- 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
-
- AbstractFileExclusion() - Constructor for class ome.formats.importer.exclusions.AbstractFileExclusion
-
- AbstractFileExclusion.Exclusion - Enum in ome.formats.importer.exclusions
-
- AbstractFileSystemService - Class in ome.io.nio
-
- AbstractFileSystemService(String) - Constructor for class ome.io.nio.AbstractFileSystemService
-
- AbstractFileTransfer - Class in ome.formats.importer.transfers
-
- AbstractFileTransfer() - Constructor for class ome.formats.importer.transfers.AbstractFileTransfer
-
- AbstractFileTransfer.Transfers - Enum in ome.formats.importer.transfers
-
- AbstractLevel1Service - Class in ome.logic
-
service level 1
- AbstractLevel1Service() - Constructor for class ome.logic.AbstractLevel1Service
-
- AbstractLevel2Service - Class in ome.logic
-
service level 2
- AbstractLevel2Service() - Constructor for class ome.logic.AbstractLevel2Service
-
- AbstractPyramidServant - Class in ome.services.blitz.impl
-
Specialization of
AbstractAmdServant
to be used by any services which
provide the
PyramidService
interface.
- AbstractPyramidServant(ServiceInterface, BlitzExecutor) - Constructor for class ome.services.blitz.impl.AbstractPyramidServant
-
- AbstractRedirector - Class in ome.services.blitz.redirect
-
- AbstractRedirector(Executor) - Constructor for class ome.services.blitz.redirect.AbstractRedirector
-
- AbstractRepositoryI - Class in ome.services.blitz.repo
-
Base repository class responsible for properly handling directory
takeover
and other lifecycle tasks.
- AbstractRepositoryI(ObjectAdapter, Registry, Executor, Principal, String, PublicRepositoryI) - Constructor for class ome.services.blitz.repo.AbstractRepositoryI
-
- AbstractRepositoryI(ObjectAdapter, Registry, Executor, Principal, FileMaker, PublicRepositoryI) - Constructor for class ome.services.blitz.repo.AbstractRepositoryI
-
- AbstractSecurityFilter - Class in ome.security.basic
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- add(Document, String, String, LuceneOptions) - Method in class ome.services.fulltext.BridgeHelper
-
Deprecated.
- add(CodomainMapContext) - Method in class omeis.providers.re.codomain.CodomainChain
-
Adds a map context to the chain.
- add(String, RType) - Method in class omero.sys.ParametersI
-
- add(Resources.Entry) - Method in class omero.util.Resources
-
- addAction(SearchAction) - Method in class ome.services.SearchBean
-
- addAlgorithm(String) - Method in class ome.parameters.Parameters
-
- addAll(Parameters) - Method in class ome.parameters.Parameters
-
adds all the information from the passed in Parameters instance to this
instance.
- addAll(QueryParameter[]) - Method in class ome.parameters.Parameters
-
adds all the information from the passed in Parameters instance to this
instance.
- addAllDisabled(String...) - Method in class ome.security.basic.CurrentDetails
-
- addAnnotationAnnotationLink(AnnotationAnnotationLink) - Method in class ome.model.annotations.Annotation
-
use instead of setAnnotationLinks .
- addAnnotationAnnotationLink(AnnotationAnnotationLink, boolean) - Method in class ome.model.annotations.Annotation
-
Adds a ome.model.annotations.AnnotationAnnotationLink to annotationLinks, allowing for recursion -- whether
or not addAnnotationAnnotationLink will be called on the addition if it is loaded
- addAnnotationAnnotationLinkSet(Collection<AnnotationAnnotationLink>) - Method in class ome.model.annotations.Annotation
-
use like addAnnotationAnnotationLink.
- addApplicationListener(ApplicationListener) - Method in class ome.services.messages.GlobalMulticaster
-
- addApplicationListenerBean(String) - Method in class ome.services.messages.GlobalMulticaster
-
- addArray(int[][], int, int, int) - Method in class 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
-
- 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
-
- 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.
- 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
-
- 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
-
- addImageToDataset(SecurityContext, ImageData, DatasetData) - Method in class omero.gateway.facility.DataManagerFacility
-
- 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
-
- 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.
- 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.
- 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
-
- 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
-
- addPropertyChangeListener(PropertyChangeListener) - Method in class omero.gateway.Gateway
-
- addReagent(Reagent) - Method in class ome.model.screen.Screen
-
use instead of setReagents .
