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

A

a00 - Variable in class ome.model.roi.AffineTransform

A00 - Static variable in class ome.model.roi.AffineTransform

a01 - Variable in class ome.model.roi.AffineTransform

A01 - Static variable in class ome.model.roi.AffineTransform

a02 - Variable in class ome.model.roi.AffineTransform

A02 - Static variable in class ome.model.roi.AffineTransform

a10 - Variable in class ome.model.roi.AffineTransform

A10 - Static variable in class ome.model.roi.AffineTransform

a11 - Variable in class ome.model.roi.AffineTransform

A11 - Static variable in class ome.model.roi.AffineTransform

a12 - Variable in class ome.model.roi.AffineTransform

A12 - Static variable in class ome.model.roi.AffineTransform

AbstractAmdServant - Class in ome.services.blitz.impl

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

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

AbstractBuffer - Class in ome.io.nio

AbstractChecksumProvider - Class in ome.util.checksum

Abstract skeleton class implementing ChecksumProvider and providing implementations of the interface methods using a universal checksum class object.

AbstractChecksumProvider(HashFunction) - Constructor for class ome.util.checksum.AbstractChecksumProvider

Protected ctor.

AbstractClassIdsOptionsQuery - Class in ome.services.query

simple abstract class that provides a common Definitions containing: IdsQueryParameterDef and ClassQueryParameterDef.

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

AbstractCloseableAmdServant - Class in ome.services.blitz.impl

Base class for all servants that must guarantee proper clean-up of held resources on close.

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

AbstractExecFileTransfer - Class in ome.formats.importer.transfers

Local-only file transfer mechanism which makes use of soft-linking.

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

AbstractFileDeletions - Class in ome.services.delete.files

Base class for managing the removal of files from disk.

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

AbstractFileExclusion - Class in ome.formats.importer.exclusions

Base FileExclusion implementation primarily providing a factory for FileExclusion implementations via AbstractFileExclusion.createExclusion(String).

AbstractFileExclusion() - Constructor for class ome.formats.importer.exclusions.AbstractFileExclusion

AbstractFileExclusion.Exclusion - Enum in ome.formats.importer.exclusions

Enum of well-known FileExclusion names.

AbstractFileSystemService - Class in ome.io.nio

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

AbstractFileTransfer - Class in ome.formats.importer.transfers

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.

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

AbstractThrottlingStrategy - Class in ome.services.throttling

Throttling implementation which uses the calling server Thread for execution.

AbstractThrottlingStrategy() - Constructor for class ome.services.throttling.AbstractThrottlingStrategy

accept(String, String) - Method in class ome.services.mail.MapAnnotationSubethaListener

Accepts all mails.

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

accept(File) - Method in class omero.gateway.util.TIFFFilter

Accepts or not the file with the declared file extensions.

accept(String) - Method in class omero.gateway.util.TIFFFilter

Accepts or not the file identified by its name.

acceptFilter(Filter) - Method in class ome.model.acquisition.Arc

acceptFilter(Filter) - Method in class ome.model.acquisition.Detector

acceptFilter(Filter) - Method in class ome.model.acquisition.DetectorSettings

acceptFilter(Filter) - Method in class ome.model.acquisition.Dichroic

acceptFilter(Filter) - Method in class ome.model.acquisition.Filament

acceptFilter(Filter) - Method in class ome.model.acquisition.Filter

acceptFilter(Filter) - Method in class ome.model.acquisition.FilterSet

acceptFilter(Filter) - Method in class ome.model.acquisition.FilterSetEmissionFilterLink

acceptFilter(Filter) - Method in class ome.model.acquisition.FilterSetExcitationFilterLink

acceptFilter(Filter) - Method in class ome.model.acquisition.GenericExcitationSource

acceptFilter(Filter) - Method in class ome.model.acquisition.ImagingEnvironment

acceptFilter(Filter) - Method in class ome.model.acquisition.Instrument

acceptFilter(Filter) - Method in class ome.model.acquisition.Laser

acceptFilter(Filter) - Method in class ome.model.acquisition.LightEmittingDiode

acceptFilter(Filter) - Method in class ome.model.acquisition.LightPath

acceptFilter(Filter) - Method in class ome.model.acquisition.LightPathEmissionFilterLink

acceptFilter(Filter) - Method in class ome.model.acquisition.LightPathExcitationFilterLink

acceptFilter(Filter) - Method in class ome.model.acquisition.LightSettings

acceptFilter(Filter) - Method in class ome.model.acquisition.LightSource

acceptFilter(Filter) - Method in class ome.model.acquisition.Microscope

acceptFilter(Filter) - Method in class ome.model.acquisition.Objective

acceptFilter(Filter) - Method in class ome.model.acquisition.ObjectiveSettings

acceptFilter(Filter) - Method in class ome.model.acquisition.OTF

acceptFilter(Filter) - Method in class ome.model.acquisition.StageLabel

acceptFilter(Filter) - Method in class ome.model.acquisition.TransmittanceRange

acceptFilter(Filter) - Method in class ome.model.annotations.Annotation

acceptFilter(Filter) - Method in class ome.model.annotations.AnnotationAnnotationLink

acceptFilter(Filter) - Method in class ome.model.annotations.BasicAnnotation

acceptFilter(Filter) - Method in class ome.model.annotations.BooleanAnnotation

acceptFilter(Filter) - Method in class ome.model.annotations.ChannelAnnotationLink

acceptFilter(Filter) - Method in class ome.model.annotations.CommentAnnotation

acceptFilter(Filter) - Method in class ome.model.annotations.DatasetAnnotationLink

acceptFilter(Filter) - Method in class ome.model.annotations.DetectorAnnotationLink

acceptFilter(Filter) - Method in class ome.model.annotations.DichroicAnnotationLink

acceptFilter(Filter) - Method in class ome.model.annotations.DoubleAnnotation

acceptFilter(Filter) - Method in class ome.model.annotations.ExperimenterAnnotationLink

acceptFilter(Filter) - Method in class ome.model.annotations.ExperimenterGroupAnnotationLink

acceptFilter(Filter) - Method in class ome.model.annotations.FileAnnotation

acceptFilter(Filter) - Method in class ome.model.annotations.FilesetAnnotationLink

acceptFilter(Filter) - Method in class ome.model.annotations.FilterAnnotationLink

acceptFilter(Filter) - Method in class ome.model.annotations.FolderAnnotationLink

acceptFilter(Filter) - Method in class ome.model.annotations.ImageAnnotationLink

acceptFilter(Filter) - Method in class ome.model.annotations.InstrumentAnnotationLink

acceptFilter(Filter) - Method in class ome.model.annotations.LightPathAnnotationLink

acceptFilter(Filter) - Method in class ome.model.annotations.LightSourceAnnotationLink

acceptFilter(Filter) - Method in class ome.model.annotations.ListAnnotation

acceptFilter(Filter) - Method in class ome.model.annotations.LongAnnotation

acceptFilter(Filter) - Method in class ome.model.annotations.MapAnnotation

acceptFilter(Filter) - Method in class ome.model.annotations.NamespaceAnnotationLink

acceptFilter(Filter) - Method in class ome.model.annotations.NodeAnnotationLink

acceptFilter(Filter) - Method in class ome.model.annotations.NumericAnnotation

acceptFilter(Filter) - Method in class ome.model.annotations.ObjectiveAnnotationLink

acceptFilter(Filter) - Method in class ome.model.annotations.OriginalFileAnnotationLink

acceptFilter(Filter) - Method in class ome.model.annotations.PlaneInfoAnnotationLink

acceptFilter(Filter) - Method in class ome.model.annotations.PlateAcquisitionAnnotationLink

acceptFilter(Filter) - Method in class ome.model.annotations.PlateAnnotationLink

acceptFilter(Filter) - Method in class ome.model.annotations.ProjectAnnotationLink

acceptFilter(Filter) - Method in class ome.model.annotations.ReagentAnnotationLink

acceptFilter(Filter) - Method in class ome.model.annotations.RoiAnnotationLink

acceptFilter(Filter) - Method in class ome.model.annotations.ScreenAnnotationLink

acceptFilter(Filter) - Method in class ome.model.annotations.SessionAnnotationLink

acceptFilter(Filter) - Method in class ome.model.annotations.ShapeAnnotationLink

acceptFilter(Filter) - Method in class ome.model.annotations.TagAnnotation

acceptFilter(Filter) - Method in class ome.model.annotations.TermAnnotation

acceptFilter(Filter) - Method in class ome.model.annotations.TextAnnotation

acceptFilter(Filter) - Method in class ome.model.annotations.TimestampAnnotation

acceptFilter(Filter) - Method in class ome.model.annotations.TypeAnnotation

acceptFilter(Filter) - Method in class ome.model.annotations.WellAnnotationLink

acceptFilter(Filter) - Method in class ome.model.annotations.XmlAnnotation

acceptFilter(Filter) - Method in class ome.model.containers.Dataset

acceptFilter(Filter) - Method in class ome.model.containers.DatasetImageLink

acceptFilter(Filter) - Method in class ome.model.containers.Folder

acceptFilter(Filter) - Method in class ome.model.containers.FolderImageLink

acceptFilter(Filter) - Method in class ome.model.containers.FolderRoiLink

acceptFilter(Filter) - Method in class ome.model.containers.Project

acceptFilter(Filter) - Method in class ome.model.containers.ProjectDatasetLink

acceptFilter(Filter) - Method in class ome.model.core.Channel

acceptFilter(Filter) - Method in class ome.model.core.Image

acceptFilter(Filter) - Method in class ome.model.core.LogicalChannel

acceptFilter(Filter) - Method in class ome.model.core.OriginalFile

acceptFilter(Filter) - Method in class ome.model.core.Pixels

acceptFilter(Filter) - Method in class ome.model.core.PixelsOriginalFileMap

acceptFilter(Filter) - Method in class ome.model.core.PlaneInfo

acceptFilter(Filter) - Method in class ome.model.display.ChannelBinding

acceptFilter(Filter) - Method in class ome.model.display.CodomainMapContext

acceptFilter(Filter) - Method in class ome.model.display.ContrastStretchingContext

acceptFilter(Filter) - Method in class ome.model.display.PlaneSlicingContext

acceptFilter(Filter) - Method in class ome.model.display.ProjectionDef

acceptFilter(Filter) - Method in class ome.model.display.QuantumDef

acceptFilter(Filter) - Method in class ome.model.display.RenderingDef

acceptFilter(Filter) - Method in class ome.model.display.ReverseIntensityContext

acceptFilter(Filter) - Method in class ome.model.display.Thumbnail

acceptFilter(Filter) - Method in class ome.model.enums.AcquisitionMode

acceptFilter(Filter) - Method in class ome.model.enums.AdminPrivilege

acceptFilter(Filter) - Method in class ome.model.enums.ArcType

acceptFilter(Filter) - Method in class ome.model.enums.Binning

acceptFilter(Filter) - Method in class ome.model.enums.ChecksumAlgorithm

acceptFilter(Filter) - Method in class ome.model.enums.ContrastMethod

acceptFilter(Filter) - Method in class ome.model.enums.Correction

acceptFilter(Filter) - Method in class ome.model.enums.DetectorType

acceptFilter(Filter) - Method in class ome.model.enums.DimensionOrder

acceptFilter(Filter) - Method in class ome.model.enums.EventType

acceptFilter(Filter) - Method in class ome.model.enums.ExperimentType

acceptFilter(Filter) - Method in class ome.model.enums.Family

acceptFilter(Filter) - Method in class ome.model.enums.FilamentType

acceptFilter(Filter) - Method in class ome.model.enums.FilterType

acceptFilter(Filter) - Method in class ome.model.enums.Format

acceptFilter(Filter) - Method in class ome.model.enums.Illumination

acceptFilter(Filter) - Method in class ome.model.enums.Immersion

acceptFilter(Filter) - Method in class ome.model.enums.LaserMedium

acceptFilter(Filter) - Method in class ome.model.enums.LaserType

acceptFilter(Filter) - Method in class ome.model.enums.Medium

acceptFilter(Filter) - Method in class ome.model.enums.MicrobeamManipulationType

acceptFilter(Filter) - Method in class ome.model.enums.MicroscopeType

acceptFilter(Filter) - Method in class ome.model.enums.PhotometricInterpretation

acceptFilter(Filter) - Method in class ome.model.enums.PixelsType

acceptFilter(Filter) - Method in class ome.model.enums.ProjectionAxis

acceptFilter(Filter) - Method in class ome.model.enums.ProjectionType

acceptFilter(Filter) - Method in class ome.model.enums.Pulse

acceptFilter(Filter) - Method in class ome.model.enums.RenderingModel

acceptFilter(Filter) - Method in class ome.model.experiment.Experiment

acceptFilter(Filter) - Method in class ome.model.experiment.MicrobeamManipulation

acceptFilter(Filter) - Method in class ome.model.fs.Fileset

acceptFilter(Filter) - Method in class ome.model.fs.FilesetEntry

acceptFilter(Filter) - Method in class ome.model.fs.FilesetJobLink

acceptFilter(Filter) - Method in class ome.model.internal.Details

acceptFilter(Filter) - Method in class ome.model.internal.Link

acceptFilter(Filter) - Method in class ome.model.jobs.ImportJob

acceptFilter(Filter) - Method in class ome.model.jobs.IndexingJob

acceptFilter(Filter) - Method in class ome.model.jobs.IntegrityCheckJob

acceptFilter(Filter) - Method in class ome.model.jobs.Job

acceptFilter(Filter) - Method in class ome.model.jobs.JobOriginalFileLink

acceptFilter(Filter) - Method in class ome.model.jobs.JobStatus

acceptFilter(Filter) - Method in class ome.model.jobs.MetadataImportJob

acceptFilter(Filter) - Method in class ome.model.jobs.ParseJob

acceptFilter(Filter) - Method in class ome.model.jobs.PixelDataJob

acceptFilter(Filter) - Method in class ome.model.jobs.ScriptJob

acceptFilter(Filter) - Method in class ome.model.jobs.ThumbnailGenerationJob

acceptFilter(Filter) - Method in class ome.model.jobs.UploadJob

acceptFilter(Filter) - Method in class ome.model.meta.DBPatch

acceptFilter(Filter) - Method in class ome.model.meta.Event

acceptFilter(Filter) - Method in class ome.model.meta.EventLog

acceptFilter(Filter) - Method in class ome.model.meta.Experimenter

acceptFilter(Filter) - Method in class ome.model.meta.ExperimenterGroup

acceptFilter(Filter) - Method in class ome.model.meta.ExternalInfo

acceptFilter(Filter) - Method in class ome.model.meta.GroupExperimenterMap

acceptFilter(Filter) - Method in class ome.model.meta.Namespace

acceptFilter(Filter) - Method in class ome.model.meta.Node

acceptFilter(Filter) - Method in class ome.model.meta.Session

acceptFilter(Filter) - Method in class ome.model.meta.Share

acceptFilter(Filter) - Method in class ome.model.meta.ShareMember

acceptFilter(Filter) - Method in class ome.model.roi.AffineTransform

acceptFilter(Filter) - Method in class ome.model.roi.Ellipse

acceptFilter(Filter) - Method in class ome.model.roi.Label

acceptFilter(Filter) - Method in class ome.model.roi.Line

acceptFilter(Filter) - Method in class ome.model.roi.Mask

acceptFilter(Filter) - Method in class ome.model.roi.Path

acceptFilter(Filter) - Method in class ome.model.roi.Point

acceptFilter(Filter) - Method in class ome.model.roi.Polygon

acceptFilter(Filter) - Method in class ome.model.roi.Polyline

acceptFilter(Filter) - Method in class ome.model.roi.Rectangle

acceptFilter(Filter) - Method in class ome.model.roi.Roi

acceptFilter(Filter) - Method in class ome.model.roi.Shape

acceptFilter(Filter) - Method in class ome.model.screen.Plate

acceptFilter(Filter) - Method in class ome.model.screen.PlateAcquisition

acceptFilter(Filter) - Method in class ome.model.screen.Reagent

acceptFilter(Filter) - Method in class ome.model.screen.Screen

acceptFilter(Filter) - Method in class ome.model.screen.ScreenPlateLink

acceptFilter(Filter) - Method in class ome.model.screen.Well

acceptFilter(Filter) - Method in class ome.model.screen.WellReagentLink

acceptFilter(Filter) - Method in class ome.model.screen.WellSample

acceptFilter(Filter) - Method in class ome.model.stats.StatsInfo

acceptFilter(Filter) - Method in class ome.model.units.ElectricPotential

acceptFilter(Filter) - Method in class ome.model.units.Frequency

acceptFilter(Filter) - Method in class ome.model.units.Length

acceptFilter(Filter) - Method in class ome.model.units.Power

acceptFilter(Filter) - Method in class ome.model.units.Pressure

acceptFilter(Filter) - Method in class ome.model.units.Temperature

acceptFilter(Filter) - Method in class ome.model.units.Time

acceptFilter(Filter) - Method in interface ome.util.Filterable

acceptFilter(Filter) - Method in class ome.util.PermDetails

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

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

acl - Variable in class ome.tools.hibernate.ProxyCleanupFilter

ACLCreateViolation - Exception in ome.conditions.acl

User does not have permissions to perform given action.

ACLCreateViolation(Class, Long, String) - Constructor for exception ome.conditions.acl.ACLCreateViolation

ACLDeleteViolation - Exception in ome.conditions.acl

User does not have permissions to perform given action.

ACLDeleteViolation(Class, Long, String) - Constructor for exception ome.conditions.acl.ACLDeleteViolation

ACLEventListener - Class in ome.security

responsible for intercepting all pre-INSERT, pre-UPDATE, pre-DELETE, and post-LOAD events to apply access control.

ACLEventListener(ACLVoter) - Constructor for class ome.security.ACLEventListener

main constructor. controls access to individual db rows..

ACLLoadViolation - Exception in ome.conditions.acl

User does not have permissions to perform given action.

ACLLoadViolation(Class, Long, String) - Constructor for exception ome.conditions.acl.ACLLoadViolation

ACLUpdateViolation - Exception in ome.conditions.acl

User does not have permissions to perform given action.

ACLUpdateViolation(Class, Long, String) - Constructor for exception ome.conditions.acl.ACLUpdateViolation

ACLViolation - Exception in ome.conditions.acl

User has attempted an action which is not permitted by the Permissions of a given instance.

ACLViolation(Class, Long, String) - Constructor for exception ome.conditions.acl.ACLViolation

aclVoter - Variable in class ome.logic.AdminImpl

ACLVoter - Interface in ome.security

helper security interface for all decisions on access control

aclVoter - Variable in class ome.services.blitz.impl.ScriptI

acquireContext() - Method in class ome.services.util.BeanHelper

Lazy loads the application context, which means that if we're not in the application server, then the OmeroContext.MANAGED_CONTEXT should never get loaded.

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

acquireLock(String) - Method in class omero.util.ServantHolder

Acquires the given lock or if necessary creates a new one.

acquireProcessor(Job, int, Current) - Method in class ome.services.blitz.impl.SharedResourcesI

acquireProcessor(Job, int, Current) - Method in interface omero.grid.ParamsHelper.Acquirer

acquirer() - Method in class ome.services.blitz.impl.ScriptI

acquisitionData - Variable in class ome.parameters.Options

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

Sets the acquisition data parameter to true.

acquisitionDate - Variable in class ome.model.core.Image

ACQUISITIONDATE - Static variable in class ome.model.core.Image

AcquisitionMode - Class in ome.model.enums

AcquisitionMode() - Constructor for class ome.model.enums.AcquisitionMode

AcquisitionMode(Long) - Constructor for class ome.model.enums.AcquisitionMode

AcquisitionMode(Long, boolean) - Constructor for class ome.model.enums.AcquisitionMode

Main constructor.

AcquisitionMode(String) - Constructor for class ome.model.enums.AcquisitionMode

AcquisitionMode.Details - Class in ome.model.enums

action - Variable in class ome.model.meta.EventLog

ACTION - Static variable in class ome.model.meta.EventLog

action - Variable in class ome.services.graphs.GraphPolicy.Details

the current plan for the object, may be mutated by GraphPolicy.review(Map, Details, Map, Set, boolean)

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

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

Action() - Constructor for class ome.tools.hibernate.EventMethodInterceptor.Action

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

Deprecated.

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

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

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

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

Does almost nothing.

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

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

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

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

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

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

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

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

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

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

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

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

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

active - Variable in class ome.model.display.ChannelBinding

ACTIVE - Static variable in class ome.model.display.ChannelBinding

active - Variable in class ome.model.display.ProjectionDef

ACTIVE - Static variable in class ome.model.display.ProjectionDef

active - Variable in class ome.model.meta.Share

ACTIVE - Static variable in class ome.model.meta.Share

activeQueries() - Method in interface ome.api.Search

Returns the number of active queries.

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

activeQueries_async(AMD_Search_activeQueries, Current) - Method in class ome.services.blitz.impl.SearchI

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

activeSession(String) - Method in class ome.util.actions.PostgresSqlAction

activeSession(String) - Method in interface ome.util.SqlAction

Returns whether the given string is the UUID of a session that is currently active.

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

Adapter - Class in ome.services.throttling

Simple adapter which takes a Executor.Work instance and executes it as a BlitzExecutor task.

Adapter(Object, Current, IceMapper, Executor, Principal, Executor.Work) - Constructor for class ome.services.throttling.Adapter

adapter - Variable in class omero.cmd.SessionI

ADD() - Constructor for class ome.formats.importer.ImportEvent.ADD

Add(Conversion...) - Static method in class ome.model.units.Conversion

Static helper for creating Conversion.Add instances.

Add(Conversion[]) - Constructor for class ome.model.units.Conversion.Add

add(QueryParameter) - Method in class ome.parameters.Parameters

add(String) - Method in class ome.parameters.Period

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

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

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

Deprecated.

Helper method which takes the parameters from the BridgeHelper.set(String, Object, Document, LuceneOptions) method (possibly modified) as well as the parsed String value which should be added to the index, and adds two fields.

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

Adds a map context to the chain.

add(String, RType) - Method in class omero.sys.ParametersI

add(Resources.Entry) - Method in class omero.util.Resources

addAction(SearchAction) - Method in class ome.services.SearchBean

addAlgorithm(String) - Method in class ome.parameters.Parameters

addAll(Parameters) - Method in class ome.parameters.Parameters

adds all the information from the passed in Parameters instance to this instance.

addAll(QueryParameter[]) - Method in class ome.parameters.Parameters

adds all the information from the passed in Parameters instance to this instance.

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

addAnnotationAnnotationLink(AnnotationAnnotationLink) - Method in class ome.model.annotations.Annotation

use instead of setAnnotationLinks .

addAnnotationAnnotationLink(AnnotationAnnotationLink, boolean) - Method in class ome.model.annotations.Annotation

Adds a ome.model.annotations.AnnotationAnnotationLink to annotationLinks, allowing for recursion -- whether or not addAnnotationAnnotationLink will be called on the addition if it is loaded

addAnnotationAnnotationLinkSet(Collection<AnnotationAnnotationLink>) - Method in class ome.model.annotations.Annotation

use like addAnnotationAnnotationLink.

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

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

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

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

addBoolean(String, Boolean) - Method in class ome.parameters.Parameters

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

addCallback(CmdCallbackPrx, Current) - Method in class omero.cmd.HandleI

addChannel(Channel) - Method in class ome.model.core.LogicalChannel

use instead of setChannels .

addChannel(Channel) - Method in class ome.model.core.Pixels

use instead of setChannels .

addChannelAnnotationLink(ChannelAnnotationLink) - Method in class ome.model.core.Channel

use instead of setAnnotationLinks .

addChannelAnnotationLink(ChannelAnnotationLink, boolean) - Method in class ome.model.core.Channel

Adds a ome.model.annotations.ChannelAnnotationLink to annotationLinks, allowing for recursion -- whether or not addChannelAnnotationLink will be called on the addition if it is loaded

addChannelAnnotationLinkSet(Collection<ChannelAnnotationLink>) - Method in class ome.model.core.Channel

use like addChannelAnnotationLink.

addChannelBinding(ChannelBinding) - Method in class ome.model.display.RenderingDef

use instead of setWaveRendering .

addChannelBindingSet(Collection<ChannelBinding>) - Method in class ome.model.display.RenderingDef

use like addChannelBinding.

addChannelSet(Collection<Channel>) - Method in class ome.model.core.LogicalChannel

use like addChannel.

addChannelSet(Collection<Channel>) - Method in class ome.model.core.Pixels

use like addChannel.

addChildFolders(Folder) - Method in class ome.model.containers.Folder

use instead of setChildFolders .

addChildFoldersSet(Collection<Folder>) - Method in class ome.model.containers.Folder

use like addFolder.

addCircle(String, double, double, double) - Method in class ome.services.blitz.measurements.MeasurementStore

addCircle(String, double, double, double) - Method in interface ome.services.blitz.measurements.OmeroMeasurementStore

addClass(Class) - Method in class ome.parameters.Parameters

addClass(String, Class) - Method in class ome.parameters.Parameters

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

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

addClientId(String) - Method in class omero.util.ServantHolder

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

Deprecated.

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

Deprecated.

addCodomainMap_async(AMD_RenderingEngine_addCodomainMap, CodomainMapContext, Current) - Method in class ome.services.blitz.impl.RenderingEngineI

addCodomainMapContext(CodomainMapContext) - Method in class ome.model.display.ChannelBinding

use instead of setSpatialDomainEnhancement .

addCodomainMapContextSet(Collection<CodomainMapContext>) - Method in class ome.model.display.ChannelBinding

use like addCodomainMapContext.

addCodomainMapToChannel(CodomainMapContext, int) - Method in class ome.services.RenderingBean

Implemented as specified by the RenderingEngine interface.

addCodomainMapToChannel(CodomainMapContext, int) - Method in interface omeis.providers.re.RenderingEngine

Adds the context to the mapping chain.

addCodomainMapToChannel_async(AMD_RenderingEngine_addCodomainMapToChannel, CodomainMapContext, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI

addComment(long, String) - Method in interface ome.api.IShare

Deprecated.

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

Deprecated.

Second helper method used when parsing files.

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

addDatasetAnnotationLink(DatasetAnnotationLink) - Method in class ome.model.containers.Dataset

use instead of setAnnotationLinks .

addDatasetAnnotationLink(DatasetAnnotationLink, boolean) - Method in class ome.model.containers.Dataset

Adds a ome.model.annotations.DatasetAnnotationLink to annotationLinks, allowing for recursion -- whether or not addDatasetAnnotationLink will be called on the addition if it is loaded

addDatasetAnnotationLinkSet(Collection<DatasetAnnotationLink>) - Method in class ome.model.containers.Dataset

use like addDatasetAnnotationLink.

addDatasetImageLink(DatasetImageLink) - Method in class ome.model.containers.Dataset

use instead of setImageLinks .

addDatasetImageLink(DatasetImageLink, boolean) - Method in class ome.model.containers.Dataset

Adds a ome.model.containers.DatasetImageLink to imageLinks, allowing for recursion -- whether or not addDatasetImageLink will be called on the addition if it is loaded

addDatasetImageLink(DatasetImageLink) - Method in class ome.model.core.Image

use instead of setDatasetLinks .

addDatasetImageLink(DatasetImageLink, boolean) - Method in class ome.model.core.Image

Adds a ome.model.containers.DatasetImageLink to datasetLinks, allowing for recursion -- whether or not addDatasetImageLink will be called on the addition if it is loaded

addDatasetImageLinkSet(Collection<DatasetImageLink>) - Method in class ome.model.containers.Dataset

use like addDatasetImageLink.

addDatasetImageLinkSet(Collection<DatasetImageLink>) - Method in class ome.model.core.Image

use like addDatasetImageLink.

addDetector(Detector) - Method in class ome.model.acquisition.Instrument

use instead of setDetector .

addDetectorAnnotationLink(DetectorAnnotationLink) - Method in class ome.model.acquisition.Detector

use instead of setAnnotationLinks .

addDetectorAnnotationLink(DetectorAnnotationLink, boolean) - Method in class ome.model.acquisition.Detector

Adds a ome.model.annotations.DetectorAnnotationLink to annotationLinks, allowing for recursion -- whether or not addDetectorAnnotationLink will be called on the addition if it is loaded

addDetectorAnnotationLinkSet(Collection<DetectorAnnotationLink>) - Method in class ome.model.acquisition.Detector

use like addDetectorAnnotationLink.

addDetectorSet(Collection<Detector>) - Method in class ome.model.acquisition.Instrument

use like addDetector.

addDichroic(Dichroic) - Method in class ome.model.acquisition.Instrument

use instead of setDichroic .

addDichroicAnnotationLink(DichroicAnnotationLink) - Method in class ome.model.acquisition.Dichroic

use instead of setAnnotationLinks .

addDichroicAnnotationLink(DichroicAnnotationLink, boolean) - Method in class ome.model.acquisition.Dichroic

Adds a ome.model.annotations.DichroicAnnotationLink to annotationLinks, allowing for recursion -- whether or not addDichroicAnnotationLink will be called on the addition if it is loaded

addDichroicAnnotationLinkSet(Collection<DichroicAnnotationLink>) - Method in class ome.model.acquisition.Dichroic

use like addDichroicAnnotationLink.

addDichroicSet(Collection<Dichroic>) - Method in class ome.model.acquisition.Instrument

use like addDichroic.

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

addElement(int, Object, Object) - Method in interface omero.gateway.cache.CacheService

Adds the specified element to the selected cache.

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

Add detailed error to error container array

addEvent(Event) - Method in class ome.model.meta.Session

use instead of setEvents .

addEventLog(EventLog) - Method in class ome.model.meta.Event

use instead of setLogs .

