, int, int, int, int, int, int) - Method in class ome.services.RawPixelsBean
setTile(byte[], int, int, int, int, int, int, int) - Method in class omero.util.RPSTileData
setTile(byte[], int, int, int, int, int, int, int) - Method in interface omero.util.TileData
setTile_async(AMD_RawPixelsStore_setTile, byte[], int, int, int, int, int, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
setTile_async(AMD_RawPixelsStore_setTile, byte[], int, int, int, int, int, int, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
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
setTimestampAnnotationAnnotator(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setTimestampAnnotationDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setTimestampAnnotationID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setTimestampAnnotationNamespace(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setTimestampAnnotationValue(Timestamp, int) - Method in class ome.formats.OMEROMetadataStoreClient
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(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setTransmittanceRangeCutInTolerance(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setTransmittanceRangeCutOut(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setTransmittanceRangeCutOutTolerance(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setTransmittanceRangeTransmittance(PercentFraction, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setTrustStore(String) - Method in class ome.security.KeyAndTrustStoreConfiguration
setTrustStorePassword(String) - Method in class ome.security.KeyAndTrustStoreConfiguration
setTypes(ITypes) - Method in class ome.services.eventlogs.PersistentEventLogLoader
setTypesService(ITypes) - Method in class ome.services.JobBean: Types service Bean injector.
setTypesService(ITypes) - Method in class ome.services.procs.ProcessorSkeleton
setUIBounds(Rectangle) - Method in class ome.formats.importer.ImportConfig
setUIBounds(Rectangle) - Method in class ome.formats.importer.util.IniFileLoader: Set ui bounds for application
setUmask(Permissions) - Method in class ome.security.basic.BasicEventContext
setUnit(UnitsElectricPotential, Current) - Method in class omero.model.ElectricPotentialI
setUnit(UnitsFrequency, Current) - Method in class omero.model.FrequencyI
setUnit(UnitsLength, Current) - Method in class omero.model.LengthI
setUnit(UnitsPower, Current) - Method in class omero.model.PowerI
setUnit(UnitsPressure, Current) - Method in class omero.model.PressureI
setUnit(UnitsTemperature, Current) - Method in class omero.model.TemperatureI
setUnit(UnitsTime, Current) - Method in class omero.model.TimeI
setUp() - Method in class ome.formats.importer.ImportFixture: checks for the necessary fields and initializes the ImportLibrary
setUp() - Method in class ome.formats.importer.util.TinyImportFixture: checks for the necessary fields and initializes the ImportLibrary
setUp() - Method in class ome.formats.OMEROImportFixture: checks for the necessary fields and initializes the ImportLibrary
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: Set the list of image file names that belong to this import container.
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
setUserAnnotate(boolean, Current) - Method in class omero.model.PermissionsI
setUserDisableHistory(boolean) - Method in class ome.formats.importer.ImportConfig
setUserDisableHistory(boolean) - Method in class ome.formats.importer.util.IniFileLoader: Set debug level for application
setUserFullPath(boolean) - Method in class ome.formats.importer.ImportConfig
setUserFullPath(boolean) - Method in class ome.formats.importer.util.IniFileLoader
setUserId(long) - Method in class ome.services.ThumbnailCtx: Sets the user ID to use for queries.
setUsername(String) - Method in class loci.ome.io.OmeroReader
setUserPixels(Double[]) - Method in class ome.formats.importer.ImportContainer
setUserRead(boolean, Current) - Method in class omero.model.PermissionsI
setUserRead(boolean) - Method in class pojos.PermissionData: Sets to true if the user has read access, false otherwise.
setUserSpecifiedAnnotations(List<Annotation>) - Method in interface ome.formats.model.IObjectContainerStore: Sets the user specified image annotations.
setUserSpecifiedAnnotations(List<Annotation>) - Method in class ome.formats.OMEROMetadataStoreClient
setUserSpecifiedDescription(String) - Method in class ome.formats.importer.ImportContainer: Sets the custom image/plate description for import.
setUserSpecifiedDescription(String) - Method in interface ome.formats.model.IObjectContainerStore: Sets the user specified image/plate description.
setUserSpecifiedDescription(String) - Method in class ome.formats.OMEROMetadataStoreClient
setUserSpecifiedName(String) - Method in class ome.formats.importer.ImportContainer: Sets the custom image/plate name for import.
setUserSpecifiedName(String) - Method in interface ome.formats.model.IObjectContainerStore: Sets the user specified image/plate name.
setUserSpecifiedName(String) - Method in class ome.formats.OMEROMetadataStoreClient
setUserSpecifiedPhysicalPixelSizes(Double, Double, Double) - Method in interface ome.formats.model.IObjectContainerStore: Sets the user specified physical pixel sizes.
setUserSpecifiedPhysicalPixelSizes(Double, Double, Double) - Method in class ome.formats.OMEROMetadataStoreClient
setUserSpecifiedTarget(IObject) - Method in interface ome.formats.model.IObjectContainerStore: Sets the user specified linkage target (usually a Dataset for Images and a Screen for Plates).
setUserSpecifiedTarget(IObject) - Method in class ome.formats.OMEROMetadataStoreClient
setUserStyleSheetURI(String) - Method in class ome.services.SVGRasterizer: Sets the uri of the user stylesheet.
setUserWrite(boolean, Current) - Method in class omero.model.PermissionsI
setUserWrite(boolean) - Method in class pojos.PermissionData: Sets to true if the user has write access, false otherwise.
setUUID(String) - Method in class ome.formats.OMEROMetadataStoreClient
setUuid(String) - Method in class ome.services.sessions.SessionManagerImpl
setUUIDFileName(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setUUIDValue(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setValue(double, Current) - Method in class omero.model.ElectricPotentialI
setValue(double, Current) - Method in class omero.model.FrequencyI
setValue(double, Current) - Method in class omero.model.LengthI
setValue(double, Current) - Method in class omero.model.PowerI
setValue(double, Current) - Method in class omero.model.PressureI
setValue(double, Current) - Method in class omero.model.TemperatureI
setValue(double, Current) - Method in class omero.model.TimeI
setValue(boolean) - Method in class pojos.BooleanAnnotationData: Returns the text.
setValue(IObject) - Method in class pojos.DataObject: Sets the IObject.
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(Color, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setWellColumn(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setWellExternalDescription(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setWellExternalIdentifier(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setWellID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setWellReagentRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setWellRow(NonNegativeInteger, 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(Length, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setWellSamplePositionY(Length, 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(Timestamp, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setWellType(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
setWellType(String) - Method in class pojos.WellData: Sets a human readable identifier for the screening status e.g. empty, positive control, etc.
setWidth(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.
setWorldAnnotate(boolean, Current) - Method in class omero.model.PermissionsI
setWorldRead(boolean, Current) - Method in class omero.model.PermissionsI
setWorldRead(boolean) - Method in class pojos.PermissionData: Sets to true if the world has read access, false otherwise.
setWorldWrite(boolean, Current) - Method in class omero.model.PermissionsI
setWorldWrite(boolean) - Method in class pojos.PermissionData: Sets to true if the world has write access, false otherwise.
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
setXMLAnnotationAnnotator(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setXMLAnnotationDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setXMLAnnotationID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setXMLAnnotationNamespace(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setXMLAnnotationValue(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
setXMLParserValidating(boolean) - Method in class ome.services.SVGRasterizer: Sets whether or not the XML parser used to parse SVG document should be validating or not, depending on the specified parameter.
setXStart(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.blitz.util.FindServiceFactoryMessage
sf - Variable in class ome.services.delete.DeleteBean
sha1(File) - Method in class omero.client: Calculates the local sha1 for a file.
SHA1ChecksumProviderImpl - Class in ome.util.checksum: An implementation of the ChecksumProvider interface using SHA1 as the secure hash algorithm.
SHA1ChecksumProviderImpl() - Constructor for class ome.util.checksum.SHA1ChecksumProviderImpl
Shape_FontSize - Static variable in class ome.formats.model.UnitsFactory
Shape_StrokeWidth - Static variable in class ome.formats.model.UnitsFactory
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.
ShareBean - Class in ome.services.sharing: Note: SessionManager should not be used to obtain the Share data since it may not be completely in sync. i.e.
ShareBean(LocalAdmin, SessionManager, ShareStore, Executor, MailUtil) - Constructor for class ome.services.sharing.ShareBean
sharedResources(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
SharedResourcesI - Class in ome.services.blitz.impl: Implementation of the SharedResources interface.
SharedResourcesI(BlitzExecutor, TopicManager, Registry, ScriptRepoHelper) - Constructor for class ome.services.blitz.impl.SharedResourcesI
SharedResourcesI(BlitzExecutor, TopicManager, Registry, ScriptRepoHelper, long) - Constructor for class ome.services.blitz.impl.SharedResourcesI
SharedResourcesI(BlitzExecutor, TopicManager, Registry, ScriptRepoHelper, long, long) - Constructor for class ome.services.blitz.impl.SharedResourcesI
ShareI - Class in ome.services.blitz.impl: Implementation of the IShare service.
ShareI(IShare, BlitzExecutor) - Constructor for class ome.services.blitz.impl.ShareI
shareId - Variable in class ome.system.SimpleEventContext
ShareRestrictionTransactionAttributeSource - Class in ome.services.sharing: Prevents methods from setting the transaction to readOnly = false when a share is activated.
ShareRestrictionTransactionAttributeSource(CurrentDetails, SessionCache) - Constructor for class ome.services.sharing.ShareRestrictionTransactionAttributeSource
ShareStore - Class in ome.services.sharing: Entry to the Ice code generated data/ directory.
ShareStore() - Constructor for class ome.services.sharing.ShareStore
sharesToSessions(List<ShareData>) - Method in class ome.services.sharing.ShareBean
shareToSession(ShareData) - Method in class ome.services.sharing.ShareBean
sharing - Variable in class ome.security.SecuritySystemHolder
SharingACLVoter - Class in ome.security.sharing
SharingACLVoter(CurrentDetails, SystemTypes, ShareStore, TokenHolder) - Constructor for class ome.security.sharing.SharingACLVoter
SharingSecuritySystem - Class in ome.security.sharing: central security interface.
SharingSecuritySystem(BasicSecuritySystem) - Constructor for class ome.security.sharing.SharingSecuritySystem
SHORT - Static variable in class omeis.providers.re.data.PlaneFactory: Identifies the type used to store pixel values.
shortName - Variable in class ome.formats.importer.ImportEvent.COUNT_EVENT
shouldBeOmitted(String) - Static method in class ome.services.util.DBEnumCheck
shutdown(boolean) - Method in class ome.services.blitz.Entry: Calls OmeroContext.closeAll() to recursively close all OMERO.blitz resources in the reverse order that they were created.
shutdown(Current) - Method in class ome.services.blitz.impl.ScriptProcessI
shutdown() - Method in class ome.services.blitz.repo.ManagedImportProcessI
shutdown() - Method in interface ome.services.blitz.repo.ProcessContainer.Process
shutdownAll() - Method in class ome.services.blitz.repo.ProcessContainer: Called on shutdown of the server.
ShutdownMessage - Class in ome.util.messages: Published when the server is shutting down.
ShutdownMessage(Object) - Constructor for class ome.util.messages.ShutdownMessage
ShutdownSafeEhcacheManagerFactoryBean - Class in ome.tools.spring: Workaround for the Spring/EHCache shutdown sequence.
ShutdownSafeEhcacheManagerFactoryBean() - Constructor for class ome.tools.spring.ShutdownSafeEhcacheManagerFactoryBean
SiftingWhileRejectingDefaultAppender - Class in ome.util.logback
SiftingWhileRejectingDefaultAppender() - Constructor for class ome.util.logback.SiftingWhileRejectingDefaultAppender
signal - Variable in class ome.util.messages.UserSignalMessage
signed - Variable in class omeis.providers.re.data.Plane2D: The sign of the type
SimilarTerms - Class in ome.services.search: Search to find similar terms to some given terms.
SimilarTerms(SearchValues, String...) - Constructor for class ome.services.search.SimilarTerms
SimpleBackOff - Class in ome.io.nio: Basic BackOff implementation which attempts several writes of the default block size on startup, and uses that as a scaling factor for all subsequent calculations.
SimpleBackOff() - Constructor for class ome.io.nio.SimpleBackOff
SimpleBackOff(TileSizes) - Constructor for class ome.io.nio.SimpleBackOff
simpleDelete(Map<String, String>, Executor, Principal, long) - Method in class ome.services.scripts.ScriptRepoHelper: Unlike ScriptRepoHelper.delete(long) this method simply performs the DB delete on the given original file id.
SimpleEventContext - Class in ome.system: simple, non-thread-safe, serializable EventContext
SimpleEventContext() - Constructor for class ome.system.SimpleEventContext: Constructor for subclasses
SimpleEventContext(EventContext) - Constructor for class ome.system.SimpleEventContext: copy constructor.
SimpleLuceneOptions - Class in ome.services.fulltext: Implementation of LuceneOptions which takes an existing instance and possible overrides for each of the values.
SimpleLuceneOptions(LuceneOptions, Float) - Constructor for class ome.services.fulltext.SimpleLuceneOptions
SimpleLuceneOptions(LuceneOptions, Field.Store) - Constructor for class ome.services.fulltext.SimpleLuceneOptions
SimpleLuceneOptions(LuceneOptions, Field.Index, Field.Store) - Constructor for class ome.services.fulltext.SimpleLuceneOptions
SimpleLuceneOptions(LuceneOptions, Float, Field.Index, Field.Store) - Constructor for class ome.services.fulltext.SimpleLuceneOptions
SimpleRoleProvider - Class in ome.security.auth: Implements RoleProvider.
SimpleRoleProvider(SecuritySystem, SessionFactory) - Constructor for class ome.security.auth.SimpleRoleProvider
SimpleRoleProvider(SecuritySystem, SessionFactory, AtomicBoolean) - Constructor for class ome.security.auth.SimpleRoleProvider
SimpleSessionStats - Class in ome.services.sessions.stats
SimpleSessionStats(ObjectsReadCounter, ObjectsWrittenCounter, MethodCounter) - Constructor for class ome.services.sessions.stats.SimpleSessionStats
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.blitz.repo.CheckedPath: Return the size of this file on the underlying filesystem.
size() - Method in class ome.services.export.ExporterIndex: Deprecated.
size() - Method in class ome.services.graphs.GraphState: Deprecated.
size() - Method in interface ome.services.graphs.GraphStep.Callback: Deprecated.
size() - Method in class ome.services.graphs.GraphSteps: Deprecated.
size() - Method in class ome.services.query.Definitions
size() - Method in class ome.services.RawFileBean
size() - Method in class ome.services.scheduler.ThreadPool
size() - Method in class ome.system.metrics.DefaultSnapshot
size() - Method in interface ome.system.metrics.Snapshot
size() - Method in class ome.tools.hibernate.ExtendedMetadata.Locks: the total number of fields for this entity.
size() - Method in class omero.util.Resources
size_async(AMD_RawFileStore_size, Current) - Method in class ome.services.blitz.impl.RawFileStoreI
sizeC - Variable in class ome.formats.importer.ImportSize
sizeC - Variable in class ome.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: Deprecated.