- addReagentAnnotationLink(ReagentAnnotationLink) - Method in class ome.model.screen.Reagent
-
use instead of setAnnotationLinks .
- addReagentAnnotationLink(ReagentAnnotationLink, boolean) - Method in class ome.model.screen.Reagent
-
Adds a ome.model.annotations.ReagentAnnotationLink to annotationLinks, allowing for recursion -- whether
or not addReagentAnnotationLink will be called on the addition if it is loaded
- addReagentAnnotationLinkSet(Collection<ReagentAnnotationLink>) - Method in class ome.model.screen.Reagent
-
use like addReagentAnnotationLink.
- addReagentSet(Collection<Reagent>) - Method in class ome.model.screen.Screen
-
use like addReagent.
- addReference(LSID, LSID) - Method in interface ome.formats.model.IObjectContainerStore
-
Adds a reference to the reference cache.
- addReference(LSID, LSID) - Method in class ome.formats.OMEROMetadataStoreClient
-
Adds a reference to the reference cache.
- addRenderingDef(RenderingDef) - Method in class ome.model.core.Pixels
-
use instead of setSettings .
- addRenderingDefSet(Collection<RenderingDef>) - Method in class ome.model.core.Pixels
-
use like addRenderingDef.
- addReply(long, String, CommentAnnotation) - Method in interface ome.api.IShare
-
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.
- 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.
- addUsers(long, Experimenter...) - Method in class ome.services.sharing.ShareBean
-
- addUsers_async(AMD_IShare_addUsers, long, List<Experimenter>, Current) - Method in class ome.services.blitz.impl.ShareI
-
- addViolation(ACLViolation) - Method in exception ome.conditions.acl.CollectedACLViolations
-
- addWell(Well) - Method in class ome.model.screen.Plate
-
use instead of setWells .
- addWellAnnotationLink(WellAnnotationLink) - Method in class ome.model.screen.Well
-
use instead of setAnnotationLinks .
- addWellAnnotationLink(WellAnnotationLink, boolean) - Method in class ome.model.screen.Well
-
Adds a ome.model.annotations.WellAnnotationLink to annotationLinks, allowing for recursion -- whether
or not addWellAnnotationLink will be called on the addition if it is loaded
- addWellAnnotationLinkSet(Collection<WellAnnotationLink>) - Method in class ome.model.screen.Well
-
use like addWellAnnotationLink.
- addWellReagentLink(WellReagentLink) - Method in class ome.model.screen.Reagent
-
use instead of setWellLinks .
- addWellReagentLink(WellReagentLink, boolean) - Method in class ome.model.screen.Reagent
-
Adds a ome.model.screen.WellReagentLink to wellLinks, allowing for recursion -- whether
or not addWellReagentLink will be called on the addition if it is loaded
- addWellReagentLink(WellReagentLink) - Method in class ome.model.screen.Well
-
use instead of setReagentLinks .
- addWellReagentLink(WellReagentLink, boolean) - Method in class ome.model.screen.Well
-
Adds a ome.model.screen.WellReagentLink to reagentLinks, allowing for recursion -- whether
or not addWellReagentLink will be called on the addition if it is loaded
- addWellReagentLinkSet(Collection<WellReagentLink>) - Method in class ome.model.screen.Reagent
-
use like addWellReagentLink.
- addWellReagentLinkSet(Collection<WellReagentLink>) - Method in class ome.model.screen.Well
-
use like addWellReagentLink.
- addWellSample(WellSample) - Method in class ome.model.core.Image
-
use instead of setWellSamples .
- addWellSample(WellSample) - Method in class ome.model.screen.PlateAcquisition
-
use instead of setWellSample .
- addWellSample(WellSample) - Method in class ome.model.screen.Well
-
use instead of setWellSamples .
- addWellSampleSet(Collection<WellSample>) - Method in class ome.model.core.Image
-
use like addWellSample.
- addWellSampleSet(Collection<WellSample>) - Method in class ome.model.screen.PlateAcquisition
-
use like addWellSample.
- addWellSampleSet(Collection<WellSample>) - Method in class ome.model.screen.Well
-
use like addWellSample.
- addWellSet(Collection<Well>) - Method in class ome.model.screen.Plate
-
use like addWell.