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

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

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

Only schedule a new backlog event if there is no currently registered event of that type.

addEventLogSet(Collection<EventLog>) - Method in class ome.model.meta.Event

use like addEventLog.

addEventSet(Collection<Event>) - Method in class ome.model.meta.Session

use like addEvent.

addExperimenterAnnotationLink(ExperimenterAnnotationLink) - Method in class ome.model.meta.Experimenter

use instead of setAnnotationLinks .

addExperimenterAnnotationLink(ExperimenterAnnotationLink, boolean) - Method in class ome.model.meta.Experimenter

Adds a ome.model.annotations.ExperimenterAnnotationLink to annotationLinks, allowing for recursion -- whether or not addExperimenterAnnotationLink will be called on the addition if it is loaded

addExperimenterAnnotationLinkSet(Collection<ExperimenterAnnotationLink>) - Method in class ome.model.meta.Experimenter

use like addExperimenterAnnotationLink.

addExperimenterGroupAnnotationLink(ExperimenterGroupAnnotationLink) - Method in class ome.model.meta.ExperimenterGroup

use instead of setAnnotationLinks .

addExperimenterGroupAnnotationLink(ExperimenterGroupAnnotationLink, boolean) - Method in class ome.model.meta.ExperimenterGroup

Adds a ome.model.annotations.ExperimenterGroupAnnotationLink to annotationLinks, allowing for recursion -- whether or not addExperimenterGroupAnnotationLink will be called on the addition if it is loaded

addExperimenterGroupAnnotationLinkSet(Collection<ExperimenterGroupAnnotationLink>) - Method in class ome.model.meta.ExperimenterGroup

use like addExperimenterGroupAnnotationLink.

addExtendedRestrictions(Set<String>) - Method in class ome.model.internal.Permissions

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

addFilesetAnnotationLink(FilesetAnnotationLink) - Method in class ome.model.fs.Fileset

use instead of setAnnotationLinks .

addFilesetAnnotationLink(FilesetAnnotationLink, boolean) - Method in class ome.model.fs.Fileset

Adds a ome.model.annotations.FilesetAnnotationLink to annotationLinks, allowing for recursion -- whether or not addFilesetAnnotationLink will be called on the addition if it is loaded

addFilesetAnnotationLinkSet(Collection<FilesetAnnotationLink>) - Method in class ome.model.fs.Fileset

use like addFilesetAnnotationLink.

addFilesetEntry(FilesetEntry) - Method in class ome.model.core.OriginalFile

use instead of setFilesetEntries .

addFilesetEntry(FilesetEntry) - Method in class ome.model.fs.Fileset

use instead of setUsedFiles .

addFilesetEntrySet(Collection<FilesetEntry>) - Method in class ome.model.core.OriginalFile

use like addFilesetEntry.

addFilesetEntrySet(Collection<FilesetEntry>) - Method in class ome.model.fs.Fileset

use like addFilesetEntry.

addFilesetJobLink(FilesetJobLink) - Method in class ome.model.fs.Fileset

use instead of setJobLinks .

addFilesetJobLink(FilesetJobLink, boolean) - Method in class ome.model.fs.Fileset

Adds a ome.model.fs.FilesetJobLink to jobLinks, allowing for recursion -- whether or not addFilesetJobLink will be called on the addition if it is loaded

addFilesetJobLinkSet(Collection<FilesetJobLink>) - Method in class ome.model.fs.Fileset

use like addFilesetJobLink.

addFilter(Filter) - Method in class ome.model.acquisition.Instrument

use instead of setFilter .

addFilterAnnotationLink(FilterAnnotationLink) - Method in class ome.model.acquisition.Filter

use instead of setAnnotationLinks .

addFilterAnnotationLink(FilterAnnotationLink, boolean) - Method in class ome.model.acquisition.Filter

Adds a ome.model.annotations.FilterAnnotationLink to annotationLinks, allowing for recursion -- whether or not addFilterAnnotationLink will be called on the addition if it is loaded

addFilterAnnotationLinkSet(Collection<FilterAnnotationLink>) - Method in class ome.model.acquisition.Filter

use like addFilterAnnotationLink.

addFiltered(String) - Method in class ome.model.internal.Details

consider the collection named by collectionName to be a "filtered" representation of the DB.

addFiltered(Collection<String>) - Method in class ome.model.internal.Details

consider all the collections named by the elements of collection to be a "filtered" representation of the DB.

addFilterSet(Collection<Filter>) - Method in class ome.model.acquisition.Instrument

use like addFilter.

addFilterSet(FilterSet) - Method in class ome.model.acquisition.Instrument

use instead of setFilterSet .

addFilterSetEmissionFilterLink(FilterSetEmissionFilterLink) - Method in class ome.model.acquisition.Filter

use instead of setEmissionFilterLink .

addFilterSetEmissionFilterLink(FilterSetEmissionFilterLink, boolean) - Method in class ome.model.acquisition.Filter

Adds a ome.model.acquisition.FilterSetEmissionFilterLink to emissionFilterLink, allowing for recursion -- whether or not addFilterSetEmissionFilterLink will be called on the addition if it is loaded

addFilterSetEmissionFilterLink(FilterSetEmissionFilterLink) - Method in class ome.model.acquisition.FilterSet

use instead of setEmissionFilterLink .

addFilterSetEmissionFilterLink(FilterSetEmissionFilterLink, boolean) - Method in class ome.model.acquisition.FilterSet

Adds a ome.model.acquisition.FilterSetEmissionFilterLink to emissionFilterLink, allowing for recursion -- whether or not addFilterSetEmissionFilterLink will be called on the addition if it is loaded

addFilterSetEmissionFilterLinkSet(Collection<FilterSetEmissionFilterLink>) - Method in class ome.model.acquisition.Filter

use like addFilterSetEmissionFilterLink.

addFilterSetEmissionFilterLinkSet(Collection<FilterSetEmissionFilterLink>) - Method in class ome.model.acquisition.FilterSet

use like addFilterSetEmissionFilterLink.

addFilterSetExcitationFilterLink(FilterSetExcitationFilterLink) - Method in class ome.model.acquisition.Filter

use instead of setExcitationFilterLink .

addFilterSetExcitationFilterLink(FilterSetExcitationFilterLink, boolean) - Method in class ome.model.acquisition.Filter

Adds a ome.model.acquisition.FilterSetExcitationFilterLink to excitationFilterLink, allowing for recursion -- whether or not addFilterSetExcitationFilterLink will be called on the addition if it is loaded

addFilterSetExcitationFilterLink(FilterSetExcitationFilterLink) - Method in class ome.model.acquisition.FilterSet

use instead of setExcitationFilterLink .

addFilterSetExcitationFilterLink(FilterSetExcitationFilterLink, boolean) - Method in class ome.model.acquisition.FilterSet

Adds a ome.model.acquisition.FilterSetExcitationFilterLink to excitationFilterLink, allowing for recursion -- whether or not addFilterSetExcitationFilterLink will be called on the addition if it is loaded

addFilterSetExcitationFilterLinkSet(Collection<FilterSetExcitationFilterLink>) - Method in class ome.model.acquisition.Filter

use like addFilterSetExcitationFilterLink.

addFilterSetExcitationFilterLinkSet(Collection<FilterSetExcitationFilterLink>) - Method in class ome.model.acquisition.FilterSet

use like addFilterSetExcitationFilterLink.

addFilterSetSet(Collection<FilterSet>) - Method in class ome.model.acquisition.Instrument

use like addFilterSet.

addFolderAnnotationLink(FolderAnnotationLink) - Method in class ome.model.containers.Folder

use instead of setAnnotationLinks .

addFolderAnnotationLink(FolderAnnotationLink, boolean) - Method in class ome.model.containers.Folder

Adds a ome.model.annotations.FolderAnnotationLink to annotationLinks, allowing for recursion -- whether or not addFolderAnnotationLink will be called on the addition if it is loaded

addFolderAnnotationLinkSet(Collection<FolderAnnotationLink>) - Method in class ome.model.containers.Folder

use like addFolderAnnotationLink.

addFolderImageLink(FolderImageLink) - Method in class ome.model.containers.Folder

use instead of setImageLinks .

addFolderImageLink(FolderImageLink, boolean) - Method in class ome.model.containers.Folder

Adds a ome.model.containers.FolderImageLink to imageLinks, allowing for recursion -- whether or not addFolderImageLink will be called on the addition if it is loaded

addFolderImageLink(FolderImageLink) - Method in class ome.model.core.Image

use instead of setFolderLinks .

addFolderImageLink(FolderImageLink, boolean) - Method in class ome.model.core.Image

Adds a ome.model.containers.FolderImageLink to folderLinks, allowing for recursion -- whether or not addFolderImageLink will be called on the addition if it is loaded

addFolderImageLinkSet(Collection<FolderImageLink>) - Method in class ome.model.containers.Folder

use like addFolderImageLink.

addFolderImageLinkSet(Collection<FolderImageLink>) - Method in class ome.model.core.Image

use like addFolderImageLink.

addFolderRoiLink(FolderRoiLink) - Method in class ome.model.containers.Folder

use instead of setRoiLinks .

addFolderRoiLink(FolderRoiLink, boolean) - Method in class ome.model.containers.Folder

Adds a ome.model.containers.FolderRoiLink to roiLinks, allowing for recursion -- whether or not addFolderRoiLink will be called on the addition if it is loaded

addFolderRoiLink(FolderRoiLink) - Method in class ome.model.roi.Roi

use instead of setFolderLinks .

addFolderRoiLink(FolderRoiLink, boolean) - Method in class ome.model.roi.Roi

Adds a ome.model.containers.FolderRoiLink to folderLinks, allowing for recursion -- whether or not addFolderRoiLink will be called on the addition if it is loaded

addFolderRoiLinkSet(Collection<FolderRoiLink>) - Method in class ome.model.containers.Folder

use like addFolderRoiLink.

addFolderRoiLinkSet(Collection<FolderRoiLink>) - Method in class ome.model.roi.Roi

use like addFolderRoiLink.

addGroupExperimenterMap(GroupExperimenterMap) - Method in class ome.model.meta.Experimenter

use instead of setGroupExperimenterMap .

addGroupExperimenterMap(GroupExperimenterMap, boolean) - Method in class ome.model.meta.Experimenter

Adds a ome.model.meta.GroupExperimenterMap to groupExperimenterMap, allowing for recursion -- whether or not addGroupExperimenterMap will be called on the addition if it is loaded

addGroupExperimenterMap(GroupExperimenterMap) - Method in class ome.model.meta.ExperimenterGroup

use instead of setGroupExperimenterMap .

addGroupExperimenterMap(GroupExperimenterMap, boolean) - Method in class ome.model.meta.ExperimenterGroup

Adds a ome.model.meta.GroupExperimenterMap to groupExperimenterMap, allowing for recursion -- whether or not addGroupExperimenterMap will be called on the addition if it is loaded

addGroupExperimenterMapSet(Collection<GroupExperimenterMap>) - Method in class ome.model.meta.Experimenter

use like addGroupExperimenterMap.

addGroupExperimenterMapSet(Collection<GroupExperimenterMap>) - Method in class ome.model.meta.ExperimenterGroup

use like addGroupExperimenterMap.

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

adds the given users to the owner list for this group.

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

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

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

adds a user to the given groups.

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

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

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

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

addGuest(long, String) - Method in interface ome.api.IShare

Deprecated.

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

Deprecated.

Adds guest email addresses to the share.

addGuests(long, String...) - Method in class ome.services.sharing.ShareBean

addGuests_async(AMD_IShare_addGuests, long, List<String>, Current) - Method in class ome.services.blitz.impl.ShareI

addId(Long) - Method in class ome.parameters.Parameters

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

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

addIds(Collection) - Method in class ome.parameters.Parameters

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

addImage(Image) - Method in class ome.model.fs.Fileset

use instead of setImages .

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

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

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

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

addImageAnnotationLink(ImageAnnotationLink) - Method in class ome.model.core.Image

use instead of setAnnotationLinks .

addImageAnnotationLink(ImageAnnotationLink, boolean) - Method in class ome.model.core.Image

Adds a ome.model.annotations.ImageAnnotationLink to annotationLinks, allowing for recursion -- whether or not addImageAnnotationLink will be called on the addition if it is loaded

addImageAnnotationLinkSet(Collection<ImageAnnotationLink>) - Method in class ome.model.core.Image

use like addImageAnnotationLink.

addImageSet(Collection<Image>) - Method in class ome.model.fs.Fileset

use like addImage.

addImagesToDataset(SecurityContext, Collection<ImageData>, DatasetData) - Method in class omero.gateway.facility.DataManagerFacility

Adds the ImageDatas to the given DatasetData

addImageToDataset(SecurityContext, ImageData, DatasetData) - Method in class omero.gateway.facility.DataManagerFacility

Adds the ImageData to the given DatasetData

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

Switch between the adding and the removing states.

addInstrumentAnnotationLink(InstrumentAnnotationLink) - Method in class ome.model.acquisition.Instrument

use instead of setAnnotationLinks .

addInstrumentAnnotationLink(InstrumentAnnotationLink, boolean) - Method in class ome.model.acquisition.Instrument

Adds a ome.model.annotations.InstrumentAnnotationLink to annotationLinks, allowing for recursion -- whether or not addInstrumentAnnotationLink will be called on the addition if it is loaded

addInstrumentAnnotationLinkSet(Collection<InstrumentAnnotationLink>) - Method in class ome.model.acquisition.Instrument

use like addInstrumentAnnotationLink.

addInteger(String, Integer) - Method in class ome.parameters.Parameters

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

addJobOriginalFileLink(JobOriginalFileLink) - Method in class ome.model.jobs.Job

use instead of setOriginalFileLinks .

addJobOriginalFileLink(JobOriginalFileLink, boolean) - Method in class ome.model.jobs.Job

Adds a ome.model.jobs.JobOriginalFileLink to originalFileLinks, allowing for recursion -- whether or not addJobOriginalFileLink will be called on the addition if it is loaded

addJobOriginalFileLinkSet(Collection<JobOriginalFileLink>) - Method in class ome.model.jobs.Job

use like addJobOriginalFileLink.

addLightPathAnnotationLink(LightPathAnnotationLink) - Method in class ome.model.acquisition.LightPath

use instead of setAnnotationLinks .

addLightPathAnnotationLink(LightPathAnnotationLink, boolean) - Method in class ome.model.acquisition.LightPath

Adds a ome.model.annotations.LightPathAnnotationLink to annotationLinks, allowing for recursion -- whether or not addLightPathAnnotationLink will be called on the addition if it is loaded

addLightPathAnnotationLinkSet(Collection<LightPathAnnotationLink>) - Method in class ome.model.acquisition.LightPath

use like addLightPathAnnotationLink.

addLightPathEmissionFilterLink(LightPathEmissionFilterLink) - Method in class ome.model.acquisition.LightPath

use instead of setEmissionFilterLink .

addLightPathEmissionFilterLink(LightPathEmissionFilterLink, boolean) - Method in class ome.model.acquisition.LightPath

Adds a ome.model.acquisition.LightPathEmissionFilterLink to emissionFilterLink, allowing for recursion -- whether or not addLightPathEmissionFilterLink will be called on the addition if it is loaded

addLightPathEmissionFilterLinkSet(Collection<LightPathEmissionFilterLink>) - Method in class ome.model.acquisition.LightPath

use like addLightPathEmissionFilterLink.

addLightPathExcitationFilterLink(LightPathExcitationFilterLink) - Method in class ome.model.acquisition.LightPath

use instead of setExcitationFilterLink .

addLightPathExcitationFilterLink(LightPathExcitationFilterLink, boolean) - Method in class ome.model.acquisition.LightPath

Adds a ome.model.acquisition.LightPathExcitationFilterLink to excitationFilterLink, allowing for recursion -- whether or not addLightPathExcitationFilterLink will be called on the addition if it is loaded

addLightPathExcitationFilterLinkSet(Collection<LightPathExcitationFilterLink>) - Method in class ome.model.acquisition.LightPath

use like addLightPathExcitationFilterLink.

addLightSettings(LightSettings) - Method in class ome.model.experiment.MicrobeamManipulation

use instead of setLightSourceSettings .

addLightSettingsSet(Collection<LightSettings>) - Method in class ome.model.experiment.MicrobeamManipulation

use like addLightSettings.

addLightSource(LightSource) - Method in class ome.model.acquisition.Instrument

use instead of setLightSource .

addLightSourceAnnotationLink(LightSourceAnnotationLink) - Method in class ome.model.acquisition.LightSource

use instead of setAnnotationLinks .

addLightSourceAnnotationLink(LightSourceAnnotationLink, boolean) - Method in class ome.model.acquisition.LightSource

Adds a ome.model.annotations.LightSourceAnnotationLink to annotationLinks, allowing for recursion -- whether or not addLightSourceAnnotationLink will be called on the addition if it is loaded

addLightSourceAnnotationLinkSet(Collection<LightSourceAnnotationLink>) - Method in class ome.model.acquisition.LightSource

use like addLightSourceAnnotationLink.

addLightSourceSet(Collection<LightSource>) - Method in class ome.model.acquisition.Instrument

use like addLightSource.

addList(String, List) - Method in class ome.parameters.Parameters

addLocalFile(File, long) - Method in class ome.services.delete.files.AbstractFileDeletions

Called during the creation of instances if a particular file should be handled by AbstractFileDeletions.deleteLocal().

addLog(String, Class, Long) - Method in class ome.security.basic.BasicSecuritySystem

addLog(String, Class, Long) - Method in class ome.security.basic.CurrentDetails

addLong(String, Long) - Method in class ome.parameters.Parameters

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

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

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

addMap(String, Map) - Method in class ome.parameters.Parameters

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

Adds the Masks in the maskSet to the component.

addMessageWithinDbPatchEnd(String, int, String) - Method in interface ome.util.SqlAction

Add a unique message to the DB patch table within the current patch.

addMessageWithinDbPatchEnd(String, int, String) - Method in class ome.util.SqlAction.Impl

addMessageWithinDbPatchStart(String, int, String) - Method in interface ome.util.SqlAction

Add a unique message to the DB patch table within the current patch.

addMessageWithinDbPatchStart(String, int, String) - Method in class ome.util.SqlAction.Impl

addMicrobeamManipulation(MicrobeamManipulation) - Method in class ome.model.experiment.Experiment

use instead of setMicrobeamManipulation .

addMicrobeamManipulationSet(Collection<MicrobeamManipulation>) - Method in class ome.model.experiment.Experiment

use like addMicrobeamManipulation.

addMimetypes(Collection<String>, Map<String, Object>) - Method in class ome.util.SqlAction.Impl

Returns the "and_mimetype" clause which must be appended to a given query.

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

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

addNamespaceAnnotationLink(NamespaceAnnotationLink) - Method in class ome.model.meta.Namespace

use instead of setAnnotationLinks .

addNamespaceAnnotationLink(NamespaceAnnotationLink, boolean) - Method in class ome.model.meta.Namespace

Adds a ome.model.annotations.NamespaceAnnotationLink to annotationLinks, allowing for recursion -- whether or not addNamespaceAnnotationLink will be called on the addition if it is loaded

addNamespaceAnnotationLinkSet(Collection<NamespaceAnnotationLink>) - Method in class ome.model.meta.Namespace

use like addNamespaceAnnotationLink.

addNodeAnnotationLink(NodeAnnotationLink) - Method in class ome.model.meta.Node

use instead of setAnnotationLinks .

addNodeAnnotationLink(NodeAnnotationLink, boolean) - Method in class ome.model.meta.Node

Adds a ome.model.annotations.NodeAnnotationLink to annotationLinks, allowing for recursion -- whether or not addNodeAnnotationLink will be called on the addition if it is loaded

addNodeAnnotationLinkSet(Collection<NodeAnnotationLink>) - Method in class ome.model.meta.Node

use like addNodeAnnotationLink.

addObject(long, T) - Method in interface ome.api.IShare

Deprecated.

Adds new item to share.

addObject(ObjectPrx) - Method in interface ome.services.blitz.fire.Registry

addObject(ObjectPrx) - Method in class ome.services.blitz.fire.Registry.Impl

addObject(String, IObject) - Method in class ome.services.blitz.measurements.MeasurementStore

addObject(String, IObject) - Method in interface ome.services.blitz.measurements.OmeroMeasurementStore

addObject(long, T) - Method in class ome.services.sharing.ShareBean

addObject_async(AMD_IShare_addObject, long, IObject, Current) - Method in class ome.services.blitz.impl.ShareI

addObjective(Objective) - Method in class ome.model.acquisition.Instrument

use instead of setObjective .

addObjectiveAnnotationLink(ObjectiveAnnotationLink) - Method in class ome.model.acquisition.Objective

use instead of setAnnotationLinks .

addObjectiveAnnotationLink(ObjectiveAnnotationLink, boolean) - Method in class ome.model.acquisition.Objective

Adds a ome.model.annotations.ObjectiveAnnotationLink to annotationLinks, allowing for recursion -- whether or not addObjectiveAnnotationLink will be called on the addition if it is loaded

addObjectiveAnnotationLinkSet(Collection<ObjectiveAnnotationLink>) - Method in class ome.model.acquisition.Objective

use like addObjectiveAnnotationLink.

addObjectiveSet(Collection<Objective>) - Method in class ome.model.acquisition.Instrument

use like addObjective.

addObjects(long, T...) - Method in interface ome.api.IShare

Deprecated.

Adds new items to share.

addObjects(Map<String, IObject>) - Method in class ome.services.blitz.measurements.MeasurementStore

addObjects(Map<String, IObject>) - Method in interface ome.services.blitz.measurements.OmeroMeasurementStore

addObjects(long, T...) - Method in class ome.services.sharing.ShareBean

addObjects_async(AMD_IShare_addObjects, long, List<IObject>, Current) - Method in class ome.services.blitz.impl.ShareI

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

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

Add observer for notification

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

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

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

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

A path from the target entity which will be added to the current stack of order statements applied to the query.

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

addOrderByAsc_async(AMD_Search_addOrderByAsc, String, Current) - Method in class ome.services.blitz.impl.SearchI

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

A path from the target entity which will be added to the current stack of order statements applied to the query.

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

addOrderByDesc_async(AMD_Search_addOrderByDesc, String, Current) - Method in class ome.services.blitz.impl.SearchI

addOriginalFileAnnotationLink(OriginalFileAnnotationLink) - Method in class ome.model.core.OriginalFile

use instead of setAnnotationLinks .

addOriginalFileAnnotationLink(OriginalFileAnnotationLink, boolean) - Method in class ome.model.core.OriginalFile

Adds a ome.model.annotations.OriginalFileAnnotationLink to annotationLinks, allowing for recursion -- whether or not addOriginalFileAnnotationLink will be called on the addition if it is loaded

addOriginalFileAnnotationLinkSet(Collection<OriginalFileAnnotationLink>) - Method in class ome.model.core.OriginalFile

use like addOriginalFileAnnotationLink.

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

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

addOTF(OTF) - Method in class ome.model.acquisition.Instrument

use instead of setOtf .

addOTFSet(Collection<OTF>) - Method in class ome.model.acquisition.Instrument

use like addOTF.

addParameters(Parameters) - Method in class ome.services.SearchBean

addPixels(Pixels) - Method in class ome.model.core.Image

use instead of setPixels .

addPixelsOriginalFileMap(PixelsOriginalFileMap) - Method in class ome.model.core.OriginalFile

use instead of setPixelsFileMaps .

addPixelsOriginalFileMap(PixelsOriginalFileMap, boolean) - Method in class ome.model.core.OriginalFile

Adds a ome.model.core.PixelsOriginalFileMap to pixelsFileMaps, allowing for recursion -- whether or not addPixelsOriginalFileMap will be called on the addition if it is loaded

addPixelsOriginalFileMap(PixelsOriginalFileMap) - Method in class ome.model.core.Pixels

use instead of setPixelsFileMaps .

addPixelsOriginalFileMap(PixelsOriginalFileMap, boolean) - Method in class ome.model.core.Pixels

Adds a ome.model.core.PixelsOriginalFileMap to pixelsFileMaps, allowing for recursion -- whether or not addPixelsOriginalFileMap will be called on the addition if it is loaded

addPixelsOriginalFileMapSet(Collection<PixelsOriginalFileMap>) - Method in class ome.model.core.OriginalFile

use like addPixelsOriginalFileMap.

addPixelsOriginalFileMapSet(Collection<PixelsOriginalFileMap>) - Method in class ome.model.core.Pixels

use like addPixelsOriginalFileMap.

addPixelsSet(Collection<Pixels>) - Method in class ome.model.core.Image

use like addPixels.

addPlaneInfo(PlaneInfo) - Method in class ome.model.core.Pixels

use instead of setPlaneInfo .

addPlaneInfoAnnotationLink(PlaneInfoAnnotationLink) - Method in class ome.model.core.PlaneInfo

use instead of setAnnotationLinks .

addPlaneInfoAnnotationLink(PlaneInfoAnnotationLink, boolean) - Method in class ome.model.core.PlaneInfo

Adds a ome.model.annotations.PlaneInfoAnnotationLink to annotationLinks, allowing for recursion -- whether or not addPlaneInfoAnnotationLink will be called on the addition if it is loaded

addPlaneInfoAnnotationLinkSet(Collection<PlaneInfoAnnotationLink>) - Method in class ome.model.core.PlaneInfo

use like addPlaneInfoAnnotationLink.

addPlaneInfoSet(Collection<PlaneInfo>) - Method in class ome.model.core.Pixels

use like addPlaneInfo.

addPlateAcquisition(PlateAcquisition) - Method in class ome.model.screen.Plate

use instead of setPlateAcquisitions .

addPlateAcquisitionAnnotationLink(PlateAcquisitionAnnotationLink) - Method in class ome.model.screen.PlateAcquisition

use instead of setAnnotationLinks .

addPlateAcquisitionAnnotationLink(PlateAcquisitionAnnotationLink, boolean) - Method in class ome.model.screen.PlateAcquisition

Adds a ome.model.annotations.PlateAcquisitionAnnotationLink to annotationLinks, allowing for recursion -- whether or not addPlateAcquisitionAnnotationLink will be called on the addition if it is loaded

addPlateAcquisitionAnnotationLinkSet(Collection<PlateAcquisitionAnnotationLink>) - Method in class ome.model.screen.PlateAcquisition

use like addPlateAcquisitionAnnotationLink.

addPlateAcquisitionSet(Collection<PlateAcquisition>) - Method in class ome.model.screen.Plate

use like addPlateAcquisition.

addPlateAnnotationLink(PlateAnnotationLink) - Method in class ome.model.screen.Plate

use instead of setAnnotationLinks .

addPlateAnnotationLink(PlateAnnotationLink, boolean) - Method in class ome.model.screen.Plate

Adds a ome.model.annotations.PlateAnnotationLink to annotationLinks, allowing for recursion -- whether or not addPlateAnnotationLink will be called on the addition if it is loaded

addPlateAnnotationLinkSet(Collection<PlateAnnotationLink>) - Method in class ome.model.screen.Plate

use like addPlateAnnotationLink.

addProcess(ProcessContainer.Process) - Method in class ome.services.blitz.repo.ProcessContainer

Called once the ManagedImportProcessI service is created.

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

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

addProjectAnnotationLink(ProjectAnnotationLink) - Method in class ome.model.containers.Project

use instead of setAnnotationLinks .

addProjectAnnotationLink(ProjectAnnotationLink, boolean) - Method in class ome.model.containers.Project

Adds a ome.model.annotations.ProjectAnnotationLink to annotationLinks, allowing for recursion -- whether or not addProjectAnnotationLink will be called on the addition if it is loaded

addProjectAnnotationLinkSet(Collection<ProjectAnnotationLink>) - Method in class ome.model.containers.Project

use like addProjectAnnotationLink.

addProjectDatasetLink(ProjectDatasetLink) - Method in class ome.model.containers.Dataset

use instead of setProjectLinks .

addProjectDatasetLink(ProjectDatasetLink, boolean) - Method in class ome.model.containers.Dataset

Adds a ome.model.containers.ProjectDatasetLink to projectLinks, allowing for recursion -- whether or not addProjectDatasetLink will be called on the addition if it is loaded

addProjectDatasetLink(ProjectDatasetLink) - Method in class ome.model.containers.Project

use instead of setDatasetLinks .

addProjectDatasetLink(ProjectDatasetLink, boolean) - Method in class ome.model.containers.Project

Adds a ome.model.containers.ProjectDatasetLink to datasetLinks, allowing for recursion -- whether or not addProjectDatasetLink will be called on the addition if it is loaded

addProjectDatasetLinkSet(Collection<ProjectDatasetLink>) - Method in class ome.model.containers.Dataset

use like addProjectDatasetLink.

addProjectDatasetLinkSet(Collection<ProjectDatasetLink>) - Method in class ome.model.containers.Project

use like addProjectDatasetLink.

addProjectionDef(ProjectionDef) - Method in class ome.model.display.RenderingDef

use instead of setProjections .

addProjectionDefSet(Collection<ProjectionDef>) - Method in class ome.model.display.RenderingDef

use like addProjectionDef.

addPropertyChangeListener(PropertyChangeListener) - Method in class omero.gateway.facility.Facility

Adds a PropertyChangeListener

addPropertyChangeListener(PropertyChangeListener) - Method in class omero.gateway.Gateway

Adds a PropertyChangeListener

addReagent(Reagent) - Method in class ome.model.screen.Screen

use instead of setReagents .

addReagentAnnotationLink(ReagentAnnotationLink) - Method in class ome.model.screen.Reagent

use instead of setAnnotationLinks .

addReagentAnnotationLink(ReagentAnnotationLink, boolean) - Method in class ome.model.screen.Reagent

Adds a ome.model.annotations.ReagentAnnotationLink to annotationLinks, allowing for recursion -- whether or not addReagentAnnotationLink will be called on the addition if it is loaded

addReagentAnnotationLinkSet(Collection<ReagentAnnotationLink>) - Method in class ome.model.screen.Reagent

use like addReagentAnnotationLink.

addReagentSet(Collection<Reagent>) - Method in class ome.model.screen.Screen

use like addReagent.

addReference(LSID, LSID) - Method in interface ome.formats.model.IObjectContainerStore

Adds a reference to the reference cache.

addReference(LSID, LSID) - Method in class ome.formats.OMEROMetadataStoreClient

Adds a reference to the reference cache.

addRenderingDef(RenderingDef) - Method in class ome.model.core.Pixels

use instead of setSettings .

addRenderingDefSet(Collection<RenderingDef>) - Method in class ome.model.core.Pixels

use like addRenderingDef.

addReply(long, String, CommentAnnotation) - Method in interface ome.api.IShare

Deprecated.

