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AbstractAmdServant - Class in ome.services.blitz.impl
throttled implementation base class which can be used by _ServiceInterfaceOperations implementors and injected into a tie servant.
AbstractAmdServant(ServiceInterface, BlitzExecutor) - Constructor for class ome.services.blitz.impl.AbstractAmdServant
 
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
 
AbstractFileExclusion - Class in ome.formats.importer.exclusions
Base FileExclusion implementation primarily providing a factory for FileExclusion implementations via AbstractFileExclusion.createExclusion(String).
AbstractFileExclusion() - Constructor for class ome.formats.importer.exclusions.AbstractFileExclusion
 
AbstractFileExclusion.Exclusion - Enum in ome.formats.importer.exclusions
Enum of well-known FileExclusion names.
AbstractFileTransfer - Class in ome.formats.importer.transfers
AbstractFileTransfer() - Constructor for class ome.formats.importer.transfers.AbstractFileTransfer
 
AbstractFileTransfer.Transfers - Enum in ome.formats.importer.transfers
Enum of well-known FileTransfer names.
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
Deprecated.
AbstractRepositoryI(ObjectAdapter, Registry, Executor, Principal, FileMaker, PublicRepositoryI) - Constructor for class ome.services.blitz.repo.AbstractRepositoryI
Deprecated.
AbstractRepositoryI(ObjectAdapter, Registry, Executor, Principal, String, ReadOnlyStatus, PublicRepositoryI) - Constructor for class ome.services.blitz.repo.AbstractRepositoryI
 
AbstractRepositoryI(ObjectAdapter, Registry, Executor, Principal, FileMaker, ReadOnlyStatus, PublicRepositoryI) - Constructor for class ome.services.blitz.repo.AbstractRepositoryI
 
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(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.
access(File) - Method in class omero.util.TempFileManager
Returns true if the current user can write to the give directory.
aclVoter - Variable in class ome.services.blitz.impl.ScriptI
 
acquireLock(String) - Method in class omero.util.ServantHolder
Acquires the given lock or if necessary creates a new one.
acquireProcessor(Job, int, Current) - Method in class ome.services.blitz.impl.SharedResourcesI
 
acquireProcessor(Job, int, Current) - Method in interface omero.grid.ParamsHelper.Acquirer
 
acquirer() - Method in class ome.services.blitz.impl.ScriptI
 
acquisitionData() - Method in class omero.sys.ParametersI
Sets the acquisition data parameter to true.
activate_async(AMD_StatefulServiceInterface_activate, Current) - Method in class ome.services.blitz.impl.AbstractAmdServant
 
activate_async(AMD_IShare_activate, long, Current) - Method in class ome.services.blitz.impl.ShareI
 
activate_async(AMD_StatefulServiceInterface_activate, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
activateAndWait(Current) - Method in class ome.services.blitz.impl.ProcessorCallbackI
Generates a UUID-based Identity with the category of PROCESSORCALLBACK.value and then calls ProcessorCallbackI.activateAndWait(Current, Ice.Identity).
activateAndWait(Current, Identity) - Method in class ome.services.blitz.impl.ProcessorCallbackI
Primary method which adds this instance to IceStorm, waits for a response from any active processor services, and finally unregister itself before returning the first processor instance which responded.
activeQueries_async(AMD_Search_activeQueries, Current) - Method in class ome.services.blitz.impl.SearchI
 
activeServices(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
adapter - Variable in class ome.services.blitz.fire.SessionManagerI
 
Adapter - Class in ome.services.throttling
Simple adapter which takes a Executor.Work instance and executes it as a BlitzExecutor task.
Adapter(Object, Current, IceMapper, Executor, Principal, Executor.Work) - Constructor for class ome.services.throttling.Adapter
 
adapter - Variable in class omero.cmd.SessionI
 
ADD() - Constructor for class ome.formats.importer.ImportEvent.ADD
 
add(String, RType) - Method in class omero.sys.ParametersI
 
add(Resources.Entry) - Method in class omero.util.Resources
 
addAdminPrivileges(SecurityContext, ExperimenterData, Collection<String>) - Method in class omero.gateway.facility.AdminFacility
Grant an user additional admin privileges.
addArray(int[][], int, int, int) - Method in class omero.gateway.util.UploadMask
Adds a Mask Shape to the appropriate ROIClass, creating one if necessary.
addCallback(CmdCallbackPrx, Current) - Method in class omero.cmd.HandleI
 
addCircle(String, double, double, double) - Method in class ome.services.blitz.measurements.MeasurementStore
 
addCircle(String, double, double, double) - Method in interface ome.services.blitz.measurements.OmeroMeasurementStore
 
addClientId(String) - Method in class omero.util.ServantHolder
 
addCodomainMap_async(AMD_RenderingEngine_addCodomainMap, CodomainMapContext, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
addCodomainMapToChannel_async(AMD_RenderingEngine_addCodomainMapToChannel, CodomainMapContext, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
addComment_async(AMD_IShare_addComment, long, String, Current) - Method in class ome.services.blitz.impl.ShareI
 
addDataset(String, String, Project) - Method in class ome.formats.OMEROMetadataStoreClient
 
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
addFile(String) - Method in class ome.formats.importer.util.ErrorContainer
 
addGroupOwners_async(AMD_IAdmin_addGroupOwners, ExperimenterGroup, List<Experimenter>, Current) - Method in class ome.services.blitz.impl.AdminI
 
addGroups_async(AMD_IAdmin_addGroups, Experimenter, List<ExperimenterGroup>, Current) - Method in class ome.services.blitz.impl.AdminI
 
addGuest_async(AMD_IShare_addGuest, long, String, Current) - Method in class ome.services.blitz.impl.ShareI
 
addGuests_async(AMD_IShare_addGuests, long, List<String>, Current) - Method in class ome.services.blitz.impl.ShareI
 
addId(long) - Method in class omero.sys.ParametersI
 
addId(RLong) - Method in class omero.sys.ParametersI
 
addIds(Collection<Long>) - Method in class omero.sys.ParametersI
 
addImage(Image) - Method in class ome.services.blitz.impl.OmeroMetadata
 
addImage(byte[], int, int, int) - Method in class 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
 
addImagesToDataset(SecurityContext, Collection<ImageData>, DatasetData) - Method in class omero.gateway.facility.DataManagerFacility
Adds the ImageDatas to the given DatasetData
addImageToDataset(SecurityContext, ImageData, DatasetData) - Method in class omero.gateway.facility.DataManagerFacility
Adds the ImageData to the given DatasetData
addLong(String, long) - Method in class omero.sys.ParametersI
 
addLong(String, RLong) - Method in class omero.sys.ParametersI
 
addLongs(String, Collection<Long>) - Method in class omero.sys.ParametersI
 
addMasks(Map<Integer, MaskData>) - Method in class omero.gateway.util.ROIComponent
Adds the Masks in the maskSet to the component.
addModelProcessor(ModelProcessor) - Method in class ome.formats.OMEROMetadataStoreClient
Adds a model processor to the end of the processing chain.
addObject(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_async(AMD_IShare_addObject, long, IObject, Current) - Method in class ome.services.blitz.impl.ShareI
 
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_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_async(AMD_Search_addOrderByAsc, String, Current) - Method in class ome.services.blitz.impl.SearchI
 
addOrderByDesc_async(AMD_Search_addOrderByDesc, String, Current) - Method in class ome.services.blitz.impl.SearchI
 
addProcess(ProcessContainer.Process) - Method in class ome.services.blitz.repo.ProcessContainer
Called once the ManagedImportProcessI service is created.
addProcessor(ProcessorPrx, Current) - Method in class ome.services.blitz.impl.SharedResourcesI
 
addProject(String, String) - Method in class ome.formats.OMEROMetadataStoreClient
 
addPropertyChangeListener(PropertyChangeListener) - Method in class omero.gateway.facility.Facility
Adds a PropertyChangeListener
addPropertyChangeListener(PropertyChangeListener) - Method in class omero.gateway.Gateway
Adds a PropertyChangeListener
addReference(LSID, LSID) - Method in interface ome.formats.model.IObjectContainerStore
Adds a reference to the reference cache.
addReference(LSID, LSID) - Method in class ome.formats.OMEROMetadataStoreClient
Adds a reference to the reference cache.
addReply_async(AMD_IShare_addReply, long, String, TextAnnotation, Current) - Method in class ome.services.blitz.impl.ShareI
 
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
 
addShapeData(ShapeData) - Method in class omero.gateway.model.ROIData
Adds ShapeData object to ROIData.
addTable(SecurityContext, DataObject, String, TableData) - Method in class omero.gateway.facility.TablesFacility
Adds a new table with the provided data
addUser_async(AMD_IShare_addUser, long, Experimenter, Current) - Method in class ome.services.blitz.impl.ShareI
 
addUsers_async(AMD_IShare_addUsers, long, List<Experimenter>, Current) - Method in class ome.services.blitz.impl.ShareI
 
adjustGraphPolicy(Function<GraphPolicy, GraphPolicy>) - Method in class omero.cmd.graphs.Chgrp2I
 
adjustGraphPolicy(Function<GraphPolicy, GraphPolicy>) - Method in class omero.cmd.graphs.Chmod2I
 
adjustGraphPolicy(Function<GraphPolicy, GraphPolicy>) - Method in class omero.cmd.graphs.Chown2I
 
adjustGraphPolicy(Function<GraphPolicy, GraphPolicy>) - Method in class omero.cmd.graphs.Delete2I
 
adjustGraphPolicy(Function<GraphPolicy, GraphPolicy>) - Method in 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.
AdminFacility - Class in omero.gateway.facility
Facility for handling admin issues, e.g. creating users, groups, etc.
AdminI - Class in ome.services.blitz.impl
Implementation of the IAdmin service.
AdminI(IAdmin, BlitzExecutor) - Constructor for class ome.services.blitz.impl.AdminI
 
advUsage() - Static method in class ome.formats.importer.cli.CommandLineImporter
Prints advanced usage to STDERR and exits with return code 1.
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
 
ALL_GROUPS_ID - Static variable in class omero.gateway.model.SearchParameters
The ID for searching across all groups
ALL_SCOPE - Static variable in class omero.gateway.model.SearchParameters
 
ALL_TYPES - Static variable in class omero.gateway.model.SearchParameters
 
allEnumerations_async(AMD_ITypes_allEnumerations, String, Current) - Method in class ome.services.blitz.impl.TypesI
 
allExps() - Method in class omero.sys.ParametersI
Removes the experimenter parameter from the map.
allGrps() - Method in class omero.sys.ParametersI
Removes the group parameter from the map.
allow(ObjectPrx) - Method in class omero.cmd.SessionI
 
allowAdministration() - Method in class ome.services.blitz.Router
 
allowGuests() - Method in class omero.cmd.Helper
Must be called before setSteps if access by the guest user is to be allowed.
allTimes() - Method in class omero.sys.ParametersI
Removes the time parameters from the map.
allTypes_async(AMD_Search_allTypes, Current) - Method in class ome.services.blitz.impl.SearchI
 
ALPHA_INDEX - Static variable in class ome.formats.model.ColorsFactory
Index of the red component of a color.
ALPHA_TEXT - Static variable in class ome.formats.model.ChannelProcessor
Name of the alpha component when it is a graphics image.
alreadyRouted(Current) - Method in class ome.services.blitz.redirect.AbstractRedirector
 
AMD_submit() - Constructor for class ome.services.blitz.repo.PublicRepositoryI.AMD_submit
 
and_async(AMD_Search_and, Current) - Method in class ome.services.blitz.impl.SearchI
 
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.
AnnotationListValue(String, ImportConfig, List<Annotation>) - Constructor for class ome.formats.importer.ImportConfig.AnnotationListValue
 
annotations - Variable in class ome.formats.importer.ImportConfig
 
ANNOTATIONS - Static variable in class omero.gateway.model.ChannelData
Identifies the Channel.ANNOTATIONLINKS field.
ANNOTATIONS - Static variable in class omero.gateway.model.DatasetData
Identifies the DatasetI.ANNOTATIONLINKS field.
ANNOTATIONS - Static variable in class omero.gateway.model.ImageData
Identifies the ImageI.ANNOTATIONLINKS field.
ANNOTATIONS - Static variable in class omero.gateway.model.PlateData
Identifies the PlateI.ANNOTATIONLINKS field.
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
 
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
 
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
applyHardWiredInterceptors(List<HardWiredInterceptor>, AopContextInitializer) - Method in class ome.services.blitz.impl.AbstractAmdServant
Applies the hard-wired intercepting to this instance.
applySettingsToDataset_async(AMD_IRenderingSettings_applySettingsToDataset, long, long, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
 
applySettingsToImage_async(AMD_IRenderingSettings_applySettingsToImage, long, long, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
 
applySettingsToImages_async(AMD_IRenderingSettings_applySettingsToImages, long, List<Long>, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
 
applySettingsToPixels_async(AMD_IRenderingSettings_applySettingsToPixels, long, long, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
 
applySettingsToProject_async(AMD_IRenderingSettings_applySettingsToProject, long, long, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
 
applySettingsToSet_async(AMD_IRenderingSettings_applySettingsToSet, long, String, List<Long>, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
 
ARC - Static variable in class omero.gateway.model.LightSourceData
Indicates that the light source is a arc.
areaPoints(SmartShape.PointCallback) - Method in class omero.model.SmartEllipseI
 
areaPoints(SmartShape.PointCallback) - Method in class omero.model.SmartLineI
 
areaPoints(SmartShape.PointCallback) - Method in class omero.model.SmartMaskI
 
areaPoints(SmartShape.PointCallback) - Method in class omero.model.SmartPathI
 
areaPoints(SmartShape.PointCallback) - Method in class omero.model.SmartPointI
 
areaPoints(SmartShape.PointCallback) - Method in class omero.model.SmartPolygonI
 
areaPoints(SmartShape.PointCallback) - Method in class omero.model.SmartPolylineI
 
areaPoints(SmartShape.PointCallback) - Method in class omero.model.SmartRectI
 
areaPoints(SmartShape.PointCallback) - Method in interface omero.model.SmartShape
Calls the SmartShape.PointCallback with all of the x/y coordinates which are within the shape.
areaPoints(SmartShape.PointCallback) - Method in class omero.model.SmartTextI
 
areTablesEnabled(Current) - Method in class ome.services.blitz.impl.SharedResourcesI
 
asAnnotation() - Method in class omero.gateway.model.DataObject
Returns the hosted IObject as an Annotation.
asAwtShape() - Method in class omero.model.SmartEllipseI
 
asAwtShape() - Method in class omero.model.SmartLineI
 
asAwtShape() - Method in class omero.model.SmartMaskI
 
asAwtShape() - Method in class omero.model.SmartPathI
 
asAwtShape() - Method in class omero.model.SmartPointI
 
asAwtShape() - Method in class omero.model.SmartPolygonI
 
asAwtShape() - Method in class omero.model.SmartPolylineI
 
asAwtShape() - Method in class omero.model.SmartRectI
 
asAwtShape() - Method in interface omero.model.SmartShape
Converts the current SmartShape to a Shape.
asAwtShape() - Method in class omero.model.SmartTextI
 
asCastedDataObjects(List) - Static method in class omero.gateway.util.PojoMapper
Converts each element of the collection into its corresponding DataObject.
ASCENDING_LETTER - Static variable in class omero.gateway.model.PlateData
Indicates that the column or row is a letter starting from A.
ASCENDING_NUMBER - Static variable in class omero.gateway.model.PlateData
Indicates that the column or row is a number starting from 1.
asChannel() - Method in class omero.gateway.model.DataObject
Returns the hosted IObject as a Well.
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(Map) - Static method in class omero.gateway.util.PojoMapper
Converts each pair (key, value) of the map.
asDataset() - Method in class omero.gateway.model.DataObject
Returns the hosted IObject as a Dataset.
asExperimenter() - Method in class omero.gateway.model.DataObject
Returns the hosted IObject as an Experimenter.
asFolder() - Method in class omero.gateway.model.DataObject
Returns the hosted IObject as a Folder.
asGroup() - Method in class omero.gateway.model.DataObject
Returns the hosted IObject as an Experimenter Group.
asIAnnotated() - Method in class omero.gateway.model.DataObject
not null; may throw class-cast exception
asImage() - Method in class omero.gateway.model.DataObject
Returns the hosted IObject as an Image.
asIObject() - Method in class omero.gateway.model.DataObject
not null; no exceptions.
asOriginalFile(String) - Method in class ome.services.blitz.repo.CheckedPath
Creates an OriginalFile instance for the given CheckedPath even if it doesn't exist.
asPixels() - Method in class omero.gateway.model.DataObject
Returns the hosted IObject as a Pixels.
asPlate() - Method in class omero.gateway.model.DataObject
Returns the hosted IObject as a Plate.
asPoints() - Method in class omero.model.SmartEllipseI
 
asPoints() - Method in class omero.model.SmartLineI
 
asPoints() - Method in class omero.model.SmartMaskI
 
asPoints() - Method in class omero.model.SmartPathI
 
asPoints() - Method in class omero.model.SmartPointI
 
asPoints() - Method in class omero.model.SmartPolygonI
 
asPoints() - Method in class omero.model.SmartPolylineI
 
asPoints() - Method in class omero.model.SmartRectI
 
asPoints() - Method in interface omero.model.SmartShape
Provides some, possibly lossy, bounding polygon of this SmartShape via points.
asPoints() - Method in class omero.model.SmartTextI
 
asPojo(IObject) - Static method in class omero.gateway.model.DataObject
Converts the passed IObject into its corresponding Pojo object.
asPojos(Collection) - Static method in class omero.gateway.model.DataObject
Converts the collection of IObjects into the corresponding DataObjects
asPojos(Map) - Static method in class omero.gateway.model.DataObject
Converts the map of IObjects into the corresponding DataObjects
asProject() - Method in class omero.gateway.model.DataObject
Returns the hosted IObject as a Project.
asScreen() - Method in class omero.gateway.model.DataObject
Returns the hosted IObject as a Screen.
assertMayProcess(String, long, Details) - Method in class omero.cmd.graphs.BaseGraphTraversalProcessor
 
assertMayProcess(String, long, Details) - Method in class omero.cmd.graphs.NullGraphTraversalProcessor
 
assertNodes(Set<String>) - Method in class ome.services.blitz.fire.Ring
 
assertResponse(int) - Method in class omero.cmd.Helper
Checks the given steps against the number of times that this method has been called on this instance and then increments the call count.
assertStep(int, int) - Method in class omero.cmd.Helper
Throws an exception if the current step is not the expected value.
assertStep(int) - Method in class omero.cmd.Helper
Checks the given steps against the number of times that this method has been called on this instance and then increments the call count.
asWell() - Method in class 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.
attach_async(AMD_JobHandle_attach, long, Current) - Method in class ome.services.blitz.impl.JobHandleI
 
attachAnnotation(SecurityContext, T, DataObject) - Method in class omero.gateway.facility.DataManagerFacility
Create/attach an AnnotationData to a given DataObject
attachFile(SecurityContext, File, String, String, String, DataObject) - Method in class omero.gateway.facility.DataManagerFacility
Attaches a File to a DataObject
autoClose - Variable in class ome.formats.importer.ImportConfig
 

B

base - Variable in class omero.util.ReadOnlyByteArray
The original array.
BaseGraphPolicyAdjuster - Class in omero.cmd.graphs
The base class assists adjustment of an existing graph traversal policy.
BaseGraphPolicyAdjuster(GraphPolicy) - Constructor for class omero.cmd.graphs.BaseGraphPolicyAdjuster
Construct a new graph policy adjuster.
BaseGraphTraversalProcessor - Class in omero.cmd.graphs
Useful methods for GraphTraversal.Processor instances to share.
BaseGraphTraversalProcessor(Session) - Constructor for class omero.cmd.graphs.BaseGraphTraversalProcessor
 
be - Variable in class ome.services.blitz.impl.AbstractAmdServant
 
BEGIN_POST_PROCESS(int, ImportContainer, IObject, Long, int, ImportSize) - Constructor for class ome.formats.importer.ImportEvent.BEGIN_POST_PROCESS
 
BEGIN_SAVE_TO_DB(int, ImportContainer, IObject, Long, int, ImportSize) - Constructor for class ome.formats.importer.ImportEvent.BEGIN_SAVE_TO_DB
 
BfPixelsStoreI - Class in ome.services.blitz.repo
 
BfPixelsStoreI(String, ImageReader) - Constructor for class ome.services.blitz.repo.BfPixelsStoreI
 
bfSetId(ReaderWrapper) - Method in class ome.services.blitz.repo.CheckedPath
Perform BioFormats ReaderWrapper.setId(String) for this file.
BlitzConfiguration - Class in ome.services.blitz.util
Factory bean which creates an Communicator instance as well as the proper ObjectAdapter and adds initial, well-known servants.
BlitzConfiguration(Ring, SessionManager, SessionProvider, SecuritySystem, Executor, int) - Constructor for class ome.services.blitz.util.BlitzConfiguration
Single constructor which builds all Ice instances needed for the server runtime based on arguments provided.
BlitzConfiguration(InitializationData, Ring, SessionManager, SessionProvider, SecuritySystem, Executor, int) - Constructor for class ome.services.blitz.util.BlitzConfiguration
BlitzExecutor - Interface in ome.services.blitz.util
Single-point of execution for all AMD blitz calls.
BlitzInstanceProvider - Class in ome.formats.model
An instance provider which uses reflection to fulfill the contract of an InstanceProvider.
BlitzInstanceProvider(EnumerationProvider) - Constructor for class ome.formats.model.BlitzInstanceProvider
Default constructor.
BlitzOnly - Interface in ome.services.blitz.util
Marker interface which specifies that an servant should not be checked for api consistency via ApiConsistencyCheck.
block(long) - Method in class omero.cmd.CmdCallbackI
Blocks for the given number of milliseconds unless CmdCallbackI.finished(Response, Status, Current) has been called in which case it returns immediately with true.
block(long) - Method in class omero.grid.ProcessCallbackI
Should only be used if the default logic of the process methods is kept in place.
BLUE_INDEX - Static variable in class ome.formats.model.ColorsFactory
Index of the red component of a color.
BLUE_TEXT - Static variable in class ome.formats.model.ChannelProcessor
Name of the blue component when it is a graphics image.
BooleanAnnotationData - Class in omero.gateway.model
Boolean annotation.
BooleanAnnotationData() - Constructor for class omero.gateway.model.BooleanAnnotationData
Creates a new instance.
BooleanAnnotationData(boolean) - Constructor for class omero.gateway.model.BooleanAnnotationData
Creates a new instance.
BooleanAnnotationData(BooleanAnnotation) - Constructor for class omero.gateway.model.BooleanAnnotationData
Creates a new instance.
BoolValue(String, ImportConfig, boolean) - Constructor for class ome.formats.importer.ImportConfig.BoolValue
 
BrowseFacility - Class in omero.gateway.facility
A Facility for browsing the data hierarchy and retrieving ProjectData, DatasetData, etc.
BTF - Static variable in class omero.gateway.util.TIFFFilter
Possible file extension.
build() - Method in class ome.formats.importer.targets.TargetBuilder
 
buildParseJob(long) - Method in class omero.grid.ParamsHelper
Build a job for the script with id.
buildResponse(int, Object) - Method in class ome.services.blitz.impl.commands.SaveI
 
buildResponse(int, Object) - Method in class ome.services.blitz.repo.ManagedImportRequestI
 
buildResponse(int, Object) - Method in class ome.services.blitz.repo.RawAccessRequestI
 
buildResponse(int, Object) - Method in class omero.cmd.admin.CurrentSessionsRequestI
 
buildResponse(int, Object) - Method in class omero.cmd.admin.ResetPasswordRequestI
 
buildResponse(int, Object) - Method in class omero.cmd.admin.UpdateSessionTimeoutRequestI
 
buildResponse(int, Object) - Method in class omero.cmd.basic.DoAllI
 
buildResponse(int, Object) - Method in class omero.cmd.basic.ListRequestsI
 
buildResponse(int, Object) - Method in class omero.cmd.basic.TimingI
 
buildResponse(int, Object) - Method in class omero.cmd.fs.FindPyramidsI
 
buildResponse(int, Object) - Method in class omero.cmd.fs.ManageImageBinariesI
 
buildResponse(int, Object) - Method in class omero.cmd.fs.OriginalMetadataRequestI
 
buildResponse(int, Object) - Method in class omero.cmd.fs.UsedFilesRequestI
 
buildResponse(int, Object) - Method in class omero.cmd.graphs.Chgrp2I
 
buildResponse(int, Object) - Method in class omero.cmd.graphs.Chmod2I
 
buildResponse(int, Object) - Method in class omero.cmd.graphs.Chown2I
 
buildResponse(int, Object) - Method in class omero.cmd.graphs.Delete2I
 
buildResponse(int, Object) - Method in class omero.cmd.graphs.DiskUsage2I
 
buildResponse(int, Object) - Method in class omero.cmd.graphs.DiskUsageI
Deprecated.
 
buildResponse(int, Object) - Method in class omero.cmd.graphs.DuplicateI
 
buildResponse(int, Object) - Method in class omero.cmd.graphs.FindChildrenI
 
buildResponse(int, Object) - Method in class omero.cmd.graphs.FindParentsI
 
buildResponse(int, Object) - Method in class omero.cmd.graphs.LegalGraphTargetsI
 
buildResponse(int, Object) - Method in class omero.cmd.graphs.SkipHeadI
 
buildResponse(int, Object) - Method in interface omero.cmd.IRequest
Post-transaction chance to map from the return value of IRequest.step(int) to a Response object.
buildResponse(int, Object) - Method in class omero.cmd.mail.SendEmailRequestI
 
BULK_ANNOTATIONS_NS - Static variable in class omero.gateway.model.FileAnnotationData
The name space used to indicate that the FileAnnotation is a Bulk Annotations file.
byAnnotatedWith_async(AMD_Search_byAnnotatedWith, List<Annotation>, Current) - Method in class ome.services.blitz.impl.SearchI
 
byFullText_async(AMD_Search_byFullText, String, Current) - Method in class ome.services.blitz.impl.SearchI
 
byGroupForTags_async(AMD_Search_byGroupForTags, String, Current) - Method in class ome.services.blitz.impl.SearchI
 
byHqlQuery_async(AMD_Search_byHqlQuery, String, Parameters, Current) - Method in class ome.services.blitz.impl.SearchI
 
byLuceneQueryBuilder_async(AMD_Search_byLuceneQueryBuilder, String, String, String, String, String, Current) - Method in class ome.services.blitz.impl.SearchI
 
bySimilarTerms_async(AMD_Search_bySimilarTerms, List<String>, Current) - Method in class ome.services.blitz.impl.SearchI
 
bySomeMustNone_async(AMD_Search_bySomeMustNone, List<String>, List<String>, List<String>, Current) - Method in class ome.services.blitz.impl.SearchI
 
byTagForGroups_async(AMD_Search_byTagForGroups, String, Current) - Method in class ome.services.blitz.impl.SearchI
 

C

c2c() - Method in class omero.util.IceMapper
 
cache - Variable in class ome.services.blitz.impl.ScriptI
 
cache() - Method in class omero.sys.ParametersI
Deprecated.
experimental: may be wholly removed in next major version
CACHE_SIZE - Static variable in interface omero.gateway.cache.CacheService
The default size of a cache.
CacheService - Interface in omero.gateway.cache
Defines the caching service interface.
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
 
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, Current) - Constructor for class omero.cmd.CallContext
 
CallContext(OmeroContext, String) - Constructor for class omero.cmd.CallContext
 
CallContext(CurrentDetails, String) - Constructor for class omero.cmd.CallContext
 
callContextWrapper(Object, Current) - Method in class omero.cmd.SessionI
 
callInvokerOnMappedArgs(IceMapper, Object, Current, Object...) - Method in class ome.services.blitz.impl.AbstractAmdServant
 
callInvokerOnRawArgs(Object, Current, Object...) - Method in class ome.services.blitz.impl.AbstractAmdServant
 
callInvokerOnRawArgs(ServiceInterface, IceMethodInvoker, Object, Current, Object...) - Method in interface ome.services.blitz.util.BlitzExecutor
Uses the given IceMethodInvoker to make the method call.
callInvokerOnRawArgs(ServiceInterface, IceMethodInvoker, Object, Current, Object...) - Method in class ome.services.throttling.InThreadThrottlingStrategy
 
callInvokerOnRawArgs(ServiceInterface, IceMethodInvoker, Object, Current, Object...) - Method in class ome.services.throttling.SerialThrottlingStrategy
 
callInvokerWithMappedArgs(ServiceInterface, IceMethodInvoker, IceMapper, Object, Current, Object...) - Method in interface ome.services.blitz.util.BlitzExecutor
Passes the given arguments to IceMethodInvoker with the assumption that all conversion from omero.* to ome.* has taken place.
callInvokerWithMappedArgs(ServiceInterface, IceMethodInvoker, IceMapper, Object, Current, Object...) - Method in class ome.services.throttling.InThreadThrottlingStrategy
 
callInvokerWithMappedArgs(ServiceInterface, IceMethodInvoker, IceMapper, Object, Current, Object...) - Method in class ome.services.throttling.SerialThrottlingStrategy
 
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(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_async(AMD_JobHandle_cancelJob, Current) - Method in class ome.services.blitz.impl.JobHandleI
 
cancelUploads - Variable in class ome.formats.importer.util.ErrorHandler
 
canChgrp() - Method in class omero.gateway.model.DataObject
Returns true if the object can be moved by the user currently logged in, false otherwise, depending on permissions level.
canChgrp(Current) - Method in class omero.model.PermissionsI
 
canChown() - Method in class omero.gateway.model.DataObject
Returns true if the object can be given by the user currently logged in, false otherwise, depending on permissions level.
canChown(Current) - Method in class omero.model.PermissionsI
 
canCreate(SecurityContext) - Method in class omero.gateway.Gateway
Get the read-only status of the server.
canDelete() - Method in class omero.gateway.model.DataObject
Returns true if the object can be deleted by the user currently logged in, false otherwise, depending on permissions level.
canDelete(Current) - Method in class omero.model.PermissionsI
 
canEdit() - Method in class ome.services.blitz.repo.CheckedPath
 
canEdit() - Method in class omero.gateway.model.DataObject
Returns true if the object can be edited by the user currently logged in false otherwise, depending on permissions level.
canEdit(Current) - Method in class omero.model.PermissionsI
 
canLink() - Method in class omero.gateway.model.DataObject
Returns true if the object can be linked e.g. image add to dataset, by the user currently logged in, false otherwise, depending on permissions level.
canLink(Current) - Method in class omero.model.PermissionsI
 
canLogin() - Method in class ome.formats.importer.ImportConfig
Confirm all information for login is supplied
canMapReturnValue() - Method in class omero.util.IceMapper
True if this instance has a IceMapper.ReturnMapping
canRead() - Method in class ome.services.blitz.repo.CheckedPath
Check if this file is actually readable on the underlying filesystem.
canRunScript_async(AMD_IScript_canRunScript, long, Current) - Method in class ome.services.blitz.impl.ScriptI
 
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.
castChildOptions(Collection<ChildOption>) - Static method in class omero.cmd.graphs.ChildOptionI
Cast ChildOption[] to ChildOptionI[].
cb - Variable in class ome.services.throttling.Task
 
changeExpiredCredentials_async(AMD_IAdmin_changeExpiredCredentials, String, String, String, Current) - Method in class ome.services.blitz.impl.AdminI
 
changeGroup_async(AMD_IAdmin_changeGroup, IObject, String, Current) - Method in class ome.services.blitz.impl.AdminI
 
changeOwner_async(AMD_IAdmin_changeOwner, IObject, String, Current) - Method in class ome.services.blitz.impl.AdminI
 
changePassword_async(AMD_IAdmin_changePassword, RString, Current) - Method in class ome.services.blitz.impl.AdminI
 
changePasswordWithOldPassword_async(AMD_IAdmin_changePasswordWithOldPassword, RString, RString, Current) - Method in class ome.services.blitz.impl.AdminI
 
changePermissions_async(AMD_IAdmin_changePermissions, IObject, Permissions, Current) - Method in class ome.services.blitz.impl.AdminI
 
changeUserPassword_async(AMD_IAdmin_changeUserPassword, String, RString, Current) - Method in class ome.services.blitz.impl.AdminI
 
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.
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.
ChannelProcessor - Class in ome.formats.model
Processes the pixels sets of an IObjectContainerStore and ensures that LogicalChannel containers are present in the container cache, and populating channel name and colour where appropriate.
ChannelProcessor() - Constructor for class ome.formats.model.ChannelProcessor
 
check() - 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
 
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.
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
 
checkIndex(int) - Method in class omero.util.ReadOnlyByteArray
Makes sure that i is in [0, length).
checkIsAdministrator(AdminPrivilege) - Method in class omero.cmd.graphs.GraphHelper
Check if the current user is an administrator.
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.
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().
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
 
checksum(String, ChecksumAlgorithm) - Method in class ome.formats.importer.exclusions.AbstractFileExclusion
 
CHECKSUM_ALGORITHM_NAMER - Static variable in class ome.services.blitz.util.ChecksumAlgorithmMapper
 
checksumAlgorithm - Variable in class ome.formats.importer.ImportConfig
 
ChecksumAlgorithmMapper - Class in ome.services.blitz.util
Work with ChecksumAlgorithm enumeration instances, including mapping their values back to ChecksumTypes.
ChecksumAlgorithmMapper() - Constructor for class ome.services.blitz.util.ChecksumAlgorithmMapper
 
checksumAlgorithms - Variable in class ome.services.blitz.repo.PublicRepositoryI
 
checksumProviderFactory - Variable in class ome.services.blitz.repo.PublicRepositoryI
 
checksums - Variable in class ome.formats.importer.ImportEvent.FILESET_UPLOAD_END
 
checkTarget(File, TransferState) - Method in class ome.formats.importer.transfers.AbstractExecFileTransfer
Check that the server can properly read the copied file.
checkUpgrade - Variable in class ome.formats.importer.ImportConfig
 
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.
Chgrp2I(ACLVoter, Roles, GraphPathBean, LightAdminPrivileges, Deletion, Set<Class<? extends IObject>>, GraphPolicy, SetMultimap<String, String>, ApplicationContext) - Constructor for class omero.cmd.graphs.Chgrp2I
Construct a new chgrp request; called from GraphRequestFactory.getRequest(Class).
child(String) - Method in class ome.services.blitz.repo.CheckedPath
Returns a new CheckedPath that has the given path appended to the end of this instances path.
ChildOptionI - Class in omero.cmd.graphs
Child options adjust how child objects are treated according to their type and, if annotations, namespace, overriding the default graph traversal policy for orphans.
ChildOptionI(GraphPathBean, ImmutableSet<String>) - Constructor for class omero.cmd.graphs.ChildOptionI
Construct a new child option instance.
ChildOptionI(ChildOptionI) - Constructor for class omero.cmd.graphs.ChildOptionI
Construct a new child option instance identical to that given.
ChildOptionsPolicy - Class in omero.cmd.graphs
Adjust graph traversal policy for child objects according to their type and, if annotations, namespace.
ChildOptionsPolicy() - Constructor for class omero.cmd.graphs.ChildOptionsPolicy
 
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() - 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.
Chmod2I(ACLVoter, Roles, GraphPathBean, LightAdminPrivileges, Deletion, Set<Class<? extends IObject>>, GraphPolicy, SetMultimap<String, String>, ApplicationContext) - Constructor for class omero.cmd.graphs.Chmod2I
Construct a new chmod request; called from GraphRequestFactory.getRequest(Class).
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() - 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.
Chown2I(ACLVoter, Roles, GraphPathBean, LightAdminPrivileges, Deletion, Set<Class<? extends IObject>>, GraphPolicy, SetMultimap<String, String>, ApplicationContext) - Constructor for class omero.cmd.graphs.Chown2I
Construct a new chown request; called from GraphRequestFactory.getRequest(Class).
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.
cleanup() - Method in class ome.formats.importer.cli.CommandLineImporter
Cleans up after a successful or unsuccessful image import.
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 class ome.formats.importer.ImportLibrary
 
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.
clearCache(int) - Method in interface omero.gateway.cache.CacheService
Clears the specified cache.
clearErrors(int) - Method in class ome.formats.importer.util.ErrorHandler
 
clearFiles() - Method in class ome.formats.importer.util.ErrorContainer
Clear the list of files to upload.
clearQueries_async(AMD_Search_clearQueries, Current) - Method in class ome.services.blitz.impl.SearchI
 
client - Class in omero
Central client-side blitz entry point.
client() - Constructor for class omero.client
Calls client.client(Ice.InitializationData) with a new InitializationData
client(InitializationData) - Constructor for class omero.client
Creates an Communicator from a InitializationData instance.
client(String) - Constructor for class omero.client
Creates an Communicator pointing at the given server using the Server.DEFAULT_PORT.
client(String, int) - Constructor for class omero.client
Creates an Communicator pointing at the given server with the non-standard port.
client(String[]) - Constructor for class omero.client
Calls client.client(String[], Ice.InitializationData) with a new InitializationData
client(String[], InitializationData) - Constructor for class omero.client
Creates an Communicator from command-line arguments.
client(File...) - Constructor for class omero.client
Creates an Communicator from multiple files.
client(Map) - Constructor for class omero.client
Creates an Communicator from a Map instance.
client - Variable in class omero.model.DetailsI
 
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
 
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
 
close(boolean) - Method in class loci.ome.io.OmeroReader
Deprecated.
 
close() - Method in class ome.formats.importer.OMEROWrapper
 
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(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.Gateway
 
close() - Method in class omero.gateway.rnd.DataSink
 
close(Current) - Method in class omero.grid.InteractiveProcessorI
 
close() - Method in class omero.grid.ProcessCallbackI
 
close(Current) - Method in interface omero.util.CloseableServant
 
close() - Method in class omero.util.RPSTileData
 
close() - Method in interface omero.util.TileData
 
close_async(AMD_StatefulServiceInterface_close, Current) - Method in class ome.services.blitz.impl.AbstractCloseableAmdServant
SessionHandler also specially catches close() calls, but cannot remove the servant from the ObjectAdapter and thereby prevent any further communication.
close_async(AMD_StatefulServiceInterface_close, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
CloseableServant - Interface in omero.util
Marker interface which distinguishes a servant which wants to have CloseableServant.close(Ice.Current) called on SessionI.doDestroy()
closeCalled(int) - Method in class ome.services.blitz.repo.ManagedImportProcessI
 
closeCompleted(ImportConfig) - Static method in class ome.formats.importer.cli.CommandLineImporter
Look for all ImportProcessPrx in the current session and close them if they return a non-null Response (i.e. they are done).
closeConnector(SecurityContext) - Method in class omero.gateway.Gateway
Close a connector for a certain SecurityContext
closeImport(SecurityContext, String) - Method in class omero.gateway.Gateway
Close Import for a certain user
closeOnDestroy(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
closeService(SecurityContext, StatefulServiceInterfacePrx) - Method in class omero.gateway.Gateway
Close a service
closeServices() - Method in class ome.formats.OMEROMetadataStoreClient
Closes all stateful services.
closeSession() - Method in class omero.client
Closes the session and nulls out the communicator.
closeSession() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
closeSession_async(AMD_ISession_closeSession, Session, Current) - Method in class ome.services.blitz.impl.SessionI
 
closeShare_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.
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
 
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
 
combineFilePathRestrictions(FilePathRestrictions...) - Static method in class ome.services.blitz.repo.path.FilePathRestrictions
Combine sets of rules to form a set that satisfies them all and that include transformations away from Unicode control characters.
CommandLineImporter - Class in ome.formats.importer.cli
The base entry point for the CLI version of the OMERO importer.
CommandLineImporter(ImportConfig, String[], boolean) - Constructor for class ome.formats.importer.cli.CommandLineImporter
Legacy constructor which uses a UploadFileTransfer.
CommandLineImporter(ImportConfig, String[], boolean, FileTransfer, int) - Constructor for class ome.formats.importer.cli.CommandLineImporter
Legacy constructor without any file exclusions.
CommandLineImporter(ImportConfig, String[], boolean, FileTransfer, List<FileExclusion>, int) - Constructor for class ome.formats.importer.cli.CommandLineImporter
Main entry class for the application.
commonRoot(List<FsFile>) - Method in class ome.services.blitz.repo.ManagedRepositoryI
From a list of paths, calculate the common root path that all share.
COMPANION_FILE_NS - Static variable in class omero.gateway.model.FileAnnotationData
The name space used to indicate that the FileAnnotation is a companion file.
compare(LSID, LSID) - Method in class ome.formats.OMEXMLModelComparator
 
compare(Dataset, Dataset) - Method in class ome.formats.SortDatasetsByName
 
compare(Project, Project) - Method in class ome.formats.SortProjectsByName
 
compare(Object, Object) - Method in class omero.gateway.model.ROICoordinate
Implemented as specified by the Comparator I/F.
complete() - Method in class ome.formats.OverlayMetadataStore
Completes overlay population, flushing in memory ROI.
COMPLEX_TYPE - Static variable in class omero.gateway.model.PixelsData
Identifies the type used to store pixel values.
concatenate(FsFile...) - Static method in class ome.services.blitz.repo.path.FsFile
Concatenate paths.
ConcurrentStatisticsImpl - Class in org.hibernate.stat
Implementation of Statistics, as well as StatisticsImplementor, based on the java.util.concurrent package introduced in Java 5.
ConcurrentStatisticsImpl() - Constructor for class org.hibernate.stat.ConcurrentStatisticsImpl
 
ConcurrentStatisticsImpl(SessionFactoryImplementor) - Constructor for class org.hibernate.stat.ConcurrentStatisticsImpl
 
config - Variable in class ome.formats.importer.cli.CommandLineImporter
Configuration used by all components
config - Variable in class ome.formats.importer.util.ErrorHandler
 
ConfigI - Class in ome.services.blitz.impl
Implementation of the IConfig service.
ConfigI(IConfig, BlitzExecutor) - Constructor for class ome.services.blitz.impl.ConfigI
 
ConfigRedirector - Class in ome.services.blitz.redirect
Redirector implementation which uses the REDIRECT config key via LocalConfig to know which Node is currently active.
ConfigRedirector(Executor) - Constructor for class ome.services.blitz.redirect.ConfigRedirector
 
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.
configureServant(Object) - Method in class omero.cmd.SessionI
Apply proper AOP and call setters for any known injection properties.
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
containedExperimenters_async(AMD_IAdmin_containedExperimenters, long, Current) - Method in class ome.services.blitz.impl.AdminI
 
containedGroups_async(AMD_IAdmin_containedGroups, long, Current) - Method in class ome.services.blitz.impl.AdminI
 
container - Variable in class ome.formats.importer.ImportEvent.PROGRESS_EVENT
 
ContainerI - Class in ome.services.blitz.impl
Implementation of the IContainer service.
ContainerI(IContainer, BlitzExecutor) - Constructor for class ome.services.blitz.impl.ContainerI
 
contains(Object) - Method in class omero.gateway.model.SearchResultCollection
 
contentLength - Variable in class ome.formats.importer.ImportEvent.FILE_UPLOAD_EVENT
 
context - Variable in class ome.services.blitz.fire.SessionManagerI
 
context - Variable in class ome.services.blitz.repo.PublicRepositoryI
 
context - Variable in class omero.cmd.SessionI
 
contexts - Variable in class omero.cmd.admin.CurrentSessionsRequestI
 
contOnError - Variable in class ome.formats.importer.ImportConfig
 
control - Variable in class omero.cmd.SessionI
 
convert(ElectricPotential) - Static method in class omero.model.ElectricPotentialI
FIXME: this should likely take a default so that locations which don't want an exception can have log.warn("Using new PositiveFloat(1.0)!"
convert(Frequency) - Static method in class omero.model.FrequencyI
FIXME: this should likely take a default so that locations which don't want an exception can have log.warn("Using new PositiveFloat(1.0)!"
convert(Length) - Static method in class omero.model.LengthI
FIXME: this should likely take a default so that locations which don't want an exception can have log.warn("Using new PositiveFloat(1.0)!"
convert(Power) - Static method in class omero.model.PowerI
FIXME: this should likely take a default so that locations which don't want an exception can have log.warn("Using new PositiveFloat(1.0)!"
convert(Pressure) - Static method in class omero.model.PressureI
FIXME: this should likely take a default so that locations which don't want an exception can have log.warn("Using new PositiveFloat(1.0)!"
convert(Temperature) - Static method in class omero.model.TemperatureI
FIXME: this should likely take a default so that locations which don't want an exception can have log.warn("Using new PositiveFloat(1.0)!"
convert(Time) - Static method in class omero.model.TimeI
FIXME: this should likely take a default so that locations which don't want an exception can have log.warn("Using new PositiveFloat(1.0)!"
convert(IceMapper) - Method in interface omero.rtypes.Conversion
Convert the "val" field on the given RType instance to an ome.model.* representation.
convert(EventContext) - Static method in class omero.util.IceMapper
 
convert(RGBBuffer) - Static method in class omero.util.IceMapper
 
convert(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
 
convertElectricPotentialXML(ElectricPotential, String) - Static method in class ome.formats.model.UnitsFactory
 
convertFrequency(Frequency) - Static method in class ome.formats.model.UnitsFactory
Convert a Bio-Formats Frequency to an OMERO Frequency.
convertFrequency(Frequency) - Static method in class ome.formats.model.UnitsFactory
 
convertFrequency(Frequency, Unit<Frequency>) - Static method in class ome.formats.model.UnitsFactory
 
convertFrequencyXML(Frequency, String) - Static method in class ome.formats.model.UnitsFactory
 
convertLength(Length) - Static method in class ome.formats.model.UnitsFactory
Convert a Bio-Formats Length to an OMERO Length.
convertLength(Length) - Static method in class ome.formats.model.UnitsFactory
 
convertLength(Length, Unit<Length>) - Static method in class ome.formats.model.UnitsFactory
 
convertLengthXML(Length, String) - Static method in class ome.formats.model.UnitsFactory
 
convertMapPairs(List<MapPair>) - Static method in class omero.util.IceMapper
 
convertNamedValueList(List<NamedValue>) - Static method in class omero.util.IceMapper
 
convertPower(Power) - Static method in class ome.formats.model.UnitsFactory
Convert a Bio-Formats Power to an OMERO Power.
convertPower(Power) - Static method in class ome.formats.model.UnitsFactory
 
convertPower(Power, Unit<Power>) - Static method in class ome.formats.model.UnitsFactory
 
convertPowerXML(Power, String) - Static method in class ome.formats.model.UnitsFactory
 
convertPressure(Pressure) - Static method in class ome.formats.model.UnitsFactory
Convert a Bio-Formats Pressure to an OMERO Pressure.
convertPressure(Pressure) - Static method in class ome.formats.model.UnitsFactory
 
convertPressure(Pressure, Unit<Pressure>) - Static method in class ome.formats.model.UnitsFactory
 
convertPressureXML(Pressure, String) - Static method in class ome.formats.model.UnitsFactory
 
convertRTypeToJava(RType) - Static method in class omero.gateway.util.ModelMapper
Converts the passed OMERO type into its corresponding Java type.
convertStringStringMap(Map<String, String>) - Static method in class omero.util.IceMapper
Convert a String→String map's values to RStrings.
convertTemperature(Temperature) - Static method in class ome.formats.model.UnitsFactory
Convert a Bio-Formats Temperature to an OMERO Temperature.
convertTemperature(Temperature) - Static method in class ome.formats.model.UnitsFactory
 
convertTemperature(Temperature, Unit<Temperature>) - Static method in class ome.formats.model.UnitsFactory
 
convertTemperatureXML(Temperature, String) - Static method in class ome.formats.model.UnitsFactory
 
convertTime(Time) - Static method in class ome.formats.model.UnitsFactory
Convert a Bio-Formats Time to an OMERO Time.
convertTime(Time) - Static method in class ome.formats.model.UnitsFactory
 
convertTime(Time, Unit<Time>) - Static method in class ome.formats.model.UnitsFactory
 
convertTimeXML(Time, String) - Static method in class ome.formats.model.UnitsFactory
 
ConvertToBlitzExceptionMessage - Class in ome.services.blitz.util
Internal event which gives third party services a chance to map their exceptions to a blitz exception.
ConvertToBlitzExceptionMessage(Object, Throwable) - Constructor for class ome.services.blitz.util.ConvertToBlitzExceptionMessage
 
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.
convertXml(MetadataRetrieve) - Method in class ome.services.blitz.impl.ExporterI
 
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_async(AMD_IPixels_copyAndResizeImage, long, RInt, RInt, RInt, RInt, List<Integer>, String, boolean, Current) - Method in class ome.services.blitz.impl.PixelsI
 
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()
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
 
copyImageLinks() - Method in class omero.gateway.model.FolderData
Copy the list of image links, see Folder.copyImageLinks()
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 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
 
copyROILinks() - Method in class omero.gateway.model.FolderData
Copy the list of roi links, see Folder.copyRoiLinks()
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
 
countSpecifiedAnnotations_async(AMD_IMetadata_countSpecifiedAnnotations, String, List<String>, List<String>, Parameters, Current) - Method in class ome.services.blitz.impl.MetadataI
 
cpf - Variable in class ome.services.blitz.impl.ScriptI
 
create(String, SessionControlPrx, Current) - Method in class ome.services.blitz.fire.SessionManagerI
 
create(String) - Method in class omero.util.ObjectFactoryRegistry.ObjectFactory
 
create(File) - Method in class omero.util.TempFileManager
If the given directory doesn't exist, creates it and returns true.
create_path() - Static method in class omero.util.TempFileManager
Calls TempFileManager.createPath(String, String, boolean) with defaults of "omero", ".tmp", and false.
create_path(String) - Static method in class omero.util.TempFileManager
Calls TempFileManager.createPath(String, String, boolean) with defaults of ".tmp", and false.
create_path(String, String) - Static method in class omero.util.TempFileManager
Calls TempFileManager.createPath(String, String, boolean) with ".tmp", and false arguments.
create_path(String, String, boolean) - Static method in class omero.util.TempFileManager
createAdapter() - Method in class ome.services.blitz.util.BlitzConfiguration
Creates an adapter with the name "BlitzAdapter", which must be properly configured via --Ice.Config or ICE_CONFIG or similar.
createAndRegisterManager(SessionManager, SecuritySystem, Executor) - Method in class ome.services.blitz.util.BlitzConfiguration
 
createAndRegisterVerifier(SessionManager, SessionProvider, 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.
createByName(String, Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
createByName(String, Current, boolean) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
createCache() - Method in interface omero.gateway.cache.CacheService
Creates a default cache.
createCache(int, int) - Method in interface omero.gateway.cache.CacheService
Creates a cache of a given type.
createCache(int) - Method in interface omero.gateway.cache.CacheService
Creates a cache of a given type.
createCallback(ImportProcessPrx, HandlePrx, ImportContainer) - Method in class ome.formats.importer.ImportLibrary
 
createChildOption() - Method in class omero.cmd.graphs.GraphRequestFactory
 
createClient(boolean) - Method in class omero.client
Creates a possibly insecure client instance and calls client.joinSession(String) using the current session id.
createCommunicator() - Method in class ome.services.blitz.util.BlitzConfiguration
 
createCommunicator(String, String[]) - Method in class ome.services.blitz.util.BlitzConfiguration
 
createData() - Method in class omero.util.RPSTileLoop
 
createData() - Method in class omero.util.TileLoop
Subclasses must provide a fresh instance of TileData.
createDataObject_async(AMD_IContainer_createDataObject, IObject, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI
 
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)
createEnumeration_async(AMD_ITypes_createEnumeration, IObject, Current) - Method in class ome.services.blitz.impl.TypesI
 
createExclusion(String) - Static method in class ome.formats.importer.exclusions.AbstractFileExclusion
Factory method for instantiating FileTransfer objects from a string.
createExperimenter(SecurityContext, ExperimenterData, String, String, List<GroupData>, boolean, boolean) - Method in class omero.gateway.facility.AdminFacility
Creates an experimenter and returns it.
createExperimenter(SecurityContext, ExperimenterData, String, String, List<GroupData>, boolean, boolean, List<String>) - 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_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
 
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
 
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.
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
 
createNewRenderingDef_async(AMD_IRenderingSettings_createNewRenderingDef, Pixels, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
 
createOrFixUserDir(String, List<CheckedPath>, Session, ServiceFactory, SqlAction) - Method in interface ome.services.blitz.repo.RepositoryDao
Checks that the given CheckedPath objects exist (via RepositoryDao.findRepoFile(String, CheckedPath, String, Ice.Current)) and are in the "user" group.
createOrFixUserDir(String, List<CheckedPath>, Session, ServiceFactory, SqlAction) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
 
createOriginalFile(ServiceFactory, SqlAction, String, List<CheckedPath>, ChecksumAlgorithm, String, Session) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
Primary location for creating original files from a CheckedPath instance.
createPath(String, String, boolean) - Method in class omero.util.TempFileManager
Uses File.createTempFile(String, String, File) to create temporary files and folders under the top-level temporary directory.
createPixelsStore(SecurityContext) - Method in class omero.gateway.Gateway
Create a RawPixelsStorePrx
createProcessBuilder(File, File) - Method in class ome.formats.importer.transfers.AbstractExecFileTransfer
Creates a ProcessBuilder instance ready to have ProcessBuilder.start() called on it.
createProcessBuilder(File, File) - Method in class ome.formats.importer.transfers.CopyFileTransfer
Executes "cp file location" (Unix) or "cp file location" (Windows) and fails on non-0 return codes.
createProcessBuilder(File, File) - Method in class ome.formats.importer.transfers.HardlinkFileTransfer
Executes "ln file location" (Unix) or "mklink /H location file" (Windows) and fails on non-0 return codes.
createProcessBuilder(File, File) - Method in class ome.formats.importer.transfers.SymlinkFileTransfer
Executes "ln -s file location" (Unix) or "mklink location file" (Windows) and fails on non-0 return codes.
createRawFileStore(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
createRawFileStore(OriginalFile, Current) - Method in class ome.services.blitz.repo.AbstractRepositoryI
 
createRawPixelsStore(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
createRawPixelsStore(OriginalFile, Current) - Method in class ome.services.blitz.repo.AbstractRepositoryI
 
createRenderingEngine(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
createRenderingEngine(OriginalFile, Current) - Method in class ome.services.blitz.repo.AbstractRepositoryI
 
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).
createRestrictedSystemUser_async(AMD_IAdmin_createRestrictedSystemUser, Experimenter, List<AdminPrivilege>, Current) - Method in class ome.services.blitz.impl.AdminI
 
createRestrictedSystemUserWithPassword_async(AMD_IAdmin_createRestrictedSystemUserWithPassword, Experimenter, List<AdminPrivilege>, RString, Current) - Method in class ome.services.blitz.impl.AdminI
 
createRoot() - Method in class ome.formats.OMEROMetadataStoreClient
 
createRoot_async(AMD_MetadataStore_createRoot, Current) - Method in class ome.services.blitz.impl.MetadataStoreI
 
createSearchService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
createServantDelegate(String) - Method in class omero.cmd.SessionI
Creates a proxy according to the servant definition for the given name.
createSession() - Method in class omero.client
createSession(String, String) - Method in class omero.client
Performs the actual logic of logging in, which is done via the client.getRouter(Ice.Communicator).
createSession_async(AMD_ISession_createSession, Principal, String, Current) - Method in class ome.services.blitz.impl.SessionI
 
createSessionWithTimeout_async(AMD_ISession_createSessionWithTimeout, Principal, long, Current) - Method in class ome.services.blitz.impl.SessionI
 
createSessionWithTimeouts_async(AMD_ISession_createSessionWithTimeouts, Principal, long, long, Current) - Method in class ome.services.blitz.impl.SessionI
 
createShare_async(AMD_IShare_createShare, String, RTime, List<IObject>, List<Experimenter>, List<String>, boolean, Current) - Method in class ome.services.blitz.impl.ShareI
 
createStore() - Method in class ome.formats.importer.ImportConfig
Create and return a new OMEROMetadataStoreClient
createSystemUser_async(AMD_IAdmin_createSystemUser, Experimenter, Current) - Method in class ome.services.blitz.impl.AdminI
 
createTableResult(TablePrx, String, long) - Static method in class omero.gateway.util.PyTablesUtils
Transforms the passed table data for a given image.
createTableResult(TablePrx, long[]) - Static method in class omero.gateway.util.PyTablesUtils
Transforms a set of rows for the passed table.
createTempFile(String, String) - Static method in class omero.util.TempFileManager
Emulates File.createTempFile(String, String) by calling TempFileManager.create_path(String, String).
createTemplatePath(Object, Current) - Method in class ome.services.blitz.repo.ManagedRepositoryI
Expand the template path and create its directories with the correct ownership.
createThumbnail_async(AMD_ThumbnailStore_createThumbnail, RInt, RInt, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
 
createThumbnails_async(AMD_ThumbnailStore_createThumbnails, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
 
createThumbnailsByLongestSideSet_async(AMD_ThumbnailStore_createThumbnailsByLongestSideSet, RInt, List<Long>, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
 
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_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
 
createUserSession_async(AMD_ISession_createUserSession, long, long, String, Current) - Method in class ome.services.blitz.impl.SessionI
 
CSV - Static variable in class omero.gateway.model.FileAnnotationData
Identifies the CSV file formats.
ctx - Variable in class ome.services.blitz.impl.AbstractAmdServant
 
ctx - Variable in class ome.services.throttling.AbstractThrottlingStrategy
 
curr - Variable in class ome.services.blitz.util.FindServiceFactoryMessage
 
current - Variable in class ome.services.throttling.Task
 
current - Variable in class omero.cmd.admin.CurrentSessionsRequestI
 
current - Variable in class omero.cmd.admin.UpdateSessionTimeoutRequestI
 
currentMetadata_async(AMD_Search_currentMetadata, Current) - Method in class ome.services.blitz.impl.SearchI
 
currentMetadataList_async(AMD_Search_currentMetadataList, Current) - Method in class ome.services.blitz.impl.SearchI
 
CurrentPlatform - Class in ome.services.blitz.util
Test under which platform OMERO is currently running.
CurrentPlatform() - Constructor for class ome.services.blitz.util.CurrentPlatform
 
CurrentSessionsRequestI - Class in omero.cmd.admin
 
CurrentSessionsRequestI(CurrentDetails, SessionManager, SessionProvider) - Constructor for class omero.cmd.admin.CurrentSessionsRequestI
 
CurrentSessionsRequestI.Factory - Class in omero.cmd.admin
 
currentUser(Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
 

D

data - Variable in class ome.services.roi.GeomTool
 
data - Variable in class ome.services.roi.PixelData
 
DATA_STORED(int, ImportContainer, IObject, Long, int, ImportSize) - Constructor for class ome.formats.importer.ImportEvent.DATA_STORED
 
DataManagerFacility - Class in omero.gateway.facility
A Facility for saving, deleting and updating data objects
DataObject - Class in omero.gateway.model
Abstract superclass for objects that hold OMEDS data.
DataObject() - Constructor for class omero.gateway.model.DataObject
 
DATASET_LINKS - Static variable in class omero.gateway.model.ImageData
Identifies the ImageI.DATASETLINKS field.
DATASET_LINKS - Static variable in class omero.gateway.model.ProjectData
Identifies the ProjectI.DATASETLINKS field.
DATASET_STORED(int, ImportContainer, IObject, Long, int, ImportSize, Integer, Integer) - Constructor for class ome.formats.importer.ImportEvent.DATASET_STORED
 
DatasetData - Class in omero.gateway.model
The data that makes up an OME Dataset along with links to its contained Images and enclosing Project as well as the Experimenter that owns this Dataset.
DatasetData() - Constructor for class omero.gateway.model.DatasetData
Creates a new instance.
DatasetData(Dataset) - Constructor for class omero.gateway.model.DatasetData
Creates a new instance.
DataSink - Class in omero.gateway.rnd
Encapsulates access to the image raw data.
DataSink(SecurityContext, PixelsData, Gateway) - Constructor for class omero.gateway.rnd.DataSink
Creates a new instance.
DataSourceException - Exception in omero.gateway.exception
Reports an error occurred while trying to pull out data from the pixels data repository.
DataSourceException() - Constructor for exception omero.gateway.exception.DataSourceException
Creates a new exception.
DataSourceException(String) - Constructor for exception omero.gateway.exception.DataSourceException
Constructs a new exception with the specified detail message.
DataSourceException(Throwable) - Constructor for exception omero.gateway.exception.DataSourceException
Constructs a new exception with the specified cause.
DataSourceException(String, Throwable) - Constructor for exception omero.gateway.exception.DataSourceException
Constructs a new exception with the specified detail message and cause.
DATE_ACQUISITION - Static variable in class omero.gateway.model.SearchParameters
Indicates that the date has to be interpreted as acquisition date
DATE_IMPORT - Static variable in class omero.gateway.model.SearchParameters
Indicates that the date has to be interpreted as import date
dbPath(Shape) - Method in class ome.services.roi.GeomTool
 
dbVersion - Static variable in class ome.formats.importer.Version
Deprecated.
 
deactivate_async(AMD_IShare_deactivate, Current) - Method in class ome.services.blitz.impl.ShareI
 
debug - Variable in class ome.formats.importer.ImportConfig
 
debug(String, Object...) - Method in class omero.cmd.Helper
 
debug(Object, String) - Method in interface omero.log.Logger
Logs a debug message.
debug(Object, LogMessage) - Method in interface omero.log.Logger
Logs a debug message.
debug(Object, String) - Method in class omero.log.NullLogger
 
debug(Object, LogMessage) - Method in class omero.log.NullLogger
 
debug(Object, String) - Method in class omero.log.SimpleLogger
 
debug(Object, LogMessage) - Method in class omero.log.SimpleLogger
 
DEBUG_SEND(boolean, boolean) - Constructor for class ome.formats.importer.ImportEvent.DEBUG_SEND
 
DEFAULT - Static variable in interface omero.gateway.cache.CacheService
Indicates to create a default cache.
DEFAULT - Static variable in class omero.gateway.model.GroupData
Identifies the default group.
DEFAULT_FILL_COLOUR - Static variable in class omero.gateway.model.ShapeSettingsData
The default fill color.
DEFAULT_FILL_COLOUR_ALPHA - Static variable in class omero.gateway.model.ShapeSettingsData
The default fill color.
DEFAULT_FONT_FAMILY - Static variable in class omero.gateway.model.ShapeSettingsData
The default font family.
DEFAULT_FONT_SIZE - Static variable in class omero.gateway.model.ShapeSettingsData
The default font size in "pt".
DEFAULT_MAX_ROWS_TO_FETCH - Static variable in class omero.gateway.facility.TablesFacility
Maximum number of rows to fetch if not specified otherwise
DEFAULT_PORT - Static variable in class loci.ome.io.OmeroReader
Deprecated.
 