- adjustGraphPolicy(Function<GraphPolicy, GraphPolicy>) - Method in class omero.cmd.graphs.Chgrp2I
-
- adjustGraphPolicy(Function<GraphPolicy, GraphPolicy>) - Method in class omero.cmd.graphs.Chmod2I
-
- adjustGraphPolicy(Function<GraphPolicy, GraphPolicy>) - Method in class omero.cmd.graphs.Chown2I
-
- adjustGraphPolicy(Function<GraphPolicy, GraphPolicy>) - Method in class omero.cmd.graphs.Delete2I
-
- adjustGraphPolicy(Function<GraphPolicy, GraphPolicy>) - Method in class omero.cmd.graphs.DuplicateI
-
- adjustGraphPolicy(Function<GraphPolicy, GraphPolicy>) - Method in interface omero.cmd.graphs.WrappableRequest
-
Transform the currently applicable graph policy for this request by the given function.
- Adler32ChecksumProviderImpl - Class in ome.util.checksum
-
An implementation of the
ChecksumProvider
interface using Adler32
as the message digest algorithm.
- Adler32ChecksumProviderImpl() - Constructor for class ome.util.checksum.Adler32ChecksumProviderImpl
-
- admin - Variable in class ome.services.delete.DeleteBean
-
- admin - Variable in class ome.services.sharing.ShareBean
-
- AdminAction - Interface in ome.security
-
- AdminFacility - Class in omero.gateway.facility
-
Facility
for handling admin issues, e.g. creating users, groups,
etc.
- adminFlush() - Method in class ome.services.sharing.ShareBean
-
- AdminI - Class in ome.services.blitz.impl
-
Implementation of the IAdmin
service.
- AdminI(IAdmin, BlitzExecutor) - Constructor for class ome.services.blitz.impl.AdminI
-
- AdminImpl - Class in ome.logic
-
Provides methods for administering user accounts, passwords, as well as
methods which require special privileges.
- AdminImpl(SqlAction, SessionFactory, MailSender, SimpleMailMessage, ACLVoter, PasswordProvider, RoleProvider, LdapImpl, PasswordUtil, ChmodStrategy, ChecksumProviderFactory) - Constructor for class ome.logic.AdminImpl
-
- 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
-
- AllGroupsSecurityFilter(SqlAction) - Constructor for class ome.security.basic.AllGroupsSecurityFilter
-
Default constructor which calls all the necessary setters for this
FactoryBean
.
- AllGroupsSecurityFilter(SqlAction, Roles) - Constructor for class ome.security.basic.AllGroupsSecurityFilter
-
- allGrps() - Method in class omero.sys.ParametersI
-
Removes the group
parameter from the map.
- allObjects(Collection<Set<GraphPolicy.Details>>, GraphPolicy.Details, Collection<Set<GraphPolicy.Details>>) - Static method in class ome.services.graphs.GraphPolicy
-
Utility method to return all the objects for review as a single set of objects.
- allow(ObjectPrx) - Method in class omero.cmd.SessionI
-
- ALLOW_LEADING_WILDCARD - Static variable in interface ome.api.Search
-
- allowAdministration() - Method in class ome.services.blitz.Router
-
- allowAnnotate(IObject, Details) - Method in interface ome.security.ACLVoter
-
test whether the given object should be annotatable given the trusted
details
.
- allowAnnotate(IObject, Details) - Method in class ome.security.basic.BasicACLVoter
-
- allowAnnotate(IObject, Details) - Method in class ome.security.CompositeACLVoter
-
- allowAnnotate(IObject, Details) - Method in class ome.security.sharing.SharingACLVoter
-
- allowChmod(IObject) - Method in interface ome.security.ACLVoter
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- asDataObjects(List) - Static method in class omero.gateway.util.PojoMapper
-
- asDataObjects(IObject[]) - Static method in class omero.gateway.util.PojoMapper
-
- 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
-
- 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
-
- 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
IObject
s into the corresponding
DataObject
s
- asPojos(Map) - Static method in class omero.gateway.model.DataObject
-
Converts the map of
IObject
s into the corresponding
DataObject
s
- 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
-
- 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
-
- attachFile(SecurityContext, File, String, String, String, DataObject) - Method in class omero.gateway.facility.DataManagerFacility
-
- 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
-
- 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
-
- 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
-
- 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
-
- canAnnotate(IObject) - Method in class ome.logic.AdminImpl
-
- canAnnotate() - Method in class omero.gateway.model.DataObject
-
Returns true
if the object can be annotated
false
otherwise, depending on permissions level.
- canAnnotate(Current) - Method in class omero.model.PermissionsI
-
- CANCEL() - Constructor for exception ome.formats.importer.ImportCandidates.CANCEL
-
- cancel() - Method in class ome.formats.importer.ImportCandidates.SCANNING
-
Can be called to cancel the current action.