Creates comment which replies to an existing comment.

addReply(long, String, CommentAnnotation) - Method in class ome.services.sharing.ShareBean

addReply_async(AMD_IShare_addReply, long, String, TextAnnotation, Current) - Method in class ome.services.blitz.impl.ShareI

addResult(List<IObject>) - Method in class ome.services.SearchBean

addRoi(Roi) - Method in class ome.model.core.Image

use instead of setRois .

addRoiAnnotationLink(RoiAnnotationLink) - Method in class ome.model.roi.Roi

use instead of setAnnotationLinks .

addRoiAnnotationLink(RoiAnnotationLink, boolean) - Method in class ome.model.roi.Roi

Adds a ome.model.annotations.RoiAnnotationLink to annotationLinks, allowing for recursion -- whether or not addRoiAnnotationLink will be called on the addition if it is loaded

addRoiAnnotationLinkSet(Collection<RoiAnnotationLink>) - Method in class ome.model.roi.Roi

use like addRoiAnnotationLink.

addRoiSet(Collection<Roi>) - Method in class ome.model.core.Image

use like addRoi.

addRoisToFolders(SecurityContext, long, Collection<ROIData>, Collection<FolderData>) - Method in class omero.gateway.facility.ROIFacility

Adds ROIs to Folders

addRoisToFolders(SecurityContext, long, Collection<ROIData>, Collection<FolderData>, boolean) - Method in class omero.gateway.facility.ROIFacility

Adds ROIs to Folders

addRows(Object[][]) - Method in class ome.services.blitz.measurements.MeasurementStore

addRows(Object[][]) - Method in interface ome.services.blitz.measurements.OmeroMeasurementStore

Adds an array of rows (Object[]) to the store.

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

addScreenAnnotationLink(ScreenAnnotationLink) - Method in class ome.model.screen.Screen

use instead of setAnnotationLinks .

addScreenAnnotationLink(ScreenAnnotationLink, boolean) - Method in class ome.model.screen.Screen

Adds a ome.model.annotations.ScreenAnnotationLink to annotationLinks, allowing for recursion -- whether or not addScreenAnnotationLink will be called on the addition if it is loaded

addScreenAnnotationLinkSet(Collection<ScreenAnnotationLink>) - Method in class ome.model.screen.Screen

use like addScreenAnnotationLink.

addScreenPlateLink(ScreenPlateLink) - Method in class ome.model.screen.Plate

use instead of setScreenLinks .

addScreenPlateLink(ScreenPlateLink, boolean) - Method in class ome.model.screen.Plate

Adds a ome.model.screen.ScreenPlateLink to screenLinks, allowing for recursion -- whether or not addScreenPlateLink will be called on the addition if it is loaded

addScreenPlateLink(ScreenPlateLink) - Method in class ome.model.screen.Screen

use instead of setPlateLinks .

addScreenPlateLink(ScreenPlateLink, boolean) - Method in class ome.model.screen.Screen

Adds a ome.model.screen.ScreenPlateLink to plateLinks, allowing for recursion -- whether or not addScreenPlateLink will be called on the addition if it is loaded

addScreenPlateLinkSet(Collection<ScreenPlateLink>) - Method in class ome.model.screen.Plate

use like addScreenPlateLink.

addScreenPlateLinkSet(Collection<ScreenPlateLink>) - Method in class ome.model.screen.Screen

use like addScreenPlateLink.

addSeen(Object) - Method in class ome.util.ContextFilter

addSession(Session) - Method in class ome.model.meta.Node

use instead of setSessions .

addSessionAnnotationLink(SessionAnnotationLink) - Method in class ome.model.meta.Session

use instead of setAnnotationLinks .

addSessionAnnotationLink(SessionAnnotationLink, boolean) - Method in class ome.model.meta.Session

Adds a ome.model.annotations.SessionAnnotationLink to annotationLinks, allowing for recursion -- whether or not addSessionAnnotationLink will be called on the addition if it is loaded

addSessionAnnotationLinkSet(Collection<SessionAnnotationLink>) - Method in class ome.model.meta.Session

use like addSessionAnnotationLink.

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

addSessionSet(Collection<Session>) - Method in class ome.model.meta.Node

use like addSession.

addSet(String, Set) - Method in class ome.parameters.Parameters

addShape(Shape) - Method in class ome.model.roi.Roi

use instead of setShapes .

addShapeAnnotationLink(ShapeAnnotationLink) - Method in class ome.model.roi.Shape

use instead of setAnnotationLinks .

addShapeAnnotationLink(ShapeAnnotationLink, boolean) - Method in class ome.model.roi.Shape

Adds a ome.model.annotations.ShapeAnnotationLink to annotationLinks, allowing for recursion -- whether or not addShapeAnnotationLink will be called on the addition if it is loaded

addShapeAnnotationLinkSet(Collection<ShapeAnnotationLink>) - Method in class ome.model.roi.Shape

use like addShapeAnnotationLink.

addShapeData(ShapeData) - Method in class omero.gateway.model.ROIData

Adds ShapeData object to ROIData.

addShapeSet(Collection<Shape>) - Method in class ome.model.roi.Roi

use like addShape.

addString(String, String) - Method in class ome.parameters.Parameters

addTable(SecurityContext, DataObject, String, TableData) - Method in class omero.gateway.facility.TablesFacility

Adds a new table with the provided data

addThumbnail(Thumbnail) - Method in class ome.model.core.Pixels

use instead of setThumbnails .

addThumbnailSet(Collection<Thumbnail>) - Method in class ome.model.core.Pixels

use like addThumbnail.

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

Deprecated.

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

Deprecated.

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

addViolation(ACLViolation) - Method in exception ome.conditions.acl.CollectedACLViolations

addWell(Well) - Method in class ome.model.screen.Plate

use instead of setWells .

addWellAnnotationLink(WellAnnotationLink) - Method in class ome.model.screen.Well

use instead of setAnnotationLinks .

addWellAnnotationLink(WellAnnotationLink, boolean) - Method in class ome.model.screen.Well

Adds a ome.model.annotations.WellAnnotationLink to annotationLinks, allowing for recursion -- whether or not addWellAnnotationLink will be called on the addition if it is loaded

addWellAnnotationLinkSet(Collection<WellAnnotationLink>) - Method in class ome.model.screen.Well

use like addWellAnnotationLink.

addWellReagentLink(WellReagentLink) - Method in class ome.model.screen.Reagent

use instead of setWellLinks .

addWellReagentLink(WellReagentLink, boolean) - Method in class ome.model.screen.Reagent

Adds a ome.model.screen.WellReagentLink to wellLinks, allowing for recursion -- whether or not addWellReagentLink will be called on the addition if it is loaded

addWellReagentLink(WellReagentLink) - Method in class ome.model.screen.Well

use instead of setReagentLinks .

addWellReagentLink(WellReagentLink, boolean) - Method in class ome.model.screen.Well

Adds a ome.model.screen.WellReagentLink to reagentLinks, allowing for recursion -- whether or not addWellReagentLink will be called on the addition if it is loaded

addWellReagentLinkSet(Collection<WellReagentLink>) - Method in class ome.model.screen.Reagent

use like addWellReagentLink.

addWellReagentLinkSet(Collection<WellReagentLink>) - Method in class ome.model.screen.Well

use like addWellReagentLink.

addWellSample(WellSample) - Method in class ome.model.core.Image

use instead of setWellSamples .

addWellSample(WellSample) - Method in class ome.model.screen.PlateAcquisition

use instead of setWellSample .

addWellSample(WellSample) - Method in class ome.model.screen.Well

use instead of setWellSamples .

addWellSampleSet(Collection<WellSample>) - Method in class ome.model.core.Image

use like addWellSample.

addWellSampleSet(Collection<WellSample>) - Method in class ome.model.screen.PlateAcquisition

use like addWellSample.

addWellSampleSet(Collection<WellSample>) - Method in class ome.model.screen.Well

use like addWellSample.

addWellSet(Collection<Well>) - Method in class ome.model.screen.Plate

use like addWell.

adjustGraphPolicy(Function<GraphPolicy, GraphPolicy>) - Method in class omero.cmd.graphs.Chgrp2I

adjustGraphPolicy(Function<GraphPolicy, GraphPolicy>) - Method in class omero.cmd.graphs.Chmod2I

adjustGraphPolicy(Function<GraphPolicy, GraphPolicy>) - Method in class omero.cmd.graphs.Chown2I

adjustGraphPolicy(Function<GraphPolicy, GraphPolicy>) - Method in class omero.cmd.graphs.Delete2I

adjustGraphPolicy(Function<GraphPolicy, GraphPolicy>) - Method in class omero.cmd.graphs.DuplicateI

adjustGraphPolicy(Function<GraphPolicy, GraphPolicy>) - Method in interface omero.cmd.graphs.WrappableRequest

Transform the currently applicable graph policy for this request by the given function.

Adler32ChecksumProviderImpl - Class in ome.util.checksum

An implementation of the ChecksumProvider interface using Adler32 as the message digest algorithm.

Adler32ChecksumProviderImpl() - Constructor for class ome.util.checksum.Adler32ChecksumProviderImpl

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

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

AdminAction - Interface in ome.security

action for passing to SecuritySystem.runAsAdmin(AdminAction).

AdminFacility - Class in omero.gateway.facility

Facility for handling admin issues, e.g. creating users, groups, etc.

adminFlush() - Method in class ome.services.sharing.ShareBean

AdminI - Class in ome.services.blitz.impl

Implementation of the IAdmin service.

AdminI(IAdmin, BlitzExecutor) - Constructor for class ome.services.blitz.impl.AdminI

AdminImpl - Class in ome.logic

Provides methods for administering user accounts, passwords, as well as methods which require special privileges.

AdminImpl(SqlAction, SessionFactory, MailSender, SimpleMailMessage, ACLVoter, PasswordProvider, RoleProvider, LdapImpl, PasswordUtil, ChmodStrategy, ChecksumProviderFactory) - Constructor for class ome.logic.AdminImpl

AdminPrivilege - Class in ome.model.enums

AdminPrivilege() - Constructor for class ome.model.enums.AdminPrivilege

AdminPrivilege(Long) - Constructor for class ome.model.enums.AdminPrivilege

AdminPrivilege(Long, boolean) - Constructor for class ome.model.enums.AdminPrivilege

Main constructor.

AdminPrivilege(String) - Constructor for class ome.model.enums.AdminPrivilege

AdminPrivilege.Details - Class in ome.model.enums

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.

AffineTransform - Class in ome.model.roi

These filter definitions are used by the security system to eliminate non-readable objects from queries.

AffineTransform() - Constructor for class ome.model.roi.AffineTransform

AffineTransform(Long) - Constructor for class ome.model.roi.AffineTransform

AffineTransform(Long, boolean) - Constructor for class ome.model.roi.AffineTransform

Main constructor.

AffineTransform(Double, Double, Double, Double, Double, Double) - Constructor for class ome.model.roi.AffineTransform

AffineTransform.Details - Class in ome.model.roi

afs - Variable in class ome.services.delete.Deletion.Builder

afs - Variable in class ome.services.delete.files.AbstractFileDeletions

afterFilter(String, Object) - Method in class ome.util.ContextFilter

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

afterPropertiesSet() - Method in class ome.system.metrics.DefaultMetrics

afterPropertiesSet() - Method in class ome.util.MapPut

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

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

afterTransfer(int, List<String>) - Method in class ome.formats.importer.transfers.CopyFileTransfer

No cleanup action is taken.

afterTransfer(int, List<String>) - Method in class ome.formats.importer.transfers.CopyMoveFileTransfer

Deletes all copied files if there were no errors.

afterTransfer(int, List<String>) - Method in interface ome.formats.importer.transfers.FileTransfer

Callback which must be invoked after a related set of files has been processed.

afterTransfer(int, List<String>) - Method in class ome.formats.importer.transfers.HardlinkFileTransfer

No cleanup action is taken.

afterTransfer(int, List<String>) - Method in class ome.formats.importer.transfers.MoveFileTransfer

Deletes all hard-linked files if there were no errors.

afterTransfer(int, List<String>) - Method in class ome.formats.importer.transfers.SymlinkFileTransfer

No cleanup is needed for soft-linking.

afterTransfer(int, List<String>) - Method in class ome.formats.importer.transfers.UploadFileTransfer

Since the RawFileStorePrx instances are cleaned up after each transfer, there's no need to cleanup per File.

afterTransfer(int, List<String>) - Method in class ome.formats.importer.transfers.UploadRmFileTransfer

Deletes all uploaded files if there were no errors.

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

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

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

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

airPressure - Variable in class ome.model.acquisition.ImagingEnvironment

AIRPRESSURE - Static variable in class ome.model.acquisition.ImagingEnvironment

ALGORITHM - Static variable in class ome.parameters.Parameters

named parameter "algorithm".

ALL_GROUPS_ID - Static variable in class omero.gateway.model.SearchParameters

The ID for searching across all groups

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

ALL_SCOPE - Static variable in class omero.gateway.model.SearchParameters

ALL_TYPES - Static variable in class omero.gateway.model.SearchParameters

AllEntitiesPseudoLogLoader<T extends IObject> - Class in ome.services.eventlogs

EventLogLoader which iterates through each object model type (in no particular order) and returns each object from lowest to highest id.

AllEntitiesPseudoLogLoader() - Constructor for class ome.services.eventlogs.AllEntitiesPseudoLogLoader

allEnumerations(Class<T>) - Method in interface ome.api.ITypes

allEnumerations(Class<T>) - Method in class ome.logic.TypesImpl

allEnumerations_async(AMD_ITypes_allEnumerations, String, Current) - Method in class ome.services.blitz.impl.TypesI

AllEventsLogLoader - Class in ome.services.eventlogs

AllEventsLogLoader() - Constructor for class ome.services.eventlogs.AllEventsLogLoader

allExps() - Method in class ome.parameters.Parameters

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

Removes the experimenter parameter from the map.

allgroups - Variable in class ome.security.SecurityFilterHolder

AllGroupsSecurityFilter - Class in ome.security.basic

overrides FilterDefinitionFactoryBean in order to construct our security filter in code and not in XML.

AllGroupsSecurityFilter(SqlAction) - Constructor for class ome.security.basic.AllGroupsSecurityFilter

Default constructor which calls all the necessary setters for this FactoryBean.

AllGroupsSecurityFilter(SqlAction, Roles) - Constructor for class ome.security.basic.AllGroupsSecurityFilter

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

Removes the group parameter from the map.

allObjects(Collection<Set<GraphPolicy.Details>>, GraphPolicy.Details, Collection<Set<GraphPolicy.Details>>) - Static method in class ome.services.graphs.GraphPolicy

Utility method to return all the objects for review as a single set of objects.

allow(ObjectPrx) - Method in class omero.cmd.SessionI

ALLOW_LEADING_WILDCARD - Static variable in interface ome.api.Search

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 - Variable in class ome.model.core.Channel

ALPHA - Static variable in class ome.model.core.Channel

alpha - Variable in class ome.model.display.ChannelBinding

ALPHA - Static variable in class ome.model.display.ChannelBinding

alpha - Variable in class ome.model.screen.Well

ALPHA - Static variable in class ome.model.screen.Well

ALPHA_INDEX - Static variable in class ome.formats.model.ColorsFactory

Index of the red component of a color.

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

Index of the red component of a color.

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

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

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

We can do alphaless rendering

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

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

AMD_submit() - Constructor for class ome.services.blitz.repo.PublicRepositoryI.AMD_submit

amplificationGain - Variable in class ome.model.acquisition.Detector

AMPLIFICATIONGAIN - Static variable in class ome.model.acquisition.Detector

analyzer - Variable in class ome.logic.QueryImpl

and() - Method in interface ome.api.Search

Applies the next by* method to the previous by* method, so that a call Search.hasNext(), Search.next(), or Search.results() sees only the intersection of the two calls.

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

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

Appends "and" plus your string unless this is the first where-spec in which case it is simply appended.

and_async(AMD_Search_and, Current) - Method in class ome.services.blitz.impl.SearchI

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

Calculates the angle between this vector and the specified argument, provided none of these vectors is the null vector.

annotatedBetween(AnnotationCriteria) - Method in class ome.services.search.SearchAction

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

annotatedBy(AnnotationCriteria) - Method in class ome.services.search.SearchAction

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

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

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

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

AnnotatedWith - Class in ome.services.search

Query for Search which uses an example Annotation instance as the basis for comparison.

AnnotatedWith(SearchValues, Annotation[], boolean, boolean) - Constructor for class ome.services.search.AnnotatedWith

ANNOTATERESTRICTION - Static variable in class ome.model.internal.Permissions

Annotation - Class in ome.model.annotations

These filter definitions are used by the security system to eliminate non-readable objects from queries.

Annotation() - Constructor for class ome.model.annotations.Annotation

Annotation(Long) - Constructor for class ome.model.annotations.Annotation

Annotation(Long, boolean) - Constructor for class ome.model.annotations.Annotation

Main constructor.

Annotation.Details - Class in ome.model.annotations

AnnotationAnnotationLink - Class in ome.model.annotations

These filter definitions are used by the security system to eliminate non-readable objects from queries.

AnnotationAnnotationLink() - Constructor for class ome.model.annotations.AnnotationAnnotationLink

AnnotationAnnotationLink(Long) - Constructor for class ome.model.annotations.AnnotationAnnotationLink

AnnotationAnnotationLink(Long, boolean) - Constructor for class ome.model.annotations.AnnotationAnnotationLink

Main constructor.

AnnotationAnnotationLink(IObject, IObject) - Constructor for class ome.model.annotations.AnnotationAnnotationLink

AnnotationAnnotationLink.Details - Class in ome.model.annotations

AnnotationData - Class in omero.gateway.model

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

AnnotationData(Class<? extends Annotation>) - Constructor for class omero.gateway.model.AnnotationData

Creates a new instance.

AnnotationData(A) - Constructor for class omero.gateway.model.AnnotationData

Creates a new instance.

annotationLinks - Variable in class ome.model.acquisition.Detector

ANNOTATIONLINKS - Static variable in class ome.model.acquisition.Detector

annotationLinks - Variable in class ome.model.acquisition.Dichroic

ANNOTATIONLINKS - Static variable in class ome.model.acquisition.Dichroic

annotationLinks - Variable in class ome.model.acquisition.Filter

ANNOTATIONLINKS - Static variable in class ome.model.acquisition.Filter

annotationLinks - Variable in class ome.model.acquisition.Instrument

ANNOTATIONLINKS - Static variable in class ome.model.acquisition.Instrument

annotationLinks - Variable in class ome.model.acquisition.LightPath

ANNOTATIONLINKS - Static variable in class ome.model.acquisition.LightPath

annotationLinks - Variable in class ome.model.acquisition.LightSource

ANNOTATIONLINKS - Static variable in class ome.model.acquisition.LightSource

annotationLinks - Variable in class ome.model.acquisition.Objective

ANNOTATIONLINKS - Static variable in class ome.model.acquisition.Objective

annotationLinks - Variable in class ome.model.annotations.Annotation

ANNOTATIONLINKS - Static variable in class ome.model.annotations.Annotation

annotationLinks - Variable in class ome.model.containers.Dataset

ANNOTATIONLINKS - Static variable in class ome.model.containers.Dataset

annotationLinks - Variable in class ome.model.containers.Folder

ANNOTATIONLINKS - Static variable in class ome.model.containers.Folder

annotationLinks - Variable in class ome.model.containers.Project

ANNOTATIONLINKS - Static variable in class ome.model.containers.Project

annotationLinks - Variable in class ome.model.core.Channel

ANNOTATIONLINKS - Static variable in class ome.model.core.Channel

annotationLinks - Variable in class ome.model.core.Image

ANNOTATIONLINKS - Static variable in class ome.model.core.Image

annotationLinks - Variable in class ome.model.core.OriginalFile

ANNOTATIONLINKS - Static variable in class ome.model.core.OriginalFile

annotationLinks - Variable in class ome.model.core.PlaneInfo

ANNOTATIONLINKS - Static variable in class ome.model.core.PlaneInfo

annotationLinks - Variable in class ome.model.fs.Fileset

ANNOTATIONLINKS - Static variable in class ome.model.fs.Fileset

annotationLinks - Variable in class ome.model.meta.Experimenter

ANNOTATIONLINKS - Static variable in class ome.model.meta.Experimenter

annotationLinks - Variable in class ome.model.meta.ExperimenterGroup

ANNOTATIONLINKS - Static variable in class ome.model.meta.ExperimenterGroup

annotationLinks - Variable in class ome.model.meta.Namespace

ANNOTATIONLINKS - Static variable in class ome.model.meta.Namespace

annotationLinks - Variable in class ome.model.meta.Node

ANNOTATIONLINKS - Static variable in class ome.model.meta.Node

annotationLinks - Variable in class ome.model.meta.Session

ANNOTATIONLINKS - Static variable in class ome.model.meta.Session

annotationLinks - Variable in class ome.model.roi.Roi

ANNOTATIONLINKS - Static variable in class ome.model.roi.Roi

annotationLinks - Variable in class ome.model.roi.Shape

ANNOTATIONLINKS - Static variable in class ome.model.roi.Shape

annotationLinks - Variable in class ome.model.screen.Plate

ANNOTATIONLINKS - Static variable in class ome.model.screen.Plate

annotationLinks - Variable in class ome.model.screen.PlateAcquisition

ANNOTATIONLINKS - Static variable in class ome.model.screen.PlateAcquisition

annotationLinks - Variable in class ome.model.screen.Reagent

ANNOTATIONLINKS - Static variable in class ome.model.screen.Reagent

annotationLinks - Variable in class ome.model.screen.Screen

ANNOTATIONLINKS - Static variable in class ome.model.screen.Screen

annotationLinks - Variable in class ome.model.screen.Well

ANNOTATIONLINKS - Static variable in class ome.model.screen.Well

ANNOTATIONLINKSCOUNTPEROWNER - Static variable in class ome.model.acquisition.Detector

ANNOTATIONLINKSCOUNTPEROWNER - Static variable in class ome.model.acquisition.Dichroic

ANNOTATIONLINKSCOUNTPEROWNER - Static variable in class ome.model.acquisition.Filter

ANNOTATIONLINKSCOUNTPEROWNER - Static variable in class ome.model.acquisition.Instrument

ANNOTATIONLINKSCOUNTPEROWNER - Static variable in class ome.model.acquisition.LightPath

ANNOTATIONLINKSCOUNTPEROWNER - Static variable in class ome.model.acquisition.LightSource

ANNOTATIONLINKSCOUNTPEROWNER - Static variable in class ome.model.acquisition.Objective

ANNOTATIONLINKSCOUNTPEROWNER - Static variable in class ome.model.annotations.Annotation

ANNOTATIONLINKSCOUNTPEROWNER - Static variable in class ome.model.containers.Dataset

ANNOTATIONLINKSCOUNTPEROWNER - Static variable in class ome.model.containers.Folder

ANNOTATIONLINKSCOUNTPEROWNER - Static variable in class ome.model.containers.Project

ANNOTATIONLINKSCOUNTPEROWNER - Static variable in class ome.model.core.Channel

ANNOTATIONLINKSCOUNTPEROWNER - Static variable in class ome.model.core.Image

ANNOTATIONLINKSCOUNTPEROWNER - Static variable in class ome.model.core.OriginalFile

ANNOTATIONLINKSCOUNTPEROWNER - Static variable in class ome.model.core.PlaneInfo

ANNOTATIONLINKSCOUNTPEROWNER - Static variable in class ome.model.fs.Fileset

ANNOTATIONLINKSCOUNTPEROWNER - Static variable in class ome.model.meta.Experimenter

ANNOTATIONLINKSCOUNTPEROWNER - Static variable in class ome.model.meta.ExperimenterGroup

ANNOTATIONLINKSCOUNTPEROWNER - Static variable in class ome.model.meta.Namespace

ANNOTATIONLINKSCOUNTPEROWNER - Static variable in class ome.model.meta.Node

ANNOTATIONLINKSCOUNTPEROWNER - Static variable in class ome.model.meta.Session

ANNOTATIONLINKSCOUNTPEROWNER - Static variable in class ome.model.roi.Roi

ANNOTATIONLINKSCOUNTPEROWNER - Static variable in class ome.model.roi.Shape

ANNOTATIONLINKSCOUNTPEROWNER - Static variable in class ome.model.screen.Plate

ANNOTATIONLINKSCOUNTPEROWNER - Static variable in class ome.model.screen.PlateAcquisition

ANNOTATIONLINKSCOUNTPEROWNER - Static variable in class ome.model.screen.Reagent

ANNOTATIONLINKSCOUNTPEROWNER - Static variable in class ome.model.screen.Screen

ANNOTATIONLINKSCOUNTPEROWNER - Static variable in class ome.model.screen.Well

AnnotationListValue(String, ImportConfig, List<Annotation>) - Constructor for class ome.formats.importer.ImportConfig.AnnotationListValue

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

ANNOTATIONS - Static variable in class omero.gateway.model.ChannelData

Identifies the Channel.ANNOTATIONLINKS field.

ANNOTATIONS - Static variable in class omero.gateway.model.DatasetData

Identifies the DatasetI.ANNOTATIONLINKS field.

ANNOTATIONS - Static variable in class omero.gateway.model.ImageData

Identifies the ImageI.ANNOTATIONLINKS field.

ANNOTATIONS - Static variable in class omero.gateway.model.PlateData

Identifies the PlateI.ANNOTATIONLINKS field.

AnnotationUtils - Class in ome.annotations

Checks metadata constraints on API calls.

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

AopContextInitializer - Class in ome.services.blitz.fire

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

ApiConsistencyCheck - Class in ome.services.blitz.util

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

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

ApiConstraintChecker - Class in ome.annotations

Checks metadata constraints on API calls.

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

ApiUsageException - Exception in ome.conditions

Alerts a user to a misuse of an Omero method call.

ApiUsageException(String) - Constructor for exception ome.conditions.ApiUsageException

append(String, Object...) - Method in class ome.security.basic.EventListenersFactoryBean

appends the objects to the existing list identified by key.

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

Simple delegate method to allow appending arbitrary strings.

append(ILoggingEvent) - Method in class ome.util.logback.SiftingWhileRejectingDefaultAppender

appendDate(StringBuilder, Date) - Method in class ome.tools.hibernate.SqlArray

appendDbPoint(StringBuilder, Point) - Static method in class omero.model.SmartShape.Util

appendDbPoint(StringBuilder, double, double) - Static method in class omero.model.SmartShape.Util

appendSegment(StringBuilder, boolean, double, double) - Static method in class omero.model.SmartShape.Util

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

appendSvgPoint(StringBuilder, Point) - Static method in class omero.model.SmartShape.Util

appendSvgPoint(StringBuilder, double, double) - Static method in class omero.model.SmartShape.Util

apply(String) - Method in class ome.services.blitz.repo.path.MakePathComponentSafe

applyBeanPropertyValues(Object, String) - Method in class ome.system.OmeroContext

Uses the methods of this context's BeanFactory to autowire any Object based on the given beanName.

applyBeanPropertyValues(Object, Class<? extends ServiceInterface>) - Method in class ome.system.OmeroContext

Uses the methods of this context's BeanFactory to autowire any Object based on the service class.

applyContext(Details, boolean) - Method in class ome.security.basic.CurrentDetails

applyHardWiredInterceptors(List<HardWiredInterceptor>, AopContextInitializer) - Method in class ome.services.blitz.impl.AbstractAmdServant

Applies the hard-wired intercepting to this instance.

applyIfShareAccessible(QueryBuilder) - Method in class ome.services.sharing.ShareBean

If the current user is not an admin, then this methods adds a subclause to the HQL: AND ( share.owner.id = :userId or user.id = :userId ) QueryBuilder.where() should already have been called.

applySettingsToDataset(long, long) - Method in interface ome.api.IRenderingSettings

Applies rendering settings to all images in a given Dataset.

applySettingsToDataset(long, long) - Method in class ome.logic.RenderingSettingsImpl

Implemented as specified by the IRenderingSettings I/F.

applySettingsToDataset_async(AMD_IRenderingSettings_applySettingsToDataset, long, long, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI

applySettingsToImage(long, long) - Method in interface ome.api.IRenderingSettings

Applies rendering settings to a given Image.

applySettingsToImage(long, long) - Method in class ome.logic.RenderingSettingsImpl

Implemented as specified by the IRenderingSettings I/F

applySettingsToImage_async(AMD_IRenderingSettings_applySettingsToImage, long, long, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI

applySettingsToImages(long, List<Long>) - Method in interface ome.api.IRenderingSettings

Applies rendering settings to a given Image.

applySettingsToImages(long, List<Long>) - Method in class ome.logic.RenderingSettingsImpl

Implemented as specified by the IRenderingSettings I/F

applySettingsToImages_async(AMD_IRenderingSettings_applySettingsToImages, long, List<Long>, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI

applySettingsToPixels(long, long) - Method in interface ome.api.IRenderingSettings

Applies rendering settings to a given Pixels.

applySettingsToPixels(long, long) - Method in class ome.logic.RenderingSettingsImpl

Implemented as specified by the IRenderingSettings I/F

applySettingsToPixels_async(AMD_IRenderingSettings_applySettingsToPixels, long, long, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI

applySettingsToProject(long, long) - Method in interface ome.api.IRenderingSettings

Applies rendering settings to all images in all Datasets of a given Project.

applySettingsToProject(long, long) - Method in class ome.logic.RenderingSettingsImpl

Implemented as specified by the IRenderingSettings I/F.

applySettingsToProject_async(AMD_IRenderingSettings_applySettingsToProject, long, long, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI

applySettingsToSet(long, Class<T>, Set<Long>) - Method in interface ome.api.IRenderingSettings

Applies rendering settings to one or many containers.

applySettingsToSet(long, Class<T>, Set<Long>) - Method in class ome.logic.RenderingSettingsImpl

Implemented as specified by the IRenderingSettings I/F.

applySettingsToSet_async(AMD_IRenderingSettings_applySettingsToSet, long, String, List<Long>, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI

Arc - Class in ome.model.acquisition

Arc() - Constructor for class ome.model.acquisition.Arc

Arc(Long) - Constructor for class ome.model.acquisition.Arc

Arc(Long, boolean) - Constructor for class ome.model.acquisition.Arc

Main constructor.