A KEEP setting is a way of putting a KEEP suggestion to vote.
skipFrom() - Method in class ome.tools.hibernate.QueryBuilder
SkipHeadI - Class in omero.cmd.graphs: The skip-head request performs the wrapped request twice: once in dry run mode to discover from which model objects to start, and then actually starting from those objects.
SkipHeadI(GraphPathBean, GraphRequestFactory) - Constructor for class omero.cmd.graphs.SkipHeadI: Construct a new skip-head request; called from GraphRequestFactory.getRequest(Class).
SkipHeadPolicy - Class in omero.cmd.graphs: Adjust graph traversal policy to prevent descent into inclusions beyond certain types.
SkipHeadPolicy() - Constructor for class omero.cmd.graphs.SkipHeadPolicy
skipWhere() - Method in class ome.tools.hibernate.QueryBuilder
sleepFor(long) - Static method in class ome.services.util.SleepTimer: Sleep for the given number of milliseconds.
SleepTimer - Class in ome.services.util: Provides a timer for having a thread sleep that prematurely awakens when the server is to shut down, so the sleeping does not keep the server running.
SleepTimer() - Constructor for class ome.services.util.SleepTimer
slice - Variable in class omeis.providers.re.data.Plane2D: The slice we're working with
Slot - Class in ome.services.throttling: Worker which consumes from the Queue.
Slot(Queue) - Constructor for class ome.services.throttling.Slot
sm - Variable in class ome.services.blitz.impl.TimelineI
SmartEllipseI - Class in omero.model
SmartEllipseI() - Constructor for class omero.model.SmartEllipseI
SmartLineI - Class in omero.model
SmartLineI() - Constructor for class omero.model.SmartLineI
SmartMaskI - Class in omero.model
SmartMaskI() - Constructor for class omero.model.SmartMaskI
SmartPathI - Class in omero.model
SmartPathI() - Constructor for class omero.model.SmartPathI
SmartPointI - Class in omero.model
SmartPointI() - Constructor for class omero.model.SmartPointI
SmartPolygonI - Class in omero.model
SmartPolygonI() - Constructor for class omero.model.SmartPolygonI
SmartPolylineI - Class in omero.model
SmartPolylineI() - Constructor for class omero.model.SmartPolylineI
SmartRectI - Class in omero.model
SmartRectI() - Constructor for class omero.model.SmartRectI
SmartShape - Interface in omero.model: Orthogonal interface hierarchy of types for working with the Shape hierarchy.
SmartShape.PointCallback - Interface in omero.model: Callback interface passed every point which is within the area of this shape.
SmartShape.Util - Class in omero.model: Utility class used as a mixin by all of the SmartShape implementations.
SmartShape.Util() - Constructor for class omero.model.SmartShape.Util
SmartTextI - Class in omero.model: THIS CLASS IS CURRENTLY BROKEN.
SmartTextI() - Constructor for class omero.model.SmartTextI
SmtpAuthenticator - Class in ome.security
SmtpAuthenticator(String, String) - Constructor for class ome.security.SmtpAuthenticator
Snapshot - Interface in ome.system.metrics: Thin wrapper around Snapshot
SomeMustNone - Class in ome.services.search: FullText subclass which parses 3 arrays of strings into into a single Lucene query.
SomeMustNone(SearchValues, String[], String[], String[], Class<? extends Analyzer>) - Constructor for class ome.services.search.SomeMustNone
SortDatasetsByName - Class in ome.formats
SortDatasetsByName() - Constructor for class ome.formats.SortDatasetsByName
sortOriginalFileIds(Session, Collection<Long>) - Static method in class ome.services.graphs.ModelObjectSequencer: Sort a list of original file IDs such that files precede containing directories.
SortProjectsByName - Class in ome.formats
SortProjectsByName() - Constructor for class ome.formats.SortProjectsByName
source - Variable in class ome.formats.importer.util.ErrorHandler.UNKNOWN_FORMAT
source - Variable in class ome.formats.importer.util.ErrorHandler.UNREADABLE_FILE
sources - Variable in class ome.services.query.QueryFactory: sources available for lookups.
spec - Variable in class ome.services.graphs.GraphStep: Deprecated.

GraphSpec instance which is active for this step.
specs - Variable in class ome.services.delete.Deletion.Builder: Deprecated.
sql - Variable in class ome.logic.AdminImpl
sql - Variable in class ome.security.basic.EventHandler
sql - Variable in class ome.services.blitz.impl.MetadataStoreI
sql - Variable in class ome.services.blitz.impl.RoiI
sql - Variable in class ome.services.eventlogs.PersistentEventLogLoader
sql - Variable in class ome.services.OmeroFilePathResolver: SQL action instance for this class.
sql - Variable in class ome.services.roi.GeomTool
sqlAction - Variable in class ome.services.sharing.BlobShareStore
sqlAction - Variable in class ome.services.util.Executor.Impl
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
srcFiles - Variable in class ome.formats.importer.ImportEvent.FILESET_UPLOAD_END
ss - Variable in class ome.services.blitz.impl.TimelineI
stack - Variable in class ome.services.graphs.GraphStep: Deprecated.

Stack of other GraphStep instances which show where this step is in the entire graph.
stackTraceAsString(Throwable) - Method in class ome.services.blitz.repo.PublicRepositoryI
StageLabel_X - Static variable in class ome.formats.model.UnitsFactory
StageLabel_Y - Static variable in class ome.formats.model.UnitsFactory
StageLabel_Z - Static variable in class ome.formats.model.UnitsFactory
standalone(String[]) - Static method in class ome.services.fulltext.Main: Starts up and simply waits until told by the grid to disconnect.
start() - Method in class ome.formats.importer.cli.CommandLineImporter
start(TransferState) - Method in class ome.formats.importer.transfers.AbstractFileTransfer: Minimal start method which logs the file, calls TransferState.start(), and loads the RawFileStorePrx which any implementation will need.
start() - Method in class ome.formats.importer.transfers.TransferState
start() - Method in class ome.formats.importer.util.ProportionalTimeEstimatorImpl
start() - Method in interface ome.formats.importer.util.TimeEstimator: Starts the time counting.
start() - Method in class ome.services.blitz.Entry: Obtains the named OmeroContext, creating it if necessary, and then delegates to Communicator.waitForShutdown() until either it is externally shutdown, or until a signal is caught.
start() - Method in class ome.services.blitz.Router
start(EventContext, SqlAction, Session, String, long, Map<String, String>) - Method in class ome.services.delete.Deletion: Deprecated.