- cancel(Current) - Method in class ome.services.blitz.impl.ScriptProcessI
-
- cancel() - Method in interface ome.services.procs.Process
-
- cancel() - Method in class ome.services.procs.ProcessSkeleton
-
- cancel(String) - Method in class ome.services.sessions.events.ChangeSecurityContextEvent
-
- cancel(Current) - Method in class omero.cmd.HandleI
-
- Cancel(String) - Constructor for exception omero.cmd.HandleI.Cancel
-
- cancel(ERR, Throwable, String, String...) - Method in class omero.cmd.Helper
-
- cancel(ERR, Throwable, String, Map<String, String>) - Method in class omero.cmd.Helper
-
- cancelJob() - Method in interface ome.api.JobHandle
-
Marks a job for cancellation.
- cancelJob() - Method in class ome.services.JobBean
-
- cancelJob_async(AMD_JobHandle_cancelJob, Current) - Method in class ome.services.blitz.impl.JobHandleI
-
- CANCELLED - Static variable in interface ome.api.JobHandle
-
- cancelUploads - Variable in class ome.formats.importer.util.ErrorHandler
-
- canDelete() - Method in class omero.gateway.model.DataObject
-
Returns true
if the object can be deleted by the user
currently logged in,
false
otherwise, depending on permissions level.
- canDelete(Current) - Method in class omero.model.PermissionsI
-
- canEdit() - Method in class ome.services.blitz.repo.CheckedPath
-
- canEdit() - Method in class omero.gateway.model.DataObject
-
Returns true
if the object can be edited by the user
currently logged in false
otherwise,
depending on permissions level.
- canEdit(Current) - Method in class omero.model.PermissionsI
-
- canLink() - Method in class omero.gateway.model.DataObject
-
Returns true
if the object can be linked e.g. image
add to dataset, by the user currently logged in,
false
otherwise, depending on
permissions level.
- canLink(Current) - Method in class omero.model.PermissionsI
-
- canLogin() - Method in class ome.formats.importer.ImportConfig
-
Confirm all information for login is supplied
- canMapReturnValue() - Method in class omero.util.IceMapper
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- changeUserPasswordById(Long, String, PasswordUtil.METHOD) - Method in class ome.security.auth.PasswordUtil
-
- Channel - Class in ome.model.core
-
These filter definitions are used by the security system
to eliminate non-readable objects from queries.
- Channel() - Constructor for class ome.model.core.Channel
-
- Channel(Long) - Constructor for class ome.model.core.Channel
-
- Channel(Long, boolean) - Constructor for class ome.model.core.Channel
-
Main constructor.
- Channel(LogicalChannel, Pixels) - Constructor for class ome.model.core.Channel
-
- Channel.Details - Class in ome.model.core
-
- Channel_EmissionWavelength - Static variable in class ome.formats.model.UnitsFactory
-
- Channel_ExcitationWavelength - Static variable in class ome.formats.model.UnitsFactory
-
- Channel_PinholeSize - Static variable in class ome.formats.model.UnitsFactory
-
- ChannelAcquisitionData - Class in omero.gateway.model
-
Object hosting the acquisition related to a logical channel.
- ChannelAcquisitionData(LogicalChannel) - Constructor for class omero.gateway.model.ChannelAcquisitionData
-
Creates a new instance.
- ChannelAnnotationLink - Class in ome.model.annotations
-
These filter definitions are used by the security system
to eliminate non-readable objects from queries.
- ChannelAnnotationLink() - Constructor for class ome.model.annotations.ChannelAnnotationLink
-
- ChannelAnnotationLink(Long) - Constructor for class ome.model.annotations.ChannelAnnotationLink
-
- ChannelAnnotationLink(Long, boolean) - Constructor for class ome.model.annotations.ChannelAnnotationLink
-
Main constructor.
- ChannelAnnotationLink(IObject, IObject) - Constructor for class ome.model.annotations.ChannelAnnotationLink
-
- ChannelAnnotationLink.Details - Class in ome.model.annotations
-
- ChannelBinding - Class in ome.model.display
-
These filter definitions are used by the security system
to eliminate non-readable objects from queries.
- ChannelBinding() - Constructor for class ome.model.display.ChannelBinding
-
- ChannelBinding(Long) - Constructor for class ome.model.display.ChannelBinding
-
- ChannelBinding(Long, boolean) - Constructor for class ome.model.display.ChannelBinding
-
Main constructor.