DEFAULT_QABASEURL - Static variable in class ome.formats.importer.ImportConfig
 
DEFAULT_STROKE_COLOUR - Static variable in class omero.gateway.model.ShapeSettingsData
The default stroke color.
DEFAULT_STROKE_WIDTH - Static variable in class omero.gateway.model.ShapeSettingsData
The default stroke width.
DEFAULT_TIMEOUT - Static variable in class ome.services.blitz.impl.SharedResourcesI
If no value is passed to this instance, this is the time (1 hour) which will be used for a script session.
DEFAULT_WAIT - Static variable in class ome.formats.importer.cli.CommandLineImporter
 
delete(SecurityContext, IObject) - Method in class omero.gateway.facility.DataManagerFacility
Deletes the specified object asynchronously
delete(SecurityContext, List<IObject>) - Method in class omero.gateway.facility.DataManagerFacility
Deletes the specified objects asynchronously
delete() - Static method in class omero.gateway.util.Requests
 
Delete2Builder() - Constructor for class omero.gateway.util.Requests.Delete2Builder
Instantiate a new Delete2.
Delete2I - Class in omero.cmd.graphs
Request to delete model objects.
Delete2I(ACLVoter, Roles, GraphPathBean, LightAdminPrivileges, Deletion, Set<Class<? extends IObject>>, GraphPolicy, SetMultimap<String, String>, ApplicationContext) - Constructor for class omero.cmd.graphs.Delete2I
Construct a new delete request; called from GraphRequestFactory.getRequest(Class).
deleteComment_async(AMD_IShare_deleteComment, Annotation, Current) - Method in class ome.services.blitz.impl.ShareI
 
deleteEntity(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
deleteEnumeration_async(AMD_ITypes_deleteEnumeration, IObject, Current) - Method in class ome.services.blitz.impl.TypesI
 
deleteExperimenter_async(AMD_IAdmin_deleteExperimenter, Experimenter, Current) - Method in class ome.services.blitz.impl.AdminI
 
deleteFilesFromRepository(ImportContainer) - Method in class ome.formats.importer.ImportLibrary
Delete files from the managed repository.
deleteFolders(SecurityContext, Collection<FolderData>, boolean, boolean) - Method in class omero.gateway.facility.DataManagerFacility
Delete Folders (asynchronous)
deleteGroup_async(AMD_IAdmin_deleteGroup, ExperimenterGroup, Current) - Method in class ome.services.blitz.impl.AdminI
 
deleteInstances(String, Collection<Long>) - Method in class omero.cmd.graphs.BaseGraphTraversalProcessor
 
deleteInstances(String, Collection<Long>) - Method in class omero.cmd.graphs.NullGraphTraversalProcessor
 
deleteObject_async(AMD_IUpdate_deleteObject, IObject, Current) - Method in class ome.services.blitz.impl.UpdateI
 
deleteObserver(IObserver) - Method in class ome.formats.importer.ImportLibrary
 
deleteObserver(IObserver) - Method in interface ome.formats.importer.IObservable
Delete observer
deleteObserver(IObserver) - Method in class ome.formats.importer.util.ClientKeepAlive
 
deleteObserver(IObserver) - Method in class ome.formats.importer.util.ErrorHandler
 
deleteObserver(IObserver) - Method in class ome.formats.importer.util.FileUploader
 
deletePaths(String[], boolean, boolean, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
Delete paths recursively as described in Repositories.ice.
deleteRepoDeleteLogs(SqlAction.DeleteLog, Current) - Method in interface ome.services.blitz.repo.RepositoryDao
Call SqlAction.deleteRepoDeleteLogs(DeleteLog) with the current context.
deleteRepoDeleteLogs(List<SqlAction.DeleteLog>, Current) - Method in interface ome.services.blitz.repo.RepositoryDao
Call SqlAction.deleteRepoDeleteLogs(DeleteLog) with the current context for a number of templates.
deleteRepoDeleteLogs(SqlAction.DeleteLog, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
 
deleteRepoDeleteLogs(List<SqlAction.DeleteLog>, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
 
deleteScript_async(AMD_IScript_deleteScript, long, Current) - Method in class ome.services.blitz.impl.ScriptI
Delete the script with id from the server.
deleteTransferredFiles(int, List<String>) - Method in class ome.formats.importer.transfers.AbstractFileTransfer
Method used by subclasses during FileTransfer.afterTransfer(int, List) if they would like to remove all the files transferred in the set.
DEPTH - Static variable in class ome.formats.importer.ImportCandidates
 
depth - Variable in class ome.formats.importer.ImportCandidates.SCANNING
 
DESCENDING_LETTER - Static variable in class omero.gateway.model.PlateData
Indicates that the column or row is a letter starting from Z or P.
DESCENDING_NUMBER - Static variable in class omero.gateway.model.PlateData
Indicates that the column or row is a letter starting from 26 or 16.
DESCRIPTION - Static variable in class omero.gateway.model.DatasetData
Identifies the DatasetI.DESCRIPTION field.
DESCRIPTION - Static variable in class omero.gateway.model.GroupData
Identifies the ExperimenterGroupI.DESCRIPTION field.
DESCRIPTION - Static variable in class omero.gateway.model.ImageData
Identifies the ImageI.DESCRIPTION field.
DESCRIPTION - Static variable in class omero.gateway.model.PlateData
Identifies the PlateI.DESCRIPTION field.
DESCRIPTION - Static variable in class omero.gateway.model.ProjectData
Identifies the ProjectI.DESCRIPTION field.
DESCRIPTION - Static variable in class omero.gateway.model.ScreenData
Identifies the ScreenI.DESCRIPTION field.
destroy() - Method in class ome.services.blitz.fire.Ring
 
destroy() - Method in class ome.services.blitz.util.BlitzConfiguration
 
destroy() - Method in class ome.services.throttling.Queue
 
destroy(Current) - Method in class omero.cmd.SessionI
Destruction simply decrements the reference count for a session to allow reconnecting to it.
destroy() - Method in class omero.util.ObjectFactoryRegistry.ObjectFactory
 
detachOnDestroy(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
DetailsI - Class in omero.model
 
DetailsI() - Constructor for class omero.model.DetailsI
 
DetailsI(client) - Constructor for class omero.model.DetailsI
 
Detector_Voltage - Static variable in class ome.formats.model.UnitsFactory
 
DetectorData - Class in omero.gateway.model
Hosts a detector.
DetectorData(Detector) - Constructor for class omero.gateway.model.DetectorData
Creates a new instance.
DetectorSettings_ReadOutRate - Static variable in class ome.formats.model.UnitsFactory
 
DetectorSettings_Voltage - Static variable in class ome.formats.model.UnitsFactory
 
determineColor(Length) - Static method in class ome.formats.model.ColorsFactory
Determines the color corresponding to the passed value.
DichroicData - Class in omero.gateway.model
Hosts the dichroic.
DichroicData(Dichroic) - Constructor for class omero.gateway.model.DichroicData
Creates a new instance.
dimOrder - Variable in class ome.formats.importer.ImportSize
 
DIRECTORY_MIMETYPE - Static variable in class ome.services.blitz.repo.PublicRepositoryI
Mimetype used to connote a directory OriginalFile object.
disconnect() - Method in class omero.gateway.Gateway
Disconnects from the server
discover_async(AMD_ILdap_discover, Current) - Method in class ome.services.blitz.impl.LdapI
 
discoverGroups_async(AMD_ILdap_discoverGroups, Current) - Method in class ome.services.blitz.impl.LdapI
 
discriminator(String) - Method in class ome.services.roi.GeomTool
Maps from multiple possible user-provided names of shapes (e.g.
diskUsage() - Static method in class omero.gateway.util.Requests
 
DiskUsage2I - Class in omero.cmd.graphs
Calculate the disk usage entailed by the given objects.
DiskUsage2I(ACLVoter, Roles, GraphPathBean, LightAdminPrivileges, Set<Class<? extends IObject>>, GraphPolicy) - Constructor for class omero.cmd.graphs.DiskUsage2I
Construct a new disk usage request; called from GraphRequestFactory.getRequest(Class).
DiskUsageI - Class in omero.cmd.graphs
Deprecated.
will be removed in OMERO 5.4, use DiskUsage2 instead
DiskUsageI(PixelsService, ThumbnailService, GraphPathBean) - Constructor for class omero.cmd.graphs.DiskUsageI
Deprecated.
Construct a disk usage request.
DoAllI - Class in omero.cmd.basic
Permits performing multiple operations
DoAllI(OmeroContext) - Constructor for class omero.cmd.basic.DoAllI
 
doClose - Variable in class omero.cmd.SessionI
 
doDestroy() - Method in class omero.cmd.SessionI
Performs the actual cleanup operation on all the resources shared between this and other ServiceFactoryI instances in the same Session.
doImport() - Method in class ome.formats.importer.ImportFixture
Runs import by looping through all files and then calling ImportLibrary.importImage(ImportContainer, int, int, int).
doImport() - Method in class ome.formats.OMEROImportFixture
Deprecated.
Runs import by looping through all files and then calling ImportLibrary.importCandidates(ImportConfig, ImportCandidates).
doStop() - Method in class omero.grid.InteractiveProcessorI
 
doThumbnails - Variable in class ome.formats.importer.ImportConfig
 
DOUBLE - Static variable in class omero.gateway.rnd.DataSink
Identifies the type used to store pixel values.
DOUBLE_COMPLEX_TYPE - Static variable in class omero.gateway.model.PixelsData
Identifies the type used to store pixel values.
DOUBLE_TYPE - Static variable in class omero.gateway.model.PixelsData
Identifies the type used to store pixel values.
DoubleAnnotationData - Class in omero.gateway.model
Wraps a double annotation.
DoubleAnnotationData(double) - Constructor for class omero.gateway.model.DoubleAnnotationData
Creates a new instance.
DoubleAnnotationData() - Constructor for class omero.gateway.model.DoubleAnnotationData
Creates a new instance.
DoubleAnnotationData(DoubleAnnotation) - Constructor for class omero.gateway.model.DoubleAnnotationData
Creates a new instance.
DoubleArrayValue(String, ImportConfig, Double[]) - Constructor for class ome.formats.importer.ImportConfig.DoubleArrayValue
 
DoubleConverter - Class in omero.gateway.rnd
Packs a sequence of bytes representing a big-endian double into a double value of appropriate integer type.
DoubleConverter() - Constructor for class omero.gateway.rnd.DoubleConverter
 
down(String, Current) - Method in class ome.services.blitz.fire.Ring
Called when any node goes down.
download(long, File) - Method in class omero.client
 
download(long, File, int) - Method in class omero.client
 
downloadImage(SecurityContext, String, long) - Method in class omero.gateway.facility.TransferFacility
Downloads the original file of an image from the server.
DSAccessException - Exception in omero.gateway.exception
Reports an error occurred while trying to pull out data from the server.
DSAccessException(String) - Constructor for exception omero.gateway.exception.DSAccessException
Constructs a new exception with the specified detail message.
DSAccessException(String, Throwable) - Constructor for exception omero.gateway.exception.DSAccessException
Constructs a new exception with the specified detail message and cause.
DSOutOfServiceException - Exception in omero.gateway.exception
Reports an error occurred while trying to access the OMERO service.
DSOutOfServiceException(String) - Constructor for exception omero.gateway.exception.DSOutOfServiceException
Constructs a new exception with the specified detail message.
DSOutOfServiceException(String, ConnectionStatus) - Constructor for exception omero.gateway.exception.DSOutOfServiceException
Constructs a new exception with the specified detail message.
DSOutOfServiceException(String, Throwable) - Constructor for exception omero.gateway.exception.DSOutOfServiceException
Constructs a new exception with the specified detail message and cause.
DSOutOfServiceException(String, Throwable, ConnectionStatus) - Constructor for exception omero.gateway.exception.DSOutOfServiceException
Constructs a new exception with the specified detail message and cause.
duplicate() - Static method in class omero.gateway.util.Requests
 
DuplicateBuilder() - Constructor for class omero.gateway.util.Requests.DuplicateBuilder
Instantiate a new Duplicate and initialize its collection containers.
DuplicateI - Class in omero.cmd.graphs
Request to duplicate model objects.
DuplicateI(ACLVoter, Roles, GraphPathBean, LightAdminPrivileges, Deletion, Set<Class<? extends IObject>>, GraphPolicy, SetMultimap<String, String>, ApplicationContext) - Constructor for class omero.cmd.graphs.DuplicateI
Construct a new duplicate request; called from GraphRequestFactory.getRequest(Class).
duplicateType(Iterable<String>) - Method in class omero.gateway.util.Requests.DuplicateBuilder
 
duplicateType(Class<? extends IObject>...) - Method in class omero.gateway.util.Requests.DuplicateBuilder
 
duplicateType(String...) - Method in class omero.gateway.util.Requests.DuplicateBuilder
 

E

editScript_async(AMD_IScript_editScript, OriginalFile, String, Current) - Method in class ome.services.blitz.impl.ScriptI
 
ElectricPotentialI - Class in omero.model
Blitz wrapper around the ElectricPotential class.
ElectricPotentialI() - Constructor for class omero.model.ElectricPotentialI
 
ElectricPotentialI(double, UnitsElectricPotential) - Constructor for class omero.model.ElectricPotentialI
 
ElectricPotentialI(double, Unit<ElectricPotential>) - Constructor for class omero.model.ElectricPotentialI
 
ElectricPotentialI(ElectricPotential, Unit<ElectricPotential>) - Constructor for class omero.model.ElectricPotentialI
Copy constructor that converts the given ElectricPotential based on the given ome-xml enum
ElectricPotentialI(double, UnitsElectricPotential) - Constructor for class omero.model.ElectricPotentialI
Copy constructor that converts the given ElectricPotential based on the given ome.model enum
ElectricPotentialI(ElectricPotential, String) - Constructor for class omero.model.ElectricPotentialI
Copy constructor that converts the given ElectricPotential based on the given enum string.
ElectricPotentialI(ElectricPotential, UnitsElectricPotential) - Constructor for class omero.model.ElectricPotentialI
Copy constructor that converts between units if possible.
ElectricPotentialI(ElectricPotential) - Constructor for class omero.model.ElectricPotentialI
Convert a Bio-Formats Length to an OMERO Length.
ellipse(double, double, double, double) - Method in class ome.services.roi.GeomTool
 
ellipse(double, double, double, double, int, int) - Method in class ome.services.roi.GeomTool
 
EllipseData - Class in omero.gateway.model
Represents an ellipse in the Euclidean space R2.
EllipseData(Shape) - Constructor for class omero.gateway.model.EllipseData
Creates a new instance of Ellipse data from an existing shape.
EllipseData() - Constructor for class omero.gateway.model.EllipseData
Creates a new instance of EllipseData.
EllipseData(double, double, double, double) - Constructor for class omero.gateway.model.EllipseData
Creates a new instance of the EllipseData.
email - Variable in class ome.formats.importer.ImportConfig
 
EMAIL - Static variable in class omero.gateway.model.ExperimenterData
Identifies the ExperimenterI.EMAIL field.
empty() - Method in class ome.formats.importer.ImportConfig.StrValue
 
empty() - Method in class ome.formats.importer.ImportConfig.Value
 
emptyPath - Static variable in class ome.services.blitz.repo.path.FsFile
the FsFile that has no path components
enableKeepAlive(int) - Method in class omero.client
Resets the "omero.keep_alive" property on the current Communicator which is used on initialization to determine the time-period between checks.
encryptedConnection - Variable in class ome.formats.importer.ImportConfig
 
END_POST_PROCESS(int, ImportContainer, IObject, Long, int, ImportSize) - Constructor for class ome.formats.importer.ImportEvent.END_POST_PROCESS
 
END_SAVE_TO_DB(int, ImportContainer, IObject, Long, int, ImportSize) - Constructor for class ome.formats.importer.ImportEvent.END_SAVE_TO_DB
 
endTime(RTime) - Method in class omero.sys.ParametersI
Sets the value of the end time parameter.
endTransaction(boolean) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
Entry - Class in ome.services.blitz
OMERO.blitz startup code.
Entry(String) - Constructor for class ome.services.blitz.Entry
Stores name of the OmeroContext which is to be used by this instance.
EnumerationException - Exception in ome.formats.enums
 
EnumerationException(String, Class<? extends IObject>, String) - Constructor for exception ome.formats.enums.EnumerationException
 
EnumerationHandler - Interface in ome.formats.enums.handler
An enumeration handler whose purpose is to provide extra logic, such as regular expression matching, for the lookup of enumerations for a specific type.
EnumerationProvider - Interface in ome.formats.enums
An enumeration provider, whose job is to make OMERO enumerations available to a consumer based on a set of criteria.
EnumHandlerFactory - Class in ome.formats.enums.handler
Factory for all available enumeration handlers.
EnumHandlerFactory() - Constructor for class ome.formats.enums.handler.EnumHandlerFactory
 
env() - Method in class omero.client
Helper method to access session environment
equals(Object) - Method in class ome.services.blitz.repo.CheckedPath
Instances are equal if their string representations match.
equals(Object) - Method in class ome.services.blitz.repo.path.FsFile
Instances are equal if their string representations match.
equals(Object) - Method in class omero.gateway.model.ROICoordinate
Overridden to control if the passed object equals the current one.
equals(Object) - Method in class omero.gateway.model.TableData
 
equals(Object) - Method in class omero.gateway.model.TableDataColumn
 
equals(Object) - Method in class omero.gateway.SecurityContext
Overridden to control if the passed object equals the current one.
equals(Object) - Method in class omero.gateway.ServerInformation
 
equals(Object) - Method in class omero.model.ElectricPotentialI
 
equals(Object) - Method in class omero.model.FrequencyI
 
equals(Object) - Method in class omero.model.LengthI
 
equals(Object) - Method in class omero.model.PowerI
 
equals(Object) - Method in class omero.model.PressureI
 
equals(Object) - Method in class omero.model.TemperatureI
 
equals(Object) - Method in class omero.model.TimeI
 
error(String, Object...) - Method in class omero.cmd.Helper
 
error(Throwable, String, Object...) - Method in class omero.cmd.Helper
 
error(Object, String) - Method in interface omero.log.Logger
Logs an error message.
error(Object, LogMessage) - Method in interface omero.log.Logger
Logs an error message.
error(Object, String) - Method in class omero.log.NullLogger
 
error(Object, LogMessage) - Method in class omero.log.NullLogger
 
error(Object, String) - Method in class omero.log.SimpleLogger
 
error(Object, LogMessage) - Method in class omero.log.SimpleLogger
 
ErrorContainer - Class in ome.formats.importer.util
Container for errors
ErrorContainer() - Constructor for class ome.formats.importer.util.ErrorContainer
 
errorCount - Variable in class ome.formats.importer.ImportEvent.IMPORT_SUMMARY
 
errorCount() - Method in class ome.formats.importer.util.ErrorHandler
 
ErrorHandler - Class in ome.formats.importer.cli
IObserver based on the gui ErrorHandler code which collects all exceptions during ImportLibrary.importCandidates(ome.formats.importer.ImportConfig, ome.formats.importer.ImportCandidates) and after the import is finished offers to submit them via the feedback system.
ErrorHandler(ImportConfig) - Constructor for class ome.formats.importer.cli.ErrorHandler
 
ErrorHandler - Class in ome.formats.importer.util
Top of the error handling hierarchy.
ErrorHandler(ImportConfig) - Constructor for class ome.formats.importer.util.ErrorHandler
Initialize
ErrorHandler.EXCEPTION_EVENT - Class in ome.formats.importer.util
 
ErrorHandler.FILE_EXCEPTION - Class in ome.formats.importer.util
ErrorHandler.FILE_EXCEPTIONs are thrown any time in the context of a particular file and otherwise unspecified exception takes place.
ErrorHandler.INTERNAL_EXCEPTION - Class in ome.formats.importer.util
 
ErrorHandler.MISSING_LIBRARY - Class in ome.formats.importer.util
A ErrorHandler.FILE_EXCEPTION caused specifically by some library (native or otherwise) not being installed locally.
ErrorHandler.UNKNOWN_FORMAT - Class in ome.formats.importer.util
Unlike ErrorHandler.FILE_EXCEPTION, UNKNOWN_FORMAT does not have a reader since bio-formats is telling us that it does not know how to handle the given file.
ErrorHandler.UNREADABLE_FILE - Class in ome.formats.importer.util
Similar to ErrorHandler.UNKNOWN_FORMAT UNREADABLE_FILE specifies that the file which is being accessed is unreadable (does not exist or canRead is false), so if the user is specifically saying that the file should be imported, there may be some underlying issue.
errors - Variable in class ome.formats.importer.util.ErrorHandler
 
ERRORS_COMPLETE() - Constructor for class ome.formats.importer.ImportEvent.ERRORS_COMPLETE
 
ERRORS_FAILED() - Constructor for class ome.formats.importer.ImportEvent.ERRORS_FAILED
 
ERRORS_PENDING() - Constructor for class ome.formats.importer.ImportEvent.ERRORS_PENDING
 
ex - Variable in class ome.services.roi.GeomTool
 
exception - Variable in class ome.formats.importer.ImportEvent.FILE_UPLOAD_EVENT
 
exception - Variable in class ome.formats.importer.util.ErrorHandler.EXCEPTION_EVENT
 
exception - Variable in class ome.services.throttling.Task
 
exception(Throwable, OmeroContext) - Method in class ome.services.throttling.Task
 
EXCEPTION_EVENT(Exception) - Constructor for class ome.formats.importer.util.ErrorHandler.EXCEPTION_EVENT
 
excludeNs(Iterable<String>) - Method in class omero.gateway.util.Requests.ChildOptionBuilder
 
excludeNs(String...) - Method in class omero.gateway.util.Requests.ChildOptionBuilder
 
excludeType(Iterable<String>) - Method in class omero.gateway.util.Requests.ChildOptionBuilder
 
excludeType(Class<? extends IObject>...) - Method in class omero.gateway.util.Requests.ChildOptionBuilder
 
excludeType(String...) - Method in class omero.gateway.util.Requests.ChildOptionBuilder
 
exclusions - Variable in class ome.formats.importer.cli.CommandLineImporter
FileExclusion mechanisms for skipping candidates
exec(File, File) - Method in class ome.formats.importer.transfers.AbstractExecFileTransfer
Executes a local command and fails on non-0 return codes.
execute(String[]) - Method in class ome.formats.importer.ImportCandidates
Method called during ImportCandidates.ImportCandidates(OMEROWrapper, String[], IObserver) to operate on all the given paths.
execute(RMap, Current) - Method in class omero.grid.InteractiveProcessorI
 
executePost(String, Map<String, String>) - Method in class ome.formats.importer.util.ErrorHandler
Execute a post with the given post list.
executePost() - Method in class ome.formats.importer.util.HtmlMessenger
Execute a post action and retrieve server reply This method executes the post created when this class is instantiated
executor - Variable in class ome.services.blitz.fire.SessionManagerI
 
executor - Variable in class ome.services.blitz.redirect.AbstractRedirector
 
executor - Variable in class ome.services.blitz.repo.RepositoryDaoImpl
 
executor - Variable in class omero.cmd.SessionI
Executor to be used by servant implementations which do not delegate to the server package where all instances are wrapped with AOP for dealing with Hibernate.
executorWorkCall(Executor.Work) - Method in class ome.services.blitz.impl.AbstractAmdServant
 
exists() - Method in class ome.services.blitz.repo.CheckedPath
Check if this file actually exists on the underlying filesystem.
exists_async(AMD_RawFileStore_exists, Current) - Method in class ome.services.blitz.impl.RawFileStoreI
 
exp(RLong) - Method in class omero.sys.ParametersI
Sets the value of the experimenter parameter.
expandTemplateRootOwnedPath(EventContext, ServiceFactory) - Method in class ome.services.blitz.repo.ManagedRepositoryI
Expand the root-owned segment of the template path.
EXPERIMENTER_PHOTO_NS - Static variable in class omero.gateway.model.FileAnnotationData
The name space used to identify the experimenter photo.
ExperimenterData - Class in omero.gateway.model
The data that makes up an OME Experimenter along with information about the Group the Experimenter belongs in.
ExperimenterData() - Constructor for class omero.gateway.model.ExperimenterData
Creates a new instance.
ExperimenterData(Experimenter) - Constructor for class omero.gateway.model.ExperimenterData
Creates a new instance.
ExpiredServantMessage - Class in ome.services.blitz.util
ApplicationEvent which gets raised on CacheEventListener.notifyElementExpired(net.sf.ehcache.Ehcache, net.sf.ehcache.Element)
ExpiredServantMessage(Object, String) - Constructor for class ome.services.blitz.util.ExpiredServantMessage
 
expires(Current) - Method in class omero.grid.InteractiveProcessorI
 
ExporterI - Class in ome.services.blitz.impl
Implementation of the Exporter service.
ExporterI(BlitzExecutor, DatabaseIdentity, PixelsService) - Constructor for class ome.services.blitz.impl.ExporterI
 
extensions - Static variable in class omero.gateway.util.TIFFFilter
The possible extensions.
extractIds(Collection<? extends DataObject>) - Static method in class omero.gateway.util.Pojos
Extract the (distinct) ids from a collection of DataObjects

F

Facility - Class in omero.gateway.facility
A Facility encapsulates a certain set of functionality for dealing with an OMERO server
factory - Variable in class ome.services.blitz.impl.RoiI
 
factory - Variable in class ome.services.blitz.impl.ScriptI
 
factory - Variable in class ome.services.blitz.impl.TimelineI
 
factory - Variable in class ome.services.roi.GeomTool
 
Factory(CurrentDetails, SessionManager, SessionProvider) - Constructor for class omero.cmd.admin.CurrentSessionsRequestI.Factory
 
Factory(CurrentDetails, SessionManager, SecuritySystem) - Constructor for class omero.cmd.admin.UpdateSessionTimeoutRequestI.Factory
 
Factory - Static variable in class omero.model.DetailsI
 
Factory - Static variable in class omero.model.ElectricPotentialI
 
Factory - Static variable in class omero.model.FrequencyI
 
Factory - Static variable in class omero.model.LengthI
 
Factory - Static variable in class omero.model.PermissionsI
 
Factory - Static variable in class omero.model.PowerI
 
Factory - Static variable in class omero.model.PressureI
 
Factory - Static variable in class omero.model.TemperatureI
 
Factory - Static variable in class omero.model.TimeI
 
fail(ERR, Throwable, String, String...) - Method in class omero.cmd.Helper
fail(ERR, Throwable, String, Map<String, String>) - Method in class omero.cmd.Helper
Sets the status.flags and the ERR properties appropriately and also stores the message and stacktrace of the throwable in the parameters.
failingChecksums - Variable in class ome.formats.importer.ImportEvent.FILESET_UPLOAD_END
 
failLocationCheck(File, String) - Method in class ome.formats.importer.transfers.AbstractExecFileTransfer
 
fatal(Object, String) - Method in interface omero.log.Logger
Logs a fatal message.
fatal(Object, LogMessage) - Method in interface omero.log.Logger
Logs a fatal message.
fatal(Object, String) - Method in class omero.log.NullLogger
 
fatal(Object, LogMessage) - Method in class omero.log.NullLogger
 
fatal(Object, String) - Method in class omero.log.SimpleLogger
 
fatal(Object, LogMessage) - Method in class omero.log.SimpleLogger
 
fetchAlso_async(AMD_Search_fetchAlso, List<String>, Current) - Method in class ome.services.blitz.impl.SearchI
 
fetchAnnotations_async(AMD_Search_fetchAnnotations, List<String>, Current) - Method in class ome.services.blitz.impl.SearchI
 
fetchCollection(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
fetchEntity(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
FILAMENT - Static variable in class omero.gateway.model.LightSourceData
Indicates that the light source is a filament.
file - Variable in class ome.formats.importer.ImportCandidates.SCANNING
 
file(String, String, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
 
FILE_EXCEPTION(String, Exception, String[], String) - Constructor for class ome.formats.importer.util.ErrorHandler.FILE_EXCEPTION
 
FILE_TRANSFER_NS - Static variable in class omero.gateway.model.AnnotationData
The name space used to identify the file transfer type.
FILE_UPLOAD_BYTES(String, int, int, Long, Long, Long, Exception) - Constructor for class ome.formats.importer.ImportEvent.FILE_UPLOAD_BYTES
 
FILE_UPLOAD_CANCELLED(String, int, int, Long, Long, Exception) - Constructor for class ome.formats.importer.ImportEvent.FILE_UPLOAD_CANCELLED
 
FILE_UPLOAD_COMPLETE(String, int, int, Long, Long, Exception) - Constructor for class ome.formats.importer.ImportEvent.FILE_UPLOAD_COMPLETE
 
FILE_UPLOAD_ERROR(String, int, int, Long, Long, Exception) - Constructor for class ome.formats.importer.ImportEvent.FILE_UPLOAD_ERROR
 
FILE_UPLOAD_FAILED(String, int, int, Long, Long, Exception) - Constructor for class ome.formats.importer.ImportEvent.FILE_UPLOAD_FAILED
 
FILE_UPLOAD_FINISHED(String, int, int, Long, Long, Exception) - Constructor for class ome.formats.importer.ImportEvent.FILE_UPLOAD_FINISHED
 
FILE_UPLOAD_STARTED(String, int, int, Long, Long, Exception) - Constructor for class ome.formats.importer.ImportEvent.FILE_UPLOAD_STARTED
 
FileAnnotationData - Class in omero.gateway.model
Annotation to upload files to the server.
FileAnnotationData(File) - Constructor for class omero.gateway.model.FileAnnotationData
Creates a new instance.
FileAnnotationData(FileAnnotation) - Constructor for class omero.gateway.model.FileAnnotationData
Creates a new instance.
fileById(long, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
 
fileContext(long, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
Create a String-String map which can be used as the context for a call to Executor.execute based on the group of the file object.
FileData - Class in omero.gateway.model
DataObject used to handle the file visible via FS.
FileData(OriginalFile) - Constructor for class omero.gateway.model.FileData
Creates a new instance.
FileData(OriginalFile, boolean) - Constructor for class omero.gateway.model.FileData
Creates a new instance.
FileData(OriginalFile, boolean, boolean) - Constructor for class omero.gateway.model.FileData
Creates a new instance.
FileExclusion - Interface in ome.formats.importer.exclusions
Voter given the opportunity by the ImportLibrary to cancel the importing of a given file.
fileExists(String, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
 
fileIndex - Variable in class ome.formats.importer.ImportEvent.FILE_UPLOAD_EVENT
 
FileMaker - Class in ome.services.blitz.repo
Utility class for creating and cleaning up a repository lock file.
FileMaker(String) - Constructor for class ome.services.blitz.repo.FileMaker
 
filename - Variable in class ome.formats.importer.ImportEvent.FILE_UPLOAD_EVENT
 
fileName - Variable in class ome.formats.importer.ImportSize
 
filename - Variable in class ome.formats.importer.util.ErrorHandler.FILE_EXCEPTION
 
filename - Variable in class ome.formats.importer.util.ErrorHandler.INTERNAL_EXCEPTION
 
filename - Variable in class ome.formats.importer.util.ErrorHandler.UNKNOWN_FORMAT
 
filename - Variable in class ome.formats.importer.util.ErrorHandler.UNREADABLE_FILE
 
FILENAME_KEY - Static variable in class omero.cmd.CallContext
 
FilenameExclusion - Class in ome.formats.importer.exclusions
Voter which checks the filename (not full path) of a given File along with the checksum to detect duplicates.
FilenameExclusion() - Constructor for class ome.formats.importer.exclusions.FilenameExclusion
 
FilePathNamingValidator - Class in ome.services.blitz.repo.path
 
FilePathNamingValidator(FilePathRestrictions...) - Constructor for class ome.services.blitz.repo.path.FilePathNamingValidator
 
FilePathRestrictionInstance - Enum in ome.services.blitz.repo.path
 
FilePathRestrictions - Class in ome.services.blitz.repo.path
Capture a set of rules by which local files may not be named on the file-system.
FilePathRestrictions(SetMultimap<Integer, Integer>, Set<String>, Set<String>, Set<String>, Set<Character>) - Constructor for class ome.services.blitz.repo.path.FilePathRestrictions
Construct a set of rules by which local files may not be named on the file-system.
filePathRestrictions - Variable in class ome.services.blitz.repo.PublicRepositoryI
 
fileRepoSecretKey - Variable in class ome.services.blitz.repo.RepositoryDaoImpl
 
fileset - Variable in class ome.formats.importer.ImportEvent.IMPORT_DONE
 
FILESET_EXCLUSION(String, int, int) - Constructor for class ome.formats.importer.ImportEvent.FILESET_EXCLUSION
 
FILESET_UPLOAD_END(String, int, int, Long, Long, String[], List<String>, Map<Integer, String>, Exception) - Constructor for class ome.formats.importer.ImportEvent.FILESET_UPLOAD_END
 
FILESET_UPLOAD_PREPARATION(String, int, int, Long, Long, Exception) - Constructor for class ome.formats.importer.ImportEvent.FILESET_UPLOAD_PREPARATION
 
FILESET_UPLOAD_START(String, int, int, Long, Long, Exception) - Constructor for class ome.formats.importer.ImportEvent.FILESET_UPLOAD_START
 
FilesetData - Class in omero.gateway.model
Wraps a file set object.
FilesetData(Fileset) - Constructor for class omero.gateway.model.FilesetData
Creates a new instance.
filesService - Variable in class ome.services.blitz.impl.MetadataStoreI
 
filesToString(File...) - Static method in class omero.client
 
fileTotal - Variable in class ome.formats.importer.ImportEvent.FILE_UPLOAD_EVENT
 
FileTransfer - Interface in ome.formats.importer.transfers
Abstracted concept of "getting the file to the server".
FileUploader - Class in ome.formats.importer.util
 
FileUploader(CloseableHttpClient) - Constructor for class ome.formats.importer.util.FileUploader
Initialize upload with httpClient
fileUploadErrors - Variable in class ome.formats.importer.util.ErrorHandler
 
FileValue(String, ImportConfig) - Constructor for class ome.formats.importer.ImportConfig.FileValue
 
fillData(ImportSettings, Fileset, ClientFilePathTransformer) - Method in class ome.formats.importer.ImportContainer
 
fillData(ImportSettings, Fileset, ClientFilePathTransformer, FileTransfer) - Method in class ome.formats.importer.ImportContainer
 
fillData(ImportConfig, ImportSettings, Fileset, ClientFilePathTransformer) - Method in class ome.formats.importer.ImportContainer
 
fillData(ImportConfig, ImportSettings, Fileset, ClientFilePathTransformer, FileTransfer) - Method in class ome.formats.importer.ImportContainer
 
fillIObject(IObject, IObject) - Static method in class omero.gateway.util.ModelMapper
Fills the new IObject with data from the old one.
fillObject(ReverseModelMapper) - Method in class omero.model.DetailsI
 
fillObject(ReverseModelMapper) - Method in class omero.model.ElectricPotentialI
 
fillObject(ReverseModelMapper) - Method in class omero.model.FrequencyI
 
fillObject(ReverseModelMapper) - Method in class omero.model.LengthI
 
fillObject(ReverseModelMapper) - Method in class omero.model.PermissionsI
 
fillObject(ReverseModelMapper) - Method in class omero.model.PowerI
 
fillObject(ReverseModelMapper) - Method in class omero.model.PressureI
 
fillObject(ReverseModelMapper) - Method in class omero.model.TemperatureI
 
fillObject(ReverseModelMapper) - Method in class omero.model.TimeI
 
fillServerError(ServerError, Throwable) - Static method in class omero.util.IceMapper
 
fillVersionInfo(List<NamedValue>) - Method in class ome.formats.importer.ImportConfig
Note useful version information that can be extracted from this system, as provenance that is useful for debugging.
filter(String, Filterable) - Method in class omero.util.IceMapper
 
FILTERABLE - Static variable in class omero.util.IceMapper
 
FILTERABLE_ARRAY - Static variable in class omero.util.IceMapper
 
FILTERABLE_COLLECTION - Static variable in class omero.util.IceMapper
 
FILTERABLE_PRIMITIVE_MAP - Static variable in class omero.util.IceMapper
 
FilterData - Class in omero.gateway.model
Object hosting a filter.
FilterData(Filter) - Constructor for class omero.gateway.model.FilterData
Creates a new instance.
filterFilesByRepository(String, List<Long>, Current) - Method in interface ome.services.blitz.repo.RepositoryDao
Find the original file IDs among those given that are in the given repository.
filterFilesByRepository(String, List<Long>, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
 
FilterSetData - Class in omero.gateway.model
Object hosting a filterSet.
FilterSetData(FilterSet) - Constructor for class omero.gateway.model.FilterSetData
Creates a new instance.
finalize() - Method in class omero.cmd.fs.UsedFilesRequestI
 
finalizePixelStore() - Method in class ome.formats.OMEROMetadataStoreClient
Closes the active raw pixels store.
find_async(AMD_IQuery_find, String, long, Current) - Method in class ome.services.blitz.impl.QueryI
 
findAll_async(AMD_IQuery_findAll, String, Filter, Current) - Method in class ome.services.blitz.impl.QueryI
 
findAllByExample_async(AMD_IQuery_findAllByExample, IObject, Filter, Current) - Method in class ome.services.blitz.impl.QueryI
 
findAllByFullText_async(AMD_IQuery_findAllByFullText, String, String, Parameters, Current) - Method in class ome.services.blitz.impl.QueryI
 
findAllByQuery_async(AMD_IQuery_findAllByQuery, String, Parameters, Current) - Method in class ome.services.blitz.impl.QueryI
 
findAllByString_async(AMD_IQuery_findAllByString, String, String, String, boolean, Filter, Current) - Method in class ome.services.blitz.impl.QueryI
 
findByExample_async(AMD_IQuery_findByExample, IObject, Current) - Method in class ome.services.blitz.impl.QueryI
 
findByImage_async(AMD_IRoi_findByImage, long, RoiOptions, Current) - Method in class ome.services.blitz.impl.RoiI
 
findByPlane_async(AMD_IRoi_findByPlane, long, int, int, RoiOptions, Current) - Method in class ome.services.blitz.impl.RoiI
 
findByQuery_async(AMD_IQuery_findByQuery, String, Parameters, Current) - Method in class ome.services.blitz.impl.QueryI
 
findByRoi_async(AMD_IRoi_findByRoi, long, RoiOptions, Current) - Method in class ome.services.blitz.impl.RoiI
 
findByString_async(AMD_IQuery_findByString, String, String, String, Current) - Method in class ome.services.blitz.impl.QueryI
 
findChildren() - Static method in class omero.gateway.util.Requests
 
FindChildrenBuilder() - Constructor for class omero.gateway.util.Requests.FindChildrenBuilder
Instantiate a new FindChildren and initialize its collection containers.
FindChildrenI - Class in omero.cmd.graphs
Request to identify children or contents of model objects, whether direct or indirect.
FindChildrenI(ACLVoter, Roles, GraphPathBean, LightAdminPrivileges, Set<Class<? extends IObject>>, GraphPolicy) - Constructor for class omero.cmd.graphs.FindChildrenI
Construct a new find-children request; called from GraphRequestFactory.getRequest(Class).
findCollection(Collection) - Method in class omero.util.IceMapper
Overrides the findCollection logic of ModelMapper, since all Collections should be Lists in Ice.
findCollectionTarget(Object) - Method in class omero.util.RTypeMapper
 
findContainerHierarchies_async(AMD_IContainer_findContainerHierarchies, String, List<Long>, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI
 
findDN_async(AMD_ILdap_findDN, String, Current) - Method in class ome.services.blitz.impl.LdapI
 
findEnumeration(HashMap<String, IObject>, String) - Method in interface ome.formats.enums.handler.EnumerationHandler
Attempt to find an enumeration from an existing set of enumeration values.
findExperimenter_async(AMD_ILdap_findExperimenter, String, Current) - Method in class ome.services.blitz.impl.LdapI
 
findGroup_async(AMD_ILdap_findGroup, String, Current) - Method in class ome.services.blitz.impl.LdapI
 
findGroupDN_async(AMD_ILdap_findGroupDN, String, Current) - Method in class ome.services.blitz.impl.LdapI
 
findInDb(CheckedPath, String, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
Find the given path in the DB or create.
findIObject(SecurityContext, String, long) - Method in class omero.gateway.facility.BrowseFacility
Retrieves an updated version of the specified object.
findIObject(SecurityContext, String, long, boolean) - Method in class omero.gateway.facility.BrowseFacility
Retrieves an updated version of the specified object.
findIObject(SecurityContext, IObject) - Method in class omero.gateway.facility.BrowseFacility
Retrieves an updated version of the specified object.
findKeyTarget(Object) - Method in class omero.util.RTypeMapper
 
findMinMax_async(AMD_RawPixelsStore_findMinMax, int[], Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
findMinMax_async(AMD_RawPixelsStore_findMinMax, int[], Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
findObject(SecurityContext, Class<T>, long) - Method in class omero.gateway.facility.BrowseFacility
Retrieves an updated version of the specified object.
findObject(SecurityContext, Class<T>, long, boolean) - Method in class omero.gateway.facility.BrowseFacility
Retrieves an updated version of the specified object.
findObject(SecurityContext, String, long) - Method in class omero.gateway.facility.BrowseFacility
Retrieves an updated version of the specified object.
findObject(SecurityContext, String, long, boolean) - Method in class omero.gateway.facility.BrowseFacility
Retrieves an updated version of the specified object.
findOrCreateInDb(CheckedPath, String, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
 
findOrCreateInDb(CheckedPath, String, String, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
 
findParents() - Static method in class omero.gateway.util.Requests
 
FindParentsBuilder() - Constructor for class omero.gateway.util.Requests.FindParentsBuilder
Instantiate a new FindParents and initialize its collection containers.
FindParentsI - Class in omero.cmd.graphs
Request to identify parents or containers of model objects, whether direct or indirect.
FindParentsI(ACLVoter, Roles, GraphPathBean, LightAdminPrivileges, Set<Class<? extends IObject>>, GraphPolicy) - Constructor for class omero.cmd.graphs.FindParentsI
Construct a new find-parents request; called from GraphRequestFactory.getRequest(Class).
findProxy(Redirector.Context, String) - Method in class ome.services.blitz.redirect.AbstractRedirector
 
FindPyramidsI - Class in omero.cmd.fs
Retrieves pyramid files
FindPyramidsI(PixelsService) - Constructor for class omero.cmd.fs.FindPyramidsI
 
findRepoDeleteLogs(SqlAction.DeleteLog, Current) - Method in interface ome.services.blitz.repo.RepositoryDao
Call SqlAction.findRepoDeleteLogs(DeleteLog) with the current context.
findRepoDeleteLogs(List<SqlAction.DeleteLog>, Current) - Method in interface ome.services.blitz.repo.RepositoryDao
As findRepoDeleteLogs(DeleteLog, Current) but for a collection of templates.
findRepoDeleteLogs(SqlAction.DeleteLog, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
 
findRepoDeleteLogs(List<SqlAction.DeleteLog>, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
 
findRepoFile(String, CheckedPath, String, Current) - Method in interface ome.services.blitz.repo.RepositoryDao
Delegate to SqlAction.findRepoFile(String, String, String, String) for looking up the id of the file, and then load it normally via IQuery.
findRepoFile(ServiceFactory, SqlAction, String, CheckedPath, String) - Method in interface ome.services.blitz.repo.RepositoryDao
As RepositoryDao.findRepoFile(String, CheckedPath, String, Current) but can be called from within a transaction.
findRepoFile(String, CheckedPath, String, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
 
findRepoFile(ServiceFactory, SqlAction, String, CheckedPath, String) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
 
FindServiceFactoryMessage - Class in ome.services.blitz.util
InternalMessage raised when a servant needs to find the ServiceFactoryI instance that the current user is working with.
FindServiceFactoryMessage(Object, Identity) - Constructor for class ome.services.blitz.util.FindServiceFactoryMessage
 
FindServiceFactoryMessage(Object, Current) - Constructor for class ome.services.blitz.util.FindServiceFactoryMessage
 
finish(TransferState, long) - Method in class ome.formats.importer.transfers.AbstractFileTransfer
Save the current state to disk and finish all timing and logging.
finish() - Method in class ome.services.blitz.impl.commands.SaveI
 
finish() - Method in class ome.services.blitz.repo.ManagedImportRequestI
 
finish() - Method in class ome.services.blitz.repo.RawAccessRequestI
 
finish() - Method in class omero.cmd.admin.CurrentSessionsRequestI
 
finish() - Method in class omero.cmd.admin.ResetPasswordRequestI
 
finish() - Method in class omero.cmd.admin.UpdateSessionTimeoutRequestI
 
finish() - Method in class omero.cmd.basic.DoAllI
 
finish() - Method in class omero.cmd.basic.ListRequestsI
 
finish() - Method in class omero.cmd.basic.TimingI
 
finish() - Method in class omero.cmd.fs.FindPyramidsI
 
finish() - Method in class omero.cmd.fs.ManageImageBinariesI
 
finish() - Method in class omero.cmd.fs.OriginalMetadataRequestI
 
finish() - Method in class omero.cmd.fs.UsedFilesRequestI
 
finish() - Method in class omero.cmd.graphs.Chgrp2I
 
finish() - Method in class omero.cmd.graphs.Chmod2I
 
finish() - Method in class omero.cmd.graphs.Chown2I
 
finish() - Method in class omero.cmd.graphs.Delete2I
 
finish() - Method in class omero.cmd.graphs.DiskUsage2I
 
finish() - Method in class omero.cmd.graphs.DiskUsageI
Deprecated.
 
finish() - Method in class omero.cmd.graphs.DuplicateI
 
finish() - Method in class omero.cmd.graphs.FindChildrenI
 
finish() - Method in class omero.cmd.graphs.FindParentsI
 
finish() - Method in class omero.cmd.graphs.LegalGraphTargetsI
 
finish() - Method in class omero.cmd.graphs.SkipHeadI
 
finish() - Method in interface omero.cmd.IRequest
Method within the transaction boundaries after all processing has occurred.
finish() - Method in class omero.cmd.mail.SendEmailRequestI
 
finishCancelled() - Method in class ome.formats.importer.util.ErrorHandler
Action to take when finish cancelled
finishComplete() - Method in class ome.formats.importer.util.ErrorHandler
Action to take when finish completed
finished(Response, Status, Current) - Method in class omero.cmd.CmdCallbackI
Called when the command has completed.
finishWithErroredFiles() - Method in class ome.formats.importer.util.ErrorHandler
Action to take when finish completed but with some errors (For example, missing files)
firePropertyChanged(PropertyChangeEvent) - Method in class omero.gateway.facility.Facility
Fires a PropertyChangeEvent
firePropertyChanged(String, Object, Object) - Method in class omero.gateway.facility.Facility
Fires a PropertyChangeEvent
firstIdOrNull(String) - Method in class omero.cmd.fs.OriginalMetadataRequestI
Use IQuery.projection(String, Parameters) to load the first long which matches the given query.
FIRSTNAME - Static variable in class omero.gateway.model.ExperimenterData
Identifies the ExperimenterI.FIRSTNAME field.
firstPlane() - Method in class omero.gateway.model.ROIData
Deprecated.
Will be removed in future. Does not work as expected if the ROI contains shapes which are associated with all planes (Z, C, T == -1)
FLIM_NS - Static variable in class omero.gateway.model.FileAnnotationData
Identifies the FLIM namespace.
FLOAT - Static variable in class omero.gateway.rnd.DataSink
Identifies the type used to store pixel values.
FLOAT_TYPE - Static variable in class omero.gateway.model.PixelsData
Identifies the type used to store pixel values.
FloatConverter - Class in omero.gateway.rnd
Packs a sequence of bytes representing a big-endian float into a double value of appropriate integer type.
FloatConverter() - Constructor for class omero.gateway.rnd.FloatConverter
 
flush() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
flushPreferences() - Method in class ome.formats.importer.util.IniFileLoader
Flush preferences to disk
FolderData - Class in omero.gateway.model
Pojo wrapper for an OME Folder.
FolderData() - Constructor for class omero.gateway.model.FolderData
Creates a new instance.
FolderData(Folder) - Constructor for class omero.gateway.model.FolderData
Creates a new instance.
FONT_BOLD - Static variable in class omero.gateway.model.ShapeSettingsData
Set if font bold.
FONT_BOLD_ITALIC - Static variable in class omero.gateway.model.ShapeSettingsData
Set if font bold.
FONT_ITALIC - Static variable in class omero.gateway.model.ShapeSettingsData
Set if font italic.
FONT_REGULAR - Static variable in class omero.gateway.model.ShapeSettingsData
Set if font bold.
forEachTile(int, int, TileLoopIteration) - Method in class omero.util.RPSTileLoop
Iterates over every tile in a given pixel based on the over arching dimensions and a requested maximum tile width and height.
forEachTile(int, int, int, int, int, int, int, TileLoopIteration) - Method in class omero.util.TileLoop
Iterates over every tile in a given pixel based on the over arching dimensions and a requested maximum tile width and height.
FrequencyI - Class in omero.model
Blitz wrapper around the Frequency class.
FrequencyI() - Constructor for class omero.model.FrequencyI
 
FrequencyI(double, UnitsFrequency) - Constructor for class omero.model.FrequencyI
 
FrequencyI(double, Unit<Frequency>) - Constructor for class omero.model.FrequencyI
 
FrequencyI(Frequency, Unit<Frequency>) - Constructor for class omero.model.FrequencyI
Copy constructor that converts the given Frequency based on the given ome-xml enum
FrequencyI(double, UnitsFrequency) - Constructor for class omero.model.FrequencyI
Copy constructor that converts the given Frequency based on the given ome.model enum
FrequencyI(Frequency, String) - Constructor for class omero.model.FrequencyI
Copy constructor that converts the given Frequency based on the given enum string.
FrequencyI(Frequency, UnitsFrequency) - Constructor for class omero.model.FrequencyI
Copy constructor that converts between units if possible.
FrequencyI(Frequency) - Constructor for class omero.model.FrequencyI
Convert a Bio-Formats Length to an OMERO Length.
from - Variable in class ome.services.blitz.util.ConvertToBlitzExceptionMessage
 
fromClass(Class) - Static method in class ome.services.blitz.measurements.Helper
Factory method to generate Helper instances from the Class of a given column.
fromEnum(Collection<E>) - Static method in class omero.gateway.util.Utils
Convert a list of omero.model.enums instances to their corresponding String values.
fromLsid(String) - Static method in class ome.services.blitz.measurements.Helper
Factory method to generate Helper instances from the LSID of a given column.
fromObjectContainerStore(IObjectContainerStore, int, int) - Static method in class ome.formats.model.ChannelData
Retrieves channel data from an object container store.
fromPoints(String) - Method in class omero.gateway.model.ShapeData
Parses out the type from the points string.
fromRType(RType) - Method in class omero.util.IceMapper
Uses the omero.rtypes hierarchy to properly convert any RType to its internal representation.
fromString(String) - Method in class ome.formats.importer.ImportConfig.AnnotationListValue
 
fromString(String) - Method in class ome.formats.importer.ImportConfig.BoolValue
 
fromString(String) - Method in class ome.formats.importer.ImportConfig.DoubleArrayValue
 
fromString(String) - Method in class ome.formats.importer.ImportConfig.FileValue
 
fromString(String) - Method in class ome.formats.importer.ImportConfig.IntValue
 
fromString(String) - Method in class ome.formats.importer.ImportConfig.LongValue
 
fromString(String) - Method in class ome.formats.importer.ImportConfig.StrValue
 
fromString(String) - Method in class ome.formats.importer.ImportConfig.Value
 
fsFile - Variable in class ome.services.blitz.repo.CheckedPath
 
FsFile - Class in ome.services.blitz.repo.path
An analog of File representing an FS repository file-path.
FsFile(Collection<String>) - Constructor for class ome.services.blitz.repo.path.FsFile
Construct an instance.
FsFile(String...) - Constructor for class ome.services.blitz.repo.path.FsFile
Construct an instance.
FsFile(FsFile, int) - Constructor for class ome.services.blitz.repo.path.FsFile
Construct an instance by trimming parent directories from an existing instance such that the depth does not exceed the given maximum.
FsFile(File) - Constructor for class ome.services.blitz.repo.path.FsFile
Construct an instance.
FsFile(String) - Constructor for class ome.services.blitz.repo.path.FsFile
Construct an instance.
fullImport(File, String) - Method in class ome.formats.OMEROImportFixture
Deprecated.
Provides one complete import cycle.

G

Gateway - Class in omero.gateway
A Gateway for simplifying access to an OMERO server
Gateway(Logger) - Constructor for class omero.gateway.Gateway
Creates a new Gateway instance
Gateway(Logger, CacheService) - Constructor for class omero.gateway.Gateway
Creates a new Gateway instance
Gateway(Logger, CacheService, ExecutorService, boolean) - Constructor for class omero.gateway.Gateway
Creates a new Gateway instance
GENERAL_ERROR - Static variable in class omero.gateway.model.SearchResultCollection
Some other error
generateRepoUuid() - Method in class ome.services.blitz.repo.AbstractRepositoryI
Called when this repository is creating a new OriginalFile repository object.
generateRepoUuid() - Method in class ome.services.blitz.repo.ScriptRepositoryI
 
generateScriptParams(long, boolean, Current) - Method in class omero.grid.ParamsHelper
Acquires an InteractiveProcessorPrx and runs a ParseJob.
generateThumbnails(ThumbnailGenerationJob) - Method in class ome.services.blitz.repo.ManagedImportRequestI
 
generateTiff_async(AMD_Exporter_generateTiff, Current) - Method in class ome.services.blitz.impl.ExporterI
 
generateXml(MetadataRetrieve) - Method in class ome.services.blitz.impl.ExporterI
 
generateXml_async(AMD_Exporter_generateXml, Current) - Method in class ome.services.blitz.impl.ExporterI
Generate XML and return the length
geomTool - Variable in class ome.services.blitz.impl.RoiI
 
GeomTool - Class in ome.services.roi
Strategy for handling the conversion between shapes and database-specific geometries.
GeomTool(PixelData, SqlAction, SessionFactory) - Constructor for class ome.services.roi.GeomTool
 
GeomTool(PixelData, SqlAction, SessionFactory, Executor, String) - Constructor for class ome.services.roi.GeomTool
 
get() - Method in class ome.formats.importer.ImportConfig.FileValue
 
get() - Method in class ome.formats.importer.ImportConfig.Value
Returns the generic type contained by this holder.
get() - Method in class ome.services.blitz.util.ResultHolder
 
get(PixelBuffer, int, int, int, int, int) - Method in class ome.services.roi.PixelData
 
get(int) - Method in class omero.util.ReadOnlyByteArray
Reads the element at the index position within this slice.
get(Identity) - Method in class omero.util.ServantHolder
 
get_async(AMD_IQuery_get, String, long, Current) - Method in class ome.services.blitz.impl.QueryI
 
getAbsolutePath() - Method in class ome.formats.importer.util.ErrorContainer
get path for file
getAbsolutePath() - Method in class omero.gateway.model.FileData
Returns the absolute path.
getAbsolutePaths() - Method in class omero.gateway.model.FilesetData
Returns the collections of absolute paths.
getAcquisitionData() - Method in class omero.sys.ParametersI
 
getAcquisitionDate() - Method in class omero.gateway.model.ImageData
Returns the acquisition date.
getActionForStarting() - Method in class omero.cmd.graphs.Chgrp2I
 
getActionForStarting() - Method in class omero.cmd.graphs.Chmod2I
 
getActionForStarting() - Method in class omero.cmd.graphs.Chown2I
 
getActionForStarting() - Method in class omero.cmd.graphs.Delete2I
 
getActionForStarting() - Method in class omero.cmd.graphs.DuplicateI
 
getActionForStarting() - Method in interface omero.cmd.graphs.WrappableRequest
 
getActiveConnections_async(AMD_IShare_getActiveConnections, long, Current) - Method in class ome.services.blitz.impl.ShareI
 
getAdapter() - Method in class omero.client
 
getAdapter() - Method in class omero.cmd.SessionI
 
getAdminPrivileges(SecurityContext) - Method in class omero.gateway.facility.AdminFacility
Get the logged in user's admin privileges (see omero.model.enums)
getAdminPrivileges(SecurityContext, ExperimenterData) - Method in class omero.gateway.facility.AdminFacility
Get the admin privileges of a certain user (see omero.model.enums)
getAdminPrivileges_async(AMD_IAdmin_getAdminPrivileges, Experimenter, Current) - Method in class ome.services.blitz.impl.AdminI
 
getAdminService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
getAdminService(SecurityContext) - Method in class omero.gateway.Gateway
Returns the IAdminPrx service.
getAdminService(SecurityContext, boolean) - Method in class omero.gateway.Gateway
Returns the IAdminPrx service.
getAdminSession() - Method in interface ome.services.blitz.fire.Registry
Create a new AdminSessionPrx with the RegistryPrx.
getAdminSession() - Method in class ome.services.blitz.fire.Registry.Impl
 
getAdminsWithPrivileges_async(AMD_IAdmin_getAdminsWithPrivileges, List<AdminPrivilege>, Current) - Method in class ome.services.blitz.impl.AdminI
 
getAgent(Current) - Method in class ome.services.blitz.fire.SessionManagerI
 
getAirPressure(UnitsPressure) - Method in class omero.gateway.model.ImageAcquisitionData
Returns the air pressure.
getAllChecksumAlgorithms() - Static method in class ome.services.blitz.util.ChecksumAlgorithmMapper
 
getAllEnumerations_async(AMD_IPixels_getAllEnumerations, String, Current) - Method in class ome.services.blitz.impl.PixelsI
 
getAllGuests_async(AMD_IShare_getAllGuests, long, Current) - Method in class ome.services.blitz.impl.ShareI
 
getAllMembers_async(AMD_IShare_getAllMembers, long, Current) - Method in class ome.services.blitz.impl.ShareI
 
getAllPixels() - Method in class omero.gateway.model.ImageData
Returns all the sets of pixels related to this image.
getAllUsers_async(AMD_IShare_getAllUsers, long, Current) - Method in class ome.services.blitz.impl.ShareI
 
getAlpha() - Method in class omero.gateway.model.WellData
Returns the alpha component of the color associated to the well, or -1.
getAmplificationGain() - Method in class omero.gateway.model.DetectorData
Returns the amplification gain of the detector.
getAnnotatedObject(IObject) - Static method in class omero.gateway.util.ModelMapper
Returns the annotated IObject related to the specified annotation.
getAnnotationObject(IObject) - Static method in class omero.gateway.util.ModelMapper
Returns the annotation represented by the specified link
getAnnotations(SecurityContext, DataObject) - Method in class omero.gateway.facility.MetadataFacility
Get all annotations for the given DataObject
getAnnotations(SecurityContext, DataObject, List<Class<? extends AnnotationData>>, List<Long>) - Method in class omero.gateway.facility.MetadataFacility
Get the annotations for the given DataObject
getAnnotations(SecurityContext, List<? extends DataObject>, List<Class<? extends AnnotationData>>, List<Long>) - Method in class omero.gateway.facility.MetadataFacility
Get the annotations for the given DataObjects
getAnnotations() - Method in class omero.gateway.model.DatasetData
Returns the annotations related to this dataset.
getAnnotations() - Method in class omero.gateway.model.ImageData
Returns the annotations
getAnnotationsCounts() - Method in class omero.gateway.model.DatasetData
Returns the number of annotations linked to the object, key: id of the user, value: number of annotation.
getAnnotationsCounts() - Method in class omero.gateway.model.ImageData
Returns the number of annotations linked to the object, key: id of the user, value: number of annotation.
getAnnotationsCounts() - Method in class omero.gateway.model.PlateAcquisitionData
Returns the number of annotations linked to the object, key: id of the user, value: number of annotation.
getAnnotationsCounts() - Method in class omero.gateway.model.PlateData
Returns the number of annotations linked to the object, key: id of the user, value: number of annotation.
getAnnotationsCounts() - Method in class omero.gateway.model.ProjectData
Returns the number of annotations linked to the object, key: id of the user, value: number of annotation.
getAnnotationsCounts() - Method in class omero.gateway.model.ScreenData
Returns the number of annotations linked to the object, key: id of the user, value: number of annotation.
getAnnotationsCounts() - Method in class omero.gateway.model.WellData
Returns the number of annotations linked to the object, key: id of the user, value: number of annotation.
getAnnotationTypes_async(AMD_ITypes_getAnnotationTypes, Current) - Method in class ome.services.blitz.impl.TypesI
 
getApplicationName() - Method in class omero.gateway.LoginCredentials
 
getAppTitle() - Method in class ome.formats.importer.ImportConfig
 
getAppTitle() - Method in class ome.formats.importer.util.IniFileLoader
 
getAppVersion() - Method in class ome.formats.importer.util.ErrorContainer
 
getArguments() - Method in class omero.gateway.LoginCredentials
Returns the arguments if set as a read-only list.
getAttachedFile() - Method in class omero.gateway.model.FileAnnotationData
Returns the file to upload to the server.
getAuthoritativeContainerCache() - Method in interface ome.formats.model.IObjectContainerStore
Returns the current authoritative LSID container cache.
getAuthoritativeContainerCache() - Method in class ome.formats.OMEROMetadataStoreClient
 
getAvailableAdminPrivileges(SecurityContext) - Method in class omero.gateway.facility.AdminFacility
Get all available admin privileges
getAvailableFamilies_async(AMD_RenderingEngine_getAvailableFamilies, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
getAvailableGroups(SecurityContext, ExperimenterData) - Method in class omero.gateway.facility.BrowseFacility
Retrieves the groups visible by the current experimenter.
getAvailableModels_async(AMD_RenderingEngine_getAvailableModels, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
getAvailableTables(SecurityContext, DataObject) - Method in class omero.gateway.facility.TablesFacility
Get all available tables for a the specified object
getAwtTransform(AffineTransform) - Static method in class omero.model.SmartShape.Util
 
getBatchSize_async(AMD_Search_getBatchSize, Current) - Method in class ome.services.blitz.impl.SearchI
 
getBioFormatsVersion() - Method in class ome.formats.importer.ImportConfig
 
getBit(byte[], int) - Method in class omero.gateway.model.MaskData
Sets the bit value in a byte array at position bit to be the value value.
getBitDepth_async(AMD_IPixels_getBitDepth, PixelsType, Current) - Method in class ome.services.blitz.impl.PixelsI
 
getBlitzAdapter() - Method in class ome.services.blitz.util.BlitzConfiguration
 
getBlitzManager() - Method in class ome.services.blitz.util.BlitzConfiguration
 
getBlitzVerifier() - Method in class ome.services.blitz.util.BlitzConfiguration
 
getBlue() - Method in class omero.gateway.model.WellData
Returns the blue component of the color associated to the well, or -1.
getBooleanAnnotationCount() - Method in class ome.services.blitz.impl.OmeroMetadata
 
getBooleanAnnotationDescription(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getBooleanAnnotationID(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getBooleanAnnotationNamespace(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getBooleanAnnotationValue(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getBuffer() - Method in class ome.formats.importer.transfers.TransferState
(Not thread safe) Get a moderately large buffer for use in reading/writing data.
getBuffer(long) - Method in class ome.services.roi.PixelData
 
getByGroup() - Method in class omero.gateway.model.SearchResultCollection
Get a perGroup map representation of the results
getByGroup(Class<? extends DataObject>) - Method in class omero.gateway.model.SearchResultCollection
Get a perGroup map representation of the results, filtered by type
getByName(String, Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
getByName(String, Current, boolean) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
getByPeriod_async(AMD_ITimeline_getByPeriod, List<String>, RTime, RTime, Parameters, boolean, Current) - Method in class ome.services.blitz.impl.TimelineI
 
getByteWidth_async(AMD_RawPixelsStore_getByteWidth, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
getByteWidth_async(AMD_RawPixelsStore_getByteWidth, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
getC() - Method in class omero.gateway.model.ShapeData
Returns the channel. -1 if the shape applies to all channels of the image.
getCache() - Method in class omero.sys.ParametersI
 
getCacheService() - Method in class omero.gateway.Gateway
Provides access to the CacheService
getCalibratedMagnification() - Method in class omero.gateway.model.ObjectiveData
Returns the objective's calibrated magnification factor.
getCallContext() - Method in class ome.services.blitz.impl.commands.SaveI
 
getCallContext() - Method in class ome.services.blitz.repo.ManagedImportRequestI
 
getCallContext() - Method in class ome.services.blitz.repo.RawAccessRequestI
 
getCallContext() - Method in class omero.cmd.admin.CurrentSessionsRequestI
 
getCallContext() - Method in class omero.cmd.admin.ResetPasswordRequestI
 
getCallContext() - Method in class omero.cmd.admin.UpdateSessionTimeoutRequestI
 
getCallContext() - Method in class omero.cmd.basic.DoAllI
 
getCallContext() - Method in class omero.cmd.basic.ListRequestsI
 
getCallContext() - Method in class omero.cmd.basic.TimingI
 
getCallContext() - Method in class omero.cmd.fs.FindPyramidsI
 
getCallContext() - Method in class omero.cmd.fs.ManageImageBinariesI
 
getCallContext() - Method in class omero.cmd.fs.OriginalMetadataRequestI
 
getCallContext() - Method in class omero.cmd.fs.UsedFilesRequestI
 
getCallContext() - Method in class omero.cmd.graphs.Chgrp2I
 
getCallContext() - Method in class omero.cmd.graphs.Chmod2I
 
getCallContext() - Method in class omero.cmd.graphs.Chown2I
 
getCallContext() - Method in class omero.cmd.graphs.Delete2I
 
getCallContext() - Method in class omero.cmd.graphs.DiskUsage2I
 
getCallContext() - Method in class omero.cmd.graphs.DiskUsageI
Deprecated.
 