Arc(ArcType) - Constructor for class ome.model.acquisition.Arc

ARC - Static variable in class omero.gateway.model.LightSourceData

Indicates that the light source is a arc.

archived - Variable in class ome.model.core.Image

ARCHIVED - Static variable in class ome.model.core.Image

ArcType - Class in ome.model.enums

ArcType() - Constructor for class ome.model.enums.ArcType

ArcType(Long) - Constructor for class ome.model.enums.ArcType

ArcType(Long, boolean) - Constructor for class ome.model.enums.ArcType

Main constructor.

ArcType(String) - Constructor for class ome.model.enums.ArcType

ArcType.Details - Class in ome.model.enums

areaPoints(SmartShape.PointCallback) - Method in class omero.model.SmartEllipseI

areaPoints(SmartShape.PointCallback) - Method in class omero.model.SmartLineI

areaPoints(SmartShape.PointCallback) - Method in class omero.model.SmartMaskI

areaPoints(SmartShape.PointCallback) - Method in class omero.model.SmartPathI

areaPoints(SmartShape.PointCallback) - Method in class omero.model.SmartPointI

areaPoints(SmartShape.PointCallback) - Method in class omero.model.SmartPolygonI

areaPoints(SmartShape.PointCallback) - Method in class omero.model.SmartPolylineI

areaPoints(SmartShape.PointCallback) - Method in class omero.model.SmartRectI

areaPoints(SmartShape.PointCallback) - Method in interface omero.model.SmartShape

Calls the SmartShape.PointCallback with all of the x/y coordinates which are within the shape.

areaPoints(SmartShape.PointCallback) - Method in class omero.model.SmartTextI

areTablesEnabled(Current) - Method in class ome.services.blitz.impl.SharedResourcesI

args() - Method in class ome.util.SqlAction.DeleteLog

asAnnotation() - Method in class omero.gateway.model.DataObject

Returns the hosted IObject as an Annotation.

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

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

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

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

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

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

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

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

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

Converts the current SmartShape to a Shape.

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

asCastedDataObjects(List) - Static method in class omero.gateway.util.PojoMapper

Converts each element of the collection into its corresponding DataObject.

ASCENDING_LETTER - Static variable in class omero.gateway.model.PlateData

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

ASCENDING_NUMBER - Static variable in class omero.gateway.model.PlateData

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

asChannel() - Method in class omero.gateway.model.DataObject

Returns the hosted IObject as a Well.

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

Deprecated.

asDataObject(IObject) - Static method in class omero.gateway.util.PojoMapper

Converts the specified IObject into its corresponding DataObject.

asDataObjectMap(Class<K>, Class<V>, String, List) - Static method in class omero.gateway.util.PojoMapper

Converts each element of the list to a pair (key, value) in the map.

asDataObjects(Collection) - Static method in class omero.gateway.util.PojoMapper

Deprecated.

Use PojoMapper.convertToDataObjects(Collection) instead

asDataObjects(List) - Static method in class omero.gateway.util.PojoMapper

Deprecated.

Use PojoMapper.convertToDataObjects(Collection) instead

asDataObjects(IObject[]) - Static method in class omero.gateway.util.PojoMapper

Deprecated.

Use PojoMapper.convertToDataObjects(Collection) instead

asDataObjects(Map) - Static method in class omero.gateway.util.PojoMapper

Converts each pair (key, value) of the map.

asDataObjectsAsList(Collection) - Static method in class omero.gateway.util.PojoMapper

Deprecated.

Use PojoMapper.convertToDataObjects(Collection) instead

asDataset() - Method in class omero.gateway.model.DataObject

Returns the hosted IObject as a Dataset.

asExperimenter() - Method in class omero.gateway.model.DataObject

Returns the hosted IObject as an Experimenter.

asFolder() - Method in class omero.gateway.model.DataObject

Returns the hosted IObject as a Folder.

asGroup() - Method in class omero.gateway.model.DataObject

Returns the hosted IObject as an Experimenter Group.

asIAnnotated() - Method in class omero.gateway.model.DataObject

not null; may throw class-cast exception

asImage() - Method in class omero.gateway.model.DataObject

Returns the hosted IObject as an Image.

asIObject() - Method in class omero.gateway.model.DataObject

not null; no exceptions.

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

Creates an OriginalFile instance for the given CheckedPath even if it doesn't exist.

asPixels() - Method in class omero.gateway.model.DataObject

Returns the hosted IObject as a Pixels.

asPlate() - Method in class omero.gateway.model.DataObject

Returns the hosted IObject as a Plate.

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

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

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

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

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

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

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

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

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

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

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

asPojo(IObject) - Static method in class omero.gateway.model.DataObject

Converts the passed IObject into its corresponding Pojo object.

asPojos(Collection) - Static method in class omero.gateway.model.DataObject

Converts the collection of IObjects into the corresponding DataObjects

asPojos(Map) - Static method in class omero.gateway.model.DataObject

Converts the map of IObjects into the corresponding DataObjects

asProject() - Method in class omero.gateway.model.DataObject

Returns the hosted IObject as a Project.

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

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

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

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

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

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

asScreen() - Method in class omero.gateway.model.DataObject

Returns the hosted IObject as a Screen.

assemble(Serializable, Object) - Method in class ome.model.units.GenericEnumType

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

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

assertMayProcess(String, long, Details) - Method in interface ome.services.graphs.GraphTraversal.Processor

Assert that an object with the given details may be processed.

assertMayProcess(String, long, Details) - Method in class omero.cmd.graphs.BaseGraphTraversalProcessor

assertMayProcess(String, long, Details) - Method in class omero.cmd.graphs.NullGraphTraversalProcessor

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

assertNoPolicyViolations() - Method in class ome.services.graphs.GraphTraversal

Check that there are no policy violations matched by p:error policy rules.

assertNoUnlinking() - Method in class ome.services.graphs.GraphTraversal

Assert that GraphTraversal.unlinkTargets(boolean) need not be called.

assertResponse(int) - Method in class omero.cmd.Helper

Checks the given steps against the number of times that this method has been called on this instance and then increments the call count.

assertStep(int, int) - Method in class omero.cmd.Helper

Throws an exception if the current step is not the expected value.

assertStep(int) - Method in class omero.cmd.Helper

Checks the given steps against the number of times that this method has been called on this instance and then increments the call count.

asWell() - Method in class omero.gateway.model.DataObject

Returns the hosted IObject as a Well.

asWellSample() - Method in class omero.gateway.model.DataObject

Returns the hosted IObject as a Well.

atime - Variable in class ome.model.core.OriginalFile

ATIME - Static variable in class ome.model.core.OriginalFile

attach(long) - Method in interface ome.api.JobHandle

attach(long) - Method in class ome.services.JobBean

attach_async(AMD_JobHandle_attach, long, Current) - Method in class ome.services.blitz.impl.JobHandleI

attachAnnotation(SecurityContext, T, DataObject) - Method in class omero.gateway.facility.DataManagerFacility

Create/attach an AnnotationData to a given DataObject

attachFile(SecurityContext, File, String, String, String, DataObject) - Method in class omero.gateway.facility.DataManagerFacility

Attaches a File to a DataObject

attenuation - Variable in class ome.model.acquisition.LightSettings

ATTENUATION - Static variable in class ome.model.acquisition.LightSettings

AttributeNewUserGroupBean - Class in ome.security.auth

Handles the "*_attribute" specifiers from etc/omero.properties.

AttributeNewUserGroupBean(String, boolean, boolean) - Constructor for class ome.security.auth.AttributeNewUserGroupBean

AttributeSet - Class in ome.security.auth

Specialized handling of all the attributes, multi or single valued.

AttributeSet(DirContextAdapter) - Constructor for class ome.security.auth.AttributeSet

AuthenticationException - Exception in ome.conditions

Invalid username and/or credential provided.

AuthenticationException(String) - Constructor for exception ome.conditions.AuthenticationException

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

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

AWTScaleService - Class in ome.logic

Provides methods for scaling buffered images.

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

axis - Variable in class ome.model.display.ProjectionDef

AXIS - Static variable in class ome.model.display.ProjectionDef

B

B_BAND - Static variable in class omeis.providers.re.RGBBuffer

Index of the blue band in the image's data buffer.

backOff - Variable in exception ome.conditions.ConcurrencyException

BackOff - Interface in ome.io.nio

Strategy interface which is used by PixelsService to calculate the appropriate backoff to report to users when pixel data is not available.

backOff - Variable in class ome.io.nio.PixelsService

BackOff implementation for calculating MissingPyramidExceptions

base - Variable in class ome.util.mem.ReadOnlyByteArray

The original array.

base - Variable in class omero.util.ReadOnlyByteArray

The original array.

BASE_SCRIPT_FILTER - Static variable in class ome.services.scripts.ScriptRepoHelper

IOFileFilter instance used during ScriptRepoHelper.iterate() to find the matching scripts in the given directory.

BaseGraphPolicyAdjuster - Class in omero.cmd.graphs

The base class assists adjustment of an existing graph traversal policy.

BaseGraphPolicyAdjuster(GraphPolicy) - Constructor for class omero.cmd.graphs.BaseGraphPolicyAdjuster

Construct a new graph policy adjuster.

BaseGraphTraversalProcessor - Class in omero.cmd.graphs

Useful methods for GraphTraversal.Processor instances to share.

BaseGraphTraversalProcessor(Session) - Constructor for class omero.cmd.graphs.BaseGraphTraversalProcessor

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

BasePolicy - Class in ome.security.policy

Simple base class for Policy implementations which always returns true for BasePolicy.isRestricted(IObject) and always fails on BasePolicy.checkRestriction(IObject).

BasePolicy(Set<Class<IObject>>) - Constructor for class ome.security.policy.BasePolicy

basic - Variable in class ome.security.SecuritySystemHolder

BasicACLVoter - Class in ome.security.basic

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

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

BasicAnnotation - Class in ome.model.annotations

BasicAnnotation() - Constructor for class ome.model.annotations.BasicAnnotation

BasicAnnotation(Long) - Constructor for class ome.model.annotations.BasicAnnotation

BasicAnnotation(Long, boolean) - Constructor for class ome.model.annotations.BasicAnnotation

Main constructor.

BasicEventContext - Class in ome.security.basic

EventContext implementation for use within the security system.

BasicEventContext(Principal, SessionStats) - Constructor for class ome.security.basic.BasicEventContext

BasicEventContext(Principal, SessionStats, EventContext) - Constructor for class ome.security.basic.BasicEventContext

Copy-constructor to not have to allow the mutator SimpleEventContext.copy(EventContext) or copyContext(EventContext) out of the EventContext hierarchy.

BasicMethodSecurity - Class in ome.security.basic

Implementation of MethodSecurity which checks method security based on the RolesAllowed annotations of our implementation methods.

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

BasicMethodSecurity(boolean) - Constructor for class ome.security.basic.BasicMethodSecurity

BasicSecuritySystem - Class in ome.security.basic

simplest implementation of SecuritySystem.

BasicSecuritySystem(OmeroInterceptor, SystemTypes, CurrentDetails, SessionManager, Roles, ServiceFactory, TokenHolder, SecurityFilter, PolicyService) - Constructor for class ome.security.basic.BasicSecuritySystem

Main public constructor for this SecuritySystem implementation.

BasicSecurityWiring - Class in ome.security.basic

Responsible for logging users in and out via the Principal before and after the actual invocation of OMERO methods.

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

BasicSecurityWiring.CloseOnNoSessionContext - Class in ome.security.basic

batch - Variable in class ome.services.fulltext.FullTextIndexer

Deprecated.

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

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

batchTimer - Variable in class ome.services.fulltext.FullTextIndexer

Deprecated.

be - Variable in class ome.services.blitz.impl.AbstractAmdServant

BeanHelper - Class in ome.services.util

Helper for all bean implementations.

BeanHelper(Class) - Constructor for class ome.services.util.BeanHelper

beforeFilter(String, Object) - Method in class ome.util.ContextFilter

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

BEGIN_POST_PROCESS(int, ImportContainer, IObject, Long, int, ImportSize) - Constructor for class ome.formats.importer.ImportEvent.BEGIN_POST_PROCESS

BEGIN_SAVE_TO_DB(int, ImportContainer, IObject, Long, int, ImportSize) - Constructor for class ome.formats.importer.ImportEvent.BEGIN_SAVE_TO_DB

BfPixelBuffer - Class in ome.io.bioformats

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

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

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

BfPixelsStoreI - Class in ome.services.blitz.repo

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

BfPixelsWrapper - Class in ome.io.bioformats

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

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

BfPyramidPixelBuffer - Class in ome.io.bioformats

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

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

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

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

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

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

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

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

Perform BioFormats ReaderWrapper.setId(String) for this file.

BigResult - Exception in ome.model.units

Checked exception which is thrown from unit methods which can possibly overflow.

BigResult(BigDecimal, String) - Constructor for exception ome.model.units.BigResult

BinaryAccessPolicy - Class in ome.security.policy

Policy which should be checked anytime access to original binary files in OMERO is being attempted.

BinaryAccessPolicy(Set<Class<IObject>>, ACLVoter) - Constructor for class ome.security.policy.BinaryAccessPolicy

BinaryAccessPolicy(Set<Class<IObject>>, ACLVoter, String[]) - Constructor for class ome.security.policy.BinaryAccessPolicy

BinaryMaskQuantizer - Class in omeis.providers.re.quantum

Quantization process for binary masks.

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

Creates a new strategy.

binning - Variable in class ome.model.acquisition.DetectorSettings

BINNING - Static variable in class ome.model.acquisition.DetectorSettings

Binning - Class in ome.model.enums

Binning() - Constructor for class ome.model.enums.Binning

Binning(Long) - Constructor for class ome.model.enums.Binning

Binning(Long, boolean) - Constructor for class ome.model.enums.Binning

Main constructor.

Binning(String) - Constructor for class ome.model.enums.Binning

Binning.Details - Class in ome.model.enums

bit(Permissions.Flag) - Static method in class ome.model.internal.Permissions

returns the order of the bit representing the given Permissions.Flag.

bit(Permissions.Role, Permissions.Right) - Static method in class ome.model.internal.Permissions

returns the order of the bit representing the given Permissions.Role and Permissions.Right.

BIT - Static variable in class ome.util.PixelData

Identifies the type used to store pixel values.

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

Deprecated.

BIT_EIGHT - Static variable in class omeis.providers.re.codomain.PlaneSlicingContext

Identifies the bit-plane 8 i.e.

BIT_FIVE - Static variable in class omeis.providers.re.codomain.PlaneSlicingContext

Identifies the bit-plane 5 i.e.

BIT_FOUR - Static variable in class omeis.providers.re.codomain.PlaneSlicingContext

Identifies the bit-plane 4 i.e.

BIT_ONE - Static variable in class omeis.providers.re.codomain.PlaneSlicingContext

Identifies the bit-plane 1 i.e.

BIT_SEVEN - Static variable in class omeis.providers.re.codomain.PlaneSlicingContext

Identifies the bit-plane 7 i.e.

BIT_SIX - Static variable in class omeis.providers.re.codomain.PlaneSlicingContext

Identifies the bit-plane 6 i.e.

BIT_THREE - Static variable in class omeis.providers.re.codomain.PlaneSlicingContext

Identifies the bit-plane 3 i.e.

BIT_TWO - Static variable in class omeis.providers.re.codomain.PlaneSlicingContext

Identifies the bit-plane 2 i.e.

BIT_ZERO - Static variable in class omeis.providers.re.codomain.PlaneSlicingContext

Identifies the bit-plane 0 i.e.

bitResolution - Variable in class ome.model.display.QuantumDef

BITRESOLUTION - Static variable in class ome.model.display.QuantumDef

bitSize - Variable in class ome.model.enums.PixelsType

BITSIZE - Static variable in class ome.model.enums.PixelsType

BlitzConfiguration - Class in ome.services.blitz.util

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

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

Single constructor which builds all Ice instances needed for the server runtime based on arguments provided.

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

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

BlitzExecutor - Interface in ome.services.blitz.util

Single-point of execution for all AMD blitz calls.

BlitzInstanceProvider - Class in ome.formats.model

An instance provider which uses reflection to fulfill the contract of an InstanceProvider.

BlitzInstanceProvider(EnumerationProvider) - Constructor for class ome.formats.model.BlitzInstanceProvider

Default constructor.

BlitzOnly - Interface in ome.services.blitz.util

Marker interface which specifies that an servant should not be checked for api consistency via ApiConsistencyCheck.

BlobShareStore - Class in ome.services.sharing

Implements ShareStore and provides functionality to work with binary Ice data from the share.

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

block(long) - Method in class omero.cmd.CmdCallbackI

Blocks for the given number of milliseconds unless CmdCallbackI.finished(Response, Status, Current) has been called in which case it returns immediately with true.

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

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

blue - Variable in class ome.model.core.Channel

BLUE - Static variable in class ome.model.core.Channel

blue - Variable in class ome.model.display.ChannelBinding

BLUE - Static variable in class ome.model.display.ChannelBinding

blue - Variable in class ome.model.screen.Well

BLUE - Static variable in class ome.model.screen.Well

BLUE_INDEX - Static variable in class ome.formats.model.ColorsFactory

Index of the red component of a color.

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

Index of the red component of a color.

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

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

blues - Variable in class omeis.providers.re.lut.LutReader

Holds the blues values.

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

BOOLEAN() - Constructor for class ome.tools.hibernate.ListAsSQLArrayUserType.BOOLEAN

BOOLEAN(List<Boolean>) - Constructor for class ome.tools.hibernate.SqlArray.BOOLEAN

BooleanAnnotation - Class in ome.model.annotations

BooleanAnnotation() - Constructor for class ome.model.annotations.BooleanAnnotation

BooleanAnnotation(Long) - Constructor for class ome.model.annotations.BooleanAnnotation

BooleanAnnotation(Long, boolean) - Constructor for class ome.model.annotations.BooleanAnnotation

Main constructor.

BooleanAnnotationData - Class in omero.gateway.model

Boolean annotation.

BooleanAnnotationData() - Constructor for class omero.gateway.model.BooleanAnnotationData

Creates a new instance.

BooleanAnnotationData(boolean) - Constructor for class omero.gateway.model.BooleanAnnotationData

Creates a new instance.

BooleanAnnotationData(BooleanAnnotation) - Constructor for class omero.gateway.model.BooleanAnnotationData

Creates a new instance.

BoolValue(String, ImportConfig, boolean) - Constructor for class ome.formats.importer.ImportConfig.BoolValue

boolValue - Variable in class ome.model.annotations.BooleanAnnotation

BOOLVALUE - Static variable in class ome.model.annotations.BooleanAnnotation

breakSharing() - Method in class ome.util.mem.Handle

Subclasses must call this method before forwarding any call that modifies the Body's state.

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

Deprecated.

BridgeHelper - Class in ome.services.fulltext

Deprecated.

BridgeHelper() - Constructor for class ome.services.fulltext.BridgeHelper

Deprecated.

BrowseFacility - Class in omero.gateway.facility

A Facility for browsing the data hierarchy and retrieving ProjectData, DatasetData, etc.

BTF - Static variable in class omero.gateway.util.TIFFFilter

Possible file extension.

build() - Method in class ome.formats.importer.targets.TargetBuilder

Builder(AbstractFileSystemService, ExtendedMetadata) - Constructor for class ome.services.delete.Deletion.Builder

buildLuceneQuery(List<String>, Date, Date, String, String) - Static method in class ome.util.search.LuceneQueryBuilder

Builds a query with the provided input terms over the given fields

buildLuceneQuery(List<String>, String) - Static method in class ome.util.search.LuceneQueryBuilder

Builds a query with the provided input terms over the given fields

buildOrObtainSession() - Method in class ome.tools.hibernate.CurrentSessionContext

buildParseJob(long) - Method in class omero.grid.ParamsHelper

Build a job for the script with id.

buildQuery(Session) - Method in class ome.services.query.CollectionCountQueryDefinition

buildQuery(Session) - Method in class ome.services.query.IObjectClassQuery

buildQuery(Session) - Method in class ome.services.query.PojosFindAnnotationsQueryDefinition

buildQuery(Session) - Method in class ome.services.query.PojosFindHierarchiesQueryDefinition

buildQuery(Session) - Method in class ome.services.query.PojosGetImagesByOptionsQueryDefinition

buildQuery(Session) - Method in class ome.services.query.PojosGetImagesQueryDefinition

buildQuery(Session) - Method in class ome.services.query.PojosGetUserImagesQueryDefinition

buildQuery(Session) - Method in class ome.services.query.PojosLoadHierarchyQueryDefinition

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

main point of entry for subclasses.

buildQuery(Session) - Method in class ome.services.query.StringQuery

buildQuery(QueryBuilder) - Method in class ome.services.scripts.ScriptRepoHelper

Adds a single clause of the form "AND (A OR B ...)" where each ScriptFileType A, B, etc. is given a chance to define its own clause.

buildResponse(int, Object) - Method in class ome.services.blitz.impl.commands.SaveI

buildResponse(int, Object) - Method in class ome.services.blitz.repo.ManagedImportRequestI

buildResponse(int, Object) - Method in class ome.services.blitz.repo.RawAccessRequestI

buildResponse(int, Object) - Method in class omero.cmd.admin.CurrentSessionsRequestI

buildResponse(int, Object) - Method in class omero.cmd.admin.ResetPasswordRequestI

buildResponse(int, Object) - Method in class omero.cmd.admin.UpdateSessionTimeoutRequestI

buildResponse(int, Object) - Method in class omero.cmd.basic.DoAllI

buildResponse(int, Object) - Method in class omero.cmd.basic.ListRequestsI

buildResponse(int, Object) - Method in class omero.cmd.basic.TimingI

buildResponse(int, Object) - Method in class omero.cmd.fs.ManageImageBinariesI

buildResponse(int, Object) - Method in class omero.cmd.fs.OriginalMetadataRequestI

buildResponse(int, Object) - Method in class omero.cmd.fs.UsedFilesRequestI

buildResponse(int, Object) - Method in class omero.cmd.graphs.Chgrp2I

buildResponse(int, Object) - Method in class omero.cmd.graphs.Chmod2I

buildResponse(int, Object) - Method in class omero.cmd.graphs.Chown2I

buildResponse(int, Object) - Method in class omero.cmd.graphs.Delete2I

buildResponse(int, Object) - Method in class omero.cmd.graphs.DiskUsage2I

buildResponse(int, Object) - Method in class omero.cmd.graphs.DiskUsageI

Deprecated.

buildResponse(int, Object) - Method in class omero.cmd.graphs.DuplicateI

buildResponse(int, Object) - Method in class omero.cmd.graphs.FindChildrenI

buildResponse(int, Object) - Method in class omero.cmd.graphs.FindParentsI

buildResponse(int, Object) - Method in class omero.cmd.graphs.LegalGraphTargetsI

buildResponse(int, Object) - Method in class omero.cmd.graphs.SkipHeadI

buildResponse(int, Object) - Method in interface omero.cmd.IRequest

Post-transaction chance to map from the return value of IRequest.step(int) to a Response object.

buildResponse(int, Object) - Method in class omero.cmd.mail.SendEmailRequestI

BULK_ANNOTATIONS_NS - Static variable in class omero.gateway.model.FileAnnotationData

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

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

Finds entities annotated with an Annotation similar to the example.

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

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

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

Passes the query as is to the Lucene backend.

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

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

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

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

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

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

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

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

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

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

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

Builds a Lucene query and passes it to the Lucene backend.

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

byLuceneQueryBuilder_async(AMD_Search_byLuceneQueryBuilder, String, String, String, String, String, Current) - Method in class ome.services.blitz.impl.SearchI

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

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

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

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

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

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

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

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

bySymbol(String) - Static method in enum ome.model.enums.UnitsElectricPotential

bySymbol(String) - Static method in enum ome.model.enums.UnitsFrequency

bySymbol(String) - Static method in enum ome.model.enums.UnitsLength

bySymbol(String) - Static method in enum ome.model.enums.UnitsPower

bySymbol(String) - Static method in enum ome.model.enums.UnitsPressure

bySymbol(String) - Static method in enum ome.model.enums.UnitsTemperature

bySymbol(String) - Static method in enum ome.model.enums.UnitsTime

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

Creates a query which will return transient (without ID) TagAnnotation instances which represent all the tag groups which the given tag belongs to.

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

byTagForGroups_async(AMD_Search_byTagForGroups, String, Current) - Method in class ome.services.blitz.impl.SearchI

BYTE - Static variable in class ome.util.PixelData

Identifies the type used to store pixel values.

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

Identifies the type used to store pixel values.

ByteArray - Class in ome.util.mem

A read-write slice of a given array.

ByteArray(byte[], int, int) - Constructor for class ome.util.mem.ByteArray

Creates a read-write slice of base.

bytes - Variable in class ome.model.roi.Mask

BYTES - Static variable in class ome.model.roi.Mask

bytesPerPixel - Variable in class ome.util.PixelData

The number of bytes per pixel.

bytesPerPixel() - Method in class ome.util.PixelData

Returns the number of byte per pixel for the pixel data.

bytesPerPixel - Variable in class omeis.providers.re.data.Plane2D

How many bytes make up a pixel value.

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

C

c2c() - Method in class ome.util.ModelMapper

TODO identity versus null mappings

c2c() - Method in class omero.util.IceMapper

cache - Variable in class ome.services.blitz.impl.ScriptI

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

CACHE_SIZE - Static variable in interface omero.gateway.cache.CacheService

The default size of a cache.

CacheFactory - Class in ome.services.sessions.state

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

CacheListener - Class in ome.services.sessions.state

Basic CacheEventListener which does nothing.

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

CacheService - Interface in omero.gateway.cache

Defines the caching service interface.

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

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

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

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

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

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

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

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

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

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

Implemented as specified by PixelBuffer I/F.

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

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

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

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

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

calibratedMagnification - Variable in class ome.model.acquisition.Objective

CALIBRATEDMAGNIFICATION - Static variable in class ome.model.acquisition.Objective

call(String, String, boolean) - Method in class ome.services.db.SelfCorrectingDataSource

call(MethodInvocation) - Method in class ome.tools.hibernate.EventMethodInterceptor.Action

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

call(IObject) - Method in interface ome.util.CBlock

invoke this block.

call(IObject) - Method in class ome.util.IdBlock

call() - Method in interface omeis.providers.re.RenderingTask

Renders wavelength.

Callback - Class in ome.services.throttling

Manages AMD-based method dispatches from blitz.

Callback(Boolean, Boolean, ServiceInterface, IceMethodInvoker, Object, IceMapper, Current, Object...) - Constructor for class ome.services.throttling.Callback

Callback(ServiceInterface, IceMethodInvoker, IceMapper, Object, Current, Object...) - Constructor for class ome.services.throttling.Callback

callback - Variable in class omero.cmd.SessionI

Callback2<R> - Class in ome.services.throttling

Callable-based callback which guarantees that ice_response or ice_exception is called.

Callback2(Current, Object, boolean, Callable<R>) - Constructor for class ome.services.throttling.Callback2

CallContext - Class in omero.cmd

Interceptor which takes any context provided by the client and calls setContext on CurrentDetails.