- ChannelBinding(RenderingDef, Family, Double, Double, Double, Boolean, Boolean, Integer, Integer, Integer, Integer) - Constructor for class ome.model.display.ChannelBinding
-
- channelBinding - 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
-
- check(String) - Method in class ome.services.query.Query
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- checkPassword(String, String, boolean) - Method in class ome.security.auth.LdapPasswordProvider
-
- checkPassword(String, String, boolean) - Method in interface ome.security.auth.PasswordProvider
-
Authenticates the give user given the password token.
- checkPassword(String, String, boolean) - Method in class ome.security.auth.PasswordProviders
-
- checkPassword(String, String, boolean) - Method in class ome.security.auth.providers.LdapPasswordProvider431
-
- checkPassword(String) - Method in class ome.services.blitz.fire.Ring
-
Currently only returns false since if the regular password check
performed by
SessionManager
cannot find the
session, then the cluster has no extra information.
- checkPath(String, ChecksumAlgorithm, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
-
Create a new
CheckedPath
object based on the given user input.
- checkPermissions(String, String, StringHolder, Current) - Method in class ome.services.blitz.fire.PermissionsVerifierI
-
- checkProperty(String, String) - Method in interface ome.api.local.LocalQuery
-
Checks if a property is defined on a mapped Hibernate type.
- checkProperty(String, String) - Method in class ome.logic.PojosImpl
-
- checkProperty(String, String) - Method in class ome.logic.QueryImpl
-
- checkReady(String) - Method in class ome.security.basic.BasicSecuritySystem
-
- checkRestriction(String, IObject) - Method in class ome.security.basic.BasicSecuritySystem
-
- checkRestriction(IObject) - Method in class ome.security.policy.BasePolicy
-
- checkRestriction(IObject) - Method in class ome.security.policy.BinaryAccessPolicy
-
- checkRestriction(String, IObject) - Method in class ome.security.policy.DefaultPolicyService
-
- checkRestriction(IObject) - Method in interface ome.security.policy.Policy
-
- checkRestriction(String, IObject) - Method in interface ome.security.policy.PolicyService
-
- 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
ChecksumType
s.
- 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
-
- ChecksumProviderFactoryImpl - Class in ome.util.checksum
-
- 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
-
- chgrp(String, Long, ChildOption, long) - Static method in class omero.gateway.util.Requests
-
- chgrp(String, Long, List<ChildOption>, long) - Static method in class omero.gateway.util.Requests
-
- chgrp(String, Long, boolean, long) - Static method in class omero.gateway.util.Requests
-
- chgrp(String, Long, ChildOption, boolean, long) - Static method in class omero.gateway.util.Requests
-
- chgrp(String, Long, List<ChildOption>, boolean, long) - Static method in class omero.gateway.util.Requests
-
- chgrp(String, List<Long>, long) - Static method in class omero.gateway.util.Requests
-
- chgrp(String, List<Long>, ChildOption, long) - Static method in class omero.gateway.util.Requests
-
- chgrp(String, List<Long>, List<ChildOption>, long) - Static method in class omero.gateway.util.Requests
-
- chgrp(String, List<Long>, boolean, long) - Static method in class omero.gateway.util.Requests
-
- chgrp(String, List<Long>, ChildOption, boolean, long) - Static method in class omero.gateway.util.Requests
-
- chgrp(String, List<Long>, List<ChildOption>, boolean, long) - Static method in class omero.gateway.util.Requests
-
- chgrp(Map<String, List<Long>>, long) - Static method in class omero.gateway.util.Requests
-
- chgrp(Map<String, List<Long>>, ChildOption, long) - Static method in class omero.gateway.util.Requests
-
- chgrp(Map<String, List<Long>>, List<ChildOption>, long) - Static method in class omero.gateway.util.Requests
-
- chgrp(Map<String, List<Long>>, boolean, long) - Static method in class omero.gateway.util.Requests
-
- chgrp(Map<String, List<Long>>, ChildOption, boolean, long) - Static method in class omero.gateway.util.Requests
-
- chgrp(Map<String, List<Long>>, List<ChildOption>, boolean, long) - Static method in class omero.gateway.util.Requests
-
- 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
-
- 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
-
- chmod(String, Long, ChildOption, String) - Static method in class omero.gateway.util.Requests
-
- chmod(String, Long, List<ChildOption>, String) - Static method in class omero.gateway.util.Requests
-
- chmod(String, Long, boolean, String) - Static method in class omero.gateway.util.Requests
-
- chmod(String, Long, ChildOption, boolean, String) - Static method in class omero.gateway.util.Requests