getCallContext() - Method in class omero.cmd.graphs.DuplicateI
 
getCallContext() - Method in class omero.cmd.graphs.FindChildrenI
 
getCallContext() - Method in class omero.cmd.graphs.FindParentsI
 
getCallContext() - Method in class omero.cmd.graphs.LegalGraphTargetsI
 
getCallContext() - Method in class omero.cmd.graphs.SkipHeadI
 
getCallContext() - Method in interface omero.cmd.IRequest
Returns the desired call context for this request.
getCallContext() - Method in class omero.cmd.mail.SendEmailRequestI
 
getCallContext() - Method in class omero.model.DetailsI
 
getCategory() - Method in class omero.client
Returns the category which should be used for all callbacks passed to the server.
getChannel() - Method in class ome.formats.model.ChannelData
Returns the channel this channel data is for.
getChannel(int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
getChannelAcquisitionMode(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getChannelColor(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getChannelContrastMethod(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getChannelCount(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getChannelCurveCoefficient_async(AMD_RenderingEngine_getChannelCurveCoefficient, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
getChannelData(SecurityContext, long) - Method in class omero.gateway.facility.MetadataFacility
Get the ChannelData for a specific image
getChannelEmissionWavelength(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getChannelExcitationWavelength(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getChannelFamily_async(AMD_RenderingEngine_getChannelFamily, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
getChannelFluor(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getChannelID(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getChannelIlluminationType(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getChannelIndex() - Method in class ome.formats.model.ChannelData
Returns the index of the channel this channel data is for.
getChannelLabeling() - Method in class omero.gateway.model.ChannelData
Returns the label of the channel.
getChannelLookupTable_async(AMD_RenderingEngine_getChannelLookupTable, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
getChannelName(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getChannelNDFilter(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getChannelNoiseReduction_async(AMD_RenderingEngine_getChannelNoiseReduction, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
getChannelPinholeSize(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getChannelPockelCellSetting(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getChannelSamplesPerPixel(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getChannelStats_async(AMD_RenderingEngine_getChannelStats, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
getChannelWindowEnd_async(AMD_RenderingEngine_getChannelWindowEnd, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
getChannelWindowStart_async(AMD_RenderingEngine_getChannelWindowStart, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
getChecksum() - Method in class ome.formats.importer.transfers.TransferState
Get the digest string for the local file.
getChecksumAlgorithm() - Method in class ome.formats.importer.ImportContainer
 
getChecksumAlgorithm(String, Current) - Method in interface ome.services.blitz.repo.RepositoryDao
Retrieve the checksum algorithm of the given name.
getChecksumAlgorithm(String, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
 
getChecksumAlgorithm(String) - Static method in class ome.services.blitz.util.ChecksumAlgorithmMapper
 
getChecksumProvider() - Method in class ome.formats.importer.transfers.TransferState
Get the ChecksumProvider passed to the constructor.
getChecksumType(ChecksumAlgorithm) - Static method in class ome.services.blitz.util.ChecksumAlgorithmMapper
 
getChecksumType(ChecksumAlgorithm) - Static method in class ome.services.blitz.util.ChecksumAlgorithmMapper
 
getChildFromLink(IObject) - Static method in class omero.gateway.util.ModelMapper
Returns the child from the passed link.
getChildOptionsPolicy(GraphPolicy, Collection<ChildOptionI>, Set<GraphPolicy.Ability>) - Static method in class omero.cmd.graphs.ChildOptionsPolicy
Adjust an existing graph traversal policy so that child objects may be included or excluded regardless of if they are truly orphans.
getClassesFromNames(Collection<String>) - Method in class omero.cmd.graphs.GraphHelper
Given class names provided by the user, find the corresponding set of actual classes.
getCleanInstance() - Method in class omero.cmd.graphs.BaseGraphPolicyAdjuster
 
getClient() - Method in class ome.formats.importer.util.ClientKeepAlive
 
getClient() - Method in class omero.model.DetailsI
 
getClientConfigDefaults_async(AMD_IConfig_getClientConfigDefaults, Current) - Method in class ome.services.blitz.impl.ConfigI
 
getClientConfigValues_async(AMD_IConfig_getClientConfigValues, Current) - Method in class ome.services.blitz.impl.ConfigI
 
getClientIds() - Method in class omero.util.ServantHolder
 
getCloseStatementCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
getCo2Percent() - Method in class omero.gateway.model.ImageAcquisitionData
Returns the Co2 level, this is a percent value in the interval [0, 1].
getCodomainMapContext_async(AMD_RenderingEngine_getCodomainMapContext, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
getCol_async(AMD_RawPixelsStore_getCol, int, int, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
getCol_async(AMD_RawPixelsStore_getCol, int, int, int, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
getCollectionCount_async(AMD_IContainer_getCollectionCount, String, String, List<Long>, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI
 
getCollectionFetchCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
getCollectionLoadCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
getCollectionRecreateCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
getCollectionRemoveCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
getCollectionRoleNames() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
Get the names of all collection roles
getCollectionStatistics(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
Get collection statistics per role
getCollectionUpdateCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
getColor(ChannelData) - Static method in class ome.formats.model.ColorsFactory
Determines the color usually associated to the specified wavelength or explicitly defined for a particular channel.
getColor(int) - Static method in class omero.gateway.model.ShapeSettingsData
Creates a Color object from an RGBA integer value
getColumn() - Method in class omero.gateway.model.WellData
Returns the column used to indicate the location of the well on the grid.
getColumnIndex(Integer) - Method in class omero.gateway.model.TableResult
Returns the index of the column corresponding to the specified value.
getColumns() - Method in class omero.gateway.model.TableData
Get the headers
getColumnSequenceIndex() - Method in class omero.gateway.model.PlateData
Returns the index indicating how to label a column.
getComment() - Method in class ome.formats.importer.util.ErrorContainer
 
getCommentAnnotationCount() - Method in class ome.services.blitz.impl.OmeroMetadata
 
getCommentAnnotationDescription(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getCommentAnnotationID(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getCommentAnnotationNamespace(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getCommentAnnotationValue(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getCommentCount_async(AMD_IShare_getCommentCount, List<Long>, Current) - Method in class ome.services.blitz.impl.ShareI
 
getComments_async(AMD_IShare_getComments, long, Current) - Method in class ome.services.blitz.impl.ShareI
 
getCommentType() - Method in class ome.formats.importer.util.ErrorContainer
 
getCommunicationLink(String) - Method in class ome.formats.importer.util.HtmlMessenger
Creates a client to communicate.
getCommunicator() - Method in class ome.services.blitz.fire.Ring
 
getCommunicator() - Method in interface ome.services.blitz.redirect.Redirector.Context
Active communicator for use by the Redirector instance.
getCommunicator() - Method in class ome.services.blitz.repo.AbstractRepositoryI
 
getCommunicator() - Method in class ome.services.blitz.repo.InternalRepositoryConfig
 
getCommunicator() - Method in class ome.services.blitz.util.BlitzConfiguration
 
getCommunicator() - Method in class omero.client
Returns the Communicator for this instance or throws an exception if null.
getComponents() - Method in class ome.services.blitz.repo.path.FsFile
Get the path components of this instance.
getCompression() - Method in class omero.gateway.LoginCredentials
Returns the compression level.
getCompression() - Method in class omero.gateway.SecurityContext
Get the compression level (A percentage compression level from 1.00 (100%) to 0.01 (1%) (the default is 85%))
getCompressionLevel_async(AMD_RenderingEngine_getCompressionLevel, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
getConfig() - Method in class ome.formats.importer.OMEROWrapper
 
getConfigDefaults_async(AMD_IConfig_getConfigDefaults, Current) - Method in class ome.services.blitz.impl.ConfigI
 
getConfigService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
getConfigService(SecurityContext) - Method in class omero.gateway.Gateway
Returns the IConfigPrx service.
getConfigValue(String) - Method in class ome.formats.OMEROMetadataStoreClient
Retrieves a configuration value from the IConfig service.
getConfigValue_async(AMD_IConfig_getConfigValue, String, Current) - Method in class ome.services.blitz.impl.ConfigI
 
getConfigValues_async(AMD_IConfig_getConfigValues, String, Current) - Method in class ome.services.blitz.impl.ConfigI
 
getConnectCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
getConnectionStatus() - Method in exception omero.gateway.exception.DSOutOfServiceException
getConnector(SecurityContext) - Method in class omero.gateway.Gateway
Get a connector for a certain SecurityContext
getConnector(SecurityContext, boolean, boolean) - Method in class omero.gateway.Gateway
Returns the connector corresponding to the passed context.
getContainerCache() - Method in interface ome.formats.model.IObjectContainerStore
Returns the current container cache.
getContainerCache() - Method in class ome.formats.OMEROMetadataStoreClient
 
getContainers() - Method in class ome.formats.importer.ImportCandidates
 
getContainerService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
getContent() - Method in class omero.gateway.model.AnnotationData
Returns the content of the annotation.
getContent() - Method in class omero.gateway.model.BooleanAnnotationData
Returns the textual content of the annotation.
getContent() - Method in class omero.gateway.model.DoubleAnnotationData
Returns the value.
getContent() - Method in class omero.gateway.model.FileAnnotationData
Returns the original file.
getContent() - Method in class omero.gateway.model.LongAnnotationData
Returns the rating value.
getContent() - Method in class omero.gateway.model.MapAnnotationData
 
getContent() - Method in class omero.gateway.model.RatingAnnotationData
Returns the rating value.
getContent() - Method in class omero.gateway.model.TagAnnotationData
Returns the textual content of the annotation.
getContent() - Method in class omero.gateway.model.TermAnnotationData
Returns the textual content of the annotation.
getContent() - Method in class omero.gateway.model.TextualAnnotationData
Returns the textual content of the annotation.
getContent() - Method in class omero.gateway.model.TimeAnnotationData
Returns the timestamp of the annotation.
getContent() - Method in class omero.gateway.model.XMLAnnotationData
Returns the content of the annotation.
getContentAsString() - Method in class omero.gateway.model.AnnotationData
Returns the content of the annotation as a String, which is parsed on a Class-by-Class basis.
getContentAsString() - Method in class omero.gateway.model.BooleanAnnotationData
Returns the textual content of the annotation.
getContentAsString() - Method in class omero.gateway.model.DoubleAnnotationData
Returns the value as a string.
getContentAsString() - Method in class omero.gateway.model.FileAnnotationData
Returns the absolute path to the file
getContentAsString() - Method in class omero.gateway.model.LongAnnotationData
Returns the value as a string.
getContentAsString() - Method in class omero.gateway.model.MapAnnotationData
 
getContentAsString() - Method in class omero.gateway.model.RatingAnnotationData
Returns the rating value as a string.
getContentAsString() - Method in class omero.gateway.model.TagAnnotationData
Returns the textual content of the annotation.
getContentAsString() - Method in class omero.gateway.model.TermAnnotationData
Returns the textual content of the annotation.
getContentAsString() - Method in class omero.gateway.model.TextualAnnotationData
Returns the textual content of the annotation.
getContentAsString() - Method in class omero.gateway.model.TimeAnnotationData
Returns the time as a string.
getContentAsString() - Method in class omero.gateway.model.XMLAnnotationData
Returns the textual content of the annotation.
getContentMap_async(AMD_IShare_getContentMap, long, Current) - Method in class ome.services.blitz.impl.ShareI
 
getContents_async(AMD_IShare_getContents, long, Current) - Method in class ome.services.blitz.impl.ShareI
 
getContentSize_async(AMD_IShare_getContentSize, long, Current) - Method in class ome.services.blitz.impl.ShareI
 
getContentSubList_async(AMD_IShare_getContentSubList, long, int, int, Current) - Method in class ome.services.blitz.impl.ShareI
 
getContrastMethod() - Method in class omero.gateway.model.ChannelAcquisitionData
Returns the contrast method.
getContrastMethod() - Method in class omero.gateway.model.ChannelData
Returns the contrast method.
getContrastMethodAsEnum() - Method in class omero.gateway.model.ChannelData
Returns the contrast method enumeration value.
getCorrection() - Method in class omero.gateway.model.ObjectiveData
Returns the correction value of the objective.
getCorrectionCollar() - Method in class omero.gateway.model.ImageAcquisitionData
Returns the correction collar of the objective.
getCreated() - Method in class omero.gateway.model.DataObject
Returns the creation time of the object.
getCreationEvent(Current) - Method in class omero.model.DetailsI
 
getCurrent() - Method in class ome.services.blitz.util.FindServiceFactoryMessage
 
getCurrent() - Method in class ome.services.blitz.util.UnregisterServantMessage
 
getCurrentAdminPrivileges_async(AMD_IAdmin_getCurrentAdminPrivileges, Current) - Method in class ome.services.blitz.impl.AdminI
 
getCurrentEventContext_async(AMD_StatefulServiceInterface_getCurrentEventContext, Current) - Method in class ome.services.blitz.impl.AbstractAmdServant
 
getCurrentEventContext_async(AMD_StatefulServiceInterface_getCurrentEventContext, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
getCustomAnnotationList() - Method in class ome.formats.importer.ImportContainer
The list of custom, user specified, annotations to link to all images represented by this container.
getCustomImageNaming() - Method in class ome.formats.importer.ImportConfig
 
getCustomImageNaming() - Method in class ome.formats.importer.util.IniFileLoader
 
getCutIn(UnitsLength) - Method in class omero.gateway.model.FilterData
Returns the cut in value or null.
getCutInTolerance(UnitsLength) - Method in class omero.gateway.model.FilterData
Returns the cut in tolerance value or null.
getCutOut(UnitsLength) - Method in class omero.gateway.model.FilterData
Returns the cut out value or null.
getCutOutTolerance(UnitsLength) - Method in class omero.gateway.model.FilterData
Returns the cut out tolerance value or null.
getData() - Method in class omero.gateway.model.TableData
Get the data in form Object['column index']['row data']
getData() - Method in class omero.gateway.model.TableResult
Returns the data.
getDatabaseTime_async(AMD_IConfig_getDatabaseTime, Current) - Method in class ome.services.blitz.impl.ConfigI
 
getDatabaseUuid_async(AMD_IConfig_getDatabaseUuid, Current) - Method in class ome.services.blitz.impl.ConfigI
 
getDataObjects(int, Class<? extends DataObject>) - Method in class omero.gateway.model.SearchResultCollection
Get DataObjects filtered by scope and type
getDataObjects() - Method in class omero.gateway.model.TagAnnotationData
Returns the collection of data objects related to this tag.
getDatasets(Project) - Method in class ome.formats.OMEROMetadataStoreClient
 
getDatasets(SecurityContext) - Method in class omero.gateway.facility.BrowseFacility
Loads all datasets
getDatasets(SecurityContext, Collection<Long>) - Method in class omero.gateway.facility.BrowseFacility
Loads the datasets with the given ids
getDatasets(SecurityContext, long) - Method in class omero.gateway.facility.BrowseFacility
Loads the datasets for a particular user
getDatasets(SecurityContext, long, Collection<Long>) - Method in class omero.gateway.facility.BrowseFacility
Loads the datasets with the given ids which belong to a particular user
getDatasets() - Method in class omero.gateway.model.ImageData
Returns the datasets containing this image.
getDatasets() - Method in class omero.gateway.model.ProjectData
Returns the datasets contained in this project.
getDatasetsWithoutProjects() - Method in class ome.formats.OMEROMetadataStoreClient
 
getDataValue() - Method in class omero.gateway.model.DoubleAnnotationData
Returns the value.
getDataValue() - Method in class omero.gateway.model.LongAnnotationData
Returns the value.
getDateType() - Method in class omero.gateway.model.SearchParameters
 
getDebugLevel() - Method in class ome.formats.importer.ImportConfig
 
getDebugLevel() - Method in class ome.formats.importer.util.IniFileLoader
Returns the level of debugging which should be set on ImportConfig Any value lower than null will not call configureDebug.
getDefaultBatchSize() - Method in class ome.formats.OMEROMetadataStoreClient
 
getDefaultBlockSize() - Method in class ome.formats.OMEROMetadataStoreClient
 
getDefaultBlockSize() - Method in class omero.client
Returns the user-configured setting for "omero.block_size" or DEFAULTBLOCKSIZE if none is set.
getDefaultGroup() - Method in class omero.gateway.model.ExperimenterData
Returns the default Group for this Experimenter
getDefaultGroup_async(AMD_IAdmin_getDefaultGroup, long, Current) - Method in class ome.services.blitz.impl.AdminI
 
getDefaultGroupLevel() - Method in class ome.formats.OMEROMetadataStoreClient
Deprecated.
getDefaultGroupName() - Method in class ome.formats.OMEROMetadataStoreClient
Retrieve the default group's name
getDefaultPixels() - Method in class omero.gateway.model.ImageData
Returns the default set of pixels.
getDefaultSample() - Method in class omero.gateway.model.PlateData
Returns the currently selected field or 0.
getDefaultT_async(AMD_RenderingEngine_getDefaultT, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
getDefaultZ_async(AMD_RenderingEngine_getDefaultZ, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
getDescription(Current) - Method in class ome.services.blitz.repo.AbstractRepositoryI
 
getDescription(long) - Method in class ome.services.blitz.repo.AbstractRepositoryI
 
getDescription() - Method in class omero.gateway.model.AnnotationData
Retrieves the description of the underlying Annotation instance.
getDescription() - Method in class omero.gateway.model.DatasetData
Returns the description of the dataset.
getDescription() - Method in class omero.gateway.model.FileAnnotationData
Returns the description of the annotation.
getDescription() - Method in class omero.gateway.model.FileData
Returns the description of the file.
getDescription() - Method in class omero.gateway.model.FolderData
Get the description of the Folder
getDescription() - Method in class omero.gateway.model.GroupData
Returns the description of the group.
getDescription() - Method in class omero.gateway.model.ImageData
Returns the description of the image.
getDescription() - Method in class omero.gateway.model.PlateAcquisitionData
Returns the description of the plate acquisition.
getDescription() - Method in class omero.gateway.model.PlateData
Returns the description of the plate.
getDescription() - Method in class omero.gateway.model.ProjectData
Returns the description of the project.
getDescription() - Method in class omero.gateway.model.ScreenData
Returns the description of the screen.
getDescription() - Method in class omero.gateway.model.TableDataColumn
Get the description
getDescription() - Method in class omero.gateway.model.XMLAnnotationData
Returns the description of the annotation.
getDescription() - Method in class omero.gateway.util.TIFFFilter
Returns the description of the filter.
getDetails() - Method in class omero.gateway.model.DataObject
Returns the details of the object.
getDetector(int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
getDetector() - Method in class omero.gateway.model.ChannelAcquisitionData
Returns the detector used for that channel.
getDetectorBinningAsEnum() - Method in class omero.gateway.model.ChannelAcquisitionData
Returns the binning enumeration value.
getDetectors() - Method in class omero.gateway.model.InstrumentData
Returns the collection of detectors.
getDetectorSettingsBinning() - Method in class omero.gateway.model.ChannelAcquisitionData
Returns the Binning factor.
getDetectorSettingsGain() - Method in class omero.gateway.model.ChannelAcquisitionData
Returns the gain set on the detector.
getDetectorSettingsOffset() - Method in class omero.gateway.model.ChannelAcquisitionData
Returns the offset set on the detector.
getDetectorSettingsReadOutRate(UnitsFrequency) - Method in class omero.gateway.model.ChannelAcquisitionData
Returns the Read out rate set on the detector.
getDetectorSettingsVoltage(UnitsElectricPotential) - Method in class omero.gateway.model.ChannelAcquisitionData
Returns the voltage set on the detector.
getDichroic() - Method in class omero.gateway.model.FilterSetData
Returns the dichroic if any.
getDichroic() - Method in class omero.gateway.model.LightPathData
Returns the dichroic if any.
getDichroics() - Method in class omero.gateway.model.InstrumentData
Returns the collection of dichroics.
getDir() - Method in class ome.services.blitz.repo.FileMaker
 
getDirectProxy() - Method in class ome.services.blitz.fire.Ring
Returns the proxy information for the local SessionManager.
getDirectProxy() - Method in interface ome.services.blitz.redirect.Redirector.Context
String representation of the proxy to the local node which may be contacted to create new sessions.
getDirectProxy() - Method in class ome.services.blitz.util.BlitzConfiguration
Return a direct proxy to the session manager in this object adapter.
getDirname() - Method in class ome.services.blitz.repo.CheckedPath
Assuming this is a directory, return relative path plus name with a final slash.
getDiscriminator() - Method in class ome.formats.importer.targets.TemplateImportTarget
 
getDisplayedFileName(String, Integer) - Static method in class omero.gateway.util.Utils
Returns the name to display for a file.
getDoThumbnails() - Method in class ome.formats.importer.ImportContainer
Retrieves whether or not we are performing thumbnail creation upon import completion.
getDoubleAnnotationCount() - Method in class ome.services.blitz.impl.OmeroMetadata
 
getDoubleAnnotationDescription(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getDoubleAnnotationID(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getDoubleAnnotationNamespace(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getDoubleAnnotationValue(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getElement(int, Object) - Method in interface omero.gateway.cache.CacheService
Adds the specified element to the selected cache.
getEllipseAnnotationRef(int, int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getEllipseFillColor(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getEllipseFillRule(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getEllipseFontFamily(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getEllipseFontSize(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getEllipseFontStyle(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getEllipseID(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getEllipseLocked(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getEllipseRadiusX(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getEllipseRadiusY(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getEllipseStrokeColor(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getEllipseStrokeDashArray(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getEllipseStrokeWidth(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getEllipseText(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getEllipseTheC(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getEllipseTheT(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getEllipseTheZ(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getEllipseTransform(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getEllipseX(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getEllipseY(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getEmail() - Method in class ome.formats.importer.util.ErrorContainer
 
getEmail() - Method in class omero.gateway.model.ExperimenterData
Returns the e-mail of the experimenter.
getEmissionFilters() - Method in class omero.gateway.model.FilterSetData
Returns the collections of emission filters if any.
getEmissionFilters() - Method in class omero.gateway.model.LightPathData
Returns the collections of emission filters if any.
getEmissionWavelength(UnitsLength) - Method in class omero.gateway.model.ChannelData
Returns the emission wavelength of the channel.
getEnd() - Method in class omero.gateway.model.SearchParameters
Returns the upper bound of the time interval.
getEndTime() - Method in class omero.gateway.model.PlateAcquisitionData
Returns the time when the last image was collected.
getEndTime() - Method in class omero.sys.ParametersI
Returns the value of the end time parameter.
getEntityDeleteCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
getEntityFetchCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
getEntityInsertCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
getEntityLoadCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
getEntityNames() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
Get the names of all entities
getEntityStatistics(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
find entity statistics per name
getEntityUpdateCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
getEnumeration(Class<T>, String, boolean) - Method in interface ome.formats.enums.EnumerationProvider
Retrieves an enumeration.
getEnumeration(Class<T>, String, boolean) - Method in class ome.formats.enums.IQueryEnumProvider
 
getEnumeration_async(AMD_IPixels_getEnumeration, String, String, Current) - Method in class ome.services.blitz.impl.PixelsI
 
getEnumeration_async(AMD_ITypes_getEnumeration, String, String, Current) - Method in class ome.services.blitz.impl.TypesI
 
getEnumerationProvider() - Method in class ome.formats.OMEROMetadataStoreClient
Retrieves the active enumeration provider.
getEnumerations(Class<T>) - Method in interface ome.formats.enums.EnumerationProvider
Retrieves all enumerations of a specific type.
getEnumerations(Class<T>) - Method in class ome.formats.enums.IQueryEnumProvider
 
getEnumerationsWithEntries_async(AMD_ITypes_getEnumerationsWithEntries, Current) - Method in class ome.services.blitz.impl.TypesI
 
getEnumerationTypes_async(AMD_ITypes_getEnumerationTypes, Current) - Method in class ome.services.blitz.impl.TypesI
 
getError() - Method in class ome.formats.importer.util.ErrorContainer
 
getError() - Method in class omero.gateway.model.SearchResultCollection
Get the error code
getEvent(Current) - Method in class ome.services.blitz.fire.SessionManagerI
 
getEventContext() - Method in class ome.services.blitz.impl.ServiceFactoryI
Doesn't take current into account
getEventContext(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
Takes current into account
getEventContext(Current) - Method in interface ome.services.blitz.repo.RepositoryDao
Look up information for the current session as specified in the ctx field of the current.
getEventContext(Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
 
getEventContext() - Method in class omero.cmd.Helper
Provides an EventContext instance without reloading the session, via LocalAdmin.getEventContextQuiet().
getEventContext() - Method in class omero.model.DetailsI
 
getEventContext_async(AMD_IAdmin_getEventContext, Current) - Method in class ome.services.blitz.impl.AdminI
 
getEventLogsByPeriod_async(AMD_ITimeline_getEventLogsByPeriod, RTime, RTime, Parameters, Current) - Method in class ome.services.blitz.impl.TimelineI
 
getEvents_async(AMD_IShare_getEvents, long, Experimenter, RTime, RTime, Current) - Method in class ome.services.blitz.impl.ShareI
 
getExcitationFilters() - Method in class omero.gateway.model.FilterSetData
Returns the collections of excitation filters if any.
getExcitationFilters() - Method in class omero.gateway.model.LightPathData
Returns the collections of excitation filters if any.
getExcitationWavelength(UnitsLength) - Method in class omero.gateway.model.ChannelData
Returns the excitation wavelength of the channel.
getExecutor() - Method in class omero.cmd.SessionI
 
getExperimenter() - Method in class omero.gateway.SecurityContext
Returns the id of the experimenter.
getExperimenter() - Method in class omero.sys.ParametersI
Returns the value of the experimenter parameter.
getExperimenter_async(AMD_IAdmin_getExperimenter, long, Current) - Method in class ome.services.blitz.impl.AdminI
 
getExperimenterData() - Method in class omero.gateway.SecurityContext
Returns the experimenter.
getExperimenterID() - Method in class ome.formats.OMEROMetadataStoreClient
 
getExperimenters() - Method in class omero.gateway.model.GroupData
Returns the experimenters contained in this group.
getExporterService(SecurityContext) - Method in class omero.gateway.Gateway
Returns the ExporterPrx service.
getExtendedMessage() - Method in exception omero.gateway.exception.RenderingServiceException
Prints the stack trace and returns it as a string.
getExtension() - Method in class omero.gateway.util.TIFFFilter
Returns the extension of the filter.
getExternalDescription() - Method in class omero.gateway.model.WellData
Returns the external description of the well.
getExternalIdentifier() - Method in class omero.gateway.model.PlateData
Returns the external identifier of the plate.
getExternalInfo(Current) - Method in class omero.model.DetailsI
 
getExtra() - Method in class ome.formats.importer.util.ErrorContainer
 
getFacility(Class<T>, Gateway) - Static method in class omero.gateway.facility.Facility
Get a reference to a certain Facility
getFacility(Class<T>) - Method in class omero.gateway.Gateway
Get a Facility to perform further operations with the server
getFactory(String, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
 
getFailedFiles() - Method in exception ome.formats.importer.transfers.CleanupFailure
 
getFailureClass() - Method in exception ome.formats.enums.EnumerationException
 
getFailureClass() - Method in exception ome.formats.model.ModelException
Returns the class that was used during a failed instantiation.
getFeedbackUrl() - Method in class ome.formats.importer.ImportConfig
 
getFilament(int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
getFile() - Method in class ome.formats.importer.ImportContainer
 
getFile() - Method in class ome.formats.importer.transfers.TransferState
Return the target file passed to the constructor.
getFile(long, Current, String) - Method in interface ome.services.blitz.repo.RepositoryDao
Get an FsFile object based on its ID.
getFile(long, Current, String) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
 
getFile(ServiceFactory) - Method in class ome.services.scripts.ScriptFinder
 
getFileBuffer(String) - Method in class ome.services.blitz.repo.CheckedPath
Get a FileBuffer corresponding to this instance.
getFileFormat() - Method in class ome.formats.importer.util.ErrorContainer
get the file format for import
getFileFormat() - Method in class omero.gateway.model.FileAnnotationData
Returns the format of the uploaded file.
getFileID() - Method in class omero.gateway.model.FileAnnotationData
Returns the id of the file.
getFileID() - Method in class omero.gateway.model.ROIResult
Returns the id of the file.
getFileId_async(AMD_RawFileStore_getFileId, Current) - Method in class ome.services.blitz.impl.RawFileStoreI
 
getFileKind() - Method in class omero.gateway.model.FileAnnotationData
Returns a user readable description of the file.
getFileName() - Method in class omero.gateway.model.FileAnnotationData
Returns the name of the file.
getFilePath(OriginalFile, Current) - Method in class ome.services.blitz.repo.AbstractRepositoryI
 
getFilePath(OriginalFile, Current) - Method in class ome.services.blitz.repo.InternalRepositoryI
 
getFilePath(OriginalFile, Current) - Method in class ome.services.blitz.repo.LegacyRepositoryI
TODO CACHING
getFilePath(OriginalFile, Current) - Method in class ome.services.blitz.repo.ScriptRepositoryI
 
getFilePath(OriginalFile, Current) - Method in class ome.services.blitz.repo.TemporaryRepositoryI
 
getFilePath() - Method in class omero.gateway.model.FileAnnotationData
Returns the absolute path to the file.
getFilePathRestrictions(String...) - Static method in enum ome.services.blitz.repo.path.FilePathRestrictionInstance
Get a set of rules by which local files may not be named on the file-system, formed by combining the rules of the given names with rules against control characters.
getFilePathRestrictions(FilePathRestrictionInstance...) - Static method in enum ome.services.blitz.repo.path.FilePathRestrictionInstance
Get a set of rules by which local files may not be named on the file-system, formed by combining the given rules identifiers with rules against control characters.
getFileRepo(OriginalFile) - Method in class ome.services.blitz.repo.AbstractRepositoryI
 
getFiles() - Method in class ome.formats.importer.util.ErrorContainer
 
getFileset() - Method in class ome.services.blitz.repo.ManagedImportProcessI
 
getFileset() - Method in interface ome.services.blitz.repo.ProcessContainer.Process
 
getFilesetId() - Method in class omero.gateway.model.ImageData
Returns the ID of the fileset to which this image belongs.
getFileSize() - Method in class omero.gateway.model.FileAnnotationData
Returns the size of the file.
getFileType() - Method in class ome.formats.importer.util.ErrorContainer
 
getFill() - Method in class omero.gateway.model.ShapeSettingsData
Returns the fill color.
getFillRule() - Method in class omero.gateway.model.ShapeSettingsData
Returns the fill rule.
getFilters() - Method in class omero.gateway.model.InstrumentData
Returns the collection of filters.
getFilterSet() - Method in class ome.formats.model.ChannelData
Returns the filter set for the logical channel of this channel data.
getFilterSet(int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
getFilterSet() - Method in class omero.gateway.model.ChannelAcquisitionData
Returns the filter set or null.
getFilterSet() - Method in class omero.gateway.model.OTFData
Returns the associated filter set.
getFilterSetEmissionFilter() - Method in class ome.formats.model.ChannelData
Returns the filter set's emission filter for the logical channel of this channel data.
getFilterSetExcitationFilter() - Method in class ome.formats.model.ChannelData
Returns the filter set's excitation filter for the logical channel of this channel data.
getFilterSets() - Method in class omero.gateway.model.InstrumentData
Returns the collection of filter sets.
getFilterWheel() - Method in class omero.gateway.model.FilterData
Returns the wheel.
getFirstName() - Method in class omero.gateway.model.ExperimenterData
Returns the first name of the experimenter.
getFluor() - Method in class omero.gateway.model.ChannelData
Returns the Fluorophore used.
getFlushCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
getFolderAsContainerName(File) - Static method in class omero.gateway.util.Utils
Returns the name as container if option is on.
getFolderPathString() - Method in class omero.gateway.model.FolderData
Returns the folder path as string
getFolderPathString(char) - Method in class omero.gateway.model.FolderData
Returns the folder path as string using a custom path separator
getFolders(SecurityContext) - Method in class omero.gateway.facility.BrowseFacility
Get all folders the logged in user has access to.
getFolders(SecurityContext, Collection<Long>) - Method in class omero.gateway.facility.BrowseFacility
Get the folders for the given folder ids.
getFolders(SecurityContext, long) - Method in class omero.gateway.facility.BrowseFacility
Get the folders which belong to the given user.
getFolders() - Method in class omero.gateway.model.ROIData
Get the folders this ROI is part of
getFolders() - Method in class omero.gateway.model.ROIResult
Get the available folders
getFont() - Method in class omero.gateway.model.ShapeSettingsData
Get the style of the font for Shape.
getFontFamily() - Method in class omero.gateway.model.ShapeSettingsData
Returns the stroke.
getFontSize(UnitsLength) - Method in class omero.gateway.model.ShapeSettingsData
Returns the stroke.
getFontStyle() - Method in class omero.gateway.model.ShapeSettingsData
Returns the font style.
getForceFileArchiveOn() - Method in class ome.formats.importer.ImportConfig
 
getForceFileArchiveOn() - Method in class ome.formats.importer.util.IniFileLoader
 
getFormat() - Method in class omero.gateway.model.ImageData
Returns the format of the image.
getForumUrl() - Method in class ome.formats.importer.ImportConfig
 
getForumUrl() - Method in class ome.formats.importer.util.IniFileLoader
 
getFreeSpaceInKilobytes_async(AMD_IRepositoryInfo_getFreeSpaceInKilobytes, Current) - Method in class ome.services.blitz.impl.RepositoryInfoI
 
getFsFileFromClientFile(File, int) - Method in class ome.services.blitz.repo.path.ClientFilePathTransformer
Given a client-local File, and a path component depth, returns the corresponding repository path.
getFsFileFromServerFile(File) - Method in class ome.services.blitz.repo.path.ServerFilePathTransformer
Given a server-local File, returns the corresponding repository path.
getFullFsPath() - Method in class ome.services.blitz.repo.CheckedPath
The full path of the entity to which this path corresponds.
getGain() - Method in class omero.gateway.model.DetectorData
Returns the gain of the detector.
getGlobalMax() - Method in class omero.gateway.model.ChannelData
Returns the global maximum of the channel i.e. the maximum of all maxima.
getGlobalMin() - Method in class omero.gateway.model.ChannelData
Returns the global minimum of the channel i.e. the minimum of all minima.
getGraphPathBean() - Method in class omero.cmd.graphs.GraphRequestFactory
 
getGraphType(Class<? extends DataObject>) - Static method in class omero.gateway.util.PojoMapper
Returns the name of the data type which has to used for Graph actions, see Requests
getGreen() - Method in class omero.gateway.model.WellData
Returns the green component of the color associated to the well, or -1.
getGridColumns() - Method in class omero.gateway.facility.TablesFacilityHelper
Get the grid columns; (TablesFacilityHelper.parseTableData(TableData) needs to be called first)
getGridQuery() - Method in interface ome.services.blitz.fire.Registry
Returns an active QueryPrx or null if none is available.
getGridQuery() - Method in class ome.services.blitz.fire.Registry.Impl
 
getGroup(Current) - Method in class ome.services.blitz.fire.SessionManagerI
 
getGroup() - Method in class ome.services.blitz.repo.ManagedImportProcessI
 
getGroup() - Method in interface ome.services.blitz.repo.ProcessContainer.Process
 
getGroup(Current) - Method in class omero.model.DetailsI
 
getGroup() - Method in class omero.sys.ParametersI
Returns the value of the group parameter.
getGroup_async(AMD_IAdmin_getGroup, long, Current) - Method in class ome.services.blitz.impl.AdminI
 
getGroupID() - Method in class omero.gateway.LoginCredentials
Returns the OMERO group identifier.
getGroupId() - Method in class omero.gateway.model.DataObject
Returns the id of the group.
getGroupId() - Method in class omero.gateway.model.ExperimenterData
Overridden to return the id of the default group.
getGroupId() - Method in class omero.gateway.model.GroupData
Overridden to return the id of the object.
getGroupId() - Method in class omero.gateway.model.SearchParameters
 
getGroupId() - Method in class omero.gateway.model.SearchResult
Get the group id of the object
getGroupID() - Method in class omero.gateway.SecurityContext
Returns the identifier of the group.
getGroups() - Method in class omero.gateway.model.ExperimenterData
Returns the groups the experimenter is a member of.
getHandle(Current) - Method in class ome.services.blitz.repo.ManagedImportProcessI
 
getHandler(Class<? extends IObject>) - Method in class ome.formats.enums.handler.EnumHandlerFactory
Returns an enumeration handler for a specific enumeration type.
getHandler(Class<? extends IObject>) - Method in class ome.formats.model.handler.ModelObjectHandlerFactory
Returns an enumeration handler for a specific enumeration type.
getHeaders() - Method in class omero.gateway.model.TableResult
Returns the name of the columns.
getHeadersDescription() - Method in class omero.gateway.model.TableResult
Returns the name of the columns.
getHeight() - Method in class omero.gateway.model.MaskData
Returns the height of the mask.
getHeight() - Method in class omero.gateway.model.RectangleData
Returns the height untransformed rectangle.
getHierarchy(SecurityContext, Class, long) - Method in class omero.gateway.facility.BrowseFacility
Retrieves hierarchy trees rooted by a given node.
getHierarchy(SecurityContext, Class, List<Long>, Parameters) - Method in class omero.gateway.facility.BrowseFacility
Retrieves hierarchy trees rooted by a given node i.e. the requested node as root and all of its descendants.
getHistogram(SecurityContext, PixelsData, int[], int, int) - Method in class omero.gateway.facility.RawDataFacility
Get the histogram data for the given image, using default 256 bins and the channels global min/max for the histogram range.
getHistogram(SecurityContext, PixelsData, int[], int, boolean, PlaneDef) - Method in class omero.gateway.facility.RawDataFacility
Get the histogram data for the given image.
getHistogram(int[], int, boolean, PlaneDef) - Method in class omero.gateway.rnd.DataSink
Get the histogram data for the given image.
getHistogram_async(AMD_RawPixelsStore_getHistogram, int[], int, boolean, PlaneDef, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
getHistogram_async(AMD_RawPixelsStore_getHistogram, int[], int, boolean, PlaneDef, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
getHolder() - Method in class ome.services.blitz.util.UnregisterServantMessage
 
getHomeUrl() - Method in class ome.formats.importer.ImportConfig
 
getHomeUrl() - Method in class ome.formats.importer.util.IniFileLoader
 
getHostname() - Method in class omero.gateway.ServerInformation
Return the hostname.
getHumidity() - Method in class omero.gateway.model.ImageAcquisitionData
Returns the humidity level, this is a value in the interval [0, 1].
getHypercube_async(AMD_RawPixelsStore_getHypercube, List<Integer>, List<Integer>, List<Integer>, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
getHypercube_async(AMD_RawPixelsStore_getHypercube, List<Integer>, List<Integer>, List<Integer>, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
getId() - Method in class ome.services.blitz.repo.CheckedPath
 
getId() - Method in class omero.gateway.model.DataObject
Returns the database id of the IObject or -1 if null
getIdentity() - Method in class ome.services.blitz.util.FindServiceFactoryMessage
 
getIdentity(String) - Method in class omero.cmd.SessionI
 
getIdentity(String) - Method in class omero.util.ServantHolder
Constructs an Identity from the current session and from the given String which for stateful services are defined by UUIDs.
getIgnoreTypePolicy(GraphPolicy, Collection<Class<? extends IObject>>) - Static method in class omero.cmd.graphs.IgnoreTypePolicy
Deprecated.
Adjust an existing graph traversal policy so that objects of certain types may be ignored.
getIllumination() - Method in class omero.gateway.model.ChannelAcquisitionData
Returns the illumination.
getIllumination() - Method in class omero.gateway.model.ChannelData
Returns the illumination.
getIlluminationAsEnum() - Method in class omero.gateway.model.ChannelData
Returns the illumination enumeration value.
getImage(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getImage(SecurityContext, long) - Method in class omero.gateway.facility.BrowseFacility
Loads a image
getImage(SecurityContext, long, ParametersI) - Method in class omero.gateway.facility.BrowseFacility
Loads a image
getImage() - Method in class omero.gateway.model.PixelsData
Returns the image linked to this pixels' set.
getImage() - Method in class omero.gateway.model.ROIData
Returns the image for the ROI.
getImage() - Method in class omero.gateway.model.WellSampleData
Returns the image related to that sample if any.
getImageAcquisitionData(SecurityContext, long) - Method in class omero.gateway.facility.MetadataFacility
Loads the ImageAcquisitionData for a specific image
getImageAcquisitionDate(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getImageAnnotationRef(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getImageAnnotationRefCount(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getImageCount() - Method in class ome.services.blitz.impl.OmeroMetadata
 
getImageDescription(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getImageID(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getImageIds() - Method in class omero.gateway.model.FilesetData
Returns the collection of images related to the file set.
getImageName(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getImageNames() - Method in class ome.formats.ImageNameMetadataStore
Retrieves the current map of Image names held.
getImageReader() - Method in class ome.formats.importer.OMEROWrapper
Return the base image reader
getImageROIRef(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getImageROIRefCount(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getImages(SecurityContext, Collection<Long>) - Method in class omero.gateway.facility.BrowseFacility
Loads the images with the given ids
getImages(SecurityContext, Collection<Long>, ParametersI) - Method in class omero.gateway.facility.BrowseFacility
Loads the images with the given ids
getImages(SecurityContext, long, Collection<Long>) - Method in class omero.gateway.facility.BrowseFacility
Loads the images for a particular user
getImages() - Method in class omero.gateway.model.DatasetData
Returns a set of images contained in the dataset.
getImages_async(AMD_IContainer_getImages, String, List<Long>, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI
 
getImagesByOptions_async(AMD_IContainer_getImagesByOptions, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI
 
getImagesBySplitFilesets_async(AMD_IContainer_getImagesBySplitFilesets, Map<String, List<Long>>, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI
 
getImagesForDatasets(SecurityContext, Collection<Long>) - Method in class omero.gateway.facility.BrowseFacility
Load all images belonging to particular datasets
getImagesForProjects(SecurityContext, Collection<Long>) - Method in class omero.gateway.facility.BrowseFacility
Load all images belonging to particular projects
getImagingEnvironment(int) - Method in class ome.formats.OMEROMetadataStoreClient
 
getImagingEnvironmentId() - Method in class omero.gateway.model.ImageAcquisitionData
Returns the id of the StageLabel or -1 if not already linked to the image.
getImmersion() - Method in class omero.gateway.model.ObjectiveData
Returns the immersion value of the objective.
getImplicitContext() - Method in class omero.client
Returns the ImplicitContext which defines what properties will be sent on every method invocation.
getImportResponse() - Method in class ome.formats.importer.ImportLibrary.ImportCallback
Assumes that users have already waited on proper completion, i.e. that ImportLibrary.ImportCallback.onFinished(Response, Status, Current) has been called.
getImportSettings(Current) - Method in class ome.services.blitz.repo.ManagedImportProcessI
 
getImportStore(SecurityContext) - Method in class omero.gateway.Gateway
Creates or recycles the import store.
getImportStore(SecurityContext, String) - Method in class omero.gateway.Gateway
Creates or recycles the import store.
getIndex() - Method in class ome.formats.importer.util.ErrorContainer
get the index for this error container
getIndex() - Method in exception omero.gateway.exception.RenderingServiceException
Returns the index.
getIndex() - Method in class omero.gateway.model.ChannelData
Returns the channel's index.
getIndex() - Method in class omero.gateway.model.ImageData
Returns the index of the image within the multi-images file.
getIndex() - Method in class omero.gateway.model.TableDataColumn
Get the index
getIniVersionNumber() - Method in class ome.formats.importer.ImportConfig
 
getInput(String) - Method in class omero.client
Retrieves an item from the "input" shared (session) memory.
getInput_async(AMD_ISession_getInput, String, String, Current) - Method in class ome.services.blitz.impl.SessionI
 
getInputKeys() - Method in class omero.client
Returns a list of keys for all items in the "input" shared (session) memory
getInputKeys_async(AMD_ISession_getInputKeys, String, Current) - Method in class ome.services.blitz.impl.SessionI
 
getInputs_async(AMD_ISession_getInputs, String, Current) - Method in class ome.services.blitz.impl.SessionI
 
getInserted() - Method in class omero.gateway.model.ImageData
Returns the insertion time of the image.
getInstance(Class<T>) - Method in class ome.formats.model.BlitzInstanceProvider
 
getInstance(Class<T>) - Method in interface ome.formats.model.InstanceProvider
Retrieves an instance.
getInstanceProvider() - Method in class ome.formats.OMEROMetadataStoreClient
Retrieves the active instance provider.
getInstitution() - Method in class omero.gateway.model.ExperimenterData
Returns the institution where the experimenter works.
getInstrumentId() - Method in class omero.gateway.model.ImageData
Returns the id of the instrument if any.
getInternalServiceFactory(String, Long, int, int, String) - Method in interface ome.services.blitz.fire.Registry
Try to return a ServiceFactory from the grid.
getInternalServiceFactory(String, Long, int, int, String) - Method in class ome.services.blitz.fire.Registry.Impl
 
getIObjectContainer(Class<? extends IObject>, LinkedHashMap<Index, Integer>) - Method in interface ome.formats.model.IObjectContainerStore
Retrieves an IObject container for a given class and location within the OME-XML data model.
getIObjectContainer(Class<? extends IObject>, LinkedHashMap<Index, Integer>) - Method in class ome.formats.OMEROMetadataStoreClient
 
getIObjectContainers(Class<? extends IObject>) - Method in interface ome.formats.model.IObjectContainerStore
Retrieves all IObject containers of a given class.
getIObjectContainers(Class<? extends IObject>) - Method in class ome.formats.OMEROMetadataStoreClient
 
getIP(Current) - Method in class ome.services.blitz.fire.SessionManagerI
 
getIQuery() - Method in class ome.formats.OMEROMetadataStoreClient
 
getIsSPW() - Method in class ome.formats.importer.ImportContainer
Return true if this import container contains a Screen/Plate/Well image group.
getIterator() - Method in class omero.gateway.model.ROIData
Returns the iterator of the collection of the map.
getJavaClasspath() - Method in class ome.formats.importer.util.ErrorContainer
 
getJavaVersion() - Method in class ome.formats.importer.util.ErrorContainer
 
getJob(Current) - Method in class ome.services.blitz.impl.ScriptProcessI
 
getJob(Current) - Method in class omero.grid.InteractiveProcessorI
 
getJob_async(AMD_JobHandle_getJob, Current) - Method in class ome.services.blitz.impl.JobHandleI
 
getKeepAlive() - Method in class ome.formats.OMEROMetadataStoreClient
Returns clientKeepAlive created in store
getKind() - Method in class omero.gateway.model.LightSourceData
Returns the kind of light source.
getLabel() - Method in class omero.gateway.model.PlateAcquisitionData
Returns the label associated to the plate acquisition.
getLabelAnnotationRef(int, int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getLabelFillColor(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getLabelFillRule(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getLabelFontFamily(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getLabelFontSize(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getLabelFontStyle(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getLabelID(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getLabelLocked(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getLabelName() - Method in class omero.gateway.model.ImageAcquisitionData
Returns the name of the stage label.
getLabelStrokeColor(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getLabelStrokeDashArray(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getLabelStrokeWidth(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getLabelText(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getLabelTheC(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getLabelTheT(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getLabelTheZ(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getLabelTransform(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getLabelX(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getLabelY(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getLaser(int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
getLaserFrequencyMultiplication() - Method in class omero.gateway.model.LightSourceData
Returns the frequency multiplication of the laser.
getLaserMedium() - Method in class omero.gateway.model.LightSourceData
Returns the laser's medium.
getLaserPockelCell() - Method in class omero.gateway.model.LightSourceData
Returns the pockel cell flag of the laser.
getLaserPulse() - Method in class omero.gateway.model.LightSourceData
Returns the pulse of the laser.
getLaserPump() - Method in class omero.gateway.model.LightSourceData
Returns the pump.
getLaserRepetitionRate(UnitsFrequency) - Method in class omero.gateway.model.LightSourceData
Returns the repetition rate (Hz) if the laser is repetitive.
getLaserTuneable() - Method in class omero.gateway.model.LightSourceData
Returns the value of the tuneable field or null if no value set.
getLaserWavelength(UnitsLength) - Method in class omero.gateway.model.LightSourceData
Returns the laser's wavelength.
getLastModified() - Method in class omero.gateway.model.AnnotationData
Returns the time when the annotation was last modified.
getLastName() - Method in class omero.gateway.model.ExperimenterData
Returns the last name of the experimenter.
getLdapService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
getLeaderOfGroupIds_async(AMD_IAdmin_getLeaderOfGroupIds, Experimenter, Current) - Method in class ome.services.blitz.impl.AdminI
 
getLeaders() - Method in class omero.gateway.model.GroupData
Returns the experimenters contained in this group.
getLeaves() - Method in class omero.sys.ParametersI
 
getLegalTargets(Class<R>) - Method in class omero.cmd.graphs.GraphRequestFactory
Get the legal target object classes for the given request.
getLength() - Method in class ome.formats.importer.transfers.TransferState
Return the length of the target file.
getLensNA() - Method in class omero.gateway.model.ObjectiveData
Returns the objective's LensNA.
getLightEmittingDiode(int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
getLightPath() - Method in class omero.gateway.model.ChannelAcquisitionData
Returns the light path or null.
getLightPathEmissionFilters() - Method in class ome.formats.model.ChannelData
Returns the collection of emission filters in the light path.
getLightPathExcitationFilters() - Method in class ome.formats.model.ChannelData
Returns the collection of excitation filters in the light path.
getLightSettingsAttenuation() - Method in class omero.gateway.model.ChannelAcquisitionData
Returns the attenuation of the light source, percent value between 0 and 1.
getLightSettingsWavelength(UnitsLength) - Method in class omero.gateway.model.ChannelAcquisitionData
Returns the wavelength of the light source.
getLightSource() - Method in class ome.formats.model.ChannelData
Returns the light source for the light source settings of this channel data.
getLightSource() - Method in class omero.gateway.model.ChannelAcquisitionData
Returns the source of light.
getLightSourceModel() - Method in class omero.gateway.model.LightSourceData
Returns the model of the light source.
getLightSources() - Method in class omero.gateway.model.InstrumentData
Returns the collection of light sources.
getLightSourceSettings() - Method in class ome.formats.model.ChannelData
Returns the light source settings for the logical channel of this channel data.
getLimit() - Method in class omero.sys.ParametersI
Returns the value of the limit parameter.
getLine(int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
getLine() - Method in class ome.services.blitz.repo.FileMaker
 
getLineAnnotationRef(int, int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getLineFillColor(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getLineFillRule(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getLineFontFamily(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getLineFontSize(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getLineFontStyle(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getLineID(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getLineLocked(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getLineMarkerEnd(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getLineMarkerStart(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getLineStrokeColor(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getLineStrokeDashArray(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getLineStrokeWidth(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getLineText(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getLineTheC(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getLineTheT(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getLineTheZ(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getLineTransform(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getLineX1(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getLineX2(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getLineY1(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getLineY2(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getListAnnotation(int) - Method in class ome.formats.OMEROMetadataStoreClient
 
getLocalLocation(OriginalFile, OriginalFile) - Method in class ome.formats.importer.transfers.AbstractExecFileTransfer
Build a path of the form "root.path/root.name/file.path/file.name".
getLogFile() - Method in class ome.formats.importer.ImportConfig
 
getLogFile() - Method in class ome.formats.importer.util.IniFileLoader
 
getLogFile() - Method in class ome.services.blitz.repo.ManagedImportLocationI
Return the server-side CheckedPath instance which can be used for writing a log file for a fileset.
getLogFile() - Method in interface omero.log.Logger
Returns the log file.
getLogFile() - Method in class omero.log.NullLogger
 
getLogFile() - Method in class omero.log.SimpleLogger
 
getLoggedInUser() - Method in class omero.gateway.Gateway
Get the currently logged in user
getLogger() - Method in class omero.gateway.Gateway
Provides access to the Logger
getLogicalChannel() - Method in class ome.formats.model.ChannelData
Returns the logical channel for this channel data.
getLongAnnotation(int) - Method in class ome.formats.OMEROMetadataStoreClient
 
getLongAnnotationCount() - Method in class ome.services.blitz.impl.OmeroMetadata
 
getLongAnnotationDescription(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getLongAnnotationID(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getLongAnnotationNamespace(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getLongAnnotationValue(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getLookupTables(SecurityContext) - Method in class omero.gateway.facility.BrowseFacility
Get the available lookup tables
getLotNumber() - Method in class omero.gateway.model.DetectorData
Returns the lot number of the detector.
getLotNumber() - Method in class omero.gateway.model.DichroicData
Returns the lot number.
getLotNumber() - Method in class omero.gateway.model.FilterData
Returns the lot number.
getLotNumber() - Method in class omero.gateway.model.FilterSetData
Returns the lot number.
getLotNumber() - Method in class omero.gateway.model.LightSourceData
Returns the lot of number the light source.
getLotNumber() - Method in class omero.gateway.model.ObjectiveData
Returns the lot number of the detector.
getManagerList(boolean) - Method in class ome.services.blitz.fire.Ring
 
getManagerList(boolean) - Method in interface ome.services.blitz.redirect.Redirector.Context
Return all known managers in the current cluster context, possibly filtering out the inactive ones.
getManufacturer() - Method in class omero.gateway.model.DetectorData
Returns the manufacturer of the detector.
getManufacturer() - Method in class omero.gateway.model.DichroicData
Returns the manufacturer.
getManufacturer() - Method in class omero.gateway.model.FilterData
Returns the manufacturer.
getManufacturer() - Method in class omero.gateway.model.FilterSetData
Returns the manufacturer.
getManufacturer() - Method in class omero.gateway.model.LightSourceData
Returns the manufacturer of the light source.
getManufacturer() - Method in class omero.gateway.model.ObjectiveData
Returns the manufacturer of the detector.
getMarkerEnd() - Method in class omero.gateway.model.ShapeSettingsData
Returns the marker end.
getMarkerStart() - Method in class omero.gateway.model.ShapeSettingsData
Returns the marker start.
getMask(int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
getMask() - Method in class omero.gateway.model.MaskData
Returns the mask as a byte array.
getMaskAnnotationRef(int, int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getMaskAsBinaryArray() - Method in class omero.gateway.model.MaskData
Returns the mask image.
getMaskAsBufferedImage() - Method in class omero.gateway.model.MaskData
Returns the mask image.
getMaskFillColor(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getMaskFillRule(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getMaskFontFamily(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getMaskFontSize(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getMaskFontStyle(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getMaskID(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getMaskLocked(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getMaskPoints() - Method in class omero.gateway.model.PolygonData
Returns the points in the polygon.
getMaskStrokeColor(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getMaskStrokeDashArray(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getMaskStrokeWidth(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getMaskTheC(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getMaskTheT(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getMaskTheZ(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getMaskTransform(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getMaximumFieldCount() - Method in class omero.gateway.model.PlateAcquisitionData
Returns the maximum number of fields in any well.
getMeasuredRois_async(AMD_IRoi_getMeasuredRois, long, long, RoiOptions, Current) - Method in class ome.services.blitz.impl.RoiI
 
getMeasuredRoisMap_async(AMD_IRoi_getMeasuredRoisMap, long, List<Long>, RoiOptions, Current) - Method in class ome.services.blitz.impl.RoiI
 
getMedium() - Method in class omero.gateway.model.ImageAcquisitionData
Returns the medium of the objective.
getMediumAsEnum() - Method in class omero.gateway.model.ImageAcquisitionData
Returns the medium enumeration value.
getMemberCount_async(AMD_IShare_getMemberCount, List<Long>, Current) - Method in class ome.services.blitz.impl.ShareI
 
getMemberOfGroupIds_async(AMD_IAdmin_getMemberOfGroupIds, Experimenter, Current) - Method in class ome.services.blitz.impl.AdminI
 
getMemberShares_async(AMD_IShare_getMemberShares, boolean, Current) - Method in class ome.services.blitz.impl.ShareI
 
getMemberSharesFor_async(AMD_IShare_getMemberSharesFor, Experimenter, boolean, Current) - Method in class ome.services.blitz.impl.ShareI
 
getMembersOnly() - Method in class omero.gateway.model.GroupData
Returns the list of experimenters that are not owners of the group.
getMetadataOptions() - Method in class ome.formats.importer.OMEROWrapper
 
getMetadataService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
getMetadataService(SecurityContext) - Method in class omero.gateway.Gateway
Returns the IMetadataPrx service.
getMethod(String) - Method in class ome.services.blitz.util.IceMethodInvoker
For testing the cached method.
getMicrobeamManipulation(int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
getMicrobeamManipulationLightSourceSettings(int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
getMicroscopeLotNumber() - Method in class omero.gateway.model.InstrumentData
Returns the lot number of the microscope.
getMicroscopeManufacturer() - Method in class omero.gateway.model.InstrumentData
Returns the model of the microscope.
getMicroscopeModel() - Method in class omero.gateway.model.InstrumentData
Returns the model of the microscope.
getMicroscopeSerialNumber() - Method in class omero.gateway.model.InstrumentData
Returns the serial number of the microscope.
getMicroscopeType() - Method in class omero.gateway.model.InstrumentData
Returns the type of microscope.
getMiddleName() - Method in class omero.gateway.model.ExperimenterData
Returns the middle name of the experimenter.
getMimetype() - Method in class ome.services.blitz.repo.CheckedPath
Get the mimetype for a file.
getMIMEType() - Method in class omero.gateway.util.TIFFFilter
Returns the MIME type.
getMinimumDepth(Collection<File>) - Method in class ome.services.blitz.repo.path.ClientFilePathTransformer
Get the smallest path component depth that allows the given set of Files to be disambiguated.
getMode() - Method in class omero.gateway.model.ChannelAcquisitionData
Returns the mode.
getMode() - Method in class omero.gateway.model.ChannelData
Returns the mode.
getModeAsEnum() - Method in class omero.gateway.model.ChannelData
Returns the acquisition enumeration value.
getModel() - Method in class omero.gateway.model.DetectorData
Returns the manufacturer of the detector.
getModel() - Method in class omero.gateway.model.DichroicData
Returns the model.
getModel() - Method in class omero.gateway.model.FilterData
Returns the model.
getModel() - Method in class omero.gateway.model.FilterSetData
Returns the model.
getModel() - Method in class omero.gateway.model.ObjectiveData
Returns the model of the objective.
getModel_async(AMD_RenderingEngine_getModel, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
getModelProcessors() - Method in class ome.formats.OMEROMetadataStoreClient
Retrieves the current list of model processors the metadata store is using.
getModelType(String) - Static method in class omero.gateway.util.PojoMapper
Converts the specified POJO into the corresponding model class, see PojoMapper.getModelType(Class)
getModelType(Class<? extends DataObject>) - Static method in class omero.gateway.util.PojoMapper
Converts the specified POJO into the corresponding model class.
getMostRecentAnnotationLinks_async(AMD_ITimeline_getMostRecentAnnotationLinks, List<String>, List<String>, List<String>, Parameters, Current) - Method in class ome.services.blitz.impl.TimelineI
 
getMostRecentObjects_async(AMD_ITimeline_getMostRecentObjects, List<String>, Parameters, boolean, Current) - Method in class ome.services.blitz.impl.TimelineI
 
getMostRecentShareCommentLinks_async(AMD_ITimeline_getMostRecentShareCommentLinks, Parameters, Current) - Method in class ome.services.blitz.impl.TimelineI
 
getMyOpenAgentSessions_async(AMD_ISession_getMyOpenAgentSessions, String, Current) - Method in class ome.services.blitz.impl.SessionI
 
getMyOpenClientSessions_async(AMD_ISession_getMyOpenClientSessions, Current) - Method in class ome.services.blitz.impl.SessionI
 
getMyOpenSessions_async(AMD_ISession_getMyOpenSessions, Current) - Method in class ome.services.blitz.impl.SessionI
 
getMyUserPhotos_async(AMD_IAdmin_getMyUserPhotos, Current) - Method in class ome.services.blitz.impl.AdminI
 
getName() - Method in class ome.services.blitz.repo.CheckedPath
Get the last component of this path, the entity to which the path corresponds.
getName() - Method in class ome.services.roi.PopulateRoiJob
 
getName() - Method in class ome.services.scripts.ScriptFinder
Subclasses should override to return the name of the file under scripts/ which should be uploaded.
getName() - Method in class omero.gateway.model.ChannelData
Returns the name of the channel.
getName() - Method in class omero.gateway.model.DatasetData
Returns the name of the dataset.
getName() - Method in class omero.gateway.model.FileData
Returns the name of the file.
getName() - Method in class omero.gateway.model.FolderData
Get the name of the Folder
getName() - Method in class omero.gateway.model.GroupData
Returns the name of the group.
getName() - Method in class omero.gateway.model.ImageData
Returns the name of the image.
getName() - Method in class omero.gateway.model.PlateAcquisitionData
Returns the name of the plate acquisition.
getName() - Method in class omero.gateway.model.PlateData
Returns the name of the plate.
getName() - Method in class omero.gateway.model.ProjectData
Returns the name of the project.
getName() - Method in class omero.gateway.model.ScreenData
Returns the name of the screen.
getName() - Method in class omero.gateway.model.TableDataColumn
Get the header
getNameSpace() - Method in class omero.gateway.model.AnnotationData
Retrieves the nameSpace of the underlying Annotation instance.
getNDFilter() - Method in class omero.gateway.model.ChannelData
Returns the ND filter wavelength of the channel.
getNodeUuid(Current) - Method in class ome.services.blitz.fire.Ring
 
getNominalMagnification() - Method in class omero.gateway.model.ObjectiveData
Returns the objective's nominal magnification factor.
getNoStatsInfo() - Method in class ome.formats.importer.ImportContainer
Retrieves whether or not we disabling StatsInfo population.
getNumberOfRows() - Method in class omero.gateway.model.TableData
 
getNumOfDirectories() - Method in class ome.formats.importer.ImportConfig
 
getNumOfDirectories() - Method in class ome.formats.importer.util.IniFileLoader
 
getObject() - Method in class omero.gateway.model.SearchResult
Get the found object
getObjectAdapter() - Method in class ome.services.blitz.repo.AbstractRepositoryI
 
getObjectAdapter() - Method in class ome.services.blitz.repo.InternalRepositoryConfig
 
getObjectId() - Method in class ome.formats.importer.targets.ModelImportTarget
 
getObjectId() - Method in class omero.gateway.model.SearchResult
Get the Id of the found object
getObjective(int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
getObjective() - Method in class omero.gateway.model.ImageAcquisitionData
Returns the objective used to capture the image.
getObjective() - Method in class omero.gateway.model.OTFData
Returns the associated objective.
getObjectives() - Method in class omero.gateway.model.InstrumentData
Returns the collection of objectives.
getObjectiveSettings(int) - Method in class ome.formats.OMEROMetadataStoreClient
 
getObjectiveSettingsId() - Method in class omero.gateway.model.ImageAcquisitionData
Returns the id of the Objective settings or -1 if not already linked to the image.
getObjectType() - Method in class ome.formats.importer.targets.ModelImportTarget
 
getOffset() - Method in class omero.gateway.model.DetectorData
Returns the offset of the detector.
getOffset() - Method in class omero.gateway.model.TableData
Get the row offset (if this TableData represents only a subset of the original table)
getOffset() - Method in class omero.sys.ParametersI
Returns the value of the offset parameter.
getOmeroVersion() - Method in class ome.formats.importer.ImportConfig
 
getOptimisticFailureCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
getOrCreateParams(long, Current) - Method in class omero.grid.ParamsHelper
Get the script params for the file.
getOriginalEnumerations_async(AMD_ITypes_getOriginalEnumerations, Current) - Method in class ome.services.blitz.impl.TypesI
 
getOriginalFile() - Method in class ome.formats.importer.transfers.TransferState
Find original file as defined by the ID in the RawFileStorePrx regardless of group.
getOriginalFile(long, Current) - Method in interface ome.services.blitz.repo.RepositoryDao
Gets the original file instance for a given file ID.
getOriginalFile(long, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
 
getOriginalFileId() - Method in class omero.gateway.model.TableData
Get the original file id
getOriginalFiles(String, CheckedPath, Current) - Method in interface ome.services.blitz.repo.RepositoryDao
Return a non-null, possibly empty list of OriginalFile elements which are accessible to the given user at the given path.
getOriginalFiles(String, CheckedPath, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
 
getOriginalFiles(ServiceFactory, SqlAction, String, CheckedPath) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
 
getOriginalFileWithHasher(long, Current) - Method in interface ome.services.blitz.repo.RepositoryDao
Retrieve the original file of the given ID.
getOriginalFileWithHasher(long, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
 
getOriginalMimetype() - Method in class omero.gateway.model.FileAnnotationData
Returns the format of the original file.
getOrphan() - Method in class omero.sys.ParametersI
 
getOrphanedImages(SecurityContext, long) - Method in class omero.gateway.facility.BrowseFacility
Get orphaned images for a certain user
getOSArch() - Method in class ome.formats.importer.util.ErrorContainer
 
getOSName() - Method in class ome.formats.importer.util.ErrorContainer
 
getOSVersion() - Method in class ome.formats.importer.util.ErrorContainer
 
getOTF() - Method in class omero.gateway.model.ChannelAcquisitionData
Returns the OTF used for that channel.
getOTF() - Method in class omero.gateway.model.InstrumentData
Returns the collection of OTFs.
getOutput(String) - Method in class omero.client
Retrieves an item from the "output" shared (session) memory.
getOutput_async(AMD_ISession_getOutput, String, String, Current) - Method in class ome.services.blitz.impl.SessionI
 
getOutputKeys() - Method in class omero.client
Returns a list of keys for all items in the "output" shared (session) memory
getOutputKeys_async(AMD_ISession_getOutputKeys, String, Current) - Method in class ome.services.blitz.impl.SessionI
 
getOutputs_async(AMD_ISession_getOutputs, String, Current) - Method in class ome.services.blitz.impl.SessionI
 
getOwner() - Method in class omero.gateway.model.DataObject
Returns the owner of the object.
getOwner(Current) - Method in class omero.model.DetailsI
 
getOwnShares_async(AMD_IShare_getOwnShares, boolean, Current) - Method in class ome.services.blitz.impl.ShareI
 
getParams(Long, String, Current) - Method in class ome.services.blitz.util.ParamsCache
Lookup a cached JobParams instance for the given key.
getParams_async(AMD_IScript_getParams, long, Current) - Method in class ome.services.blitz.impl.ScriptI
Get the Parameters of the script.
getParentFilePath() - Method in class omero.gateway.model.ImageData
Returns the path to the file hosting the image.
getParentFolder() - Method in class omero.gateway.model.FolderData
Get the the parent folder
getParentFromLink(IObject) - Static method in class omero.gateway.util.ModelMapper
Returns the child from the passed link.
getPassword() - Method in class omero.gateway.UserCredentials
Returns the password.
getPastConnections_async(AMD_IShare_getPastConnections, long, Current) - Method in class ome.services.blitz.impl.ShareI
 
getPath() - Method in class omero.gateway.model.FileData
Returns the (relative) path of the file.
getPath() - Method in class omero.gateway.model.OTFData
Returns the path.
getPathFor(long) - Method in class ome.services.blitz.repo.path.MakeNextDirectory
Get the subdirectories to create for the given index, the first directories to be created corresponding to index == 0.
getPathFrom(FsFile) - Method in class ome.services.blitz.repo.path.FsFile
Find the relative path of this path from a given parent.
getPaths() - Method in class ome.formats.importer.ImportCandidates
 
getPathSanitizer() - Method in class ome.services.blitz.repo.path.ServerFilePathTransformer
Get the string transformer that is used to make file-path components safe across platforms.
getPathToFile() - Method in class omero.gateway.model.ImageData
Returns the path to the file.
getPerm1(Current) - Method in class omero.model.PermissionsI
 
getPermissions() - Method in class omero.gateway.model.DataObject
Returns the permission of the object.
getPermissions(Current) - Method in class omero.model.DetailsI
 
getPermissionsLevel() - Method in class omero.gateway.model.PermissionData
Returns the permissions level.
getPinholeSize(UnitsLength) - Method in class omero.gateway.model.ChannelData
Returns the pin hole size of the channel.
getPixels() - Method in class ome.formats.OMEROImportFixture
Deprecated.
Accessor for the created pixels.
getPixels() - Method in class omero.util.RPSTileLoop
After saving the binary data, the update event of the Pixels instance will be updated and therefore need to be reloaded.
getPixels_async(AMD_RenderingEngine_getPixels, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
getPixelsBinDataBigEndian(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPixelsDimensionOrder(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPixelsID(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPixelsId_async(AMD_RawPixelsStore_getPixelsId, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
getPixelsId_async(AMD_RawPixelsStore_getPixelsId, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
getPixelSizeX(UnitsLength) - Method in class omero.gateway.model.PixelsData
Returns the dimension of a pixel along the X-axis.
getPixelSizeY(UnitsLength) - Method in class omero.gateway.model.PixelsData
Returns the dimension of a pixel along the Y-axis.
getPixelSizeZ(UnitsLength) - Method in class omero.gateway.model.PixelsData
Returns the dimension of a pixel along the Z-axis
getPixelsPath_async(AMD_RawPixelsStore_getPixelsPath, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
getPixelsPath_async(AMD_RawPixelsStore_getPixelsPath, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
getPixelsPhysicalSizeX(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPixelsPhysicalSizeY(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPixelsPhysicalSizeZ(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPixelsService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
getPixelsService(SecurityContext) - Method in class omero.gateway.Gateway
Returns the IPixelsPrx service.
getPixelsSizeC(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPixelsSizeT(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPixelsSizeX(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPixelsSizeY(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPixelsSizeZ(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPixelsStore(SecurityContext) - Method in class omero.gateway.Gateway
Returns the RawPixelsStorePrx service.
getPixelsTimeIncrement(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPixelsType(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPixelsType() - Method in class omero.gateway.model.OTFData
Returns the pixels type.
getPixelsTypeLowerBound_async(AMD_RenderingEngine_getPixelsTypeLowerBound, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
getPixelsTypeUpperBound_async(AMD_RenderingEngine_getPixelsTypeUpperBound, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
getPixelType() - Method in class omero.gateway.model.PixelsData
Returns the pixels type.
getPixelValue(int, int) - Method in class omero.gateway.rnd.Plane2D
Returns the pixels value at the point specified by the x-coordinate and y-coordinate.
getPixelValues() - Method in class omero.gateway.rnd.Plane2D
Returns the pixels values
getPlane(PixelBuffer, int, int, int) - Method in class ome.services.roi.PixelData
Returns the PixelData for plane given its z, c and t as well as a PixelBuffer
getPlane(SecurityContext, PixelsData, int, int, int) - Method in class omero.gateway.facility.RawDataFacility
Extracts a 2D plane from the pixels set.
getPlane(int, int, int) - Method in class omero.gateway.rnd.DataSink
Extracts a 2D plane from the pixels set this object is working for.
getPlane_async(AMD_RawPixelsStore_getPlane, int, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
getPlane_async(AMD_RawPixelsStore_getPlane, int, int, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
getPlaneCount(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPlaneCount() - Method in class omero.gateway.model.ROIData
Deprecated.
Will be removed in future. Does not work as expected if the ROI contains shapes which are associated with all planes (Z, C, T == -1)
getPlaneDeltaT(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPlaneExposureTime(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPlaneOffset_async(AMD_RawPixelsStore_getPlaneOffset, int, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
getPlaneOffset_async(AMD_RawPixelsStore_getPlaneOffset, int, int, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
getPlanePositionX(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPlanePositionY(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPlanePositionZ(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPlaneRegion_async(AMD_RawPixelsStore_getPlaneRegion, int, int, int, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
getPlaneRegion_async(AMD_RawPixelsStore_getPlaneRegion, int, int, int, int, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
getPlaneSize_async(AMD_RawPixelsStore_getPlaneSize, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
getPlaneSize_async(AMD_RawPixelsStore_getPlaneSize, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
getPlaneTheC(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPlaneTheT(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPlaneTheZ(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPlate() - Method in class omero.gateway.model.WellData
Returns the plate containing this Well.
getPlateAcquisitions() - Method in class omero.gateway.model.PlateData
Returns the plate acquisitions related to this plate.
getPlates(SecurityContext) - Method in class omero.gateway.facility.BrowseFacility
Loads all plates
getPlates(SecurityContext, Collection<Long>) - Method in class omero.gateway.facility.BrowseFacility
Loads the plates with the given ids
getPlates(SecurityContext, long) - Method in class omero.gateway.facility.BrowseFacility
Loads the plates for a particular user
getPlates(SecurityContext, long, Collection<Long>) - Method in class omero.gateway.facility.BrowseFacility
Loads the plates with the given ids which belong to a particular user
getPlates() - Method in class omero.gateway.model.ScreenData
Returns the plates contained in this screen.
getPlateType() - Method in class omero.gateway.model.PlateData
Returns the type of plate e.g.
getPockelCell() - Method in class omero.gateway.model.ChannelData
Returns the Pockel cell settings.
getPointAnnotationRef(int, int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPointFillColor(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPointFillRule(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPointFontFamily(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPointFontSize(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPointFontStyle(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPointID(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPointLocked(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPoints(long, Session) - Method in class ome.services.roi.GeomTool
 
getPoints() - Method in class omero.gateway.model.PolygonData
Returns the points in the polygon.
getPoints() - Method in class omero.gateway.model.PolylineData
Returns the points in the Polyline.
getPoints_async(AMD_IRoi_getPoints, long, Current) - Method in class ome.services.blitz.impl.RoiI
 
getPointStrokeColor(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPointStrokeDashArray(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPointStrokeWidth(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPointText(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPointTheC(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPointTheT(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPointTheZ(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPointTransform(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPointX(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPointY(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPojosService(SecurityContext) - Method in class omero.gateway.Gateway
Returns the IContainerPrx service.
getPojoType(Class<? extends IObject>) - Static method in class omero.gateway.util.PojoMapper
Get the pojo type for a an IObject class (Reverse of PojoMapper.getModelType(Class))
getPolygonAnnotationRef(int, int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPolygonFillColor(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPolygonFillRule(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPolygonFontFamily(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPolygonFontSize(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPolygonFontStyle(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPolygonID(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPolygonLocked(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPolygonPoints(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPolygonStrokeColor(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPolygonStrokeDashArray(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPolygonStrokeWidth(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPolygonText(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPolygonTheC(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPolygonTheT(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPolygonTheZ(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPolygonTransform(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPolylineAnnotationRef(int, int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPolylineFillColor(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPolylineFillRule(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPolylineFontFamily(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPolylineFontSize(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPolylineFontStyle(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPolylineID(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPolylineLocked(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPolylineMarkerEnd(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPolylineMarkerStart(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPolylinePoints(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPolylineStrokeColor(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPolylineStrokeDashArray(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPolylineStrokeWidth(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPolylineText(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPolylineTheC(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPolylineTheT(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPolylineTheZ(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPolylineTransform(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getPort() - Method in class omero.gateway.ServerInformation
Return the port
getPositionX(UnitsLength) - Method in class omero.gateway.model.ImageAcquisitionData
Returns the x-coordinate in the frame microscope.
getPositionX(UnitsLength) - Method in class omero.gateway.model.WellSampleData
Returns the position X.
getPositionY(UnitsLength) - Method in class omero.gateway.model.ImageAcquisitionData
Returns the y-coordinate in the frame microscope.
getPositionY(UnitsLength) - Method in class omero.gateway.model.WellSampleData
Returns the position Y.
getPositionZ(UnitsLength) - Method in class omero.gateway.model.ImageAcquisitionData
Returns the z-coordinate in the frame microscope.
getPower(UnitsPower) - Method in class omero.gateway.model.LightSourceData
Returns the power of the light source.
getPredicateFromClasses(Iterable<Class<? extends IObject>>) - Static method in class omero.cmd.graphs.GraphUtil
Construct a predicate to test if an object's class is of any of the given classes.
getPrepareStatementCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
getPrincipal() - Method in class omero.cmd.SessionI
 