Returns the number of steps that are available.
start() - Method in class ome.services.fulltext.FullTextThread: Called by Spring on creation.
start(GraphStep.Callback) - Method in class ome.services.graphs.GraphStep: Deprecated.
start() - Method in class ome.services.mail.SubethaSMTP
start() - Method in class ome.services.pixeldata.PixelDataThread: Called by Spring on creation.
start() - Method in class ome.services.util.DBPatchCheck
start() - Method in class ome.services.util.ServerVersionCheck: Prints simple banner with OMERO version.
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.
statefulExecutor - Variable in class ome.services.blitz.repo.RepositoryDaoImpl
StatefulServiceInterface - Interface in ome.api: OMERO API Interface with stateful semantics.
stats() - Method in interface ome.services.sessions.SessionContext: Return a SessionStats implementation for this session.
stats() - Method in class ome.services.sessions.SessionContextImpl
stats() - Method in class ome.services.sessions.stats.CurrentSessionStats
stats() - Method in class ome.services.sessions.stats.DelegatingStats: Intended to be overwritten by subclasses.
stats() - Method in class ome.services.sessions.stats.PerSessionStats
stats() - Method in class ome.services.sessions.stats.PerThreadStats
StatsFactory - Class in omeis.providers.re.metadata: Computes two types of statistics: The PixelsStats and the location stats.
StatsFactory() - Constructor for class omeis.providers.re.metadata.StatsFactory
status() - Method in class ome.services.blitz.Entry
Status - Class in ome.services.blitz: Status check for OMERO.blitz.
Status(String[]) - Constructor for class ome.services.blitz.Status
STDIN - Static variable in class prefs: Storing the standard in as a Properties instance as early as possible to prevent lost data.
step - Variable in class ome.formats.importer.ImportEvent.IMPORT_STEP
step(int, int, Current) - Method in class ome.formats.importer.ImportLibrary.ImportCallback
step(int) - Method in class ome.services.blitz.impl.commands.SaveI
step(int) - Method in class ome.services.blitz.repo.ManagedImportRequestI
step(int) - Method in class ome.services.blitz.repo.RawAccessRequestI
step(int) - Method in class omero.cmd.admin.CurrentSessionsRequestI
step(int) - Method in class omero.cmd.admin.ResetPasswordRequestI
step(int) - Method in class omero.cmd.admin.UpdateSessionTimeoutRequestI
step(int) - Method in class omero.cmd.basic.DoAllI
step(int) - Method in class omero.cmd.basic.ListRequestsI
step(int) - Method in class omero.cmd.basic.TimingI
step(int, int, Current) - Method in class omero.cmd.CmdCallbackI: Called periodically by the server to signal that processing is moving forward.
step(int) - Method in class omero.cmd.fs.ManageImageBinariesI
step(int) - Method in class omero.cmd.fs.OriginalMetadataRequestI
step(int) - Method in class omero.cmd.fs.UsedFilesRequestI
step(int) - Method in class omero.cmd.graphs.Chgrp2I
step(int) - Method in class omero.cmd.graphs.ChgrpFacadeI: Deprecated.
step(int) - Method in class omero.cmd.graphs.ChgrpI: Deprecated.
step(int) - Method in class omero.cmd.graphs.Chmod2I
step(int) - Method in class omero.cmd.graphs.ChmodFacadeI: Deprecated.
step(int) - Method in class omero.cmd.graphs.ChmodI: Deprecated.
step(int) - Method in class omero.cmd.graphs.Chown2I
step(int) - Method in class omero.cmd.graphs.ChownFacadeI: Deprecated.
step(int) - Method in class omero.cmd.graphs.ChownI: Deprecated.
step(int) - Method in class omero.cmd.graphs.Delete2I
step(int) - Method in class omero.cmd.graphs.DeleteFacadeI: Deprecated.
step(int) - Method in class omero.cmd.graphs.DeleteI: Deprecated.
step(int) - Method in class omero.cmd.graphs.DiskUsageI
step(int) - Method in class omero.cmd.graphs.GraphSpecListI: Deprecated.
step(int) - Method in class omero.cmd.graphs.SkipHeadI
step(int) - Method in interface omero.cmd.IRequest: Single uncancellable action which will be performed by this IRequest.
step(int) - Method in class omero.cmd.mail.SendEmailRequestI
steps(SqlAction, Session, ServiceFactory) - Method in class omero.cmd.HandleI
stop() - Method in class ome.formats.importer.transfers.TransferState
stop(long) - Method in class ome.formats.importer.transfers.TransferState
stop() - Method in class ome.formats.importer.util.ProportionalTimeEstimatorImpl
stop(long) - Method in class ome.formats.importer.util.ProportionalTimeEstimatorImpl
stop() - Method in interface ome.formats.importer.util.TimeEstimator: Stops the time counting and updates the internal time counter.
stop(long) - Method in interface ome.formats.importer.util.TimeEstimator: Stops the time counting and updates the internal updates the internal time counter and counter of total number of transmitted bytes.
stop() - Method in class ome.services.delete.Deletion: Deprecated.
stop() - Method in class ome.services.fulltext.FullTextThread: Called by Spring on destruction.
stop() - Method in class ome.services.mail.SubethaSMTP
stop() - Method in class ome.services.pixeldata.PixelDataThread: Called by Spring on destruction.
stop() - Method in class ome.services.util.ServerVersionCheck: Prints simple banner with "Stopping OMERO"
stop() - Method in class ome.system.metrics.DefaultTimer.Context
stop() - Method in interface ome.system.metrics.Timer.Context
stop() - Method in class omeis.providers.re.RenderingStats: Notifies this object that the rendering process has finished.
stop(Current) - Method in class omero.grid.InteractiveProcessorI: Cancels the current process, nulls the value, and returns immediately if detach is false.
store() - Method in class ome.formats.importer.ImportConfig.PassValue
store() - Method in class ome.formats.importer.ImportConfig.Value: Stores the current value back to some medium.
store - Variable in class ome.formats.OMEROImportFixture
store - Variable in class ome.security.basic.BasicSecuritySystem
store - Variable in class ome.services.blitz.impl.MetadataStoreI
store - Variable in class ome.services.sharing.ShareBean
store(Object, Object) - Method in class omero.util.IceMapper
storeShareData(long, ShareData) - Method in class ome.services.sharing.ShareBean
STRING - Static variable in class ome.services.query.StringQuery: parameter name for the definition of the HQL string.
STRING(Connection, List<String>) - Method in interface ome.tools.hibernate.ListAsSQLArrayUserType.ArrayFactory
STRING2(Connection, List<String[]>) - Method in interface ome.tools.hibernate.ListAsSQLArrayUserType.ArrayFactory
STRING_TO_RSTRING - Static variable in class omero.util.IceMapper
stringFromSvnString(String) - Static method in class ome.system.Version: Parses the given String to remove the leading "$", keyword name, and colons.
stringLongToEntity(String, long) - Method in class ome.services.query.HierarchyNavigatorWrap: Convert the given type string and database ID to the model object.
StringQuery - Class in ome.services.query: simple HQL query.
StringQuery(Parameters) - Constructor for class ome.services.query.StringQuery: Default constructor, used primarily for testing.
StringQuery(SqlAction, Parameters) - Constructor for class ome.services.query.StringQuery
StringQuerySource - Class in ome.services.query: interprets the query id as an HQL query.
StringQuerySource() - Constructor for class ome.services.query.StringQuerySource: Default constructor, used primarily for testing.
StringQuerySource(SqlAction) - Constructor for class ome.services.query.StringQuerySource
stringToType(String) - Method in class ome.services.query.HierarchyNavigatorWrap: Convert the given type string to the object type.
subcancel(HandleI.Cancel, DoAllI.X) - Method in class omero.cmd.basic.DoAllI
SubethaSMTP - Class in ome.services.mail: Simple server bean which can be started on Spring context creation and shutdown when the application is editing.
SubethaSMTP(MessageHandlerFactory) - Constructor for class ome.services.mail.SubethaSMTP
SubethaSMTP(MessageHandlerFactory, int) - Constructor for class ome.services.mail.SubethaSMTP
subhelper(Request, Status) - Method in class omero.cmd.Helper: Run IRequest.init(Helper) on a sub-command by creating a new Helper instance.
subject - Variable in class ome.services.graphs.GraphPolicy.Details: the unloaded instance
submit(Job) - Method in interface ome.api.JobHandle: Submits a Job and returns its database id.
submit(Job) - Method in class ome.services.JobBean
submit(Callable<T>) - Method in class ome.services.util.Executor.Impl
submit(Map<String, String>, Callable<T>) - Method in class ome.services.util.Executor.Impl
submit(Executor.Priority, Callable<T>) - Method in class ome.services.util.Executor.Impl
submit(Executor.Priority, Map<String, String>, Callable<T>) - Method in class ome.services.util.Executor.Impl
submit(Callable<T>) - Method in interface ome.services.util.Executor: Call Executor.submit(Map, Callable) with a null callContext.
submit(Map<String, String>, Callable<T>) - Method in interface ome.services.util.Executor: Simple submission method which can be used in conjunction with a call to Executor.execute(Principal, Work) to overcome the no-multiple-login rule.
submit(Executor.Priority, Callable<T>) - Method in interface ome.services.util.Executor: Simple submission method with a Executor.Priority.
submit(Executor.Priority, Map<String, String>, Callable<T>) - Method in interface ome.services.util.Executor: Like Executor.submit(Map, Callable) but provide info to which priority queue should be used.
submit_async(AMD_JobHandle_submit, Job, Current) - Method in class ome.services.blitz.impl.JobHandleI
submit_async(AMD_Session_submit, Request, Current) - Method in class omero.cmd.SessionI
submitRequest(ServiceFactoryI, Request, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
SUBMITTED - Static variable in interface ome.api.JobHandle
subscribe(String, ObjectPrx, Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
subselect(QueryBuilder) - Method in class ome.tools.hibernate.QueryBuilder: Appends the string representation of the QueryBuilder argument inside of parentheses.
subtypeEquals(int, int, String) - Method in class ome.tools.hibernate.ExtendedMetadata.Locks: returns true is the indexed subtype returns the same class type as the klass argument.
subtypeName(int, int) - Method in class ome.tools.hibernate.ExtendedMetadata.Locks: retrieves the full Hibernate path for this component field.
succeeded(GraphStep) - Method in class ome.services.graphs.GraphSteps: Deprecated.
success(SqlAction.DeleteLog) - Method in class ome.services.messages.DeleteLogMessage
success - Variable in class ome.services.messages.LoginAttemptMessage
sudo(Current, String) - Method in class ome.services.blitz.repo.PublicRepositoryI: Provide a Current like the given one, except with the request context session UUID replaced.
suggestChecksumAlgorithm(List<ChecksumAlgorithm>, Current) - Method in class ome.services.blitz.repo.ManagedRepositoryI
suggestExclusion(ServiceFactoryPrx, ImportContainer) - Method in interface ome.formats.importer.exclusions.FileExclusion: Given the current session attempt to discover if the given container should be skipped, i.e.
suggestExclusion(ServiceFactoryPrx, ImportContainer) - Method in class ome.formats.importer.exclusions.FilenameExclusion
suggestImportPaths(FsFile, FsFile, List<FsFile>, Class<? extends FormatReader>, ChecksumAlgorithm, Current) - Method in class ome.services.blitz.repo.ManagedRepositoryI: Take a relative path that the user would like to see in his or her upload area, and provide an import location instance whose paths correspond to existing directories corresponding to the sanitized file paths.
sum(PlanePoint) - Method in class ome.util.math.geom2D.PlanePoint: Calculates the sum of this vector with the specified argument.
SUM_INTENSITY - Static variable in interface ome.api.IProjection: Sum intensity projection
superspec - Variable in class ome.services.graphs.BaseGraphSpec: Deprecated.