CallContext(OmeroContext, String) - Constructor for class omero.cmd.CallContext

CallContext(CurrentDetails, String) - Constructor for class omero.cmd.CallContext

callContextWrapper(Object) - Method in class omero.cmd.SessionI

callInvokerOnMappedArgs(IceMapper, Object, Current, Object...) - Method in class ome.services.blitz.impl.AbstractAmdServant

callInvokerOnRawArgs(Object, Current, Object...) - Method in class ome.services.blitz.impl.AbstractAmdServant

callInvokerOnRawArgs(ServiceInterface, IceMethodInvoker, Object, Current, Object...) - Method in interface ome.services.blitz.util.BlitzExecutor

Uses the given IceMethodInvoker to make the method call.

callInvokerOnRawArgs(ServiceInterface, IceMethodInvoker, Object, Current, Object...) - Method in class ome.services.throttling.InThreadThrottlingStrategy

callInvokerOnRawArgs(ServiceInterface, IceMethodInvoker, Object, Current, Object...) - Method in class ome.services.throttling.SerialThrottlingStrategy

callInvokerWithMappedArgs(ServiceInterface, IceMethodInvoker, IceMapper, Object, Current, Object...) - Method in interface ome.services.blitz.util.BlitzExecutor

Passes the given arguments to IceMethodInvoker with the assumption that all conversion from omero.* to ome.* has taken place.

callInvokerWithMappedArgs(ServiceInterface, IceMethodInvoker, IceMapper, Object, Current, Object...) - Method in class ome.services.throttling.InThreadThrottlingStrategy

callInvokerWithMappedArgs(ServiceInterface, IceMethodInvoker, IceMapper, Object, Current, Object...) - Method in class ome.services.throttling.SerialThrottlingStrategy

callWithRetries(String, String, boolean) - Method in class ome.services.db.SelfCorrectingDataSource

canAnnotate(IObject) - Method in interface ome.api.local.LocalAdmin

Companion to IAdmin.canUpdate(IObject) but not yet remotely accessible.

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

canAnnotate() - Method in class omero.gateway.model.DataObject

Returns true if the object can be annotated false otherwise, depending on permissions level.

canAnnotate(Current) - Method in class omero.model.PermissionsI

CANCEL() - Constructor for exception ome.formats.importer.ImportCandidates.CANCEL

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

Can be called to cancel the current action.

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

cancel() - Method in interface ome.services.procs.Process

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

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

cancel(Current) - Method in class omero.cmd.HandleI

Cancel(String) - Constructor for exception omero.cmd.HandleI.Cancel

cancel(ERR, Throwable, String, String...) - Method in class omero.cmd.Helper

Calls Helper.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 Helper.fail(ERR, Throwable, 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() - Method in class omero.gateway.model.DataObject

Returns true if the object can be deleted by the user currently logged in, false otherwise, depending on permissions level.

canDelete(Current) - Method in class omero.model.PermissionsI

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

canEdit() - Method in class omero.gateway.model.DataObject

Returns true if the object can be edited by the user currently logged in false otherwise, depending on permissions level.

canEdit(Current) - Method in class omero.model.PermissionsI

canLink() - Method in class omero.gateway.model.DataObject

Returns true if the object can be linked e.g. image add to dataset, by the user currently logged in, false otherwise, depending on permissions level.

canLink(Current) - Method in class omero.model.PermissionsI

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

Confirm all information for login is supplied

canMapReturnValue() - Method in class omero.util.IceMapper

True if this instance has a IceMapper.ReturnMapping

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

Check if this file is actually readable on the underlying filesystem.

canRead(EventContext, String) - Method in class ome.system.PreferenceContext

canRunScript_async(AMD_IScript_canRunScript, long, Current) - Method in class ome.services.blitz.impl.ScriptI

canUpdate(IObject) - Method in interface ome.api.IAdmin

Returns true if the currently logged in user can modify the given IObject.

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

canUpdate(IObject, Current) - Method in interface ome.services.blitz.repo.RepositoryDao

Delegates to IAdmin#canUpdate

canUpdate(IObject, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl

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

canWriteParentDirectory(ServiceFactory, SqlAction, String, CheckedPath) - Method in class ome.services.blitz.repo.RepositoryDaoImpl

Throw a SecurityViolation if the current context cannot write to the parent directory.

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

castChildOptions(Collection<ChildOption>) - Static method in class omero.cmd.graphs.ChildOptionI

Cast ChildOption[] to ChildOptionI[].

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

CBlock<E> - Interface in ome.util

Block template used to "C"ollect the results of some function called on each IObject in a collection.

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

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

cd - Variable in class ome.security.SecurityFilterHolder

cdEnd - Variable in class ome.model.display.QuantumDef

CDEND - Static variable in class ome.model.display.QuantumDef

cdStart - Variable in class ome.model.display.QuantumDef

CDSTART - Static variable in class ome.model.display.QuantumDef

ceId - Variable in class ome.system.SimpleEventContext

ceType - Variable in class ome.system.SimpleEventContext

cgId - Variable in class ome.system.SimpleEventContext

CGLIB_IDENTIFIER - Static variable in class ome.util.Utils

cgName - Variable in class ome.system.SimpleEventContext

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

List of IObject instances which have currently been found.

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

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

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

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

Used after an ExpiredCredentialException instance is thrown.

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

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

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

call details.setGroup() on this instance.

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

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

changeGroupPermissions(Long, Long) - Method in interface ome.util.SqlAction

changeGroupPermissions(Long, Long) - Method in class ome.util.SqlAction.Impl

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

call details.setOwner() on this instance.

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

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

changePassword(String) - Method in interface ome.api.IAdmin

change the password for the current user.

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

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

Throws by default.

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

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

changePassword(String, String, PasswordUtil.METHOD) - Method in class ome.security.auth.JdbcPasswordProvider

Actually perform the password change in the database and log the event against the user.

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

Attempts to change the password for the given user.

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

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

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

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

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

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

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

call defaults.setPermissions() on this instance.

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

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

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

ChangeSecurityContextEvent - Class in ome.services.sessions.events

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

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

changeTablePermissionsForGroup(String, Long, Long) - Method in interface ome.util.SqlAction

changeTablePermissionsForGroup(String, Long, Long) - Method in class ome.util.SqlAction.Impl

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

change the password for the a given user.

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

changeUserPassword_async(AMD_IAdmin_changeUserPassword, String, RString, Current) - Method in class ome.services.blitz.impl.AdminI

changeUserPasswordById(Long, String) - Method in class ome.security.auth.PasswordUtil

Calls PasswordUtil.changeUserPasswordById(Long, String, METHOD) with "false" as the value of the salt argument in order to provide backwards compatibility.

changeUserPasswordById(Long, String, PasswordUtil.METHOD) - Method in class ome.security.auth.PasswordUtil

Calls either PasswordUtil.preparePassword(String) or PasswordUtil.prepareSaltedPassword(Long, String) and passes the resulting value to SqlAction.setUserPassword(Long, String).

Channel - Class in ome.model.core

These filter definitions are used by the security system to eliminate non-readable objects from queries.

Channel() - Constructor for class ome.model.core.Channel

Channel(Long) - Constructor for class ome.model.core.Channel

Channel(Long, boolean) - Constructor for class ome.model.core.Channel

Main constructor.

Channel(LogicalChannel, Pixels) - Constructor for class ome.model.core.Channel

Channel.Details - Class in ome.model.core

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

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

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

ChannelAcquisitionData - Class in omero.gateway.model

Object hosting the acquisition related to a logical channel.

ChannelAcquisitionData(LogicalChannel) - Constructor for class omero.gateway.model.ChannelAcquisitionData

Creates a new instance.

ChannelAnnotationLink - Class in ome.model.annotations

These filter definitions are used by the security system to eliminate non-readable objects from queries.

ChannelAnnotationLink() - Constructor for class ome.model.annotations.ChannelAnnotationLink

ChannelAnnotationLink(Long) - Constructor for class ome.model.annotations.ChannelAnnotationLink

ChannelAnnotationLink(Long, boolean) - Constructor for class ome.model.annotations.ChannelAnnotationLink

Main constructor.

ChannelAnnotationLink(IObject, IObject) - Constructor for class ome.model.annotations.ChannelAnnotationLink

ChannelAnnotationLink.Details - Class in ome.model.annotations

ChannelBinding - Class in ome.model.display

These filter definitions are used by the security system to eliminate non-readable objects from queries.

ChannelBinding() - Constructor for class ome.model.display.ChannelBinding

ChannelBinding(Long) - Constructor for class ome.model.display.ChannelBinding

ChannelBinding(Long, boolean) - Constructor for class ome.model.display.ChannelBinding

Main constructor.

ChannelBinding(RenderingDef, Family, Double, Double, Double, Boolean, Boolean, Integer, Integer, Integer, Integer) - Constructor for class ome.model.display.ChannelBinding

channelBinding - Variable in class ome.model.display.CodomainMapContext

CHANNELBINDING - Static variable in class ome.model.display.CodomainMapContext

ChannelBinding.Details - Class in ome.model.display

ChannelData - Class in ome.formats.model

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

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

ChannelData - Class in omero.gateway.model

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

ChannelData(int) - Constructor for class omero.gateway.model.ChannelData

Creates a new instance.

ChannelData(int, Channel) - Constructor for class omero.gateway.model.ChannelData

Creates a new instance.

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

ChannelProcessor - Class in ome.formats.model

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

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

channels - Variable in class ome.model.core.LogicalChannel

CHANNELS - Static variable in class ome.model.core.LogicalChannel

channels - Variable in class ome.model.core.Pixels

CHANNELS - Static variable in class ome.model.core.Pixels

check(IObject, Object) - Method in class ome.security.basic.GroupChmodStrategy

Here we used the checks returned from ExtendedMetadata to iterate through every non-system table and check that it has no FKs which point to back to its rows and violate the read permissions which are being reduced.

check(IObject, Object) - Method in interface ome.security.ChmodStrategy

Performs one of the checks returned by ChmodStrategy.getChecks(IObject obj, String permissions).

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

check that there is a definition for this Query with the provided argument as its name.

check() - Method in interface omero.util.Resources.Entry

Called during each cycle.

CheckAllJobs - Class in ome.services.blitz.util

CheckAllJobs(Executor, ObjectAdapter, TopicManager) - Constructor for class ome.services.blitz.util.CheckAllJobs

CheckAllJobs(Executor, ObjectAdapter, TopicManager, long) - Constructor for class ome.services.blitz.util.CheckAllJobs

checkAndCollapseGraph() - Method in class ome.formats.OMEROMetadataStore

Checks the entire object graph for sections that may be collapsed if the data is derived from a Plate.

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

checkBounds(Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer

checkBounds(Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelsWrapper

checkBounds(Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

checkBounds(Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

checkBounds(Integer, Integer, Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer

Checks to ensure that no one particular axis has an offset out of bounds.

checkBounds(Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

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

Method called during initialization to get all the active uuids within the cluster, and remove any dead nodes.

checkDatabase(String) - Method in class ome.system.PreferenceContext

checkDelayedCallContext(BasicEventContext) - Method in class ome.security.basic.CurrentDetails

CheckedPath - Class in ome.services.blitz.repo

To prevent frequently re-calculating paths and re-creating File objects, CheckedPath objects store various interpretations of paths that are passed in by users.

CheckedPath(ServerFilePathTransformer, String, ChecksumProviderFactory, ChecksumAlgorithm) - Constructor for class ome.services.blitz.repo.CheckedPath

Construct a CheckedPath from a relative "/"-delimited path rooted at the repository.

checkedPaths - Variable in class ome.services.blitz.repo.ManagedImportLocationI

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

Returns all entities which would prevent the given Image id from being deleted.

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

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

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

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

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

checkLocation(File, RawFileStorePrx) - Method in class ome.formats.importer.transfers.AbstractExecFileTransfer

Check that the target location: 1) doesn't exist and 2) is properly written to by the server.

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

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

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

Like OmeroInterceptor.checkManagedDetails(IObject, Details, Details) but allows passing in a specific Details instance.

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

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

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

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

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

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

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

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

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

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

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

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

Checks password for given user.

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

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

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

If this was constructed with the ignoreUnknown argument set to true, returns null, since the base class knows no users.

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

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

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

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

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

Authenticates the give user given the password token.

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

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

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

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

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

Create a new CheckedPath object based on the given user input.

checkPermissions(String, String, StringHolder, Current) - Method in class ome.services.blitz.fire.PermissionsVerifierI

checkProperty(String, String) - Method in interface ome.api.local.LocalQuery

Checks if a property is defined on a mapped Hibernate type.

checkProperty(String, String) - Method in class ome.logic.PojosImpl

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

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

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 Policy.isRestricted(IObject) but throws an appropriate SecurityViolation subclass if the restriction is active.

checkRestriction(String, IObject) - Method in interface ome.security.policy.PolicyService

Give each configured Policy instance the chance to throw a SecurityViolation from its Policy.checkRestriction(IObject) method.

checkRestriction(String, IObject) - Method in interface ome.security.SecuritySystem

Checks whether or not a Policy instance of matching name has been registered, considers itself active, and considers the passed context object to be restricted.

checkRestriction(String, IObject) - Method in class ome.security.SecuritySystemHolder

checkRestriction(String, IObject) - Method in class ome.security.sharing.SharingSecuritySystem

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

checksum(String, ChecksumAlgorithm) - Method in class ome.formats.importer.exclusions.AbstractFileExclusion

CHECKSUM_ALGORITHM_NAMER - Static variable in class ome.services.blitz.util.ChecksumAlgorithmMapper

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

ChecksumAlgorithm - Class in ome.model.enums

ChecksumAlgorithm() - Constructor for class ome.model.enums.ChecksumAlgorithm

ChecksumAlgorithm(Long) - Constructor for class ome.model.enums.ChecksumAlgorithm

ChecksumAlgorithm(Long, boolean) - Constructor for class ome.model.enums.ChecksumAlgorithm

Main constructor.

ChecksumAlgorithm(String) - Constructor for class ome.model.enums.ChecksumAlgorithm

ChecksumAlgorithm.Details - Class in ome.model.enums

ChecksumAlgorithmMapper - Class in ome.services.blitz.util

Work with ChecksumAlgorithm enumeration instances, including mapping their values back to ChecksumTypes.

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

checksumAlgorithms - Variable in class ome.services.blitz.repo.PublicRepositoryI

checksumAsBytes() - Method in class ome.util.checksum.AbstractChecksumProvider

checksumAsBytes() - Method in interface ome.util.checksum.ChecksumProvider

Returns a byte array representation of the calculated checksum.

checksumAsBytes() - Method in class ome.util.checksum.FileSizeChecksumProviderImpl

checksumAsString() - Method in class ome.util.checksum.AbstractChecksumProvider

checksumAsString() - Method in interface ome.util.checksum.ChecksumProvider

Returns a String representing the checksum in hex form.

checksumAsString() - Method in class ome.util.checksum.FileSizeChecksumProviderImpl

ChecksumProvider - Interface in ome.util.checksum

An interface producing checksums or message digests (depending on the implementing class) of a given type of input.

checksumProviderFactory - Variable in class ome.services.blitz.repo.PublicRepositoryI

ChecksumProviderFactory - Interface in ome.util.checksum

A factory producing throw-away objects of the ChecksumProvider type.

ChecksumProviderFactoryImpl - Class in ome.util.checksum

An implementation of the ChecksumProviderFactory interface.

ChecksumProviderFactoryImpl() - Constructor for class ome.util.checksum.ChecksumProviderFactoryImpl

checksums - Variable in class ome.formats.importer.ImportEvent.FILESET_UPLOAD_END

ChecksumType - Enum in ome.util.checksum

Enumeration defining the possible algorithms used for calculating checksums.

checkTarget(File, TransferState) - Method in class ome.formats.importer.transfers.AbstractExecFileTransfer

Check that the server can properly read the copied file.

checkType(String) - Method in interface ome.api.local.LocalQuery

Checks if a type has been mapped in Hibernate.

checkType(String) - Method in class ome.logic.PojosImpl

checkType(String) - Method in class ome.logic.QueryImpl

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

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

chgrp(String, Long, long) - Static method in class omero.gateway.util.Requests

Deprecated.

use Requests.Chgrp2Builder from Requests.chgrp(), see this method for an example

chgrp(String, Long, ChildOption, long) - Static method in class omero.gateway.util.Requests

Deprecated.

use Requests.Chgrp2Builder from Requests.chgrp(), see this method for an example

chgrp(String, Long, List<ChildOption>, long) - Static method in class omero.gateway.util.Requests

Deprecated.

use Requests.Chgrp2Builder from Requests.chgrp(), see this method for an example

chgrp(String, Long, boolean, long) - Static method in class omero.gateway.util.Requests

Deprecated.

use Requests.Chgrp2Builder from Requests.chgrp(), see this method for an example

chgrp(String, Long, ChildOption, boolean, long) - Static method in class omero.gateway.util.Requests

Deprecated.

use Requests.Chgrp2Builder from Requests.chgrp(), see this method for an example

chgrp(String, Long, List<ChildOption>, boolean, long) - Static method in class omero.gateway.util.Requests

Deprecated.

use Requests.Chgrp2Builder from Requests.chgrp(), see this method for an example

chgrp(String, List<Long>, long) - Static method in class omero.gateway.util.Requests

Deprecated.

use Requests.Chgrp2Builder from Requests.chgrp(), see this method for an example

chgrp(String, List<Long>, ChildOption, long) - Static method in class omero.gateway.util.Requests

Deprecated.

use Requests.Chgrp2Builder from Requests.chgrp(), see this method for an example

chgrp(String, List<Long>, List<ChildOption>, long) - Static method in class omero.gateway.util.Requests

Deprecated.

use Requests.Chgrp2Builder from Requests.chgrp(), see this method for an example

chgrp(String, List<Long>, boolean, long) - Static method in class omero.gateway.util.Requests

Deprecated.

use Requests.Chgrp2Builder from Requests.chgrp(), see this method for an example

chgrp(String, List<Long>, ChildOption, boolean, long) - Static method in class omero.gateway.util.Requests

Deprecated.

use Requests.Chgrp2Builder from Requests.chgrp(), see this method for an example

chgrp(String, List<Long>, List<ChildOption>, boolean, long) - Static method in class omero.gateway.util.Requests

Deprecated.

use Requests.Chgrp2Builder from Requests.chgrp(), see this method for an example

chgrp(Map<String, List<Long>>, long) - Static method in class omero.gateway.util.Requests

Deprecated.

use Requests.Chgrp2Builder from Requests.chgrp(), see this method for an example

chgrp(Map<String, List<Long>>, ChildOption, long) - Static method in class omero.gateway.util.Requests

Deprecated.

use Requests.Chgrp2Builder from Requests.chgrp(), see this method for an example

chgrp(Map<String, List<Long>>, List<ChildOption>, long) - Static method in class omero.gateway.util.Requests

Deprecated.

use Requests.Chgrp2Builder from Requests.chgrp(), see this method for an example

chgrp(Map<String, List<Long>>, boolean, long) - Static method in class omero.gateway.util.Requests

Deprecated.

use Requests.Chgrp2Builder from Requests.chgrp(), see this method for an example

chgrp(Map<String, List<Long>>, ChildOption, boolean, long) - Static method in class omero.gateway.util.Requests

Deprecated.

use Requests.Chgrp2Builder from Requests.chgrp(), see this method for an example

chgrp(Map<String, List<Long>>, List<ChildOption>, boolean, long) - Static method in class omero.gateway.util.Requests

Deprecated.

use Requests.Chgrp2Builder from Requests.chgrp(), see this method for an example

chgrp() - Static method in class omero.gateway.util.Requests

Chgrp2Builder() - Constructor for class omero.gateway.util.Requests.Chgrp2Builder

Instantiate a new Chgrp2.

Chgrp2I - Class in omero.cmd.graphs

Request to move model objects to a different experiment group, replacing version 5.0's ChgrpI.

Chgrp2I(ACLVoter, Roles, SystemTypes, GraphPathBean, Deletion, Set<Class<? extends IObject>>, GraphPolicy, SetMultimap<String, String>, ApplicationContext) - Constructor for class omero.cmd.graphs.Chgrp2I

Deprecated.

from OMERO 5.4 the systemTypes argument is no longer included

child - Variable in class ome.model.acquisition.FilterSetEmissionFilterLink

CHILD - Static variable in class ome.model.acquisition.FilterSetEmissionFilterLink

child() - Method in class ome.model.acquisition.FilterSetEmissionFilterLink

child - Variable in class ome.model.acquisition.FilterSetExcitationFilterLink

CHILD - Static variable in class ome.model.acquisition.FilterSetExcitationFilterLink

child() - Method in class ome.model.acquisition.FilterSetExcitationFilterLink

child - Variable in class ome.model.acquisition.LightPathEmissionFilterLink

CHILD - Static variable in class ome.model.acquisition.LightPathEmissionFilterLink

child() - Method in class ome.model.acquisition.LightPathEmissionFilterLink

child - Variable in class ome.model.acquisition.LightPathExcitationFilterLink

CHILD - Static variable in class ome.model.acquisition.LightPathExcitationFilterLink

child() - Method in class ome.model.acquisition.LightPathExcitationFilterLink

child - Variable in class ome.model.annotations.AnnotationAnnotationLink

CHILD - Static variable in class ome.model.annotations.AnnotationAnnotationLink

child() - Method in class ome.model.annotations.AnnotationAnnotationLink

child - Variable in class ome.model.annotations.ChannelAnnotationLink

CHILD - Static variable in class ome.model.annotations.ChannelAnnotationLink

child() - Method in class ome.model.annotations.ChannelAnnotationLink

child - Variable in class ome.model.annotations.DatasetAnnotationLink

CHILD - Static variable in class ome.model.annotations.DatasetAnnotationLink

child() - Method in class ome.model.annotations.DatasetAnnotationLink

child - Variable in class ome.model.annotations.DetectorAnnotationLink

CHILD - Static variable in class ome.model.annotations.DetectorAnnotationLink

child() - Method in class ome.model.annotations.DetectorAnnotationLink

child - Variable in class ome.model.annotations.DichroicAnnotationLink

CHILD - Static variable in class ome.model.annotations.DichroicAnnotationLink

child() - Method in class ome.model.annotations.DichroicAnnotationLink

child - Variable in class ome.model.annotations.ExperimenterAnnotationLink

CHILD - Static variable in class ome.model.annotations.ExperimenterAnnotationLink

child() - Method in class ome.model.annotations.ExperimenterAnnotationLink

child - Variable in class ome.model.annotations.ExperimenterGroupAnnotationLink

CHILD - Static variable in class ome.model.annotations.ExperimenterGroupAnnotationLink

child() - Method in class ome.model.annotations.ExperimenterGroupAnnotationLink

child - Variable in class ome.model.annotations.FilesetAnnotationLink

CHILD - Static variable in class ome.model.annotations.FilesetAnnotationLink

child() - Method in class ome.model.annotations.FilesetAnnotationLink

child - Variable in class ome.model.annotations.FilterAnnotationLink

CHILD - Static variable in class ome.model.annotations.FilterAnnotationLink

child() - Method in class ome.model.annotations.FilterAnnotationLink

child - Variable in class ome.model.annotations.FolderAnnotationLink

CHILD - Static variable in class ome.model.annotations.FolderAnnotationLink

child() - Method in class ome.model.annotations.FolderAnnotationLink

child - Variable in class ome.model.annotations.ImageAnnotationLink

CHILD - Static variable in class ome.model.annotations.ImageAnnotationLink

child() - Method in class ome.model.annotations.ImageAnnotationLink

child - Variable in class ome.model.annotations.InstrumentAnnotationLink

CHILD - Static variable in class ome.model.annotations.InstrumentAnnotationLink

child() - Method in class ome.model.annotations.InstrumentAnnotationLink

child - Variable in class ome.model.annotations.LightPathAnnotationLink

CHILD - Static variable in class ome.model.annotations.LightPathAnnotationLink

child() - Method in class ome.model.annotations.LightPathAnnotationLink

child - Variable in class ome.model.annotations.LightSourceAnnotationLink

CHILD - Static variable in class ome.model.annotations.LightSourceAnnotationLink

child() - Method in class ome.model.annotations.LightSourceAnnotationLink

child - Variable in class ome.model.annotations.NamespaceAnnotationLink

CHILD - Static variable in class ome.model.annotations.NamespaceAnnotationLink

child() - Method in class ome.model.annotations.NamespaceAnnotationLink

child - Variable in class ome.model.annotations.NodeAnnotationLink

CHILD - Static variable in class ome.model.annotations.NodeAnnotationLink

child() - Method in class ome.model.annotations.NodeAnnotationLink

child - Variable in class ome.model.annotations.ObjectiveAnnotationLink

CHILD - Static variable in class ome.model.annotations.ObjectiveAnnotationLink

child() - Method in class ome.model.annotations.ObjectiveAnnotationLink

child - Variable in class ome.model.annotations.OriginalFileAnnotationLink

CHILD - Static variable in class ome.model.annotations.OriginalFileAnnotationLink

child() - Method in class ome.model.annotations.OriginalFileAnnotationLink

child - Variable in class ome.model.annotations.PlaneInfoAnnotationLink

CHILD - Static variable in class ome.model.annotations.PlaneInfoAnnotationLink

child() - Method in class ome.model.annotations.PlaneInfoAnnotationLink

child - Variable in class ome.model.annotations.PlateAcquisitionAnnotationLink

CHILD - Static variable in class ome.model.annotations.PlateAcquisitionAnnotationLink

child() - Method in class ome.model.annotations.PlateAcquisitionAnnotationLink

child - Variable in class ome.model.annotations.PlateAnnotationLink

CHILD - Static variable in class ome.model.annotations.PlateAnnotationLink

child() - Method in class ome.model.annotations.PlateAnnotationLink

child - Variable in class ome.model.annotations.ProjectAnnotationLink

CHILD - Static variable in class ome.model.annotations.ProjectAnnotationLink

child() - Method in class ome.model.annotations.ProjectAnnotationLink

child - Variable in class ome.model.annotations.ReagentAnnotationLink

CHILD - Static variable in class ome.model.annotations.ReagentAnnotationLink

child() - Method in class ome.model.annotations.ReagentAnnotationLink

child - Variable in class ome.model.annotations.RoiAnnotationLink

CHILD - Static variable in class ome.model.annotations.RoiAnnotationLink

child() - Method in class ome.model.annotations.RoiAnnotationLink

child - Variable in class ome.model.annotations.ScreenAnnotationLink

CHILD - Static variable in class ome.model.annotations.ScreenAnnotationLink

child() - Method in class ome.model.annotations.ScreenAnnotationLink

child - Variable in class ome.model.annotations.SessionAnnotationLink

CHILD - Static variable in class ome.model.annotations.SessionAnnotationLink

child() - Method in class ome.model.annotations.SessionAnnotationLink

child - Variable in class ome.model.annotations.ShapeAnnotationLink

CHILD - Static variable in class ome.model.annotations.ShapeAnnotationLink

child() - Method in class ome.model.annotations.ShapeAnnotationLink

child - Variable in class ome.model.annotations.WellAnnotationLink

CHILD - Static variable in class ome.model.annotations.WellAnnotationLink

child() - Method in class ome.model.annotations.WellAnnotationLink

child - Variable in class ome.model.containers.DatasetImageLink

CHILD - Static variable in class ome.model.containers.DatasetImageLink

child() - Method in class ome.model.containers.DatasetImageLink

child - Variable in class ome.model.containers.FolderImageLink

CHILD - Static variable in class ome.model.containers.FolderImageLink

child() - Method in class ome.model.containers.FolderImageLink

child - Variable in class ome.model.containers.FolderRoiLink

CHILD - Static variable in class ome.model.containers.FolderRoiLink

child() - Method in class ome.model.containers.FolderRoiLink

child - Variable in class ome.model.containers.ProjectDatasetLink

CHILD - Static variable in class ome.model.containers.ProjectDatasetLink

child() - Method in class ome.model.containers.ProjectDatasetLink

child - Variable in class ome.model.core.PixelsOriginalFileMap

CHILD - Static variable in class ome.model.core.PixelsOriginalFileMap

child() - Method in class ome.model.core.PixelsOriginalFileMap

child - Variable in class ome.model.fs.FilesetJobLink

CHILD - Static variable in class ome.model.fs.FilesetJobLink

child() - Method in class ome.model.fs.FilesetJobLink

child - Variable in class ome.model.jobs.JobOriginalFileLink

CHILD - Static variable in class ome.model.jobs.JobOriginalFileLink

child() - Method in class ome.model.jobs.JobOriginalFileLink

child - Variable in class ome.model.meta.GroupExperimenterMap

CHILD - Static variable in class ome.model.meta.GroupExperimenterMap

child() - Method in class ome.model.meta.GroupExperimenterMap

child - Variable in class ome.model.meta.ShareMember

CHILD - Static variable in class ome.model.meta.ShareMember

child() - Method in class ome.model.meta.ShareMember

child - Variable in class ome.model.screen.ScreenPlateLink

CHILD - Static variable in class ome.model.screen.ScreenPlateLink

child() - Method in class ome.model.screen.ScreenPlateLink

child - Variable in class ome.model.screen.WellReagentLink

CHILD - Static variable in class ome.model.screen.WellReagentLink

child() - Method in class ome.model.screen.WellReagentLink

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

Returns a new CheckedPath that has the given path appended to the end of this instances path.

childFolders - Variable in class ome.model.containers.Folder

CHILDFOLDERS - Static variable in class ome.model.containers.Folder

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

childType(Iterable<String>) - Method in class omero.gateway.util.Requests.FindChildrenBuilder

childType(Class<? extends IObject>...) - Method in class omero.gateway.util.Requests.FindChildrenBuilder

childType(String...) - Method in class omero.gateway.util.Requests.FindChildrenBuilder

chmod - Variable in class ome.logic.AdminImpl

chmod(IObject, String) - Method in class ome.security.basic.GroupChmodStrategy

chmod(IObject, String) - Method in interface ome.security.ChmodStrategy

Change the permissions for the given object.

chmod(String, Long, String) - Static method in class omero.gateway.util.Requests

Deprecated.

use Requests.Chmod2Builder from Requests.chmod(), see this method for an example

chmod(String, Long, ChildOption, String) - Static method in class omero.gateway.util.Requests

Deprecated.

use Requests.Chmod2Builder from Requests.chmod(), see this method for an example

chmod(String, Long, List<ChildOption>, String) - Static method in class omero.gateway.util.Requests

Deprecated.

use Requests.Chmod2Builder from Requests.chmod(), see this method for an example

chmod(String, Long, boolean, String) - Static method in class omero.gateway.util.Requests

Deprecated.

use Requests.Chmod2Builder from Requests.chmod(), see this method for an example

chmod(String, Long, ChildOption, boolean, String) - Static method in class omero.gateway.util.Requests

Deprecated.

use Requests.Chmod2Builder from Requests.chmod(), see this method for an example

chmod(String, Long, List<ChildOption>, boolean, String) - Static method in class omero.gateway.util.Requests

Deprecated.

use Requests.Chmod2Builder from Requests.chmod(), see this method for an example

chmod(String, List<Long>, String) - Static method in class omero.gateway.util.Requests

Deprecated.

use Requests.Chmod2Builder from Requests.chmod(), see this method for an example

chmod(String, List<Long>, ChildOption, String) - Static method in class omero.gateway.util.Requests

Deprecated.

use Requests.Chmod2Builder from Requests.chmod(), see this method for an example

chmod(String, List<Long>, List<ChildOption>, String) - Static method in class omero.gateway.util.Requests

Deprecated.

use Requests.Chmod2Builder from Requests.chmod(), see this method for an example

chmod(String, List<Long>, boolean, String) - Static method in class omero.gateway.util.Requests

Deprecated.

use Requests.Chmod2Builder from Requests.chmod(), see this method for an example

chmod(String, List<Long>, ChildOption, boolean, String) - Static method in class omero.gateway.util.Requests

Deprecated.

use Requests.Chmod2Builder from Requests.chmod(), see this method for an example

chmod(String, List<Long>, List<ChildOption>, boolean, String) - Static method in class omero.gateway.util.Requests

Deprecated.

use Requests.Chmod2Builder from Requests.chmod(), see this method for an example

chmod(Map<String, List<Long>>, String) - Static method in class omero.gateway.util.Requests

Deprecated.

use Requests.Chmod2Builder from Requests.chmod(), see this method for an example

chmod(Map<String, List<Long>>, ChildOption, String) - Static method in class omero.gateway.util.Requests

Deprecated.

use Requests.Chmod2Builder from Requests.chmod(), see this method for an example

chmod(Map<String, List<Long>>, List<ChildOption>, String) - Static method in class omero.gateway.util.Requests

Deprecated.

use Requests.Chmod2Builder from Requests.chmod(), see this method for an example

chmod(Map<String, List<Long>>, boolean, String) - Static method in class omero.gateway.util.Requests

Deprecated.

use Requests.Chmod2Builder from Requests.chmod(), see this method for an example

chmod(Map<String, List<Long>>, ChildOption, boolean, String) - Static method in class omero.gateway.util.Requests

Deprecated.

use Requests.Chmod2Builder from Requests.chmod(), see this method for an example

chmod(Map<String, List<Long>>, List<ChildOption>, boolean, String) - Static method in class omero.gateway.util.Requests

Deprecated.

use Requests.Chmod2Builder from Requests.chmod(), see this method for an example

chmod() - Static method in class omero.gateway.util.Requests

Chmod2Builder() - Constructor for class omero.gateway.util.Requests.Chmod2Builder

Instantiate a new Chmod2.