getProject(long) - Method in class ome.formats.OMEROMetadataStoreClient
 
getProjectionService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
getProjectionService(SecurityContext) - Method in class omero.gateway.Gateway
Returns the IProjectionPrx service.
getProjects() - Method in class ome.formats.OMEROMetadataStoreClient
 
getProjects(SecurityContext) - Method in class omero.gateway.facility.BrowseFacility
Get all projects
getProjects(SecurityContext, Collection<Long>) - Method in class omero.gateway.facility.BrowseFacility
Get the projects for the given project ids
getProjects(SecurityContext, long) - Method in class omero.gateway.facility.BrowseFacility
Get the projects of a certain user
getProjects(SecurityContext, long, Collection<Long>) - Method in class omero.gateway.facility.BrowseFacility
Get the projects for the given project ids which belong to a certain user
getProjects() - Method in class omero.gateway.model.DatasetData
Returns a set of projects containing the dataset.
getProperties() - Method in class omero.client
Returns the active properties for this instance.
getProperty(String) - Method in class omero.client
Returns the property value for this key or the empty string if none.
getPropertyChangeListeners() - Method in class omero.gateway.Gateway
Get the PropertyChangeListeners
getPropertyMap() - Method in class omero.client
Returns all properties which are prefixed with "omero." or "Ice."
getPropertyMap(Properties) - Method in class omero.client
Returns all properties which are prefixed with "omero." or "Ice."
getProtocolDescription() - Method in class omero.gateway.model.ScreenData
Returns the description of the protocol.
getProtocolIdentifier() - Method in class omero.gateway.model.ScreenData
Returns the identifier of the protocol.
getProxy() - Method in class ome.services.blitz.impl.ScriptProcessI
 
getProxy(Current) - Method in class ome.services.blitz.repo.AbstractRepositoryI
 
getProxy() - Method in class ome.services.blitz.repo.ManagedImportProcessI
 
getProxy() - Method in interface ome.services.blitz.repo.ProcessContainer.Process
 
getProxy() - Method in class ome.services.blitz.util.RegisterServantMessage
 
getProxyOrNull(String, SessionControlPrx, Current) - Method in class ome.services.blitz.fire.Ring
Delegates to the Ring.redirector strategy configured for this instance.
getProxyOrNull(Redirector.Context, String, SessionControlPrx, Current) - Method in class ome.services.blitz.redirect.AbstractRedirector
Returns null early if the Current has already once been routed by a Redirector implementation, returns an existing session if it can be found, or returns a null.
getProxyOrNull(Redirector.Context, String, SessionControlPrx, Current) - Method in class ome.services.blitz.redirect.ConfigRedirector
Create or retrieve and returns a SessionPrx which the current method takes control of.
getProxyOrNull(Redirector.Context, String, SessionControlPrx, Current) - Method in class ome.services.blitz.redirect.NullRedirector
Always returns null
getProxyOrNull(Redirector.Context, String, SessionControlPrx, Current) - Method in interface ome.services.blitz.redirect.Redirector
Create or retrieve and returns a SessionPrx which the current method takes control of.
getProxyOrNull(Redirector.Context, String, SessionControlPrx, Current) - Method in class ome.services.blitz.redirect.ScaleRedirector
 
getQuantizedLinePoints(Line2D, Set<Point2D>) - Static method in class omero.model.SmartShape.Util
 
getQuantumDef_async(AMD_RenderingEngine_getQuantumDef, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
getQueries() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
Get all executed query strings
getQuery() - Method in class omero.gateway.model.SearchParameters
Returns the query terms to search for
getQueryCacheHitCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
getQueryCacheMissCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
getQueryCachePutCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
getQueryExecutionCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
getQueryExecutionMaxTime() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
getQueryExecutionMaxTimeQueryString() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
getQueryService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
getQueryService(SecurityContext) - Method in class omero.gateway.Gateway
Returns the IQueryPrx service.
getQueryStatistics(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
Query statistics from query string (HQL or SQL)
getRadiusX() - Method in class omero.gateway.model.EllipseData
Returns the radius along the X-axis.
getRadiusY() - Method in class omero.gateway.model.EllipseData
Returns the radius along the Y-axis.
getRating() - Method in class omero.gateway.model.RatingAnnotationData
Returns the rating value.
getRawFileService(SecurityContext) - Method in class omero.gateway.Gateway
Returns the RawFileStorePrx service.
getRawFileStore(long, CheckedPath, String, Current) - Method in interface ome.services.blitz.repo.RepositoryDao
Create a RawFileBean (i.e. an implementation of RawFileStore which can be passed to RepoRawFileStoreI for performing internal functions.
getRawFileStore(long, CheckedPath, String, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
 
getRawValue(int) - Method in class omero.gateway.rnd.Plane2D
Returns the raw data value at the given offset
getReader() - Method in class ome.formats.importer.ImportContainer
Return the reader class name used for reading the contents of this import container.
getReader() - Method in interface ome.formats.model.IObjectContainerStore
Returns the current Bio-Formats reader that has been used to populate the container store.
getReader() - Method in class ome.formats.OMEROMetadataStoreClient
 
getReaderClass(Fileset, Current) - Method in class ome.services.blitz.repo.ManagedRepositoryI
Get the suggested BioFormats Reader for the given Fileset.
getReaderType(String) - Method in class ome.formats.importer.ImportCandidates
Retrieve reader type for file specified in path
getReagentsCounts() - Method in class omero.gateway.model.WellData
Returns the number of reagents linked to the object, key: id of the user, value: number of annotation.
getReagentSetDescripion() - Method in class omero.gateway.model.ScreenData
Returns the description of the reagent set.
getReagentSetIdentifier() - Method in class omero.gateway.model.ScreenData
Returns the identifier of the Reagent set.
getRectangleAnnotationRef(int, int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getRectangleFillColor(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getRectangleFillRule(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getRectangleFontFamily(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getRectangleFontSize(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getRectangleFontStyle(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getRectangleHeight(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getRectangleID(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getRectangleLocked(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getRectangleStrokeColor(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getRectangleStrokeDashArray(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getRectangleStrokeWidth(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getRectangleText(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getRectangleTheC(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getRectangleTheT(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getRectangleTheZ(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getRectangleTransform(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getRectangleWidth(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getRectangleX(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getRectangleY(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getRed() - Method in class omero.gateway.model.WellData
Returns the red component of the color associated to the well, or -1.
getRedirect(Redirector.Context) - Method in class ome.services.blitz.redirect.AbstractRedirector
Returns the current redirect, to which all calls to Redirector.getProxyOrNull(Context, String, Glacier2.SessionControlPrx, Ice.Current) will be pointed.
getReference() - Method in class omero.gateway.model.ImageData
Returns the reference to the file to register.
getReferenceCache() - Method in interface ome.formats.model.IObjectContainerStore
Returns the current reference cache.
getReferenceCache() - Method in class ome.formats.OMEROMetadataStoreClient
 
getReferenceCount_async(AMD_ISession_getReferenceCount, String, Current) - Method in class ome.services.blitz.impl.SessionI
 
getReferenceStringCache() - Method in interface ome.formats.model.IObjectContainerStore
Returns the current string based reference cache.
getReferenceStringCache() - Method in class ome.formats.OMEROMetadataStoreClient
 
getRefPlateId() - Method in class omero.gateway.model.PlateAcquisitionData
Returns the id of the plate of reference.
getRefractiveIndex() - Method in class omero.gateway.model.ImageAcquisitionData
Returns the refractive index of the objective.
getRegion_async(AMD_RawPixelsStore_getRegion, int, long, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
getRegion_async(AMD_RawPixelsStore_getRegion, int, long, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
getRegistry() - Method in class ome.services.blitz.repo.InternalRepositoryConfig
 
getRegistry() - Method in class ome.services.blitz.util.BlitzConfiguration
 
getRelativePath() - Method in class ome.services.blitz.repo.CheckedPath
Get the parent path of the entity to which this path corresponds.
getRenderingDefId_async(AMD_RenderingEngine_getRenderingDefId, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
getRenderingDefId_async(AMD_ThumbnailStore_getRenderingDefId, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
 
getRenderingEngines() - Method in class omero.gateway.Gateway
Returns the rendering engines to re-activate.
getRenderingService(SecurityContext, long) - Method in class omero.gateway.Gateway
Returns the Rendering service.
getRenderingSettings_async(AMD_IRenderingSettings_getRenderingSettings, long, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
 
getRenderingSettingsService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
getRenderingSettingsService(SecurityContext) - Method in class omero.gateway.Gateway
Returns the IRenderingSettingsPrx service.
getRepositoryInfoService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
getRepositoryService(SecurityContext) - Method in class omero.gateway.Gateway
Returns the IRepositoryInfoPrx service.
getRepositorySpace() - Method in class ome.formats.OMEROMetadataStoreClient
 
getRepoUuid() - Method in class ome.services.blitz.repo.AbstractRepositoryI
 
getRepoUuid() - Method in class ome.services.blitz.repo.PublicRepositoryI
 
getRequest(Class<R>) - Method in class omero.cmd.graphs.GraphRequestFactory
Construct a request.
getRequest(Current) - Method in class omero.cmd.HandleI
 
getRequiredPermissions() - Method in class omero.cmd.graphs.NullGraphTraversalProcessor
 
getResolutionDescriptions_async(AMD_PyramidService_getResolutionDescriptions, Current) - Method in class ome.services.blitz.impl.AbstractPyramidServant
 
getResolutionDescriptions_async(AMD_PyramidService_getResolutionDescriptions, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
getResolutionLevel_async(AMD_PyramidService_getResolutionLevel, Current) - Method in class ome.services.blitz.impl.AbstractPyramidServant
 
getResolutionLevel_async(AMD_PyramidService_getResolutionLevel, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
getResolutionLevels_async(AMD_PyramidService_getResolutionLevels, Current) - Method in class ome.services.blitz.impl.AbstractPyramidServant
 
getResolutionLevels_async(AMD_PyramidService_getResolutionLevels, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
getResponse() - Method in class ome.services.blitz.impl.commands.SaveI
 
getResponse() - Method in class ome.services.blitz.repo.ManagedImportRequestI
 
getResponse() - Method in class ome.services.blitz.repo.RawAccessRequestI
 
getResponse() - Method in class omero.cmd.admin.CurrentSessionsRequestI
 
getResponse() - Method in class omero.cmd.admin.ResetPasswordRequestI
 
getResponse() - Method in class omero.cmd.admin.UpdateSessionTimeoutRequestI
 
getResponse() - Method in class omero.cmd.basic.DoAllI
 
getResponse() - Method in class omero.cmd.basic.ListRequestsI
 
getResponse() - Method in class omero.cmd.basic.TimingI
 
getResponse() - Method in class omero.cmd.CmdCallbackI
Returns possibly null Response value.
getResponse() - Method in class omero.cmd.fs.FindPyramidsI
 
getResponse() - Method in class omero.cmd.fs.ManageImageBinariesI
 
getResponse() - Method in class omero.cmd.fs.OriginalMetadataRequestI
 
getResponse() - Method in class omero.cmd.fs.UsedFilesRequestI
 
getResponse() - Method in class omero.cmd.graphs.Chgrp2I
 
getResponse() - Method in class omero.cmd.graphs.Chmod2I
 
getResponse() - Method in class omero.cmd.graphs.Chown2I
 
getResponse() - Method in class omero.cmd.graphs.Delete2I
 
getResponse() - Method in class omero.cmd.graphs.DiskUsage2I
 
getResponse() - Method in class omero.cmd.graphs.DiskUsageI
Deprecated.
 
getResponse() - Method in class omero.cmd.graphs.DuplicateI
 
getResponse() - Method in class omero.cmd.graphs.FindChildrenI
 
getResponse() - Method in class omero.cmd.graphs.FindParentsI
 
getResponse() - Method in class omero.cmd.graphs.LegalGraphTargetsI
 
getResponse() - Method in class omero.cmd.graphs.SkipHeadI
 
getResponse(Current) - Method in class omero.cmd.HandleI
 
getResponse() - Method in class omero.cmd.Helper
 
getResponse() - Method in interface omero.cmd.IRequest
Returns the current response value.
getResponse() - Method in class omero.cmd.mail.SendEmailRequestI
 
getResponses() - Method in class ome.services.blitz.impl.ProcessorCallbackI
Return the number of times this instance has been called in a thread safe manner.
getResult() - Method in class omero.gateway.model.ROIResult
Returns the result.
getResults(int, Current) - Method in class ome.services.blitz.impl.ScriptProcessI
 
getResults(int, Class<? extends DataObject>) - Method in class omero.gateway.model.SearchResultCollection
Get all results of a certain scope and/or type
getResults(ProcessPrx, Current) - Method in class omero.grid.InteractiveProcessorI
 
getRGBA(Color) - Static method in class omero.gateway.model.ShapeSettingsData
Returns the Color's RGBA value as integer
getRGBA_async(AMD_RenderingEngine_getRGBA, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
getRing() - Method in class ome.services.blitz.util.BlitzConfiguration
 
getROI() - Method in class omero.gateway.util.ROIComponent
Returns all the ROI in the component as a list.
getROI() - Method in class omero.gateway.util.UploadMask
Returns the ROIs created from uploading the images.
getROIAnnotationRef(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getROIAnnotationRefCount(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getROICoordinate() - Method in class omero.gateway.model.ShapeData
Returns the ROICoordinate for the ShapeData.
getROICount() - Method in class ome.services.blitz.impl.OmeroMetadata
 
getROICount(SecurityContext, long) - Method in class omero.gateway.facility.ROIFacility
Get the number of ROIs for an image (-1 in case of error)
getROIDescription(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getROIFolders(SecurityContext, long) - Method in class omero.gateway.facility.ROIFacility
Get all ROI folders for a certain image
getROIID(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getRoiIds() - Method in class ome.services.blitz.measurements.MeasurementStore
 
getRoiIds() - Method in interface ome.services.blitz.measurements.OmeroMeasurementStore
Returns the ids of all Roi instances created during the save method.
getRoiMeasurements_async(AMD_IRoi_getRoiMeasurements, long, RoiOptions, Current) - Method in class ome.services.blitz.impl.RoiI
 
getROIName(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getROIs() - Method in class omero.gateway.model.ROIResult
Returns the collection of ROIs.
getRoiService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
getROIService(SecurityContext) - Method in class omero.gateway.Gateway
Returns the IRoiPrx service.
getRoiStats_async(AMD_IRoi_getRoiStats, long, Current) - Method in class ome.services.blitz.impl.RoiI
 
getRoot() - Method in class ome.formats.OMEROMetadataStoreClient
 
getRoot() - Method in class ome.services.blitz.impl.OmeroMetadata
 
getRootFile() - Method in class ome.formats.importer.transfers.TransferState
Find original file represented by the managed repository that import is taking place to.
getRouter(Communicator) - Static method in class omero.client
Acquires the default router, and throws an exception if it is not of type {Glacier2.RouterPrx}.
getRow() - Method in class omero.gateway.model.WellData
Returns the row used to indicate the location of the well on the grid.
getRow_async(AMD_RawPixelsStore_getRow, int, int, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
getRow_async(AMD_RawPixelsStore_getRow, int, int, int, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
getRowOffset_async(AMD_RawPixelsStore_getRowOffset, int, int, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
getRowOffset_async(AMD_RawPixelsStore_getRowOffset, int, int, int, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
getRowSequenceIndex() - Method in class omero.gateway.model.PlateData
Returns the index indicating how to label a row.
getRowSize_async(AMD_RawPixelsStore_getRowSize, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
getRowSize_async(AMD_RawPixelsStore_getRowSize, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
getScope() - Method in class omero.gateway.model.SearchParameters
Returns the scope of the search.
getScopeId() - Method in class omero.gateway.model.SearchResult
The Id of the search scope, e.g. name, description, ...
getScreens() - Method in class ome.formats.OMEROMetadataStoreClient
 
getScreens(SecurityContext) - Method in class omero.gateway.facility.BrowseFacility
Loads all screens
getScreens(SecurityContext, Collection<Long>) - Method in class omero.gateway.facility.BrowseFacility
Loads the screens with the given ids
getScreens(SecurityContext, long) - Method in class omero.gateway.facility.BrowseFacility
Loads the screens for a particular user
getScreens(SecurityContext, long, Collection<Long>) - Method in class omero.gateway.facility.BrowseFacility
Loads the screens with the given ids which belong to a particular user
getScreens() - Method in class omero.gateway.model.PlateData
Returns a set of screens containing the plate.
getScriptID_async(AMD_IScript_getScriptID, String, Current) - Method in class ome.services.blitz.impl.ScriptI
Get the id of the official script with given path.
getScriptRepository(Current) - Method in class ome.services.blitz.impl.SharedResourcesI
 
getScripts_async(AMD_IScript_getScripts, Current) - Method in class ome.services.blitz.impl.ScriptI
Get Scripts will return all the scripts by id and name available on the server.
getScriptsByMimetype_async(AMD_IScript_getScriptsByMimetype, String, Current) - Method in class ome.services.blitz.impl.ScriptI
Get Scripts will return all the scripts by id and name available on the server.
getScriptService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
getScriptService(SecurityContext) - Method in class omero.gateway.Gateway
Returns the IScriptPrx service.
getScriptText_async(AMD_IScript_getScriptText, long, Current) - Method in class ome.services.blitz.impl.ScriptI
Return the script with the name to the user.
getScriptWithDetails_async(AMD_IScript_getScriptWithDetails, long, Current) - Method in class ome.services.blitz.impl.ScriptI
Return the script with the name to the user.
getSearchService(SecurityContext) - Method in class omero.gateway.Gateway
Returns the SearchPrx service.
getSecondLevelCacheHitCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
getSecondLevelCacheMissCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
getSecondLevelCachePutCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
getSecondLevelCacheRegionNames() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
Get all second-level cache region names
getSecondLevelCacheStatistics(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
Second level cache statistics per region
getSecurityContexts(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
getSecurityRoles_async(AMD_IAdmin_getSecurityRoles, Current) - Method in class ome.services.blitz.impl.AdminI
 
getSelectedFile() - Method in class ome.formats.importer.util.ErrorContainer
 
getSerialNumber() - Method in class omero.gateway.model.DetectorData
Returns the serial number of the detector.
getSerialNumber() - Method in class omero.gateway.model.DichroicData
Returns the serial number.
getSerialNumber() - Method in class omero.gateway.model.FilterData
Returns the serial number.
getSerialNumber() - Method in class omero.gateway.model.FilterSetData
Returns the serial number.
getSerialNumber() - Method in class omero.gateway.model.LightSourceData
Returns the serial number of the light source.
getSerialNumber() - Method in class omero.gateway.model.ObjectiveData
Returns the serial number of the objective.
getSeries() - Method in class omero.gateway.model.ImageData
Returns the series.
getServant(Identity) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
getServant() - Method in class ome.services.blitz.util.RegisterServantMessage
 
getServantList() - Method in class omero.util.ServantHolder
 
getServer() - Method in class omero.gateway.LoginCredentials
Returns the server information.
getServerFileFromFsFile(FsFile) - Method in class ome.services.blitz.repo.path.ServerFilePathTransformer
Given a repository path, returns the corresponding server-local File.
getServerFileMimetype() - Method in class omero.gateway.model.FileAnnotationData
Returns the file format as defined by the specification, corresponding to the file extension.
getServerInformation() - Method in class omero.gateway.SecurityContext
 
getServerPort() - Method in class ome.formats.importer.util.IniFileLoader
 
getServerTime_async(AMD_IConfig_getServerTime, Current) - Method in class ome.services.blitz.impl.ConfigI
 
getServerVersion() - Method in class omero.gateway.Gateway
Get the version of the server the Gateway is connected to
getServiceFactory() - Method in class ome.formats.OMEROMetadataStoreClient
Returns the currently active service factory.
getServiceFactory(String, String) - Method in class ome.services.blitz.fire.SessionManagerI
 
getServiceFactory(Identity) - Method in class ome.services.blitz.fire.SessionManagerI
 
getServiceFactory() - Method in class ome.services.blitz.impl.RawFileStoreI
 
getServiceFactory() - Method in class ome.services.blitz.util.FindServiceFactoryMessage
 
getServiceFactory() - Method in class omero.cmd.Helper
 
getServiceFactoryIdentity(Current) - Method in class ome.services.blitz.fire.SessionManagerI
 
getServiceKey() - Method in class ome.services.blitz.util.ExpiredServantMessage
 
getSession() - Method in class omero.client
Returns the current active session or throws an exception if none has been created since the last client.closeSession()
getSession() - Method in class omero.cmd.Helper
 
getSession() - Method in class omero.model.DetailsI
 
getSession() - Method in class omero.util.RPSTileLoop
 
getSession() - Method in class omero.util.ServantHolder
 
getSession_async(AMD_ISession_getSession, String, Current) - Method in class ome.services.blitz.impl.SessionI
 
getSessionCloseCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
getSessionId() - Method in class omero.client
Returns the UUID for the current session without making a remote call.
getSessionId(ExperimenterData) - Method in class omero.gateway.Gateway
Get the ID of the current session
getSessionOpenCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
getSessionService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
getSetting_async(AMD_ILdap_getSetting, Current) - Method in class ome.services.blitz.impl.LdapI
 
getShapeAnnotationRefCount(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getShapeCount(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getShapeCount() - Method in class omero.gateway.model.ROIData
Returns the number of shapes in the ROI.
getShapes(int, int) - Method in class omero.gateway.model.ROIData
Returns the list of shapes on a given plane.
getShapeSettings() - Method in class omero.gateway.model.ShapeData
Returns the settings associated to the shape.
getShapesInRange(ROICoordinate, ROICoordinate) - Method in class omero.gateway.model.ROIData
Deprecated.
Will be removed in future. Does not work as expected if the ROI contains shapes which are associated with all planes (Z, C, T == -1)
getShapeStats_async(AMD_IRoi_getShapeStats, long, Current) - Method in class ome.services.blitz.impl.RoiI
 
getShapeStatsList_async(AMD_IRoi_getShapeStatsList, List<Long>, Current) - Method in class ome.services.blitz.impl.RoiI
 
getShapeStatsRestricted_async(AMD_IRoi_getShapeStatsRestricted, List<Long>, int, int, int[], Current) - Method in class ome.services.blitz.impl.RoiI
 
getShapeType(int, int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getShare_async(AMD_IShare_getShare, long, Current) - Method in class ome.services.blitz.impl.ShareI
 
getSharedResources(SecurityContext) - Method in class omero.gateway.Gateway
Returns the SharedResourcesPrx service.
getShareService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
getSharesOwnedBy_async(AMD_IShare_getSharesOwnedBy, Experimenter, boolean, Current) - Method in class ome.services.blitz.impl.ShareI
 
getSizeC() - Method in class omero.gateway.model.PixelsData
Returns the number of channels.
getSizeT() - Method in class omero.gateway.model.PixelsData
Returns the number of time-points.
getSizeX() - Method in class omero.gateway.model.OTFData
Returns the size along the X-axis.
getSizeX() - Method in class omero.gateway.model.PixelsData
Returns the number of pixels along the X-axis.
getSizeY() - Method in class omero.gateway.model.OTFData
Returns the size along the Y-axis.
getSizeY() - Method in class omero.gateway.model.PixelsData
Returns the number of pixels along the Y-axis.
getSizeZ() - Method in class omero.gateway.model.PixelsData
Returns the number of pixels along the Z-axis.
getSkipHeadPolicyPerform(GraphPolicy, SetMultimap<String, Long>) - Static method in class omero.cmd.graphs.SkipHeadPolicy
Adjust an existing graph traversal policy so that for specific model objects permissions are not checked.
getSkipHeadPolicySkip(GraphPolicy, GraphPathBean, Collection<String>, GraphPolicy.Action, SetMultimap<String, Long>) - Static method in class omero.cmd.graphs.SkipHeadPolicy
Adjust an existing graph traversal policy so that orphaned model objects will always or never be included, according to their type.
getSkipTailPolicy(GraphPolicy, Predicate<Class<? extends IObject>>) - Static method in class omero.cmd.graphs.SkipTailPolicy
Adjust an existing graph traversal policy so that processing stops at certain model object classes.
getSourceObject(LSID) - Method in interface ome.formats.model.IObjectContainerStore
Retrieves an OMERO Blitz source object for a given LSID.
getSourceObject(LSID) - Method in class ome.formats.OMEROMetadataStoreClient
 
getSourceObjects(Class<T>) - Method in interface ome.formats.model.IObjectContainerStore
Retrieves all OMERO Blitz source objects of a given class.
getSourceObjects(Class<T>) - Method in class ome.formats.OMEROMetadataStoreClient
 
getSql() - Method in class omero.cmd.Helper
 
getStack_async(AMD_RawPixelsStore_getStack, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
getStack_async(AMD_RawPixelsStore_getStack, int, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
getStackOffset_async(AMD_RawPixelsStore_getStackOffset, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
getStackOffset_async(AMD_RawPixelsStore_getStackOffset, int, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
getStackSize_async(AMD_RawPixelsStore_getStackSize, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
getStackSize_async(AMD_RawPixelsStore_getStackSize, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
getStackTrace(Throwable) - Static method in class ome.formats.importer.util.ErrorHandler
Return the stack trace from a Throwable.
getStageLabelId() - Method in class omero.gateway.model.ImageAcquisitionData
Returns the id of the StageLabel or -1 if not already linked to the image.
getStart() - Method in class omero.gateway.model.SearchParameters
Returns the lower bound of the time interval.
getStartFrom(Response) - Method in class omero.cmd.graphs.Chgrp2I
 
getStartFrom(Response) - Method in class omero.cmd.graphs.Chmod2I
 
getStartFrom(Response) - Method in class omero.cmd.graphs.Chown2I
 
getStartFrom(Response) - Method in class omero.cmd.graphs.Delete2I
 
getStartFrom(Response) - Method in class omero.cmd.graphs.DuplicateI
 
getStartFrom(Response) - Method in interface omero.cmd.graphs.WrappableRequest
From the response of the head-skipping request, determine which model objects are the targets of the operation.
getStartTime() - Method in class omero.gateway.model.PlateAcquisitionData
Returns the time when the first image was collected.
getStartTime() - Method in class omero.gateway.model.WellSampleData
Returns the time at which the field was acquired.
getStartTime() - Method in class omero.sys.ParametersI
Returns the value of the start time parameter.
getStartTime() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
getStatefulServiceCount() - Method in class ome.services.blitz.impl.ServiceFactoryI
NB: Much of the logic here is similar to SessionI.doClose and should be pushed down.
getStatefulServiceCount() - Method in class omero.util.ServantHolder
 
getStatefulServices() - Method in class omero.client
Returns all active StatefulServiceInterface proxies.
getStaticDisableHistory() - Method in class ome.formats.importer.ImportConfig
 
getStaticDisableHistory() - Method in class ome.formats.importer.util.IniFileLoader
 
getStats(List<Long>) - Method in class ome.services.roi.GeomTool
 
getStatsRestricted(List<Long>, int, int, int[]) - Method in class ome.services.roi.GeomTool
 
getStatus() - Method in class ome.formats.importer.util.ErrorContainer
return the error status
getStatus() - Method in class omero.cmd.CmdCallbackI
Returns possibly null Status value.
getStatus(Current) - Method in class omero.cmd.HandleI
 
getStatus() - Method in class omero.cmd.Helper
 
getStatus() - Method in class omero.gateway.model.PlateData
Returns the status of the plate.
getStatus() - Method in class omero.gateway.model.WellData
Returns the status of the well.
getStatusOrThrow() - Method in class omero.cmd.CmdCallbackI
 
getStepProvidingCompleteResponse() - Method in class omero.cmd.graphs.Chgrp2I
 
getStepProvidingCompleteResponse() - Method in class omero.cmd.graphs.Chmod2I
 
getStepProvidingCompleteResponse() - Method in class omero.cmd.graphs.Chown2I
 
getStepProvidingCompleteResponse() - Method in class omero.cmd.graphs.Delete2I
 
getStepProvidingCompleteResponse() - Method in class omero.cmd.graphs.DuplicateI
 
getStepProvidingCompleteResponse() - Method in interface omero.cmd.graphs.WrappableRequest
Get the step of this request that suffices for assembling the request's response.
getSteps() - Method in class omero.cmd.Helper
 
getStringRepresentation() - Method in enum omero.gateway.model.SearchScope
Get a String representation of this scope which can be used in a lucene search
getStringRepresentation(Collection<SearchScope>) - Static method in enum omero.gateway.model.SearchScope
Get a String representation of the given scopes which can be used in a lucence search
getStringSeparator(String) - Static method in class omero.gateway.util.Utils
Returns the separator or null.
getStroke() - Method in class omero.gateway.model.ShapeSettingsData
Returns the color of the stroke.
getStrokeDashArray() - Method in class omero.gateway.model.ShapeSettingsData
Returns the stroke dashes.
getStrokeWidth(UnitsLength) - Method in class omero.gateway.model.ShapeSettingsData
Returns the stroke's width (or 1 px if it's not set or <= 0)
getSuccessfulTransactionCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
getSupportedMetadataLevels() - Method in class ome.formats.importer.OMEROWrapper
 
getSymbol(Current) - Method in class omero.model.ElectricPotentialI
 
getSymbol(Current) - Method in class omero.model.FrequencyI
 
getSymbol(Current) - Method in class omero.model.LengthI
 
getSymbol(Current) - Method in class omero.model.PowerI
 
getSymbol(Current) - Method in class omero.model.PressureI
 
getSymbol(Current) - Method in class omero.model.TemperatureI
 
getSymbol(Current) - Method in class omero.model.TimeI
 
getT() - Method in class omero.gateway.model.ShapeData
Returns the time-point. -1 if the shape applies to all time-points of the image.
getTable() - Method in class ome.services.blitz.measurements.MeasurementStore
 
getTable() - Method in interface ome.services.blitz.measurements.OmeroMeasurementStore
Returns the Table proxy which is in use by this service.
getTable(SecurityContext, long) - Method in class omero.gateway.facility.TablesFacility
Load the data from a table (Note: limited to TablesFacility.DEFAULT_MAX_ROWS_TO_FETCH number of rows)
getTable(SecurityContext, long, long, long, int...) - Method in class omero.gateway.facility.TablesFacility
Load data from a table
getTable(SecurityContext, long, List<Long>) - Method in class omero.gateway.facility.TablesFacility
Load data from a table
getTable(SecurityContext, long, long...) - Method in class omero.gateway.facility.TablesFacility
Load data from a table
getTable(SecurityContext, long, long, long, long...) - Method in class omero.gateway.facility.TablesFacility
Load data from a table
getTable_async(AMD_IRoi_getTable, long, Current) - Method in class ome.services.blitz.impl.RoiI
 
getTableID() - Method in class omero.gateway.model.TableResult
Returns the id of the table.
getTableInfo(SecurityContext, long) - Method in class omero.gateway.facility.TablesFacility
Get basic information about a table.
getTagAnnotationCount() - Method in class ome.services.blitz.impl.OmeroMetadata
 
getTagAnnotationDescription(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getTagAnnotationID(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getTagAnnotationNamespace(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getTagAnnotationValue(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getTagDescription() - Method in class omero.gateway.model.TagAnnotationData
Returns the description of the tag.
getTagDescriptions() - Method in class omero.gateway.model.TagAnnotationData
Returns the descriptions linked to that tag.
getTaggedObjectsCount_async(AMD_IMetadata_getTaggedObjectsCount, List<Long>, Parameters, Current) - Method in class ome.services.blitz.impl.MetadataI
 
getTags() - Method in class omero.gateway.model.TagAnnotationData
Returns the collection of tags related to this tag.
getTagValue() - Method in class omero.gateway.model.TagAnnotationData
Returns the text of the tag.
getTarget() - Method in class ome.formats.importer.ImportConfig
 
getTarget() - Method in class ome.formats.importer.ImportContainer
 
getTarget(Class<T>, long) - Method in class ome.formats.OMEROMetadataStoreClient
Helper method to retrieve an object from iQuery
getTarget() - Method in class ome.services.blitz.repo.ManagedImportLocationI
Return the server-side CheckedPath instance which can be passed to a Bio-Formats reader.
getTargetMultimap(Set<Class<? extends IObject>>, Map<String, List<Long>>) - Method in class omero.cmd.graphs.GraphHelper
Converts the Ice StringLongListMap to a multimap.
getTargetSet(Set<Class<? extends IObject>>, Collection<String>) - Method in class omero.cmd.graphs.GraphHelper
Converts the Ice StringSet to a set.
getTempDir() - Method in class omero.util.TempFileManager
Returns the directory under which all temporary files and folders will be created.
gettempdir() - Static method in class omero.util.TempFileManager
getTemperature(UnitsTemperature) - Method in class omero.gateway.model.ImageAcquisitionData
Returns the temperature.
getTemplate() - Method in class ome.formats.importer.targets.TemplateImportTarget
 
getTerm() - Method in class omero.gateway.model.TermAnnotationData
Returns the term.
getTermAnnotationCount() - Method in class ome.services.blitz.impl.OmeroMetadata
 
getTermAnnotationDescription(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getTermAnnotationID(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getTermAnnotationNamespace(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getTermAnnotationValue(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getTermDescription() - Method in class omero.gateway.model.TermAnnotationData
Returns the description of the term.
getText() - Method in class omero.gateway.model.EllipseData
Returns the text of the shape.
getText() - Method in class omero.gateway.model.LineData
Returns the text of the shape.
getText() - Method in class omero.gateway.model.MaskData
Returns the text of the shape.
getText() - Method in class omero.gateway.model.PointData
Returns the text of the shape.
getText() - Method in class omero.gateway.model.PolygonData
Returns the text of the shape.
getText() - Method in class omero.gateway.model.PolylineData
Returns the text of the shape.
getText() - Method in class omero.gateway.model.RectangleData
Returns the text of the shape.
getText() - Method in class omero.gateway.model.TextData
Returns the text of the shape.
getText() - Method in class omero.gateway.model.TextualAnnotationData
Returns the text of this annotation.
getText() - Method in class omero.gateway.model.XMLAnnotationData
Returns the text of this annotation.
getThumbnail_async(AMD_ThumbnailStore_getThumbnail, RInt, RInt, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
 
getThumbnailByLongestSide_async(AMD_ThumbnailStore_getThumbnailByLongestSide, RInt, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
 
getThumbnailByLongestSideDirect_async(AMD_ThumbnailStore_getThumbnailByLongestSideDirect, RInt, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
 
getThumbnailByLongestSideSet_async(AMD_ThumbnailStore_getThumbnailByLongestSideSet, RInt, List<Long>, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
 
getThumbnailDirect_async(AMD_ThumbnailStore_getThumbnailDirect, RInt, RInt, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
 
getThumbnailForSectionByLongestSideDirect_async(AMD_ThumbnailStore_getThumbnailForSectionByLongestSideDirect, int, int, RInt, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
 
getThumbnailForSectionDirect_async(AMD_ThumbnailStore_getThumbnailForSectionDirect, int, int, RInt, RInt, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
 
getThumbnailService(SecurityContext) - Method in class omero.gateway.Gateway
Returns the ThumbnailStorePrx service.
getThumbnailSet_async(AMD_ThumbnailStore_getThumbnailSet, RInt, RInt, List<Long>, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
 
getThumbnailWithoutDefault_async(AMD_ThumbnailStore_getThumbnailWithoutDefault, RInt, RInt, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
 
getTie(Identity) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
getTile(SecurityContext, PixelsData, int, int, int, int, int, int, int) - Method in class omero.gateway.facility.RawDataFacility
Extracts a 2D tile from the pixels set
getTile(int, int, int, int, int, int, int) - Method in class omero.gateway.rnd.DataSink
Extracts a 2D tile from the pixels set this object is working for.
getTile(int, int, int, int, int, int, int) - Method in class omero.util.RPSTileData
 
getTile(int, int, int, int, int, int, int) - Method in interface omero.util.TileData
 
getTile_async(AMD_RawPixelsStore_getTile, int, int, int, int, int, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
getTile_async(AMD_RawPixelsStore_getTile, int, int, int, int, int, int, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
getTileSize(Long) - Method in class ome.formats.OMEROMetadataStoreClient
Retrieves the suggested tile size for a pixels set.
getTileSize_async(AMD_PyramidService_getTileSize, Current) - Method in class ome.services.blitz.impl.AbstractPyramidServant
 
getTileSize_async(AMD_PyramidService_getTileSize, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
getTime() - Method in class omero.gateway.model.TimeAnnotationData
Returns the time value.
getTimelineService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
getTimePoint() - Method in class omero.gateway.model.ROICoordinate
Returns the timepoint. (-1 == all timepoints)
getTimepoint_async(AMD_RawPixelsStore_getTimepoint, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
getTimepoint_async(AMD_RawPixelsStore_getTimepoint, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
getTimepointOffset_async(AMD_RawPixelsStore_getTimepointOffset, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
getTimepointOffset_async(AMD_RawPixelsStore_getTimepointOffset, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
getTimepointSize_async(AMD_RawPixelsStore_getTimepointSize, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
getTimepointSize_async(AMD_RawPixelsStore_getTimepointSize, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
getTimestampAnnotationCount() - Method in class ome.services.blitz.impl.OmeroMetadata
 
getTimestampAnnotationDescription(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getTimestampAnnotationID(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getTimestampAnnotationNamespace(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getTimestampAnnotationValue(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getToken() - Method in class ome.formats.importer.util.ErrorContainer
 
getTokenUrl() - Method in class ome.formats.importer.ImportConfig
 
getTooSimilarFiles(Set<File>) - Method in class ome.services.blitz.repo.path.ClientFilePathTransformer
Get the files that are too similarly named.
getTopicManager() - Method in class ome.services.blitz.util.BlitzConfiguration
 
getTopLevelNames(Iterable<Class<? extends IObject>>) - Method in class omero.cmd.graphs.GraphHelper
Get the simple names of the top-level superclasses of the given classes.
getTotalSize_async(AMD_RawPixelsStore_getTotalSize, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
getTotalSize_async(AMD_RawPixelsStore_getTotalSize, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
getTransactionCount() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
getTransform() - Method in class omero.gateway.model.ShapeData
Returns the transformation.
getTransmittance() - Method in class omero.gateway.model.FilterData
Returns the cut out tolerance value or -1.
getType() - Method in class omero.gateway.model.DetectorData
Returns the type of the detector.
getType() - Method in class omero.gateway.model.FilterData
Returns the type.
getType() - Method in class omero.gateway.model.LightSourceData
Returns the type of light.
getType() - Method in class omero.gateway.model.SearchResult
Get the type (class) of objects to search for see DataObject
getType() - Method in class omero.gateway.model.TableDataColumn
Get the data type
getTypes() - Method in class omero.gateway.model.SearchParameters
Returns the types to search on.
getTypesService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
getTypesService(SecurityContext) - Method in class omero.gateway.Gateway
Returns the ITypesPrx service.
getUIBounds() - Method in class ome.formats.importer.ImportConfig
 
getUIBounds() - Method in class ome.formats.importer.util.IniFileLoader
 
getUnique() - Method in class omero.sys.ParametersI
 
getUnit(Current) - Method in class omero.model.ElectricPotentialI
 
getUnit(Current) - Method in class omero.model.FrequencyI
 
getUnit(Current) - Method in class omero.model.LengthI
 
getUnit(Current) - Method in class omero.model.PowerI
 
getUnit(Current) - Method in class omero.model.PressureI
 
getUnit(Current) - Method in class omero.model.TemperatureI
 
getUnit(Current) - Method in class omero.model.TimeI
 
getUntied(Identity) - Method in class omero.util.ServantHolder
 
getUpdated() - Method in class omero.gateway.model.DataObject
Returns the updated time of the object.
getUpdateEvent(Current) - Method in class omero.model.DetailsI
 
getUpdateService(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
getUpdateService(SecurityContext) - Method in class omero.gateway.Gateway
Returns the IUpdatePrx service.
getUpdateService(SecurityContext, String) - Method in class omero.gateway.Gateway
Returns the IUpdatePrx service.
getUploader() - Method in class ome.formats.importer.transfers.TransferState
 
getUploader(String) - Method in class ome.formats.importer.transfers.TransferState
Return the RawFileStorePrx instance for this index setting the mode if not null.
getUploader(int, Current) - Method in class ome.services.blitz.repo.ManagedImportProcessI
 
getUploaderUrl() - Method in class ome.formats.importer.ImportConfig
 
getUploadOffset(int, Current) - Method in class ome.services.blitz.repo.ManagedImportProcessI
 
getUploadTimeLeft() - Method in class ome.formats.importer.transfers.TransferState
 
getUploadTimeLeft() - Method in class ome.formats.importer.util.ProportionalTimeEstimatorImpl
 
getUploadTimeLeft() - Method in interface ome.formats.importer.util.TimeEstimator
Return the estimated time left in milliseconds based on the calls to start and stop methods.
getUploadUrl() - Method in class ome.formats.importer.util.ErrorContainer
 
getUsageFraction_async(AMD_IRepositoryInfo_getUsageFraction, Current) - Method in class ome.services.blitz.impl.RepositoryInfoI
 
getUsedFilePaths() - Method in class omero.gateway.model.FilesetData
Returns the collection of file paths used for importing the files (in case of in-place imports these are the targets of the (sym)links)
getUsedFiles(String) - Method in class ome.formats.importer.ImportCandidates
Return string of files used by container item at path
getUsedFiles() - Method in class ome.formats.importer.ImportContainer
Return a list of file names that belong to this import container.
getUsedFilesTotalSize() - Method in class ome.formats.importer.ImportContainer
Returns the total size in bytes (based on File.length()) of all files in this import container.
getUsedSpaceInKilobytes_async(AMD_IRepositoryInfo_getUsedSpaceInKilobytes, Current) - Method in class ome.services.blitz.impl.RepositoryInfoI
 
getUseQuaqua() - Method in class ome.formats.importer.ImportConfig
 
getUseQuaqua() - Method in class ome.formats.importer.util.IniFileLoader
 
getUser() - Method in class omero.gateway.LoginCredentials
Returns the credentials.
getUserDetails(SecurityContext, String) - Method in class omero.gateway.Gateway
Get the user details of a certain user
getUserDisableHistory() - Method in class ome.formats.importer.ImportConfig
 
getUserDisableHistory() - Method in class ome.formats.importer.util.IniFileLoader
 
getUserFullPath() - Method in class ome.formats.importer.ImportConfig
Deprecated.
getUserFullPath() - Method in class ome.formats.importer.util.IniFileLoader
Deprecated.
getUserId() - Method in class omero.gateway.model.SearchParameters
 
getUserImages(SecurityContext) - Method in class omero.gateway.facility.BrowseFacility
Loads all images of the logged in user
getUserImages_async(AMD_IContainer_getUserImages, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI
 
getUserInstitution(long, Current) - Method in interface ome.services.blitz.repo.RepositoryDao
Get the current user's institution.
getUserInstitution(long, ServiceFactory) - Method in interface ome.services.blitz.repo.RepositoryDao
Get the current user's institution.
getUserInstitution(long, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
 
getUserInstitution(long, ServiceFactory) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
 
getUserName() - Method in class omero.gateway.model.ExperimenterData
Returns the last name of the experimenter.
getUsername() - Method in class omero.gateway.UserCredentials
Returns the user name (or session ID, if it was set before instead of an username)
getUserPixels() - Method in class ome.formats.importer.ImportContainer
 
getUserScripts_async(AMD_IScript_getUserScripts, List<IObject>, Current) - Method in class ome.services.blitz.impl.ScriptI
 
getUserSettingsDirectory() - Method in class ome.formats.importer.ImportConfig
 
getUserSettingsDirectory() - Method in class ome.formats.importer.util.IniFileLoader
 
getUserSpecifiedAnnotations() - Method in interface ome.formats.model.IObjectContainerStore
Returns the user specified annotations.
getUserSpecifiedAnnotations() - Method in class ome.formats.OMEROMetadataStoreClient
 
getUserSpecifiedDescription() - Method in class ome.formats.importer.ImportContainer
Retrieves the current custom image/plate description string.
getUserSpecifiedDescription() - Method in interface ome.formats.model.IObjectContainerStore
Returns the user specified image/plate description.
getUserSpecifiedDescription() - Method in class ome.formats.OMEROMetadataStoreClient
 
getUserSpecifiedImageName() - Method in class ome.formats.OMEROMetadataStoreClient
 
getUserSpecifiedName() - Method in class ome.formats.importer.ImportContainer
Retrieves the current custom image/plate name string.
getUserSpecifiedName() - Method in interface ome.formats.model.IObjectContainerStore
Returns the user specified image/plate name.
getUserSpecifiedName() - Method in class ome.formats.OMEROMetadataStoreClient
 
getUserSpecifiedPhysicalPixelSizes() - Method in interface ome.formats.model.IObjectContainerStore
Returns the user specified physical pixel sizes.
getUserSpecifiedPhysicalPixelSizes() - Method in class ome.formats.OMEROMetadataStoreClient
 
getUserSpecifiedTarget() - Method in interface ome.formats.model.IObjectContainerStore
Returns the user-specified linkage target (usually a Dataset for Images) and a Screen for Plates).
getUserSpecifiedTarget() - Method in class ome.formats.OMEROMetadataStoreClient
 
getUuid() - Method in class omero.gateway.model.ROIData
Get the UUID
getValue() - Method in exception ome.formats.enums.EnumerationException
 
getValue() - Method in enum ome.formats.Index
 
getValue(Class<? extends IObject>, int) - Method in class ome.formats.OMEXMLModelComparator
Assigns a value to a particular class based on its location in the OME-XML hierarchy.
getValue() - Method in class omero.gateway.model.BooleanAnnotationData
Returns the text of this annotation.
getValue(Current) - Method in class omero.model.ElectricPotentialI
 
getValue(Current) - Method in class omero.model.FrequencyI
 
getValue(Current) - Method in class omero.model.LengthI
 
getValue(Current) - Method in class omero.model.PowerI
 
getValue(Current) - Method in class omero.model.PressureI
 
getValue(Current) - Method in class omero.model.TemperatureI
 
getValue(Current) - Method in class omero.model.TimeI
 
getVersion() - Method in class omero.gateway.model.DataObject
Returns the version of the object if the object is immutable, false otherwise.
getVersion_async(AMD_IConfig_getVersion, Current) - Method in class ome.services.blitz.impl.ConfigI
 
getVersionNote() - Method in class ome.formats.importer.util.IniFileLoader
 
getVersionNumber() - Method in class ome.formats.importer.ImportConfig
 
getVersionNumber() - Method in class ome.formats.importer.util.IniFileLoader
 
getVoltage(UnitsElectricPotential) - Method in class omero.gateway.model.DetectorData
Returns the voltage of the detector.
getWellOriginX(UnitsLength) - Method in class omero.gateway.model.PlateData
Returns the x-coordinate in 2D-space of the well.
getWellOriginY(UnitsLength) - Method in class omero.gateway.model.PlateData
Returns the y-coordinate in 2D-space of the well.
getWells(SecurityContext, Collection<Long>) - Method in class omero.gateway.facility.BrowseFacility
Loads the wells
getWells(SecurityContext, long) - Method in class omero.gateway.facility.BrowseFacility
Loads the wells for a given plate
getWellSamples() - Method in class omero.gateway.model.WellData
Returns the well samples linked to the well.
getWellType() - Method in class omero.gateway.model.WellData
Returns a human readable identifier for the screening status e.g. empty, positive control, etc.
getWidth() - Method in class omero.gateway.model.MaskData
Returns the width of the mask.
getWidth() - Method in class omero.gateway.model.RectangleData
Returns the width untransformed rectangle.
getWorkingDistance(UnitsLength) - Method in class omero.gateway.model.ObjectiveData
Returns the working distance.
getX() - Method in class omero.gateway.model.EllipseData
Returns the x-coordinate of the center of the ellipse.
getX() - Method in class omero.gateway.model.MaskData
Returns the x-coordinate of the top-left corner of the mask.
getX() - Method in class omero.gateway.model.PointData
Returns the x-coordinate of the shape.
getX() - Method in class omero.gateway.model.RectangleData
Returns the x-coordinate of the top-left corner of an untransformed rectangle.
getX() - Method in class omero.gateway.model.TextData
Returns the x-coordinate text field.
getX1() - Method in class omero.gateway.model.LineData
Returns the x-coordinate of the starting point of an untransformed line.
getX2() - Method in class omero.gateway.model.LineData
Returns the x-coordinate of the end point of an untransformed line.
getXMLAnnotationCount() - Method in class ome.services.blitz.impl.OmeroMetadata
 
getXMLAnnotationDescription(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getXMLAnnotationID(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getXMLAnnotationNamespace(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getXMLAnnotationValue(int) - Method in class ome.services.blitz.impl.OmeroMetadata
 
getY() - Method in class omero.gateway.model.EllipseData
Returns the y-coordinate of the center of the ellipse.
getY() - Method in class omero.gateway.model.MaskData
Returns the y-coordinate of the top-left corner of the mask.
getY() - Method in class omero.gateway.model.PointData
Returns the y coordinate of the shape.
getY() - Method in class omero.gateway.model.RectangleData
Returns the y-coordinate of the top-left corner of an untransformed rectangle.
getY() - Method in class omero.gateway.model.TextData
Returns the y-coordinate text field.
getY1() - Method in class omero.gateway.model.LineData
Returns the y-coordinate of the starting point of an untransformed line.
getY2() - Method in class omero.gateway.model.LineData
Returns the y-coordinate of the end point of an untransformed line.
getZ() - Method in class omero.gateway.model.ShapeData
Returns the z-section. -1 if the shape applies to all z-sections of the image.
getZoom() - Method in class omero.gateway.model.DetectorData
Returns the offset of the detector.
getZSection() - Method in class omero.gateway.model.ROICoordinate
Returns the z-section. (-1 == all z-sections)
granted(int, int) - Method in class omero.model.PermissionsI
 
GraphHelper - Class in omero.cmd.graphs
Factors common code out of GraphQuery implementations for reuse.
GraphHelper(Helper, GraphPathBean) - Constructor for class omero.cmd.graphs.GraphHelper
Construct a helper for a graph request instance.
GraphRequestFactory - Class in omero.cmd.graphs
Create request objects that are executed using the GraphPathBean.
GraphRequestFactory(ACLVoter, Roles, GraphPathBean, LightAdminPrivileges, Deletion, Map<Class<? extends Request>, List<String>>, Map<Class<? extends Request>, List<GraphPolicyRule>>, List<String>, Set<String>) - Constructor for class omero.cmd.graphs.GraphRequestFactory
Construct a new graph request factory.
GraphUtil - Class in omero.cmd.graphs
Static utility methods for model graph operations.
GraphUtil() - Constructor for class omero.cmd.graphs.GraphUtil
 
GREEN_INDEX - Static variable in class ome.formats.model.ColorsFactory
Index of the red component of a color.
GREEN_TEXT - Static variable in class ome.formats.model.ChannelProcessor
Name of the green component when it is a graphics image.
group - Variable in class ome.formats.importer.ImportConfig
 
GROUP_COLLAB_READ - Static variable in class ome.formats.importer.ImportEvent
 
GROUP_COLLAB_READ_LINK - Static variable in class ome.formats.importer.ImportEvent
 
GROUP_EXPERIMENTER_MAP - Static variable in class omero.gateway.model.ExperimenterData
Identifies the ExperimenterI.GROUPEXPERIMENTERMAP field.
GROUP_EXPERIMENTER_MAP - Static variable in class omero.gateway.model.GroupData
Identifies the ExperimenterGroupI.GROUPEXPERIMENTERMAP field.
GROUP_PRIVATE - Static variable in class ome.formats.importer.ImportEvent
 
GROUP_PUBLIC - Static variable in class ome.formats.importer.ImportEvent
 
GROUP_SYSTEM - Static variable in class ome.formats.importer.ImportEvent
 
groupContext(Long, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
Creates a copy of the Current.ctx map and if groupId is not null, sets the "omero.group" key to be a string version of the id.
GroupData - Class in omero.gateway.model
The data that makes up an OME Group along with the various members of the Group
GroupData() - Constructor for class omero.gateway.model.GroupData
Creates a new instance.
GroupData(ExperimenterGroup) - Constructor for class omero.gateway.model.GroupData
Creates a new instance.
grp(RLong) - Method in class omero.sys.ParametersI
Sets the value of the group parameter.
GUEST - Static variable in class omero.gateway.model.GroupData
Identifies the Guest group.

H

handle(IObject) - Method in interface ome.formats.model.handler.ModelObjectHandler
Attempt to handle the model object of this type.
handle - Variable in class ome.services.blitz.repo.ManagedImportRequestI
Set by ManagedImportProcessI when verifyUpload has been called.
handle - Variable in class omero.cmd.CmdCallbackI
Proxy passed to this instance on creation.
handle(int, int) - Method in interface omero.model.SmartShape.PointCallback
 
handleCallbackException(Exception) - Method in class omero.cmd.SessionI
Reusable method for logging an exception that occurs on one-way communication with clients during callback notification.
handleContextRefreshedEvent(ContextRefreshedEvent) - Method in class ome.services.blitz.util.CheckAllJobs
 
handleException(Throwable) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
handleException(Throwable, OmeroContext) - Method in class omero.util.IceMapper
 
HandleFactory - Class in omero.cmd
SPIOrthogonal interface hierarchy of types for working with the Request hierarchy.
HandleFactory(long) - Constructor for class omero.cmd.HandleFactory
 
handleFile(File, int, Collection) - Method in class ome.formats.importer.ImportCandidates
Handle a file import
HandleI - Class in omero.cmd
Servant for the handle proxy from the Command API.
HandleI(int) - Constructor for class omero.cmd.HandleI
Deprecated.
HandleI(ReadOnlyStatus, int) - Constructor for class omero.cmd.HandleI
Create a HandleI (at CREATED in the state diagram) with the given cancel timeout in milliseconds.
HandleI.Cancel - Exception in omero.cmd
Signals that HandleI.run() has noticed that the state diagram wants a cancellation or that the Request implementation wishes to stop execution.
handleInput(Class<?>, Object) - Method in class omero.util.IceMapper
 
handleLsid(IObject) - Method in class ome.services.blitz.impl.OmeroMetadata
 
handleOutput(Class, Object) - Method in class omero.util.IceMapper
 
handler - Variable in class ome.formats.importer.cli.CommandLineImporter
ErrorHandler which is also responsible for uploading files
handleRingShutdown(Redirector.Context, String) - Method in class ome.services.blitz.redirect.ConfigRedirector
 
handleRingShutdown(Redirector.Context, String) - Method in class ome.services.blitz.redirect.NullRedirector
Does nothing.
handleRingShutdown(Redirector.Context, String) - Method in interface ome.services.blitz.redirect.Redirector
Gives the Redirector a chance to remove the current Ring when it is being shutdown.
handleRingShutdown(Redirector.Context, String) - Method in class ome.services.blitz.redirect.ScaleRedirector
Nothing needs to be done on shutdown, since the Ring implementation will properly disable the Node table queried during the next call to Redirector.getProxyOrNull(Context, String, Glacier2.SessionControlPrx, Ice.Current)
handleServerError(Throwable, OmeroContext) - Method in class omero.util.IceMapper
wraps any non-ServerError returned by IceMapper.handleException(Throwable, OmeroContext) in an InternalException.
HardlinkFileTransfer - Class in ome.formats.importer.transfers
Local-only file transfer mechanism which makes use of hard-linking.
HardlinkFileTransfer() - Constructor for class ome.formats.importer.transfers.HardlinkFileTransfer
 
hasDectector() - Method in class omero.gateway.model.ChannelAcquisitionData
Returns true if there is a detector for that channel, false otherwise.
hasEmissionData(ChannelData) - Static method in class ome.formats.model.ColorsFactory
Returns true if the channel has emission metadata, false otherwise.
hasFilter() - Method in class omero.gateway.model.ChannelAcquisitionData
Returns true if there is a filter set linked to the channel false otherwise.
hash - Variable in class ome.services.blitz.repo.CheckedPath
 
hash() - Method in class ome.services.blitz.repo.CheckedPath
 
hashCode() - Method in class ome.services.blitz.repo.CheckedPath
On Windows systems the calculation is not case-sensitive.
hashCode() - Method in class ome.services.blitz.repo.path.FsFile
hashCode() - Method in class omero.gateway.model.ROICoordinate
Calculate the hashCode for the data, The hashcode is generated by bitshifting z by ZTBITSPLIT bits and adding t.
hashCode() - Method in class omero.gateway.model.TableData
 
hashCode() - Method in class omero.gateway.model.TableDataColumn
 
hashCode() - Method in class omero.gateway.SecurityContext
Calculate the hashCode for the data.
hashCode() - Method in class omero.gateway.ServerInformation
 
hashCode() - Method in class omero.model.ElectricPotentialI
 
hashCode() - Method in class omero.model.FrequencyI
 
hashCode() - Method in class omero.model.LengthI
 
hashCode() - Method in class omero.model.PowerI
 
hashCode() - Method in class omero.model.PressureI
 
hashCode() - Method in class omero.model.TemperatureI
 
hashCode() - Method in class omero.model.TimeI
 
hasID(DataObject) - Static method in class omero.gateway.util.Pojos
Checks if a DataObject Pojo is not null and has an ID
hasIris() - Method in class omero.gateway.model.ObjectiveData
Returns a boolean flag if the value has been set, null otherwise.
hasLightPath() - Method in class omero.gateway.model.ChannelAcquisitionData
Returns true if there is a light path described for that channel, false otherwise.
hasNext_async(AMD_Search_hasNext, Current) - Method in class ome.services.blitz.impl.SearchI
 
hasntSeen(Object) - Method in class omero.util.IceMapper
 
hasOpticalAxisAveraged() - Method in class omero.gateway.model.OTFData
Returns a boolean flag if the value has been set
hasPump() - Method in class omero.gateway.model.LightSourceData
Returns true if the light source is a laser with a pump, false otherwise.
hasReference(LSID, LSID) - Method in interface ome.formats.model.IObjectContainerStore
Checks to see if there is currently an active reference for two LSIDs.
hasReference(LSID, LSID) - Method in class ome.formats.OMEROMetadataStoreClient
 
hasShapes - Variable in class ome.services.roi.GeomTool
 
hasStats() - Method in class omero.gateway.model.ChannelData
Returns true if the channel has some channel information false otherwise.
hasTextToSearch() - Method in class omero.gateway.model.SearchParameters
Returns true if text to search for, false otherwise.
Helper - Class in ome.services.blitz.measurements
Parallel type hierarchy to Column to facilitate (and speed-up) working with columns without adding methods to the slice definitions.
Helper() - Constructor for class ome.services.blitz.measurements.Helper
 
helper - Variable in class ome.services.blitz.repo.RawAccessRequestI
 
helper - Variable in class omero.cmd.admin.CurrentSessionsRequestI
 
helper - Variable in class omero.cmd.admin.UpdateSessionTimeoutRequestI
 
Helper - Class in omero.cmd
Helper object for all omero.cmd implementations.
Helper(Request, Status, SqlAction, Session, ServiceFactory) - Constructor for class omero.cmd.Helper
 
holder - Variable in class ome.services.blitz.impl.AbstractAmdServant
 
holder - Variable in class omero.cmd.SessionI
 
hostname - Variable in class ome.formats.importer.ImportConfig
 
HTM - Static variable in class omero.gateway.model.FileAnnotationData
Identifies the HTM file formats.
HTML - Static variable in class omero.gateway.model.FileAnnotationData
Identifies the HTML file formats.
HtmlMessenger - Class in ome.formats.importer.util
This class allows you to submit a URL and a String hash map of key-value pairs to be posted to the URL in question.
HtmlMessenger(String, Map<String, String>) - Constructor for class ome.formats.importer.util.HtmlMessenger
Instantiate messenger
HtmlMessengerException - Exception in ome.formats.importer.util
 
HtmlMessengerException(String, Exception) - Constructor for exception ome.formats.importer.util.HtmlMessengerException
Creates a new instance.
HtmlMessengerException(String) - Constructor for exception ome.formats.importer.util.HtmlMessengerException
Creates a new instance.

I

ice_exception(Exception) - Method in class ome.services.blitz.repo.PublicRepositoryI.AMD_submit
 
ice_postUnmarshal() - Method in class omero.model.PermissionsI
Called as Ice converts from a binary stream to a PermissionsI object.
ice_response(HandlePrx) - Method in class ome.services.blitz.repo.PublicRepositoryI.AMD_submit
 
IceMapper - Class in omero.util
Responsible for the mapping of ome.* types to omero.* types and back again.
IceMapper() - Constructor for class omero.util.IceMapper
 
IceMapper(IceMapper.ReturnMapping) - Constructor for class omero.util.IceMapper
 
IceMapper.ReturnMapping - Interface in omero.util
 
IceMethodInvoker - Class in ome.services.blitz.util
Method-cache primed either with an ServiceInterface instance or with a Class with generic type ServiceInterface.
IceMethodInvoker(ServiceInterface, OmeroContext) - Constructor for class ome.services.blitz.util.IceMethodInvoker
Create an IceMethodInvoker instance using the Class of the passed argument to call IceMethodInvoker.IceMethodInvoker(Class, OmeroContext).
IceMethodInvoker(Class<S>, OmeroContext) - Constructor for class ome.services.blitz.util.IceMethodInvoker
Creates an IceMethodInvoker instance by using reflection on the Class argument.
icMap - Variable in class ome.formats.importer.util.ErrorHandler
Host information about the file and its corresponding import candidate.
id - Variable in class ome.services.blitz.repo.CheckedPath
 
id - Variable in class ome.services.blitz.util.FindServiceFactoryMessage
 
ignoreAnnotator(String, Object...) - Method in class ome.formats.OMEROMetadataStoreClient
For all cases of an annotator being ignore (WARN).
ignoreInsecure(String, Object...) - Method in class ome.formats.OMEROMetadataStoreClient
Called when saving a property to OMERO would result in a SecurityViolation (DEBUG).
ignoreMissing(String, Object...) - Method in class ome.formats.OMEROMetadataStoreClient
Called when a property is missing from the OMERO model (WARN).
ignoreType(Iterable<String>) - Method in class omero.gateway.util.Requests.DuplicateBuilder
 
ignoreType(Class<? extends IObject>...) - Method in class omero.gateway.util.Requests.DuplicateBuilder
 
ignoreType(String...) - Method in class omero.gateway.util.Requests.DuplicateBuilder
 
IgnoreTypePolicy - Class in omero.cmd.graphs
Deprecated.
experimental: may be wholly removed in next major version
IgnoreTypePolicy() - Constructor for class omero.cmd.graphs.IgnoreTypePolicy
Deprecated.
 
ignoreUnneeded(String, Object...) - Method in class ome.formats.OMEROMetadataStoreClient
Called when a property is not needed in OMERO since the data can be gotten elsewhere, as in directly from the file itself (DEBUG).
ignoreUnsupported(String, Object...) - Method in class ome.formats.OMEROMetadataStoreClient
Called when a property is not expected in a file to be imported.
IHandle - Interface in omero.cmd
SPIOrthogonal interface hierarchy of types for working with the Request hierarchy.
IllegalArgumentException - Exception in omero
 
IllegalArgumentException(String) - Constructor for exception omero.IllegalArgumentException
 
IMAGE - Static variable in class omero.gateway.model.PixelsData
Identifies the PixelsI.IMAGE field.
IMAGE_COLUMN_INDEX - Static variable in class omero.gateway.model.TableResult
Identifies the index of the Image column.
IMAGE_LINKS - Static variable in class omero.gateway.model.DatasetData
Identifies the DatasetI.IMAGELINKS field.
ImageAcquisitionData - Class in omero.gateway.model
Object hosting the acquisition metadata.
ImageAcquisitionData(Image) - Constructor for class omero.gateway.model.ImageAcquisitionData
Creates a new instance.
imageCount - Variable in class ome.formats.importer.ImportSize
 
imageCount() - Method in class omero.gateway.model.FolderData
Get the number of images linked to this folder
ImageData - Class in omero.gateway.model
The data that makes up an OME Image along with links to its Pixels, enclosing Datasets, and the Experimenter that owns this Image.
ImageData() - Constructor for class omero.gateway.model.ImageData
Creates a new instance.
ImageData(Image) - Constructor for class omero.gateway.model.ImageData
Creates a new instance.
imageID - Variable in class loci.ome.io.OMECredentials
Deprecated.
 