Path of the superspec.
SVGRasterizer - Class in ome.services: This class provides a simple and method based API for converting a SVG document fragment to a BufferedImage.
SVGRasterizer(String) - Constructor for class ome.services.SVGRasterizer: Constructs a new SVGRasterizer.
SVGRasterizer(URL) - Constructor for class ome.services.SVGRasterizer: Constructs a new SVGRasterizer.
SVGRasterizer(InputStream) - Constructor for class ome.services.SVGRasterizer: Constructs a new SVGRasterizer converter.
SVGRasterizer(Reader) - Constructor for class ome.services.SVGRasterizer: Constructs a new SVGRasterizer converter.
SVGRasterizer.Rasterizer - Class in ome.services: An image transcoder that stores the resulting image.
SVGRasterizer.Rasterizer() - Constructor for class ome.services.SVGRasterizer.Rasterizer
SVN_DATE_FORMAT - Static variable in class ome.system.Version: Date format used by Subversions "Date" keyword.
swapIfRequired(byte[]) - Method in class ome.io.bioformats.BfPixelsWrapper: cgb - stolen from ImportLibrary - slightly modified Examines a byte array to see if it needs to be byte swapped and modifies the byte array directly.
SymlinkFileTransfer - Class in ome.formats.importer.transfers: Local-only file transfer mechanism which makes use of soft-linking.
SymlinkFileTransfer() - Constructor for class ome.formats.importer.transfers.SymlinkFileTransfer
synchronizeJobs() - Method in class ome.services.blitz.util.CheckAllJobs
synchronizeLdapUser(String) - Method in class ome.logic.LdapImpl
synchronizeLoginCache() - Method in interface ome.api.IAdmin: uses JMX to refresh the login cache if supported.
synchronizeLoginCache() - Method in class ome.logic.AdminImpl
synchronizeLoginCache_async(AMD_IAdmin_synchronizeLoginCache, Current) - Method in class ome.services.blitz.impl.AdminI
sys(String[]) - Static method in class prefs: Replaces the user Preferences instance with the system Preferences and continues dispatching.
SYSTEM - Static variable in class pojos.GroupData: Identifies the System group.
systemService - Variable in class ome.services.util.Executor.Impl
SystemTypes - Class in ome.security: Defines what IObject classes are considered "system" types.
SystemTypes() - Constructor for class ome.security.SystemTypes
SystemTypes(Roles) - Constructor for class ome.security.SystemTypes
sysTypes - Variable in class ome.security.basic.BasicACLVoter
sysTypes - Variable in class ome.security.basic.BasicSecuritySystem

T

t - Variable in exception ome.util.messages.MessageException

table - Variable in class ome.services.graphs.GraphStep

Deprecated.

Parsed table name used for the SQL/HQL statements.

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

targetId - Variable in class omero.cmd.graphs.Preprocessor.GraphModifyTarget

Deprecated.

TargetProcessor - Class in ome.formats.model

Processes the IObjectContainerStore and populates references for the linkage target object of choice.

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

targetType - Variable in class omero.cmd.graphs.Preprocessor.GraphModifyTarget

Deprecated.

targetTypeHierarchy - Static variable in class omero.cmd.graphs.Preprocessor

Deprecated.

the target type hierarchy, an ordered list descending from higher to lower

Task - Class in ome.services.throttling

Simple base task which contains logic for routing calls reflectively to ice_response and ice_exception of any AMD callback.

Task(Object, Current, boolean) - Constructor for class ome.services.throttling.Task

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

sets ImportLibrary, OMEROMetadataStoreClient, and file array to null.

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

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

sets ImportLibrary, OMEROMetadataStore, and file array to null.

TemperatureI - Class in omero.model

Blitz wrapper around the Temperature class.

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

TemperatureI(double, UnitsTemperature) - Constructor for class omero.model.TemperatureI

TemperatureI(double, Unit<Temperature>) - Constructor for class omero.model.TemperatureI

TemperatureI(Temperature, Unit<Temperature>) - Constructor for class omero.model.TemperatureI

Copy constructor that converts the given Temperature based on the given ome-xml enum

TemperatureI(double, UnitsTemperature) - Constructor for class omero.model.TemperatureI

Copy constructor that converts the given Temperature based on the given ome.model enum

TemperatureI(Temperature, String) - Constructor for class omero.model.TemperatureI

Copy constructor that converts the given Temperature based on the given enum string.

TemperatureI(Temperature, UnitsTemperature) - Constructor for class omero.model.TemperatureI

Copy constructor that converts between units if possible.

TemperatureI(Temperature) - Constructor for class omero.model.TemperatureI

Convert a Bio-Formats Length to an OMERO Length.

TempFileManager - Class in omero.util

Creates temporary files and folders and makes a best effort to remove them on exit (or sooner).

TempFileManager() - Constructor for class omero.util.TempFileManager

Default constructor, passes "omero" to TempFileManager.TempFileManager(String)

TempFileManager(String) - Constructor for class omero.util.TempFileManager

Initializes a TempFileManager instance with a userDir containing the given prefix value.

templateMessage - Variable in class ome.logic.AdminImpl

templateRoot - Variable in class ome.services.blitz.repo.ManagedRepositoryI

TemporaryRepositoryI - Class in ome.services.blitz.repo

Simple repository service to make the ${java.io.tmpdir} available at runtime.

TemporaryRepositoryI(ObjectAdapter, Registry, Executor, Principal, PublicRepositoryI) - Constructor for class ome.services.blitz.repo.TemporaryRepositoryI

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.

throwable - Variable in class ome.services.eventlogs.EventLogFailure

throwCreationViolation(IObject) - Method in interface ome.security.ACLVoter

throws a SecurityViolation based on the given IObject and the context of the current user.

throwCreationViolation(IObject) - Method in class ome.security.basic.BasicACLVoter

throwCreationViolation(IObject) - Method in class ome.security.CompositeACLVoter

throwCreationViolation(IObject) - Method in class ome.security.sharing.SharingACLVoter

throwDeleteViolation(IObject) - Method in interface ome.security.ACLVoter

throws a SecurityViolation based on the given IObject and the context of the current user.

throwDeleteViolation(IObject) - Method in class ome.security.basic.BasicACLVoter

throwDeleteViolation(IObject) - Method in class ome.security.CompositeACLVoter

throwDeleteViolation(IObject) - Method in class ome.security.sharing.SharingACLVoter

throwDisabled(String) - Method in class ome.security.sharing.SharingACLVoter

throwIfAlreadySet(Object, Object) - Method in class ome.services.util.BeanHelper

throwIfCancelled() - Method in class ome.services.sessions.events.ChangeSecurityContextEvent

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

If this configuration is finished and BlitzConfiguration.communicator is not-null, throw a IllegalStateException

throwLoadViolation(IObject) - Method in interface ome.security.ACLVoter

throws a SecurityViolation based on the given IObject and the context of the current user.

throwLoadViolation(IObject) - Method in class ome.security.basic.BasicACLVoter

throwLoadViolation(IObject) - Method in class ome.security.CompositeACLVoter

throwLoadViolation(IObject) - Method in class ome.security.sharing.SharingACLVoter

throwMissingPyramidException(String, Pixels) - Method in interface ome.io.nio.BackOff

throwMissingPyramidException(String, Pixels) - Method in class ome.io.nio.SimpleBackOff

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

ThumbnailBean - Class in ome.services

Provides methods for directly querying object graphs.

ThumbnailBean() - Constructor for class ome.services.ThumbnailBean

default constructor

ThumbnailBean(boolean) - Constructor for class ome.services.ThumbnailBean

overridden to allow Spring to set boolean

ThumbnailCtx - Class in ome.services

ThumbnailCtx(IQuery, IUpdate, IPixels, IRenderingSettings, ThumbnailService, SecuritySystem, long) - Constructor for class ome.services.ThumbnailCtx

Default constructor.

ThumbnailCtx.NoThumbnail - Exception in ome.services

Marker exception which is thrown by all methods which wish to tell their callers that for whatever reason the desired Thumbnail is not available, in which case the caller can use a *Direct method instead.

ThumbnailCtx.NoThumbnail(String) - Constructor for exception ome.services.ThumbnailCtx.NoThumbnail

thumbnailExists(Integer, Integer) - Method in interface ome.api.ThumbnailStore

Checks if a thumbnail of a particular size exists for a pixels set.

thumbnailExists(Integer, Integer) - Method in class ome.services.ThumbnailBean

thumbnailExists_async(AMD_ThumbnailStore_thumbnailExists, RInt, RInt, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI

ThumbnailFileDeletions - Class in ome.services.delete.files

Helper class which sorts through a number of file-based deletions before processing them.

ThumbnailFileDeletions(AbstractFileSystemService, Set<Long>) - Constructor for class ome.services.delete.files.ThumbnailFileDeletions

THUMBNAILS_PATH - Static variable in class ome.io.nio.AbstractFileSystemService

ThumbnailService - Class in ome.io.nio

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

Constructor

ThumbnailStore - Interface in ome.api

Provides methods for dealing with thumbnails.

ThumbnailStoreI - Class in ome.services.blitz.impl

Implementation of the ThumbnailStore service.

ThumbnailStoreI(ThumbnailStore, BlitzExecutor) - Constructor for class ome.services.blitz.impl.ThumbnailStoreI

tie() - Method in class ome.services.blitz.repo.ManagedRepositoryI

tie() - Method in class ome.services.blitz.repo.PublicRepositoryI

Wrap the current instance with an TieBase so that it can be turned into a proxy.

TieAware - Interface in omero.util

Servant which is aware of the TieBase-instance which it belongs to and will have it injected on instantiation.

TileData - Interface in omero.util

Access strategy which can be implemented by diverse resources

TileLoop - Class in omero.util

TileLoop() - Constructor for class omero.util.TileLoop

TileLoopIteration - Interface in ome.io.nio

A single iteration of a tile for each loop.

TileLoopIteration - Interface in omero.util

A single iteration of a tile for each loop.