-
- chmod(String, Long, List<ChildOption>, boolean, String) - Static method in class omero.gateway.util.Requests
-
- chmod(String, List<Long>, String) - Static method in class omero.gateway.util.Requests
-
- chmod(String, List<Long>, ChildOption, String) - Static method in class omero.gateway.util.Requests
-
- chmod(String, List<Long>, List<ChildOption>, String) - Static method in class omero.gateway.util.Requests
-
- chmod(String, List<Long>, boolean, String) - Static method in class omero.gateway.util.Requests
-
- chmod(String, List<Long>, ChildOption, boolean, String) - Static method in class omero.gateway.util.Requests
-
- chmod(String, List<Long>, List<ChildOption>, boolean, String) - Static method in class omero.gateway.util.Requests
-
- chmod(Map<String, List<Long>>, String) - Static method in class omero.gateway.util.Requests
-
- chmod(Map<String, List<Long>>, ChildOption, String) - Static method in class omero.gateway.util.Requests
-
- chmod(Map<String, List<Long>>, List<ChildOption>, String) - Static method in class omero.gateway.util.Requests
-
- chmod(Map<String, List<Long>>, boolean, String) - Static method in class omero.gateway.util.Requests
-
- chmod(Map<String, List<Long>>, ChildOption, boolean, String) - Static method in class omero.gateway.util.Requests
-
- chmod(Map<String, List<Long>>, List<ChildOption>, boolean, String) - Static method in class omero.gateway.util.Requests
-
- 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
-
- ChmodStrategy - Interface in ome.security
-
Strategy for changing the permissions of objects in the database
as well as verifying that the permissions for the modified objects
are sensible after the change.
- choose() - Method in class ome.security.CompositeACLVoter
-
- choose() - Method in class ome.security.SecurityFilterHolder
-
- choose() - Method in class ome.security.SecuritySystemHolder
-
- chooseNextRedirect(Redirector.Context, Set<String>) - Method in class ome.services.blitz.redirect.ConfigRedirector
-
- chooseNextRedirect(Redirector.Context, Set<String>) - Method in class ome.services.blitz.redirect.NullRedirector
-
Does nothing.
- chooseNextRedirect(Redirector.Context, Set<String>) - Method in interface ome.services.blitz.redirect.Redirector
-
Gives the
Redirector
a chance to configure the next appropriate
redirect based on the
Set
of current
Node
uuids.
- chooseNextRedirect(Redirector.Context, Set<String>) - Method in class ome.services.blitz.redirect.ScaleRedirector
-
- chown(String, Long, long) - Static method in class omero.gateway.util.Requests
-
- chown(String, Long, ChildOption, long) - Static method in class omero.gateway.util.Requests
-
- chown(String, Long, List<ChildOption>, long) - Static method in class omero.gateway.util.Requests
-
- chown(String, Long, boolean, long) - Static method in class omero.gateway.util.Requests
-
- chown(String, Long, ChildOption, boolean, long) - Static method in class omero.gateway.util.Requests
-
- chown(String, Long, List<ChildOption>, boolean, long) - Static method in class omero.gateway.util.Requests
-
- chown(String, List<Long>, long) - Static method in class omero.gateway.util.Requests
-
- chown(String, List<Long>, ChildOption, long) - Static method in class omero.gateway.util.Requests
-
- chown(String, List<Long>, List<ChildOption>, long) - Static method in class omero.gateway.util.Requests
-
- chown(String, List<Long>, boolean, long) - Static method in class omero.gateway.util.Requests
-
- chown(String, List<Long>, ChildOption, boolean, long) - Static method in class omero.gateway.util.Requests
-
- chown(String, List<Long>, List<ChildOption>, boolean, long) - Static method in class omero.gateway.util.Requests
-
- chown(Map<String, List<Long>>, long) - Static method in class omero.gateway.util.Requests
-
- chown(Map<String, List<Long>>, ChildOption, long) - Static method in class omero.gateway.util.Requests
-
- chown(Map<String, List<Long>>, List<ChildOption>, long) - Static method in class omero.gateway.util.Requests
-
- chown(Map<String, List<Long>>, boolean, long) - Static method in class omero.gateway.util.Requests
-
- chown(Map<String, List<Long>>, ChildOption, boolean, long) - Static method in class omero.gateway.util.Requests
-
- chown(Map<String, List<Long>>, List<ChildOption>, boolean, long) - Static method in class omero.gateway.util.Requests
-
- 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
-
- 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
-
- 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
-
- 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
-
- client(InitializationData) - Constructor for class omero.client
-
Creates an Communicator
from a InitializationData
instance.