Chmod2I - Class in omero.cmd.graphs

Request to change the permissions on model objects, replacing version 5.0's ChmodI.

Chmod2I(ACLVoter, Roles, SystemTypes, GraphPathBean, Deletion, Set<Class<? extends IObject>>, GraphPolicy, SetMultimap<String, String>, ApplicationContext) - Constructor for class omero.cmd.graphs.Chmod2I

Deprecated.

from OMERO 5.4 the systemTypes argument is no longer included

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)

chown(String, Long, long) - Static method in class omero.gateway.util.Requests

Deprecated.

use Requests.Chown2Builder from Requests.chown(), see this method for an example

chown(String, Long, ChildOption, long) - Static method in class omero.gateway.util.Requests

Deprecated.

use Requests.Chown2Builder from Requests.chown(), see this method for an example

chown(String, Long, List<ChildOption>, long) - Static method in class omero.gateway.util.Requests

Deprecated.

use Requests.Chown2Builder from Requests.chown(), see this method for an example

chown(String, Long, boolean, long) - Static method in class omero.gateway.util.Requests

Deprecated.

use Requests.Chown2Builder from Requests.chown(), see this method for an example

chown(String, Long, ChildOption, boolean, long) - Static method in class omero.gateway.util.Requests

Deprecated.

use Requests.Chown2Builder from Requests.chown(), see this method for an example

chown(String, Long, List<ChildOption>, boolean, long) - Static method in class omero.gateway.util.Requests

Deprecated.

use Requests.Chown2Builder from Requests.chown(), see this method for an example

chown(String, List<Long>, long) - Static method in class omero.gateway.util.Requests

Deprecated.

use Requests.Chown2Builder from Requests.chown(), see this method for an example

chown(String, List<Long>, ChildOption, long) - Static method in class omero.gateway.util.Requests

Deprecated.

use Requests.Chown2Builder from Requests.chown(), see this method for an example

chown(String, List<Long>, List<ChildOption>, long) - Static method in class omero.gateway.util.Requests

Deprecated.

use Requests.Chown2Builder from Requests.chown(), see this method for an example

chown(String, List<Long>, boolean, long) - Static method in class omero.gateway.util.Requests

Deprecated.

use Requests.Chown2Builder from Requests.chown(), see this method for an example

chown(String, List<Long>, ChildOption, boolean, long) - Static method in class omero.gateway.util.Requests

Deprecated.

use Requests.Chown2Builder from Requests.chown(), see this method for an example

chown(String, List<Long>, List<ChildOption>, boolean, long) - Static method in class omero.gateway.util.Requests

Deprecated.

use Requests.Chown2Builder from Requests.chown(), see this method for an example

chown(Map<String, List<Long>>, long) - Static method in class omero.gateway.util.Requests

Deprecated.

use Requests.Chown2Builder from Requests.chown(), see this method for an example

chown(Map<String, List<Long>>, ChildOption, long) - Static method in class omero.gateway.util.Requests

Deprecated.

use Requests.Chown2Builder from Requests.chown(), see this method for an example

chown(Map<String, List<Long>>, List<ChildOption>, long) - Static method in class omero.gateway.util.Requests

Deprecated.

use Requests.Chown2Builder from Requests.chown(), see this method for an example

chown(Map<String, List<Long>>, boolean, long) - Static method in class omero.gateway.util.Requests

Deprecated.

use Requests.Chown2Builder from Requests.chown(), see this method for an example

chown(Map<String, List<Long>>, ChildOption, boolean, long) - Static method in class omero.gateway.util.Requests

Deprecated.

use Requests.Chown2Builder from Requests.chown(), see this method for an example

chown(Map<String, List<Long>>, List<ChildOption>, boolean, long) - Static method in class omero.gateway.util.Requests

Deprecated.

use Requests.Chown2Builder from Requests.chown(), see this method for an example

chown() - Static method in class omero.gateway.util.Requests

Chown2Builder() - Constructor for class omero.gateway.util.Requests.Chown2Builder

Instantiate a new Chown2 and initialize its collection containers.

Chown2I - Class in omero.cmd.graphs

Request to give model objects to a different experimenter, replacing version 5.0's ChownI.

Chown2I(ACLVoter, Roles, SystemTypes, GraphPathBean, Deletion, Set<Class<? extends IObject>>, GraphPolicy, SetMultimap<String, String>, ApplicationContext) - Constructor for class omero.cmd.graphs.Chown2I

Deprecated.

from OMERO 5.4 the systemTypes argument is no longer included

CLASS - Static variable in class ome.parameters.Parameters

named parameter "class".

classes - Variable in class ome.services.fulltext.FullTextBridge

Deprecated.

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 the top-level temporary directory.

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

cleanup() - Method in class ome.formats.importer.cli.CommandLineImporter

Cleans up after a successful or unsuccessful image import.

cleanup() - Method in class ome.services.util.ServiceHandler

cleanup() - Method in class omero.util.Resources

cleanup() - Method in interface omero.util.Resources.Entry

Gives an Resources.Entry a chance to cleanup resources before it is removed from checking.

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

Releases the lock and deletes the top-level temporary directory.

CleanupFailure - Exception in ome.formats.importer.transfers

Exception thrown when cleaning up resources after transfer fails partially or completely.

CleanupFailure(List<File>) - Constructor for exception ome.formats.importer.transfers.CleanupFailure

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

Called if this isn't a kill-everything event.

cleanupUpload(RawFileStorePrx, FileInputStream) - Method in class ome.formats.importer.transfers.AbstractFileTransfer

Utility method for closing resources.

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

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

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

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

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

clear() - Static method in class omero.gateway.facility.Facility

Clears the Facility object cache

clear() - Method in class omero.gateway.model.SearchResultCollection

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

reset all statistics

clearAllCaches() - Method in interface omero.gateway.cache.CacheService

Clears all the caches.

clearAnnotationLinks() - Method in class ome.model.acquisition.Detector

clears the set.

clearAnnotationLinks() - Method in class ome.model.acquisition.Dichroic

clears the set.

clearAnnotationLinks() - Method in class ome.model.acquisition.Filter

clears the set.

clearAnnotationLinks() - Method in class ome.model.acquisition.Instrument

clears the set.

clearAnnotationLinks() - Method in class ome.model.acquisition.LightPath

clears the set.

clearAnnotationLinks() - Method in class ome.model.acquisition.LightSource

clears the set.

clearAnnotationLinks() - Method in class ome.model.acquisition.Objective

clears the set.

clearAnnotationLinks() - Method in class ome.model.annotations.Annotation

clears the set.

clearAnnotationLinks() - Method in class ome.model.containers.Dataset

clears the set.

clearAnnotationLinks() - Method in class ome.model.containers.Folder

clears the set.

clearAnnotationLinks() - Method in class ome.model.containers.Project

clears the set.

clearAnnotationLinks() - Method in class ome.model.core.Channel

clears the set.

clearAnnotationLinks() - Method in class ome.model.core.Image

clears the set.

clearAnnotationLinks() - Method in class ome.model.core.OriginalFile

clears the set.

clearAnnotationLinks() - Method in class ome.model.core.PlaneInfo

clears the set.

clearAnnotationLinks() - Method in class ome.model.fs.Fileset

clears the set.

clearAnnotationLinks() - Method in interface ome.model.IAnnotated

clearAnnotationLinks() - Method in class ome.model.meta.Experimenter

clears the set.

clearAnnotationLinks() - Method in class ome.model.meta.ExperimenterGroup

clears the set.

clearAnnotationLinks() - Method in class ome.model.meta.Namespace

clears the set.

clearAnnotationLinks() - Method in class ome.model.meta.Node

clears the set.

clearAnnotationLinks() - Method in class ome.model.meta.Session

clears the set.

clearAnnotationLinks() - Method in class ome.model.roi.Roi

clears the set.

clearAnnotationLinks() - Method in class ome.model.roi.Shape

clears the set.

clearAnnotationLinks() - Method in class ome.model.screen.Plate

clears the set.

clearAnnotationLinks() - Method in class ome.model.screen.PlateAcquisition

clears the set.

clearAnnotationLinks() - Method in class ome.model.screen.Reagent

clears the set.

clearAnnotationLinks() - Method in class ome.model.screen.Screen

clears the set.

clearAnnotationLinks() - Method in class ome.model.screen.Well

clears the set.

clearCache(int) - Method in interface omero.gateway.cache.CacheService

Clears the specified cache.

clearChannels() - Method in class ome.model.core.LogicalChannel

clears the set.

clearChannels() - Method in class ome.model.core.Pixels

clears the set.

clearChildFolders() - Method in class ome.model.containers.Folder

clears the set.

clearDatasetLinks() - Method in class ome.model.containers.Project

clears the set.

clearDatasetLinks() - Method in class ome.model.core.Image

clears the set.

clearDetector() - Method in class ome.model.acquisition.Instrument

clears the set.

clearDichroic() - Method in class ome.model.acquisition.Instrument

clears the set.

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

clearEmissionFilterLinks() - Method in class ome.model.acquisition.Filter

clears the set.

clearEmissionFilterLinks() - Method in class ome.model.acquisition.FilterSet

clears the set.

clearEmissionFilterLinks() - Method in class ome.model.acquisition.LightPath

clears the set.

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

clearEvents() - Method in class ome.model.meta.Session

clears the set.

clearExcitationFilterLinks() - Method in class ome.model.acquisition.Filter

clears the set.

clearExcitationFilterLinks() - Method in class ome.model.acquisition.FilterSet

clears the set.

clearExcitationFilterLinks() - Method in class ome.model.acquisition.LightPath

clears the set.

clearExperimenterGroupLinks() - Method in class ome.model.meta.Experimenter

clears the set.

clearExperimenterLinks() - Method in class ome.model.meta.ExperimenterGroup

clears the set.

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

Clear the list of files to upload.

clearFilesetEntries() - Method in class ome.model.core.OriginalFile

clears the set.

clearFilter() - Method in class ome.model.acquisition.Instrument

clears the set.

clearFiltered() - Method in class ome.model.internal.Details

all currently marked collections are released.

clearFilterSet() - Method in class ome.model.acquisition.Instrument

clears the set.

clearFolderLinks() - Method in class ome.model.core.Image

clears the set.

clearFolderLinks() - Method in class ome.model.roi.Roi

clears the set.

clearImageLinks() - Method in class ome.model.containers.Dataset

clears the set.

clearImageLinks() - Method in class ome.model.containers.Folder

clears the set.

clearImages() - Method in class ome.model.fs.Fileset

clears the set.

clearJobLinks() - Method in class ome.model.fs.Fileset

clears the set.

clearLightSource() - Method in class ome.model.acquisition.Instrument

clears the set.

clearLightSourceSettings() - Method in class ome.model.experiment.MicrobeamManipulation

clears the set.

clearLogs() - Method in class ome.model.meta.Event

clears the set.

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

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

clearMicrobeamManipulation() - Method in class ome.model.experiment.Experiment

clears the set.

clearObjective() - Method in class ome.model.acquisition.Instrument

clears the set.

clearOriginalFileLinks() - Method in class ome.model.core.Pixels

clears the set.

clearOriginalFileLinks() - Method in class ome.model.jobs.Job

clears the set.

clearOtf() - Method in class ome.model.acquisition.Instrument

clears the set.

clearPermissionsBit(String, long, int) - Method in interface ome.util.SqlAction

Sets the given permissions bit to 0.

clearPermissionsBit(String, long, int) - Method in class ome.util.SqlAction.Impl

clearPixels() - Method in class ome.model.core.Image

clears the set.

clearPixelsLinks() - Method in class ome.model.core.OriginalFile

clears the set.

clearPlaneInfo() - Method in class ome.model.core.Pixels

clears the set.

clearPlateAcquisitions() - Method in class ome.model.screen.Plate

clears the set.

clearPlateLinks() - Method in class ome.model.screen.Screen

clears the set.

clearProjections() - Method in class ome.model.display.RenderingDef

clears the set.

clearProjectLinks() - Method in class ome.model.containers.Dataset

clears the set.

clearQueries() - Method in interface ome.api.Search

Removes all active queries (leaving settings alone), such that Search.activeQueries() will return 0.

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

clearQueries_async(AMD_Search_clearQueries, Current) - Method in class ome.services.blitz.impl.SearchI

clearReagentLinks() - Method in class ome.model.screen.Well

clears the set.

clearReagents() - Method in class ome.model.screen.Screen

clears the set.

clearRoiLinks() - Method in class ome.model.containers.Folder

clears the set.

clearRois() - Method in class ome.model.core.Image

clears the set.

clearScreenLinks() - Method in class ome.model.screen.Plate

clears the set.

clearSessions() - Method in class ome.model.meta.Node

clears the set.

clearSettings() - Method in class ome.model.core.Pixels

clears the set.

clearShapes() - Method in class ome.model.roi.Roi

clears the set.

clearSpatialDomainEnhancement() - Method in class ome.model.display.ChannelBinding

clears the set.

clearThumbnails() - Method in class ome.model.core.Pixels

clears the set.

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

clearUsedFiles() - Method in class ome.model.fs.Fileset

clears the set.

clearWaveRendering() - Method in class ome.model.display.RenderingDef

clears the set.

clearWellLinks() - Method in class ome.model.screen.Reagent

clears the set.

clearWells() - Method in class ome.model.screen.Plate

clears the set.

clearWellSample() - Method in class ome.model.screen.PlateAcquisition

clears the set.

clearWellSamples() - Method in class ome.model.core.Image

clears the set.

clearWellSamples() - Method in class ome.model.screen.Well

clears the set.

client - Class in omero

Central client-side blitz entry point.

client() - Constructor for class omero.client

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

client(InitializationData) - Constructor for class omero.client

Creates an Communicator from a InitializationData instance.

client(String) - Constructor for class omero.client

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

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

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

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

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

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

Creates an Communicator from command-line arguments.

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

Creates an Communicator from multiple files.

client(Map) - Constructor for class omero.client

Creates an Communicator from a Map instance.

client - Variable in class omero.model.DetailsI

CLIENT_CONTEXT - Static variable in class ome.system.OmeroContext

identifier for an OmeroContext configured in classpath*:beanRefContext.xml for use by remote (via JNDI/RMI) clients.

ClientError - Exception in omero

abstract superclass of all Omero exceptions.

ClientError(String) - Constructor for exception omero.ClientError

ClientFilePathTransformer - Class in ome.services.blitz.repo.path

Transform client-local File to repository FsFile path.

ClientFilePathTransformer(Function<String, String>) - Constructor for class ome.services.blitz.repo.path.ClientFilePathTransformer

Construct a new client-side file path transformer.

clientId - Variable in class omero.cmd.SessionI

clientId(Current) - Static method in class omero.cmd.SessionI

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

clientIds - Variable in class omero.util.ServantHolder

An internal mapping to all client ids from SessionI for a given DB session since there is no method on ObjectAdapter to retrieve all servants.

ClientKeepAlive - Class in ome.formats.importer.util

A Runnable which keeps a Connector's server-side resources from timing out.

ClientKeepAlive() - Constructor for class ome.formats.importer.util.ClientKeepAlive

clientPath - Variable in class ome.model.fs.FilesetEntry

CLIENTPATH - Static variable in class ome.model.fs.FilesetEntry

ClientPathExclusion - Class in ome.formats.importer.exclusions

Voter which checks the original filepath from the client (FilesetEntry.getClientPath()) for existence.

ClientPathExclusion() - Constructor for class ome.formats.importer.exclusions.ClientPathExclusion

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

close(boolean) - Method in class loci.ome.io.OmeroReader

Deprecated.

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() - 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() - Method in class omero.gateway.facility.RawDataFacility

close() - Method in class omero.gateway.rnd.DataSink

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

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

close(Current) - Method in interface omero.util.CloseableServant

close() - Method in class omero.util.RPSTileData

close() - Method in interface omero.util.TileData

close_async(AMD_StatefulServiceInterface_close, Current) - Method in class ome.services.blitz.impl.AbstractCloseableAmdServant

SessionHandler also specially catches close() calls, but cannot remove the servant from the ObjectAdapter and thereby prevent any further communication.

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

CloseableServant - Interface in omero.util

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

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

Close all sessions with checking for the necessary reference counts.

closeAll() - Method in class ome.services.sessions.SessionManagerImpl

closeAll() - Method in class ome.system.OmeroContext

closes all the nested OmeroContexts within this instance.

closeCalled(int) - Method in class ome.services.blitz.repo.ManagedImportProcessI

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

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

closeConnector(SecurityContext) - Method in class omero.gateway.Gateway

Close a connector for a certain SecurityContext

closed - Variable in class ome.model.meta.Session

CLOSED - Static variable in class ome.model.meta.Session

closeImport(SecurityContext, String) - Method in class omero.gateway.Gateway

Close Import for a certain user

closeNode(String) - Method in interface ome.util.SqlAction

closeNode(String) - Method in class ome.util.SqlAction.Impl

closeNodeSessions(String) - Method in interface ome.util.SqlAction

closeNodeSessions(String) - Method in class ome.util.SqlAction.Impl

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

CloseOnNoSessionContext() - Constructor for class ome.security.basic.BasicSecurityWiring.CloseOnNoSessionContext

closeParsedFiles() - Method in class ome.services.fulltext.ParserSession

Deprecated.

closeQuietly(Closeable) - Static method in class ome.util.Utils

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

closeService(SecurityContext, StatefulServiceInterfacePrx) - Method in class omero.gateway.Gateway

Close a service

closeServices() - Method in class ome.formats.OMEROMetadataStoreClient

Closes all stateful services.

closeSession(Session) - Method in interface ome.api.ISession

Closes session and releases all resources.

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

closeSession() - Method in class ome.system.ServiceFactory

closeSession() - Method in class omero.client

Closes the session and nulls out the communicator.

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

closeSession_async(AMD_ISession_closeSession, Session, Current) - Method in class ome.services.blitz.impl.SessionI

closeSessions(String) - Method in class ome.util.actions.PostgresSqlAction

closeSessions(String) - Method in interface ome.util.SqlAction

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

Deprecated.

Closes share.

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

closeShare_async(AMD_IShare_closeShare, long, Current) - Method in class ome.services.blitz.impl.ShareI

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

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

Call StatefulServiceInterfacePrx.close() on the cached uploader instance if non-null and null the instance.

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

This method should never exit without releasing the lock.

CmdCallbackI - Class in omero.cmd

Callback servant used to wait until a HandlePrx would return non-null on getReponse.

CmdCallbackI(client, HandlePrx) - Constructor for class omero.cmd.CmdCallbackI

CmdCallbackI(CmdCallbackI) - Constructor for class omero.cmd.CmdCallbackI

CmdCallbackI(ObjectAdapter, String, HandlePrx) - Constructor for class omero.cmd.CmdCallbackI

co2percent - Variable in class ome.model.acquisition.ImagingEnvironment

CO2PERCENT - Static variable in class ome.model.acquisition.ImagingEnvironment

CodomainChain - Class in omeis.providers.re.codomain

Queues the contexts that define the spatial domain transformations that have to be applied to the image.

CodomainChain(int, int) - Constructor for class omeis.providers.re.codomain.CodomainChain

Creates a new chain.

CodomainChain(int, int, List<CodomainMapContext>) - Constructor for class omeis.providers.re.codomain.CodomainChain

Creates a new chain.

CodomainMap - Interface in omeis.providers.re.codomain

Declares the interface common to all codomain maps.

CodomainMapContext - Class in ome.model.display

These filter definitions are used by the security system to eliminate non-readable objects from queries.

CodomainMapContext() - Constructor for class ome.model.display.CodomainMapContext

CodomainMapContext(Long) - Constructor for class ome.model.display.CodomainMapContext

CodomainMapContext(Long, boolean) - Constructor for class ome.model.display.CodomainMapContext

Main constructor.

CodomainMapContext(ChannelBinding) - Constructor for class ome.model.display.CodomainMapContext

CodomainMapContext - Class in omeis.providers.re.codomain

Each concrete subclass defines transformation parameters for a CodomainMap implementation.

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

CodomainMapContext.Details - Class in ome.model.display

coefficient - Variable in class ome.model.display.ChannelBinding

COEFFICIENT - Static variable in class ome.model.display.ChannelBinding

COLLAB_READLINK - Static variable in class ome.model.internal.Permissions

an immutable Permissions instance with read and write permissions for group members.

COLLAB_READONLY - Static variable in class ome.model.internal.Permissions

an immutable Permissions instance with permissions for group members to read other members' data.

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

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

collectAnnotationLinks(CBlock<E>) - Method in class ome.model.acquisition.Detector

takes a CBlock and calls the block once for each ome.model.annotations.DetectorAnnotationLink while collecting the results.

collectAnnotationLinks(CBlock<E>) - Method in class ome.model.acquisition.Dichroic

takes a CBlock and calls the block once for each ome.model.annotations.DichroicAnnotationLink while collecting the results.

collectAnnotationLinks(CBlock<E>) - Method in class ome.model.acquisition.Filter

takes a CBlock and calls the block once for each ome.model.annotations.FilterAnnotationLink while collecting the results.

collectAnnotationLinks(CBlock<E>) - Method in class ome.model.acquisition.Instrument

takes a CBlock and calls the block once for each ome.model.annotations.InstrumentAnnotationLink while collecting the results.

collectAnnotationLinks(CBlock<E>) - Method in class ome.model.acquisition.LightPath

takes a CBlock and calls the block once for each ome.model.annotations.LightPathAnnotationLink while collecting the results.

collectAnnotationLinks(CBlock<E>) - Method in class ome.model.acquisition.LightSource

takes a CBlock and calls the block once for each ome.model.annotations.LightSourceAnnotationLink while collecting the results.

collectAnnotationLinks(CBlock<E>) - Method in class ome.model.acquisition.Objective

takes a CBlock and calls the block once for each ome.model.annotations.ObjectiveAnnotationLink while collecting the results.

collectAnnotationLinks(CBlock<E>) - Method in class ome.model.annotations.Annotation

takes a CBlock and calls the block once for each ome.model.annotations.AnnotationAnnotationLink while collecting the results.

collectAnnotationLinks(CBlock<E>) - Method in class ome.model.containers.Dataset

takes a CBlock and calls the block once for each ome.model.annotations.DatasetAnnotationLink while collecting the results.

collectAnnotationLinks(CBlock<E>) - Method in class ome.model.containers.Folder

takes a CBlock and calls the block once for each ome.model.annotations.FolderAnnotationLink while collecting the results.

collectAnnotationLinks(CBlock<E>) - Method in class ome.model.containers.Project

takes a CBlock and calls the block once for each ome.model.annotations.ProjectAnnotationLink while collecting the results.

collectAnnotationLinks(CBlock<E>) - Method in class ome.model.core.Channel

takes a CBlock and calls the block once for each ome.model.annotations.ChannelAnnotationLink while collecting the results.

collectAnnotationLinks(CBlock<E>) - Method in class ome.model.core.Image

takes a CBlock and calls the block once for each ome.model.annotations.ImageAnnotationLink while collecting the results.

collectAnnotationLinks(CBlock<E>) - Method in class ome.model.core.OriginalFile

takes a CBlock and calls the block once for each ome.model.annotations.OriginalFileAnnotationLink while collecting the results.

collectAnnotationLinks(CBlock<E>) - Method in class ome.model.core.PlaneInfo

takes a CBlock and calls the block once for each ome.model.annotations.PlaneInfoAnnotationLink while collecting the results.

collectAnnotationLinks(CBlock<E>) - Method in class ome.model.fs.Fileset

takes a CBlock and calls the block once for each ome.model.annotations.FilesetAnnotationLink while collecting the results.

collectAnnotationLinks(CBlock<E>) - Method in interface ome.model.IAnnotated

collectAnnotationLinks(CBlock<E>) - Method in class ome.model.meta.Experimenter

takes a CBlock and calls the block once for each ome.model.annotations.ExperimenterAnnotationLink while collecting the results.

collectAnnotationLinks(CBlock<E>) - Method in class ome.model.meta.ExperimenterGroup

takes a CBlock and calls the block once for each ome.model.annotations.ExperimenterGroupAnnotationLink while collecting the results.

collectAnnotationLinks(CBlock<E>) - Method in class ome.model.meta.Namespace

takes a CBlock and calls the block once for each ome.model.annotations.NamespaceAnnotationLink while collecting the results.

collectAnnotationLinks(CBlock<E>) - Method in class ome.model.meta.Node

takes a CBlock and calls the block once for each ome.model.annotations.NodeAnnotationLink while collecting the results.

collectAnnotationLinks(CBlock<E>) - Method in class ome.model.meta.Session

takes a CBlock and calls the block once for each ome.model.annotations.SessionAnnotationLink while collecting the results.

collectAnnotationLinks(CBlock<E>) - Method in class ome.model.roi.Roi

takes a CBlock and calls the block once for each ome.model.annotations.RoiAnnotationLink while collecting the results.

collectAnnotationLinks(CBlock<E>) - Method in class ome.model.roi.Shape

takes a CBlock and calls the block once for each ome.model.annotations.ShapeAnnotationLink while collecting the results.

collectAnnotationLinks(CBlock<E>) - Method in class ome.model.screen.Plate

takes a CBlock and calls the block once for each ome.model.annotations.PlateAnnotationLink while collecting the results.

collectAnnotationLinks(CBlock<E>) - Method in class ome.model.screen.PlateAcquisition

takes a CBlock and calls the block once for each ome.model.annotations.PlateAcquisitionAnnotationLink while collecting the results.

collectAnnotationLinks(CBlock<E>) - Method in class ome.model.screen.Reagent

takes a CBlock and calls the block once for each ome.model.annotations.ReagentAnnotationLink while collecting the results.

collectAnnotationLinks(CBlock<E>) - Method in class ome.model.screen.Screen

takes a CBlock and calls the block once for each ome.model.annotations.ScreenAnnotationLink while collecting the results.

collectAnnotationLinks(CBlock<E>) - Method in class ome.model.screen.Well

takes a CBlock and calls the block once for each ome.model.annotations.WellAnnotationLink while collecting the results.

collectChannels(CBlock<E>) - Method in class ome.model.core.LogicalChannel

takes a CBlock and calls the block once for each ome.model.core.Channel while collecting the results.

collectChannels(CBlock<E>) - Method in class ome.model.core.Pixels

takes a CBlock and calls the block once for each ome.model.core.Channel while collecting the results.

collectChildFolders(CBlock<E>) - Method in class ome.model.containers.Folder

takes a CBlock and calls the block once for each ome.model.containers.Folder while collecting the results.

collectDatasetLinks(CBlock<E>) - Method in class ome.model.containers.Project

takes a CBlock and calls the block once for each ome.model.containers.ProjectDatasetLink while collecting the results.

collectDatasetLinks(CBlock<E>) - Method in class ome.model.core.Image

takes a CBlock and calls the block once for each ome.model.containers.DatasetImageLink while collecting the results.

collectDetector(CBlock<E>) - Method in class ome.model.acquisition.Instrument

takes a CBlock and calls the block once for each ome.model.acquisition.Detector while collecting the results.

collectDichroic(CBlock<E>) - Method in class ome.model.acquisition.Instrument

takes a CBlock and calls the block once for each ome.model.acquisition.Dichroic while collecting the results.