TileSizes - Interface in ome.io.nio

Strategy interface which is used by PixelsService to specify the default tile sizes as well as when tiling is necessary.

time() - Method in class ome.system.metrics.DefaultTimer

time() - Method in interface ome.system.metrics.Timer

TimeAnnotationData - Class in pojos

Basic time annotation.

TimeAnnotationData() - Constructor for class pojos.TimeAnnotationData

Creates a default instance.

TimeAnnotationData(TimestampAnnotation) - Constructor for class pojos.TimeAnnotationData

Creates a new instance.

TimeEstimator - Interface in ome.formats.importer.util

Estimates the time left (ETA) during image resource upload to the server.

TimeI - Class in omero.model

Blitz wrapper around the Time class.

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

TimeI(double, UnitsTime) - Constructor for class omero.model.TimeI

TimeI(double, Unit<Time>) - Constructor for class omero.model.TimeI

TimeI(Time, Unit<Time>) - Constructor for class omero.model.TimeI

Copy constructor that converts the given Time based on the given ome-xml enum

TimeI(double, UnitsTime) - Constructor for class omero.model.TimeI

Copy constructor that converts the given Time based on the given ome.model enum

TimeI(Time, String) - Constructor for class omero.model.TimeI

Copy constructor that converts the given Time based on the given enum string.

TimeI(Time, UnitsTime) - Constructor for class omero.model.TimeI

Copy constructor that converts between units if possible.

TimeI(Time) - Constructor for class omero.model.TimeI

Convert a Bio-Formats Length to an OMERO Length.

timeLeft - Variable in class ome.formats.importer.ImportEvent.FILE_UPLOAD_BYTES

TimelineI - Class in ome.services.blitz.impl

implementation of the ITimeline service interface.

TimelineI(BlitzExecutor) - Constructor for class ome.services.blitz.impl.TimelineI

timeOfEvent(Event) - Method in class pojos.DataObject

timer(Object, String) - Method in class ome.system.metrics.DefaultMetrics

timer(Object, String) - Method in interface ome.system.metrics.Metrics

timer(Object, String) - Method in class ome.system.metrics.NullMetrics

Timer - Interface in ome.system.metrics

Thin wrapper around Timer

Timer.Context - Interface in ome.system.metrics

timeToIdle - Variable in class ome.services.sessions.SessionManager.CreationRequest

timeToLive - Variable in class ome.services.sessions.SessionManager.CreationRequest

TimingI - Class in omero.cmd.basic

Diagnostic tool for testing call overhead.

TimingI() - Constructor for class omero.cmd.basic.TimingI

TinyImportFixture - Class in ome.formats.importer.util

test fixture which uses a hard-coded file ("tinyTest.d3d.dv") from the classpath, and adds them to a new UUID-named dataset.

TinyImportFixture(ServiceFactory) - Constructor for class ome.formats.importer.util.TinyImportFixture

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

Returns a platform-specific user-writable temporary directory.

to - Variable in class ome.services.blitz.util.ConvertToBlitzExceptionMessage

TO - Static variable in class ome.services.mail.MapAnnotationSubethaListener

toFile(File) - Method in class ome.services.blitz.repo.path.FsFile

Convert this instance to a File relative to the given File.

toJavaType(RInt) - Method in class ome.services.blitz.impl.MetadataStoreI

Transforms an OMERO RType into the corresponding Java type.

toJavaType(RLong) - Method in class ome.services.blitz.impl.MetadataStoreI

Transforms an OMERO RType into the corresponding Java type.

toJavaType(RBool) - Method in class ome.services.blitz.impl.MetadataStoreI

Transforms an OMERO RType into the corresponding Java type.

toJavaType(RFloat) - Method in class ome.services.blitz.impl.MetadataStoreI

Transforms an OMERO RType into the corresponding Java type.

toJavaType(RDouble) - Method in class ome.services.blitz.impl.MetadataStoreI

Transforms an OMERO RType into the corresponding Java type.

toJavaType(RString) - Method in class ome.services.blitz.impl.MetadataStoreI

Transforms an OMERO RType into the corresponding Java type.

token - Variable in class omero.cmd.SessionI

Token in the form of a UUID for securing method invocations.

tokenHolder - Variable in class ome.security.basic.BasicACLVoter

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

TokenHolder - Class in ome.security.basic

Manages a special token (a unique object) which can be inserted into IObject instances for special almost-administrative handling.

TokenHolder() - Constructor for class ome.security.basic.TokenHolder

tokenStream(String, Reader) - Method in class ome.services.fulltext.FullTextAnalyzer

Returns a LowercaseAlphaNumericTokenizer

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

toLog() - Method in class ome.formats.importer.ImportEvent.FILE_UPLOAD_BYTES

toLog() - Method in class ome.formats.importer.ImportEvent.IMPORT_DONE

toLog() - Method in class ome.formats.importer.ImportEvent.IMPORT_STARTED

toLog() - Method in class ome.formats.importer.ImportEvent.IMPORT_STEP

toLog() - Method in class ome.formats.importer.ImportEvent.LOADED_IMAGE

toLog() - Method in class ome.formats.importer.ImportEvent.LOADING_IMAGE

toLog() - Method in class ome.formats.importer.ImportEvent.POST_UPLOAD_EVENT

toLog() - Method in class ome.formats.importer.ImportEvent.PROGRESS_EVENT

toLog() - Method in class ome.formats.importer.ImportEvent

toLog() - Method in class ome.formats.importer.util.ErrorHandler.FILE_EXCEPTION

toLog() - Method in class ome.formats.importer.util.ErrorHandler.INTERNAL_EXCEPTION

toLog() - Method in class ome.formats.importer.util.ErrorHandler.UNKNOWN_FORMAT

toLog() - Method in class ome.formats.importer.util.ErrorHandler.UNREADABLE_FILE

toNumber(double) - Static method in class pojos.ShapeData

Returns a double array as a number attribute value.

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

TopicManager - Interface in ome.services.blitz.fire

Local dispatcher to TopicManager

TopicManager.Impl - Class in ome.services.blitz.fire

TopicManager.Impl(Communicator) - Constructor for class ome.services.blitz.fire.TopicManager.Impl

TopicManager.TopicMessage - Class in ome.services.blitz.fire

TopicManager.TopicMessage(Object, String, ObjectPrxHelperBase, String, Object...) - Constructor for class ome.services.blitz.fire.TopicManager.TopicMessage

topicOrNull(String) - Method in class ome.services.blitz.fire.TopicManager.Impl

toPoints(Point2D.Double[]) - Static method in class pojos.ShapeData

Returns a Point2D.Double array as a Points attribute value. as specified in http://www.w3.org/TR/SVGMobile12/shapes.html#PointsBNF

toRType(Integer) - Method in class ome.formats.OMEROMetadataStoreClient

Transforms a Java type into the corresponding OMERO RType.

toRType(NonNegativeInteger) - Method in class ome.formats.OMEROMetadataStoreClient

Transforms a Java type into the corresponding OMERO RType.

toRType(NonNegativeLong) - Method in class ome.formats.OMEROMetadataStoreClient

Transforms a Java type into the corresponding OMERO RType.

toRType(PositiveFloat) - Method in class ome.formats.OMEROMetadataStoreClient

Transforms a Java type into the corresponding OMERO RType.

toRType(PercentFraction) - Method in class ome.formats.OMEROMetadataStoreClient

Transforms a Java type into the corresponding OMERO RType.

toRType(Long) - Method in class ome.formats.OMEROMetadataStoreClient

Transforms a Java type into the corresponding OMERO RType.

toRType(String) - Method in class ome.formats.OMEROMetadataStoreClient

Transforms a Java type into the corresponding OMERO RType.

toRType(Boolean) - Method in class ome.formats.OMEROMetadataStoreClient

Transforms a Java type into the corresponding OMERO RType.

toRType(Double) - Method in class ome.formats.OMEROMetadataStoreClient

Transforms a Java type into the corresponding OMERO RType.

toRType(Float) - Method in class ome.formats.OMEROMetadataStoreClient

Transforms a Java type into the corresponding OMERO RType.

toRType(Timestamp) - Method in class ome.formats.OMEROMetadataStoreClient

Transforms a Java type into the corresponding OMERO RType.

toRType(NamingConvention) - Method in class ome.formats.OMEROMetadataStoreClient

Transforms a Java type into the corresponding OMERO RType.

toRType(AffineTransform) - Method in class ome.formats.OMEROMetadataStoreClient

Transforms a Java type into the corresponding OMERO RType.

toRType(Color) - Method in class ome.formats.OMEROMetadataStoreClient

Transforms a Java type into the corresponding OMERO RType.

toRType(Object) - Method in class omero.util.IceMapper

toString() - Method in exception ome.formats.enums.EnumerationException

toString() - Method in class ome.formats.importer.ImportConfig.Value

toString() - Method in enum ome.formats.Index

toString() - Method in exception ome.formats.model.ModelException

toString() - Method in class ome.io.nio.AbstractBuffer

toString() - Method in class ome.io.nio.ConfiguredTileSizes

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

toString() - Method in class ome.security.basic.BasicEventContext

toString() - Method in class ome.services.blitz.repo.CheckedPath

toString() - Method in class ome.services.blitz.repo.path.FsFile

Provides repository path with components separated by FsFile.separatorChar.

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

Deprecated.

toString() - Method in class ome.services.graphs.GraphEntry

Deprecated.

toString() - Method in exception ome.services.graphs.GraphException

toString() - Method in class ome.services.graphs.GraphPolicyRule

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

Deprecated.

toString() - Method in class ome.services.graphs.GraphTables

Deprecated.

toString() - Method in class ome.services.scripts.RepoFile.FsFile

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

toString() - Method in class ome.services.throttling.Task

toString() - Method in class ome.system.Principal

returns only the name of the instance because that is the expected behavior of Principal implementations

toString() - Method in class ome.tools.FileSystem

Public toString implementation

toString() - Method in class ome.tools.hibernate.QueryBuilder

toString() - Method in class ome.tools.hibernate.SqlArray

toString() - Method in class ome.tools.spring.InternalServiceFactory

toString() - Method in class omeis.providers.re.codomain.CodomainChain

Overrides the toString method.

toString() - Method in class omeis.providers.re.data.PlaneDef

Overrides generic toString method to provide a specific string representation of this object.

toString() - Method in class omeis.providers.re.data.RegionDef

Overridden to return the region as a string.

toString() - Method in class omero.cmd.graphs.Preprocessor.GraphModifyTarget

Deprecated.

toString() - Method in class omero.cmd.SessionI

toString() - Method in class omero.model.ElectricPotentialI

toString() - Method in class omero.model.FrequencyI

toString() - Method in class omero.model.LengthI

toString() - Method in class omero.model.PermissionsI

produces a String representation of the PermissionsI similar to those on a Unix filesystem.

toString() - Method in class omero.model.PowerI

toString() - Method in class omero.model.PressureI

toString() - Method in class omero.model.TemperatureI

toString() - Method in class omero.model.TimeI

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

toString() - Method in class pojos.DataObject

Overridden to return the name of the class and the object id.

toString() - Method in class pojos.ROICoordinate

Returns the string of the coordinates.

total - Variable in class ome.formats.importer.ImportEvent.COUNT_EVENT

total - Variable in class ome.formats.importer.ImportEvent.PROGRESS_EVENT

total() - Method in class ome.tools.hibernate.ExtendedMetadata.Locks

as opposed to ExtendedMetadata.Locks.size(), the returns the actual number of fields that will need to be checked.