ImageNameMetadataStore - Class in ome.formats
Stores all Image names consumed by the interface.
ImageNameMetadataStore() - Constructor for class ome.formats.ImageNameMetadataStore
 
ImagingEnvironment_AirPressure - Static variable in class ome.formats.model.UnitsFactory
 
ImagingEnvironment_Temperature - Static variable in class ome.formats.model.UnitsFactory
 
Impl(Communicator) - Constructor for class ome.services.blitz.fire.Registry.Impl
 
Impl(Communicator) - Constructor for class ome.services.blitz.fire.TopicManager.Impl
 
IMPORT_ARCHIVING(int, ImportContainer, IObject, Long, int, ImportSize) - Constructor for class ome.formats.importer.ImportEvent.IMPORT_ARCHIVING
 
IMPORT_DONE(int, ImportContainer, IObject, Long, int, ImportSize, List<Pixels>, Fileset, List<IObject>) - Constructor for class ome.formats.importer.ImportEvent.IMPORT_DONE
 
IMPORT_LOG_MIMETYPE - Static variable in class ome.services.blitz.repo.PublicRepositoryI
media type for import logs
IMPORT_OVERLAYS(int, ImportContainer, IObject, Long, int, ImportSize) - Constructor for class ome.formats.importer.ImportEvent.IMPORT_OVERLAYS
 
IMPORT_PROCESSING(int, ImportContainer, IObject, Long, int, ImportSize) - Constructor for class ome.formats.importer.ImportEvent.IMPORT_PROCESSING
 
IMPORT_STARTED(int, ImportContainer, IObject, Long, int, ImportSize, Integer, Integer, Long) - Constructor for class ome.formats.importer.ImportEvent.IMPORT_STARTED
 
IMPORT_STEP(int, int, int) - Constructor for class ome.formats.importer.ImportEvent.IMPORT_STEP
 
IMPORT_SUMMARY(long, int) - Constructor for class ome.formats.importer.ImportEvent.IMPORT_SUMMARY
 
ImportCallback(ImportProcessPrx, HandlePrx, ImportContainer) - Constructor for class ome.formats.importer.ImportLibrary.ImportCallback
 
ImportCandidates - Class in ome.formats.importer
Utility class which given any File object will determine the correct number and members of a given import.
ImportCandidates(OMEROWrapper, String[], IObserver) - Constructor for class ome.formats.importer.ImportCandidates
ImportCandidates(int, OMEROWrapper, String[], IObserver) - Constructor for class ome.formats.importer.ImportCandidates
Main constructor which starts depth-first descent into all the paths and permits a descent to the given depth.
importCandidates(ImportConfig, ImportCandidates) - Method in class ome.formats.importer.ImportLibrary
Primary user method for importing a number of import candidates.
ImportCandidates.CANCEL - Exception in ome.formats.importer
Marker exception raised if the ImportCandidates.SCANNING.cancel() method is called by an IObserver instance.
ImportCandidates.SCANNING - Class in ome.formats.importer
Event raised during a pass through the directory structure given to ImportCandidates.
ImportConfig - Class in ome.formats.importer
Utility class which configures the Import.
ImportConfig() - Constructor for class ome.formats.importer.ImportConfig
Simplest constructor which use calls ImportConfig.ImportConfig(File) with null.
ImportConfig(File) - Constructor for class ome.formats.importer.ImportConfig
Calls ImportConfig.ImportConfig(Preferences, IniFileLoader, Properties) with user preferences, a local PreferenceContext, an IniFileLoader initialized with the given argument, and System.getProperties().
ImportConfig(Preferences, IniFileLoader, Properties) - Constructor for class ome.formats.importer.ImportConfig
Complete constructor.
ImportConfig.AnnotationListValue - Class in ome.formats.importer
 
ImportConfig.BoolValue - Class in ome.formats.importer
 
ImportConfig.DoubleArrayValue - Class in ome.formats.importer
 
ImportConfig.FileValue - Class in ome.formats.importer
 
ImportConfig.IntValue - Class in ome.formats.importer
 
ImportConfig.LongValue - Class in ome.formats.importer
 
ImportConfig.PassValue - Class in ome.formats.importer
 
ImportConfig.StrValue - Class in ome.formats.importer
 
ImportConfig.Value<T> - Class in ome.formats.importer
Container which thread-safely makes a generic configuration value available, without requiring getters and setters.
ImportConfig.VersionInfo - Enum in ome.formats.importer
Keys for fileset version information entries.
ImportContainer - Class in ome.formats.importer
 
ImportContainer(File, IObject, Double[], String, String[], Boolean) - Constructor for class ome.formats.importer.ImportContainer
 
ImportContainer(ImportConfig, File, IObject, Double[], String, String[], Boolean) - Constructor for class ome.formats.importer.ImportContainer
 
ImportEvent - Class in ome.formats.importer
Simple event base-class used by IObservable and IObserver implementations.
ImportEvent() - Constructor for class ome.formats.importer.ImportEvent
 
ImportEvent.ADD - Class in ome.formats.importer
 
ImportEvent.BEGIN_POST_PROCESS - Class in ome.formats.importer
 
ImportEvent.BEGIN_SAVE_TO_DB - Class in ome.formats.importer
 
ImportEvent.COUNT_EVENT - Class in ome.formats.importer
 
ImportEvent.DATA_STORED - Class in ome.formats.importer
 
ImportEvent.DATASET_STORED - Class in ome.formats.importer
 
ImportEvent.DEBUG_SEND - Class in ome.formats.importer
 
ImportEvent.END_POST_PROCESS - Class in ome.formats.importer
 
ImportEvent.END_SAVE_TO_DB - Class in ome.formats.importer
 
ImportEvent.ERRORS_COMPLETE - Class in ome.formats.importer
 
ImportEvent.ERRORS_FAILED - Class in ome.formats.importer
 
ImportEvent.ERRORS_PENDING - Class in ome.formats.importer
 
ImportEvent.FILE_UPLOAD_BYTES - Class in ome.formats.importer
 
ImportEvent.FILE_UPLOAD_CANCELLED - Class in ome.formats.importer
 
ImportEvent.FILE_UPLOAD_COMPLETE - Class in ome.formats.importer
 
ImportEvent.FILE_UPLOAD_ERROR - Class in ome.formats.importer
 
ImportEvent.FILE_UPLOAD_EVENT - Class in ome.formats.importer
 
ImportEvent.FILE_UPLOAD_FAILED - Class in ome.formats.importer
 
ImportEvent.FILE_UPLOAD_FINISHED - Class in ome.formats.importer
 
ImportEvent.FILE_UPLOAD_STARTED - Class in ome.formats.importer
 
ImportEvent.FILESET_EXCLUSION - Class in ome.formats.importer
 
ImportEvent.FILESET_UPLOAD_END - Class in ome.formats.importer
 
ImportEvent.FILESET_UPLOAD_PREPARATION - Class in ome.formats.importer
 
ImportEvent.FILESET_UPLOAD_START - Class in ome.formats.importer
 
ImportEvent.IMPORT_ARCHIVING - Class in ome.formats.importer
 
ImportEvent.IMPORT_DONE - Class in ome.formats.importer
 
ImportEvent.IMPORT_OVERLAYS - Class in ome.formats.importer
 
ImportEvent.IMPORT_PROCESSING - Class in ome.formats.importer
 
ImportEvent.IMPORT_STARTED - Class in ome.formats.importer
 
ImportEvent.IMPORT_STEP - Class in ome.formats.importer
 
ImportEvent.IMPORT_SUMMARY - Class in ome.formats.importer
 
ImportEvent.LOADED_IMAGE - Class in ome.formats.importer
 
ImportEvent.LOADING_IMAGE - Class in ome.formats.importer
 
ImportEvent.LOGGED_IN - Class in ome.formats.importer
 
ImportEvent.LOGGED_OUT - Class in ome.formats.importer
 
ImportEvent.METADATA_IMPORTED - Class in ome.formats.importer
 
ImportEvent.METADATA_PROCESSED - Class in ome.formats.importer
 
ImportEvent.OBJECTS_RETURNED - Class in ome.formats.importer
 
ImportEvent.PIXELDATA_PROCESSED - Class in ome.formats.importer
 
ImportEvent.POST_UPLOAD_EVENT - Class in ome.formats.importer
 
ImportEvent.PROGRESS_EVENT - Class in ome.formats.importer
 
ImportEvent.REIMPORT - Class in ome.formats.importer
 
ImportEvent.THUMBNAILS_GENERATED - Class in ome.formats.importer
 
importFileset(Fileset, ImportSettings, Current) - Method in class ome.services.blitz.repo.ManagedRepositoryI
Return a template based directory path.
ImportFixture - Class in ome.formats.importer
test fixture for importing files without a GUI.
ImportFixture(OMEROMetadataStoreClient, OMEROWrapper) - Constructor for class ome.formats.importer.ImportFixture
 
importImage(ImportContainer, int, int, int) - Method in class ome.formats.importer.ImportLibrary
Deprecated.
now used by tests only
importImage(ImportContainer, ExecutorService, int) - Method in class ome.formats.importer.ImportLibrary
Perform an image import uploading files if necessary.
ImportLibrary - Class in ome.formats.importer
support class for the proper usage of OMEROMetadataStoreClient and FormatReader instances.
ImportLibrary(OMEROMetadataStoreClient, OMEROWrapper) - Constructor for class ome.formats.importer.ImportLibrary
The default implementation of FileTransfer performs a no-op and therefore need not have FileTransfer.afterTransfer(int, List) as with the ImportLibrary.ImportLibrary(OMEROMetadataStoreClient, OMEROWrapper, FileTransfer) constructor.
ImportLibrary(OMEROMetadataStoreClient, OMEROWrapper, FileTransfer) - Constructor for class ome.formats.importer.ImportLibrary
The library will not close the client instance.
ImportLibrary(OMEROMetadataStoreClient, OMEROWrapper, FileTransfer, int) - Constructor for class ome.formats.importer.ImportLibrary
 
ImportLibrary(OMEROMetadataStoreClient, OMEROWrapper, FileTransfer, List<FileExclusion>, int) - Constructor for class ome.formats.importer.ImportLibrary
 
ImportLibrary.ImportCallback - Class in ome.formats.importer
 
importMetadata(MetadataImportJob) - Method in class ome.services.blitz.repo.ManagedImportRequestI
Uses the OMEROMetadataStoreClient to save all metadata for the current image provided.
importPaths(List<String>, Current) - Method in class ome.services.blitz.repo.ManagedRepositoryI
 
ImportSize - Class in ome.formats.importer
Calculates the various dimensions of an image from a Pixels instance.
ImportSize(String, Pixels, String) - Constructor for class ome.formats.importer.ImportSize
 
ImportTarget - Interface in ome.formats.importer.targets
 
importTime - Variable in class ome.formats.importer.ImportEvent.IMPORT_SUMMARY
 
IN_MEMORY - Static variable in interface omero.gateway.cache.CacheService
Indicates to cache data in memory only.
includeNs(Iterable<String>) - Method in class omero.gateway.util.Requests.ChildOptionBuilder
 
includeNs(String...) - Method in class omero.gateway.util.Requests.ChildOptionBuilder
 
includeType(Iterable<String>) - Method in class omero.gateway.util.Requests.ChildOptionBuilder
 
includeType(Class<? extends IObject>...) - Method in class omero.gateway.util.Requests.ChildOptionBuilder
 
includeType(String...) - Method in class omero.gateway.util.Requests.ChildOptionBuilder
 
index - Variable in class ome.formats.importer.ImportEvent.COUNT_EVENT
 
index - Variable in class ome.formats.importer.ImportEvent.PROGRESS_EVENT
 
Index - Enum in ome.formats
 
index(IndexingJob) - Method in class ome.services.blitz.repo.ManagedImportRequestI
 
indexObject_async(AMD_IUpdate_indexObject, IObject, Current) - Method in class ome.services.blitz.impl.UpdateI
 
info(String, Object...) - Method in class omero.cmd.Helper
 
info(Object, String) - Method in interface omero.log.Logger
Logs an info message.
info(Object, LogMessage) - Method in interface omero.log.Logger
Logs an info message.
info(Object, String) - Method in class omero.log.NullLogger
 
info(Object, LogMessage) - Method in class omero.log.NullLogger
 
info(Object, String) - Method in class omero.log.SimpleLogger
 
info(Object, LogMessage) - Method in class omero.log.SimpleLogger
 
IniFileLoader - Class in ome.formats.importer.util
This class loads in the default importer.ini file (or one specified from the command line when starting the app)
IniFileLoader(File) - Constructor for class ome.formats.importer.util.IniFileLoader
Load given file
init(String) - Method in interface ome.formats.importer.targets.ImportTarget
 
init(String) - Method in class ome.formats.importer.targets.ModelImportTarget
 
init(String) - Method in class ome.formats.importer.targets.TemplateImportTarget
 
init(ObjectAdapter, String) - Method in class ome.services.blitz.fire.Ring
Typically called from within BlitzConfiguration after the communicator and adapter have been properly setup.
init(Helper) - Method in class ome.services.blitz.impl.commands.SaveI
 
init(String) - Method in class ome.services.blitz.repo.FileMaker
 
init(String, boolean) - Method in class ome.services.blitz.repo.FileMaker
 
init(Helper) - Method in class ome.services.blitz.repo.ManagedImportRequestI
 
init(Helper) - Method in class ome.services.blitz.repo.RawAccessRequestI
 
init(Helper) - Method in class omero.cmd.admin.CurrentSessionsRequestI
 
init(Helper) - Method in class omero.cmd.admin.ResetPasswordRequestI
 
init(Helper) - Method in class omero.cmd.admin.UpdateSessionTimeoutRequestI
 
init(Helper) - Method in class omero.cmd.basic.DoAllI
 
init(Helper) - Method in class omero.cmd.basic.ListRequestsI
 
init(Helper) - Method in class omero.cmd.basic.TimingI
 
init(Helper) - Method in class omero.cmd.fs.FindPyramidsI
 
init(Helper) - Method in class omero.cmd.fs.ManageImageBinariesI
 
init(Helper) - Method in class omero.cmd.fs.OriginalMetadataRequestI
 
init(Helper) - Method in class omero.cmd.fs.UsedFilesRequestI
 
init(Helper) - Method in class omero.cmd.graphs.Chgrp2I
 
init() - Method in class omero.cmd.graphs.ChildOptionI
Initialize this child option instance.
init(Helper) - Method in class omero.cmd.graphs.Chmod2I
 
init(Helper) - Method in class omero.cmd.graphs.Chown2I
 
init(Helper) - Method in class omero.cmd.graphs.Delete2I
 
init(Helper) - Method in class omero.cmd.graphs.DiskUsage2I
 
init(Helper) - Method in class omero.cmd.graphs.DiskUsageI
Deprecated.
 
init(Helper) - Method in class omero.cmd.graphs.DuplicateI
 
init(Helper) - Method in class omero.cmd.graphs.FindChildrenI
 
init(Helper) - Method in class omero.cmd.graphs.FindParentsI
 
init(Helper) - Method in class omero.cmd.graphs.LegalGraphTargetsI
 
init(Helper) - Method in class omero.cmd.graphs.SkipHeadI
 
init(Helper) - Method in interface omero.cmd.IRequest
Method called within the transaction boundaries before any processing occurs.
init(Helper) - Method in class omero.cmd.mail.SendEmailRequestI
 
initFile(String) - Method in class loci.ome.io.OmeroReader
Deprecated.
 
initFile(String) - Method in class ome.services.formats.OmeroReader
 
initializationDone() - Method in class omero.cmd.CmdCallbackI
Subclasses which must perform their own initialization before CmdCallbackI.onFinished(Response, Status, Current) is called should call CmdCallbackI.initializationDone() once that setup is complete.
initialize(ServiceFactoryPrx) - Method in class ome.formats.OMEROMetadataStoreClient
Initializes the MetadataStore with an already logged in, ready to go service factory.
initialize(client) - Method in class ome.formats.OMEROMetadataStoreClient
Initializes the MetadataStore with an already logged in, ready to go service factory.
initialize(String, String, String, int) - Method in class ome.formats.OMEROMetadataStoreClient
Initializes the MetadataStore taking string parameters to feed to the OMERO Blitz client object.
initialize(String, String, String, int, boolean) - Method in class ome.formats.OMEROMetadataStoreClient
Initializes the MetadataStore taking string parameters to feed to the OMERO Blitz client object.
initialize(String, String, String, int, Long, boolean) - Method in class ome.formats.OMEROMetadataStoreClient
Initializes the MetadataStore taking string parameters to feed to the OMERO Blitz client object.
initialize(String, int, String) - Method in class ome.formats.OMEROMetadataStoreClient
Initializes the MetadataStore by joining an existing session.
initialize(String, int, String, boolean) - Method in class ome.formats.OMEROMetadataStoreClient
Initializes the MetadataStore by joining an existing session.
initialize(ServiceFactoryPrx, List<Pixels>, List<Long>) - Method in class ome.formats.OverlayMetadataStore
Initializes the metadata store implementation.
initialize(Session) - Method in class ome.services.blitz.impl.OmeroMetadata
 
initialize(String[], String[], Class[], Map<String, Object>) - Method in class ome.services.blitz.measurements.MeasurementStore
 
initialize(String[], String[], Class[], Map<String, Object>) - Method in interface ome.services.blitz.measurements.OmeroMeasurementStore
 
initialize(FileMaker, Long, String) - Method in class ome.services.blitz.repo.ManagedRepositoryI
 
initialize(FileMaker, Long, String) - Method in class ome.services.blitz.repo.PublicRepositoryI
Called by the internal repository once initialization has taken place.
initialize(Identity, IRequest, Map<String, String>) - Method in class omero.cmd.HandleI
 
initialize(Identity, IRequest, Map<String, String>) - Method in interface omero.cmd.IHandle
Must be called on all instances exactly once before processing.
initializeRedirect(Redirector.Context, String) - Method in class ome.services.blitz.redirect.AbstractRedirector
Set the new redirect value if null, or if the uuid is null or empty, then the existing redirect will be removed.
initialPoll() - Method in class omero.cmd.CmdCallbackI
Called at the end of construction to check a race condition.
insertEntity(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
INSIGHT_PUBLISHED_NS - Static variable in class omero.gateway.model.BooleanAnnotationData
The name space used to indicate that the tag is used a tag set.
INSIGHT_RATING_NS - Static variable in class omero.gateway.model.RatingAnnotationData
The name space used to identify the archived annotation linked to a set of pixels.
INSIGHT_TAGSET_NS - Static variable in class omero.gateway.model.TagAnnotationData
The name space used to indicate that the tag is used a tag set.
InstanceProvider - Interface in ome.formats.model
An instance provider, whose job is to make OMERO Blitz classes available to a consumer based on a set of criteria.
INSTITUTION - Static variable in class omero.gateway.model.ExperimenterData
Identifies the ExperimenterI.INSTITUTION field.
InstrumentData - Class in omero.gateway.model
Hosts the instrument used to capture an image.
InstrumentData(Instrument) - Constructor for class omero.gateway.model.InstrumentData
Creates a new instance.
InstrumentProcessor - Class in ome.formats.model
Processes the members of an Instrument (Objective, OTF, Arc Laser and Filament) and ensures that the Instrument containers are present in the container cache, adding them if they are missing.
InstrumentProcessor() - Constructor for class ome.formats.model.InstrumentProcessor
 
INT16_TYPE - Static variable in class omero.gateway.model.PixelsData
Identifies the type used to store pixel values.
INT32_TYPE - Static variable in class omero.gateway.model.PixelsData
Identifies the type used to store pixel values.
INT8_TYPE - Static variable in class omero.gateway.model.PixelsData
Identifies the type used to store pixel values.
INT_16 - Static variable in class omero.gateway.rnd.DataSink
Identifies the type used to store pixel values.
INT_32 - Static variable in class omero.gateway.rnd.DataSink
Identifies the type used to store pixel values.
INT_8 - Static variable in class omero.gateway.rnd.DataSink
Identifies the type used to store pixel values.
IntConverter - Class in omero.gateway.rnd
Packs a sequence of bytes representing a signed (2's complement) big-endian integer into an integer value of appropriate integer value.
IntConverter() - Constructor for class omero.gateway.rnd.IntConverter
 
InteractiveProcessorI - Class in omero.grid
Processor implementation which delegates to an omero.grid.Processor servant.
InteractiveProcessorI(Principal, SessionManager, Executor, ProcessorPrx, Job, long, SessionControlPrx, ParamsCache, ParamsHelper, ScriptRepoHelper, Current) - Constructor for class omero.grid.InteractiveProcessorI
 
interceptor - Variable in class ome.services.blitz.impl.ScriptI
 
interceptor - Variable in class ome.services.blitz.repo.RepositoryDaoImpl
 
INTERNAL_EXCEPTION(String, Exception, String[], String) - Constructor for class ome.formats.importer.util.ErrorHandler.INTERNAL_EXCEPTION
 
internalMkdir(CheckedPath) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
This method should only be used by the register public method in order to guarantee that the DB is kept in sync with the file system.
InternalRepositoryConfig - Class in ome.services.blitz.repo
Simple configuration class which is created via repository.xml Spring configuration file after the OMERO.repository context is loaded.
InternalRepositoryConfig(String) - Constructor for class ome.services.blitz.repo.InternalRepositoryConfig
 
InternalRepositoryI - Class in ome.services.blitz.repo
Standalone repository service.
InternalRepositoryI(ObjectAdapter, Registry, Executor, Principal, String, PublicRepositoryI) - Constructor for class ome.services.blitz.repo.InternalRepositoryI
Deprecated.
InternalRepositoryI(ObjectAdapter, Registry, Executor, Principal, String, ReadOnlyStatus, PublicRepositoryI) - Constructor for class ome.services.blitz.repo.InternalRepositoryI
 
internalServantConfig(Object) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
internalServantConfig(Object) - Method in class omero.cmd.SessionI
 
InThreadThrottlingStrategy - Class in ome.services.throttling
Throttling implementation which uses the calling server Thread for execution.
InThreadThrottlingStrategy(CurrentDetails) - Constructor for class ome.services.throttling.InThreadThrottlingStrategy
 
IntValue(String, ImportConfig, int) - Constructor for class ome.formats.importer.ImportConfig.IntValue
 
IntValue(String, ImportConfig, int, String) - Constructor for class ome.formats.importer.ImportConfig.IntValue
 
invalidateConnection_async(AMD_IShare_invalidateConnection, long, Experimenter, Current) - Method in class ome.services.blitz.impl.ShareI
 
invoke(MethodInvocation) - Method in class ome.services.blitz.fire.AopContextInitializer
 
invoke(Object, Current, IceMapper, Object...) - Method in class ome.services.blitz.util.IceMethodInvoker
Calls the method named in Current.operation with the arguments provided mapped via the IceMapper instance.
invoke(MethodInvocation) - Method in class omero.cmd.CallContext
 
invoker - Variable in class ome.services.blitz.impl.AbstractAmdServant
If a service is provided, then an invoker will be created to cache all of its methods.
IObjectContainerStore - Interface in ome.formats.model
An object that handles the storage and manipulation of IObject containers and their references.
IObservable - Interface in ome.formats.importer
 
IObserver - Interface in ome.formats.importer
 
IQueryEnumProvider - Class in ome.formats.enums
An enumeration provider which uses IQuery and a cache to fulfill the contract of an EnumerationProvider.
IQueryEnumProvider(IQueryPrx) - Constructor for class ome.formats.enums.IQueryEnumProvider
Default IQuery based enumeration provider constructor.
IRequest - Interface in omero.cmd
SPI Orthogonal interface hierarchy of types for working with the Request hierarchy.
isAcceptable(List<String>) - Method in class ome.services.blitz.repo.path.MakeNextDirectory
If the circumstances (filesystem, etc.) are such that it is okay to use the given subdirectories.
isAccepted(boolean, String, String, Current) - Method in class ome.services.blitz.impl.ProcessorCallbackI
Deprecated.
isActive() - Method in class omero.gateway.model.ExperimenterData
Returns true if the experimenter is active, false otherwise.
isActive_async(AMD_RenderingEngine_isActive, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
isAdjustedAfterReview(GraphPolicy.Details) - Method in class omero.cmd.graphs.BaseGraphPolicyAdjuster
An opportunity to adjust each model object after the graph policy reviews it.
isAdjustedBeforeReview(GraphPolicy.Details) - Method in class omero.cmd.graphs.BaseGraphPolicyAdjuster
An opportunity to adjust each model object before the graph policy reviews it.
isAlive(SecurityContext) - Method in class omero.gateway.Gateway
Checks if there is a Connector for a particular SecurityContext
isAllowLeadingWildcard_async(AMD_Search_isAllowLeadingWildcard, Current) - Method in class ome.services.blitz.impl.SearchI
 
isArchived() - Method in class omero.gateway.model.ImageData
Returns true if the image has been archived, false otherwise.
isAvailable() - Method in class omero.gateway.util.NetworkChecker
Checks the network is available or not.
isCancelled() - Method in class omero.cmd.CmdCallbackI
Returns whether Status::CANCELLED is contained in the flags variable of the Status instance.
isCaseSensitive_async(AMD_Search_isCaseSensitive, Current) - Method in class ome.services.blitz.impl.SearchI
 
isCheckNetwork() - Method in class omero.gateway.LoginCredentials
 
isClientObject() - Method in class omero.gateway.model.ShapeData
Returns true if the object one that has been created client side.
isClientSide() - Method in class omero.gateway.model.ROIData
Returns true if the object a client-side object, false otherwise.
isCompleted() - Method in class omero.gateway.model.TableData
 
isCondition(String) - Method in class omero.cmd.graphs.BaseGraphPolicyAdjuster
 
isConnected() - Method in class omero.gateway.Gateway
Check if the Gateway is still connected to the server
isDebugConsole() - Method in class ome.formats.importer.util.IniFileLoader
 
isDebugUI() - Method in class ome.formats.importer.util.IniFileLoader
 
isDetectorSettingsDirty() - Method in class omero.gateway.model.ChannelAcquisitionData
Returns true if the detector settings has been updated, false otherwise.
isDirectory() - Method in class ome.services.blitz.repo.CheckedPath
 
isDirectory() - Method in class omero.gateway.model.FileData
Returns true if the file is a directory, false otherwise.
isDirty() - Method in class omero.gateway.model.DataObject
Returns true if setter value has modified the value of the stored IObject, false otherwise.
isDisallow(int, Current) - Method in class omero.model.PermissionsI
 
isEmpty() - Method in class omero.gateway.model.TableData
 
isEncryptedConnection() - Method in class ome.formats.OMEROMetadataStoreClient
 
isEncryption() - Method in class omero.gateway.LoginCredentials
 
isEndTime() - Method in class omero.sys.ParametersI
Returns true if the map contains the end time parameter, false otherwise.
isError() - Method in class omero.gateway.model.SearchResultCollection
 
isExperimenter() - Method in class omero.sys.ParametersI
Returns true if the filter contains and ownerId parameter, false otherwise.
isFailure() - Method in class omero.cmd.CmdCallbackI
Returns whether Status::FAILURE is contained in the flags variable of the Status instance.
isFloat_async(AMD_RawPixelsStore_isFloat, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
isFloat_async(AMD_RawPixelsStore_isFloat, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
isFontBold() - Method in class omero.gateway.model.ShapeSettingsData
Returns true if it is bold, false otherwise.
isFontItalic() - Method in class omero.gateway.model.ShapeSettingsData
Returns true if it is italic, false otherwise.
isFSImage() - Method in class omero.gateway.model.ImageData
Returns true is the image has been imported the new import strategy known as FS import, false if imported using the previous import approach (data duplication).
isFullAdmin(SecurityContext) - Method in class omero.gateway.facility.AdminFacility
Checks if the currently logged in user has full admin privileges
isFullAdmin(SecurityContext, ExperimenterData) - Method in class omero.gateway.facility.AdminFacility
Checks if a user has full admin privileges
isGroup() - Method in class omero.sys.ParametersI
Returns true if the filter contains an groupId, false otherwise.
isGroupAnnotate() - Method in class omero.gateway.model.PermissionData
Returns true if the group has annotate access i.e.
isGroupAnnotate(Current) - Method in class omero.model.PermissionsI
 
isGroupRead() - Method in class omero.gateway.model.PermissionData
Returns true if the group has read access i.e.
isGroupRead(Current) - Method in class omero.model.PermissionsI
 
isGroupWrite() - Method in class omero.gateway.model.PermissionData
Returns true if the group has write access i.e.
isGroupWrite(Current) - Method in class omero.model.PermissionsI
 
isHidden() - Method in class omero.gateway.model.FileData
Returns true if the file is hidden, false otherwise.
isIdMatch() - Method in class omero.gateway.model.SearchResult
Indicates if this result is an ID match
isImagingEnvironmentDirty() - Method in class omero.gateway.model.ImageAcquisitionData
Returns true if the StageLabel has been updated, false otherwise.
isImmutable(Object) - Method in class omero.util.IceMapper
 
isIncludeType(Class<? extends IObject>) - Method in class omero.cmd.graphs.ChildOptionI
Test if this child option adjusts graph traversal policy for the given child object class.
isInProgress_async(AMD_ThumbnailStore_isInProgress, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
 
isLast(int) - Method in class omero.cmd.Helper
Returns true if this is the last step for the given request.
isLDAP() - Method in class omero.gateway.model.ExperimenterData
Returns true if the user is connected via LDAP.
isLegalFsFile(FsFile) - Method in class ome.services.blitz.repo.path.ServerFilePathTransformer
Test if the given FsFile has been properly sanitized by the client.
isLeicaReader() - Method in class ome.formats.importer.OMEROWrapper
 
isLifetime() - Method in class omero.gateway.model.ImageData
Returns true if the image is a lifetime image, false otherwise.
isLightSourceSettingsDirty() - Method in class omero.gateway.model.ChannelAcquisitionData
Returns true if the light source settings has been updated, false otherwise.
isLinux() - Static method in class ome.services.blitz.util.CurrentPlatform
 
isLoaded() - Method in class omero.gateway.model.DataObject
Returns true if the object is loaded, false otherwise.
isMacOSX() - Static method in class ome.services.blitz.util.CurrentPlatform
 
isMemberOfGroup(long) - Method in class omero.gateway.model.ExperimenterData
Checks if supplied group id matches any group to which the current experimenter belongs to.
isMergedBatches_async(AMD_Search_isMergedBatches, Current) - Method in class ome.services.blitz.impl.SearchI
 
isMinMaxSet() - Method in class ome.formats.importer.OMEROWrapper
 
isMovieFile() - Method in class omero.gateway.model.FileAnnotationData
Returns true if it is a movie file.
isNetworkUp(boolean) - Method in class omero.gateway.Gateway
Checks if the network interface is up.
isNetworkup(boolean) - Method in class omero.gateway.util.NetworkChecker
Returns true if the network is still up, otherwise throws an UnknownHostException.
isNullablePrimitive(Class<?>) - Static method in class omero.util.IceMapper
 
isObjectiveSettingsDirty() - Method in class omero.gateway.model.ImageAcquisitionData
Returns true if the objective settings has been updated, false otherwise.
isOMERO - Variable in class loci.ome.io.OMECredentials
Deprecated.
 
isPagination() - Method in class omero.sys.ParametersI
Returns true if the filter contains a limit OR a offset, false otherwise.
isPixelsTypeSigned_async(AMD_RenderingEngine_isPixelsTypeSigned, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
isPrimitive(Class<?>) - Method in class omero.util.IceMapper
 
isProxyAccepted(boolean, String, ProcessorPrx, Current) - Method in class ome.services.blitz.impl.ProcessorCallbackI
Callback method called by the remote processor instance.
isReadOnly(ReadOnlyStatus) - Method in class omero.cmd.admin.CurrentSessionsRequestI
 
isReadOnly(ReadOnlyStatus) - Method in class omero.cmd.basic.DoAllI
 
isReadOnly(ReadOnlyStatus) - Method in class omero.cmd.fs.FindPyramidsI
 
isReadOnly(ReadOnlyStatus) - Method in class omero.cmd.fs.OriginalMetadataRequestI
 
isReadOnly(ReadOnlyStatus) - Method in class omero.cmd.fs.UsedFilesRequestI
 
isReadOnly(ReadOnlyStatus) - Method in class omero.cmd.graphs.Chgrp2I
 
isReadOnly(ReadOnlyStatus) - Method in class omero.cmd.graphs.Chmod2I
 
isReadOnly(ReadOnlyStatus) - Method in class omero.cmd.graphs.Chown2I
 
isReadOnly(ReadOnlyStatus) - Method in class omero.cmd.graphs.Delete2I
 
isReadOnly(ReadOnlyStatus) - Method in class omero.cmd.graphs.DiskUsage2I
 
isReadOnly(ReadOnlyStatus) - Method in class omero.cmd.graphs.DiskUsageI
Deprecated.
 
isReadOnly(ReadOnlyStatus) - Method in class omero.cmd.graphs.DuplicateI
 
isReadOnly(ReadOnlyStatus) - Method in class omero.cmd.graphs.FindChildrenI
 
isReadOnly(ReadOnlyStatus) - Method in class omero.cmd.graphs.FindParentsI
 
isReadOnly(ReadOnlyStatus) - Method in class omero.cmd.graphs.LegalGraphTargetsI
 
isReadOnly(ReadOnlyStatus) - Method in class omero.cmd.graphs.SkipHeadI
 
isReadOnly(ReadOnlyStatus) - Method in class omero.cmd.mail.SendEmailRequestI
 
isReadOnly() - Method in class omero.gateway.model.ShapeData
Returns true if the object a read-only object, false otherwise.
isRestricted(String, Current) - Method in class omero.model.PermissionsI
 
isReturnUnloaded_async(AMD_Search_isReturnUnloaded, Current) - Method in class ome.services.blitz.impl.SearchI
 
isRoot - Variable in class ome.services.blitz.repo.CheckedPath
 
isSame(long) - Method in class omero.gateway.rnd.DataSink
Returns true if a data source has already been created for the specified pixels set, false otherwise.
isSecure() - Method in class omero.client
Specifies whether or not this client was created via a call to client.createClient(boolean) with a boolean of false.
isSend(int) - Method in class ome.formats.importer.util.ErrorHandler
Check if files need sending at error container index
isSigned_async(AMD_RawPixelsStore_isSigned, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
isSigned_async(AMD_RawPixelsStore_isSigned, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
isSPWReader() - Method in class ome.formats.importer.OMEROWrapper
 
isStageLabelDirty() - Method in class omero.gateway.model.ImageAcquisitionData
Returns true if the position has been updated, false otherwise.
isStartTime() - Method in class omero.sys.ParametersI
Returns true if the map contains the start time parameter, false otherwise.
isStatisticsEnabled() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
Are statistics logged
isSudo() - Method in class omero.gateway.SecurityContext
Returns true if a session has to be created for another user, false otherwise.
isTargetNamespace(String) - Method in class omero.cmd.graphs.ChildOptionI
Test if this child option adjusts graph traversal policy for child objects that are annotations in the given namespace.
isThisType(String, boolean) - Method in class loci.ome.io.OmeroReader
Deprecated.
 
isThisType(String, boolean) - Method in class ome.services.formats.OmeroReader
 
isThisType(RandomAccessInputStream) - Method in class ome.services.formats.OmeroReader
 
isUnknown() - Static method in class ome.services.blitz.util.CurrentPlatform
 
isUpgradeNeeded() - Method in class ome.formats.importer.ImportConfig
Check online to see if this is the current version
isUseProjections_async(AMD_Search_isUseProjections, Current) - Method in class ome.services.blitz.impl.SearchI
 
isUserAnnotate(Current) - Method in class omero.model.PermissionsI
 
isUserRead() - Method in class omero.gateway.model.PermissionData
Returns true if the user has read access, false otherwise.
isUserRead(Current) - Method in class omero.model.PermissionsI
 
isUserWrite() - Method in class omero.gateway.model.PermissionData
Returns true if the user has write access, false otherwise.
isUserWrite(Current) - Method in class omero.model.PermissionsI
 
isValid() - Method in class omero.gateway.model.SearchParameters
Returns true if the context of the search is valid i.e.
isVoid(Current) - Method in class ome.services.blitz.util.IceMethodInvoker
Checks for a void return type, which is needed to know what type of ice_response() method to invoke.
isVoid - Variable in class ome.services.throttling.Task
 
isVoid() - Method in class omero.util.IceMapper
Returns true only if the current mapping is the IceMapper.VOID mapping.
isWindows() - Method in class ome.formats.importer.transfers.AbstractFileTransfer
Uses os.name to determine whether or not this JVM is running under Windows.
isWindows() - Static method in class ome.services.blitz.util.CurrentPlatform
 
isWorldAnnotate(Current) - Method in class omero.model.PermissionsI
 
isWorldRead() - Method in class omero.gateway.model.PermissionData
Returns true if the world has read access, false otherwise.
isWorldRead(Current) - Method in class omero.model.PermissionsI
 
isWorldWrite() - Method in class omero.gateway.model.PermissionData
Returns true if the world has write access, false otherwise.
isWorldWrite(Current) - Method in class omero.model.PermissionsI
 
isWrapperArray(Class<?>) - Static method in class omero.util.IceMapper
 

J

jobError_async(AMD_JobHandle_jobError, Current) - Method in class ome.services.blitz.impl.JobHandleI
 
jobFinished_async(AMD_JobHandle_jobFinished, Current) - Method in class ome.services.blitz.impl.JobHandleI
 
JobHandleI - Class in ome.services.blitz.impl
Implementation of the JobHandle service.
JobHandleI(JobHandle, BlitzExecutor) - Constructor for class ome.services.blitz.impl.JobHandleI
 
jobMessage_async(AMD_JobHandle_jobMessage, Current) - Method in class ome.services.blitz.impl.JobHandleI
 
jobRunning_async(AMD_JobHandle_jobRunning, Current) - Method in class ome.services.blitz.impl.JobHandleI
 
jobStatus_async(AMD_JobHandle_jobStatus, Current) - Method in class ome.services.blitz.impl.JobHandleI
 
joinSession(String) - Method in class omero.client
Uses the given session uuid as name and password to rejoin a running session.
joinSession() - Method in class omero.gateway.Gateway
Tries to rejoin the session.
JoinSessionCredentials - Class in omero.gateway
Holds all necessary information needed for joining an active OMERO server session
JoinSessionCredentials(String, String) - Constructor for class omero.gateway.JoinSessionCredentials
Creates a new instance
JoinSessionCredentials(String, String, int) - Constructor for class omero.gateway.JoinSessionCredentials
Creates a new instance

K

keepAlive(ServiceInterfacePrx, Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
Currently ignoring the individual proxies
keepAllAlive(ServiceInterfacePrx[], Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
key - Variable in enum ome.formats.importer.ImportConfig.VersionInfo
the map key corresponding to this instance
kill(Current) - Method in class ome.services.blitz.impl.ScriptProcessI
 
killSession() - Method in class omero.client
Calls ISession.closeSession(omero.model.Session) until the returned reference count is greater than zero.
knownManagers() - Method in class ome.services.blitz.fire.Ring
 

L

LASER - Static variable in class omero.gateway.model.LightSourceData
Indicates that the light source is a laser.
Laser_RepetitionRate - Static variable in class ome.formats.model.UnitsFactory
 
Laser_Wavelength - Static variable in class ome.formats.model.UnitsFactory
 
lastModified() - Method in class omero.gateway.model.FileData
Returns when the file was last modified.
LASTNAME - Static variable in class omero.gateway.model.ExperimenterData
Identifies the ExperimenterI.LASTNAME field.
lastPlane() - Method in class omero.gateway.model.ROIData
Deprecated.
Will be removed in future. Does not work as expected if the ROI contains shapes which are associated with all planes (Z, C, T == -1)
launchProcessing() - Method in class ome.formats.OMEROMetadataStoreClient
 
LdapI - Class in ome.services.blitz.impl
Implementation of the ILdap service.
LdapI(ILdap, BlitzExecutor) - Constructor for class ome.services.blitz.impl.LdapI
 
leaves() - Method in class omero.sys.ParametersI
Sets the leaf parameter to true.
LegacyRepositoryI - Class in ome.services.blitz.repo
Repository which makes the ${omero.data.dir} directory available via the standard Repository API.
LegacyRepositoryI(ObjectAdapter, Registry, Executor, Principal, String, PublicRepositoryI) - Constructor for class ome.services.blitz.repo.LegacyRepositoryI
Deprecated.
LegacyRepositoryI(ObjectAdapter, Registry, Executor, Principal, String, ReadOnlyStatus, PublicRepositoryI) - Constructor for class ome.services.blitz.repo.LegacyRepositoryI
 
LegacyRepositoryI(ObjectAdapter, Registry, Executor, Principal, FileMaker, PublicRepositoryI) - Constructor for class ome.services.blitz.repo.LegacyRepositoryI
Deprecated.
LegacyRepositoryI(ObjectAdapter, Registry, Executor, Principal, FileMaker, ReadOnlyStatus, PublicRepositoryI) - Constructor for class ome.services.blitz.repo.LegacyRepositoryI
 
LegalGraphTargetsI - Class in omero.cmd.graphs
Query which model object classes are legal as targets for a request.
LegalGraphTargetsI(GraphRequestFactory) - Constructor for class omero.cmd.graphs.LegalGraphTargetsI
Construct a new legal graph targets query.
length - Variable in class omero.util.ReadOnlyByteArray
The length of the slice.
LengthI - Class in omero.model
Blitz wrapper around the Length class.
LengthI() - Constructor for class omero.model.LengthI
 
LengthI(double, UnitsLength) - Constructor for class omero.model.LengthI
 
LengthI(double, Unit<Length>) - Constructor for class omero.model.LengthI
 
LengthI(Length, Unit<Length>) - Constructor for class omero.model.LengthI
Copy constructor that converts the given Length based on the given ome-xml enum
LengthI(double, UnitsLength) - Constructor for class omero.model.LengthI
Copy constructor that converts the given Length based on the given ome.model enum
LengthI(Length, String) - Constructor for class omero.model.LengthI
Copy constructor that converts the given Length based on the given enum string.
LengthI(Length, UnitsLength) - Constructor for class omero.model.LengthI
Copy constructor that converts between units if possible.
LengthI(Length) - Constructor for class omero.model.LengthI
Convert a Bio-Formats Length to an OMERO Length.
LEVEL_FIVE - Static variable in class omero.gateway.model.RatingAnnotationData
Indicates the object is rated with five stars.
LEVEL_FOUR - Static variable in class omero.gateway.model.RatingAnnotationData
Indicates the object is rated with four stars.
LEVEL_ONE - Static variable in class omero.gateway.model.RatingAnnotationData
Indicates the object is rated with one star.
LEVEL_THREE - Static variable in class omero.gateway.model.RatingAnnotationData
Indicates the object is rated with three stars.
LEVEL_TWO - Static variable in class omero.gateway.model.RatingAnnotationData
Indicates the object is rated with two stars.
LEVEL_ZERO - Static variable in class omero.gateway.model.RatingAnnotationData
Indicates the object is not rated.
library - Variable in class ome.formats.importer.cli.CommandLineImporter
Base importer library, this is what we actually use to import.
LIGHT_EMITTING_DIODE - Static variable in class omero.gateway.model.LightSourceData
Indicates that the light source is a light emitting diode.
LightPathData - Class in omero.gateway.model
Object hosting a light path.
LightPathData(LightPath) - Constructor for class omero.gateway.model.LightPathData
Creates a new instance.
LightSource_Power - Static variable in class ome.formats.model.UnitsFactory
 
LightSourceData - Class in omero.gateway.model
Object hosting a light source: filament, arc, laser or light emitting diode
LightSourceData(LightSource) - Constructor for class omero.gateway.model.LightSourceData
Creates a new instance.
LightSourceSettings_Wavelength - Static variable in class ome.formats.model.UnitsFactory
 
LineData - Class in omero.gateway.model
Represents a line in the Euclidean space R2.
LineData(Shape) - Constructor for class omero.gateway.model.LineData
Creates a new instance.
LineData() - Constructor for class omero.gateway.model.LineData
Create a new instance of LineData, creating a new LineI Object.
LineData(double, double, double, double) - Constructor for class omero.gateway.model.LineData
Create a new instance of the LineData,
link_async(AMD_IContainer_link, List<IObject>, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI
 
linkAnnotation(IObject, Annotation) - Static method in class omero.gateway.util.ModelMapper
Links the annotation to the passed object.
linkParentToChild(IObject, IObject) - Static method in class omero.gateway.util.ModelMapper
Links the child to its parent.
linkParentToNewChild(IObject, IObject) - Static method in class omero.gateway.util.ModelMapper
Links the newly created child to its parent.
list(String, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
 
listChecksumAlgorithms(Current) - Method in class ome.services.blitz.repo.ManagedRepositoryI
 
listFiles(String, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
 
listImports(Current) - Method in class ome.services.blitz.repo.ManagedRepositoryI
 
LISTOBJECTARRAY_TO_RTYPESEQSEQ - Static variable in class omero.util.IceMapper
 
listProcesses(Collection<Long>) - Method in class ome.services.blitz.repo.ProcessContainer
 
ListRequestsI - Class in omero.cmd.basic
 
ListRequestsI(OmeroContext) - Constructor for class omero.cmd.basic.ListRequestsI
 
ln(double, double, double, double) - Method in class ome.services.roi.GeomTool
 
load() - Method in class ome.formats.importer.ImportConfig.Value
Loads properties from various locations.
load(OMEROMetadataStoreClient, ImportContainer) - Method in interface ome.formats.importer.targets.ImportTarget
 
load(OMEROMetadataStoreClient, ImportContainer) - Method in class ome.formats.importer.targets.ModelImportTarget
 
load(OMEROMetadataStoreClient, ImportContainer) - Method in class ome.formats.importer.targets.ServerTemplateImportTarget
 
load(OMEROMetadataStoreClient, boolean) - Method in class ome.formats.importer.targets.ServerTemplateImportTarget
 
load(OMEROMetadataStoreClient, ImportContainer) - Method in class ome.formats.importer.targets.TemplateImportTarget
 
load_async(AMD_RenderingEngine_load, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
loadAll() - Method in class ome.formats.importer.ImportConfig
Loads all the values for which it makes sense to have a preferences values.
loadAnnotation_async(AMD_IMetadata_loadAnnotation, List<Long>, Current) - Method in class ome.services.blitz.impl.MetadataI
 
loadAnnotations_async(AMD_IMetadata_loadAnnotations, String, List<Long>, List<String>, List<Long>, Parameters, Current) - Method in class ome.services.blitz.impl.MetadataI
 
loadAnnotationsUsedNotOwned_async(AMD_IMetadata_loadAnnotationsUsedNotOwned, String, long, Current) - Method in class ome.services.blitz.impl.MetadataI
 
loadChannelAcquisitionData_async(AMD_IMetadata_loadChannelAcquisitionData, List<Long>, Current) - Method in class ome.services.blitz.impl.MetadataI
 
loadCollection(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
loadContainerHierarchy_async(AMD_IContainer_loadContainerHierarchy, String, List<Long>, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI
 
loaded - Variable in class ome.services.blitz.fire.SessionManagerI
 
LOADED_IMAGE(String, Integer, Integer, Integer) - Constructor for class ome.formats.importer.ImportEvent.LOADED_IMAGE
 
loadEntity(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
loadFileAnnotation() - Method in class omero.cmd.fs.OriginalMetadataRequestI
Only called if OriginalMetadataRequestI.loadFileset() finds no Fileset.
loadFileset() - Method in class omero.cmd.fs.OriginalMetadataRequestI
Searches for a Fileset attached to this Image, and if present, uses Bio-Formats to parse the metadata into the OriginalMetadataResponse instance.
loadFilesets(List<Long>, Current) - Method in interface ome.services.blitz.repo.RepositoryDao
Load filesets by id.
loadFilesets(List<Long>, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
 
loadFolders(SecurityContext, Collection<Long>) - Method in class omero.gateway.facility.BrowseFacility
Loads the folders for the given Ids.
loadGui() - Method in class ome.formats.importer.ImportConfig
Loads gui specific values for which it makes sense to have a preferences values.
LOADING_IMAGE(String, Integer, Integer, Integer) - Constructor for class ome.formats.importer.ImportEvent.LOADING_IMAGE
 
loadInstrument_async(AMD_IMetadata_loadInstrument, long, Current) - Method in class ome.services.blitz.impl.MetadataI
 
loadLogFile() - Method in class ome.formats.importer.ImportLibrary.ImportCallback
 
loadLogFiles_async(AMD_IMetadata_loadLogFiles, String, List<Long>, Current) - Method in class ome.services.blitz.impl.MetadataI
 
loadMeasuredRois(Session, long, long) - Method in class ome.services.blitz.impl.RoiI
 
loadOriginalFile(RawFileStorePrx) - Method in class ome.formats.importer.ImportLibrary
Use RawFileStorePrx.getFileId() in order to load the OriginalFile that the service argument is acting on.
loadRenderingDef_async(AMD_RenderingEngine_loadRenderingDef, long, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
loadRndSettings_async(AMD_IPixels_loadRndSettings, long, Current) - Method in class ome.services.blitz.impl.PixelsI
 
loadROI(SecurityContext, long) - Method in class omero.gateway.facility.ROIFacility
Loads the ROI
loadROIs(SecurityContext, long) - Method in class omero.gateway.facility.ROIFacility
Loads the ROI related to the specified image.
loadROIs(SecurityContext, long, List<Long>) - Method in class omero.gateway.facility.ROIFacility
Loads the ROI related to the specified image.
loadROIs(SecurityContext, long, List<Long>, long) - Method in class omero.gateway.facility.ROIFacility
Loads the ROI related to the specified image.
loadROIsByPlane(SecurityContext, long, int, int) - Method in class omero.gateway.facility.ROIFacility
Loads the ROI related to the specified image.
loadROIsForFolder(SecurityContext, long, long) - Method in class omero.gateway.facility.ROIFacility
Get all ROIs which are part of a certain folder
loadScripts(ServiceFactory, Parameters) - Method in class ome.services.scripts.ScriptFinder
Load all scripts that match the name, hash, and format for script
loadSpecifiedAnnotations_async(AMD_IMetadata_loadSpecifiedAnnotations, String, List<String>, List<String>, Parameters, Current) - Method in class ome.services.blitz.impl.MetadataI
 
loadSpecifiedAnnotationsLinkedTo_async(AMD_IMetadata_loadSpecifiedAnnotationsLinkedTo, String, List<String>, List<String>, String, List<Long>, Parameters, Current) - Method in class ome.services.blitz.impl.MetadataI
 
loadTagContent_async(AMD_IMetadata_loadTagContent, List<Long>, Parameters, Current) - Method in class ome.services.blitz.impl.MetadataI
 
loadTagSets_async(AMD_IMetadata_loadTagSets, Parameters, Current) - Method in class ome.services.blitz.impl.MetadataI
 
local(AbstractRepositoryI, PublicRepositoryI, Current) - Method in class ome.services.blitz.repo.RawAccessRequestI
Method called locally to the repository during RawAccessRequestI.rawAccess().
loci.ome.io - package loci.ome.io
OME I/O: a library for OME database import, upload and download.
loci.ome.io.services - package loci.ome.io.services
 
log - Variable in class ome.formats.importer.exclusions.AbstractFileExclusion
 
log - Variable in class ome.formats.importer.targets.TemplateImportTarget
 
log - Variable in class ome.formats.importer.transfers.AbstractFileTransfer
 
log - Variable in class ome.formats.importer.util.ErrorHandler
 
log - Variable in class ome.services.blitz.impl.AbstractAmdServant
 
log - Variable in class ome.services.blitz.redirect.AbstractRedirector
 
log - Variable in class ome.services.roi.GeomTool
 
log - Variable in class ome.services.roi.PixelData
 
log - Variable in class ome.services.scripts.ScriptFinder
 
log - Variable in class ome.services.throttling.AbstractThrottlingStrategy
 
log - Variable in class omero.util.ObjectFactoryRegistry
 
LOG_FILE_NS - Static variable in class omero.gateway.model.FileAnnotationData
The name space used to indicate that the FileAnnotation is an import log file.
logDebug(Object, String, Throwable) - Method in class omero.gateway.facility.Facility
Helper method to simplify logging
logError(Object, String, Throwable) - Method in class omero.gateway.facility.Facility
Helper method to simplify logging
LOGFILE - Static variable in class ome.formats.importer.util.IniFileLoader
Public in order to configure LogAppenderProxy, but then the value might as well be configured in the log4j.properties file
logFile - Variable in class ome.services.blitz.repo.ManagedImportLocationI
 
logFileId - Variable in class ome.formats.importer.ImportEvent.POST_UPLOAD_EVENT
 
LOGGED_IN() - Constructor for class ome.formats.importer.ImportEvent.LOGGED_IN
 
LOGGED_OUT() - Constructor for class ome.formats.importer.ImportEvent.LOGGED_OUT
 
Logger - Interface in omero.log
Defines the log service interface.
LoggingImportMonitor - Class in ome.formats.importer.cli
Basic import process monitor that writes information to the log.
LoggingImportMonitor() - Constructor for class ome.formats.importer.cli.LoggingImportMonitor
 
LoginCredentials - Class in omero.gateway
Holds all necessary information needed for connecting to an OMERO server
LoginCredentials() - Constructor for class omero.gateway.LoginCredentials
Creates a new instance
LoginCredentials(String[]) - Constructor for class omero.gateway.LoginCredentials
Creates a new instance.
LoginCredentials(String, String, String) - Constructor for class omero.gateway.LoginCredentials
Creates a new instance with the given credentials and default port
LoginCredentials(String, String, String, int) - Constructor for class omero.gateway.LoginCredentials
Creates a new instance with the given credentials
logInfo(Object, String, Throwable) - Method in class omero.gateway.facility.Facility
Helper method to simplify logging
LogMessage - Class in omero.log
Writes a multi-line log message into a single string.
LogMessage() - Constructor for class omero.log.LogMessage
Creates a new empty message.
LogMessage(String, Throwable) - Constructor for class omero.log.LogMessage
Creates a new instance.
logout() - Method in class ome.formats.OMEROMetadataStoreClient
Destroys the sessionFactory and closes the client.
logSummary() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
log in info level the main statistics
logVersionInfo(String) - Method in class ome.formats.OMEROMetadataStoreClient
 
logWarn(Object, String, Throwable) - Method in class omero.gateway.facility.Facility
Helper method to simplify logging
LongAnnotationData - Class in omero.gateway.model
Wraps a long annotation.
LongAnnotationData(long) - Constructor for class omero.gateway.model.LongAnnotationData
Creates a new instance.
LongAnnotationData() - Constructor for class omero.gateway.model.LongAnnotationData
Creates a new instance.
LongAnnotationData(LongAnnotation) - Constructor for class omero.gateway.model.LongAnnotationData
Creates a new instance.
LongValue(String, ImportConfig, Long) - Constructor for class ome.formats.importer.ImportConfig.LongValue
 
lookup(ParamsCache.Key) - Method in class ome.services.blitz.util.ParamsCache
Called by the LoadingCache when a cache-miss occurs.
lookupAll() - Method in class ome.services.blitz.util.ParamsCache
Called from a Quartz cron trigger for periodically reloading all scripts.
lookupClusterNodes() - Method in class ome.services.blitz.fire.Registry.Impl
 
lookupClusterNodes() - Method in interface ome.services.blitz.fire.Registry
Returns all found cluster nodes or null if something goes wrong during lookup (null QueryPrx for example)
lookupExperimenter(SecurityContext, String) - Method in class omero.gateway.facility.AdminFacility
Returns the experimenter corresponding to the passed name or null.
lookupExperimenter_async(AMD_IAdmin_lookupExperimenter, String, Current) - Method in class ome.services.blitz.impl.AdminI
 
lookupExperimenters_async(AMD_IAdmin_lookupExperimenters, Current) - Method in class ome.services.blitz.impl.AdminI
 
lookupGroup(SecurityContext, String) - Method in class omero.gateway.facility.AdminFacility
Returns the group corresponding to the passed name or null.
lookupGroup_async(AMD_IAdmin_lookupGroup, String, Current) - Method in class ome.services.blitz.impl.AdminI
 
lookupGroups_async(AMD_IAdmin_lookupGroups, Current) - Method in class ome.services.blitz.impl.AdminI
 
lookupLdapAuthExperimenter_async(AMD_IAdmin_lookupLdapAuthExperimenter, long, Current) - Method in class ome.services.blitz.impl.AdminI
 
lookupLdapAuthExperimenters_async(AMD_IAdmin_lookupLdapAuthExperimenters, Current) - Method in class ome.services.blitz.impl.AdminI
 
lookupManagedRepository() - Method in class ome.formats.importer.ImportLibrary
Retrieves the first managed repository from the list of current active repositories.
lookupMonitorServers() - Method in class ome.services.blitz.fire.Registry.Impl
 
lookupMonitorServers() - Method in interface ome.services.blitz.fire.Registry
 
lookupPixels_async(AMD_RenderingEngine_lookupPixels, long, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
lookupProcessors() - Method in class ome.services.blitz.fire.Registry.Impl
 
lookupProcessors() - Method in interface ome.services.blitz.fire.Registry
 
lookupRenderingDef_async(AMD_RenderingEngine_lookupRenderingDef, long, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
lookupRepositories() - Method in class ome.services.blitz.fire.Registry.Impl
 
lookupRepositories() - Method in interface ome.services.blitz.fire.Registry
 
lookupSymbol(UnitsElectricPotential) - Static method in class omero.model.ElectricPotentialI
 
lookupSymbol(UnitsFrequency) - Static method in class omero.model.FrequencyI
 
lookupSymbol(UnitsLength) - Static method in class omero.model.LengthI
 
lookupSymbol(UnitsPower) - Static method in class omero.model.PowerI
 
lookupSymbol(UnitsPressure) - Static method in class omero.model.PressureI
 
lookupSymbol(UnitsTemperature) - Static method in class omero.model.TemperatureI
 
lookupSymbol(UnitsTime) - Static method in class omero.model.TimeI
 
lookupTables() - Method in class ome.services.blitz.fire.Registry.Impl
 
lookupTables() - Method in interface ome.services.blitz.fire.Registry
 
loop(int, long) - Method in class omero.cmd.CmdCallbackI
Calls block(long) "loops" number of times with the "ms" argument.
loop - Variable in class omero.util.RPSTileData
 

M

main(String[]) - Static method in class loci.ome.io.OmeroReader
Deprecated.
A simple command line tool for downloading images from OMERO.
main(String[]) - Static method in class ome.formats.importer.cli.CommandLineImporter
Command line application entry point which parses CLI arguments and passes them into the importer.
main(String[]) - Static method in class ome.services.blitz.Entry
Entry point to the server.
main(String[]) - Static method in class ome.services.blitz.Status
Uses the passed args to create an Communicator.
main(String[]) - Static method in class omero.cmd.fs.OriginalMetadataRequestI
 
main(String[]) - Static method in class omero.util.TempFileManager
Command-line interface to the global TempFileManager instance.
makeAdjustedCurrent(Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
 
makeCheckedDirs(LinkedList<CheckedPath>, boolean, Session, ServiceFactory, SqlAction, EventContext) - Method in class ome.services.blitz.repo.ManagedRepositoryI
makeCheckedDirs(LinkedList<CheckedPath>, boolean, Session, ServiceFactory, SqlAction, EventContext) - Method in class ome.services.blitz.repo.PublicRepositoryI
Internal method to be used by subclasses to perform any extra checks on the listed of CheckedPath instances before allowing the creation of directories.
makeDir(String, boolean, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
Create a nested path in the repository.
makeDir(CheckedPath, boolean, Session, ServiceFactory, SqlAction, EventContext) - Method in class ome.services.blitz.repo.PublicRepositoryI
 
makeDirs(PublicRepositoryI, List<CheckedPath>, boolean, Current) - Method in interface ome.services.blitz.repo.RepositoryDao
Create a number of directories in a single transaction, using the PublicRepositoryI instance as a callback for implementation specific logic.
makeDirs(PublicRepositoryI, List<CheckedPath>, boolean, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
 
makeElectricPotential(double, Unit<ElectricPotential>) - Static method in class ome.formats.model.UnitsFactory
 
makeElectricPotential(double, UnitsElectricPotential) - Static method in class ome.formats.model.UnitsFactory
 
makeElectricPotentialUnitXML(String) - Static method in class ome.formats.model.UnitsFactory
 
makeElectricPotentialXML(double, String) - Static method in class ome.formats.model.UnitsFactory
 
makeFactory(client) - Static method in class omero.model.DetailsI
 
makeFactory(client) - Static method in class omero.model.ElectricPotentialI
 
makeFactory(client) - Static method in class omero.model.FrequencyI
 
makeFactory(client) - Static method in class omero.model.LengthI
 
makeFactory(client) - Static method in class omero.model.PowerI
 
makeFactory(client) - Static method in class omero.model.PressureI
 
makeFactory(client) - Static method in class omero.model.TemperatureI
 
makeFactory(client) - Static method in class omero.model.TimeI
 
makeFrequency(double, Unit<Frequency>) - Static method in class ome.formats.model.UnitsFactory
 
makeFrequency(double, UnitsFrequency) - Static method in class ome.formats.model.UnitsFactory
 
makeFrequencyUnitXML(String) - Static method in class ome.formats.model.UnitsFactory
 
makeFrequencyXML(double, String) - Static method in class ome.formats.model.UnitsFactory
 
makeLength(double, Unit<Length>) - Static method in class ome.formats.model.UnitsFactory
 
makeLength(double, UnitsLength) - Static method in class ome.formats.model.UnitsFactory
 
makeLengthUnitXML(String) - Static method in class ome.formats.model.UnitsFactory
 
makeLengthXML(double, String) - Static method in class ome.formats.model.UnitsFactory
 
MakeNextDirectory - Class in ome.services.blitz.repo.path
Abstracts a pattern for using repository template path directories in ManagedRepositoryI.TemplateDirectoryCreator: pinpoint the next directory to use, then try to use it while watching for conflicts from other similar threads.
MakeNextDirectory() - Constructor for class ome.services.blitz.repo.path.MakeNextDirectory
 
MakePathComponentSafe - Class in ome.services.blitz.repo.path
 
MakePathComponentSafe(FilePathRestrictions...) - Constructor for class ome.services.blitz.repo.path.MakePathComponentSafe
 
makePower(double, Unit<Power>) - Static method in class ome.formats.model.UnitsFactory
 
makePower(double, UnitsPower) - Static method in class ome.formats.model.UnitsFactory
 
makePowerUnitXML(String) - Static method in class ome.formats.model.UnitsFactory
 
makePowerXML(double, String) - Static method in class ome.formats.model.UnitsFactory
 
makePressure(double, Unit<Pressure>) - Static method in class ome.formats.model.UnitsFactory
 
makePressure(double, UnitsPressure) - Static method in class ome.formats.model.UnitsFactory
 
makePressureUnitXML(String) - Static method in class ome.formats.model.UnitsFactory
 
makePressureXML(double, String) - Static method in class ome.formats.model.UnitsFactory
 
makeTemperature(double, Unit<Temperature>) - Static method in class ome.formats.model.UnitsFactory
 
makeTemperature(double, UnitsTemperature) - Static method in class ome.formats.model.UnitsFactory
 
makeTemperatureUnitXML(String) - Static method in class ome.formats.model.UnitsFactory
 
makeTemperatureXML(double, String) - Static method in class ome.formats.model.UnitsFactory
 
makeTime(double, Unit<Time>) - Static method in class ome.formats.model.UnitsFactory
 
makeTime(double, UnitsTime) - Static method in class ome.formats.model.UnitsFactory
 
makeTimeUnitXML(String) - Static method in class ome.formats.model.UnitsFactory
 
makeTimeXML(double, String) - Static method in class ome.formats.model.UnitsFactory
 
makeXMLQuantity(double, String) - Static method in class omero.model.ElectricPotentialI
 
makeXMLQuantity(double, String) - Static method in class omero.model.FrequencyI
 
makeXMLQuantity(double, String) - Static method in class omero.model.LengthI
 
makeXMLQuantity(double, String) - Static method in class omero.model.PowerI
 
makeXMLQuantity(double, String) - Static method in class omero.model.PressureI
 
makeXMLQuantity(double, String) - Static method in class omero.model.TemperatureI
 
makeXMLQuantity(double, String) - Static method in class omero.model.TimeI
 
makeXMLUnit(String) - Static method in class omero.model.ElectricPotentialI
 
makeXMLUnit(String) - Static method in class omero.model.FrequencyI
 
makeXMLUnit(String) - Static method in class omero.model.LengthI
 
makeXMLUnit(String) - Static method in class omero.model.PowerI
 
makeXMLUnit(String) - Static method in class omero.model.PressureI
 
makeXMLUnit(String) - Static method in class omero.model.TemperatureI
 
makeXMLUnit(String) - Static method in class omero.model.TimeI
 
ManagedImportLocationI - Class in ome.services.blitz.repo
Server-side implementation of ImportLocation for also storing the CheckedPath instances for each used file.
ManagedImportLocationI() - Constructor for class ome.services.blitz.repo.ManagedImportLocationI
 
ManagedImportProcessI - Class in ome.services.blitz.repo
Represents a single import within a defined-session all running server-side.
ManagedImportProcessI(ManagedRepositoryI, Fileset, ImportLocation, ImportSettings, Current, String) - Constructor for class ome.services.blitz.repo.ManagedImportProcessI
Create and register a servant for servicing the import process within a managed repository.
ManagedImportRequestI - Class in ome.services.blitz.repo
Wrapper around FilesetJobLink instances which need to be handled on the server-side.
ManagedImportRequestI(Registry, TileSizes, RepositoryDao, OMEROWrapper, String) - Constructor for class ome.services.blitz.repo.ManagedImportRequestI
 
ManagedRepositoryI - Class in ome.services.blitz.repo
Extension of the PublicRepository API which only manages files under ${omero.data.dir}/ManagedRepository.
ManagedRepositoryI(String, RepositoryDao) - Constructor for class ome.services.blitz.repo.ManagedRepositoryI
Creates a ProcessContainer internally that will not be managed by background threads.
ManagedRepositoryI(String, RepositoryDao, ProcessContainer, ChecksumProviderFactory, String, String, String, Roles, Set<String>) - Constructor for class ome.services.blitz.repo.ManagedRepositoryI
 
ManageImageBinariesI - Class in omero.cmd.fs
Workflow for converting attached original images into OMERO5+ filesets.
ManageImageBinariesI(PixelsService, ACLVoter) - Constructor for class omero.cmd.fs.ManageImageBinariesI
 
manager - Variable in class omero.cmd.admin.CurrentSessionsRequestI
 
manager - Variable in class omero.cmd.admin.UpdateSessionTimeoutRequestI
 
managerOrNull() - Method in class ome.services.blitz.fire.TopicManager.Impl
 
map() - Method in class ome.formats.importer.ImportConfig
 
map(List<String>) - Method in class ome.services.blitz.impl.MetadataI
 
map(String) - Method in class ome.services.blitz.impl.MetadataI
 
map(Filterable[]) - Method in class omero.util.IceMapper
 
MapAnnotationData - Class in omero.gateway.model
 
MapAnnotationData(MapAnnotation) - Constructor for class omero.gateway.model.MapAnnotationData
 
MapAnnotationData() - Constructor for class omero.gateway.model.MapAnnotationData
 
mapFlexServer(String, String) - Method in class ome.formats.importer.util.IniFileLoader
Append keep to server map
mapReturnValue(IceMapper, Object) - Method in class ome.services.blitz.impl.RoiI.RoiResultMapReturnMapper
 
mapReturnValue(IceMapper, Object) - Method in class ome.services.blitz.impl.RoiI.RoiResultReturnMapper
 
mapReturnValue(Object) - Method in class omero.util.IceMapper
Convert the given Object via the set IceMapper.ReturnMapping.
mapReturnValue(IceMapper, Object) - Method in interface omero.util.IceMapper.ReturnMapping
 
mapUserGroups() - Method in class ome.formats.OMEROMetadataStoreClient
Maps the user's groups for use by ScreenLogin.registerGroup() Also strips system groups from this map
markModified() - Method in class ome.services.blitz.repo.CheckedPath
Mark this existing file as having been modified at the present moment.
MaskData - Class in omero.gateway.model
Represents an Mask in the Euclidean space R2.
MaskData(Shape) - Constructor for class omero.gateway.model.MaskData
Creates a new instance.
MaskData() - Constructor for class omero.gateway.model.MaskData
Creates a new instance of MaskData.
MaskData(double, double, double, double, byte[]) - Constructor for class omero.gateway.model.MaskData
Creates a new instance of the MaskData.
matches(Class, Class) - Static method in class ome.services.blitz.util.ApiConsistencyCheck
Defines what Class types match.
MEASUREMENT_NS - Static variable in class omero.gateway.model.FileAnnotationData
The name space used to indicate that the FileAnnotation is a Measurement file.
MeasurementStore - Class in ome.services.blitz.measurements
Parser API implementation for storing result measurements from SPW companion files as ROIs and OMERO.tables.
MeasurementStore(LocalUpdate, TablePrx) - Constructor for class ome.services.blitz.measurements.MeasurementStore
 
meta - Variable in class ome.services.roi.PixelData
 
METADATA_IMPORTED(int, ImportContainer, IObject, Long, int, ImportSize, Integer, Integer, Long) - Constructor for class ome.formats.importer.ImportEvent.METADATA_IMPORTED
 
METADATA_LEVEL - Static variable in class ome.formats.importer.ImportCandidates
 
METADATA_PROCESSED(int, ImportContainer, IObject, Long, int, ImportSize, Integer, Integer, Long) - Constructor for class ome.formats.importer.ImportEvent.METADATA_PROCESSED
 
MetadataFacility - Class in omero.gateway.facility
A Facility to access the metadata.
MetadataI - Class in ome.services.blitz.impl
Implementation of the IMetadata service.
MetadataI(IMetadata, BlitzExecutor) - Constructor for class ome.services.blitz.impl.MetadataI
Creates a new instance.
MetadataStoreI - Class in ome.services.blitz.impl
 
MetadataStoreI(BlitzExecutor, PopulateRoiJob, SqlAction, OriginalFilesService, String) - Constructor for class ome.services.blitz.impl.MetadataStoreI
 
MIDDLENAME - Static variable in class omero.gateway.model.ExperimenterData
Identifies the ExperimenterI.MIDDLENAME field.
mime - Variable in class ome.services.blitz.repo.CheckedPath
 
mimetype(String, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
Get the mimetype for a file.
MIMETYPE - Static variable in class omero.gateway.util.TIFFFilter
The MIMEType associated to this type of file.
minMaxSet - Variable in class ome.formats.importer.OMEROWrapper
 
MISSING_LIBRARY(String, MissingLibraryException, String[], String) - Constructor for class ome.formats.importer.util.ErrorHandler.MISSING_LIBRARY
 
mkdir() - Method in class ome.services.blitz.repo.CheckedPath
Create this directory on the underlying filesystem.
mkdirs() - Method in class ome.services.blitz.repo.CheckedPath
Create this directory, and parents if necessary, on the underlying filesystem.
ModelException - Exception in ome.formats.model
Exception thrown when there is an object instantiation error or error processing the model.
ModelException(String) - Constructor for exception ome.formats.model.ModelException
Default constructor.
ModelException(String, Class<? extends IObject>, Exception) - Constructor for exception ome.formats.model.ModelException
Default constructor.
ModelImportTarget - Class in ome.formats.importer.targets
 
ModelImportTarget() - Constructor for class ome.formats.importer.targets.ModelImportTarget
 
ModelMapper - Class in omero.gateway.util
Helper class to map DataObjects into their corresponding IObjects.
ModelMapper() - Constructor for class omero.gateway.util.ModelMapper
 
ModelObjectHandler - Interface in ome.formats.model.handler
A model object handler whose purpose is to provide extra logic, such as enumeration not-null constraint fulfilment.
ModelObjectHandlerFactory - Class in ome.formats.model.handler
Factory for all available model handlers.
ModelObjectHandlerFactory(EnumerationProvider) - Constructor for class ome.formats.model.handler.ModelObjectHandlerFactory
Default constructor.
ModelProcessor - Interface in ome.formats.model
An object which performs post-processing on an IObjectContainerStore.
MODULO_NS - Static variable in class omero.gateway.model.XMLAnnotationData
The name space used to identify modulo concept.
MoveFileTransfer - Class in ome.formats.importer.transfers
Local-only file transfer mechanism which makes use of hard-linking followed by the deletion of the original source file.
MoveFileTransfer() - Constructor for class ome.formats.importer.transfers.MoveFileTransfer
 
moveToCommonSpace_async(AMD_IAdmin_moveToCommonSpace, List<IObject>, Current) - Method in class ome.services.blitz.impl.AdminI
 
MOVIE_NS - Static variable in class omero.gateway.model.FileAnnotationData
The name space used to indicate that the FileAnnotation is a movie.
MS_EXCEL - Static variable in class omero.gateway.model.FileAnnotationData
Identifies the Excel file formats.
MS_POWER_POINT - Static variable in class omero.gateway.model.FileAnnotationData
Identifies the Power point file formats.
MS_POWER_POINT_SHOW - Static variable in class omero.gateway.model.FileAnnotationData
Identifies the Power point file formats.
MS_POWER_POINT_X - Static variable in class omero.gateway.model.FileAnnotationData
Identifies the Power point file formats.
MS_WORD - Static variable in class omero.gateway.model.FileAnnotationData
Identifies the Word file formats.
MS_WORD_X - Static variable in class omero.gateway.model.FileAnnotationData
Identifies the Word file formats.
mustEdit() - Method in class ome.services.blitz.repo.CheckedPath
 
mustExist() - Method in class ome.services.blitz.repo.CheckedPath
Checks for existence of the original path, throwing an exception if not present.