CollectedACLViolations - Exception in ome.conditions.acl

User has attempted an action which is not permitted by the Permissions of a given instance.

CollectedACLViolations(String) - Constructor for exception ome.conditions.acl.CollectedACLViolations

collectEmissionFilterLink(CBlock<E>) - Method in class ome.model.acquisition.Filter

takes a CBlock and calls the block once for each ome.model.acquisition.FilterSetEmissionFilterLink while collecting the results.

collectEmissionFilterLink(CBlock<E>) - Method in class ome.model.acquisition.FilterSet

takes a CBlock and calls the block once for each ome.model.acquisition.FilterSetEmissionFilterLink while collecting the results.

collectEmissionFilterLink(CBlock<E>) - Method in class ome.model.acquisition.LightPath

takes a CBlock and calls the block once for each ome.model.acquisition.LightPathEmissionFilterLink while collecting the results.

collectEvents(CBlock<E>) - Method in class ome.model.meta.Session

takes a CBlock and calls the block once for each ome.model.meta.Event while collecting the results.

collectExcitationFilterLink(CBlock<E>) - Method in class ome.model.acquisition.Filter

takes a CBlock and calls the block once for each ome.model.acquisition.FilterSetExcitationFilterLink while collecting the results.

collectExcitationFilterLink(CBlock<E>) - Method in class ome.model.acquisition.FilterSet

takes a CBlock and calls the block once for each ome.model.acquisition.FilterSetExcitationFilterLink while collecting the results.

collectExcitationFilterLink(CBlock<E>) - Method in class ome.model.acquisition.LightPath

takes a CBlock and calls the block once for each ome.model.acquisition.LightPathExcitationFilterLink while collecting the results.

collectFilesetEntries(CBlock<E>) - Method in class ome.model.core.OriginalFile

takes a CBlock and calls the block once for each ome.model.fs.FilesetEntry while collecting the results.

collectFilter(CBlock<E>) - Method in class ome.model.acquisition.Instrument

takes a CBlock and calls the block once for each ome.model.acquisition.Filter while collecting the results.

collectFilterSet(CBlock<E>) - Method in class ome.model.acquisition.Instrument

takes a CBlock and calls the block once for each ome.model.acquisition.FilterSet while collecting the results.

collectFolderLinks(CBlock<E>) - Method in class ome.model.core.Image

takes a CBlock and calls the block once for each ome.model.containers.FolderImageLink while collecting the results.

collectFolderLinks(CBlock<E>) - Method in class ome.model.roi.Roi

takes a CBlock and calls the block once for each ome.model.containers.FolderRoiLink while collecting the results.

collectGroupExperimenterMap(CBlock<E>) - Method in class ome.model.meta.Experimenter

takes a CBlock and calls the block once for each ome.model.meta.GroupExperimenterMap while collecting the results.

collectGroupExperimenterMap(CBlock<E>) - Method in class ome.model.meta.ExperimenterGroup

takes a CBlock and calls the block once for each ome.model.meta.GroupExperimenterMap while collecting the results.

collectImageLinks(CBlock<E>) - Method in class ome.model.containers.Dataset

takes a CBlock and calls the block once for each ome.model.containers.DatasetImageLink while collecting the results.

collectImageLinks(CBlock<E>) - Method in class ome.model.containers.Folder

takes a CBlock and calls the block once for each ome.model.containers.FolderImageLink while collecting the results.

collectImages(CBlock<E>) - Method in class ome.model.fs.Fileset

takes a CBlock and calls the block once for each ome.model.core.Image while collecting the results.

CollectionCountQueryDefinition - Class in ome.services.query

counts the number of members in a collection.

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

CollectionQueryParameterDef - Class in ome.services.query

extension of QueryParameterDef which restricts the type to a Collection, and specifies the element types of that Collection.

CollectionQueryParameterDef(String, boolean, Class) - Constructor for class ome.services.query.CollectionQueryParameterDef

collectJobLinks(CBlock<E>) - Method in class ome.model.fs.Fileset

takes a CBlock and calls the block once for each ome.model.fs.FilesetJobLink while collecting the results.

collectLightSource(CBlock<E>) - Method in class ome.model.acquisition.Instrument

takes a CBlock and calls the block once for each ome.model.acquisition.LightSource while collecting the results.

collectLightSourceSettings(CBlock<E>) - Method in class ome.model.experiment.MicrobeamManipulation

takes a CBlock and calls the block once for each ome.model.acquisition.LightSettings while collecting the results.

collectLogs(CBlock<E>) - Method in class ome.model.meta.Event

takes a CBlock and calls the block once for each ome.model.meta.EventLog while collecting the results.

collectMicrobeamManipulation(CBlock<E>) - Method in class ome.model.experiment.Experiment

takes a CBlock and calls the block once for each ome.model.experiment.MicrobeamManipulation while collecting the results.

collectObjective(CBlock<E>) - Method in class ome.model.acquisition.Instrument

takes a CBlock and calls the block once for each ome.model.acquisition.Objective while collecting the results.

collectOriginalFileLinks(CBlock<E>) - Method in class ome.model.jobs.Job

takes a CBlock and calls the block once for each ome.model.jobs.JobOriginalFileLink while collecting the results.

collectOtf(CBlock<E>) - Method in class ome.model.acquisition.Instrument

takes a CBlock and calls the block once for each ome.model.acquisition.OTF while collecting the results.

collectPixels(CBlock<E>) - Method in class ome.model.core.Image

takes a CBlock and calls the block once for each ome.model.core.Pixels while collecting the results.

collectPixelsFileMaps(CBlock<E>) - Method in class ome.model.core.OriginalFile

takes a CBlock and calls the block once for each ome.model.core.PixelsOriginalFileMap while collecting the results.

collectPixelsFileMaps(CBlock<E>) - Method in class ome.model.core.Pixels

takes a CBlock and calls the block once for each ome.model.core.PixelsOriginalFileMap while collecting the results.

collectPlaneInfo(CBlock<E>) - Method in class ome.model.core.Pixels

takes a CBlock and calls the block once for each ome.model.core.PlaneInfo while collecting the results.

collectPlateAcquisitions(CBlock<E>) - Method in class ome.model.screen.Plate

takes a CBlock and calls the block once for each ome.model.screen.PlateAcquisition while collecting the results.

collectPlateLinks(CBlock<E>) - Method in class ome.model.screen.Screen

takes a CBlock and calls the block once for each ome.model.screen.ScreenPlateLink while collecting the results.

collectProjections(CBlock<E>) - Method in class ome.model.display.RenderingDef

takes a CBlock and calls the block once for each ome.model.display.ProjectionDef while collecting the results.

collectProjectLinks(CBlock<E>) - Method in class ome.model.containers.Dataset

takes a CBlock and calls the block once for each ome.model.containers.ProjectDatasetLink while collecting the results.

collectReagentLinks(CBlock<E>) - Method in class ome.model.screen.Well

takes a CBlock and calls the block once for each ome.model.screen.WellReagentLink while collecting the results.

collectReagents(CBlock<E>) - Method in class ome.model.screen.Screen

takes a CBlock and calls the block once for each ome.model.screen.Reagent while collecting the results.

collectRoiLinks(CBlock<E>) - Method in class ome.model.containers.Folder

takes a CBlock and calls the block once for each ome.model.containers.FolderRoiLink while collecting the results.

collectRois(CBlock<E>) - Method in class ome.model.core.Image

takes a CBlock and calls the block once for each ome.model.roi.Roi while collecting the results.

collectScreenLinks(CBlock<E>) - Method in class ome.model.screen.Plate

takes a CBlock and calls the block once for each ome.model.screen.ScreenPlateLink while collecting the results.

collectSessions(CBlock<E>) - Method in class ome.model.meta.Node

takes a CBlock and calls the block once for each ome.model.meta.Session while collecting the results.

collectSettings(CBlock<E>) - Method in class ome.model.core.Pixels

takes a CBlock and calls the block once for each ome.model.display.RenderingDef while collecting the results.

collectShapes(CBlock<E>) - Method in class ome.model.roi.Roi

takes a CBlock and calls the block once for each ome.model.roi.Shape while collecting the results.

collectSpatialDomainEnhancement(CBlock<E>) - Method in class ome.model.display.ChannelBinding

takes a CBlock and calls the block once for each ome.model.display.CodomainMapContext while collecting the results.

collectThumbnails(CBlock<E>) - Method in class ome.model.core.Pixels

takes a CBlock and calls the block once for each ome.model.display.Thumbnail while collecting the results.

collectUsedFiles(CBlock<E>) - Method in class ome.model.fs.Fileset

takes a CBlock and calls the block once for each ome.model.fs.FilesetEntry while collecting the results.

collectWaveRendering(CBlock<E>) - Method in class ome.model.display.RenderingDef

takes a CBlock and calls the block once for each ome.model.display.ChannelBinding while collecting the results.

collectWellLinks(CBlock<E>) - Method in class ome.model.screen.Reagent

takes a CBlock and calls the block once for each ome.model.screen.WellReagentLink while collecting the results.

collectWells(CBlock<E>) - Method in class ome.model.screen.Plate

takes a CBlock and calls the block once for each ome.model.screen.Well while collecting the results.

collectWellSample(CBlock<E>) - Method in class ome.model.screen.PlateAcquisition

takes a CBlock and calls the block once for each ome.model.screen.WellSample while collecting the results.

collectWellSamples(CBlock<E>) - Method in class ome.model.core.Image

takes a CBlock and calls the block once for each ome.model.screen.WellSample while collecting the results.

collectWellSamples(CBlock<E>) - Method in class ome.model.screen.Well

takes a CBlock and calls the block once for each ome.model.screen.WellSample while collecting the results.

ColorsFactory - Class in ome.formats.model

Utility class to determine the color usually associated to a specified channel depending on its emission wavelength.

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

ColorsFactory - Class in omeis.providers.re

Utility class to determine the color usually associated to a specified channel depending on its emission wavelength.

ColorsFactory() - Constructor for class omeis.providers.re.ColorsFactory

column - Variable in class ome.model.screen.Well

COLUMN - Static variable in class ome.model.screen.Well

columnNamingConvention - Variable in class ome.model.screen.Plate

COLUMNNAMINGCONVENTION - Static variable in class ome.model.screen.Plate

columns - Variable in class ome.model.screen.Plate

COLUMNS - Static variable in class ome.model.screen.Plate

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

Deprecated.

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

combineFilePathRestrictions(FilePathRestrictions...) - Static method in class ome.services.blitz.repo.path.FilePathRestrictions

Combine sets of rules to form a set that satisfies them all and that include transformations away from Unicode control characters.

CommandLineImporter - Class in ome.formats.importer.cli

The base entry point for the CLI version of the OMERO importer.

CommandLineImporter(ImportConfig, String[], boolean) - Constructor for class ome.formats.importer.cli.CommandLineImporter

Legacy constructor which uses a UploadFileTransfer.

CommandLineImporter(ImportConfig, String[], boolean, FileTransfer, int) - Constructor for class ome.formats.importer.cli.CommandLineImporter

Legacy constructor without any file exclusions.

CommandLineImporter(ImportConfig, String[], boolean, FileTransfer, List<FileExclusion>, int) - Constructor for class ome.formats.importer.cli.CommandLineImporter

Main entry class for the application.

CommentAnnotation - Class in ome.model.annotations

CommentAnnotation() - Constructor for class ome.model.annotations.CommentAnnotation

CommentAnnotation(Long) - Constructor for class ome.model.annotations.CommentAnnotation

CommentAnnotation(Long, boolean) - Constructor for class ome.model.annotations.CommentAnnotation

Main constructor.

commonRoot(List<FsFile>) - Method in class ome.services.blitz.repo.ManagedRepositoryI

From a list of paths, calculate the common root path that all share.

COMPANION_FILE_NS - Static variable in class omero.gateway.model.FileAnnotationData

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

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

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

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

compare(Object, Object) - Method in class omero.gateway.model.ROICoordinate

Implemented as specified by the Comparator I/F.

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

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

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

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

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

comparePasswords(String, String) - Method in interface ome.security.auth.PasswordUtility

Complement - Class in ome.services.search

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

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

complete() - Method in class ome.formats.OverlayMetadataStore

Completes overlay population, flushing in memory ROI.

completeFast - Variable in class ome.services.fulltext.FullTextIndexer

Deprecated.

completeSlow - Variable in class ome.services.fulltext.FullTextIndexer

Deprecated.

COMPLEX_TYPE - Static variable in class omero.gateway.model.PixelsData

Identifies the type used to store pixel values.

CompositeACLVoter - Class in ome.security

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

CompressImpl - Class in ome.logic

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

compression - Variable in class ome.model.display.RenderingDef

COMPRESSION - Static variable in class ome.model.display.RenderingDef

compressToStream(BufferedImage, OutputStream) - Method in interface ome.api.local.LocalCompress

Compresses a buffered image to an output stream.

compressToStream(BufferedImage, OutputStream) - Method in class ome.logic.CompressImpl

computeLocationStats(Pixels, PixelBuffer, PlaneDef, int) - Method in class omeis.providers.re.metadata.StatsFactory

Helper object to determine the location of the pixels' values, the inputWindow i.e.

concatenate(FsFile...) - Static method in class ome.services.blitz.repo.path.FsFile

Concatenate paths.

ConcurrencyException - Exception in ome.conditions

Error due to simultaneous access of some resource.

ConcurrencyException(String, long) - Constructor for exception ome.conditions.ConcurrencyException

ConcurrentStatisticsImpl - Class in org.hibernate.stat

Implementation of Statistics, as well as StatisticsImplementor, based on the java.util.concurrent package introduced in Java 5.

ConcurrentStatisticsImpl() - Constructor for class org.hibernate.stat.ConcurrentStatisticsImpl

ConcurrentStatisticsImpl(SessionFactoryImplementor) - Constructor for class org.hibernate.stat.ConcurrentStatisticsImpl

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

Configuration used by all components

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

config - Variable in class ome.model.meta.Experimenter

CONFIG - Static variable in class ome.model.meta.Experimenter

config - Variable in class ome.model.meta.ExperimenterGroup

CONFIG - Static variable in class ome.model.meta.ExperimenterGroup

CONFIG_KEY - Static variable in class ome.util.PixelData

configGroup(EventContext, List<Long>) - Method in class ome.security.basic.AllGroupsSecurityFilter

ConfigI - Class in ome.services.blitz.impl

Implementation of the IConfig service.

ConfigI(IConfig, BlitzExecutor) - Constructor for class ome.services.blitz.impl.ConfigI

ConfigImpl - Class in ome.logic

implementation of the IConfig service interface.

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

ConfigRedirector - Class in ome.services.blitz.redirect

Redirector implementation which uses the REDIRECT config key via LocalConfig to know which Node is currently active.

ConfigRedirector(Executor) - Constructor for class ome.services.blitz.redirect.ConfigRedirector

ConfigurablePasswordProvider - Class in ome.security.auth

Base class for most PasswordProvider implementations, providing configuration for default behaviors.

ConfigurablePasswordProvider(PasswordUtil) - Constructor for class ome.security.auth.ConfigurablePasswordProvider

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.

configure(Type, Properties, Dialect) - Method in class ome.util.TableIdGenerator

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

Modifies the logging level of everything under the ome.formats, ome.services.blitz, ome.system and loci packages hierarchically.

ConfiguredTileSizes - Class in ome.io.nio

Implementation which has all values injected during configuration.

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

ConfiguredTileSizes(int, int, int, int) - Constructor for class ome.io.nio.ConfiguredTileSizes

configureServant(Object) - Method in class omero.cmd.SessionI

Apply proper AOP and call setters for any known injection properties.

configValue(String) - Method in interface ome.util.SqlAction

configValue(String) - Method in class ome.util.SqlAction.Impl

conn - Variable in class ome.model.meta.Node

CONN - Static variable in class ome.model.meta.Node

connect(LoginCredentials) - Method in class omero.gateway.Gateway

Connect to the server

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

CONNECTION - Static variable in exception omero.gateway.exception.RenderingServiceException

Indicates that the error occurred due to a connection failure.

ConnectionStatus - Enum in omero.gateway.exception

The various connections status.

consolidate() - Method in class omero.gateway.model.SearchResultCollection

Removes results which DataObjects are not set

constant - Variable in class ome.model.display.PlaneSlicingContext

CONSTANT - Static variable in class ome.model.display.PlaneSlicingContext

containedExperimenters(long) - Method in interface ome.api.IAdmin

fetch all users contained in this group.

containedExperimenters(long) - Method in class ome.logic.AdminImpl

containedExperimenters_async(AMD_IAdmin_containedExperimenters, long, Current) - Method in class ome.services.blitz.impl.AdminI

containedGroups(long) - Method in interface ome.api.IAdmin

fetch all groups of which the given user is a member.

containedGroups(long) - Method in class ome.logic.AdminImpl

containedGroups_async(AMD_IAdmin_containedGroups, long, Current) - Method in class ome.services.blitz.impl.AdminI

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

ContainerI - Class in ome.services.blitz.impl

Implementation of the IContainer service.

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

containingEvent - Variable in class ome.model.meta.Event

CONTAININGEVENT - Static variable in class ome.model.meta.Event

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

Tests if an object is currently contained in the session.

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

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

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

Required by the Shape I/F.

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

Required by the Shape I/F.

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

Required by the Shape I/F.

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

Required by the Shape I/F.

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

Required by the Shape I/F.

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

Required by the Shape I/F.

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

Required by the Shape I/F.

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

Required by the Shape I/F.

contains(Object) - Method in class omero.gateway.model.SearchResultCollection

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

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

context - Variable in class ome.logic.AdminImpl

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

context - Variable in class ome.services.blitz.repo.PublicRepositoryI

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

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

Deprecated.

context - Variable in class ome.services.messages.ContextMessage

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

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

Context(Timer.Context) - Constructor for class ome.system.metrics.DefaultTimer.Context

context - Variable in class omero.cmd.SessionI

contextAt(int) - Method in class ome.model.internal.Details

ContextFilter - Class in ome.util

modified (hierarchical) visitor pattern.

ContextFilter() - Constructor for class ome.util.ContextFilter

ContextMessage - Class in ome.services.messages

ContextMessage(Object, Map<String, String>) - Constructor for class ome.services.messages.ContextMessage

ContextMessage.Pop - Class in ome.services.messages

Published when an internal service is finished with the context previously signaled through publishing a ContextMessage.Push.

ContextMessage.Push - Class in ome.services.messages

Published when an internal service would like to modify the current EventContext.

contexts - Variable in class ome.model.internal.Details

contexts - Variable in class omero.cmd.admin.CurrentSessionsRequestI

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

contrastMethod - Variable in class ome.model.core.LogicalChannel

CONTRASTMETHOD - Static variable in class ome.model.core.LogicalChannel

ContrastMethod - Class in ome.model.enums

ContrastMethod() - Constructor for class ome.model.enums.ContrastMethod

ContrastMethod(Long) - Constructor for class ome.model.enums.ContrastMethod

ContrastMethod(Long, boolean) - Constructor for class ome.model.enums.ContrastMethod

Main constructor.

ContrastMethod(String) - Constructor for class ome.model.enums.ContrastMethod

ContrastMethod.Details - Class in ome.model.enums

ContrastStretchingContext - Class in ome.model.display

ContrastStretchingContext() - Constructor for class ome.model.display.ContrastStretchingContext

ContrastStretchingContext(Long) - Constructor for class ome.model.display.ContrastStretchingContext

ContrastStretchingContext(Long, boolean) - Constructor for class ome.model.display.ContrastStretchingContext

Main constructor.

ContrastStretchingContext(Integer, Integer, Integer, Integer) - Constructor for class ome.model.display.ContrastStretchingContext

ContrastStretchingContext - Class in omeis.providers.re.codomain

Two points pStart and pEnd define the context of this transformation.

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

control - Variable in class omero.cmd.SessionI

Conversion - Class in ome.model.units

Base-functor like object which can be used for preparing complex equations for converting from one unit to another.

Conversion(Conversion...) - Constructor for class ome.model.units.Conversion

Primary constructor for a Conversion object.

Conversion.Add - Class in ome.model.units

Sums all Conversion instances via BigDecimal.add(BigDecimal).

Conversion.Int - Class in ome.model.units

Simply is a representation of a possibly large integer.

Conversion.Mul - Class in ome.model.units

Multiplies all Conversion instances via BigDecimal.multiply(BigDecimal).

Conversion.Pow - Class in ome.model.units

Exponentiates two Conversion instances via BigDecimal.pow(int).

Conversion.Rat - Class in ome.model.units

Divides two Conversion instances via BigDecimal.divide(BigDecimal, MathContext).

Conversion.Sym - Class in ome.model.units

Simply represents the variable of the source unit so that Conversion.Sym.convert(double) just returns the value passed in.

conversions - Variable in class ome.model.units.Conversion

Conversions, if any, which are passed into the constructor of this instance.

convert(double) - Method in class ome.model.units.Conversion.Add

convert(double) - Method in class ome.model.units.Conversion

Primary operator for Conversion instances.

convert(double) - Method in class ome.model.units.Conversion.Int

Returns a BigDecimal representation of this int.

convert(double) - Method in class ome.model.units.Conversion.Mul

convert(double) - Method in class ome.model.units.Conversion.Pow

convert(double) - Method in class ome.model.units.Conversion.Rat

convert(double) - Method in class ome.model.units.Conversion.Sym

convert(ElectricPotential) - Static method in class omero.model.ElectricPotentialI

FIXME: this should likely take a default so that locations which don't want an exception can have log.warn("Using new PositiveFloat(1.0)!"

convert(Frequency) - Static method in class omero.model.FrequencyI

FIXME: this should likely take a default so that locations which don't want an exception can have log.warn("Using new PositiveFloat(1.0)!"

convert(Length) - Static method in class omero.model.LengthI

FIXME: this should likely take a default so that locations which don't want an exception can have log.warn("Using new PositiveFloat(1.0)!"

convert(Power) - Static method in class omero.model.PowerI

FIXME: this should likely take a default so that locations which don't want an exception can have log.warn("Using new PositiveFloat(1.0)!"

convert(Pressure) - Static method in class omero.model.PressureI

FIXME: this should likely take a default so that locations which don't want an exception can have log.warn("Using new PositiveFloat(1.0)!"

convert(Temperature) - Static method in class omero.model.TemperatureI

FIXME: this should likely take a default so that locations which don't want an exception can have log.warn("Using new PositiveFloat(1.0)!"

convert(Time) - Static method in class omero.model.TimeI

FIXME: this should likely take a default so that locations which don't want an exception can have log.warn("Using new PositiveFloat(1.0)!"

convert(IceMapper) - Method in interface omero.rtypes.Conversion

Convert the "val" field on the given RType instance to an ome.model.* representation.

convert(EventContext) - Static method in class omero.util.IceMapper

convert(RGBBuffer) - Static method in class omero.util.IceMapper

convert(CodomainMapContext) - Method in class omero.util.IceMapper

Converts the passed Ice Object and returns the converted object.

convert(PlaneDef) - Static method in class omero.util.IceMapper

Converts the passed Ice Object and returns the converted object.

convert(Principal) - Static method in class omero.util.IceMapper

convert(Roles) - Static method in class omero.util.IceMapper

convert(Date) - Static method in class omero.util.IceMapper

convert(RTime) - Static method in class omero.util.IceMapper

convert(Parameters) - Method in class omero.util.IceMapper

convert(String, Object) - Method in class omero.util.IceMapper

convert(Options) - Static method in class omero.util.IceMapper

convert(Filter) - Static method in class omero.util.IceMapper

convert(Permissions) - Static method in class omero.util.IceMapper

convert(Permissions) - Static method in class omero.util.IceMapper

convertElectricPotential(ElectricPotential) - Static method in class ome.formats.model.UnitsFactory

Convert a Bio-Formats ElectricPotential to an OMERO ElectricPotential.

convertElectricPotential(ElectricPotential) - Static method in class ome.formats.model.UnitsFactory

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

convertElectricPotential(ElectricPotential) - Static method in class ome.model.units.ElectricPotential

FIXME: this should likely take a default so that locations which don't want an exception can have log.warn("Using new PositiveFloat(1.0)!"

convertElectricPotential(ElectricPotential, Unit<ElectricPotential>) - Static method in class ome.model.units.ElectricPotential

convertElectricPotential(ElectricPotential, String) - Static method in class ome.model.units.ElectricPotential

convertElectricPotentialXML(ElectricPotential, String) - Static method in class ome.formats.model.UnitsFactory

convertFrequency(Frequency) - Static method in class ome.formats.model.UnitsFactory

Convert a Bio-Formats Frequency to an OMERO Frequency.

convertFrequency(Frequency) - Static method in class ome.formats.model.UnitsFactory

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

convertFrequency(Frequency) - Static method in class ome.model.units.Frequency

FIXME: this should likely take a default so that locations which don't want an exception can have log.warn("Using new PositiveFloat(1.0)!"

convertFrequency(Frequency, Unit<Frequency>) - Static method in class ome.model.units.Frequency

convertFrequency(Frequency, String) - Static method in class ome.model.units.Frequency

convertFrequencyXML(Frequency, String) - Static method in class ome.formats.model.UnitsFactory

convertLength(Length) - Static method in class ome.formats.model.UnitsFactory

Convert a Bio-Formats Length to an OMERO Length.

convertLength(Length) - Static method in class ome.formats.model.UnitsFactory

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

convertLength(Length) - Static method in class ome.model.units.Length

FIXME: this should likely take a default so that locations which don't want an exception can have log.warn("Using new PositiveFloat(1.0)!"

convertLength(Length, Unit<Length>) - Static method in class ome.model.units.Length

convertLength(Length, String) - Static method in class ome.model.units.Length

convertLengthXML(Length, String) - Static method in class ome.formats.model.UnitsFactory

convertMapPairs(List<MapPair>) - Static method in class omero.util.IceMapper

convertNamedValueList(List<NamedValue>) - Static method in class omero.util.IceMapper

convertPower(Power) - Static method in class ome.formats.model.UnitsFactory

Convert a Bio-Formats Power to an OMERO Power.

convertPower(Power) - Static method in class ome.formats.model.UnitsFactory

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

convertPower(Power) - Static method in class ome.model.units.Power

FIXME: this should likely take a default so that locations which don't want an exception can have log.warn("Using new PositiveFloat(1.0)!"

convertPower(Power, Unit<Power>) - Static method in class ome.model.units.Power

convertPower(Power, String) - Static method in class ome.model.units.Power

convertPowerXML(Power, String) - Static method in class ome.formats.model.UnitsFactory

convertPressure(Pressure) - Static method in class ome.formats.model.UnitsFactory

Convert a Bio-Formats Pressure to an OMERO Pressure.

convertPressure(Pressure) - Static method in class ome.formats.model.UnitsFactory

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

convertPressure(Pressure) - Static method in class ome.model.units.Pressure

FIXME: this should likely take a default so that locations which don't want an exception can have log.warn("Using new PositiveFloat(1.0)!"

convertPressure(Pressure, Unit<Pressure>) - Static method in class ome.model.units.Pressure

convertPressure(Pressure, String) - Static method in class ome.model.units.Pressure

convertPressureXML(Pressure, String) - Static method in class ome.formats.model.UnitsFactory

convertRTypeToJava(RType) - Static method in class omero.gateway.util.ModelMapper

Converts the passed OMERO type into its corresponding Java type.

convertStringStringMap(Map<String, String>) - Static method in class omero.util.IceMapper

Convert a String→String map's values to RStrings.

convertTemperature(Temperature) - Static method in class ome.formats.model.UnitsFactory

Convert a Bio-Formats Temperature to an OMERO Temperature.

convertTemperature(Temperature) - Static method in class ome.formats.model.UnitsFactory

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

convertTemperature(Temperature) - Static method in class ome.model.units.Temperature

FIXME: this should likely take a default so that locations which don't want an exception can have log.warn("Using new PositiveFloat(1.0)!"

convertTemperature(Temperature, Unit<Temperature>) - Static method in class ome.model.units.Temperature

convertTemperature(Temperature, String) - Static method in class ome.model.units.Temperature

convertTemperatureXML(Temperature, String) - Static method in class ome.formats.model.UnitsFactory

convertTime(Time) - Static method in class ome.formats.model.UnitsFactory

Convert a Bio-Formats Time to an OMERO Time.

convertTime(Time) - Static method in class ome.formats.model.UnitsFactory

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

convertTime(Time) - Static method in class ome.model.units.Time

FIXME: this should likely take a default so that locations which don't want an exception can have log.warn("Using new PositiveFloat(1.0)!"

convertTime(Time, Unit<Time>) - Static method in class ome.model.units.Time

convertTime(Time, String) - Static method in class ome.model.units.Time

convertTimeXML(Time, String) - Static method in class ome.formats.model.UnitsFactory

ConvertToBlitzExceptionMessage - Class in ome.services.blitz.util

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

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

convertToDataObjects(Collection) - Static method in class omero.gateway.util.PojoMapper

Converts each element of the collection into its corresponding DataObject.

convertTypeForSearch(Class) - Static method in class omero.gateway.util.PojoMapper

Converts the specified type to its corresponding type for search.

convertTypeForSearchByQuery(Class) - Static method in class omero.gateway.util.PojoMapper

Deprecated.