TOTAL_PHYSICAL_MEMORY - Static variable in class ome.services.util.JvmSettingsCheck

TotalPhysicalMemorySize value from the OperatingSystem JMX bean at startup.

TOTAL_SIZE - Static variable in class ome.services.search.FullText

totalErrors - Variable in class ome.formats.importer.util.ErrorHandler

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

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

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

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

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

transfer - Variable in class ome.formats.importer.cli.CommandLineImporter

FileTransfer mechanism to be used for uploading

transfer(TransferState) - Method in class ome.formats.importer.transfers.AbstractExecFileTransfer

"Transfer" files by soft-linking them into place.

transfer(TransferState) - Method in interface ome.formats.importer.transfers.FileTransfer

Transfers a file and returns the appropriate checksum string for the source file.

transfer(TransferState) - Method in class ome.formats.importer.transfers.UploadFileTransfer

TransferState - Class in ome.formats.importer.transfers

Non-thread-safe argument holder for FileTransfer implementations.

TransferState(File, int, int, ImportProcessPrx, ImportLibrary, TimeEstimator, ChecksumProvider, byte[]) - Constructor for class ome.formats.importer.transfers.TransferState

State of the current file transfer.

transform(Function<String, String>) - Method in class ome.services.blitz.repo.path.FsFile

Transform each path component with the given transformer.

transform(int) - Method in class omeis.providers.re.codomain.CodomainChain

Applies the transformation.

transform(int) - Method in interface omeis.providers.re.codomain.CodomainMap

Performs the transformation.

transform(int, double) - Method in class omeis.providers.re.quantum.ExponentialMap

Implemented as specified in QuantumMap.

transform(double, double) - Method in class omeis.providers.re.quantum.ExponentialMap

Implemented as specified in QuantumMap.

transform(float, double) - Method in class omeis.providers.re.quantum.ExponentialMap

Implemented as specified in QuantumMap.

transform(int, double) - Method in class omeis.providers.re.quantum.LogarithmicMap

Implemented as specified in QuantumMap.

transform(double, double) - Method in class omeis.providers.re.quantum.LogarithmicMap

Implemented as specified in QuantumMap.

transform(float, double) - Method in class omeis.providers.re.quantum.LogarithmicMap

Implemented as specified in QuantumMap.

transform(int, double) - Method in class omeis.providers.re.quantum.PolynomialMap

Implemented as specified in QuantumMap.

transform(double, double) - Method in class omeis.providers.re.quantum.PolynomialMap

Implemented as specified in QuantumMap.

transform(float, double) - Method in class omeis.providers.re.quantum.PolynomialMap

Implemented as specified in QuantumMap.

transform(int, double) - Method in interface omeis.providers.re.quantum.QuantumMap

Maps the specified value.

transform(double, double) - Method in interface omeis.providers.re.quantum.QuantumMap

Maps the specified value.

transform(float, double) - Method in interface omeis.providers.re.quantum.QuantumMap

Maps the specified value.

transform(Predicate<Request>, Preprocessor.GraphModifyTarget, Set<Preprocessor.GraphModifyTarget>, Set<Preprocessor.GraphModifyTarget>) - Method in class omero.cmd.graphs.Preprocessor

Deprecated.

Transform the list of requests.

transformationMap - Variable in class ome.services.blitz.repo.path.FilePathRestrictions

transformationMatrix - Variable in class ome.services.blitz.repo.path.FilePathRestrictions

translateException(Throwable) - Method in class ome.services.util.BeanHelper

TransmittanceRange_CutIn - Static variable in class ome.formats.model.UnitsFactory

TransmittanceRange_CutInTolerance - Static variable in class ome.formats.model.UnitsFactory

TransmittanceRange_CutOut - Static variable in class ome.formats.model.UnitsFactory

TransmittanceRange_CutOutTolerance - Static variable in class ome.formats.model.UnitsFactory

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

treeList(String, CheckedPath, Current) - Method in interface ome.services.blitz.repo.RepositoryDao

treeList(String, CheckedPath, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl

trimPaths(FsFile, List<FsFile>, Class<? extends FormatReader>) - Method in class ome.services.blitz.repo.ManagedRepositoryI

Trim off the start of long client-side paths.

truncate(long) - Method in interface ome.api.RawFileStore

Limits the size of a file to the given length.

truncate(long) - Method in class ome.io.nio.FileBuffer

truncate(long) - Method in class ome.services.RawFileBean

truncate_async(AMD_RawFileStore_truncate, long, Current) - Method in class ome.services.blitz.impl.RawFileStoreI

truncateIfSmaller(long) - Method in class ome.io.nio.FileBuffer

Only truncate if the size of the file is less than the size argument.

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.system.Principal

type() - Method in interface omero.rtypes.Conversion

Specifies the type that can be expected from the rtypes.Conversion.convert(IceMapper) method.

types - Variable in class ome.security.policy.BasePolicy

types - Variable in class ome.services.eventlogs.PersistentEventLogLoader

types - Variable in class ome.services.graphs.AbstractHierarchyGraphSpec

Deprecated.

Type of each sub-step.

TypesI - Class in ome.services.blitz.impl

Implementation of the ITypes service.

TypesI(ITypes, BlitzExecutor) - Constructor for class ome.services.blitz.impl.TypesI

TypesImpl - Class in ome.logic

implementation of the ITypes service interface.

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

typeToString(T) - Method in class ome.services.query.HierarchyNavigatorWrap

Convert the given object type to the type strings expected by HierarchyNavigator.

U

UINT16 - Static variable in class omeis.providers.re.data.PlaneFactory

Identifies the UINT16 data type used to store pixel values, as per OME spec.

UINT16_TYPE - Static variable in class pojos.PixelsData

Identifies the type used to store pixel values.

UINT32 - Static variable in class omeis.providers.re.data.PlaneFactory

Identifies the UINT32 data type used to store pixel values, as per OME spec.

UINT32_TYPE - Static variable in class pojos.PixelsData

Identifies the type used to store pixel values.

UINT8 - Static variable in class omeis.providers.re.data.PlaneFactory

Identifies the UINT8 data type used to store pixel values, as per OME spec.

UINT8_TYPE - Static variable in class pojos.PixelsData

Identifies the type used to store pixel values.

umask - Variable in class ome.system.SimpleEventContext

Union - Class in ome.services.search

Union SearchAction which combines two other search actions into one logical unit, e.g.

Union(SearchValues, SearchAction, SearchAction) - Constructor for class ome.services.search.Union

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

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

Obtain a unique alias to be used in the SQL.

UnitsFactory - Class in ome.formats.model

Utility class to generate and convert unit objects.

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

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

unlinkTargets(boolean) - Method in class ome.services.graphs.GraphTraversal

Remove links between the targeted model objects and the remainder of the model object graph.

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 omero.cmd.SessionI

Calls SessionI.unregisterServant(Ice.Identity, Ice.ObjectAdapter, ServantHolder)

unregisterServant(Identity, ObjectAdapter, ServantHolder) - Static method in class omero.cmd.SessionI

Reverts all the additions made by #registerServant(ServantInterface, Ice.Current, Ice.Identity) Now called by SessionManagerI in response to an UnregisterServantMessage

UnregisterServantMessage - Class in ome.services.blitz.util

InternalMessage raised when a servant should be removed from the adapter.

UnregisterServantMessage(Object, Current, ServantHolder) - Constructor for class ome.services.blitz.util.UnregisterServantMessage

unsafeNames - Variable in class ome.services.blitz.repo.path.FilePathRestrictions

unsafePrefixes - Variable in class ome.services.blitz.repo.path.FilePathRestrictions

unsafeSuffixes - Variable in class ome.services.blitz.repo.path.FilePathRestrictions

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

removes the user from the owner list for this group.

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

unsetGroupOwner_async(AMD_IAdmin_unsetGroupOwner, ExperimenterGroup, Experimenter, Current) - Method in class ome.services.blitz.impl.AdminI

unwrap(RType) - Static method in class omero.rtypes

Descends into data structures unwrapping all RType objects as it goes.

unwrap(RType, Map<RType, Object>) - Static method in class omero.rtypes

Descends into data structures wrapping all elements as it goes.

unwrapCollection(Collection<RType>, Collection<Object>, Map<RType, Object>) - Static method in class omero.rtypes

unwrapRawFileBean(RawFileStore) - Method in class ome.services.blitz.repo.RepositoryDaoImpl

Loads

update(IObservable, ImportEvent) - Method in class ome.formats.importer.cli.LoggingImportMonitor

update(IObservable, ImportEvent) - Method in interface ome.formats.importer.IObserver

Update observable on event

update(IObservable, ImportEvent) - Method in class ome.formats.importer.util.ErrorHandler

update(RepoFile, Long, Map<String, String>) - Method in class ome.services.scripts.ScriptRepoHelper

update(Session) - Method in interface ome.services.sessions.SessionManager

See ISession#updateSession(Session) for the logic that's implemented here.

update(Session, boolean) - Method in interface ome.services.sessions.SessionManager

Same as SessionManager.update(Session) but some security checks can be overridden.

update(Session) - Method in class ome.services.sessions.SessionManagerImpl

update(Session, boolean) - Method in class ome.services.sessions.SessionManagerImpl

update(Share, ShareData) - Method in class ome.services.sharing.ShareStore

update(int) - Method in class ome.system.metrics.DefaultHistogram

update(int) - Method in interface ome.system.metrics.Histogram

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

update(CodomainMapContext) - Method in class omeis.providers.re.codomain.CodomainChain

Updates a map context in the chain.

update - Variable in class omero.cmd.admin.UpdateSessionTimeoutRequestI

UPDATE_EVENT - Static variable in class ome.security.basic.UpdateEventListener

updateCodomainMap(CodomainMapContext) - Method in class ome.services.RenderingBean

Implemented as specified by the RenderingEngine interface.

updateCodomainMap(CodomainMapContext) - Method in interface omeis.providers.re.RenderingEngine

Updates the specified context.

updateCodomainMap_async(AMD_RenderingEngine_updateCodomainMap, CodomainMapContext, Current) - Method in class ome.services.blitz.impl.RenderingEngineI

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

updated - Variable in class omero.cmd.admin.UpdateSessionTimeoutRequestI

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

Updates a data object.

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

Implemented as specified by the IContainer I/F

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

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

convenience method to save network calls.