N

name - Variable in enum ome.services.blitz.repo.path.FilePathRestrictionInstance
 
NAME - Static variable in class omero.gateway.model.DatasetData
Identifies the DatasetI.NAME field.
NAME - Static variable in class omero.gateway.model.GroupData
Identifies the ExperimenterGroupI.NAME field.
NAME - Static variable in class omero.gateway.model.ImageData
Identifies the ImageI.NAME field.
NAME - Static variable in class omero.gateway.model.PlateData
Identifies the PlateI.NAME field.
NAME - Static variable in class omero.gateway.model.ProjectData
Identifies the ProjectI.NAME field.
NAME - Static variable in class omero.gateway.model.ScreenData
Identifies the ScreenI.NAME field.
needsInit() - Method in class ome.services.blitz.repo.FileMaker
 
NetworkChecker - Class in omero.gateway.util
Checks if the network is still up.
NetworkChecker(String, Logger) - Constructor for class omero.gateway.util.NetworkChecker
Creates a new instance.
NEW_LINE - Static variable in class omero.log.LogMessage
The new line sequence.
newBlueColor() - Static method in class ome.formats.model.ColorsFactory
Creates a new Blue Color object.
newCurrent(Identity, String, ObjectAdapter, String) - Static method in class omero.cmd.SessionI
 
newCurrent(Identity, String) - Method in class omero.cmd.SessionI
 
newGreenColor() - Static method in class ome.formats.model.ColorsFactory
Creates a new Green Color object.
newGreyColor() - Static method in class ome.formats.model.ColorsFactory
Creates a new Grey Color object.
newOMEROReader() - Method in interface loci.ome.io.services.OMEReaderWriterService
Deprecated.
Creates a new OMERO IFormatReader implementation.
newOMEROReader() - Method in class loci.ome.io.services.OMEReaderWriterServiceImpl
 
newOMEROWriter() - Method in class loci.ome.io.services.OMEReaderWriterServiceImpl
 
newRedColor() - Static method in class ome.formats.model.ColorsFactory
Creates a new Red Color object.
newTable(long, String, Current) - Method in class ome.services.blitz.impl.SharedResourcesI
 
newWhiteColor() - Static method in class ome.formats.model.ColorsFactory
Creates a new White Color object.
next_async(AMD_Search_next, Current) - Method in class ome.services.blitz.impl.SearchI
 
NO_ERROR - Static variable in class omero.gateway.model.SearchResultCollection
No error
noAcquisitionData() - Method in class omero.sys.ParametersI
Sets the acquisition data parameter to false.
noCache() - Method in class omero.sys.ParametersI
Set queries to not be cacheable.
nodeProxyQuery(Redirector.Context, String, String) - Method in class ome.services.blitz.redirect.AbstractRedirector
 
noLeaves() - Method in class omero.sys.ParametersI
Sets the leaf parameter to false.
noOrphan() - Method in class omero.sys.ParametersI
Sets the orphan parameter to false.
noPage() - Method in class omero.sys.ParametersI
Nulls both the Filter.limit and Filter.offset values.
noStatsInfo - Variable in class ome.formats.importer.ImportConfig
 
not_async(AMD_Search_not, Current) - Method in class ome.services.blitz.impl.SearchI
 
notAnnotatedBy_async(AMD_Search_notAnnotatedBy, Details, Current) - Method in class ome.services.blitz.impl.SearchI
 
noteDetails(Session, IObject, String, long) - Method in class omero.cmd.graphs.BaseGraphPolicyAdjuster
 
notifyCallbacks() - Method in class omero.cmd.HandleI
Calls the proper notification on all callbacks based on the current position in the state diagram.
notifyMembersOfShare_async(AMD_IShare_notifyMembersOfShare, long, String, String, boolean, Current) - Method in class ome.services.blitz.impl.ShareI
 
notifyObservers(ImportEvent) - Method in class ome.formats.importer.ImportLibrary
 
notifyObservers(ImportEvent) - Method in interface ome.formats.importer.IObservable
Notify observers of event
notifyObservers(ImportEvent) - Method in class ome.formats.importer.util.ClientKeepAlive
 
notifyObservers(ImportEvent) - Method in class ome.formats.importer.util.ErrorHandler
 
notifyObservers(ImportEvent) - Method in class ome.formats.importer.util.FileUploader
 
notOwnedBy_async(AMD_Search_notOwnedBy, Details, Current) - Method in class ome.services.blitz.impl.SearchI
 
noUnique() - Method in class omero.sys.ParametersI
 
NS_CLIENT_CREATED - Static variable in class omero.gateway.model.MapAnnotationData
The name space used to identify MapAnnotations created be the user
nullDetails() - Method in class omero.gateway.model.DataObject
Returns true if the details are null otherwise false otherwise.
NullGraphTraversalProcessor - Class in omero.cmd.graphs
A GraphTraversal.Processor that does nothing whatsoever.
NullGraphTraversalProcessor(Set<GraphPolicy.Ability>) - Constructor for class omero.cmd.graphs.NullGraphTraversalProcessor
Construct a GraphTraversal.Processor that does nothing whatsoever.
NullLogger - Class in omero.log
Empty Logger implementation whichs doesn't do anything
NullLogger() - Constructor for class omero.log.NullLogger
 
nullProperties(String, String, Collection<Long>) - Method in class omero.cmd.graphs.BaseGraphTraversalProcessor
 
nullProperties(String, String, Collection<Long>) - Method in class omero.cmd.graphs.NullGraphTraversalProcessor
 
NullRedirector - Class in ome.services.blitz.redirect
Redirector implementation to effectively disable redirects.
NullRedirector() - Constructor for class ome.services.blitz.redirect.NullRedirector
 
nullSafe(Integer) - Method in class omero.gateway.model.DataObject
 
nullSafe(RInt) - Method in class omero.gateway.model.DataObject
 
nullSafe(Long) - Method in class omero.gateway.model.DataObject
 
nullSafe(Double) - Method in class omero.gateway.model.DataObject
 
nullSafe(Float) - Method in class omero.gateway.model.DataObject
 
nullSafe(RFloat) - Method in class omero.gateway.model.DataObject
 
nullSafe(RDouble) - Method in class omero.gateway.model.DataObject
 
nullSafe(Length) - Method in class omero.gateway.model.DataObject
 
numDone - Variable in class ome.formats.importer.ImportEvent.COUNT_EVENT
 
numDone - Variable in class ome.formats.importer.ImportEvent.PROGRESS_EVENT
 
numFiles - Variable in class ome.formats.importer.ImportCandidates.SCANNING
 
numOfDirectories - Variable in class ome.formats.importer.ImportConfig
 

O

OBJECT_TO_RTYPE - Static variable in class omero.util.IceMapper
 
OBJECTARRAY_TO_RTYPESEQ - Static variable in class omero.util.IceMapper
 
ObjectFactory(String) - Constructor for class omero.util.ObjectFactoryRegistry.ObjectFactory
 
ObjectFactoryRegistry - Class in omero.util
SPI type picked up from the Spring configuration and given a chance to register all its ObjectFactory instances with the Communicator.
ObjectFactoryRegistry() - Constructor for class omero.util.ObjectFactoryRegistry
 
ObjectFactoryRegistry.ObjectFactory - Class in omero.util
 
Objective_WorkingDistance - Static variable in class ome.formats.model.UnitsFactory
 
ObjectiveData - Class in omero.gateway.model
Hosts an objective used to capture an image.
ObjectiveData(Objective) - Constructor for class omero.gateway.model.ObjectiveData
Creates a new instance.
objects - Variable in class ome.formats.importer.ImportEvent.IMPORT_DONE
 
OBJECTS_RETURNED(int, ImportContainer, IObject, Long, int, ImportSize, Integer, Integer, Long) - Constructor for class ome.formats.importer.ImportEvent.OBJECTS_RETURNED
 
observers - Variable in class ome.formats.importer.util.ErrorHandler
 
obtainProxy(String, Redirector.Context, String, SessionControlPrx, Current) - Method in class ome.services.blitz.redirect.AbstractRedirector
 
offset - Variable in class omero.util.ReadOnlyByteArray
Marks the start of the slice.
ome.formats - package ome.formats
 
ome.formats.enums - package ome.formats.enums
 
ome.formats.enums.handler - package ome.formats.enums.handler
 
ome.formats.importer - package ome.formats.importer
 
ome.formats.importer.cli - package ome.formats.importer.cli
 
ome.formats.importer.exclusions - package ome.formats.importer.exclusions
FileExclusion provides a mechanism for determining which potential filesets should be excluded from import.
ome.formats.importer.targets - package ome.formats.importer.targets
 
ome.formats.importer.transfers - package ome.formats.importer.transfers
FileTransfer provides a mechanism for shipping client-side files to the server-side.
ome.formats.importer.util - package ome.formats.importer.util
 
ome.formats.model - package ome.formats.model
 
ome.formats.model.handler - package ome.formats.model.handler
 
ome.services.blitz - package ome.services.blitz
 
ome.services.blitz.fire - package ome.services.blitz.fire
 
ome.services.blitz.impl - package ome.services.blitz.impl
 
ome.services.blitz.impl.commands - package ome.services.blitz.impl.commands
 
ome.services.blitz.measurements - package ome.services.blitz.measurements
 
ome.services.blitz.redirect - package ome.services.blitz.redirect
 
ome.services.blitz.repo - package ome.services.blitz.repo
 
ome.services.blitz.repo.path - package ome.services.blitz.repo.path
 
ome.services.blitz.util - package ome.services.blitz.util
 
ome.services.formats - package ome.services.formats
 
ome.services.roi - package ome.services.roi
 
ome.services.scripts - package ome.services.scripts
 
ome.services.throttling - package ome.services.throttling
 
OMECredentials - Class in loci.ome.io
Deprecated.
As of release 5.3.0
OMECredentials(String, String, String) - Constructor for class loci.ome.io.OMECredentials
Deprecated.
 
OMECredentials(String) - Constructor for class loci.ome.io.OMECredentials
Deprecated.
Get credentials from a string.
OMENAME - Static variable in class omero.gateway.model.ExperimenterData
Identifies the ExperimenterI.OMENAME field.
OMEReaderWriterService - Interface in loci.ome.io.services
Deprecated.
As of release 5.3.0
OMEReaderWriterServiceImpl - Class in loci.ome.io.services
 
OMEReaderWriterServiceImpl() - Constructor for class loci.ome.io.services.OMEReaderWriterServiceImpl
 
omero - package omero
 
omero.cmd - package omero.cmd
 
omero.cmd.admin - package omero.cmd.admin
 
omero.cmd.basic - package omero.cmd.basic
 
omero.cmd.fs - package omero.cmd.fs
 
omero.cmd.graphs - package omero.cmd.graphs
 
omero.cmd.mail - package omero.cmd.mail
 
omero.gateway - package omero.gateway
 
omero.gateway.cache - package omero.gateway.cache
 
omero.gateway.exception - package omero.gateway.exception
 
omero.gateway.facility - package omero.gateway.facility
 
omero.gateway.model - package omero.gateway.model
 
omero.gateway.rnd - package omero.gateway.rnd
 
omero.gateway.util - package omero.gateway.util
 
omero.grid - package omero.grid
 
omero.log - package omero.log
 
omero.model - package omero.model
 
omero.sys - package omero.sys
 
omero.util - package omero.util
 
OMERO_EMISSION_FILTER_SUFFIX - Static variable in class ome.formats.OMEROMetadataStoreClient
Emission filter LSID suffix.
OMERO_EXCITATION_FILTER_SUFFIX - Static variable in class ome.formats.OMEROMetadataStoreClient
Excitation filter LSID suffix.
omeroClass(String, boolean) - Static method in class omero.util.IceMapper
 
omeroDataDir - Variable in class ome.services.blitz.impl.MetadataStoreI
 
OMEROImportFixture - Class in ome.formats
Deprecated.
to be moved to components/blitz/test/
OMEROImportFixture(OMEROMetadataStoreClient, OMEROWrapper) - Constructor for class ome.formats.OMEROImportFixture
Deprecated.
 
OmeroMeasurementStore - Interface in ome.services.blitz.measurements
Sub-interface of MeasurementStore with extended life-cycle methods for handling exceptions during saving the measurements to multiple stores.
OmeroMetadata - Class in ome.services.blitz.impl
An implementation for MetadataStore and MetadataRetrieve that knows how to read and write the OMERO object model.
OmeroMetadata(DatabaseIdentity) - Constructor for class ome.services.blitz.impl.OmeroMetadata
 
OMEROMetadataStoreClient - Class in ome.formats
Client side implementation of the Bio-Formats MetadataStore.
OMEROMetadataStoreClient() - Constructor for class ome.formats.OMEROMetadataStoreClient
 
OMEROMetadataStoreClientRoot - Class in ome.formats
MetadataRoot implementation for the client-side implementation of the Bio-Formats MetadataStore.
OMEROMetadataStoreClientRoot() - Constructor for class ome.formats.OMEROMetadataStoreClientRoot
Default constructor.
OMEROMetadataStoreClientRoot(List<Pixels>) - Constructor for class ome.formats.OMEROMetadataStoreClientRoot
Copy constructor.
OmeroReader - Class in loci.ome.io
Deprecated.
As of release 5.3.0
OmeroReader() - Constructor for class loci.ome.io.OmeroReader
Deprecated.
 
OmeroReader - Class in ome.services.formats
Implementation of IFormatReader for use in export.
OmeroReader(RawPixelsStore, Pixels) - Constructor for class ome.services.formats.OmeroReader
 
OmeroReader(RawPixelsStorePrx, Pixels) - Constructor for class ome.services.formats.OmeroReader
 
OMEROWrapper - Class in ome.formats.importer
 
OMEROWrapper(ImportConfig) - Constructor for class ome.formats.importer.OMEROWrapper
Wrapper for bio-formats
OMEROWrapper(ImportConfig, long, File) - Constructor for class ome.formats.importer.OMEROWrapper
 
OMEXMLModelComparator - Class in ome.formats
This comparator takes into account the OME-XML data model hierarchy and uses that to define equivalence.
OMEXMLModelComparator() - Constructor for class ome.formats.OMEXMLModelComparator
 
onAddError(ErrorContainer, String) - Method in class ome.formats.importer.util.ErrorHandler
Action to take on adding an error to container
onApplicationEvent(InternalMessage) - Method in class ome.services.blitz.fire.SessionManagerI
 
onApplicationEvent(ApplicationEvent) - Method in class ome.services.blitz.fire.TopicManager.Impl
 
onApplicationEvent(InternalMessage) - Method in class ome.services.blitz.repo.AbstractRepositoryI
 
onApplicationEvent(ApplicationEvent) - Method in class ome.services.throttling.AbstractThrottlingStrategy
 
onCancel() - Method in class ome.formats.importer.util.ErrorHandler
action to take on cancel
onException(Exception) - Method in class ome.formats.importer.util.ErrorHandler
Action to take on exception
onFinished(Response, Status, Current) - Method in class ome.formats.importer.ImportLibrary.ImportCallback
Overridden to handle the end of the process.
onFinished(Response, Status, Current) - Method in class omero.cmd.CmdCallbackI
Method intended to be overridden by subclasses.
onFinishedDone() - Method in class omero.cmd.CmdCallbackI
 
onHeartbeat(Runnable) - Method in class omero.client
 
onlyAnnotatedBetween_async(AMD_Search_onlyAnnotatedBetween, RTime, RTime, Current) - Method in class ome.services.blitz.impl.SearchI
 
onlyAnnotatedBy_async(AMD_Search_onlyAnnotatedBy, Details, Current) - Method in class ome.services.blitz.impl.SearchI
 
onlyAnnotatedWith_async(AMD_Search_onlyAnnotatedWith, List<String>, Current) - Method in class ome.services.blitz.impl.SearchI
 
onlyCreatedBetween_async(AMD_Search_onlyCreatedBetween, RTime, RTime, Current) - Method in class ome.services.blitz.impl.SearchI
 
onlyIds_async(AMD_Search_onlyIds, List<Long>, Current) - Method in class ome.services.blitz.impl.SearchI
 
onlyModifiedBetween_async(AMD_Search_onlyModifiedBetween, RTime, RTime, Current) - Method in class ome.services.blitz.impl.SearchI
 
onlyOwnedBy_async(AMD_Search_onlyOwnedBy, Details, Current) - Method in class ome.services.blitz.impl.SearchI
 
onlyType_async(AMD_Search_onlyType, String, Current) - Method in class ome.services.blitz.impl.SearchI
 
onlyTypes_async(AMD_Search_onlyTypes, List<String>, Current) - Method in class ome.services.blitz.impl.SearchI
 
onNotSending(int, String) - Method in class ome.formats.importer.util.ErrorHandler
 
onSending(int) - Method in class ome.formats.importer.util.ErrorHandler
 
onSent(int) - Method in class ome.formats.importer.util.ErrorHandler
 
onSessionClosed(Runnable) - Method in class omero.client
 
onSetOmeroContext(OmeroContext) - Method in class ome.services.blitz.impl.AbstractAmdServant
To be overridden by subclasses.
onSetOmeroContext(OmeroContext) - Method in class ome.services.blitz.impl.MetadataStoreI
 
onShutdown(Runnable) - Method in class omero.client
 
onUpdate(IObservable, ImportEvent) - Method in class ome.formats.importer.cli.ErrorHandler
 
onUpdate(IObservable, ImportEvent) - Method in class ome.formats.importer.util.ErrorHandler
abstract on update method
openBytes(int, byte[], int, int, int, int) - Method in class loci.ome.io.OmeroReader
Deprecated.
 
openBytes(int, byte[], int, int, int, int) - Method in class ome.services.formats.OmeroReader
 
openPlane2D(String, int, byte[]) - Method in class ome.formats.importer.OMEROWrapper
Obtains an object which represents a given sub-image of a plane within the file.
openPlane2D(String, int, byte[], int, int, int, int) - Method in class ome.formats.importer.OMEROWrapper
Obtains an object which represents a given sub-image of a plane within the file.
openSession() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
openTable(OriginalFile, Current) - Method in class ome.services.blitz.impl.SharedResourcesI
 
OPERATION_NOT_SUPPORTED - Static variable in exception omero.gateway.exception.RenderingServiceException
Indicates that the error occurred due to an operation not being supported.
optimisticFailure(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
option() - Static method in class omero.gateway.util.Requests
 
or_async(AMD_Search_or, Current) - Method in class ome.services.blitz.impl.SearchI
 
org.hibernate.stat - package org.hibernate.stat
 
ORIGINAL_METADATA_NAME - Static variable in class omero.gateway.model.FileAnnotationData
The default name for the original metadata file.
OriginalMetadataRequestI - Class in omero.cmd.fs
Original metadata loader, handling both pre-FS and post-FS data.
OriginalMetadataRequestI(PixelsService) - Constructor for class omero.cmd.fs.OriginalMetadataRequestI
 
orphan() - Method in class omero.sys.ParametersI
Sets the orphan parameter to true.
OTFData - Class in omero.gateway.model
Hosts an OTF.
OTFData(OTF) - Constructor for class omero.gateway.model.OTFData
Creates a new instance.
OverlayMetadataStore - Class in ome.formats
Client side metadata store implementation that only deals with overlays.
OverlayMetadataStore() - Constructor for class ome.formats.OverlayMetadataStore
 

P

pack(ReadOnlyByteArray, int, int) - Method in class omero.gateway.rnd.DoubleConverter
Implemented as specified by BytesConverter
pack(ReadOnlyByteArray, int, int) - Method in class omero.gateway.rnd.FloatConverter
Implemented as specified by BytesConverter
pack(ReadOnlyByteArray, int, int) - Method in class omero.gateway.rnd.IntConverter
Implemented as specified by BytesConverter
pack(ReadOnlyByteArray, int, int) - Method in class omero.gateway.rnd.UintConverter
Implemented as specified by BytesConverter
page(int, int) - Method in class omero.sys.ParametersI
Sets both the Filter.limit and Filter.offset values by wrapping the arguments in RInt and passing the values to ParametersI.page(RInt, RInt)
page(RInt, RInt) - Method in class omero.sys.ParametersI
Creates a Filter if necessary and sets both Filter.limit and Filter.offset.
parallelFileset - Variable in class ome.formats.importer.ImportConfig
 
parallelUpload - Variable in class ome.formats.importer.ImportConfig
 
ParametersI - Class in omero.sys
Helper subclass of Parameters for simplifying method parameter creation.
ParametersI() - Constructor for class omero.sys.ParametersI
Default constructor creates the Parameters.map instance to prevent later NullPointerExceptions.
ParametersI(Map<String, RType>) - Constructor for class omero.sys.ParametersI
Uses (and does not copy) the given Map<String, RType> as the named parameter store in this instance.
params(String...) - Method in class omero.cmd.Helper
Converts pairs of values from the varargs list into a map.
params(Current) - Method in class omero.grid.InteractiveProcessorI
 
ParamsCache - Class in ome.services.blitz.util
Caching replacement of ParamsHelper which maintains an OriginalFile ID+SHA1-to-JobParams mapping in memory rather than storing ParseJob instances in the database.
ParamsCache(Registry, Roles, ScriptRepoHelper, String) - Constructor for class ome.services.blitz.util.ParamsCache
 
ParamsHelper - Class in omero.grid
 
ParamsHelper(ParamsHelper.Acquirer, Executor, Principal) - Constructor for class omero.grid.ParamsHelper
 
ParamsHelper.Acquirer - Interface in omero.grid
Interface added in order to allow ParamHelper instances to use methods from SharedResourcesI.
parent() - Method in class ome.services.blitz.repo.CheckedPath
Returns a new CheckedPath using File.getParent() and passing in all other values.
parentType(Iterable<String>) - Method in class omero.gateway.util.Requests.FindParentsBuilder
 
parentType(Class<? extends IObject>...) - Method in class omero.gateway.util.Requests.FindParentsBuilder
 
parentType(String...) - Method in class omero.gateway.util.Requests.FindParentsBuilder
 
parse(String) - Method in class ome.formats.importer.targets.TargetBuilder
 
parseAndSetInt(InitializationData, String, int) - Method in class omero.client
 
parseAwtPath(String) - Static method in class omero.model.SmartShape.Util
 
parseData(String, int, ImportSize) - Method in class ome.services.blitz.repo.ManagedImportRequestI
Parse the binary data to generate min/max values and allow an md to be calculated.
parseFlexMaps(Preferences) - Method in class ome.formats.importer.util.IniFileLoader
Parse Flex reader server maps
parseOriginalMetadataTxt(File) - Method in class omero.cmd.fs.OriginalMetadataRequestI
Read the given INI-style file and populate the maps with the properties from the corresponding sections.
parsePoints(String) - Static method in class loci.ome.io.OmeroReader
Deprecated.
Parse Points String obtained from convertPoints and extract Coordinates as String
parsePoints(String) - Static method in class omero.model.SmartShape.Util
 
parsePointsToIntegerList(String) - Method in class omero.gateway.model.ShapeData
Parses the points list from the string to a list of integer objects.
parsePointsToPath(String, boolean) - Static method in class omero.model.SmartShape.Util
 
parsePointsToPoint2DList(String) - Method in class omero.gateway.model.ShapeData
Parses the points list from the string to a list of point2d objects.
passivate_async(AMD_StatefulServiceInterface_passivate, Current) - Method in class ome.services.blitz.impl.AbstractAmdServant
 
passivate_async(AMD_StatefulServiceInterface_passivate, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
PassValue(String, ImportConfig) - Constructor for class ome.formats.importer.ImportConfig.PassValue
 
password - Variable in class loci.ome.io.OMECredentials
Deprecated.
 
password - Variable in class ome.formats.importer.ImportConfig
 
PDF - Static variable in class omero.gateway.model.FileAnnotationData
Identifies the PDF file formats.
PermissionData - Class in omero.gateway.model
Simple data object to wrap a Permissions instance.
PermissionData() - Constructor for class omero.gateway.model.PermissionData
Creates a new instance.
PermissionData(Permissions) - Constructor for class omero.gateway.model.PermissionData
Creates a new instance.
PERMISSIONS_GROUP_READ - Static variable in class omero.gateway.model.GroupData
Indicates that the group is Group i.e.
PERMISSIONS_GROUP_READ_LINK - Static variable in class omero.gateway.model.GroupData
Indicates that the group is Group i.e.
PERMISSIONS_GROUP_READ_LINK_SHORT_TEXT - Static variable in class omero.gateway.model.GroupData
Indicates that the group is Group i.e.
PERMISSIONS_GROUP_READ_LINK_TEXT - Static variable in class omero.gateway.model.GroupData
Indicates that the group is Group i.e.
PERMISSIONS_GROUP_READ_SHORT_TEXT - Static variable in class omero.gateway.model.GroupData
Indicates that the group is Group i.e.
PERMISSIONS_GROUP_READ_TEXT - Static variable in class omero.gateway.model.GroupData
Indicates that the group is Group i.e.
PERMISSIONS_GROUP_READ_WRITE - Static variable in class omero.gateway.model.GroupData
Indicates that the group is Group i.e.
PERMISSIONS_GROUP_READ_WRITE_SHORT_TEXT - Static variable in class omero.gateway.model.GroupData
Indicates that the group is Group i.e.
PERMISSIONS_GROUP_READ_WRITE_TEXT - Static variable in class omero.gateway.model.GroupData
Indicates that the group is Group i.e.
PERMISSIONS_PRIVATE - Static variable in class omero.gateway.model.GroupData
Indicates that the group is Private i.e.
PERMISSIONS_PRIVATE_TEXT - Static variable in class omero.gateway.model.GroupData
Indicates that the group is Private i.e.
PERMISSIONS_PUBLIC_READ - Static variable in class omero.gateway.model.GroupData
Indicates that the group is Public i.e.
PERMISSIONS_PUBLIC_READ_TEXT - Static variable in class omero.gateway.model.GroupData
Indicates that the group is Public i.e.
PERMISSIONS_PUBLIC_READ_WRITE - Static variable in class omero.gateway.model.GroupData
Indicates that the group is Public i.e.
PERMISSIONS_PUBLIC_READ_WRITE_TEXT - Static variable in class omero.gateway.model.GroupData
Indicates that the group is Public i.e.
PermissionsI - Class in omero.model
Blitz wrapper around the Permissions class.
PermissionsI() - Constructor for class omero.model.PermissionsI
 
PermissionsI(String) - Constructor for class omero.model.PermissionsI
 
PermissionsI(PermissionsI) - Constructor for class omero.model.PermissionsI
 
PermissionsI(Permissions) - Constructor for class omero.model.PermissionsI
 
PermissionsVerifierI - Class in ome.services.blitz.fire
 
PermissionsVerifierI(Ring, SessionManager, SessionProvider, Executor, String) - Constructor for class ome.services.blitz.fire.PermissionsVerifierI
 
PERSISTENCE_ON_DISK - Static variable in interface omero.gateway.cache.CacheService
Indicates to cache data on disk.
persistLogFile(OriginalFile, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
Deprecated.
pid() - Method in class omero.util.TempFileManager
Returns some representation of the current process's id
ping() - Method in class ome.formats.OMEROMetadataStoreClient
Pings all registered OMERO Blitz proxies.
ping() - Method in class ome.services.blitz.repo.ManagedImportProcessI
 
ping() - Method in interface ome.services.blitz.repo.ProcessContainer.Process
 
pingAll() - Method in class ome.services.blitz.repo.ProcessContainer
Called periodically by quartz to keep the sessions alive.
pixelData(PixelDataJob) - Method in class ome.services.blitz.repo.ManagedImportRequestI
 
PixelData - Class in ome.services.roi
Strategy for loading and optionally caching pixel data.
PixelData(PixelsService, IPixels) - Constructor for class ome.services.roi.PixelData
 
PIXELDATA_PROCESSED(int, ImportContainer, IObject, Long, int, ImportSize, Integer, Integer, Long) - Constructor for class ome.formats.importer.ImportEvent.PIXELDATA_PROCESSED
 
pixels - Variable in class ome.formats.importer.ImportEvent.IMPORT_DONE
 
pixels - Variable in class ome.formats.importer.ImportSize
 
pixels(String, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
Deprecated.
PIXELS - Static variable in class omero.gateway.model.ImageData
Identifies the ImageI.PIXELS field.
pixels - Variable in class omero.util.RPSTileLoop
Instance will be replaced on RawPixelsStorePrx.save()
Pixels_PhysicalSizeX - Static variable in class ome.formats.model.UnitsFactory
 
Pixels_PhysicalSizeY - Static variable in class ome.formats.model.UnitsFactory
 
Pixels_PhysicalSizeZ - Static variable in class ome.formats.model.UnitsFactory
 
Pixels_TimeIncrement - Static variable in class ome.formats.model.UnitsFactory
 
PixelsData - Class in omero.gateway.model
The data that makes up an OME Pixels object along with a back pointer to the Image that owns this Pixels.
PixelsData() - Constructor for class omero.gateway.model.PixelsData
Creates a new instance.
PixelsData(Pixels) - Constructor for class omero.gateway.model.PixelsData
Creates a new instance.
PixelsI - Class in ome.services.blitz.impl
Implementation of the IPixels service.
PixelsI(IPixels, BlitzExecutor) - Constructor for class ome.services.blitz.impl.PixelsI
 
PixelsProcessor - Class in ome.formats.model
Processes the pixels sets of an IObjectContainerStore and ensures that the physical pixel dimensions, Image name and description are updated to the corresponding user-provided values, if present.
PixelsProcessor() - Constructor for class ome.formats.model.PixelsProcessor
 
pixId - Variable in class ome.formats.importer.ImportEvent.PROGRESS_EVENT
 
Plane2D - Class in omero.gateway.rnd
Holds structure used to mapped the raw pixels data.
Plane2D(ReadOnlyByteArray, int, int, int, BytesConverter) - Constructor for class omero.gateway.rnd.Plane2D
Creates a new instance.
Plane_DeltaT - Static variable in class ome.formats.model.UnitsFactory
 
Plane_ExposureTime - Static variable in class ome.formats.model.UnitsFactory
 
Plane_PositionX - Static variable in class ome.formats.model.UnitsFactory
 
Plane_PositionY - Static variable in class ome.formats.model.UnitsFactory
 
Plane_PositionZ - Static variable in class ome.formats.model.UnitsFactory
 
PlaneInfoProcessor - Class in ome.formats.model
Processes the plane info sets of an IObjectContainerStore and removes entities of this rapidly exploding object that have no metadata populated.
PlaneInfoProcessor() - Constructor for class ome.formats.model.PlaneInfoProcessor
 
planes - Variable in class ome.services.formats.OmeroReader
 
PLATE_LINKS - Static variable in class omero.gateway.model.ScreenData
Identifies the ScreenI.PLATELINKS field.
Plate_WellOriginX - Static variable in class ome.formats.model.UnitsFactory
 
Plate_WellOriginY - Static variable in class ome.formats.model.UnitsFactory
 
PlateAcquisitionData - Class in omero.gateway.model
The data that makes up an OME PlateAcquisition.
PlateAcquisitionData() - Constructor for class omero.gateway.model.PlateAcquisitionData
Creates a new instance.
PlateAcquisitionData(PlateAcquisition) - Constructor for class omero.gateway.model.PlateAcquisitionData
Creates a new instance.
PlateData - Class in omero.gateway.model
The data that makes up an OME Plate along with links to its contained Well and enclosing Screen as well as the Experimenter that owns this Plate.
PlateData() - Constructor for class omero.gateway.model.PlateData
Creates a new instance.
PlateData(Plate) - Constructor for class omero.gateway.model.PlateData
Creates a new instance.
PointData - Class in omero.gateway.model
Represents a point in the Euclidean space R2.
PointData(Shape) - Constructor for class omero.gateway.model.PointData
Creates a new instance.
PointData() - Constructor for class omero.gateway.model.PointData
Creates a new instance of PointData, creating a new pointI Object.
PointData(double, double) - Constructor for class omero.gateway.model.PointData
Create a new instance of the PointData,
points(double, double, double, double) - Static method in class omero.model.SmartShape.Util
Returns the four corner points of a rectangle
pointsByBoundingBox(Shape, Rectangle2D, SmartShape.PointCallback) - Static method in class omero.model.SmartShape.Util
 
pointsToPath(List<Point>, boolean) - Static method in class omero.model.SmartShape.Util
 
PojoMapper - Class in omero.gateway.util
Helper methods to convert IObjects into their corresponding DataObjects.
PojoMapper() - Constructor for class omero.gateway.util.PojoMapper
 
Pojos - Class in omero.gateway.util
Utility methods for the Pojo DataObjects
Pojos() - Constructor for class omero.gateway.util.Pojos
 
poll(Current) - Method in class ome.services.blitz.impl.ScriptProcessI
 
poll() - Method in class omero.cmd.CmdCallbackI
Calls HandlePrx.getResponse() in order to check for a non-null value.
PolygonData - Class in omero.gateway.model
Represents an Polygon shape in the Euclidean space R2.
PolygonData(Shape) - Constructor for class omero.gateway.model.PolygonData
Creates a new instance.
PolygonData() - Constructor for class omero.gateway.model.PolygonData
Creates a new instance of PolygonData.
PolygonData(List<Point2D.Double>) - Constructor for class omero.gateway.model.PolygonData
Create a new instance of the PolylineData, set the points in the polyline.
PolylineData - Class in omero.gateway.model
Represents an Polyline shape in the Euclidean space R2.
PolylineData(Shape) - Constructor for class omero.gateway.model.PolylineData
Creates a new instance.
PolylineData() - Constructor for class omero.gateway.model.PolylineData
Creates a new instance of polyline, creating a new PolylineI Object.
PolylineData(List<Point2D.Double>) - Constructor for class omero.gateway.model.PolylineData
Create a new instance of the PolylineData, set the points in the polyline.
popRoi - Variable in class ome.services.blitz.impl.MetadataStoreI
 
populateMinMax() - Method in class ome.formats.OMEROMetadataStoreClient
Sends all the minimums and maximums for all images processed so far to the server.
populateMinMax_async(AMD_MetadataStore_populateMinMax, double[][][], Current) - Method in class ome.services.blitz.impl.MetadataStoreI
 
PopulateRoiJob - Class in ome.services.roi
Start-up task which guarantees that lib/python/populateroi.py is added as a script to the server.
PopulateRoiJob(Roles, String, Executor) - Constructor for class ome.services.roi.PopulateRoiJob
 
PopulateRoiJob(Roles, String, Executor, File) - Constructor for class ome.services.roi.PopulateRoiJob
 
PopulateRoiJob(Roles, Principal, Executor, File) - Constructor for class ome.services.roi.PopulateRoiJob
 
port - Variable in class loci.ome.io.OMECredentials
Deprecated.
 
port - Variable in class ome.formats.importer.ImportConfig
 
POST_UPLOAD_EVENT(int, ImportContainer, IObject, Long, int, ImportSize, Integer, Integer, Long) - Constructor for class ome.formats.importer.ImportEvent.POST_UPLOAD_EVENT
 
postClose(Current) - Method in class ome.services.blitz.impl.AbstractCloseableAmdServant
Should not throw any exceptions which should be detected by clients since it is called in a finally block after the client thread has been released.
postClose(Current) - Method in class ome.services.blitz.impl.AbstractPyramidServant
 
postClose(Current) - Method in class ome.services.blitz.impl.ExporterI
 
postClose(Current) - Method in class ome.services.blitz.impl.JobHandleI
 
postClose(Current) - Method in class ome.services.blitz.impl.MetadataStoreI
 
postClose(Current) - Method in class ome.services.blitz.impl.RawFileStoreI
 
postClose(Current) - Method in class ome.services.blitz.impl.SearchI
 
postClose(Current) - Method in class ome.services.blitz.impl.SharedResourcesI
 
postClose(Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
 
postClose(Current) - Method in class ome.services.blitz.repo.ManagedImportProcessI
 
postClose(Current) - Method in class ome.services.blitz.repo.RepoRawFileStoreI
 
postProcess() - Method in class ome.formats.OMEROMetadataStoreClient
Post processes the internal structure of the client side MetadataStore.
postProcess(Object) - Method in class ome.services.throttling.Task
Can be overridden to transform the return value from the async method.
postProcess_async(AMD_MetadataStore_postProcess, Current) - Method in class ome.services.blitz.impl.MetadataStoreI
Called after some number of Passes the MetadataStoreI.savedPlates to a background processor for further work.
postProcessAfterInitialization(Object, String) - Method in class ome.services.blitz.util.ApiConsistencyCheck
 
postProcessBeforeInitialization(Object, String) - Method in class ome.services.blitz.util.ApiConsistencyCheck
No-op
PowerI - Class in omero.model
Blitz wrapper around the Power class.
PowerI() - Constructor for class omero.model.PowerI
 
PowerI(double, UnitsPower) - Constructor for class omero.model.PowerI
 
PowerI(double, Unit<Power>) - Constructor for class omero.model.PowerI
 
PowerI(Power, Unit<Power>) - Constructor for class omero.model.PowerI
Copy constructor that converts the given Power based on the given ome-xml enum
PowerI(double, UnitsPower) - Constructor for class omero.model.PowerI
Copy constructor that converts the given Power based on the given ome.model enum
PowerI(Power, String) - Constructor for class omero.model.PowerI
Copy constructor that converts the given Power based on the given enum string.
PowerI(Power, UnitsPower) - Constructor for class omero.model.PowerI
Copy constructor that converts between units if possible.
PowerI(Power) - Constructor for class omero.model.PowerI
Convert a Bio-Formats Length to an OMERO Length.
preClose(Current) - Method in class ome.services.blitz.impl.AbstractCloseableAmdServant
 
preClose(Current) - Method in class ome.services.blitz.impl.AbstractPyramidServant
 
preClose(Current) - Method in class ome.services.blitz.impl.ExporterI
 
preClose(Current) - Method in class ome.services.blitz.impl.JobHandleI
 
preClose(Current) - Method in class ome.services.blitz.impl.MetadataStoreI
 
preClose(Current) - Method in class ome.services.blitz.impl.RawFileStoreI
 
preClose(Current) - Method in class ome.services.blitz.impl.SearchI
 
preClose(Current) - Method in class ome.services.blitz.impl.SharedResourcesI
 
preClose(Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
 
preClose(Current) - Method in class ome.services.blitz.repo.ManagedImportProcessI
 
preClose(Current) - Method in class ome.services.blitz.repo.RepoRawFileStoreI
 
prepare(Map<Integer, Image>) - Method in class ome.formats.OMEROMetadataStoreClient
Prepares the metadata store using existing metadata that has been pre-registered by OMERO.fs.
prepare_async(AMD_RawPixelsStore_prepare, List<Long>, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
prepare_async(AMD_RawPixelsStore_prepare, List<Long>, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
prepareGraphTraversal(List<ChildOption>, Set<GraphPolicy.Ability>, GraphPolicy, Iterable<Function<GraphPolicy, GraphPolicy>>, ACLVoter, GraphPathBean, SetMultimap<String, String>, GraphTraversal.Processor, boolean) - Method in class omero.cmd.graphs.GraphHelper
Construct a graph traversal manager for a GraphQuery request.
preparePixelsStore(List<Long>) - Method in class ome.formats.OMEROMetadataStoreClient
Prepares the server side RawPixelsStore.
prepareStatement() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
PressureI - Class in omero.model
Blitz wrapper around the Pressure class.
PressureI() - Constructor for class omero.model.PressureI
 
PressureI(double, UnitsPressure) - Constructor for class omero.model.PressureI
 
PressureI(double, Unit<Pressure>) - Constructor for class omero.model.PressureI
 
PressureI(Pressure, Unit<Pressure>) - Constructor for class omero.model.PressureI
Copy constructor that converts the given Pressure based on the given ome-xml enum
PressureI(double, UnitsPressure) - Constructor for class omero.model.PressureI
Copy constructor that converts the given Pressure based on the given ome.model enum
PressureI(Pressure, String) - Constructor for class omero.model.PressureI
Copy constructor that converts the given Pressure based on the given enum string.
PressureI(Pressure, UnitsPressure) - Constructor for class omero.model.PressureI
Copy constructor that converts between units if possible.
PressureI(Pressure) - Constructor for class omero.model.PressureI
Convert a Bio-Formats Length to an OMERO Length.
PRIMITIVE - Static variable in class omero.util.IceMapper
 
PRIMITIVE_FILTERABLE_COLLECTION_MAP - Static variable in class omero.util.IceMapper
 
PRIMITIVE_MAP - Static variable in class omero.util.IceMapper
 
principal - Variable in class ome.services.blitz.fire.Ring
 
principal() - Method in class ome.services.blitz.fire.Ring
 
principal() - Method in interface ome.services.blitz.redirect.Redirector.Context
Principal instance which can be used for internal calls the Executor.
principal - Variable in class ome.services.blitz.repo.RepositoryDaoImpl
 
principal - Variable in class omero.cmd.SessionI
 
print() - Method in class ome.formats.importer.ImportCandidates
Prints the "standard" representation of the groups, which is parsed by other software layers.
print(Throwable) - Method in class omero.log.LogMessage
Writes a stack trace into this log message.
printLine() - Method in class ome.formats.importer.transfers.AbstractExecFileTransfer
 
printLine() - Method in class ome.formats.importer.transfers.AbstractFileTransfer
 
printYaml() - Method in class ome.formats.importer.ImportCandidates
 
process(IObjectContainerStore) - Method in class ome.formats.model.ChannelProcessor
Processes the OMERO client side metadata store.
process(IObjectContainerStore) - Method in class ome.formats.model.InstrumentProcessor
Processes the OMERO client side metadata store.
process(IObjectContainerStore) - Method in interface ome.formats.model.ModelProcessor
Processes an IObjectContainerStore.
process(IObjectContainerStore) - Method in class ome.formats.model.PixelsProcessor
Processes the OMERO client side metadata store.
process(IObjectContainerStore) - Method in class ome.formats.model.PlaneInfoProcessor
Processes the OMERO client side metadata store.
process(IObjectContainerStore) - Method in class ome.formats.model.ReferenceProcessor
 
process(IObjectContainerStore) - Method in class ome.formats.model.ShapeProcessor
Processes the OMERO client side metadata store.
process(IObjectContainerStore) - Method in class ome.formats.model.TargetProcessor
Processes the OMERO client side metadata store.
process(IObjectContainerStore) - Method in class ome.formats.model.WellProcessor
Processes the OMERO client side metadata store.
process - Variable in class omero.grid.ProcessCallbackI
Proxy passed to this instance on creation.
ProcessCallbackI - Class in omero.grid
 
ProcessCallbackI(ProcessCallbackI) - Constructor for class omero.grid.ProcessCallbackI
 
ProcessCallbackI(client, ProcessPrx) - Constructor for class omero.grid.ProcessCallbackI
 
ProcessCallbackI(client, ProcessPrx, boolean) - Constructor for class omero.grid.ProcessCallbackI
 
ProcessCallbackI(ObjectAdapter, String, ProcessPrx) - Constructor for class omero.grid.ProcessCallbackI
 
ProcessCallbackI(ObjectAdapter, String, ProcessPrx, boolean) - Constructor for class omero.grid.ProcessCallbackI
 
ProcessCallbackI.Action - Enum in omero.grid
 
processCancelled(boolean, Current) - Method in class omero.grid.ProcessCallbackI
 
ProcessContainer - Class in ome.services.blitz.repo
Helper class for holding the individual ManagedImportProcessI instances created by ManagedRepositoryI.
ProcessContainer() - Constructor for class ome.services.blitz.repo.ProcessContainer
 
ProcessContainer.Process - Interface in ome.services.blitz.repo
 
processFinished(int, Current) - Method in class omero.grid.ProcessCallbackI
 
processInstances(String, Collection<Long>) - Method in class omero.cmd.graphs.NullGraphTraversalProcessor
 
processKilled(boolean, Current) - Method in class omero.grid.ProcessCallbackI
 
ProcessorCallbackI - Class in ome.services.blitz.impl
Callback used to lookup active processors via IceStorm.
ProcessorCallbackI(ServiceFactoryI) - Constructor for class ome.services.blitz.impl.ProcessorCallbackI
Simplified constructor used to see if any usermode processor is active for either the current group or the current user.
ProcessorCallbackI(ServiceFactoryI, ResultHolder<ProcessorPrx>, Job) - Constructor for class ome.services.blitz.impl.ProcessorCallbackI
Primary constructor.
PROGRESS_EVENT(int, ImportContainer, IObject, Long, int, ImportSize, Integer, Integer) - Constructor for class ome.formats.importer.ImportEvent.PROGRESS_EVENT
 
PROJECT_LINKS - Static variable in class omero.gateway.model.DatasetData
Identifies the DatasetI.PROJECTLINKS field.
ProjectData - Class in omero.gateway.model
The data that makes up an OME Project along with links to its contained Datasets and the Experimenter that owns this Project.
ProjectData() - Constructor for class omero.gateway.model.ProjectData
Creates a new instance.
ProjectData(Project) - Constructor for class omero.gateway.model.ProjectData
Creates a new instance.
projection_async(AMD_IQuery_projection, String, Parameters, Current) - Method in class ome.services.blitz.impl.QueryI
 
ProjectionI - Class in ome.services.blitz.impl
Implementation of the IProjection service.
ProjectionI(ServiceInterface, BlitzExecutor) - Constructor for class ome.services.blitz.impl.ProjectionI
 
projectPixels_async(AMD_IProjection_projectPixels, long, PixelsType, ProjectionType, int, int, List<Integer>, int, int, int, String, Current) - Method in class ome.services.blitz.impl.ProjectionI
 
projectStack_async(AMD_IProjection_projectStack, long, PixelsType, ProjectionType, int, int, int, int, int, Current) - Method in class ome.services.blitz.impl.ProjectionI
 
prompt(ImportConfig.Value<T>, String, boolean) - Method in class ome.formats.importer.ImportConfig
Build prompt
PROP_CONNECTOR_CLOSED - Static variable in class omero.gateway.Gateway
Property to indicate that a Connector has been closed
PROP_CONNECTOR_CREATED - Static variable in class omero.gateway.Gateway
Property to indicate that a Connector has been created
PROP_FACILITY_CLOSED - Static variable in class omero.gateway.Gateway
Property to indicate that a Facility has been closed
PROP_FACILITY_CREATED - Static variable in class omero.gateway.Gateway
Property to indicate that a Facility has been created
PROP_IMPORTSTORE_CLOSED - Static variable in class omero.gateway.Gateway
Property to indicate that an import store has been closed
PROP_IMPORTSTORE_CREATED - Static variable in class omero.gateway.Gateway
Property to indicate that an import store has been created
PROP_RENDERINGENGINE_CLOSED - Static variable in class omero.gateway.Gateway
Property to indicate that a rendering engine has been closed
PROP_RENDERINGENGINE_CREATED - Static variable in class omero.gateway.Gateway
Property to indicate that a rendering engine has been created
PROP_SESSION_CLOSED - Static variable in class omero.gateway.Gateway
Property to indicate that a session has been closed
PROP_SESSION_CREATED - Static variable in class omero.gateway.Gateway
Property to indicate that a session has been created
PROP_STATEFUL_SERVICE_CLOSED - Static variable in class omero.gateway.Gateway
Property to indicate that a stateful service has been closed
PROP_STATEFUL_SERVICE_CREATED - Static variable in class omero.gateway.Gateway
Property to indicate that a stateful service has been created
PROP_STATELESS_SERVICE_CREATED - Static variable in class omero.gateway.Gateway
Property to indicate that a stateless service has been created
ProportionalTimeEstimatorImpl - Class in ome.formats.importer.util
Class implementing the TimeEstimator interface.
ProportionalTimeEstimatorImpl(long) - Constructor for class ome.formats.importer.util.ProportionalTimeEstimatorImpl
Creates a new object of this class with a defined internal buffer size.
provider - Variable in class omero.cmd.admin.CurrentSessionsRequestI
 
proxy() - Method in class ome.services.blitz.impl.ServiceFactoryI
 
proxyForSession(Redirector.Context, String) - Method in class ome.services.blitz.redirect.AbstractRedirector
 
pt(double, double) - Method in class ome.services.roi.GeomTool
 
PublicRepositoryI - Class in ome.services.blitz.repo
An implementation of the PublicRepository interface.
PublicRepositoryI(RepositoryDao, ChecksumProviderFactory, String, String) - Constructor for class ome.services.blitz.repo.PublicRepositoryI
 
PublicRepositoryI.AMD_submit - Class in ome.services.blitz.repo
 
publisherOrNull(String) - Method in class ome.services.blitz.fire.TopicManager.Impl
 
publishEventLog(ApplicationContext, String, String, Collection<Long>) - Method in class omero.cmd.graphs.GraphHelper
Publish database changes to the event log.
publishMessage(InternalMessage) - Method in class ome.services.blitz.repo.PublicRepositoryI
 
purgeNode(String) - Method in class ome.services.blitz.fire.Ring
 
put(File, Dataset) - Method in class ome.formats.importer.ImportFixture
 
put(Callback) - Method in class ome.services.throttling.Queue
 
put(Identity, Object) - Method in class omero.util.ServantHolder
 
putAll(Map<File, Dataset>) - Method in class ome.formats.importer.ImportFixture
 
PyTablesUtils - Class in omero.gateway.util
Collection of utility classes to convert OMERO tables.
PyTablesUtils() - Constructor for class omero.gateway.util.PyTablesUtils
 

Q

qaBaseURL - Variable in class ome.formats.importer.ImportConfig
 
query - Variable in class omero.cmd.admin.UpdateSessionTimeoutRequestI
 
query(SecurityContext, long, String) - Method in class omero.gateway.facility.TablesFacility
Perform a query on the table
query(SecurityContext, long, String, long, long, long) - Method in class omero.gateway.facility.TablesFacility
Perform a query on the table
queryCacheHit(String, String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
queryCacheMiss(String, String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
queryCachePut(String, String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
queryExecuted(String, int, long) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
QueryI - Class in ome.services.blitz.impl
Implementation of the IQuery service.
QueryI(IQuery, BlitzExecutor) - Constructor for class ome.services.blitz.impl.QueryI
 
Queue - Class in ome.services.throttling
Manages AMD-based method dispatches from blitz
Queue(OmeroContext) - Constructor for class ome.services.throttling.Queue
 

R

random(int) - Method in class ome.services.roi.GeomTool
 
randomize(Random) - Method in class omero.model.SmartEllipseI
 
randomize(Random) - Method in class omero.model.SmartLineI
 
randomize(Random) - Method in class omero.model.SmartMaskI
 
randomize(Random) - Method in class omero.model.SmartPathI
 
randomize(Random) - Method in class omero.model.SmartPointI
 
randomize(Random) - Method in class omero.model.SmartPolygonI
 
randomize(Random) - Method in class omero.model.SmartPolylineI
 
randomize(Random) - Method in class omero.model.SmartRectI
 
randomize(Random) - Method in interface omero.model.SmartShape
Initializes this shape with completely random data.
randomize(Random) - Method in class omero.model.SmartTextI
 
rarray(RType...) - Static method in class omero.rtypes
 
rarray(Collection<RType>) - Static method in class omero.rtypes
 
RatingAnnotationData - Class in omero.gateway.model
Annotation used to rate an object.
RatingAnnotationData() - Constructor for class omero.gateway.model.RatingAnnotationData
Creates a new instance of value LEVEL_ZERO.
RatingAnnotationData(int) - Constructor for class omero.gateway.model.RatingAnnotationData
Creates a new instance.
RatingAnnotationData(LongAnnotation) - Constructor for class omero.gateway.model.RatingAnnotationData
Creates a new instance.
rawAccess(RawAccessRequest, Current) - Method in class ome.services.blitz.repo.AbstractRepositoryI
 
rawAccess() - Method in class ome.services.blitz.repo.RawAccessRequestI
 
RawAccessRequestI - Class in ome.services.blitz.repo
Command request for accessing a repository directly.
RawAccessRequestI(Registry) - Constructor for class ome.services.blitz.repo.RawAccessRequestI
 
RawDataFacility - Class in omero.gateway.facility
A Facility for accessing raw data
RawFileStoreI - Class in ome.services.blitz.impl
Implementation of the RawFileStore service.
RawFileStoreI(RawFileStore, BlitzExecutor) - Constructor for class ome.services.blitz.impl.RawFileStoreI
 
RawPixelsStoreI - Class in ome.services.blitz.impl
Implementation of the RawPixelsStore service.
RawPixelsStoreI(RawPixelsStore, BlitzExecutor) - Constructor for class ome.services.blitz.impl.RawPixelsStoreI
 
rbool(boolean) - Static method in class omero.rtypes
 
rclass(String) - Static method in class omero.rtypes
 
rdouble(double) - Static method in class omero.rtypes
 
read_async(AMD_Exporter_read, long, int, Current) - Method in class ome.services.blitz.impl.ExporterI
 
read_async(AMD_RawFileStore_read, long, int, Current) - Method in class ome.services.blitz.impl.RawFileStoreI
 
read_async(AMD_RawFileStore_read, long, int, Current) - Method in class ome.services.blitz.repo.RepoRawFileStoreI
 
reader - Variable in class ome.formats.importer.util.ErrorHandler.FILE_EXCEPTION
 
reader - Variable in class ome.formats.importer.util.ErrorHandler.INTERNAL_EXCEPTION
 
READERS_KEY - Static variable in class ome.formats.importer.ImportConfig
Lookup key for System.getProperty(String).
readersPath - Variable in class ome.formats.importer.ImportConfig
 
READONLY_FLAG - Static variable in class omero.gateway.model.ShapeData
Flag stating that the ROI is read only.
ReadOnlyByteArray - Class in omero.util
A read-only slice of a given array.
ReadOnlyByteArray(byte[], int, int) - Constructor for class omero.util.ReadOnlyByteArray
Creates a read-only slice of base.
reapSession(String) - Method in class ome.services.blitz.fire.SessionManagerI
Destroys all the ServiceFactoryI instances based on the given sessionId.
recreateCollection(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
rect(double, double, double, double) - Method in class ome.services.roi.GeomTool
 
RectangleData - Class in omero.gateway.model
Represents a rectangle in the Euclidean space R2.
RectangleData(Shape) - Constructor for class omero.gateway.model.RectangleData
Creates a new instance.
RectangleData() - Constructor for class omero.gateway.model.RectangleData
Creates a new instance with a default rectangle.
RectangleData(double, double, double, double) - Constructor for class omero.gateway.model.RectangleData
Creates a new instance of the RectangleData.
RED_INDEX - Static variable in class ome.formats.model.ColorsFactory
Index of the red component of a color.
RED_TEXT - Static variable in class ome.formats.model.ChannelProcessor
Name of the red component when it is a graphics image.
Redirector - Interface in ome.services.blitz.redirect
Strategy interface for helping a Ring instance decide whether to redirect SessionPrx creation to another SessionManagerI instance.
Redirector.Context - Interface in ome.services.blitz.redirect
Interface implemented by Ring instances to allow passing in the context necessary for making strategy decisions.
ReferenceProcessor - Class in ome.formats.model
Processes the references of an IObjectContainerStore and ensures that container references are consistent with the LSID stored in the IObjectContainer itself.
ReferenceProcessor() - Constructor for class ome.formats.model.ReferenceProcessor
 
referenceType(Iterable<String>) - Method in class omero.gateway.util.Requests.DuplicateBuilder
 
referenceType(Class<? extends IObject>...) - Method in class omero.gateway.util.Requests.DuplicateBuilder
 
referenceType(String...) - Method in class omero.gateway.util.Requests.DuplicateBuilder
 
refresh_async(AMD_IQuery_refresh, IObject, Current) - Method in class ome.services.blitz.impl.QueryI
 
register(String, ObjectPrx, boolean) - Method in class ome.services.blitz.fire.TopicManager.Impl
 
register(String, ObjectPrx, boolean) - Method in interface ome.services.blitz.fire.TopicManager
Enforces no security constraints.
register(String, RString, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
Register an OriginalFile using its path
register(String, CheckedPath, String, Current) - Method in interface ome.services.blitz.repo.RepositoryDao
Register an OriginalFile object
register(String, CheckedPath, String, ServiceFactory, SqlAction, Session) - Method in interface ome.services.blitz.repo.RepositoryDao
Like RepositoryDao.register(String, CheckedPath, String, Ice.Current) but does not create a new transaction.
register(String, CheckedPath, String, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
 
register(String, CheckedPath, String, ServiceFactory, SqlAction, Session) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
Returns original file object is "live" within the Hibernate session.
register(Logger, Communicator, boolean) - Method in class omero.util.ObjectFactoryRegistry.ObjectFactory
 
registerCallback(ProcessCallbackPrx, Current) - Method in class ome.services.blitz.impl.ScriptProcessI
 
registerCallback(RawFileStorePrx, int) - Method in class ome.services.blitz.repo.ManagedImportProcessI
 
registerKeepAlive() - Method in class ome.services.blitz.repo.ManagedImportRequestI
If the ManagedImportRequestI.setResources(Resources) has been called with a non-null value, then create an Resources.Entry which will ping the ServiceFactoryPrx instance periodically to keep the import from timing out.
registerPredicate(GraphPolicyRulePredicate) - Method in class omero.cmd.graphs.BaseGraphPolicyAdjuster
 
registerProxy(Current) - Method in class ome.services.blitz.repo.ManagedImportProcessI
Adds this instance to the current session so that clients can communicate with it.
registerServant(Identity, Object) - Method in class omero.cmd.SessionI
Registers the servant with the adapter (or throws an exception if one is already registered) as well as configures the servant in any post-Spring way necessary, based on the type of the servant.
registerServant(Identity, Object, Current) - Method in class omero.cmd.SessionI
Additionally stores information from the Current argument in the CallContext so that information from the creation of a servant can be recorded server-side without the need for clients to re-send the information or even for values which clients should not know.
RegisterServantMessage - Class in ome.services.blitz.util
InternalMessage raised when a servant should be registered for clean.
RegisterServantMessage(Object, Object, Current) - Constructor for class ome.services.blitz.util.RegisterServantMessage
 
RegisterServantMessage(Object, Object, String, Current) - Constructor for class ome.services.blitz.util.RegisterServantMessage
 
Registry - Interface in ome.services.blitz.fire
Helper class which makes the RegistryPrx available within OmeroBlitz.
registry - Variable in class ome.services.blitz.fire.SessionManagerI
 
Registry.Impl - Class in ome.services.blitz.fire
 
REIMPORT() - Constructor for class ome.formats.importer.ImportEvent.REIMPORT
 
relativeComplement(Collection<T>, Collection<T>) - Static method in class omero.gateway.util.Pojos
Get the relative complement of coll1 in coll2
releaseDate - Static variable in class ome.formats.importer.Version
Deprecated.
The data of the last release date.
releaseLock(String) - Method in class omero.util.ServantHolder
Releases the given lock if found, otherwise throws an InternalException
remove(Resources.Entry) - Method in class omero.util.Resources
 
remove(Identity) - Method in class omero.util.ServantHolder
 
remove_async(AMD_Search_remove, Current) - Method in class ome.services.blitz.impl.SearchI
 
remove_path(File) - Static method in class omero.util.TempFileManager
removeAdminPrivileges(SecurityContext, ExperimenterData, Collection<String>) - Method in class omero.gateway.facility.AdminFacility
Revoke admin privileges for a user
removeCache(int) - Method in interface omero.gateway.cache.CacheService
Removes the cache corresponding to the passed id.
removeCallback(CmdCallbackPrx, Current) - Method in class omero.cmd.HandleI
 
removeClientId(String) - Method in class omero.util.ServantHolder
 
removeCodomainMap_async(AMD_RenderingEngine_removeCodomainMap, CodomainMapContext, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
removeCodomainMapFromChannel_async(AMD_RenderingEngine_removeCodomainMapFromChannel, CodomainMapContext, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
removeCollection(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
removeGroupOwners_async(AMD_IAdmin_removeGroupOwners, ExperimenterGroup, List<Experimenter>, Current) - Method in class ome.services.blitz.impl.AdminI
 
removeGroups_async(AMD_IAdmin_removeGroups, Experimenter, List<ExperimenterGroup>, Current) - Method in class ome.services.blitz.impl.AdminI
 
removeGuest_async(AMD_IShare_removeGuest, long, String, Current) - Method in class ome.services.blitz.impl.ShareI
 
removeGuests_async(AMD_IShare_removeGuests, long, List<String>, Current) - Method in class ome.services.blitz.impl.ShareI
 
removeIObject(IObject, IObject) - Static method in class omero.gateway.util.ModelMapper
Unlinks the specified child and the parent and returns the updated child IObject.
removeIObjectContainer(LSID) - Method in interface ome.formats.model.IObjectContainerStore
Removes an IObject container from within the OME-XML data model store.
removeIObjectContainer(LSID) - Method in class ome.formats.OMEROMetadataStoreClient
 
removeModelProcessor(ModelProcessor) - Method in class ome.formats.OMEROMetadataStoreClient
Removes a model processor from use.
removeObject(Identity) - Method in class ome.services.blitz.fire.Registry.Impl
 
removeObject(Identity) - Method in interface ome.services.blitz.fire.Registry
 
removeObject_async(AMD_IShare_removeObject, long, IObject, Current) - Method in class ome.services.blitz.impl.ShareI
 
removeObjects_async(AMD_IShare_removeObjects, long, List<IObject>, Current) - Method in class ome.services.blitz.impl.ShareI
 
removeObjectSafely(Identity) - Method in class ome.services.blitz.fire.Registry.Impl
 
removeObjectSafely(Identity) - Method in interface ome.services.blitz.fire.Registry
 
removeParams(Long) - Method in class ome.services.blitz.util.ParamsCache
Remove a cached JobParams instance.
removePath(File) - Method in class omero.util.TempFileManager
If the given file is under the top-level temporary directory then it is deleted whether file or folder.
removeProcess(ProcessContainer.Process) - Method in class ome.services.blitz.repo.ProcessContainer
Removes the process.
removeProcessor(ProcessorPrx, Current) - Method in class ome.services.blitz.impl.SharedResourcesI
 
removePropertyChangeListener(PropertyChangeListener) - Method in class omero.gateway.facility.Facility
Removes a PropertyChangeListener (Pass null to remove all PropertyChangeListeners)
removePropertyChangeListener(PropertyChangeListener) - Method in class omero.gateway.Gateway
Removes a PropertyChangeListener
removeRoisFromFolders(SecurityContext, long, Collection<ROIData>, Collection<FolderData>) - Method in class omero.gateway.facility.ROIFacility
Remove the ROIs from the folders
removeShapeData(ShapeData) - Method in class omero.gateway.model.ROIData
Removes the ShapeData object from ROIData.
removeUnusedFiles_async(AMD_IRepositoryInfo_removeUnusedFiles, Current) - Method in class ome.services.blitz.impl.RepositoryInfoI
 
removeUser_async(AMD_IShare_removeUser, long, Experimenter, Current) - Method in class ome.services.blitz.impl.ShareI
 
removeUsers_async(AMD_IShare_removeUsers, long, List<Experimenter>, Current) - Method in class ome.services.blitz.impl.ShareI
 
render_async(AMD_RenderingEngine_render, PlaneDef, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
renderAsPackedInt_async(AMD_RenderingEngine_renderAsPackedInt, PlaneDef, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
renderCompressed_async(AMD_RenderingEngine_renderCompressed, PlaneDef, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
RenderingEngineI - Class in ome.services.blitz.impl
Implementation of the RenderingEngine service.
RenderingEngineI(RenderingEngine, BlitzExecutor) - Constructor for class ome.services.blitz.impl.RenderingEngineI
 
RenderingServiceException - Exception in omero.gateway.exception
Reports an error occurred while trying to render a plane.
RenderingServiceException() - Constructor for exception omero.gateway.exception.RenderingServiceException
Creates a new exception.
RenderingServiceException(String) - Constructor for exception omero.gateway.exception.RenderingServiceException
Constructs a new exception with the specified detail message.
RenderingServiceException(Throwable) - Constructor for exception omero.gateway.exception.RenderingServiceException
Constructs a new exception with the specified cause.
RenderingServiceException(String, Throwable) - Constructor for exception omero.gateway.exception.RenderingServiceException
Constructs a new exception with the specified detail message and cause.
RenderingSettingsI - Class in ome.services.blitz.impl
Implementation of the IRenderingSettings service.
RenderingSettingsI(IRenderingSettings, BlitzExecutor) - Constructor for class ome.services.blitz.impl.RenderingSettingsI
 
renderProjectedAsPackedInt_async(AMD_RenderingEngine_renderProjectedAsPackedInt, ProjectionType, int, int, int, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
renderProjectedCompressed_async(AMD_RenderingEngine_renderProjectedCompressed, ProjectionType, int, int, int, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
repo - Variable in class ome.services.blitz.repo.RawAccessRequestI
 
RepoRawFileStoreI - Class in ome.services.blitz.repo
An implementation of the RepoRawFileStore interface
RepoRawFileStoreI(BlitzExecutor, RawFileStore, Current) - Constructor for class ome.services.blitz.repo.RepoRawFileStoreI
 
reportForgottenPassword_async(AMD_IAdmin_reportForgottenPassword, String, String, Current) - Method in class ome.services.blitz.impl.AdminI
 
repositories(Current) - Method in class ome.services.blitz.impl.SharedResourcesI
 
repositoryDao - Variable in class ome.services.blitz.repo.PublicRepositoryI
 
RepositoryDao - Interface in ome.services.blitz.repo
 
RepositoryDaoImpl - Class in ome.services.blitz.repo
DAO class for encapsulating operations related to resource access inside the repository.
RepositoryDaoImpl(Principal, Roles, Executor, Executor, OmeroInterceptor, String) - Constructor for class ome.services.blitz.repo.RepositoryDaoImpl
Primary constructor which takes all final fields.
RepositoryDaoImpl(Principal, Executor) - Constructor for class ome.services.blitz.repo.RepositoryDaoImpl
Previous constructor which should no longer be used.
RepositoryInfoI - Class in ome.services.blitz.impl
Implementation of the IRepositoryInfo service.
RepositoryInfoI(IRepositoryInfo, BlitzExecutor) - Constructor for class ome.services.blitz.impl.RepositoryInfoI
 
request(GraphModify2) - Method in class omero.gateway.util.Requests.SkipHeadBuilder
 
request(Class<? extends GraphModify2>) - Method in class omero.gateway.util.Requests.SkipHeadBuilder
 
requestFromUser() - Method in class ome.formats.importer.ImportConfig
if can't log in request needed information
requestHeartBeats() - Method in class ome.services.blitz.fire.SessionManagerI
Destroys all the ServiceFactoryI instances based on the given sessionId.
RequestObjectFactoryRegistry - Class in ome.services.blitz.impl.commands
Types which rely on the omero.model and omero.api objects rather than just the omero.cmd types.
RequestObjectFactoryRegistry() - Constructor for class ome.services.blitz.impl.commands.RequestObjectFactoryRegistry
 