- client(String) - Constructor for class omero.client
-
- 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
-
- 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
-
- 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
-
- 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.
- 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
-
- 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
-
- 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
-
- 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
-
- ConfigRedirector(Executor) - Constructor for class ome.services.blitz.redirect.ConfigRedirector
-
- ConfigurablePasswordProvider - Class in ome.security.auth
-
Base class for most
PasswordProvider
implementations, providing
configuration for default behaviors.
- ConfigurablePasswordProvider(PasswordUtil) - Constructor for class ome.security.auth.ConfigurablePasswordProvider
-
- ConfigurablePasswordProvider(PasswordUtil, boolean) - Constructor for class ome.security.auth.ConfigurablePasswordProvider
-
- ConfigurablePasswordProvider(PasswordUtil, boolean, boolean) - Constructor for class ome.security.auth.ConfigurablePasswordProvider
-
- configure(List<HardWiredInterceptor>, OmeroContext) - Static method in class ome.logic.HardWiredInterceptor
-
- configure(SelfConfigurableService) - Method in class ome.services.util.BeanHelper
-
- configure(Type, Properties, Dialect) - Method in class ome.tools.hibernate.MySeqGenerator
-
If the parameters do not contain a SequenceGenerator.SEQUENCE
name, we assign one based on the table name.
- configure(Type, Properties, Dialect) - Method in class ome.util.TableIdGenerator
-
- configureDebug(String) - Method in class ome.formats.importer.ImportConfig
-
Modifies the logging level of everything under the
ome.formats
, ome.services.blitz
,
ome.system
and loci
packages hierarchically.
- ConfiguredTileSizes - Class in ome.io.nio
-
Implementation which has all values injected during configuration.
- ConfiguredTileSizes() - Constructor for class ome.io.nio.ConfiguredTileSizes
-
- ConfiguredTileSizes(int, int, int, int) - Constructor for class ome.io.nio.ConfiguredTileSizes
-
- configureServant(Object) - Method in class omero.cmd.SessionI
-
Apply proper AOP and call setters for any known injection properties.
- configValue(String) - Method in interface ome.util.SqlAction
-
- configValue(String) - Method in class ome.util.SqlAction.Impl
-
- conn - Variable in class ome.model.meta.Node
-
- CONN - Static variable in class ome.model.meta.Node
-
- connect(LoginCredentials) - Method in class omero.gateway.Gateway
-
Connect to the server
- connect() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
-
- CONNECTION - Static variable in exception omero.gateway.exception.RenderingServiceException
-
Indicates that the error occurred due to a connection failure.
- ConnectionStatus - Enum in omero.gateway.exception
-
The various connections status.
- consolidate() - Method in class omero.gateway.model.SearchResultCollection
-
Removes results which DataObjects are not set
- constant - Variable in class ome.model.display.PlaneSlicingContext
-
- CONSTANT - Static variable in class ome.model.display.PlaneSlicingContext
-
- containedExperimenters(long) - Method in interface ome.api.IAdmin
-
fetch all
users
contained in this group.
- containedExperimenters(long) - Method in class ome.logic.AdminImpl
-
- containedExperimenters_async(AMD_IAdmin_containedExperimenters, long, Current) - Method in class ome.services.blitz.impl.AdminI
-
- containedGroups(long) - Method in interface ome.api.IAdmin
-
fetch all
groups
of which the given user is a
member.
- containedGroups(long) - Method in class ome.logic.AdminImpl
-
- containedGroups_async(AMD_IAdmin_containedGroups, long, Current) - Method in class ome.services.blitz.impl.AdminI
-
- container - Variable in class ome.formats.importer.ImportEvent.PROGRESS_EVENT
-
- ContainerI - Class in ome.services.blitz.impl
-
Implementation of the IContainer service.
- ContainerI(IContainer, BlitzExecutor) - Constructor for class ome.services.blitz.impl.ContainerI
-
- containingEvent - Variable in class ome.model.meta.Event
-
- CONTAININGEVENT - Static variable in class ome.model.meta.Event
-
- contains(Object) - Method in interface ome.api.local.LocalQuery
-
Tests if an object is currently contained in the session.