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

Implemented as specified by the IContainer I/F

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

updatedObjects(int) - Method in class ome.services.sessions.stats.DelegatingStats

updatedObjects(int) - Method in class ome.services.sessions.stats.NullSessionStats

updatedObjects(int) - Method in interface ome.services.sessions.stats.SessionStats

updatedObjects(int) - Method in class ome.services.sessions.stats.SimpleSessionStats

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

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

updates enumeration value specified by object

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

updateEnumeration_async(AMD_ITypes_updateEnumeration, IObject, Current) - Method in class ome.services.blitz.impl.TypesI

updateEnumerations(List<T>) - Method in interface ome.api.ITypes

updates enumeration value specified by object

updateEnumerations(List<T>) - Method in class ome.logic.TypesImpl

updateEnumerations_async(AMD_ITypes_updateEnumerations, List<IObject>, Current) - Method in class ome.services.blitz.impl.TypesI

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

Marks a new update request in State#lastUpdateRequest.

UpdateEventListener - Class in ome.security.basic

responsible for setting the updat event on all events shortly before being saved.

UpdateEventListener(CurrentDetails) - Constructor for class ome.security.basic.UpdateEventListener

main constructor. controls access to individual db rows..

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

Updates an experimenter if admin or owner of group.

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

updateExperimenter_async(AMD_IAdmin_updateExperimenter, Experimenter, Current) - Method in class ome.services.blitz.impl.AdminI

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

Updates an experimenter if admin or owner of group.

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

updateExperimenterWithPassword_async(AMD_IAdmin_updateExperimenterWithPassword, Experimenter, RString, Current) - Method in class ome.services.blitz.impl.AdminI

updateField(Session, String, RLong, boolean) - Method in class omero.cmd.admin.UpdateSessionTimeoutRequestI

updateFileSize(OriginalFile, long) - Method in class ome.formats.OMEROMetadataStoreClient

UpdateFilter - Class in ome.tools.hibernate

responsible for correlating entity identities during multiple calls to merge.

UpdateFilter() - Constructor for class ome.tools.hibernate.UpdateFilter

updateFlexReaderServerMaps() - Method in class ome.formats.importer.util.IniFileLoader

Updates the Flex reader server maps from the configuration file.

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

Updates an experimenter group if admin or owner of group.

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

updateGroup_async(AMD_IAdmin_updateGroup, ExperimenterGroup, Current) - Method in class ome.services.blitz.impl.AdminI

UpdateI - Class in ome.services.blitz.impl

Implementation of the IUpdate service.

UpdateI(IUpdate, BlitzExecutor) - Constructor for class ome.services.blitz.impl.UpdateI

UpdateImpl - Class in ome.logic

implementation of the IUpdate service interface

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

updateJob(Job, String, String, Current) - Method in interface ome.services.blitz.repo.RepositoryDao

Set both the message and the status of the given job.

updateJob(Job, String, String, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl

updateMinMax(int, byte[], int) - Method in class ome.formats.importer.OMEROWrapper

updateObject(String, IObject, Map<String, Integer>) - Method in class ome.formats.OMEROMetadataStore

Updates a given model object in our object graph.

updateObject(T...) - Method in interface ome.security.SecureAction

executes with special privilegs within the SecuritySystem.

updateObject(T...) - Method in class ome.tools.hibernate.SecureMerge

updateObjects_async(AMD_MetadataStore_updateObjects, IObjectContainer[], Current) - Method in class ome.services.blitz.impl.MetadataStoreI

updatePixels(List<Pixels>) - Method in class ome.formats.OMEROMetadataStoreClient

Updates a list of Pixels.

updateQuantumManager() - Method in class omeis.providers.re.Renderer

Updates the QuantumManager and configures it according to the current quantum definition.

updateReadFilter(Session) - Method in class ome.security.basic.BasicSecuritySystem

updateReferences(Map<String, String[]>) - Method in class ome.formats.OMEROMetadataStore

Updates our object graph references.

updateReferences_async(AMD_MetadataStore_updateReferences, Map<String, String[]>, Current) - Method in class ome.services.blitz.impl.MetadataStoreI

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

Allows a user to update his/her own information.

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

updateSelf_async(AMD_IAdmin_updateSelf, Experimenter, Current) - Method in class ome.services.blitz.impl.AdminI

updateSession(Session) - Method in class ome.services.sessions.SessionBean

updateSession() - Method in class omero.cmd.admin.UpdateSessionTimeoutRequestI

UpdateSessionTimeoutRequestI - Class in omero.cmd.admin

UpdateSessionTimeoutRequestI(CurrentDetails, SessionManager, SecuritySystem) - Constructor for class omero.cmd.admin.UpdateSessionTimeoutRequestI

UpdateSessionTimeoutRequestI.Factory - Class in omero.cmd.admin

UpdateSessionTimeoutRequestI.Factory(CurrentDetails, SessionManager, SecuritySystem) - Constructor for class omero.cmd.admin.UpdateSessionTimeoutRequestI.Factory

updateUsedFilesTotalSize() - Method in class ome.formats.importer.ImportContainer

UpgradeCheck - Class in ome.system

Contacts a given URL which should be an OME server which will return either an empty String or a URL which points to a needed upgrade.

UpgradeCheck(String, String, String) - Constructor for class ome.system.UpgradeCheck

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

uploadBytes(long) - Method in class ome.formats.importer.transfers.TransferState

Raise the ImportEvent.FILE_UPLOAD_BYTES event to all observers.

uploadComplete(long) - Method in class ome.formats.importer.transfers.TransferState

Raise the ImportEvent.FILE_UPLOAD_COMPLETE event to all observers.

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

uploadFile(ImportProcessPrx, String[], int, TimeEstimator) - Method in class ome.formats.importer.ImportLibrary

uploadFile(ImportProcessPrx, String[], int, ChecksumProviderFactory, TimeEstimator, byte[]) - Method in class ome.formats.importer.ImportLibrary

uploadFile(ErrorContainer) - Method in class ome.formats.importer.util.ErrorHandler

Upload a single ErrorContainer.

uploadFiles(String, int, ErrorContainer) - Method in class ome.formats.importer.util.FileUploader

Upload files from error container to url

uploadFileset(Fileset, ImportSettings, Current) - Method in class ome.services.blitz.repo.ManagedRepositoryI

Return a template based directory path.

uploadFilesToRepository(String[], ImportProcessPrx) - Method in class ome.formats.importer.ImportLibrary

Upload files to the managed repository.

UploadFileTransfer - Class in ome.formats.importer.transfers

Traditional file transfer mechanism which uploads files using the API.

UploadFileTransfer() - Constructor for class ome.formats.importer.transfers.UploadFileTransfer

UploadMask - Class in pojos.util

Uploaded for masks.

UploadMask(long) - Constructor for class pojos.util.UploadMask

Creates a new instance.

uploadMask_async(AMD_IRoi_uploadMask, long, int, int, byte[], Current) - Method in class ome.services.blitz.impl.RoiI

uploadMyUserPhoto(String, String, byte[]) - Method in interface ome.api.IAdmin

Uploads a photo for the user which will be displayed on his/her profile.

uploadMyUserPhoto(String, String, byte[]) - Method in class ome.logic.AdminImpl

uploadMyUserPhoto_async(AMD_IAdmin_uploadMyUserPhoto, String, String, byte[], Current) - Method in class ome.services.blitz.impl.AdminI

uploadOfficialScript_async(AMD_IScript_uploadOfficialScript, String, String, Current) - Method in class ome.services.blitz.impl.ScriptI

UploadRmFileTransfer - Class in ome.formats.importer.transfers

Version of the default UploadFileTransfer which deletes all files in a transfer set if the upload is successful.

UploadRmFileTransfer() - Constructor for class ome.formats.importer.transfers.UploadRmFileTransfer

uploadScript_async(AMD_IScript_uploadScript, String, String, Current) - Method in class ome.services.blitz.impl.ScriptI

Upload script to the server.

uploadStarted() - Method in class ome.formats.importer.transfers.TransferState

Raise the ImportEvent.FILE_UPLOAD_STARTED event to all observers.

usage() - Static method in class ome.formats.importer.cli.CommandLineImporter

Prints usage to STDERR and exits with return code 1.

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

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

Returns a usage string array.

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

usedFiles - Variable in class ome.formats.importer.util.ErrorHandler.FILE_EXCEPTION

usedFiles - Variable in class ome.formats.importer.util.ErrorHandler.INTERNAL_EXCEPTION

UsedFilesRequestI - Class in omero.cmd.fs

Lists the IDs of the original files associated with an image.

UsedFilesRequestI(PixelsService) - Constructor for class omero.cmd.fs.UsedFilesRequestI

Construct a new used files request.

useFirstAcceptable() - Method in class ome.services.blitz.repo.path.MakeNextDirectory

Use the first acceptable path (that with the lowest index for MakeNextDirectory.getPathFor(long)) and return the corresponding subdirectories.

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

usePath(List<String>) - Method in class ome.services.blitz.repo.path.MakeNextDirectory

Actually use the path.

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

user - Variable in class ome.services.messages.LoginAttemptMessage

USER - Static variable in class pojos.GroupData

Identifies the User group.

userGroups(String) - Method in class ome.security.auth.PasswordUtil

UserGroupUpdateEvent - Class in ome.services.sessions.events

InteralMessage published by the SecuritySystem when an Experimenter, ExperimenterGroup, or GroupExperimenterMap is inserted or updated.

UserGroupUpdateEvent(Object) - Constructor for class ome.services.sessions.events.UserGroupUpdateEvent

userId(String) - Method in class ome.security.auth.PasswordUtil

Get the user's ID

username - Variable in class loci.ome.io.OMECredentials

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

userName(long) - Method in class ome.security.auth.PasswordUtil

Get the user's name

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

Returns the current OS-user's name.

usernameFilter(String) - Method in class ome.security.auth.LdapConfig

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

userProxy(String) - Method in interface ome.api.local.LocalAdmin

returns a possibly uninitialized proxy for the given user name.

userProxy(Long) - Method in interface ome.api.local.LocalAdmin

returns a possibly uninitialized proxy for the given user id.

userProxy(Long) - Method in class ome.logic.AdminImpl

userProxy(String) - Method in class ome.logic.AdminImpl

UserSignalMessage - Class in ome.util.messages

Published if the Posix USR1 or USR2 signal is received.

UserSignalMessage(Object, int) - Constructor for class ome.util.messages.UserSignalMessage

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

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

util - Variable in class ome.security.auth.ConfigurablePasswordProvider

Utils - Class in ome.io.nio

General utility methods for working with ROMIO classes.

Utils() - Constructor for class ome.io.nio.Utils

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

validate(GraphState, Session, SqlAction, GraphOpts) - Method in class ome.services.chgrp.ChgrpStep

Deprecated.

validate(Session, GraphOpts) - Method in class ome.services.chown.ChownStep

Deprecated.

validate(int) - Method in class ome.services.graphs.GraphState

Deprecated.

validate(GraphState, Session, SqlAction, GraphOpts) - Method in class ome.services.graphs.GraphStep

Deprecated.