RequestObjectFactoryRegistry - Class in ome.services.blitz.repo
Requests which are handled by the repository servants.
RequestObjectFactoryRegistry(Registry, TileSizes, RepositoryDao, Ring, PixelsService) - Constructor for class ome.services.blitz.repo.RequestObjectFactoryRegistry
 
RequestObjectFactoryRegistry(Registry, TileSizes, RepositoryDao, Ring, PixelsService, Resources) - Constructor for class ome.services.blitz.repo.RequestObjectFactoryRegistry
 
RequestObjectFactoryRegistry - Class in omero.cmd
SPI type picked up from the Spring configuration and given a chance to register all its ObjectFactory instances with the Communicator.
RequestObjectFactoryRegistry(ExtendedMetadata, ACLVoter, Roles, PixelsService, ThumbnailService, MailUtil, PasswordUtil, SecuritySystem, PasswordProvider, GraphRequestFactory) - Constructor for class omero.cmd.RequestObjectFactoryRegistry
 
Requests - Class in omero.gateway.util
A utility class of factory methods with various signatures for clients to use in generating requests for graph operations.
Requests() - Constructor for class omero.gateway.util.Requests
 
Requests.Chgrp2Builder - Class in omero.gateway.util
A builder for Chgrp2 instances.
Requests.ChildOptionBuilder - Class in omero.gateway.util
A builder for ChildOption instances.
Requests.Chmod2Builder - Class in omero.gateway.util
A builder for Chmod2 instances.
Requests.Chown2Builder - Class in omero.gateway.util
A builder for Chown2 instances.
Requests.Delete2Builder - Class in omero.gateway.util
A builder for Delete2 instances.
Requests.DiskUsageBuilder - Class in omero.gateway.util
A builder for DiskUsage2 instances.
Requests.DuplicateBuilder - Class in omero.gateway.util
A builder for Duplicate instances.
Requests.FindChildrenBuilder - Class in omero.gateway.util
A builder for FindChildren instances.
Requests.FindParentsBuilder - Class in omero.gateway.util
A builder for FindParents instances.
Requests.SkipHeadBuilder - Class in omero.gateway.util
A builder for SkipHead instances.
requiresPixelsPyramid(Pixels) - Method in class ome.services.roi.PixelData
Returns whether a pyramid should be used for the given Pixels.
requiresPixelsPyramid_async(AMD_PyramidService_requiresPixelsPyramid, Current) - Method in class ome.services.blitz.impl.AbstractPyramidServant
 
requiresPixelsPyramid_async(AMD_PyramidService_requiresPixelsPyramid, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
resetDefaults_async(AMD_IRenderingSettings_resetDefaults, RenderingDef, Pixels, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
 
resetDefaults_async(AMD_Search_resetDefaults, Current) - Method in class ome.services.blitz.impl.SearchI
 
resetDefaults_async(AMD_ThumbnailStore_resetDefaults, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
 
resetDefaultsAndGenerateThumbnails(List<Long>, List<Long>) - Method in class ome.formats.OMEROMetadataStoreClient
Resets the defaults and generates thumbnails for a given set of Pixels IDs.
resetDefaultsByOwnerInSet_async(AMD_IRenderingSettings_resetDefaultsByOwnerInSet, String, List<Long>, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
 
resetDefaultSettings_async(AMD_RenderingEngine_resetDefaultSettings, boolean, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
resetDefaultsForPixels_async(AMD_IRenderingSettings_resetDefaultsForPixels, long, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
 
resetDefaultsInDataset_async(AMD_IRenderingSettings_resetDefaultsInDataset, long, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
 
resetDefaultsInImage_async(AMD_IRenderingSettings_resetDefaultsInImage, long, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
 
resetDefaultsInSet_async(AMD_IRenderingSettings_resetDefaultsInSet, String, List<Long>, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
 
resetDefaultsNoSave_async(AMD_IRenderingSettings_resetDefaultsNoSave, RenderingDef, Pixels, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
 
resetEnumerations_async(AMD_ITypes_resetEnumerations, String, Current) - Method in class ome.services.blitz.impl.TypesI
 
resetMinMaxInSet_async(AMD_IRenderingSettings_resetMinMaxInSet, String, List<Long>, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
 
ResetPasswordRequestI - Class in omero.cmd.admin
Callback interface allowing to reset password for the given user.
ResetPasswordRequestI(MailUtil, PasswordUtil, SecuritySystem, PasswordProvider) - Constructor for class omero.cmd.admin.ResetPasswordRequestI
 
RESOLUTION_DESCRIPTIONS - Static variable in class ome.services.blitz.impl.AbstractPyramidServant
This is a fairly brittle mapping from the List> created by the PixelBuffers to the List which is remotely provided by Blitz.
resolveConfigFile(String) - Method in class ome.services.blitz.util.BlitzConfiguration
Resolve the given config file to a concrete location, possibly throwing an exception if stored in a jar.
Resources - Class in omero.util
Container class for storing resources which should be cleaned up on close and periodically checked.
Resources() - Constructor for class omero.util.Resources
As Resources.Resources(int) but specifies a 60 second sleep period between task execution.
Resources(int) - Constructor for class omero.util.Resources
As Resources.Resources(int, ScheduledExecutorService) but uses a Executors.newSingleThreadExecutor().
Resources(int, ScheduledExecutorService) - Constructor for class omero.util.Resources
 
Resources.Entry - Interface in omero.util
Interface to be implemented by any object which wants to be managed by the Resources class.
response - Variable in class ome.services.throttling.Task
 
response(Object, OmeroContext) - Method in class ome.services.throttling.Task
Calls the response method
responseRunning(List<Long>, Current) - Method in class ome.services.blitz.impl.ProcessorCallbackI
Callback method which should not be called for this instance.
ResultHolder<U> - Class in ome.services.blitz.util
 
ResultHolder(long) - Constructor for class ome.services.blitz.util.ResultHolder
 
results_async(AMD_Search_results, Current) - Method in class ome.services.blitz.impl.SearchI
 
retrieveAllRndSettings_async(AMD_IPixels_retrieveAllRndSettings, long, long, Current) - Method in class ome.services.blitz.impl.PixelsI
 
retrieveCollection_async(AMD_IContainer_retrieveCollection, IObject, String, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI
 
retrievePixDescription_async(AMD_IPixels_retrievePixDescription, long, Current) - Method in class ome.services.blitz.impl.PixelsI
 
retrieveRndSettings_async(AMD_IPixels_retrieveRndSettings, long, Current) - Method in class ome.services.blitz.impl.PixelsI
 
retrieveRndSettingsFor_async(AMD_IPixels_retrieveRndSettingsFor, long, long, Current) - Method in class ome.services.blitz.impl.PixelsI
 
reusedSession - Variable in class omero.cmd.SessionI
 
reverse(Object) - Method in class omero.util.IceMapper
 
reverse(Collection) - Method in class omero.util.IceMapper
Copied from ModelMapper.findCollection(Collection) This could be unified in that a method findCollection(Collection, Map) was added with ModelMapper calling findCollection(source, model2target) and reverseCollection(Collection) calling findCollection(source,target2model).
reverse(Collection, Class) - Method in class omero.util.IceMapper
Creates a collection assignable to the given type.
reverse(Map) - Method in class omero.util.IceMapper
 
reverse(ModelBased) - Method in class omero.util.IceMapper
Copied from ReverseModelMapper.
reverseArray(List, Class) - Method in class omero.util.IceMapper
Supports the separate case of reversing for arrays.
reverseNamedList(List<NamedValue>) - Static method in class omero.util.IceMapper
 
reverseStringStringMap(Map<String, RString>) - Static method in class omero.util.IceMapper
Reverse a String→String map's values from RStrings.
review(Map<String, Set<GraphPolicy.Details>>, GraphPolicy.Details, Map<String, Set<GraphPolicy.Details>>, Set<String>, boolean) - Method in class omero.cmd.graphs.BaseGraphPolicyAdjuster
 
revision - Static variable in class ome.formats.importer.Version
Deprecated.
The repository revision.
revisionDate - Static variable in class ome.formats.importer.Version
Deprecated.
The data of the last repository revision.
rfloat(float) - Static method in class omero.rtypes
 
Ring - Class in ome.services.blitz.fire
Distributed ring of BlitzConfiguration objects which manages lookups of sessions and other resources from all the blitzes which take part in the cluster.
Ring(String, Executor) - Constructor for class ome.services.blitz.fire.Ring
 
Ring(String, Executor, Redirector, ScriptRepoHelper, NodeProvider) - Constructor for class ome.services.blitz.fire.Ring
 
ring - Variable in class ome.services.blitz.fire.SessionManagerI
 
rint(int) - Static method in class omero.rtypes
 
rinternal(Internal) - Static method in class omero.rtypes
 
rlist(RType...) - Static method in class omero.rtypes
 
rlist(Collection<RType>) - Static method in class omero.rtypes
 
rlong(long) - Static method in class omero.rtypes
 
rmap() - Static method in class omero.rtypes
 
rmap(Map<String, RType>) - Static method in class omero.rtypes
 
rmap(String, RType) - Static method in class omero.rtypes
 
robject(IObject) - Static method in class omero.rtypes
 
ROI_COLUMN_INDEX - Static variable in class omero.gateway.model.TableResult
Identifies the index of the ROI column.
ROIComponent - Class in omero.gateway.util
Component hosting the ROI.
ROIComponent(long) - Constructor for class omero.gateway.util.ROIComponent
Instantiate the ROIComponent.
ROICoordinate - Class in omero.gateway.model
Defines a plane.
ROICoordinate() - Constructor for class omero.gateway.model.ROICoordinate
Creates a default instance.
ROICoordinate(int, int) - Constructor for class omero.gateway.model.ROICoordinate
Creates a new instance.
roiCount() - Method in class omero.gateway.model.FolderData
Get the number of ROIs linked to this folder
ROIData - Class in omero.gateway.model
Converts the ROI object.
ROIData(Roi) - Constructor for class omero.gateway.model.ROIData
Creates a new instance.
ROIData() - Constructor for class omero.gateway.model.ROIData
Create a new instance of an ROIData object.
ROIFacility - Class in omero.gateway.facility
A Facility for ROI.
RoiI - Class in ome.services.blitz.impl
implementation of the IRoi service interface.
RoiI(BlitzExecutor, GeomTool, SqlAction) - Constructor for class ome.services.blitz.impl.RoiI
 
RoiI.RoiResultMapper - Class in ome.services.blitz.impl
 
RoiI.RoiResultMapReturnMapper - Class in ome.services.blitz.impl
 
RoiI.RoiResultReturnMapper - Class in ome.services.blitz.impl
 
ROIResult - Class in omero.gateway.model
Hosts the results of a call loading the ROI.
ROIResult(Collection<ROIData>) - Constructor for class omero.gateway.model.ROIResult
Creates a new instance.
ROIResult(Collection<ROIData>, long) - Constructor for class omero.gateway.model.ROIResult
Creates a new instance.
ROIResult(Collection<ROIData>, long, Object) - Constructor for class omero.gateway.model.ROIResult
Creates a new instance.
RoiResultMapper(RoiOptions) - Constructor for class ome.services.blitz.impl.RoiI.RoiResultMapper
 
RoiResultMapReturnMapper(RoiOptions) - Constructor for class ome.services.blitz.impl.RoiI.RoiResultMapReturnMapper
 
RoiResultReturnMapper(RoiOptions) - Constructor for class ome.services.blitz.impl.RoiI.RoiResultReturnMapper
 
RoiTypes - Class in ome.services.roi
Intelligent server-side representations of the Roi and Shape types.
RoiTypes() - Constructor for class ome.services.roi.RoiTypes
 
RoiTypes.RoiTypesObjectFactoryRegistry - Class in ome.services.roi
 
RoiTypesObjectFactoryRegistry() - Constructor for class ome.services.roi.RoiTypes.RoiTypesObjectFactoryRegistry
 
roles - Variable in class ome.services.blitz.repo.RepositoryDaoImpl
 
root(Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
 
ROUTED_FROM - Static variable in class ome.services.blitz.redirect.AbstractRedirector
 
Router - Class in ome.services.blitz
Wrapper around a call to 'glacier2router' to permit Java control over the process.
Router() - Constructor for class ome.services.blitz.Router
 
rps - Variable in class omero.util.RPSTileData
 
RPSTileData - Class in omero.util
Access strategy which can be implemented by diverse resources
RPSTileData(RPSTileLoop, RawPixelsStorePrx) - Constructor for class omero.util.RPSTileData
 
RPSTileLoop - Class in omero.util
Helper subclass of TileLoop which handles unloaded Pixels instances and manages the creation of the RPSTileData.
RPSTileLoop(ServiceFactoryPrx, Pixels) - Constructor for class omero.util.RPSTileLoop
 
rset(RType...) - Static method in class omero.rtypes
 
rset(Collection<RType>) - Static method in class omero.rtypes
 
rstring(String) - Static method in class omero.rtypes
 
RTF - Static variable in class omero.gateway.model.FileAnnotationData
Identifies the RTF file formats.
rtime(long) - Static method in class omero.rtypes
 
rtime(Date) - Static method in class omero.rtypes
 
rtime_max() - Static method in class omero.rtypes
 
rtime_min() - Static method in class omero.rtypes
 
rtime_str(String) - Static method in class omero.rtypes
 
rtype(Object) - Static method in class omero.rtypes
Attempts to dispatch to the other omero.rtypes.* static methods to create a proper RType subclass by checking the type of the input.
RTYPEDICT - Static variable in class omero.util.IceMapper
 
RTypeMapper - Class in omero.util
Extension of IceMapper which guarantees that RCollection and RMap instances are properly created.
RTypeMapper(IceMapper.ReturnMapping) - Constructor for class omero.util.RTypeMapper
 
RTypeObjectFactoryRegistry() - Constructor for class omero.rtypes.RTypeObjectFactoryRegistry
 
rtypes - Class in omero
Abstract class similar to Arrays or Collections which is responsible for creating RTypes from static factory methods.
rtypes() - Constructor for class omero.rtypes
 
rtypes.Conversion - Interface in omero
SPI-style interface which helps the omero server to properly convert omero.RType objects into Java-native objects for use in Hibernate.
rtypes.RTypeObjectFactoryRegistry - Class in omero
 
rules - Variable in class ome.services.blitz.repo.path.FilePathNamingValidator
 
rules - Variable in class ome.services.blitz.repo.path.MakePathComponentSafe
 
run() - Method in class ome.formats.importer.util.ClientKeepAlive
 
run() - Method in class ome.services.blitz.Status
 
run() - Method in class ome.services.blitz.util.CheckAllJobs
 
run(OmeroContext) - Method in class ome.services.throttling.Adapter
 
run(OmeroContext) - Method in class ome.services.throttling.Callback
 
run(OmeroContext) - Method in class ome.services.throttling.Callback2
 
run() - Method in class ome.services.throttling.Slot
 
run(OmeroContext) - Method in class ome.services.throttling.Task
 
run() - Method in class omero.cmd.HandleI
NB: Executes only if at CREATED in the state diagram.
run(TileData, int, int, int, int, int, int, int, int) - Method in interface omero.util.TileLoopIteration
Invoke a single loop iteration.
runnableCall(Current, Task) - Method in class ome.services.blitz.impl.AbstractAmdServant
 
runnableCall(Current, Task) - Method in interface ome.services.blitz.util.BlitzExecutor
 
runnableCall(Current, Task) - Method in class ome.services.throttling.InThreadThrottlingStrategy
 
runnableCall(Current, Task) - Method in class ome.services.throttling.SerialThrottlingStrategy
 
runScript(SecurityContext, long, Map<String, RType>) - Method in class omero.gateway.Gateway
Run a script on the server
runScript_async(AMD_IScript_runScript, long, Map<String, RType>, RInt, Current) - Method in class ome.services.blitz.impl.ScriptI
 

S

safeCharacter - Variable in class ome.services.blitz.repo.path.FilePathRestrictions
 
safeCharacters - Variable in class ome.services.blitz.repo.path.FilePathRestrictions
 
safeRunnableCall(Current, Object, boolean, Callable<R>) - Method in class ome.services.blitz.impl.AbstractAmdServant
 
safeRunnableCall(Current, Object, boolean, Callable<R>) - Method in interface ome.services.blitz.util.BlitzExecutor
 
safeRunnableCall(Current, Object, boolean, Callable<R>) - Method in class ome.services.throttling.InThreadThrottlingStrategy
 
safeRunnableCall(Current, Object, boolean, Callable<R>) - Method in class ome.services.throttling.SerialThrottlingStrategy
 
sanityCheckPixels_async(AMD_IRenderingSettings_sanityCheckPixels, Pixels, Pixels, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
 
sanityCheckRepository_async(AMD_IRepositoryInfo_sanityCheckRepository, Current) - Method in class ome.services.blitz.impl.RepositoryInfoI
 
save() - Method in class ome.formats.importer.transfers.TransferState
Calls RawFileStorePrx.save() and stores the resultant OriginalFile for future inspection along with the local checksum.
save() - Method in class ome.services.blitz.measurements.MeasurementStore
 
save() - Method in interface ome.services.blitz.measurements.OmeroMeasurementStore
 
save_async(AMD_RawFileStore_save, Current) - Method in class ome.services.blitz.impl.RawFileStoreI
 
save_async(AMD_RawPixelsStore_save, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
save_async(AMD_RawPixelsStore_save, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
saveAll() - Method in class ome.formats.importer.ImportConfig
 
saveAndReturnArray_async(AMD_IUpdate_saveAndReturnArray, List<IObject>, Current) - Method in class ome.services.blitz.impl.UpdateI
 
saveAndReturnIds_async(AMD_IUpdate_saveAndReturnIds, List<IObject>, Current) - Method in class ome.services.blitz.impl.UpdateI
 
saveAndReturnObject(SecurityContext, IObject, Map) - Method in class omero.gateway.facility.DataManagerFacility
Updates the specified object.
saveAndReturnObject(SecurityContext, DataObject) - Method in class omero.gateway.facility.DataManagerFacility
Updates the specified object.
saveAndReturnObject(SecurityContext, IObject) - Method in class omero.gateway.facility.DataManagerFacility
Updates the specified object.
saveAndReturnObject(SecurityContext, IObject, Map, String) - Method in class omero.gateway.facility.DataManagerFacility
Updates the specified object.
saveAndReturnObject(SecurityContext, DataObject, String) - Method in class omero.gateway.facility.DataManagerFacility
Updates the specified object.
saveAndReturnObject(SecurityContext, IObject, String) - Method in class omero.gateway.facility.DataManagerFacility
Updates the specified object.
saveAndReturnObject(SecurityContext, List<IObject>, Map, String) - Method in class omero.gateway.facility.DataManagerFacility
Updates the specified object.
saveAndReturnObject_async(AMD_IUpdate_saveAndReturnObject, IObject, Current) - Method in class ome.services.blitz.impl.UpdateI
 
saveArray_async(AMD_IUpdate_saveArray, List<IObject>, Current) - Method in class ome.services.blitz.impl.UpdateI
 
saveAsNewSettings_async(AMD_RenderingEngine_saveAsNewSettings, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
saveCollection_async(AMD_IUpdate_saveCollection, List<IObject>, Current) - Method in class ome.services.blitz.impl.UpdateI
 
saveCurrentSettings_async(AMD_RenderingEngine_saveCurrentSettings, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
savedDataset - Variable in class ome.formats.importer.ImportConfig
 
savedDirectory - Variable in class ome.formats.importer.ImportConfig
 
savedImagesNotInPlates - Variable in class ome.services.blitz.impl.MetadataStoreI
 
savedPlates - Variable in class ome.services.blitz.impl.MetadataStoreI
 
savedProject - Variable in class ome.formats.importer.ImportConfig
 
savedScreen - Variable in class ome.formats.importer.ImportConfig
 
saveFileset(String, Fileset, ChecksumAlgorithm, List<CheckedPath>, Current) - Method in interface ome.services.blitz.repo.RepositoryDao
Fill the various fields of the Fileset and then save the entire instance into the database.
saveFileset(String, Fileset, ChecksumAlgorithm, List<CheckedPath>, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
 
saveGui() - Method in class ome.formats.importer.ImportConfig
Saves gui specific values for which it makes sense to have a preferences values.
SaveI - Class in ome.services.blitz.impl.commands
Permits saving a single IObject instance.
SaveI() - Constructor for class ome.services.blitz.impl.commands.SaveI
 
saveJob(T, Current) - Method in interface ome.services.blitz.repo.RepositoryDao
Create a job from an instance provided by either the client or the server.
saveJob(Job, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
 
saveObject(IObject, Current) - Method in interface ome.services.blitz.repo.RepositoryDao
Save the given model object.
saveObject(IObject, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
 
saveObject_async(AMD_IUpdate_saveObject, IObject, Current) - Method in class ome.services.blitz.impl.UpdateI
 
saveOmeroRoiToMetadataStore(List<Roi>, MetadataStore) - Static method in class loci.ome.io.OmeroReader
Deprecated.
Converts omero.model.Roi to ome.xml.model.* and updates the MetadataStore
saveRndSettings_async(AMD_IPixels_saveRndSettings, RenderingDef, Current) - Method in class ome.services.blitz.impl.PixelsI
 
saveROIs(SecurityContext, long, Collection<ROIData>) - Method in class omero.gateway.facility.ROIFacility
Save the ROI for the image to the server.
saveROIs(SecurityContext, long, long, Collection<ROIData>) - Method in class omero.gateway.facility.ROIFacility
Save the ROI for the image to the server.
saveToDB(FilesetJobLink) - Method in class ome.formats.OMEROMetadataStoreClient
Updates the server side MetadataStore with a list of our objects and references and saves them into the database.
saveToDB_async(AMD_MetadataStore_saveToDB, FilesetJobLink, Current) - Method in class ome.services.blitz.impl.MetadataStoreI
 
ScaleRedirector - Class in ome.services.blitz.redirect
Planned implementation (NYI): will use the "Node.scale" column to randomly choose a target.
ScaleRedirector(Executor) - Constructor for class ome.services.blitz.redirect.ScaleRedirector
 
SCANNING(File, int, int, int) - Constructor for class ome.formats.importer.ImportCandidates.SCANNING
 
SCREEN_LINKS - Static variable in class omero.gateway.model.PlateData
Identifies the PlateI.SCREENLINKS field.
ScreenData - Class in omero.gateway.model
The data that makes up an OME Screen along with links to its contained Plates and the Experimenter that owns this Screen.
ScreenData() - Constructor for class omero.gateway.model.ScreenData
Creates a new instance.
ScreenData(Screen) - Constructor for class omero.gateway.model.ScreenData
Creates a new instance.
script(ScriptJob) - Method in class ome.services.blitz.repo.ManagedImportRequestI
 
ScriptFinder - Class in ome.services.scripts
Looks up an official script based on path for internal use.
ScriptFinder(Roles, String, Executor, File) - Constructor for class ome.services.scripts.ScriptFinder
 
ScriptFinder(Roles, Principal, Executor, File) - Constructor for class ome.services.scripts.ScriptFinder
 
ScriptI - Class in ome.services.blitz.impl
implementation of the IScript service interface.
ScriptI(BlitzExecutor, ScriptRepoHelper, ACLVoter, OmeroInterceptor, ChecksumProviderFactory, ParamsCache) - Constructor for class ome.services.blitz.impl.ScriptI
 
ScriptProcessI - Class in ome.services.blitz.impl
 
ScriptProcessI(ServiceFactoryI, Current, InteractiveProcessorPrx, _InteractiveProcessorOperations, ProcessPrx) - Constructor for class ome.services.blitz.impl.ScriptProcessI
 
ScriptRepositoryI - Class in ome.services.blitz.repo
Repository which makes the included script files available to users.
ScriptRepositoryI(ObjectAdapter, Registry, Executor, Principal, ScriptRepoHelper, PublicRepositoryI, Set<String>) - Constructor for class ome.services.blitz.repo.ScriptRepositoryI
Deprecated.
ScriptRepositoryI(ObjectAdapter, Registry, Executor, Principal, ScriptRepoHelper, ReadOnlyStatus, PublicRepositoryI, Set<String>) - Constructor for class ome.services.blitz.repo.ScriptRepositoryI
 
scripts - Variable in class ome.services.blitz.impl.ScriptI
 
search(SecurityContext, SearchParameters) - Method in class omero.gateway.facility.SearchFacility
Searches for data.
searchAll_async(AMD_ILdap_searchAll, Current) - Method in class ome.services.blitz.impl.LdapI
 
searchByAttribute_async(AMD_ILdap_searchByAttribute, String, String, String, Current) - Method in class ome.services.blitz.impl.LdapI
 
searchByAttributes_async(AMD_ILdap_searchByAttributes, String, List<String>, List<String>, Current) - Method in class ome.services.blitz.impl.LdapI
 
searchByDN_async(AMD_ILdap_searchByDN, String, Current) - Method in class ome.services.blitz.impl.LdapI
 
searchDnInGroups_async(AMD_ILdap_searchDnInGroups, String, String, Current) - Method in class ome.services.blitz.impl.LdapI
 
SearchFacility - Class in omero.gateway.facility
A Facility for performing searches
SearchI - Class in ome.services.blitz.impl
Implementation of the Search service.
SearchI(Search, BlitzExecutor) - Constructor for class ome.services.blitz.impl.SearchI
 
SearchParameters - Class in omero.gateway.model
Holds all parameters needed to perform a search operation; See SearchFacility.search(omero.gateway.SecurityContext, SearchParameters)
SearchParameters(Set<SearchScope>, List<Class<? extends DataObject>>, String) - Constructor for class omero.gateway.model.SearchParameters
Creates a new instance.
SearchResult - Class in omero.gateway.model
Encapsulates a single object found by a search together with the search scope (name, description, etc.) it was found with.
SearchResult() - Constructor for class omero.gateway.model.SearchResult
Create a new instance
SearchResult(int, Class<? extends DataObject>, long, long) - Constructor for class omero.gateway.model.SearchResult
Create a new instance
SearchResultCollection - Class in omero.gateway.model
Holds the results of a search; a collection of SearchResults
SearchResultCollection() - Constructor for class omero.gateway.model.SearchResultCollection
 
SearchScope - Enum in omero.gateway.model
Defines the scope of a search, i.e. in which fields to search (name, description, etc.); See SearchParameters
secondLevelCacheHit(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
secondLevelCacheMiss(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
secondLevelCachePut(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
security - Variable in class omero.cmd.admin.UpdateSessionTimeoutRequestI
 
SecurityContext - Class in omero.gateway
Hosts information required to access correct connector.
SecurityContext(long) - Constructor for class omero.gateway.SecurityContext
Creates a new instance.
securitySystem - Variable in class ome.services.blitz.fire.SessionManagerI
 
SendEmailRequestI - Class in omero.cmd.mail
Callback interface allowing to send email using JavaMailSender, supporting MIME messages through preparation callbacks.
SendEmailRequestI(MailUtil) - Constructor for class omero.cmd.mail.SendEmailRequestI
 
sendErrors() - Method in class ome.formats.importer.util.ErrorHandler
Send existing errors in ErrorContainer array to server
sendFiles - Variable in class ome.formats.importer.ImportConfig
 
sendFiles - Variable in class ome.formats.importer.ImportEvent.DEBUG_SEND
 
sendFiles - Variable in class ome.formats.importer.util.ErrorHandler
 
sendLogFile - Variable in class ome.formats.importer.ImportConfig
 
sendLogs - Variable in class ome.formats.importer.ImportEvent.DEBUG_SEND
 
sendLogs - Variable in class ome.formats.importer.util.ErrorHandler
 
sendReport - Variable in class ome.formats.importer.ImportConfig
 
separatorChar - Static variable in class ome.services.blitz.repo.path.FsFile
the separator character for delimiting repository path components
SerialThrottlingStrategy - Class in ome.services.throttling
Throttling implementation which only allows a single invocation to be run at any given time.
SerialThrottlingStrategy(OmeroContext) - Constructor for class ome.services.throttling.SerialThrottlingStrategy
 
series - Variable in class ome.formats.importer.ImportEvent.IMPORT_STEP
 
series - Variable in class ome.formats.importer.ImportEvent.PROGRESS_EVENT
 
seriesCount - Variable in class ome.formats.importer.ImportEvent.IMPORT_STEP
 
ServantHolder - Class in omero.util
Manager for all active servants in a single session.
ServantHolder(String) - Constructor for class omero.util.ServantHolder
 
ServantHolder(String, int) - Constructor for class omero.util.ServantHolder
 
servantsPerSession - Variable in class ome.services.blitz.fire.SessionManagerI
 
server - Variable in class loci.ome.io.OMECredentials
Deprecated.
 
SERVER_NAME_SEPARATOR - Static variable in class ome.formats.importer.ImportConfig
Delimiter used to encode multiple servers in one preferences value.
ServerFilePathTransformer - Class in ome.services.blitz.repo.path
Transform between repository FsFile path and server-local File.
ServerFilePathTransformer() - Constructor for class ome.services.blitz.repo.path.ServerFilePathTransformer
 
ServerInformation - Class in omero.gateway
Holds hostname and port of an OMERO server
ServerInformation() - Constructor for class omero.gateway.ServerInformation
Creates an empty instance
ServerInformation(String, int) - Constructor for class omero.gateway.ServerInformation
Creates a new instance
serverPaths - Variable in class ome.services.blitz.repo.PublicRepositoryI
 
ServerTemplateImportTarget - Class in ome.formats.importer.targets
 
ServerTemplateImportTarget(String) - Constructor for class ome.formats.importer.targets.ServerTemplateImportTarget
 
service - Variable in class ome.services.blitz.impl.AbstractAmdServant
If there is no undering ome.* service, then this value can be null.
ServiceFactoryAware - Interface in ome.services.blitz.util
Servant which is aware of the ServiceFactoryI-instance which it belongs to and will have it injected on instantiation.
ServiceFactoryI - Class in ome.services.blitz.impl
Responsible for maintaining all servants for a single session.
ServiceFactoryI(Current, ServantHolder, SessionControlPrx, OmeroContext, SessionManager, Executor, Principal, List<HardWiredInterceptor>, TopicManager, Registry) - Constructor for class ome.services.blitz.impl.ServiceFactoryI
 
ServiceFactoryI(boolean, Current, ServantHolder, SessionControlPrx, OmeroContext, SessionManager, Executor, Principal, List<HardWiredInterceptor>, TopicManager, Registry, String) - Constructor for class ome.services.blitz.impl.ServiceFactoryI
 
session - Variable in class omero.cmd.graphs.BaseGraphTraversalProcessor
 
session - Variable in class omero.model.DetailsI
 
session - Variable in class omero.util.RPSTileLoop
 
SessionAware - Interface in omero.cmd
Servant which is aware of the SessionI-instance which it belongs to and will have it injected on instantiation.
SessionI - Class in ome.services.blitz.impl
Implementation of the ISession service.
SessionI(ISession, BlitzExecutor) - Constructor for class ome.services.blitz.impl.SessionI
 
SessionI - Class in omero.cmd
 
SessionI(boolean, Current, ServantHolder, SessionControlPrx, OmeroContext, SessionManager, Executor, Principal, String) - Constructor for class omero.cmd.SessionI
 
sessionId(String, String) - Static method in class omero.cmd.SessionI
Definition of session ids: "session-<CLIENTID>/<UUID>"
sessionId() - Method in class omero.cmd.SessionI
Returns the Identity for this instance as defined by SessionI.sessionId(String, String)
sessionKey - Variable in class ome.formats.importer.ImportConfig
 
sessionManager - Variable in class ome.services.blitz.fire.SessionManagerI
 
sessionManager - Variable in class omero.cmd.SessionI
 
SessionManagerI - Class in ome.services.blitz.fire
Central login logic for all OMERO.blitz clients.
SessionManagerI(Ring, ObjectAdapter, SecuritySystem, SessionManager, Executor, TopicManager, Registry, int) - Constructor for class ome.services.blitz.fire.SessionManagerI
 
sessionToHolder - Variable in class ome.services.blitz.fire.SessionManagerI
An internal mapping to all ServiceFactoryI instances for a given session since there is no method on ObjectAdapter to retrieve all servants.
set(T) - Method in class ome.formats.importer.ImportConfig.Value
Sets the in-memory value, which will get persisted on ImportConfig.Value.store() when ImportConfig.saveAll() is called.
set(U) - Method in class ome.services.blitz.util.ResultHolder
 
set(int, int, boolean) - Method in class omero.model.PermissionsI
 
setAbsolutePath(String) - Method in class ome.formats.importer.util.ErrorContainer
set path for file
setActive_async(AMD_RenderingEngine_setActive, int, boolean, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
setActive_async(AMD_IShare_setActive, long, boolean, Current) - Method in class ome.services.blitz.impl.ShareI
 
setAdminPrivileges(SecurityContext, ExperimenterData, Collection<String>) - Method in class omero.gateway.facility.AdminFacility
Set the admin privileges of a certain user (see omero.model.enums)
setAdminPrivileges_async(AMD_IAdmin_setAdminPrivileges, Experimenter, List<AdminPrivilege>, Current) - Method in class ome.services.blitz.impl.AdminI
 
setAgent(String) - Method in class omero.client
Sets the user agent string for this client.
setAirPressure(Pressure) - Method in class omero.gateway.model.ImageAcquisitionData
Sets the air pressure.
setAllowLeadingWildcard_async(AMD_Search_setAllowLeadingWildcard, boolean, Current) - Method in class ome.services.blitz.impl.SearchI
 
setAllPixels(List<PixelsData>) - Method in class omero.gateway.model.ImageData
Sets the set of pixels related to this image.
setAlpha(Integer) - Method in class omero.gateway.model.WellData
Sets the alpha component of the color associated to the well.
setAnnotations(Set) - Method in class omero.gateway.model.DatasetData
Sets the annotations related to this dataset.
setAnnotations(Set) - Method in class omero.gateway.model.ImageData
Sets the image's annotations.
setApplicationContext(ApplicationContext) - Method in class ome.services.blitz.fire.SessionManagerI
 
setApplicationContext(ApplicationContext) - Method in class ome.services.blitz.impl.AbstractAmdServant
Creates an IceMethodInvoker for this instance if AbstractAmdServant.service is non-null.
setApplicationContext(ApplicationContext) - Method in class ome.services.blitz.impl.commands.RequestObjectFactoryRegistry
 
setApplicationContext(ApplicationContext) - Method in class ome.services.blitz.repo.PublicRepositoryI
 
setApplicationContext(ApplicationContext) - Method in class ome.services.blitz.repo.RequestObjectFactoryRegistry
 
setApplicationContext(ApplicationContext) - Method in class ome.services.blitz.util.ParamsCache
 
setApplicationContext(ApplicationContext) - Method in class ome.services.throttling.AbstractThrottlingStrategy
 
setApplicationContext(ApplicationContext) - Method in class omero.cmd.graphs.GraphRequestFactory
 
setApplicationContext(ApplicationContext) - Method in class omero.cmd.RequestObjectFactoryRegistry
 
setApplicationName(String) - Method in class omero.gateway.LoginCredentials
Set the application name
setAppVersion(String) - Method in class ome.formats.importer.util.ErrorContainer
 
setArcAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setArcID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setArcLotNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setArcManufacturer(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setArcModel(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setArcPower(Power, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setArcSerialNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setArcType(ArcType, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setArgument(Map<String, Boolean>, String) - Static method in class ome.formats.importer.cli.CommandLineImporter
Set a conflicting argument and return the usage if the key is already set
setBaseDirFile(File) - Method in class ome.services.blitz.repo.path.ServerFilePathTransformer
Set the repository root directory, to which FsFile instances are considered to be relative.
setBatchSize_async(AMD_Search_setBatchSize, int, Current) - Method in class ome.services.blitz.impl.SearchI
 
setBinaryFileBinData(byte[], int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setBinaryFileBinDataBigEndian(Boolean, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setBinaryFileBinDataCompression(Compression, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setBinaryFileBinDataLength(NonNegativeLong, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setBinaryFileFileName(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setBinaryFileMIMEType(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setBinaryFileSize(NonNegativeLong, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setBinaryOnlyMetadataFile(String) - Method in class ome.formats.OMEROMetadataStoreClient
 
setBinaryOnlyUUID(String) - Method in class ome.formats.OMEROMetadataStoreClient
 
setBit(byte[], int, int) - Method in class omero.gateway.model.MaskData
Sets the bit value in a byte array at position bit to be the value value.
setBlue(Integer) - Method in class omero.gateway.model.WellData
Sets the blue component of the color associated to the well.
setBooleanAnnotationAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setBooleanAnnotationAnnotator(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setBooleanAnnotationDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setBooleanAnnotationID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setBooleanAnnotationNamespace(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setBooleanAnnotationValue(Boolean, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setC(int) - Method in class omero.gateway.model.ShapeData
Sets the channel.
setCacheEntries(int, int) - Method in interface omero.gateway.cache.CacheService
Resets the number of items in memory of the cache, when a new cache is created or deleted.
setCallback(ClientCallbackPrx, Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
setCallback(RepoRawFileStoreI.Callback) - Method in class ome.services.blitz.repo.RepoRawFileStoreI
 
setCallContext(Map<String, String>) - Method in class ome.services.blitz.repo.ManagedImportRequestI
 
setCaseSentivice_async(AMD_Search_setCaseSentivice, boolean, Current) - Method in class ome.services.blitz.impl.SearchI
 
setChannelAcquisitionMode(AcquisitionMode, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setChannelAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setChannelColor(Color, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setChannelContrastMethod(ContrastMethod, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setChannelEmissionWavelength(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setChannelExcitationWavelength(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setChannelFilterSetRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setChannelFluor(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setChannelGlobalMinMax(int, double, double, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setChannelGlobalMinMax_async(AMD_IPixels_setChannelGlobalMinMax, long, int, double, double, Current) - Method in class ome.services.blitz.impl.PixelsI
 
setChannelID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setChannelIlluminationType(IlluminationType, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setChannelLightSourceSettingsAttenuation(PercentFraction, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setChannelLightSourceSettingsID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setChannelLightSourceSettingsWavelength(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setChannelLookupTable_async(AMD_RenderingEngine_setChannelLookupTable, int, String, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
setChannelName(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setChannelNDFilter(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setChannelPinholeSize(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setChannelPockelCellSetting(Integer, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setChannelSamplesPerPixel(PositiveInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setChannelWindow_async(AMD_RenderingEngine_setChannelWindow, int, double, double, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
setCheckNetwork(boolean) - Method in class omero.gateway.LoginCredentials
Enable/Disable network checks
setChecksumAlgorithm(String) - Method in class ome.formats.importer.ImportContainer
 
setChecksumAlgorithm(ChecksumAlgorithm, List<Long>, Current) - Method in class ome.services.blitz.repo.ManagedRepositoryI
 
setClient(OMEROMetadataStoreClient) - Method in class ome.formats.importer.util.ClientKeepAlive
 
setClientEndpoints(String, int) - Method in class ome.services.blitz.Router
 
setClientObject(boolean) - Method in class omero.gateway.model.ShapeData
Sets to true if the object one that has been created client side, false otherwise.
setClientSide(boolean) - Method in class omero.gateway.model.ROIData
Sets the flag indicating if the object is a client-side object or not.
setCo2Percent(double) - Method in class omero.gateway.model.ImageAcquisitionData
Sets the co2 level.
setCodomainInterval_async(AMD_RenderingEngine_setCodomainInterval, int, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
setComment(String) - Method in class ome.formats.importer.util.ErrorContainer
 
setCommentAnnotationAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setCommentAnnotationAnnotator(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setCommentAnnotationDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setCommentAnnotationID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setCommentAnnotationNamespace(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setCommentAnnotationValue(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setCommentType(String) - Method in class ome.formats.importer.util.ErrorContainer
 
setCompleted() - Method in class omero.gateway.model.TableData
Manually set completed state (sets the TableData.numberOfRows to the last row in the TableData.data array)
setCompression(float) - Method in class omero.gateway.LoginCredentials
Sets the compression level
setCompression(float) - Method in class omero.gateway.SecurityContext
Set the compression level
setCompressionLevel_async(AMD_RenderingEngine_setCompressionLevel, float, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
setCondition(String) - Method in class omero.cmd.graphs.BaseGraphPolicyAdjuster
 
setConfigValue_async(AMD_IConfig_setConfigValue, String, String, Current) - Method in class ome.services.blitz.impl.ConfigI
 
setConfigValueIfEquals_async(AMD_IConfig_setConfigValueIfEquals, String, String, String, Current) - Method in class ome.services.blitz.impl.ConfigI
 
setContent(Object) - Method in class omero.gateway.model.AnnotationData
Sets the annotation value.
setContent(Object) - Method in class omero.gateway.model.BooleanAnnotationData
Sets the text annotation.
setContent(Object) - Method in class omero.gateway.model.DoubleAnnotationData
Sets the text annotation.
setContent(Object) - Method in class omero.gateway.model.FileAnnotationData
Sets the text annotation.
setContent(Object) - Method in class omero.gateway.model.LongAnnotationData
Sets the text annotation.
setContent(Object) - Method in class omero.gateway.model.MapAnnotationData
 
setContent(Object) - Method in class omero.gateway.model.RatingAnnotationData
Sets the text annotation.
setContent(Object) - Method in class omero.gateway.model.TagAnnotationData
Sets the text annotation.
setContent(Object) - Method in class omero.gateway.model.TermAnnotationData
Sets the text annotation.
setContent(Object) - Method in class omero.gateway.model.TextualAnnotationData
Sets the text annotation.
setContent(Object) - Method in class omero.gateway.model.TimeAnnotationData
Sets the time annotation.
setContent(Object) - Method in class omero.gateway.model.XMLAnnotationData
Sets the annotation.
setContrastMethod(ContrastMethod) - Method in class omero.gateway.model.ChannelData
Sets the contrast method value.
setCorrectionCollar(double) - Method in class omero.gateway.model.ImageAcquisitionData
Sets the correction of the objective.
setCreationEvent(Event, Current) - Method in class omero.model.DetailsI
 
setCurrentGroup(long) - Method in class ome.formats.OMEROMetadataStoreClient
Changes the default group of the currently logged in user.
setCurrentLogFile(String, String) - Method in class ome.formats.OMEROMetadataStoreClient
 
setCustomAnnotationList(List<Annotation>) - Method in class ome.formats.importer.ImportContainer
Sets the list of custom, user specified, annotations to link to all images represented by this container.
setCustomImageNaming(boolean) - Method in class ome.formats.importer.ImportConfig
 
setCustomImageNaming(boolean) - Method in class ome.formats.importer.util.IniFileLoader
 
setDataObjects(Set<DataObject>) - Method in class omero.gateway.model.TagAnnotationData
Sets the collection of data objects related to that tag.
setDatasetAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDatasetDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDatasetExperimenterGroupRef(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDatasetExperimenterRef(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDatasetID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDatasetImageRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDatasetName(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDatasets(Set) - Method in class omero.gateway.model.ImageData
Sets the datasets containing the image.
setDatasets(Set<DatasetData>) - Method in class omero.gateway.model.ProjectData
Sets the datasets contained in this project.
setDataValue(double) - Method in class omero.gateway.model.DoubleAnnotationData
Sets the rating value.
setDataValue(long) - Method in class omero.gateway.model.LongAnnotationData
Sets the rating value.
setDateType(int) - Method in class omero.gateway.model.SearchParameters
 
setDebugLevel(int) - Method in class ome.formats.importer.ImportConfig
 
setDebugLevel(int) - Method in class ome.formats.importer.util.IniFileLoader
Set debug level for application
setDefaultGroup_async(AMD_IAdmin_setDefaultGroup, Experimenter, ExperimenterGroup, Current) - Method in class ome.services.blitz.impl.AdminI
 
setDefaultPixels(PixelsData) - Method in class omero.gateway.model.ImageData
Sets the default set of pixels.
setDefaultSample(int) - Method in class omero.gateway.model.PlateData
Sets the default sample.
setDefaultT_async(AMD_RenderingEngine_setDefaultT, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
setDefaultZ_async(AMD_RenderingEngine_setDefaultZ, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
setDescription(String) - Method in class omero.gateway.model.AnnotationData
Sets the description of the underlying Annotation instance.
setDescription(String) - Method in class omero.gateway.model.DatasetData
Sets the description of the dataset.
setDescription(String) - Method in class omero.gateway.model.FileAnnotationData
Sets the description of the annotation.
setDescription(String) - Method in class omero.gateway.model.FileData
Sets the description.
setDescription(String) - Method in class omero.gateway.model.FolderData
Set the description of the Folder
setDescription(String) - Method in class omero.gateway.model.GroupData
Sets the name of the group.
setDescription(String) - Method in class omero.gateway.model.ImageData
Sets the description of the image.
setDescription(String) - Method in class omero.gateway.model.PlateAcquisitionData
Sets the name of the acquisition.
setDescription(String) - Method in class omero.gateway.model.PlateData
Sets the description of the plate.
setDescription(String) - Method in class omero.gateway.model.ProjectData
Sets the description of the project.
setDescription(String) - Method in class omero.gateway.model.ScreenData
Sets the description of the screen.
setDescription(String) - Method in class omero.gateway.model.TableDataColumn
Set the description
setDescription(String) - Method in class omero.gateway.model.XMLAnnotationData
Sets the description of the annotation.
setDescription_async(AMD_IShare_setDescription, long, String, Current) - Method in class ome.services.blitz.impl.ShareI
 
setDetach(boolean, Current) - Method in class omero.grid.InteractiveProcessorI
 
setDetectorAmplificationGain(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDetectorAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDetectorGain(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDetectorID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDetectorLotNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDetectorManufacturer(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDetectorModel(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDetectorOffset(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDetectorSerialNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDetectorSettingBinning(Binning) - Method in class omero.gateway.model.ChannelAcquisitionData
Sets the detector's binning.
setDetectorSettingOffset(double) - Method in class omero.gateway.model.ChannelAcquisitionData
Sets the detector's setting offset.
setDetectorSettingsBinning(Binning, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDetectorSettingsGain(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDetectorSettingsGain(double) - Method in class omero.gateway.model.ChannelAcquisitionData
Sets the detector setting's gain.
setDetectorSettingsID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDetectorSettingsIntegration(PositiveInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDetectorSettingsOffset(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDetectorSettingsReadOutRate(Frequency, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDetectorSettingsReadOutRate(Frequency) - Method in class omero.gateway.model.ChannelAcquisitionData
Sets the detector setting's read out rate.
setDetectorSettingsVoltage(ElectricPotential, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDetectorSettingsVoltage(ElectricPotential) - Method in class omero.gateway.model.ChannelAcquisitionData
Sets the detector setting's voltage.
setDetectorSettingsZoom(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDetectorType(DetectorType, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDetectorVoltage(ElectricPotential, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDetectorZoom(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDichroicAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDichroicID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDichroicLotNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDichroicManufacturer(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDichroicModel(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDichroicSerialNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDirty(boolean) - Method in class omero.gateway.model.DataObject
Sets to true if the value has been modified, otherwise.
setDirty(boolean) - Method in class omero.gateway.model.ShapeData
Sets to true if the figure been changed from the server side version, false otherwise.
setDN_async(AMD_ILdap_setDN, RLong, String, Current) - Method in class ome.services.blitz.impl.LdapI
 
setDoThumbnails(boolean) - Method in class ome.formats.importer.ImportContainer
Sets whether or not we are performing thumbnail creation upon import completion.
setDoubleAnnotationAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDoubleAnnotationAnnotator(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDoubleAnnotationDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDoubleAnnotationID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDoubleAnnotationNamespace(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setDoubleAnnotationValue(Double, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setEllipseAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setEllipseFillColor(Color, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setEllipseFillRule(FillRule, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setEllipseFontFamily(FontFamily, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setEllipseFontSize(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setEllipseFontStyle(FontStyle, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setEllipseID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setEllipseLocked(Boolean, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setEllipseRadiusX(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setEllipseRadiusY(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setEllipseStrokeColor(Color, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setEllipseStrokeDashArray(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setEllipseStrokeWidth(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setEllipseText(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setEllipseTheC(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setEllipseTheT(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setEllipseTheZ(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setEllipseTransform(AffineTransform, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setEllipseX(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setEllipseY(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setEmail(String) - Method in class ome.formats.importer.util.ErrorContainer
 
setEmail(String) - Method in class omero.gateway.model.ExperimenterData
Sets the e-mail of the experimenter.
setEmissionWavelength(Length) - Method in class omero.gateway.model.ChannelData
Sets the emission wavelength.
setEncrypted(boolean) - Method in class loci.ome.io.OmeroReader
Deprecated.
 
setEncryptedConnection(boolean) - Method in class ome.formats.OMEROMetadataStoreClient
 
setEncryption(boolean) - Method in class omero.gateway.LoginCredentials
Enable/Disable encryption
setEnumerationProvider(EnumerationProvider) - Method in class ome.formats.OMEROMetadataStoreClient
Sets the active enumeration provider.
setError(Throwable) - Method in class ome.formats.importer.util.ErrorContainer
 
setError(int) - Method in class omero.gateway.model.SearchResultCollection
Set the error state
setExcitationWavelength(Length) - Method in class omero.gateway.model.ChannelData
Sets the excitation wavelength.
setExperimentDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setExperimenter(ExperimenterData) - Method in class omero.gateway.SecurityContext
Sets the experimenter
setExperimenterAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setExperimenterEmail(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setExperimenterFirstName(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setExperimenterGroupAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setExperimenterGroupDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setExperimenterGroupExperimenterRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setExperimenterGroupID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setExperimenterGroupLeader(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setExperimenterGroupName(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setExperimenterID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setExperimenterInstitution(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setExperimenterLastName(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setExperimenterMiddleName(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setExperimenters(Set<ExperimenterData>) - Method in class omero.gateway.model.GroupData
Sets the experimenters contained in this group.
setExperimenterUserName(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setExperimentExperimenterRef(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setExperimentID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setExperimentType(ExperimentType, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setExpiration_async(AMD_IShare_setExpiration, long, RTime, Current) - Method in class ome.services.blitz.impl.ShareI
 
setExternalDescription(String) - Method in class omero.gateway.model.WellData
Sets the external description of the well.
setExternalIdentifier(String) - Method in class omero.gateway.model.PlateData
Sets the external identifier.
setExternalInfo(ExternalInfo, Current) - Method in class omero.model.DetailsI
 
setExtra(String) - Method in class ome.formats.importer.util.ErrorContainer
 
setFastShutdown(boolean) - Method in class omero.client
Sets the fastShutdown flag.
setFilamentAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFilamentID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFilamentLotNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFilamentManufacturer(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFilamentModel(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFilamentPower(Power, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFilamentSerialNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFilamentType(FilamentType, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFile(File) - Method in class ome.formats.OMEROImportFixture
Deprecated.
 
setFileAnnotationAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFileAnnotationAnnotator(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFileAnnotationDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFileAnnotationID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFileAnnotationNamespace(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFileId_async(AMD_RawFileStore_setFileId, long, Current) - Method in class ome.services.blitz.impl.RawFileStoreI
 
setFileId_async(AMD_RawFileStore_setFileId, long, Current) - Method in class ome.services.blitz.repo.RepoRawFileStoreI
 
setFiles(String[]) - Method in class ome.formats.importer.util.ErrorContainer
 
setFileType(String) - Method in class ome.formats.importer.util.ErrorContainer
 
setFill(Color) - Method in class omero.gateway.model.ShapeSettingsData
Set the fill color.
setFillRule(String) - Method in class omero.gateway.model.ShapeSettingsData
Set the fill rule.
setFilterAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFilterFilterWheel(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFilterID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFilterLotNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFilterManufacturer(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFilterModel(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFilterSerialNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFilterSetDichroicRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFilterSetEmissionFilterRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFilterSetExcitationFilterRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFilterSetID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFilterSetLotNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFilterSetManufacturer(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFilterSetModel(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFilterSetSerialNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFilterType(FilterType, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFirstName(String) - Method in class omero.gateway.model.ExperimenterData
Sets the first name of the experimenter.
setFluor(String) - Method in class omero.gateway.model.ChannelData
Sets the fluor.
setFolder(Folder) - Method in class omero.gateway.model.FolderData
Set the Folder
setFolderAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFolderDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFolderFolderRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFolderID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFolderImageRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFolderName(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFolderROIRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setFolders(Collection<FolderData>) - Method in class omero.gateway.model.ROIResult
Sets the available folders
setFontFamily(String) - Method in class omero.gateway.model.ShapeSettingsData
Returns the stroke.
setFontSize(Length) - Method in class omero.gateway.model.ShapeSettingsData
Set the size of the font.
setFontStyle(String) - Method in class omero.gateway.model.ShapeSettingsData
Sets the style of the font.
setGenericExcitationSourceAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setGenericExcitationSourceID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setGenericExcitationSourceLotNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setGenericExcitationSourceManufacturer(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setGenericExcitationSourceMap(List<MapPair>, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setGenericExcitationSourceModel(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setGenericExcitationSourcePower(Power, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setGenericExcitationSourceSerialNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setGreen(Integer) - Method in class omero.gateway.model.WellData
Sets the green component of the color associated to the well.
setGroup(Long) - Method in class ome.formats.OMEROMetadataStoreClient
Sets the id which will be used to set the call context for all services.
setGroup(ExperimenterGroup, Current) - Method in class omero.model.DetailsI
 
setGroupAnnotate(boolean) - Method in class omero.gateway.model.PermissionData
Sets to true if the group has annotate access, false otherwise.
setGroupAnnotate(boolean, Current) - Method in class omero.model.PermissionsI
 
setGroupID(Long) - Method in class loci.ome.io.OmeroReader
Deprecated.
 
setGroupID(long) - Method in class omero.gateway.LoginCredentials
Sets the groupID to use for the connection
setGroupId(long) - Method in class omero.gateway.model.SearchParameters
 
setGroupId(long) - Method in class omero.gateway.model.SearchResult
Set the group id of the object
setGroupName(String) - Method in class loci.ome.io.OmeroReader
Deprecated.
 
setGroupOwner_async(AMD_IAdmin_setGroupOwner, ExperimenterGroup, Experimenter, Current) - Method in class ome.services.blitz.impl.AdminI
 
setGroupRead(boolean) - Method in class omero.gateway.model.PermissionData
Sets to true if the group has read access, false otherwise.
setGroupRead(boolean, Current) - Method in class omero.model.PermissionsI
 
setGroups(List<GroupData>) - Method in class omero.gateway.model.ExperimenterData
Sets the groups the experimenter is a member of.
setGroupWrite(boolean) - Method in class omero.gateway.model.PermissionData
Sets to true if the group has write access, false otherwise.
setGroupWrite(boolean, Current) - Method in class omero.model.PermissionsI
 
setHeight(double) - Method in class omero.gateway.model.MaskData
Sets the height of an untransformed mask.
setHeight(double) - Method in class omero.gateway.model.RectangleData
Sets the height of an untransformed rectangle.
setHolder(ServantHolder) - Method in class ome.services.blitz.impl.AbstractAmdServant
Sets the ServantHolder for the current session so that on AbstractCloseableAmdServant.close_async(AMD_StatefulServiceInterface_close, Current) it will be possible to cleanup the resources.
setHostname(String) - Method in class omero.gateway.ServerInformation
Set the hostname
setHumidity(double) - Method in class omero.gateway.model.ImageAcquisitionData
Sets the humidity.
setIceCommunicator(Communicator) - Method in class omero.util.ObjectFactoryRegistry
 
setId(Long) - Method in class ome.services.blitz.repo.CheckedPath
 
setId(long) - Method in class omero.gateway.model.DataObject
Sets the database id.
setIdMatch(boolean) - Method in class omero.gateway.model.SearchResult
Set to true if this result is an ID match.
setIllumination(Illumination) - Method in class omero.gateway.model.ChannelData
Sets the illumination value.
setImage(ImageData) - Method in class omero.gateway.model.PixelsData
Sets the image linked to this pixels' set.
setImage(Image) - Method in class omero.gateway.model.ROIData
Sets the image for the ROI.
setImage(ImageData) - Method in class omero.gateway.model.WellSampleData
Sets the image linked to this well sample.
setImageAcquisitionDate(Timestamp, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setImageAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setImageDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setImageExperimenterGroupRef(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setImageExperimenterRef(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setImageExperimentRef(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setImageID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setImageInstrumentRef(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setImageMicrobeamManipulationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setImageName(String, int) - Method in class ome.formats.ImageNameMetadataStore
 
setImageName(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setImageROIRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setImageROIRef(String, int, int) - Method in class ome.formats.OverlayMetadataStore
 
setImages(Set<ImageData>) - Method in class omero.gateway.model.DatasetData
Sets the images contained in this dataset.
setImagingEnvironmentAirPressure(Pressure, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setImagingEnvironmentCO2Percent(PercentFraction, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setImagingEnvironmentHumidity(PercentFraction, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setImagingEnvironmentMap(List<MapPair>, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setImagingEnvironmentTemperature(Temperature, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setImportOutput(ImportOutput) - Method in class ome.formats.importer.cli.CommandLineImporter
Set the current ImportOutput (defaulting to null if a null value is passed).
setImportOutput(ImportOutput) - Method in class ome.formats.importer.cli.LoggingImportMonitor
Set the current ImportOutput (defaulting to null if a null value is passed).
setIndex(int) - Method in class ome.formats.importer.util.ErrorContainer
Set index
setIndex(int) - Method in exception omero.gateway.exception.RenderingServiceException
Sets the index indicating if the error occurred due to a network failure.
setIndex(int) - Method in class omero.gateway.model.TableDataColumn
Set the index
setIndexes(Map<Integer, Integer>) - Method in class omero.gateway.model.TableResult
Sets the indexes.
setInput(String, RType) - Method in class omero.client
Sets an item in the "input" shared (session) memory under the given name.
setInput_async(AMD_ISession_setInput, String, String, RType, Current) - Method in class ome.services.blitz.impl.SessionI
 
setInstanceProvider(InstanceProvider) - Method in class ome.formats.OMEROMetadataStoreClient
Sets the active instance provider.
setInstitution(String) - Method in class omero.gateway.model.ExperimenterData
Sets the institution where the experimenter works.
setInstrumentAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setInstrumentID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setIP(String) - Method in class omero.client
Sets the user ip string for this client.
setIsSPW(Boolean) - Method in class ome.formats.importer.ImportContainer
Set true if the import container is filled in with a Screen/Plate/Well image structure.
setJavaClasspath(String) - Method in class ome.formats.importer.util.ErrorContainer
 
setJavaVersion(String) - Method in class ome.formats.importer.util.ErrorContainer
 
setLabelAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLabelFillColor(Color, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLabelFillRule(FillRule, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLabelFontFamily(FontFamily, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLabelFontSize(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLabelFontStyle(FontStyle, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLabelID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLabelLocked(Boolean, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLabelName(String) - Method in class omero.gateway.model.ImageAcquisitionData
Sets the name of the stage label.
setLabelStrokeColor(Color, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLabelStrokeDashArray(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLabelStrokeWidth(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLabelText(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLabelTheC(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLabelTheT(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLabelTheZ(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLabelTransform(AffineTransform, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLabelX(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLabelY(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLaserAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLaserFrequencyMultiplication(PositiveInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLaserID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLaserLaserMedium(LaserMedium, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLaserLotNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLaserManufacturer(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLaserModel(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLaserPockelCell(Boolean, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLaserPower(Power, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLaserPulse(Pulse, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLaserPump(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLaserRepetitionRate(Frequency, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLaserSerialNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLaserTuneable(Boolean, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLaserType(LaserType, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLaserWavelength(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLastName(String) - Method in class omero.gateway.model.ExperimenterData
Sets the last name of the experimenter.
setLightEmittingDiodeAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLightEmittingDiodeID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLightEmittingDiodeLotNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLightEmittingDiodeManufacturer(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLightEmittingDiodeModel(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLightEmittingDiodePower(Power, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLightEmittingDiodeSerialNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLightPathAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLightPathDichroicRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLightPathEmissionFilterRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLightPathExcitationFilterRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLightSettingsAttenuation(double) - Method in class omero.gateway.model.ChannelAcquisitionData
Sets the attenuation of the light settings.
setLightSettingsWavelength(Length) - Method in class omero.gateway.model.ChannelAcquisitionData
Sets the wavelength of the light source.
setLightSource(LightSourceData) - Method in class omero.gateway.model.ChannelAcquisitionData
Sets the light source associated to the settings.
setLineAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLineFillColor(Color, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLineFillRule(FillRule, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLineFontFamily(FontFamily, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLineFontSize(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLineFontStyle(FontStyle, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLineID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLineLocked(Boolean, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLineMarkerEnd(Marker, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLineMarkerStart(Marker, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLineStrokeColor(Color, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLineStrokeDashArray(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLineStrokeWidth(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLineText(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLineTheC(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLineTheT(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLineTheZ(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLineTransform(AffineTransform, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLineX1(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLineX2(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLineY1(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLineY2(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setListAnnotationAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setListAnnotationAnnotator(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setListAnnotationDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setListAnnotationID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setListAnnotationNamespace(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLongAnnotationAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLongAnnotationAnnotator(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLongAnnotationDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLongAnnotationID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLongAnnotationNamespace(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setLongAnnotationValue(Long, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMapAnnotationAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMapAnnotationAnnotator(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMapAnnotationDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMapAnnotationID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMapAnnotationNamespace(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMapAnnotationValue(List<MapPair>, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMarkerEnd(String) - Method in class omero.gateway.model.ShapeSettingsData
Sets the marker end.
setMarkerStart(String) - Method in class omero.gateway.model.ShapeSettingsData
Sets the marker start.
setMask(byte[]) - Method in class omero.gateway.model.MaskData
Sets the mask image.
setMask(BufferedImage) - Method in class omero.gateway.model.MaskData
Sets the mask from the bufferedImage.
setMaskAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMaskBinData(byte[], int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMaskBinData(byte[], int, int) - Method in class ome.formats.OverlayMetadataStore
 
setMaskBinDataBigEndian(Boolean, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMaskBinDataCompression(Compression, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMaskBinDataLength(NonNegativeLong, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMaskFillColor(Color, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMaskFillRule(FillRule, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMaskFontFamily(FontFamily, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMaskFontSize(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMaskFontStyle(FontStyle, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMaskHeight(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMaskHeight(Double, int, int) - Method in class ome.formats.OverlayMetadataStore
 
setMaskID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMaskLocked(Boolean, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMaskStrokeColor(Color, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMaskStrokeColor(Color, int, int) - Method in class ome.formats.OverlayMetadataStore
 
setMaskStrokeDashArray(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMaskStrokeWidth(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMaskText(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMaskTheC(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMaskTheT(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMaskTheZ(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMaskTransform(AffineTransform, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMaskWidth(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMaskWidth(Double, int, int) - Method in class ome.formats.OverlayMetadataStore
 
setMaskX(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMaskX(Double, int, int) - Method in class ome.formats.OverlayMetadataStore
 
setMaskY(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMaskY(Double, int, int) - Method in class ome.formats.OverlayMetadataStore
 
setMedium(Medium) - Method in class omero.gateway.model.ImageAcquisitionData
Sets the medium of the objective.
setMergedBatches_async(AMD_Search_setMergedBatches, boolean, Current) - Method in class ome.services.blitz.impl.SearchI
 
setMessage(String, Current) - Method in class ome.services.blitz.impl.ScriptProcessI
 
setMessage_async(AMD_JobHandle_setMessage, String, Current) - Method in class ome.services.blitz.impl.JobHandleI
 
setMetadataOptions(MetadataOptions) - Method in class ome.formats.importer.OMEROWrapper
 
setMicrobeamManipulationDescription(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMicrobeamManipulationExperimenterRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMicrobeamManipulationID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMicrobeamManipulationLightSourceSettingsAttenuation(PercentFraction, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMicrobeamManipulationLightSourceSettingsID(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMicrobeamManipulationLightSourceSettingsWavelength(Length, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMicrobeamManipulationROIRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMicrobeamManipulationType(MicrobeamManipulationType, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMicroscopeLotNumber(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMicroscopeManufacturer(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMicroscopeModel(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMicroscopeSerialNumber(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMicroscopeType(MicroscopeType, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setMiddleName(String) - Method in class omero.gateway.model.ExperimenterData
Sets the middle name of the experimenter.
setMode(AcquisitionMode) - Method in class omero.gateway.model.ChannelData
Sets the acquisition mode value.
setModel_async(AMD_RenderingEngine_setModel, RenderingModel, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
setModelProcessors(List<ModelProcessor>) - Method in class ome.formats.OMEROMetadataStoreClient
Sets the current set of model processors.
setName(String) - Method in class ome.formats.OMEROImportFixture
Deprecated.
 
setName(String) - Method in class omero.gateway.model.ChannelData
Sets the name of the logical channel.
setName(String) - Method in class omero.gateway.model.DatasetData
Sets the name of the dataset.
setName(String) - Method in class omero.gateway.model.FolderData
Set the name of the Folder
setName(String) - Method in class omero.gateway.model.GroupData
Sets the name of the group.
setName(String) - Method in class omero.gateway.model.ImageData
Sets the name of the image.
setName(String) - Method in class omero.gateway.model.PlateAcquisitionData
Sets the name of the acquisition.
setName(String) - Method in class omero.gateway.model.PlateData
Sets the name of the plate.
setName(String) - Method in class omero.gateway.model.ProjectData
Sets the name of the project.
setName(String) - Method in class omero.gateway.model.ScreenData
Sets the name of the screen.
setName(String) - Method in class omero.gateway.model.TableDataColumn
Set the header
setNameSpace(String) - Method in class omero.gateway.model.AnnotationData
Sets the name space of the underlying Annotation instance.
setNDFilter(double) - Method in class omero.gateway.model.ChannelData
Sets the ND filter.
setNoStatsInfo(boolean) - Method in class ome.formats.importer.ImportContainer
Sets whether or not we disabling StatsInfo population.
setNumberOfRows(long) - Method in class omero.gateway.model.TableData
Set the total number of rows in the original table
setNumOfDirectories(int) - Method in class ome.formats.importer.ImportConfig
 
setNumOfDirectories(int) - Method in class ome.formats.importer.util.IniFileLoader
 
setObject(DataObject) - Method in class omero.gateway.model.SearchResult
Set the found object
setObjectId(long) - Method in class omero.gateway.model.SearchResult
Set the Id of the found object
setObjectiveAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setObjectiveCalibratedMagnification(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setObjectiveCorrection(Correction, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setObjectiveID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setObjectiveImmersion(Immersion, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setObjectiveIris(Boolean, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setObjectiveLensNA(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setObjectiveLotNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setObjectiveManufacturer(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setObjectiveModel(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setObjectiveNominalMagnification(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setObjectiveSerialNumber(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setObjectiveSettingsCorrectionCollar(Double, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setObjectiveSettingsID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setObjectiveSettingsMedium(Medium, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setObjectiveSettingsRefractiveIndex(Double, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setObjectiveWorkingDistance(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setOffset(int, long) - Method in class ome.services.blitz.repo.ManagedImportProcessI
 
setOffset(long) - Method in class omero.gateway.model.TableData
Set the row offset (if this TableData represents only a subset of the original table)
setOriginalFileId(long) - Method in class omero.gateway.model.TableData
Set the originalfile id
setOriginalSettingsForPixels_async(AMD_IRenderingSettings_setOriginalSettingsForPixels, long, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
 
setOriginalSettingsInDataset_async(AMD_IRenderingSettings_setOriginalSettingsInDataset, long, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
 
setOriginalSettingsInImage_async(AMD_IRenderingSettings_setOriginalSettingsInImage, long, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
 
setOriginalSettingsInSet_async(AMD_IRenderingSettings_setOriginalSettingsInSet, String, List<Long>, Current) - Method in class ome.services.blitz.impl.RenderingSettingsI
 
setOSArch(String) - Method in class ome.formats.importer.util.ErrorContainer
 
setOSName(String) - Method in class ome.formats.importer.util.ErrorContainer
 
setOSVersion(String) - Method in class ome.formats.importer.util.ErrorContainer
 
setOutput(String, RType) - Method in class omero.client
Sets an item in the "output" shared (session) memory under the given name.
setOutput_async(AMD_ISession_setOutput, String, String, RType, Current) - Method in class ome.services.blitz.impl.SessionI
 
setOverlays_async(AMD_RenderingEngine_setOverlays, RLong, RLong, Map<Long, Integer>, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
setOwner(Experimenter, Current) - Method in class omero.model.DetailsI
 
setParentFilePath(String, int) - Method in class omero.gateway.model.ImageData
Sets the path to the file hosting the image.
setParentFolder(Folder) - Method in class omero.gateway.model.FolderData
Set the the parent folder
setPassword(String) - Method in class loci.ome.io.OmeroReader
Deprecated.
 