Not used.

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

Copiable - Interface in ome.util.mem

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

CopiableArray - Class in ome.util.mem

This abstract class provides an implementation of the Copiable interface.

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

Creates a new instance.

copy() - Method in class ome.model.internal.Details

copy(Details) - Method in class ome.model.internal.Details

Method which takes all field values from the given Details instance and copies them into the current instance.

copy(SearchValues) - Method in class ome.services.search.SearchValues

copy(Parameters) - Method in class ome.services.search.SearchValues

Copies all known values from Parameters

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

copy(EventContext) - Method in class ome.system.SimpleEventContext

Copies all values directly from the given instance into this instance.

copy(Map) - Static method in class ome.tools.hibernate.HibernateUtils

copy(Collection) - Static method in class ome.tools.hibernate.HibernateUtils

copy() - Method in interface ome.util.mem.Copiable

Makes a copy of this object.

copy(int, int) - Method in class ome.util.mem.CopiableArray

Copies the Copiable from the specified position from into the specified position to.

copy() - Method in class ome.util.mem.CopiableArray

Implements the method as specified by Copiable.

copy() - Method in class ome.util.mem.Handle

Returns a deep copy of this object.

copy(T) - Method in class ome.util.ShallowCopy

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

Returns a deep copy of this object.

copy() - Method in class omeis.providers.re.codomain.ContrastStretchingContext

Implemented as specified by superclass.

copy() - Method in class omeis.providers.re.codomain.IdentityMapContext

Implemented as specified by superclass.

copy() - Method in class omeis.providers.re.codomain.PlaneSlicingContext

Implemented as specified by superclass.

copy() - Method in class omeis.providers.re.codomain.ReverseIntensityContext

Implemented as specified by superclass.

copy() - Method in class omero.gateway.SecurityContext

Returns a copy of the security context.

copy(Current) - Method in class omero.model.ElectricPotentialI

copy(Current) - Method in class omero.model.FrequencyI

copy(Current) - Method in class omero.model.LengthI

copy(Current) - Method in class omero.model.PowerI

copy(Current) - Method in class omero.model.PressureI

copy(Current) - Method in class omero.model.TemperatureI

copy(Current) - Method in class omero.model.TimeI

copyAndResizeImage(long, Integer, Integer, Integer, Integer, List<Integer>, String, boolean) - Method in interface ome.api.IPixels

Copies the metadata, and only the metadata linked to a Image object into a new Image object of equal or differing size across one or many of its three physical dimensions or temporal dimension.

copyAndResizeImage(long, Integer, Integer, Integer, Integer, List<Integer>, String, boolean) - Method in class ome.logic.PixelsImpl

copyAndResizeImage_async(AMD_IPixels_copyAndResizeImage, long, RInt, RInt, RInt, RInt, List<Integer>, String, boolean, Current) - Method in class ome.services.blitz.impl.PixelsI

copyAndResizePixels(long, Integer, Integer, Integer, Integer, List<Integer>, String, boolean) - Method in interface ome.api.IPixels

Copies the metadata, and only the metadata linked to a Pixels object into a new Pixels object of equal or differing size across one or many of its three physical dimensions or temporal dimension.

copyAndResizePixels(long, Integer, Integer, Integer, Integer, List<Integer>, String, boolean) - Method in class ome.logic.PixelsImpl

copyAndResizePixels_async(AMD_IPixels_copyAndResizePixels, long, RInt, RInt, RInt, RInt, List<Integer>, String, boolean, Current) - Method in class ome.services.blitz.impl.PixelsI

copyAnnotationLinks() - Method in class omero.gateway.model.FolderData

Copy the list of annotation links, see Folder.copyAnnotationLinks()

copyChildFolders() - Method in class omero.gateway.model.FolderData

Copy the list of child folders, see Folder.copyChildFolders()

copyClassListToArray(List<Class>) - Static method in class ome.services.search.SearchValues

copyDetails(Details) - Static method in class ome.services.search.SearchValues

copyExtendedRestrictions() - Method in class ome.model.internal.Permissions

Produce a copy of restrictions for use elsewhere.

copyFieldsTo(Chgrp2) - Method in class omero.cmd.graphs.Chgrp2I

copyFieldsTo(Chmod2) - Method in class omero.cmd.graphs.Chmod2I

copyFieldsTo(Chown2) - Method in class omero.cmd.graphs.Chown2I

copyFieldsTo(Delete2) - Method in class omero.cmd.graphs.Delete2I

copyFieldsTo(Duplicate) - Method in class omero.cmd.graphs.DuplicateI

copyFieldsTo(X) - Method in interface omero.cmd.graphs.WrappableRequest

Copy the fields of this request to that of the given request.

CopyFileTransfer - Class in ome.formats.importer.transfers

Local-only file transfer mechanism which makes use of the plaform copy command.

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

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

copyImageLinks() - Method in class omero.gateway.model.FolderData

Copy the list of image links, see Folder.copyImageLinks()

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

CopyMoveFileTransfer - Class in ome.formats.importer.transfers

Local-only file transfer mechanism which makes use of the local copy command followed by the deletion of the original source file.

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

copyMultimapForResponse(SetMultimap<String, Long>) - Static method in class omero.cmd.graphs.GraphUtil

Copy a multimap to a new map.

copyObject(Filterable, ModelMapper) - Method in interface ome.model.ModelBased

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

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

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

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

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

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

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

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

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

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

copyRestrictions() - Method in class ome.model.internal.Permissions

Produce a copy of restrictions for use elsewhere.

copyRestrictions(boolean[], String[]) - Method in class ome.model.internal.Permissions

Safely copy the source array.

copyRestrictions(int, Set<String>) - Method in class ome.model.internal.Permissions

Copy restrictions based on the integer returned by BasicACLVoter.

copyROILinks() - Method in class omero.gateway.model.FolderData

Copy the list of roi links, see Folder.copyRoiLinks()

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

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

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

copy a token from one IObject to another.

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

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

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

copyWhereUnset(Details, Details) - Method in class ome.model.internal.Details

For any field of this which is null (and is NOT null on mask -- assuming mask is not null), copy the same value from copyFrom into this object.

correction - Variable in class ome.model.acquisition.Objective

CORRECTION - Static variable in class ome.model.acquisition.Objective

Correction - Class in ome.model.enums

Correction() - Constructor for class ome.model.enums.Correction

Correction(Long) - Constructor for class ome.model.enums.Correction

Correction(Long, boolean) - Constructor for class ome.model.enums.Correction

Main constructor.

Correction(String) - Constructor for class ome.model.enums.Correction

Correction.Details - Class in ome.model.enums

correctionCollar - Variable in class ome.model.acquisition.ObjectiveSettings

CORRECTIONCOLLAR - Static variable in class ome.model.acquisition.ObjectiveSettings

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

count() - Method in class ome.services.messages.DeleteLogMessage

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

Returns the SessionContext.Count instance held by this context.

Count(String) - Constructor for class ome.services.sessions.SessionContext.Count

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

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

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

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

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

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

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

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

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

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

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

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

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

CountCollectionPersister - Class in ome.util

CollectionPersister which knows how to handle the count views generated by dsl/resources/ome/dsl/views.dm.

CountCollectionPersister(Collection, CollectionRegionAccessStrategy, Configuration, SessionFactoryImplementor) - Constructor for class ome.util.CountCollectionPersister

Counter - Interface in ome.system.metrics

Thin wrapper around Counter

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

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

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

CounterFactory - Class in ome.services.sessions.stats

Factory for creating counter objects.

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

countFormat(String) - Method in class ome.util.actions.PostgresSqlAction

countFormat(String) - Method in interface ome.util.SqlAction

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

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

countLocks(Session, Long, String[][], String) - Method in interface ome.tools.hibernate.ExtendedMetadata

Takes the lock checks returned by ExtendedMetadata.getLockChecks(Class) and performs the actual check returning a map from class to total number of locks.

countLocks(Session, Long, String[][], String) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl

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

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

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

Counts the number of annotation of a given type.

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

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

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

cpf - Variable in class ome.logic.AdminImpl

cpf - Variable in class ome.services.blitz.impl.ScriptI

CRC32ChecksumProviderImpl - Class in ome.util.checksum

An implementation of the ChecksumProvider interface using CRC32 as the message digest algorithm.

CRC32ChecksumProviderImpl() - Constructor for class ome.util.checksum.CRC32ChecksumProviderImpl

create() - Static method in class ome.model.internal.Details

Call Details.create(Object[]) with null.

create(Object[]) - Static method in class ome.model.internal.Details

Factory method which returns a Details implementation for passing in API calls, but cannot be stored within an IObject instance.

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

create(String) - Method in class omero.util.ObjectFactoryRegistry.ObjectFactory

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

createAnnotation(AnnotationData) - Static method in class omero.gateway.util.ModelMapper

Creates a new annotation IObject.

createAnnotationAndLink(IObject, AnnotationData) - Static method in class omero.gateway.util.ModelMapper

Creates a new annotation IObject.

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

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

createBfReader() - Method in class ome.io.nio.PixelsService

Create an IFormatReader with the appropriate ReaderWrapper instances and IFormatReader.setFlattenedResolutions(boolean) set to false.

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

Returns the image that represents the SVG document.

createBufferedImage(int[], int, int) - Static method in class ome.util.ImageUtil

Creates a buffered image from a rendering engine RGB buffer without data copying.

createByName(String, Current) - Method in class ome.services.blitz.impl.ServiceFactoryI

createCache(CacheEventListener...) - Method in class ome.services.sessions.state.CacheFactory

createCache(String, boolean, int) - Method in class ome.services.sessions.state.SessionCache

createCache() - Method in interface omero.gateway.cache.CacheService

Creates a default cache.

createCache(int, int) - Method in interface omero.gateway.cache.CacheService

Creates a cache of a given type.

createCache(int) - Method in interface omero.gateway.cache.CacheService

Creates a cache of a given type.

createCallback(ImportProcessPrx, HandlePrx, ImportContainer) - Method in class ome.formats.importer.ImportLibrary

createChildOption() - Method in class omero.cmd.graphs.GraphRequestFactory

createClient(boolean) - Method in class omero.client

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

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

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

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

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

Subclasses must provide a fresh instance of TileData.

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

Creates the specified data object.

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

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

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

convenience method to save network calls.

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

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

createDataset(SecurityContext, DatasetData, ProjectData) - Method in class omero.gateway.facility.DataManagerFacility

Creates the DatasetData on the server and attaches it to the ProjectData (if not null) (if the project doesn't exist on the server yet, it will be created, too)

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

Creates a Details object for the current security context.

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

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

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

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

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

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

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

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

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

createExclusion(String) - Static method in class ome.formats.importer.exclusions.AbstractFileExclusion

Factory method for instantiating FileTransfer objects from a string.

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

create and return a new user in the given groups.

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

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

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

createExperimenter(SecurityContext, ExperimenterData, String, String, List<GroupData>, boolean, boolean) - Method in class omero.gateway.facility.AdminFacility

Creates an experimenter and returns it.

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

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

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

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

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

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

createFactories(Communicator) - Method in class ome.services.blitz.impl.commands.RequestObjectFactoryRegistry

createFactories(Communicator) - Method in class ome.services.blitz.repo.RequestObjectFactoryRegistry

createFactories(Communicator) - Method in class ome.services.roi.RoiTypes.RoiTypesObjectFactoryRegistry

createFactories(Communicator) - Method in class omero.cmd.admin.CurrentSessionsRequestI.Factory

createFactories(Communicator) - Method in class omero.cmd.admin.UpdateSessionTimeoutRequestI.Factory

createFactories(Communicator) - Method in class omero.cmd.RequestObjectFactoryRegistry

createFactories(Communicator) - Method in class omero.rtypes.RTypeObjectFactoryRegistry

createFactories(Communicator) - Method in class omero.util.ObjectFactoryRegistry

createFromRequest(SessionManager.CreationRequest) - Method in interface ome.services.sessions.SessionManager

createFromRequest(SessionManager.CreationRequest) - Method in class ome.services.sessions.SessionManagerImpl

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

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

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

create and return a new group.

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

createGroup(ExperimenterGroup) - Method in interface ome.security.auth.RoleProvider

createGroup(String, Permissions, boolean) - Method in interface ome.security.auth.RoleProvider

createGroup(String, Permissions, boolean, boolean) - Method in interface ome.security.auth.RoleProvider

createGroup(String, Permissions, boolean) - Method in class ome.security.auth.SimpleRoleProvider

createGroup(String, Permissions, boolean, boolean) - Method in class ome.security.auth.SimpleRoleProvider

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

createGroup(SecurityContext, GroupData, ExperimenterData, int) - Method in class omero.gateway.facility.AdminFacility

Creates a group and returns it.

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

createHandle(Request) - Method in class omero.cmd.HandleFactory

createIdsTempTable(Collection<Long>) - Method in interface ome.util.SqlAction

Creates a temporary table filled with the given ids and returns its name.

createIdsTempTable(Collection<Long>) - Method in class ome.util.SqlAction.Impl

createImage(int, int, int, int, List<Integer>, PixelsType, String, String) - Method in interface ome.api.IPixels

Creates the metadata, and only the metadata linked to an Image object.

createImage(int, int, int, int, List<Integer>, PixelsType, String, String) - Method in class ome.logic.PixelsImpl

createImage(int, int) - Method in class ome.services.SVGRasterizer.Rasterizer

createImage_async(AMD_IPixels_createImage, int, int, int, int, List<Integer>, PixelsType, String, String, Current) - Method in class ome.services.blitz.impl.PixelsI

createImport(ImportContainer) - Method in class ome.formats.importer.ImportLibrary

Provide initial configuration to the server in order to create the ImportProcessPrx which will manage state server-side.

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

Creating the process will register itself in an appropriate container (i.e. a SessionI or similar) for the current user and therefore this instance no longer needs to worry about the maintenance of the object.

createInsertTrigger(String, String, String) - Method in interface ome.util.SqlAction

Creates an insert trigger of the given name, for the given table, with the given procedure.

createInsertTrigger(String, String, String) - Method in class ome.util.SqlAction.Impl

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

First, adds all default listeners.

createInstance() - Method in class ome.services.delete.Deletion.Builder

createIObject(DataObject) - Static method in class omero.gateway.util.ModelMapper

Converts the specified DataObject into its corresponding IObject.

createIObject(DataObject, DataObject) - Static method in class omero.gateway.util.ModelMapper

Converts the specified DataObject into its corresponding IObject.

createJob(ServiceFactory) - Method in class ome.services.scripts.ScriptFinder

Returns a fresh (unsaved) ScriptJob which can be passed to acquireProcessor for background processing.

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

createJobHandle() - Method in class ome.system.ServiceFactory

create a new JobHandle proxy.

createJPEG(OutputStream) - Method in class ome.services.SVGRasterizer

Returns the image that represents the SVG document as a JPEG.

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

Helper method to properly log any exceptions raised by Bio-Formats and add a min/max calculator wrapper to the reader stack.

createNewRenderingDef(Pixels) - Method in interface ome.api.IRenderingSettings

Creates a new rendering definition object along with its sub-objects.

createNewRenderingDef(Pixels) - Method in class ome.logic.RenderingSettingsImpl

Implemented as specified by the IRenderingSettings I/F

createNewRenderingDef_async(AMD_IRenderingSettings_createNewRenderingDef, Pixels, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI

createOrFixUserDir(String, List<CheckedPath>, Session, ServiceFactory, SqlAction) - Method in interface ome.services.blitz.repo.RepositoryDao

Checks that the given CheckedPath objects exist (via RepositoryDao.findRepoFile(String, CheckedPath, String, Ice.Current)) and are in the "user" group.

createOrFixUserDir(String, List<CheckedPath>, Session, ServiceFactory, SqlAction) - Method in class ome.services.blitz.repo.RepositoryDaoImpl

createOriginalFile(ServiceFactory, SqlAction, String, List<CheckedPath>, ChecksumAlgorithm, String) - Method in class ome.services.blitz.repo.RepositoryDaoImpl

Primary location for creating original files from a CheckedPath instance.

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

Uses File.createTempFile(String, String, File) to create temporary files and folders under the top-level temporary directory.

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

Creates a PixelBuffer for a given pixels set.

createPixelsStore(SecurityContext) - Method in class omero.gateway.Gateway

Create a RawPixelsStorePrx

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

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

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

createProcessBuilder(File, File) - Method in class ome.formats.importer.transfers.AbstractExecFileTransfer

Creates a ProcessBuilder instance ready to have ProcessBuilder.start() called on it.

createProcessBuilder(File, File) - Method in class ome.formats.importer.transfers.CopyFileTransfer

Executes "cp file location" (Unix) or "cp file location" (Windows) and fails on non-0 return codes.

createProcessBuilder(File, File) - Method in class ome.formats.importer.transfers.HardlinkFileTransfer

Executes "ln file location" (Unix) or "mklink /H location file" (Windows) and fails on non-0 return codes.

createProcessBuilder(File, File) - Method in class ome.formats.importer.transfers.SymlinkFileTransfer

Executes "ln -s file location" (Unix) or "mklink location file" (Windows) and fails on non-0 return codes.

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

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

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

createRawFileStore(OriginalFile, Current) - Method in class ome.services.blitz.repo.AbstractRepositoryI

createRawFileStore() - Method in class ome.system.ServiceFactory

create a new RawFileStore proxy.

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

createRawPixelsStore(OriginalFile, Current) - Method in class ome.services.blitz.repo.AbstractRepositoryI

createRawPixelsStore() - Method in class ome.system.ServiceFactory

create a new RawPixelsStore proxy.

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

createRenderingEngine(OriginalFile, Current) - Method in class ome.services.blitz.repo.AbstractRepositoryI

createRenderingEngine() - Method in class ome.system.ServiceFactory

create a new RenderingEngine proxy.

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

Create, initialize, and register an RepoRawFileStoreI with the proper setting (read or write).

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

Helper method to properlty create a RomioPixelBuffer.

createRoot() - Method in class ome.formats.OMEROMetadataStore

createRoot() - Method in class ome.formats.OMEROMetadataStoreClient

createRoot_async(AMD_MetadataStore_createRoot, Current) - Method in class ome.services.blitz.impl.MetadataStoreI

createSafeInputStream(Communicator, byte[]) - Static method in class ome.services.util.IceUtil

Creates an InputStream with the appropriate encoding.

createSafeOutputStream(Communicator) - Static method in class ome.services.util.IceUtil

Creates an OutputStream with the appropriate encoding.

createSavepoint(String) - Method in class ome.util.actions.PostgresSqlAction

createSavepoint(String) - Method in interface ome.util.SqlAction

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

createSearchService() - Method in class ome.system.ServiceFactory

create a new Search proxy.

createServantDelegate(String) - Method in class omero.cmd.SessionI

Creates a proxy according to the servant definition for the given name.

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

Creates a new session and returns it to the user.

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

createSession() - Method in class omero.client

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 client.getRouter(Ice.Communicator).

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

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

Takes a snapshot as from SessionManagerImpl.executeSessionContextLookup(ServiceFactory, Principal, Session) 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

Deprecated.

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, its subpath exists.

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

create and return a new system user.

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

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

createTableResult(TablePrx, String, long) - Static method in class omero.gateway.util.PyTablesUtils

Transforms the passed table data for a given image.

createTableResult(TablePrx, long[]) - Static method in class omero.gateway.util.PyTablesUtils

Transforms a set of rows for the passed table.

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

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

createThumbnailStore(SecurityContext) - Method in class omero.gateway.Gateway

Create a ThumbnailStorePrx

createTransfer(String) - Static method in class ome.formats.importer.transfers.AbstractFileTransfer

Factory method for instantiating FileTransfer objects from a string.

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

Creating the process will register itself in an appropriate container (i.e. a SessionI or similar) for the current user and therefore this instance no longer needs to worry about the maintenance of the object.

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

create and return a new user.

createUser(String) - Method in interface ome.api.ILdap

Creates an Experimenter entry in the OMERO DB based on the supplied LDAP username.

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

createUser(String) - Method in class ome.logic.LdapImpl

Creates an Experimenter based on the supplied LDAP username.

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

Creates an Experimenter based on the supplied LDAP username.

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

Creates an Experimenter based on the supplied LDAP username.

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

createUser_async(AMD_ILdap_createUser, String, Current) - Method in class ome.services.blitz.impl.LdapI

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

Deprecated.

createUserSession(long, long, String) - Method in interface ome.api.ISession

Allows a user to open up another session for him/herself with the given defaults without needing to re-enter password.

createUserSession(long, long, String) - Method in class ome.services.sessions.SessionBean

createUserSession_async(AMD_ISession_createUserSession, long, long, String, Current) - Method in class ome.services.blitz.impl.SessionI

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

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

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

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

CREATIONEVENT - Static variable in class ome.model.internal.Details

CreationRequest() - Constructor for class ome.services.sessions.SessionManager.CreationRequest

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

credentials - Variable in class ome.system.SessionInitializer

CRITICAL_USAGE - Static variable in class ome.logic.RepositoryInfoImpl

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

csId - Variable in class ome.system.SimpleEventContext

csName - Variable in class ome.system.SimpleEventContext

CSV - Static variable in class omero.gateway.model.FileAnnotationData

Identifies the CSV file formats.

ctime - Variable in class ome.model.core.OriginalFile

CTIME - Static variable in class ome.model.core.OriginalFile

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

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

ctx - Variable in class ome.services.blitz.impl.AbstractAmdServant

ctx - Variable in class ome.services.delete.Deletion.Builder

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

ctx - Variable in class ome.services.throttling.AbstractThrottlingStrategy

ctx - Variable in class ome.system.ServiceFactory

the context instance which this ServiceFactory uses to look up all of its state.

cuId - Variable in class ome.system.SimpleEventContext

cuName - Variable in class ome.system.SimpleEventContext

curr - Variable in class ome.services.blitz.util.FindServiceFactoryMessage

current - Variable in class ome.security.SecurityFilterHolder

current - Variable in class ome.security.SecuritySystemHolder

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

current - Variable in class ome.tools.hibernate.ProxyCleanupFilter

current - Variable in class omero.cmd.admin.CurrentSessionsRequestI

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

current_group - Static variable in class ome.security.basic.OneGroupSecurityFilter

current_user - Static variable in interface ome.security.SecurityFilter

currentContext(Principal) - Method in class ome.services.blitz.repo.RepositoryDaoImpl

Deprecated.

currentContext() - Method in class ome.util.ContextFilter

CurrentDetails - Class in ome.security.basic

Stores information related to the security context of the current thread.

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

Default constructor.

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

CurrentDetails(SessionCache, Roles) - Constructor for class ome.security.basic.CurrentDetails

currentMetadata() - Method in interface ome.api.Search

Provides access to the extra query information (for example Lucene score and boost values) for a single call to Search.next().

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

currentMetadata_async(AMD_Search_currentMetadata, Current) - Method in class ome.services.blitz.impl.SearchI

currentMetadataList() - Method in interface ome.api.Search

Provides access to the extra query information (for example Lucene score and boost values) for a single call to Search.results().

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

currentMetadataList_async(AMD_Search_currentMetadataList, Current) - Method in class ome.services.blitz.impl.SearchI

currentPatch - Variable in class ome.model.meta.DBPatch

CURRENTPATCH - Static variable in class ome.model.meta.DBPatch

CurrentPlatform - Class in ome.services.blitz.util

Test under which platform OMERO is currently running.

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

CurrentSessionContext - Class in ome.tools.hibernate

Implementation of Hibernate's current_session_context_class extension point.

CurrentSessionContext(SessionFactoryImplementor) - Constructor for class ome.tools.hibernate.CurrentSessionContext

CurrentSessionsRequestI - Class in omero.cmd.admin

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

CurrentSessionsRequestI.Factory - Class in omero.cmd.admin

CurrentSessionStats - Class in ome.services.sessions.stats

Wrapper which delegates to a SessionStats instance acquired during construction.

CurrentSessionStats(CurrentDetails, SessionManager) - Constructor for class ome.services.sessions.stats.CurrentSessionStats

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

currentUser(Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl

currentUserNames() - Method in class ome.util.actions.PostgresSqlAction

currentUserNames() - Method in interface ome.util.SqlAction

currentVersion - Variable in class ome.model.meta.DBPatch

CURRENTVERSION - Static variable in class ome.model.meta.DBPatch

currValue(String) - Method in class ome.util.actions.PostgresSqlAction

currValue(String) - Method in interface ome.util.SqlAction

cutIn - Variable in class ome.model.acquisition.TransmittanceRange

CUTIN - Static variable in class ome.model.acquisition.TransmittanceRange

cutInTolerance - Variable in class ome.model.acquisition.TransmittanceRange

CUTINTOLERANCE - Static variable in class ome.model.acquisition.TransmittanceRange

cutOut - Variable in class ome.model.acquisition.TransmittanceRange

CUTOUT - Static variable in class ome.model.acquisition.TransmittanceRange

cutOutTolerance - Variable in class ome.model.acquisition.TransmittanceRange

CUTOUTTOLERANCE - Static variable in class ome.model.acquisition.TransmittanceRange

D

d - Variable in class ome.model.roi.Path

D - Static variable in class ome.model.roi.Path

data - Variable in class ome.model.meta.Share

DATA - Static variable in class ome.model.meta.Share

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

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

data - Variable in class ome.util.PixelData

The pixels data backing buffer.

DATA_STORED(int, ImportContainer, IObject, Long, int, ImportSize) - Constructor for class ome.formats.importer.ImportEvent.DATA_STORED

DatabaseBusyException - Exception in ome.conditions

No connections are currently available for the database.

DatabaseBusyException(String, long) - Constructor for exception ome.conditions.DatabaseBusyException

DatabaseIdentity - Class in ome.services.db

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

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

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

DataManagerFacility - Class in omero.gateway.facility

A Facility for saving, deleting and updating data objects

DataObject - Class in omero.gateway.model

Abstract superclass for objects that hold OMEDS data.

DataObject() - Constructor for class omero.gateway.model.DataObject

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

Dataset - Class in ome.model.containers

These filter definitions are used by the security system to eliminate non-readable objects from queries.

Dataset() - Constructor for class ome.model.containers.Dataset

Dataset(Long) - Constructor for class ome.model.containers.Dataset

Dataset(Long, boolean) - Constructor for class ome.model.containers.Dataset

Main constructor.

Dataset(String) - Constructor for class ome.model.containers.Dataset

Dataset.Details - Class in ome.model.containers

DATASET_LINKS - Static variable in class omero.gateway.model.ImageData

Identifies the ImageI.DATASETLINKS field.

DATASET_LINKS - Static variable in class omero.gateway.model.ProjectData

Identifies the ProjectI.DATASETLINKS field.

DATASET_STORED(int, ImportContainer, IObject, Long, int, ImportSize, Integer, Integer) - Constructor for class ome.formats.importer.ImportEvent.DATASET_STORED

DatasetAnnotationLink - Class in ome.model.annotations

These filter definitions are used by the security system to eliminate non-readable objects from queries.

DatasetAnnotationLink() - Constructor for class ome.model.annotations.DatasetAnnotationLink

DatasetAnnotationLink(Long) - Constructor for class ome.model.annotations.DatasetAnnotationLink

DatasetAnnotationLink(Long, boolean) - Constructor for class ome.model.annotations.DatasetAnnotationLink

Main constructor.

DatasetAnnotationLink(IObject, IObject) - Constructor for class ome.model.annotations.DatasetAnnotationLink

DatasetAnnotationLink.Details - Class in ome.model.annotations

DatasetData - Class in omero.gateway.model

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

DatasetData() - Constructor for class omero.gateway.model.DatasetData

Creates a new instance.

DatasetData(Dataset) - Constructor for class omero.gateway.model.DatasetData

Creates a new instance.

DatasetImageLink - Class in ome.model.containers

These filter definitions are used by the security system to eliminate non-readable objects from queries.

DatasetImageLink() - Constructor for class ome.model.containers.DatasetImageLink

DatasetImageLink(Long) - Constructor for class ome.model.containers.DatasetImageLink

DatasetImageLink(Long, boolean) - Constructor for class ome.model.containers.DatasetImageLink

Main constructor.

DatasetImageLink(IObject, IObject) - Constructor for class ome.model.containers.DatasetImageLink

DatasetImageLink.Details - Class in ome.model.containers

datasetLinks - Variable in class ome.model.containers.Project

DATASETLINKS - Static variable in class ome.model.containers.Project

datasetLinks - Variable in class ome.model.core.Image

DATASETLINKS - Static variable in class ome.model.core.Image

DATASETLINKSCOUNTPEROWNER - Static variable in class ome.model.containers.Project

DATASETLINKSCOUNTPEROWNER - Static variable in class ome.model.core.Image

DataSink - Class in omero.gateway.rnd

Encapsulates access to the image raw data.

DataSink(SecurityContext, PixelsData, Gateway) - Constructor for class omero.gateway.rnd.DataSink

Creates a new instance.