Action performed at the end of the transaction to give all rows the chance to invalidate other actions.

validated(GraphStep) - Method in class ome.services.graphs.GraphSteps

Deprecated.

validateEmail(String) - Method in class ome.services.mail.MailUtil

Helper Validate that this address conforms to the syntax rules of RFC 822.

validateFilePathNaming(FsFile) - Method in class ome.services.blitz.repo.path.FilePathNamingValidator

Validate the given FS file.

validateFilePathNaming(String) - Method in class ome.services.blitz.repo.path.FilePathNamingValidator

Validate the given file path.

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

Validates password for base.

validateScript_async(AMD_IScript_validateScript, Job, List<IObject>, Current) - Method in class ome.services.blitz.impl.ScriptI

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

Deprecated.

Prepares the next phase (GraphState.validate(int)) by returning how many validation steps should be performed.

validation() - Method in class ome.services.graphs.GraphStep

Deprecated.

value(String) - Method in class ome.services.query.Query

get the Object value for this name argument.

valueMapper - Variable in class omeis.providers.re.quantum.QuantumStrategy

Reference to the value mapper.

valueOf(String) - Static method in enum ome.formats.importer.exclusions.AbstractFileExclusion.Exclusion

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ome.formats.importer.ImportConfig.VersionInfo

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ome.formats.importer.transfers.AbstractFileTransfer.Transfers

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ome.formats.Index

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ome.security.auth.PasswordUtil.METHOD

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ome.services.blitz.repo.path.FilePathRestrictionInstance

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ome.services.graphs.GraphOpts.Op

Deprecated.

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ome.services.graphs.GraphPolicy.Ability

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ome.services.graphs.GraphPolicy.Action

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ome.services.graphs.GraphPolicy.Orphan

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ome.services.util.Executor.Priority

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ome.system.Preference.Visibility

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ome.util.checksum.ChecksumType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum omero.cmd.graphs.Preprocessor.TargetType

Deprecated.

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum omero.grid.ProcessCallbackI.Action

Returns the enum constant of this type with the specified name.

values() - Static method in enum ome.formats.importer.exclusions.AbstractFileExclusion.Exclusion

Returns an array containing the constants of this enum type, in the order they are declared.

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

values() - Static method in enum ome.formats.importer.ImportConfig.VersionInfo

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum ome.formats.importer.transfers.AbstractFileTransfer.Transfers

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum ome.formats.Index

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum ome.security.auth.PasswordUtil.METHOD

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum ome.services.blitz.repo.path.FilePathRestrictionInstance

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum ome.services.graphs.GraphOpts.Op

Deprecated.

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum ome.services.graphs.GraphPolicy.Ability

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum ome.services.graphs.GraphPolicy.Action

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum ome.services.graphs.GraphPolicy.Orphan

Returns an array containing the constants of this enum type, in the order they are declared.

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

values() - Static method in enum ome.services.util.Executor.Priority

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum ome.system.Preference.Visibility

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum ome.util.checksum.ChecksumType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum omero.cmd.graphs.Preprocessor.TargetType

Deprecated.

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum omero.grid.ProcessCallbackI.Action

Returns an array containing the constants of this enum type, in the order they are declared.

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

Calculates the vector associated to this point and the specified argument.

vec(double, double) - Method in class ome.util.math.geom2D.PlanePoint

Calculates the vector associated to this point and the specified argument.

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

verifyChecksums(List<Long>, Current) - Method in class ome.services.blitz.repo.ManagedRepositoryI

verifyUpload(List<String>, Current) - Method in class ome.services.blitz.repo.ManagedImportProcessI

Version - Class in ome.formats.importer

Version() - Constructor for class ome.formats.importer.Version

Version - 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

waitCompleted(ImportConfig) - Static method in class ome.formats.importer.cli.CommandLineImporter

Look for all ImportProcessPrx in the current session and close them if they return a non-null Response (i.e. they are done).

waitForLock - Variable in class ome.services.fulltext.FullTextThread

WAITING - Static variable in interface ome.api.JobHandle

waitOnFinishedDone() - Method in class omero.cmd.CmdCallbackI

waitOnInitialization() - Method in class omero.cmd.CmdCallbackI

Subclasses which must perform their own initialization before CmdCallbackI.onFinished(Response, Status, Current) is called should call {@link #waitOnInitialization() before accessing any initialized state.

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

Deprecated.

walk(String[], GraphEntry, QueryBuilder) - Method in class ome.services.graphs.BaseGraphSpec

Deprecated.

Walks the parts given adding a new relationship between each.

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

Deprecated.

Returns an iterator over all subspecs and their subspecs, depth-first.

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

warn(String, Object...) - Method in class omero.cmd.Helper

wasCancelled() - Method in class ome.formats.importer.ImportCandidates

wasSource(EventLogLoader) - Method in class ome.services.eventlogs.EventLogFailure

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.

WellSample_PositionX - Static variable in class ome.formats.model.UnitsFactory

WellSample_PositionY - Static variable in class ome.formats.model.UnitsFactory

WellSampleData - Class in pojos

The data that makes up an OME WellSample along with links to its images and the Experimenter that owns this WellSample.

WellSampleData() - Constructor for class pojos.WellSampleData

Creates a new instance.

WellSampleData(WellSample) - Constructor for class pojos.WellSampleData

Creates a new instance.

where() - Method in class ome.tools.hibernate.QueryBuilder

Marks the end of all fetches by adding a "where" clause to the string.

whereClause() - Method in class ome.tools.hibernate.QueryBuilder

Similar to how skipFrom and skipWhere were previously used, this sets the current builder to QueryBuilder.where but without prefacing the "where " string.

willBeTriedAgain(GraphStep) - Method in class ome.services.graphs.GraphSteps

Deprecated.

work - Variable in class ome.services.util.ExecutionThread

WorkflowData - Class in pojos

The data that makes up an OME worflow object.

WorkflowData(Namespace) - Constructor for class pojos.WorkflowData

Creates a new instance.

WorkflowData(String, List<String>) - Constructor for class pojos.WorkflowData

Creates a new instance.

WorkflowData(String, String) - Constructor for class pojos.WorkflowData

Creates a new instance.

WorkflowData() - Constructor for class pojos.WorkflowData

Creates a new instance.

wrap(String, IObject) - Method in class ome.services.eventlogs.AllEntitiesPseudoLogLoader

wrap(Iterator<Reader>) - Method in class ome.services.fulltext.FileParser

Wraps an Iterator with an Iterable instance.

wrap(Reader) - Method in class ome.services.fulltext.FileParser

wrap(Hashtable<String, Object>) - Method in class omero.cmd.fs.OriginalMetadataRequestI

Use IceMapper to convert from Object instances in the given Hashtable to RType instances.

wrap(Object) - Static method in class omero.rtypes

Descends into data structures wrapping all elements as it goes.

wrap(Object, Map<Object, RType>) - Static method in class omero.rtypes

Descends into data structures wrapping all elements as it goes.

WrappableRequest<X> - Interface in omero.cmd.graphs

Requests that can be wrapped by a SkipHeadI request.

wrapSecurityViolation(SecurityViolation) - Method in class ome.services.blitz.repo.RepositoryDaoImpl

write(byte[], long, int) - Method in interface ome.api.RawFileStore

Delegates to FileBuffer

write(ByteBuffer, long) - Method in class ome.io.nio.FileBuffer

Delegates to FileChannel

write(ByteBuffer) - Method in class ome.io.nio.FileBuffer

Delegates to FileChannel

write(byte[], long, int) - Method in class ome.services.RawFileBean

write(String, String) - Method in class ome.services.scripts.ScriptRepoHelper

write(RepoFile, String) - Method in class ome.services.scripts.ScriptRepoHelper

write_async(AMD_RawFileStore_write, byte[], long, int, Current) - Method in class ome.services.blitz.impl.RawFileStoreI

write_async(AMD_RawFileStore_write, byte[], long, int, Current) - Method in class ome.services.blitz.repo.RepoRawFileStoreI

writeImage(BufferedImage, TranscoderOutput) - Method in class ome.services.SVGRasterizer.Rasterizer

writeLine(String) - Method in class ome.services.blitz.repo.FileMaker

writer - Variable in class ome.io.bioformats.BfPyramidPixelBuffer

Bio-Formats implementation used to write to the backing TIFF.

WriteStrategy - Interface in ome.security

Responsible for determining which users can modify which objects in which contexts.

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.

xmlElectricPotentialEnumToOMERO(Unit<ElectricPotential>) - Static method in class ome.formats.model.UnitsFactory

xmlElectricPotentialEnumToOMERO(String) - Static method in class ome.formats.model.UnitsFactory

xmlFrequencyEnumToOMERO(Unit<Frequency>) - Static method in class ome.formats.model.UnitsFactory

xmlFrequencyEnumToOMERO(String) - Static method in class ome.formats.model.UnitsFactory

xmlLengthEnumToOMERO(Unit<Length>) - Static method in class ome.formats.model.UnitsFactory

xmlLengthEnumToOMERO(String) - Static method in class ome.formats.model.UnitsFactory

xmlPowerEnumToOMERO(Unit<Power>) - Static method in class ome.formats.model.UnitsFactory

xmlPowerEnumToOMERO(String) - Static method in class ome.formats.model.UnitsFactory

xmlPressureEnumToOMERO(Unit<Pressure>) - Static method in class ome.formats.model.UnitsFactory

xmlPressureEnumToOMERO(String) - Static method in class ome.formats.model.UnitsFactory

xmlTemperatureEnumToOMERO(Unit<Temperature>) - Static method in class ome.formats.model.UnitsFactory

xmlTemperatureEnumToOMERO(String) - Static method in class ome.formats.model.UnitsFactory

xmlTimeEnumToOMERO(Unit<Time>) - Static method in class ome.formats.model.UnitsFactory

xmlTimeEnumToOMERO(String) - Static method in class ome.formats.model.UnitsFactory

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

ZIP_EXTENSION - Static variable in class ome.formats.importer.util.FileUploader

The extension used for the zip.

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

ZY - Static variable in class omeis.providers.re.data.PlaneDef

Flag to identify an YZ-plane.

_

__del__() - Method in class omero.client

Calls closeSession() and ignores any exceptions.

__dont_use_me_factory - Variable in class ome.services.sharing.BlobShareStore

Used indirectly to obtain sessions for querying and updating the store during normal operation.

__redirect(long, _RawFileStoreTie, Current) - Method in class ome.services.blitz.impl.RawFileStoreI

_addGraph(ShareData, ShareBean.Graph) - Method in class ome.services.sharing.ShareBean

_getPixelBuffer(Pixels, boolean) - Method in class ome.io.nio.PixelsService

_wait(Current) - Method in class ome.services.blitz.impl.ScriptProcessI

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