- contains(Object) - Method in class ome.logic.QueryImpl
-
- contains(long, Class<T>, long) - Method in class ome.services.sharing.ShareStore
-
- contains(double, double) - Method in class ome.util.math.geom2D.EllipseArea
-
Required by the
Shape
I/F.
- contains(double, double, double, double) - Method in class ome.util.math.geom2D.EllipseArea
-
Required by the
Shape
I/F.
- contains(Point2D) - Method in class ome.util.math.geom2D.EllipseArea
-
Required by the
Shape
I/F.
- contains(Rectangle2D) - Method in class ome.util.math.geom2D.EllipseArea
-
Required by the
Shape
I/F.
- contains(double, double) - Method in class ome.util.math.geom2D.RectangleArea
-
Required by the
Shape
I/F.
- contains(double, double, double, double) - Method in class ome.util.math.geom2D.RectangleArea
-
Required by the
Shape
I/F.
- contains(Point2D) - Method in class ome.util.math.geom2D.RectangleArea
-
Required by the
Shape
I/F.
- contains(Rectangle2D) - Method in class ome.util.math.geom2D.RectangleArea
-
Required by the
Shape
I/F.
- contains(Object) - Method in class omero.gateway.model.SearchResultCollection
-
- containsKey(Object) - Method in class ome.services.query.Definitions
-
- contentLength - Variable in class ome.formats.importer.ImportEvent.FILE_UPLOAD_EVENT
-
- context - Variable in class ome.logic.AdminImpl
-
- context - Variable in class ome.services.blitz.fire.SessionManagerI
-
- context - Variable in class ome.services.blitz.repo.PublicRepositoryI
-
- context - Variable in class ome.services.fulltext.FileParser
-
- context - Variable in class ome.services.fulltext.FullTextIndexer
-
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
-
- Conversion.Add - Class in ome.model.units
-
- Conversion.Int - Class in ome.model.units
-
Simply is a representation of a possibly large integer.
- Conversion.Mul - Class in ome.model.units
-
- Conversion.Pow - Class in ome.model.units
-
- Conversion.Rat - Class in ome.model.units
-
- Conversion.Sym - Class in ome.model.units
-
- 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
-
- convert(double) - Method in class ome.model.units.Conversion.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 RString
s.
- 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
-
- 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
-
- 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
-
- countLocks(Session, Long, String[][], String) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
-
- countOnDisk() - Method in class ome.services.scripts.ScriptRepoHelper
-
- 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
-
- 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
-
- create_path(String) - Static method in class omero.util.TempFileManager
-
- create_path(String, String) - Static method in class omero.util.TempFileManager
-
- create_path(String, String, boolean) - Static method in class omero.util.TempFileManager
-
- createAdapter() - Method in class ome.services.blitz.util.BlitzConfiguration
-
Creates an adapter with the name "BlitzAdapter", which must be properly
configured via --Ice.Config or ICE_CONFIG or similar.
- createAndPrepareMissingRenderingSettings(Set<Long>) - Method in class ome.services.ThumbnailCtx
-
Resets a given set of Pixels rendering settings to the default
effectively creating any which do not exist.
- createAndRegisterManager(SessionManager, SecuritySystem, Executor) - Method in class ome.services.blitz.util.BlitzConfiguration
-
- createAndRegisterVerifier(SessionManager, Executor) - Method in class ome.services.blitz.util.BlitzConfiguration
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- createServantDelegate(String) - Method in class omero.cmd.SessionI
-
Creates a proxy according to the servant definition for the given
name.
- createSession(Principal, String) - Method in interface ome.api.ISession
-
Creates a new session and returns it to the user.
- createSession(Principal, String) - Method in class ome.services.sessions.SessionBean
-
- createSession() - Method in class omero.client
-
- createSession(String, String) - Method in class omero.client
-
- createSession_async(AMD_ISession_createSession, Principal, String, Current) - Method in class ome.services.blitz.impl.SessionI
-
- createSessionContext(List<?>, SessionContext) - Method in class ome.services.sessions.SessionManagerImpl
-
- CreateSessionMessage - Class in ome.services.messages
-
Published after a successful session creation.
- CreateSessionMessage(Object, String) - Constructor for class ome.services.messages.CreateSessionMessage
-
- createSessionWithTimeout(Principal, long) - Method in interface ome.api.ISession
-
- 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
-
- 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.
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-