setPassword(String) - Method in class omero.gateway.UserCredentials
Sets the password
setPathSanitizer(Function<String, String>) - Method in class ome.services.blitz.repo.path.ServerFilePathTransformer
Set the string transformer that is used to make file-path components safe across platforms.
setPathToFile(String) - Method in class omero.gateway.model.ImageData
Sets the path to the file.
setPerm1(long, Current) - Method in class omero.model.PermissionsI
 
setPerm1(Long) - Method in class omero.model.PermissionsI
 
setPermissions(Permissions, Current) - Method in class omero.model.DetailsI
 
setPermissionsVerifier(String, int) - Method in class ome.services.blitz.Router
 
setPinholeSize(Length) - Method in class omero.gateway.model.ChannelData
Sets the pinhole size.
setPixels(Pixels) - Method in class omero.util.RPSTileLoop
Called by the TileData implementation to update the RPSTileLoop.pixels instance for re-use by the client.
setPixelsBigEndian(Boolean, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPixelsBinData(byte[], int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPixelsBinDataBigEndian(Boolean, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPixelsBinDataCompression(Compression, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPixelsBinDataLength(NonNegativeLong, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPixelsDimensionOrder(DimensionOrder, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPixelsFile(long, String, String) - Method in class ome.formats.OMEROMetadataStoreClient
Sets the path, name and repo in the pixels table.
setPixelsFile_async(AMD_MetadataStore_setPixelsFile, long, String, String, Current) - Method in class ome.services.blitz.impl.MetadataStoreI
 
setPixelsID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPixelsId_async(AMD_RawPixelsStore_setPixelsId, long, boolean, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
setPixelsId_async(AMD_ThumbnailStore_setPixelsId, long, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
 
setPixelsId_async(AMD_RawPixelsStore_setPixelsId, long, boolean, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
setPixelsInterleaved(Boolean, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPixelSizeX(Length) - Method in class omero.gateway.model.PixelsData
Sets the dimension of a pixel along the X-axis
setPixelSizeY(Length) - Method in class omero.gateway.model.PixelsData
Sets the dimension of a pixel along the Y-axis.
setPixelSizeZ(Length) - Method in class omero.gateway.model.PixelsData
Sets the dimension of a pixel along the Z-axis
setPixelsPhysicalSizeX(Length, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPixelsPhysicalSizeY(Length, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPixelsPhysicalSizeZ(Length, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPixelsService(PixelsService) - Method in class omero.cmd.graphs.DiskUsage2I
setPixelsSignificantBits(PositiveInteger, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPixelsSizeC(PositiveInteger, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPixelsSizeT(PositiveInteger, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPixelsSizeX(PositiveInteger, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPixelsSizeY(PositiveInteger, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPixelsSizeZ(PositiveInteger, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPixelsTimeIncrement(Time, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPixelsType(PixelType, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPlane(Long, byte[], int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
Writes a plane to the server.
setPlane_async(AMD_RawPixelsStore_setPlane, byte[], int, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
setPlane_async(AMD_RawPixelsStore_setPlane, byte[], int, int, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
setPlaneAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPlaneDeltaT(Time, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPlaneExposureTime(Time, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPlaneHashSHA1(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPlanePositionX(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPlanePositionY(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPlanePositionZ(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPlaneTheC(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPlaneTheT(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPlaneTheZ(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPlateAcquisition(Set<PlateAcquisitionData>) - Method in class omero.gateway.model.PlateData
Sets the plate acquisition linked to the plate.
setPlateAcquisitionAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPlateAcquisitionDescription(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPlateAcquisitionEndTime(Timestamp, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPlateAcquisitionID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPlateAcquisitionMaximumFieldCount(PositiveInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPlateAcquisitionName(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPlateAcquisitionStartTime(Timestamp, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPlateAcquisitionWellSampleRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPlateAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPlateColumnNamingConvention(NamingConvention, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPlateColumns(PositiveInteger, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPlateDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPlateExternalIdentifier(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPlateFieldIndex(NonNegativeInteger, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPlateID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPlateName(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPlateRowNamingConvention(NamingConvention, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPlateRows(PositiveInteger, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPlates(Set<PlateData>) - Method in class omero.gateway.model.ScreenData
Sets the plates contained in this screen.
setPlateStatus(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPlateWellOriginX(Length, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPlateWellOriginY(Length, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPockelCell(int) - Method in class omero.gateway.model.ChannelData
Sets the pockel cell.
setPointAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPointFillColor(Color, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPointFillRule(FillRule, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPointFontFamily(FontFamily, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPointFontSize(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPointFontStyle(FontStyle, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPointID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPointLocked(Boolean, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPoints(List<Point2D.Double>) - Method in class omero.gateway.model.PolygonData
Sets the points in the polygon.
setPoints(List<Point2D.Double>) - Method in class omero.gateway.model.PolylineData
Sets the points in the polyline.
setPointStrokeColor(Color, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPointStrokeDashArray(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPointStrokeWidth(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPointText(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPointTheC(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPointTheT(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPointTheZ(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPointTransform(AffineTransform, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPointX(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPointY(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolygonAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolygonFillColor(Color, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolygonFillRule(FillRule, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolygonFontFamily(FontFamily, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolygonFontSize(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolygonFontStyle(FontStyle, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolygonID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolygonLocked(Boolean, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolygonPoints(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolygonStrokeColor(Color, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolygonStrokeDashArray(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolygonStrokeWidth(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolygonText(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolygonTheC(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolygonTheT(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolygonTheZ(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolygonTransform(AffineTransform, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolylineAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolylineFillColor(Color, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolylineFillRule(FillRule, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolylineFontFamily(FontFamily, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolylineFontSize(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolylineFontStyle(FontStyle, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolylineID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolylineLocked(Boolean, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolylineMarkerEnd(Marker, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolylineMarkerStart(Marker, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolylinePoints(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolylineStrokeColor(Color, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolylineStrokeDashArray(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolylineStrokeWidth(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolylineText(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolylineTheC(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolylineTheT(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolylineTheZ(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPolylineTransform(AffineTransform, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setPort(int) - Method in class loci.ome.io.OmeroReader
Deprecated.
 
setPort(int) - Method in class omero.gateway.ServerInformation
Set the port
setPositionX(Length) - Method in class omero.gateway.model.ImageAcquisitionData
Sets the x-position.
setPositionY(Length) - Method in class omero.gateway.model.ImageAcquisitionData
Sets the y-position.
setPositionZ(Length) - Method in class omero.gateway.model.ImageAcquisitionData
Sets the z-position.
setProjectAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setProjectDatasetRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setProjectDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setProjectExperimenterGroupRef(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setProjectExperimenterRef(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setProjectID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setProjectName(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setProjects(Set<ProjectData>) - Method in class omero.gateway.model.DatasetData
Sets the projects containing the dataset.
setProtocolDescription(String) - Method in class omero.gateway.model.ScreenData
Sets the description of the protocol.
setProtocolIdentifier(String) - Method in class omero.gateway.model.ScreenData
Sets the identifier of the protocol.
setQuantizationMap_async(AMD_RenderingEngine_setQuantizationMap, int, Family, double, boolean, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
setQuantumStrategy_async(AMD_RenderingEngine_setQuantumStrategy, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
setRadiusX(double) - Method in class omero.gateway.model.EllipseData
Sets the radius along the X-axis.
setRadiusY(double) - Method in class omero.gateway.model.EllipseData
Sets the radius along the Y-axis.
setRating(int) - Method in class omero.gateway.model.RatingAnnotationData
Sets the rating value.
setReader(String) - Method in class ome.formats.importer.ImportContainer
Sets the reader class name used for reading the contents of this import container.
setReader(IFormatReader) - Method in interface ome.formats.model.IObjectContainerStore
Sets the Bio-Formats reader that will be used to populate the container store.
setReader(IFormatReader) - Method in class ome.formats.OMEROMetadataStoreClient
 
setReaderType(String) - Method in class ome.formats.importer.util.ErrorContainer
set file format for import
setReadOnly() - Method in class ome.services.blitz.repo.CheckedPath
Mark the underlying File as read-only and return true if the operation was successful.
setReadOnly(boolean) - Method in class omero.gateway.model.ShapeData
Sets to true if the object is a read-only object, false otherwise.
setReagentAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setReagentDescription(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setReagentID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setReagentName(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setReagentReagentIdentifier(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setReagentSetDescripion(String) - Method in class omero.gateway.model.ScreenData
Sets the identifier of the reagent.
setReagentSetIdentifier(String) - Method in class omero.gateway.model.ScreenData
Sets the identifier of the reagent.
setRectangleAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setRectangleFillColor(Color, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setRectangleFillRule(FillRule, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setRectangleFontFamily(FontFamily, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setRectangleFontSize(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setRectangleFontStyle(FontStyle, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setRectangleHeight(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setRectangleID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setRectangleLocked(Boolean, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setRectangleStrokeColor(Color, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setRectangleStrokeDashArray(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setRectangleStrokeWidth(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setRectangleText(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setRectangleTheC(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setRectangleTheT(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setRectangleTheZ(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setRectangleTransform(AffineTransform, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setRectangleWidth(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setRectangleX(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setRectangleY(Double, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setRed(Integer) - Method in class omero.gateway.model.WellData
Sets the red component of the color associated to the well.
setReference(OriginalFile) - Method in class omero.gateway.model.ImageData
Sets the reference to the file to register.
setReferenceStringCache(Map<String, String[]>) - Method in interface ome.formats.model.IObjectContainerStore
Sets the string based reference cache for this container store.
setReferenceStringCache(Map<String, String[]>) - Method in class ome.formats.OMEROMetadataStoreClient
 
setRefPlateId(long) - Method in class omero.gateway.model.PlateAcquisitionData
Sets the id of the plate this plate acquisition is for.
setRefractiveIndex(double) - Method in class omero.gateway.model.ImageAcquisitionData
Sets the refractive index of the objective.
setRegion_async(AMD_RawPixelsStore_setRegion, int, long, byte[], Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
setRegion_async(AMD_RawPixelsStore_setRegion, int, long, byte[], Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
setRegisteredFile(OriginalFile) - Method in class omero.gateway.model.FileData
Sets the registered file.
setRegisteredFile(Image) - Method in class omero.gateway.model.ImageData
Sets the registered file.
setRegistry(Registry) - Method in class ome.services.blitz.fire.Ring
Sets the Registry for this instance.
setRenderingDefId_async(AMD_ThumbnailStore_setRenderingDefId, long, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
 
setRepositoryPath(String) - Method in class omero.gateway.model.FileData
Sets the path to the parent.
setResolutionLevel_async(AMD_PyramidService_setResolutionLevel, int, Current) - Method in class ome.services.blitz.impl.AbstractPyramidServant
 
setResolutionLevel_async(AMD_PyramidService_setResolutionLevel, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
setResources(Resources) - Method in class ome.services.blitz.repo.ManagedImportRequestI
Late injection to not break the constructor
setResponseIfNull(Response) - Method in class omero.cmd.Helper
Set the response if there is not currently run, in which case true is returned.
setResult(Object) - Method in class omero.gateway.model.ROIResult
Sets the results.
setReturnUnloaded_async(AMD_Search_setReturnUnloaded, boolean, Current) - Method in class ome.services.blitz.impl.SearchI
 
setRGBA_async(AMD_RenderingEngine_setRGBA, int, int, int, int, int, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
setRightsRightsHeld(String) - Method in class ome.formats.OMEROMetadataStoreClient
 
setRightsRightsHolder(String) - Method in class ome.formats.OMEROMetadataStoreClient
 
setROIAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setROICoordinate(ROICoordinate) - Method in class omero.gateway.model.ShapeData
Sets the ROICoordinate for the ShapeData.
setROIDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setROIID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setROIID(String, int) - Method in class ome.formats.OverlayMetadataStore
 
setROIName(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setRoot(MetadataRoot) - Method in class ome.formats.OMEROMetadataStoreClient
 
setRow_async(AMD_RawPixelsStore_setRow, byte[], int, int, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
setRow_async(AMD_RawPixelsStore_setRow, byte[], int, int, int, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
setScopeId(int) - Method in class omero.gateway.model.SearchResult
Set the id of the search scope, e.g. name, description, ...
setScreenAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setScreenDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setScreenID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setScreenName(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setScreenPlateRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setScreenProtocolDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setScreenProtocolIdentifier(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setScreenReagentSetDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setScreenReagentSetIdentifier(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setScreens(Set<ScreenData>) - Method in class omero.gateway.model.PlateData
Sets the screens containing the plate.
setScreenType(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setSecurityContext(IObject, Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
setSecurityPassword(String, Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
setSecuritySystem(SecuritySystem) - Method in class ome.services.blitz.impl.TimelineI
 
setSelectedFile(File) - Method in class ome.formats.importer.util.ErrorContainer
 
setServer(String) - Method in class loci.ome.io.OmeroReader
Deprecated.
 
setServerEndpoints(String, int) - Method in class ome.services.blitz.Router
 
setServerInformation(ServerInformation) - Method in class omero.gateway.SecurityContext
setServiceFactory(ServiceFactoryI) - Method in class ome.services.blitz.impl.ExporterI
 
setServiceFactory(ServiceFactoryI) - Method in class ome.services.blitz.impl.MetadataStoreI
 
setServiceFactory(ServiceFactoryI) - Method in class ome.services.blitz.impl.RawFileStoreI
 
setServiceFactory(ServiceFactoryI) - Method in class ome.services.blitz.impl.RenderingEngineI
 
setServiceFactory(ServiceFactoryI) - Method in class ome.services.blitz.impl.RoiI
 
setServiceFactory(ServiceFactoryI) - Method in class ome.services.blitz.impl.ScriptI
 
setServiceFactory(ServiceFactoryI) - Method in class ome.services.blitz.impl.SharedResourcesI
 
setServiceFactory(ServiceFactoryI) - Method in class ome.services.blitz.impl.TimelineI
 
setServiceFactory(ServiceFactoryI) - Method in class ome.services.blitz.repo.ManagedImportProcessI
 
setServiceFactory(Identity, ServiceFactoryI) - Method in class ome.services.blitz.util.FindServiceFactoryMessage
Store the information.
setServiceFactory(Identity, ServiceFactoryI) - Method in class ome.services.blitz.util.RegisterServantMessage
 
setServiceFactory(ServiceFactoryI) - Method in interface ome.services.blitz.util.ServiceFactoryAware
 
setSession(SessionI) - Method in class omero.cmd.HandleI
 
setSession(SessionI) - Method in interface omero.cmd.SessionAware
 
setSessionID(String) - Method in class loci.ome.io.OmeroReader
Deprecated.
 
setSessionManager(SessionManager) - Method in class ome.services.blitz.impl.TimelineI
 
setSessionManager(String, int) - Method in class ome.services.blitz.Router
 
setShapeSettings(Shape) - Method in class omero.gateway.model.ShapeData
Set the settings associated to the shape.
setSizeC(int) - Method in class omero.gateway.model.PixelsData
Sets the number of channels.
setSizeT(int) - Method in class omero.gateway.model.PixelsData
Sets the number of time-points.
setSizeX(int) - Method in class omero.gateway.model.PixelsData
Sets the number of pixels along the X-axis.
setSizeY(int) - Method in class omero.gateway.model.PixelsData
Sets the number of pixels along the Y-axis.
setSizeZ(int) - Method in class omero.gateway.model.PixelsData
Sets the number of pixels along the Z-axis.
setStack_async(AMD_RawPixelsStore_setStack, byte[], int, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
setStack_async(AMD_RawPixelsStore_setStack, byte[], int, int, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
setStageLabelName(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setStageLabelX(Length, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setStageLabelY(Length, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setStageLabelZ(Length, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setStatisticsEnabled(boolean) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
Enable statistics logs (this is a dynamic parameter)
setStatus(int) - Method in class ome.formats.importer.util.ErrorContainer
set the status for this error
setStatus(String) - Method in class omero.gateway.model.PlateData
Sets the status.
setStatus(String) - Method in class omero.gateway.model.WellData
Sets the status of the well.
setStatus_async(AMD_JobHandle_setStatus, String, Current) - Method in class ome.services.blitz.impl.JobHandleI
 
setStatusAndMessage_async(AMD_JobHandle_setStatusAndMessage, String, RString, Current) - Method in class ome.services.blitz.impl.JobHandleI
 
setSteps(int) - Method in class omero.cmd.Helper
 
setStroke(Color) - Method in class omero.gateway.model.ShapeSettingsData
Set the stroke color.
setStrokeDashArray(double[]) - Method in class omero.gateway.model.ShapeSettingsData
Set the stroke dashes.
setStrokeWidth(Length) - Method in class omero.gateway.model.ShapeSettingsData
Set the stroke width.
setT(int) - Method in class omero.gateway.model.ShapeData
Sets the time-point.
setTableID(long) - Method in class omero.gateway.model.TableResult
Sets the id of the table.
setTagAnnotationAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setTagAnnotationAnnotator(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setTagAnnotationDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setTagAnnotationID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setTagAnnotationNamespace(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setTagAnnotationValue(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setTagDescription(String) - Method in class omero.gateway.model.TagAnnotationData
Sets the description of the tag.
setTagDescriptions(List<TextualAnnotationData>) - Method in class omero.gateway.model.TagAnnotationData
Sets the tag's descriptions.
setTagValue(String) - Method in class omero.gateway.model.TagAnnotationData
Sets the value of the tag.
setTarget(IObject) - Method in class ome.formats.importer.ImportContainer
 
setTemperature(Temperature) - Method in class omero.gateway.model.ImageAcquisitionData
Sets the temperature.
setTerm(String) - Method in class omero.gateway.model.TermAnnotationData
Sets the term.
setTermAnnotationAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setTermAnnotationAnnotator(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setTermAnnotationDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setTermAnnotationID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setTermAnnotationNamespace(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setTermAnnotationValue(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setTermDescription(String) - Method in class omero.gateway.model.TermAnnotationData
Sets the description of the tag.
setText(String) - Method in class omero.gateway.model.EllipseData
Sets the text of the shape.
setText(String) - Method in class omero.gateway.model.LineData
Sets the text of the shape.
setText(String) - Method in class omero.gateway.model.MaskData
Sets the text of the shape.
setText(String) - Method in class omero.gateway.model.PointData
Sets the text of the shape.
setText(String) - Method in class omero.gateway.model.PolygonData
Sets the text of the shape.
setText(String) - Method in class omero.gateway.model.PolylineData
Sets the text of the shape.
setText(String) - Method in class omero.gateway.model.RectangleData
Sets the text of the shape.
setText(String) - Method in class omero.gateway.model.TextData
Sets the text of the shape.
setText(String) - Method in class omero.gateway.model.TextualAnnotationData
Sets the text.
setText(String) - Method in class omero.gateway.model.XMLAnnotationData
Sets the text value.
setThumbnailService(ThumbnailService) - Method in class omero.cmd.graphs.DiskUsage2I
setTie(TieBase) - Method in class ome.services.blitz.impl.RawFileStoreI
 
setTie(TieBase) - Method in interface omero.util.TieAware
 
setTiffDataFirstC(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setTiffDataFirstT(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setTiffDataFirstZ(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setTiffDataIFD(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setTiffDataPlaneCount(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setTile(Long, byte[], int, int, int, int, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
Writes a tile of pixels to the server.
setTile(byte[], int, int, int, int, int, int, int) - Method in class omero.util.RPSTileData
 
setTile(byte[], int, int, int, int, int, int, int) - Method in interface omero.util.TileData
 
setTile_async(AMD_RawPixelsStore_setTile, byte[], int, int, int, int, int, int, int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
setTile_async(AMD_RawPixelsStore_setTile, byte[], int, int, int, int, int, int, int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
setTimeInterval(Timestamp, Timestamp, int) - Method in class omero.gateway.model.SearchParameters
Sets the time interval.
setTimeout(int) - Method in class ome.services.blitz.Router
 
setTimepoint_async(AMD_RawPixelsStore_setTimepoint, byte[], int, Current) - Method in class ome.services.blitz.impl.RawPixelsStoreI
 
setTimepoint_async(AMD_RawPixelsStore_setTimepoint, byte[], int, Current) - Method in class ome.services.blitz.repo.BfPixelsStoreI
 
setTimestampAnnotationAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setTimestampAnnotationAnnotator(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setTimestampAnnotationDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setTimestampAnnotationID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setTimestampAnnotationNamespace(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setTimestampAnnotationValue(Timestamp, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
settings - Variable in class omero.gateway.model.ShapeData
The representation of the shape.
setToken(String) - Method in class ome.formats.importer.util.ErrorContainer
 
setTransform(AffineTransform) - Method in class omero.gateway.model.ShapeData
Sets the Affine transform of the shape.
setTransmittanceRangeCutIn(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setTransmittanceRangeCutInTolerance(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setTransmittanceRangeCutOut(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setTransmittanceRangeCutOutTolerance(Length, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setTransmittanceRangeTransmittance(PercentFraction, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setType(Class<? extends DataObject>) - Method in class omero.gateway.model.SearchResult
Set the type (class) of objects to search for see DataObject
setType(Class<?>) - Method in class omero.gateway.model.TableDataColumn
Set the data type
setUIBounds(Rectangle) - Method in class ome.formats.importer.ImportConfig
 
setUIBounds(Rectangle) - Method in class ome.formats.importer.util.IniFileLoader
Set ui bounds for application
setUnit(UnitsElectricPotential, Current) - Method in class omero.model.ElectricPotentialI
 
setUnit(UnitsFrequency, Current) - Method in class omero.model.FrequencyI
 
setUnit(UnitsLength, Current) - Method in class omero.model.LengthI
 
setUnit(UnitsPower, Current) - Method in class omero.model.PowerI
 
setUnit(UnitsPressure, Current) - Method in class omero.model.PressureI
 
setUnit(UnitsTemperature, Current) - Method in class omero.model.TemperatureI
 
setUnit(UnitsTime, Current) - Method in class omero.model.TimeI
 
setUp() - Method in class ome.formats.importer.ImportFixture
checks for the necessary fields and initializes the ImportLibrary
setUp() - Method in class ome.formats.OMEROImportFixture
Deprecated.
checks for the necessary fields and initializes the ImportLibrary
setUpdateEvent(Event, Current) - Method in class omero.model.DetailsI
 
setUploadUrl(String) - Method in class ome.formats.importer.util.ErrorContainer
 
setUsedFiles(String[]) - Method in class ome.formats.importer.ImportContainer
Set the list of image file names that belong to this import container.
setUseProjections_async(AMD_Search_setUseProjections, boolean, Current) - Method in class ome.services.blitz.impl.SearchI
 
setUseQuaqua(boolean) - Method in class ome.formats.importer.ImportConfig
 
setUseQuaqua(boolean) - Method in class ome.formats.importer.util.IniFileLoader
 
setUserAnnotate(boolean, Current) - Method in class omero.model.PermissionsI
 
setUserDisableHistory(boolean) - Method in class ome.formats.importer.ImportConfig
 
setUserDisableHistory(boolean) - Method in class ome.formats.importer.util.IniFileLoader
Set if history should be disabled.
setUserFullPath(boolean) - Method in class ome.formats.importer.ImportConfig
Deprecated.
setUserFullPath(boolean) - Method in class ome.formats.importer.util.IniFileLoader
Deprecated.
setUserId(long) - Method in class omero.gateway.model.SearchParameters
 
setUsername(String) - Method in class loci.ome.io.OmeroReader
Deprecated.
 
setUsername(String) - Method in class omero.gateway.UserCredentials
Sets the username (or session ID)
setUserPixels(Double[]) - Method in class ome.formats.importer.ImportContainer
 
setUserRead(boolean) - Method in class omero.gateway.model.PermissionData
Sets to true if the user has read access, false otherwise.
setUserRead(boolean, Current) - Method in class omero.model.PermissionsI
 
setUserSpecifiedAnnotations(List<Annotation>) - Method in interface ome.formats.model.IObjectContainerStore
Sets the user specified image annotations.
setUserSpecifiedAnnotations(List<Annotation>) - Method in class ome.formats.OMEROMetadataStoreClient
 
setUserSpecifiedDescription(String) - Method in class ome.formats.importer.ImportContainer
Sets the custom image/plate description for import.
setUserSpecifiedDescription(String) - Method in interface ome.formats.model.IObjectContainerStore
Sets the user specified image/plate description.
setUserSpecifiedDescription(String) - Method in class ome.formats.OMEROMetadataStoreClient
 
setUserSpecifiedName(String) - Method in class ome.formats.importer.ImportContainer
Sets the custom image/plate name for import.
setUserSpecifiedName(String) - Method in interface ome.formats.model.IObjectContainerStore
Sets the user specified image/plate name.
setUserSpecifiedName(String) - Method in class ome.formats.OMEROMetadataStoreClient
 
setUserSpecifiedPhysicalPixelSizes(Double, Double, Double) - Method in interface ome.formats.model.IObjectContainerStore
Sets the user specified physical pixel sizes.
setUserSpecifiedPhysicalPixelSizes(Double, Double, Double) - Method in class ome.formats.OMEROMetadataStoreClient
 
setUserSpecifiedTarget(IObject) - Method in interface ome.formats.model.IObjectContainerStore
Sets the user-specified linkage target (usually a Dataset for Images) and a Screen for Plates).
setUserSpecifiedTarget(IObject) - Method in class ome.formats.OMEROMetadataStoreClient
 
setUserWrite(boolean) - Method in class omero.gateway.model.PermissionData
Sets to true if the user has write access, false otherwise.
setUserWrite(boolean, Current) - Method in class omero.model.PermissionsI
 
setUUID(String) - Method in class ome.formats.OMEROMetadataStoreClient
 
setUuid(String) - Method in class omero.gateway.model.ROIData
Set the UUID
setUUIDFileName(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setUUIDValue(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setValue(boolean) - Method in class omero.gateway.model.BooleanAnnotationData
Returns the text.
setValue(IObject) - Method in class omero.gateway.model.DataObject
Sets the IObject.
setValue(double, Current) - Method in class omero.model.ElectricPotentialI
 
setValue(double, Current) - Method in class omero.model.FrequencyI
 
setValue(double, Current) - Method in class omero.model.LengthI
 
setValue(double, Current) - Method in class omero.model.PowerI
 
setValue(double, Current) - Method in class omero.model.PressureI
 
setValue(double, Current) - Method in class omero.model.TemperatureI
 
setValue(double, Current) - Method in class omero.model.TimeI
 
setVersion(int) - Method in class omero.gateway.model.DataObject
Sets the version of the object if it is immutable.
setVersionNumber(String) - Method in class ome.formats.importer.ImportConfig
 
setWellAnnotationRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setWellColor(Color, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setWellColumn(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setWellExternalDescription(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setWellExternalIdentifier(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setWellID(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setWellReagentRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setWellRow(NonNegativeInteger, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setWellSampleID(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setWellSampleImageRef(String, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setWellSampleIndex(NonNegativeInteger, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setWellSamplePositionX(Length, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setWellSamplePositionY(Length, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setWellSamples(List<WellSampleData>) - Method in class omero.gateway.model.WellData
Sets the well samples linked to the well.
setWellSampleTimepoint(Timestamp, int, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setWellType(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setWellType(String) - Method in class omero.gateway.model.WellData
Sets a human readable identifier for the screening status e.g. empty, positive control, etc.
setWidth(double) - Method in class omero.gateway.model.MaskData
Sets the width of an untransformed mask.
setWidth(double) - Method in class omero.gateway.model.RectangleData
Sets width of an untransformed rectangle.
setWorldAnnotate(boolean, Current) - Method in class omero.model.PermissionsI
 
setWorldRead(boolean) - Method in class omero.gateway.model.PermissionData
Sets to true if the world has read access, false otherwise.
setWorldRead(boolean, Current) - Method in class omero.model.PermissionsI
 
setWorldWrite(boolean) - Method in class omero.gateway.model.PermissionData
Sets to true if the world has write access, false otherwise.
setWorldWrite(boolean, Current) - Method in class omero.model.PermissionsI
 
setX(double) - Method in class omero.gateway.model.EllipseData
Sets the x-coordinate of the center of the ellipse.
setX(double) - Method in class omero.gateway.model.MaskData
Sets the x-coordinate top-left corner of an untransformed mask.
setX(double) - Method in class omero.gateway.model.PointData
set the x-coordinate of the shape.
setX(double) - Method in class omero.gateway.model.RectangleData
Sets the x-coordinate of the top-left corner of an untransformed rectangle.
setX(double) - Method in class omero.gateway.model.TextData
Sets the x-coordinate of the text field.
setX1(double) - Method in class omero.gateway.model.LineData
Set the x-coordinate of the starting point of an untransformed line.
setX2(double) - Method in class omero.gateway.model.LineData
Set the x-coordinate of the end point of an untransformed line.
setXMLAnnotationAnnotationRef(String, int, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setXMLAnnotationAnnotator(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setXMLAnnotationDescription(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setXMLAnnotationID(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setXMLAnnotationNamespace(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setXMLAnnotationValue(String, int) - Method in class ome.formats.OMEROMetadataStoreClient
 
setY(double) - Method in class omero.gateway.model.EllipseData
Sets the y-coordinate of the center of the ellipse.
setY(double) - Method in class omero.gateway.model.MaskData
Sets the y-coordinate top-left corner of an untransformed mask.
setY(double) - Method in class omero.gateway.model.PointData
set the y-coordinate of the shape.
setY(double) - Method in class omero.gateway.model.RectangleData
Sets the y-coordinate of the top-left corner of an untransformed rectangle.
setY(double) - Method in class omero.gateway.model.TextData
Sets the y-coordinate of the text field.
setY1(double) - Method in class omero.gateway.model.LineData
Set the y-coordinate of the starting point of an untransformed line.
setY2(double) - Method in class omero.gateway.model.LineData
Set the y-coordinate of the end point of an untransformed line.
setZ(int) - Method in class omero.gateway.model.ShapeData
Sets the z-section.
sf - Variable in class ome.services.blitz.impl.MetadataStoreI
 
sf - Variable in class ome.services.blitz.util.FindServiceFactoryMessage
 
sha1(File) - Method in class omero.client
Calculates the local sha1 for a file.
Shape_FontSize - Static variable in class ome.formats.model.UnitsFactory
 
Shape_StrokeWidth - Static variable in class ome.formats.model.UnitsFactory
 
ShapeData - Class in omero.gateway.model
Hosts a shape.
ShapeData(Shape, boolean) - Constructor for class omero.gateway.model.ShapeData
Creates a new instance.
ShapeData(Shape) - Constructor for class omero.gateway.model.ShapeData
Creates a new instance.
ShapeProcessor - Class in ome.formats.model
Processes the shapes of a IObjectContainerStore and ensures that the ROI containers are present.
ShapeProcessor() - Constructor for class ome.formats.model.ShapeProcessor
 
ShapeSettingsData - Class in omero.gateway.model
Stores the settings related to a given shape.
sharedResources(Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
SharedResourcesI - Class in ome.services.blitz.impl
Implementation of the SharedResources interface.
SharedResourcesI(BlitzExecutor, TopicManager, Registry, ScriptRepoHelper, ParamsCache) - Constructor for class ome.services.blitz.impl.SharedResourcesI
 
SharedResourcesI(BlitzExecutor, TopicManager, Registry, ScriptRepoHelper, ParamsCache, long) - Constructor for class ome.services.blitz.impl.SharedResourcesI
 
SharedResourcesI(BlitzExecutor, TopicManager, Registry, ScriptRepoHelper, ParamsCache, long, long) - Constructor for class ome.services.blitz.impl.SharedResourcesI
 
ShareI - Class in ome.services.blitz.impl
Implementation of the IShare service.
ShareI(IShare, BlitzExecutor) - Constructor for class ome.services.blitz.impl.ShareI
 
shortName - Variable in class ome.formats.importer.ImportEvent.COUNT_EVENT
 
shutdown(boolean) - Method in class ome.services.blitz.Entry
Calls OmeroContext.closeAll() to recursively close all OMERO.blitz resources in the reverse order that they were created.
shutdown(Current) - Method in class ome.services.blitz.impl.ScriptProcessI
 
shutdown() - Method in class ome.services.blitz.repo.ManagedImportProcessI
 
shutdown() - Method in interface ome.services.blitz.repo.ProcessContainer.Process
 
shutDown() - Method in interface omero.gateway.cache.CacheService
Shuts the cache down.
shutdownAll() - Method in class ome.services.blitz.repo.ProcessContainer
Called on shutdown of the server.
shutDownDerivedConnector(SecurityContext) - Method in class omero.gateway.Gateway
Shuts down the connectors created while creating/importing data for other users.
shutdownRenderingEngine(SecurityContext, long) - Method in class omero.gateway.Gateway
Shuts down the rendering engine
SimpleLogger - Class in omero.log
A simple Logger implementation which just prints the messages to the console
SimpleLogger() - Constructor for class omero.log.SimpleLogger
 
singleFile(File, ImportConfig) - Method in class ome.formats.importer.ImportCandidates
Return an import container for a single file
size() - Method in class ome.formats.importer.ImportCandidates
 
size - Variable in class ome.formats.importer.ImportEvent.PROGRESS_EVENT
 
size() - Method in class ome.services.blitz.repo.CheckedPath
Return the size of this file on the underlying filesystem.
size() - Method in class omero.util.Resources
 
size_async(AMD_RawFileStore_size, Current) - Method in class ome.services.blitz.impl.RawFileStoreI
 
sizeC - Variable in class ome.formats.importer.ImportSize
 
sizeC - Variable in class ome.services.formats.OmeroReader
 
sizeImages() - Method in class ome.services.blitz.impl.OmeroMetadata
 
sizeT - Variable in class ome.formats.importer.ImportSize
 
sizeT - Variable in class ome.services.formats.OmeroReader
 
sizeX - Variable in class ome.formats.importer.ImportSize
 
sizeX - Variable in class ome.services.formats.OmeroReader
 
sizeY - Variable in class ome.formats.importer.ImportSize
 
sizeY - Variable in class ome.services.formats.OmeroReader
 
sizeZ - Variable in class ome.formats.importer.ImportSize
 
sizeZ - Variable in class ome.services.formats.OmeroReader
 
skipHead() - Static method in class omero.gateway.util.Requests
 
SkipHeadBuilder() - Constructor for class omero.gateway.util.Requests.SkipHeadBuilder
Instantiate a new SkipHead and initialize its collection containers.
SkipHeadI - Class in omero.cmd.graphs
The skip-head request performs the wrapped request twice: once in dry run mode to discover from which model objects to start, and then actually starting from those objects.
SkipHeadI(GraphPathBean, GraphRequestFactory) - Constructor for class omero.cmd.graphs.SkipHeadI
Construct a new skip-head request; called from GraphRequestFactory.getRequest(Class).
SkipHeadPolicy - Class in omero.cmd.graphs
Adjust graph traversal policy to prevent descent into inclusions beyond certain types.
SkipHeadPolicy() - Constructor for class omero.cmd.graphs.SkipHeadPolicy
 
SkipTailPolicy - Class in omero.cmd.graphs
Adjust graph traversal policy to avoid processing or acting on certain model object classes.
SkipTailPolicy() - Constructor for class omero.cmd.graphs.SkipTailPolicy
 
Slot - Class in ome.services.throttling
Worker which consumes from the Queue.
Slot(Queue) - Constructor for class ome.services.throttling.Slot
 
sm - Variable in class ome.services.blitz.impl.TimelineI
 
SmartEllipseI - Class in omero.model
 
SmartEllipseI() - Constructor for class omero.model.SmartEllipseI
 
SmartLineI - Class in omero.model
 
SmartLineI() - Constructor for class omero.model.SmartLineI
 
SmartMaskI - Class in omero.model
 
SmartMaskI() - Constructor for class omero.model.SmartMaskI
 
SmartPathI - Class in omero.model
 
SmartPathI() - Constructor for class omero.model.SmartPathI
 
SmartPointI - Class in omero.model
 
SmartPointI() - Constructor for class omero.model.SmartPointI
 
SmartPolygonI - Class in omero.model
 
SmartPolygonI() - Constructor for class omero.model.SmartPolygonI
 
SmartPolylineI - Class in omero.model
 
SmartPolylineI() - Constructor for class omero.model.SmartPolylineI
 
SmartRectI - Class in omero.model
 
SmartRectI() - Constructor for class omero.model.SmartRectI
 
SmartShape - Interface in omero.model
Orthogonal interface hierarchy of types for working with the Shape hierarchy.
SmartShape.PointCallback - Interface in omero.model
Callback interface passed every point which is within the area of this shape.
SmartShape.Util - Class in omero.model
Utility class used as a mixin by all of the SmartShape implementations.
SmartTextI - Class in omero.model
 
SmartTextI() - Constructor for class omero.model.SmartTextI
 
SortDatasetsByName - Class in ome.formats
 
SortDatasetsByName() - Constructor for class ome.formats.SortDatasetsByName
 
SortProjectsByName - Class in ome.formats
 
SortProjectsByName() - Constructor for class ome.formats.SortProjectsByName
 
source - Variable in class ome.formats.importer.util.ErrorHandler.UNKNOWN_FORMAT
 
source - Variable in class ome.formats.importer.util.ErrorHandler.UNREADABLE_FILE
 
splitString(String) - Static method in class omero.gateway.util.Utils
Returns the partial name of the image's name
sql - Variable in class ome.services.blitz.impl.MetadataStoreI
 
sql - Variable in class ome.services.blitz.impl.RoiI
 
sql - Variable in class ome.services.roi.GeomTool
 
srcFiles - Variable in class ome.formats.importer.ImportEvent.FILESET_UPLOAD_END
 
ss - Variable in class ome.services.blitz.impl.TimelineI
 
stackTraceAsString(Throwable) - Method in class ome.services.blitz.repo.PublicRepositoryI
 
StageLabel_X - Static variable in class ome.formats.model.UnitsFactory
 
StageLabel_Y - Static variable in class ome.formats.model.UnitsFactory
 
StageLabel_Z - Static variable in class ome.formats.model.UnitsFactory
 
start() - Method in class ome.formats.importer.cli.CommandLineImporter
 
start(TransferState) - Method in class ome.formats.importer.transfers.AbstractFileTransfer
Minimal start method which logs the file, calls TransferState.start(), and loads the RawFileStorePrx which any implementation will need.
start() - Method in class ome.formats.importer.transfers.TransferState
 
start() - Method in class ome.formats.importer.util.ProportionalTimeEstimatorImpl
 
start() - Method in interface ome.formats.importer.util.TimeEstimator
Starts the time counting.
start() - Method in class ome.services.blitz.Entry
Obtains the named OmeroContext, creating it if necessary, and then delegates to Communicator.waitForShutdown() until either it is externally shutdown, or until a signal is caught.
start() - Method in class ome.services.blitz.Router
 
startFrom(Iterable<String>) - Method in class omero.gateway.util.Requests.SkipHeadBuilder
 
startFrom(Class<? extends IObject>...) - Method in class omero.gateway.util.Requests.SkipHeadBuilder
 
startFrom(String...) - Method in class omero.gateway.util.Requests.SkipHeadBuilder
 
startTime(RTime) - Method in class omero.sys.ParametersI
Sets the value of the start time parameter.
statefulExecutor - Variable in class ome.services.blitz.repo.RepositoryDaoImpl
 
status() - Method in class ome.services.blitz.Entry
 
Status - Class in ome.services.blitz
Status check for OMERO.blitz.
Status(String[]) - Constructor for class ome.services.blitz.Status
 
step - Variable in class ome.formats.importer.ImportEvent.IMPORT_STEP
 
step(int, int, Current) - Method in class ome.formats.importer.ImportLibrary.ImportCallback
 
step(int) - Method in class ome.services.blitz.impl.commands.SaveI
 
step(int) - Method in class ome.services.blitz.repo.ManagedImportRequestI
 
step(int) - Method in class ome.services.blitz.repo.RawAccessRequestI
 
step(int) - Method in class omero.cmd.admin.CurrentSessionsRequestI
 
step(int) - Method in class omero.cmd.admin.ResetPasswordRequestI
 
step(int) - Method in class omero.cmd.admin.UpdateSessionTimeoutRequestI
 
step(int) - Method in class omero.cmd.basic.DoAllI
 
step(int) - Method in class omero.cmd.basic.ListRequestsI
 
step(int) - Method in class omero.cmd.basic.TimingI
 
step(int, int, Current) - Method in class omero.cmd.CmdCallbackI
Called periodically by the server to signal that processing is moving forward.
step(int) - Method in class omero.cmd.fs.FindPyramidsI
 
step(int) - Method in class omero.cmd.fs.ManageImageBinariesI
 
step(int) - Method in class omero.cmd.fs.OriginalMetadataRequestI
 
step(int) - Method in class omero.cmd.fs.UsedFilesRequestI
 
step(int) - Method in class omero.cmd.graphs.Chgrp2I
 
step(int) - Method in class omero.cmd.graphs.Chmod2I
 
step(int) - Method in class omero.cmd.graphs.Chown2I
 
step(int) - Method in class omero.cmd.graphs.Delete2I
 
step(int) - Method in class omero.cmd.graphs.DiskUsage2I
 
step(int) - Method in class omero.cmd.graphs.DiskUsageI
Deprecated.
 
step(int) - Method in class omero.cmd.graphs.DuplicateI
 
step(int) - Method in class omero.cmd.graphs.FindChildrenI
 
step(int) - Method in class omero.cmd.graphs.FindParentsI
 
step(int) - Method in class omero.cmd.graphs.LegalGraphTargetsI
 
step(int) - Method in class omero.cmd.graphs.SkipHeadI
 
step(int) - Method in interface omero.cmd.IRequest
Single uncancellable action which will be performed by this IRequest.
step(int) - Method in class omero.cmd.mail.SendEmailRequestI
 
steps(SqlAction, Session, ServiceFactory) - Method in class omero.cmd.HandleI
 
stop() - Method in class ome.formats.importer.transfers.TransferState
 
stop(long) - Method in class ome.formats.importer.transfers.TransferState
 
stop() - Method in class ome.formats.importer.util.ProportionalTimeEstimatorImpl
 
stop(long) - Method in class ome.formats.importer.util.ProportionalTimeEstimatorImpl
 
stop() - Method in interface ome.formats.importer.util.TimeEstimator
Stops the time counting and updates the internal time counter.
stop(long) - Method in interface ome.formats.importer.util.TimeEstimator
Stops the time counting and updates the internal updates the internal time counter and counter of total number of transmitted bytes.
stop(Current) - Method in class omero.grid.InteractiveProcessorI
Cancels the current process, nulls the value, and returns immediately if detach is false.
stopBefore(Iterable<String>) - Method in class omero.gateway.util.Requests.FindChildrenBuilder
 
stopBefore(Class<? extends IObject>...) - Method in class omero.gateway.util.Requests.FindChildrenBuilder
 
stopBefore(String...) - Method in class omero.gateway.util.Requests.FindChildrenBuilder
 
stopBefore(Iterable<String>) - Method in class omero.gateway.util.Requests.FindParentsBuilder
 
stopBefore(Class<? extends IObject>...) - Method in class omero.gateway.util.Requests.FindParentsBuilder
 
stopBefore(String...) - Method in class omero.gateway.util.Requests.FindParentsBuilder
 
StopBeforeHelper<X> - Class in omero.cmd.graphs
Calculates suggestions for the stopBefore property of FindParents and FindChildren.
StopBeforeHelper() - Constructor for class omero.cmd.graphs.StopBeforeHelper
 
store() - Method in class ome.formats.importer.ImportConfig.PassValue
 
store() - Method in class ome.formats.importer.ImportConfig.Value
Stores the current value back to some medium.
store - Variable in class ome.formats.OMEROImportFixture
Deprecated.
 
store - Variable in class ome.services.blitz.impl.MetadataStoreI
 
store(Object, Object) - Method in class omero.util.IceMapper
 
STRING_TO_RSTRING - Static variable in class omero.util.IceMapper
 
StrValue(String, ImportConfig) - Constructor for class ome.formats.importer.ImportConfig.StrValue
 
StrValue(String, ImportConfig, String) - Constructor for class ome.formats.importer.ImportConfig.StrValue
 
StrValue(String, ImportConfig, String, String) - Constructor for class ome.formats.importer.ImportConfig.StrValue
 
subcancel(HandleI.Cancel, DoAllI.X) - Method in class omero.cmd.basic.DoAllI
 
subfolderCount() - Method in class omero.gateway.model.FolderData
Get the number of sub folders
subhelper(Request, Status) - Method in class omero.cmd.Helper
Run IRequest.init(Helper) on a sub-command by creating a new Helper instance.
submit(Callable<T>) - Method in class omero.gateway.Gateway
Submits an async task
submit(SecurityContext, List<Request>, SecurityContext) - Method in class omero.gateway.Gateway
Executes the commands.
submit(SecurityContext, Request) - Method in class omero.gateway.Gateway
Directly submit a Request to the server
submit_async(AMD_JobHandle_submit, Job, Current) - Method in class ome.services.blitz.impl.JobHandleI
 
submit_async(AMD_Session_submit, Request, Current) - Method in class omero.cmd.SessionI
 
submit_async(AMD_Session_submit, Request, Current, Executor.Priority) - Method in class omero.cmd.SessionI
 
submitRequest(ServiceFactoryI, Request, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
 
submitRequest(ServiceFactoryI, Request, Current, Executor.Priority) - Method in class ome.services.blitz.repo.PublicRepositoryI
 
subscribe(String, ObjectPrx, Current) - Method in class ome.services.blitz.impl.ServiceFactoryI
 
sudo(Current, String) - Method in class ome.services.blitz.repo.PublicRepositoryI
Provide a Current like the given one, except with the request context session UUID replaced.
sudo() - Method in class omero.gateway.SecurityContext
Indicates to create a session for another user.
suggestChecksumAlgorithm(List<ChecksumAlgorithm>, Current) - Method in class ome.services.blitz.repo.ManagedRepositoryI
 
suggestExclusion(ServiceFactoryPrx, ImportContainer) - Method in class ome.formats.importer.exclusions.ClientPathExclusion
 
suggestExclusion(ServiceFactoryPrx, ImportContainer) - Method in interface ome.formats.importer.exclusions.FileExclusion
Given the current session attempt to discover if the given container should be skipped, i.e.
suggestExclusion(ServiceFactoryPrx, ImportContainer) - Method in class ome.formats.importer.exclusions.FilenameExclusion
 
suggestImportPaths(FsFile, FsFile, List<FsFile>, Class<? extends FormatReader>, ChecksumAlgorithm, Current) - Method in class ome.services.blitz.repo.ManagedRepositoryI
Take a relative path that the user would like to see in his or her upload area, and provide an import location instance whose paths correspond to existing directories corresponding to the sanitized file paths.
SymlinkFileTransfer - Class in ome.formats.importer.transfers
Local-only file transfer mechanism which makes use of soft-linking.
SymlinkFileTransfer() - Constructor for class ome.formats.importer.transfers.SymlinkFileTransfer
 
synchronizeJobs() - Method in class ome.services.blitz.util.CheckAllJobs
 
synchronizeLoginCache_async(AMD_IAdmin_synchronizeLoginCache, Current) - Method in class ome.services.blitz.impl.AdminI
 
SYSTEM - Static variable in class omero.gateway.model.GroupData
Identifies the System group.

T

TableData - Class in omero.gateway.model
A simple data 'container' for an OMERO.table
TableData(List<TableDataColumn>, List<List<Object>>) - Constructor for class omero.gateway.model.TableData
Creates a new instance
TableData(TableDataColumn[], Object[][]) - Constructor for class omero.gateway.model.TableData
Creates a new instance
TableDataColumn - Class in omero.gateway.model
Defines a column for a TableData object
TableDataColumn(String, int, Class<?>) - Constructor for class omero.gateway.model.TableDataColumn
Creates a new instance
TableDataColumn(String, String, int, Class<?>) - Constructor for class omero.gateway.model.TableDataColumn
Creates a new instance
TableResult - Class in omero.gateway.model
Store the element of the py-tables.
TableResult(Object[][], String[]) - Constructor for class omero.gateway.model.TableResult
Creates a new instance.
TableResult(Object[][], String[], String[]) - Constructor for class omero.gateway.model.TableResult
Creates a new instance.
TABLES_MIMETYPE - Static variable in class omero.gateway.facility.TablesFacility
The mimetype of an omero tables file
TablesFacility - Class in omero.gateway.facility
Facility to interact with OMERO.tables
TablesFacilityHelper - Class in omero.gateway.facility
Helper class which deals with the various conversions from omero.grid objects into plain Java, respectively gateway.model objects
TagAnnotationData - Class in omero.gateway.model
A tag annotation can either be related to an image or a tag but not to both at the same time.
TagAnnotationData(String, boolean) - Constructor for class omero.gateway.model.TagAnnotationData
Creates a new instance.
TagAnnotationData(String) - Constructor for class omero.gateway.model.TagAnnotationData
Creates a new instance.
TagAnnotationData(String, String) - Constructor for class omero.gateway.model.TagAnnotationData
Creates a new instance.
TagAnnotationData(String, String, boolean) - Constructor for class omero.gateway.model.TagAnnotationData
Creates a new instance.
TagAnnotationData(TagAnnotation) - Constructor for class omero.gateway.model.TagAnnotationData
Creates a new instance.
TagAnnotationData(TagAnnotation, List<CommentAnnotation>) - Constructor for class omero.gateway.model.TagAnnotationData
Creates a new instance.
take() - Method in class ome.services.throttling.Queue
 
takeover() - Method in class ome.services.blitz.repo.AbstractRepositoryI
Method called in a background thread which may end up waiting indefinitely on the repository lock file ("${omero.data.dir}/.omero/repository/${omero.db.uuid}/repo_uuid").
target - Variable in class ome.formats.importer.ImportConfig
 
target - Variable in class ome.formats.importer.ImportEvent.PROGRESS_EVENT
 
target2model - Variable in class omero.util.IceMapper
 
TargetBuilder - Class in ome.formats.importer.targets
 
TargetBuilder() - Constructor for class ome.formats.importer.targets.TargetBuilder
 
targetClass - Variable in class ome.formats.importer.ImportConfig
Deprecated.
targetId - Variable in class ome.formats.importer.ImportConfig
Deprecated.
TargetProcessor - Class in ome.formats.model
Processes the IObjectContainerStore and populates references for the linkage target object of choice.
TargetProcessor() - Constructor for class ome.formats.model.TargetProcessor
 
targetUsers(Iterable<Long>) - Method in class omero.gateway.util.Requests.Chown2Builder
 
targetUsers(RLong...) - Method in class omero.gateway.util.Requests.Chown2Builder
 
targetUsers(Long...) - Method in class omero.gateway.util.Requests.Chown2Builder
 
targetUsers(Experimenter) - Method in class omero.gateway.util.Requests.Chown2Builder
 
Task - Class in ome.services.throttling
Simple base task which contains logic for routing calls reflectively to ice_response and ice_exception of any AMD callback.
Task(Object, Current, boolean) - Constructor for class ome.services.throttling.Task
 
tearDown() - Method in class ome.formats.importer.ImportFixture
sets ImportLibrary, OMEROMetadataStoreClient, and file array to null.
tearDown() - Method in class ome.formats.OMEROImportFixture
Deprecated.
sets ImportLibrary, OMEROMetadataStore, and file array to null.
TemperatureI - Class in omero.model
Blitz wrapper around the Temperature class.
TemperatureI() - Constructor for class omero.model.TemperatureI
 
TemperatureI(double, UnitsTemperature) - Constructor for class omero.model.TemperatureI
 
TemperatureI(double, Unit<Temperature>) - Constructor for class omero.model.TemperatureI
 
TemperatureI(Temperature, Unit<Temperature>) - Constructor for class omero.model.TemperatureI
Copy constructor that converts the given Temperature based on the given ome-xml enum
TemperatureI(double, UnitsTemperature) - Constructor for class omero.model.TemperatureI
Copy constructor that converts the given Temperature based on the given ome.model enum
TemperatureI(Temperature, String) - Constructor for class omero.model.TemperatureI
Copy constructor that converts the given Temperature based on the given enum string.
TemperatureI(Temperature, UnitsTemperature) - Constructor for class omero.model.TemperatureI
Copy constructor that converts between units if possible.
TemperatureI(Temperature) - Constructor for class omero.model.TemperatureI
Convert a Bio-Formats Length to an OMERO Length.
TempFileManager - Class in omero.util
Creates temporary files and folders and makes a best effort to remove them on exit (or sooner).
TempFileManager() - Constructor for class omero.util.TempFileManager
Default constructor, passes "omero" to TempFileManager.TempFileManager(String)
TempFileManager(String) - Constructor for class omero.util.TempFileManager
Initializes a TempFileManager instance with the user's temporary directory containing the given prefix value.
TemplateImportTarget - Class in ome.formats.importer.targets
 
TemplateImportTarget() - Constructor for class ome.formats.importer.targets.TemplateImportTarget
 
templateRoot - Variable in class ome.services.blitz.repo.ManagedRepositoryI
 
TemporaryRepositoryI - Class in ome.services.blitz.repo
Simple repository service to make the ${java.io.tmpdir} available at runtime.
TemporaryRepositoryI(ObjectAdapter, Registry, Executor, Principal, PublicRepositoryI) - Constructor for class ome.services.blitz.repo.TemporaryRepositoryI
 
TermAnnotationData - Class in omero.gateway.model
Defines a Term Annotation.
TermAnnotationData(String) - Constructor for class omero.gateway.model.TermAnnotationData
Creates a new instance.
TermAnnotationData(TermAnnotation) - Constructor for class omero.gateway.model.TermAnnotationData
Creates a new instance.
TEXT - Static variable in class omero.gateway.model.FileAnnotationData
Identifies the Text file formats.
TextData - Class in omero.gateway.model
Represents a Text in the Euclidean space R2.
TextData(Shape) - Constructor for class omero.gateway.model.TextData
Creates a new instance of Text data from an existing shape.
TextData() - Constructor for class omero.gateway.model.TextData
Creates a new instance of TextData, creating a new TextI Object.
TextData(String, double, double) - Constructor for class omero.gateway.model.TextData
Creates a new instance of the TextData, sets the centre and major, minor axes.
TextualAnnotationData - Class in omero.gateway.model
Basic textual annotation used to add comments to a given object.
TextualAnnotationData() - Constructor for class omero.gateway.model.TextualAnnotationData
Creates a new instance.
TextualAnnotationData(String) - Constructor for class omero.gateway.model.TextualAnnotationData
Creates a new instance.
TextualAnnotationData(CommentAnnotation) - Constructor for class omero.gateway.model.TextualAnnotationData
Creates a new instance.
TF_2 - Static variable in class omero.gateway.util.TIFFFilter
Possible file extension.
TF_8 - Static variable in class omero.gateway.util.TIFFFilter
Possible file extension.
ThrottlingStrategy - Interface in ome.services.throttling
Strategy interface for controlling the execution of blitz methods.
throwIfInitialized(Object) - Method in class ome.services.blitz.util.BlitzConfiguration
If this configuration is finished and BlitzConfiguration.communicator is not-null, throw a IllegalStateException
thumbnailExists_async(AMD_ThumbnailStore_thumbnailExists, RInt, RInt, Current) - Method in class ome.services.blitz.impl.ThumbnailStoreI
 
THUMBNAILS_GENERATED(int, ImportContainer, IObject, Long, int, ImportSize, Integer, Integer, Long) - Constructor for class ome.formats.importer.ImportEvent.THUMBNAILS_GENERATED
 
ThumbnailStoreI - Class in ome.services.blitz.impl
Implementation of the ThumbnailStore service.
ThumbnailStoreI(ThumbnailStore, BlitzExecutor) - Constructor for class ome.services.blitz.impl.ThumbnailStoreI
 
tie() - Method in class ome.services.blitz.repo.ManagedRepositoryI
 
tie() - Method in class ome.services.blitz.repo.PublicRepositoryI
Wrap the current instance with an TieBase so that it can be turned into a proxy.
TieAware - Interface in omero.util
Servant which is aware of the TieBase-instance which it belongs to and will have it injected on instantiation.
TIF - Static variable in class omero.gateway.util.TIFFFilter
Possible file extension.
TIFF - Static variable in class omero.gateway.util.TIFFFilter
Possible file extension.
TIFFFilter - Class in omero.gateway.util
Methods to check if an image is a TIFF image.
TIFFFilter() - Constructor for class omero.gateway.util.TIFFFilter
 
TileData - Interface in omero.util
Access strategy which can be implemented by diverse resources
TileLoop - Class in omero.util
 
TileLoop() - Constructor for class omero.util.TileLoop
 
TileLoopIteration - Interface in omero.util
A single iteration of a tile for each loop.
TimeAnnotationData - Class in omero.gateway.model
Basic time annotation.
TimeAnnotationData() - Constructor for class omero.gateway.model.TimeAnnotationData
Creates a default instance.
TimeAnnotationData(TimestampAnnotation) - Constructor for class omero.gateway.model.TimeAnnotationData
Creates a new instance.
TimeEstimator - Interface in ome.formats.importer.util
Estimates the time left (ETA) during image resource upload to the server.
TimeI - Class in omero.model
Blitz wrapper around the Time class.
TimeI() - Constructor for class omero.model.TimeI
 
TimeI(double, UnitsTime) - Constructor for class omero.model.TimeI
 
TimeI(double, Unit<Time>) - Constructor for class omero.model.TimeI
 
TimeI(Time, Unit<Time>) - Constructor for class omero.model.TimeI
Copy constructor that converts the given Time based on the given ome-xml enum
TimeI(double, UnitsTime) - Constructor for class omero.model.TimeI
Copy constructor that converts the given Time based on the given ome.model enum
TimeI(Time, String) - Constructor for class omero.model.TimeI
Copy constructor that converts the given Time based on the given enum string.
TimeI(Time, UnitsTime) - Constructor for class omero.model.TimeI
Copy constructor that converts between units if possible.
TimeI(Time) - Constructor for class omero.model.TimeI
Convert a Bio-Formats Length to an OMERO Length.
timeLeft - Variable in class ome.formats.importer.ImportEvent.FILE_UPLOAD_BYTES
 
TimelineI - Class in ome.services.blitz.impl
implementation of the ITimeline service interface.
TimelineI(BlitzExecutor) - Constructor for class ome.services.blitz.impl.TimelineI
 
timeOfEvent(Event) - Method in class omero.gateway.model.DataObject
 
TimingI - Class in omero.cmd.basic
Diagnostic tool for testing call overhead.
TimingI() - Constructor for class omero.cmd.basic.TimingI
 
tmpdir() - Method in class omero.util.TempFileManager
Returns a platform-specific user-writable temporary directory.
to - Variable in class ome.services.blitz.util.ConvertToBlitzExceptionMessage
 
toEnum(Class<E>, Class<I>, Collection<String>) - Static method in class omero.gateway.util.Utils
Convert a list of String values to their corresponding omero.model.enums instances.
toFile(File) - Method in class ome.services.blitz.repo.path.FsFile
Convert this instance to a File relative to the given File.
toGroup(long) - Method in class omero.gateway.util.Requests.Chgrp2Builder
 
toGroup(RLong) - Method in class omero.gateway.util.Requests.Chgrp2Builder
 
toGroup(ExperimenterGroup) - Method in class omero.gateway.util.Requests.Chgrp2Builder
 
toJavaType(RInt) - Method in class ome.services.blitz.impl.MetadataStoreI
Transforms an OMERO RType into the corresponding Java type.
toJavaType(RLong) - Method in class ome.services.blitz.impl.MetadataStoreI
Transforms an OMERO RType into the corresponding Java type.
toJavaType(RBool) - Method in class ome.services.blitz.impl.MetadataStoreI
Transforms an OMERO RType into the corresponding Java type.
toJavaType(RFloat) - Method in class ome.services.blitz.impl.MetadataStoreI
Transforms an OMERO RType into the corresponding Java type.
toJavaType(RDouble) - Method in class ome.services.blitz.impl.MetadataStoreI
Transforms an OMERO RType into the corresponding Java type.
toJavaType(RString) - Method in class ome.services.blitz.impl.MetadataStoreI
Transforms an OMERO RType into the corresponding Java type.
token - Variable in class omero.cmd.SessionI
Token in the form of a UUID for securing method invocations.
TOKEN_KEY - Static variable in class omero.cmd.CallContext
 
toLog() - Method in class ome.formats.importer.ImportCandidates.SCANNING
 
toLog() - Method in class ome.formats.importer.ImportEvent.FILE_UPLOAD_BYTES
 
toLog() - Method in class ome.formats.importer.ImportEvent.IMPORT_DONE
 
toLog() - Method in class ome.formats.importer.ImportEvent.IMPORT_STARTED
 
toLog() - Method in class ome.formats.importer.ImportEvent.IMPORT_STEP
 
toLog() - Method in class ome.formats.importer.ImportEvent.LOADED_IMAGE
 
toLog() - Method in class ome.formats.importer.ImportEvent.LOADING_IMAGE
 
toLog() - Method in class ome.formats.importer.ImportEvent.POST_UPLOAD_EVENT
 
toLog() - Method in class ome.formats.importer.ImportEvent.PROGRESS_EVENT
 
toLog() - Method in class ome.formats.importer.ImportEvent
 
toLog() - Method in class ome.formats.importer.util.ErrorHandler.FILE_EXCEPTION
 
toLog() - Method in class ome.formats.importer.util.ErrorHandler.INTERNAL_EXCEPTION
 
toLog() - Method in class ome.formats.importer.util.ErrorHandler.UNKNOWN_FORMAT
 
toLog() - Method in class ome.formats.importer.util.ErrorHandler.UNREADABLE_FILE
 
toNumber(double) - Static method in class omero.gateway.model.ShapeData
Returns a double array as a number attribute value.
TOO_MANY_CLAUSES - Static variable in class omero.gateway.model.SearchResultCollection
The search has to many clauses, e.g. a 'a*' search term would expand to too many single clauses
TOO_MANY_RESULTS_ERROR - Static variable in class omero.gateway.model.SearchResultCollection
The search has to many results
toPerms(String) - Method in class omero.gateway.util.Requests.Chmod2Builder
 
topicManager - Variable in class ome.services.blitz.fire.SessionManagerI
 
TopicManager - Interface in ome.services.blitz.fire
Local dispatcher to TopicManager
TopicManager.Impl - Class in ome.services.blitz.fire
 
TopicManager.TopicMessage - Class in ome.services.blitz.fire
 
TopicMessage(Object, String, ObjectPrxHelperBase, String, Object...) - Constructor for class ome.services.blitz.fire.TopicManager.TopicMessage
 
topicOrNull(String) - Method in class ome.services.blitz.fire.TopicManager.Impl
 
toPoints(Point2D.Double[]) - Static method in class omero.gateway.model.ShapeData
Returns a Point2D.Double array as a Points attribute value. as specified in http://www.w3.org/TR/SVGMobile12/shapes.html#PointsBNF
toRType(Integer) - Method in class ome.formats.OMEROMetadataStoreClient
Transforms a Java type into the corresponding OMERO RType.
toRType(NonNegativeInteger) - Method in class ome.formats.OMEROMetadataStoreClient
Transforms a Java type into the corresponding OMERO RType.
toRType(NonNegativeLong) - Method in class ome.formats.OMEROMetadataStoreClient
Transforms a Java type into the corresponding OMERO RType.
toRType(PositiveFloat) - Method in class ome.formats.OMEROMetadataStoreClient
Transforms a Java type into the corresponding OMERO RType.
toRType(PercentFraction) - Method in class ome.formats.OMEROMetadataStoreClient
Transforms a Java type into the corresponding OMERO RType.
toRType(Long) - Method in class ome.formats.OMEROMetadataStoreClient
Transforms a Java type into the corresponding OMERO RType.
toRType(String) - Method in class ome.formats.OMEROMetadataStoreClient
Transforms a Java type into the corresponding OMERO RType.
toRType(Boolean) - Method in class ome.formats.OMEROMetadataStoreClient
Transforms a Java type into the corresponding OMERO RType.
toRType(Double) - Method in class ome.formats.OMEROMetadataStoreClient
Transforms a Java type into the corresponding OMERO RType.
toRType(Float) - Method in class ome.formats.OMEROMetadataStoreClient
Transforms a Java type into the corresponding OMERO RType.
toRType(Timestamp) - Method in class ome.formats.OMEROMetadataStoreClient
Transforms a Java type into the corresponding OMERO RType.
toRType(NamingConvention) - Method in class ome.formats.OMEROMetadataStoreClient
Transforms a Java type into the corresponding OMERO RType.
toRType(AffineTransform) - Method in class ome.formats.OMEROMetadataStoreClient
Transforms a Java type into the corresponding OMERO RType.
toRType(Color) - Method in class ome.formats.OMEROMetadataStoreClient
Transforms a Java type into the corresponding OMERO RType.
toRType(Object) - Method in class omero.util.IceMapper
 
toString() - Method in exception ome.formats.enums.EnumerationException
 
toString() - Method in class ome.formats.importer.ImportConfig.Value
 
toString() - Method in enum ome.formats.Index
 
toString() - Method in exception ome.formats.model.ModelException
 
toString() - Method in class ome.services.blitz.repo.CheckedPath
 
toString() - Method in class ome.services.blitz.repo.path.FsFile
Provides repository path with components separated by FsFile.separatorChar.
toString() - Method in class ome.services.throttling.Task
 
toString() - Method in class omero.cmd.SessionI
 
toString() - Method in class omero.gateway.model.DataObject
Overridden to return the name of the class and the object id.
toString() - Method in class omero.gateway.model.FolderData
 
toString() - Method in class omero.gateway.model.PermissionData
 
toString() - Method in class omero.gateway.model.ROICoordinate
Returns the string of the coordinates.
toString() - Method in class omero.gateway.model.SearchResult
 
toString() - Method in class omero.gateway.model.SearchResultCollection
 
toString() - Method in class omero.gateway.model.TableData
 
toString() - Method in class omero.gateway.model.TableDataColumn
 
toString() - Method in class omero.gateway.SecurityContext
 
toString() - Method in class omero.gateway.ServerInformation
 
toString() - Method in class omero.gateway.UserCredentials
Formats user name and password.
toString() - Method in class omero.log.LogMessage
Returns the current content of the message.
toString() - Method in class omero.model.ElectricPotentialI
 
toString() - Method in class omero.model.FrequencyI
 
toString() - Method in class omero.model.LengthI
 
toString() - Method in class omero.model.PermissionsI
produces a String representation of the PermissionsI similar to those on a Unix filesystem.
toString() - Method in class omero.model.PowerI
 
toString() - Method in class omero.model.PressureI
 
toString() - Method in class omero.model.TemperatureI
 
toString() - Method in class omero.model.TimeI
 
toString() - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
total - Variable in class ome.formats.importer.ImportEvent.COUNT_EVENT
 
total - Variable in class ome.formats.importer.ImportEvent.PROGRESS_EVENT
 
totalErrors - Variable in class ome.formats.importer.util.ErrorHandler
 
totalFiles - Variable in class ome.formats.importer.ImportCandidates.SCANNING
 
toUser(long) - Method in class omero.gateway.util.Requests.Chown2Builder
 
toUser(RLong) - Method in class omero.gateway.util.Requests.Chown2Builder
 
toUser(Experimenter) - Method in class omero.gateway.util.Requests.Chown2Builder
 
transfer - Variable in class ome.formats.importer.cli.CommandLineImporter
FileTransfer mechanism to be used for uploading
transfer(TransferState) - Method in class ome.formats.importer.transfers.AbstractExecFileTransfer
"Transfer" files by soft-linking them into place.
transfer(TransferState) - Method in interface ome.formats.importer.transfers.FileTransfer
Transfers a file and returns the appropriate checksum string for the source file.
transfer(TransferState) - Method in class ome.formats.importer.transfers.UploadFileTransfer
 
TransferFacility - Class in omero.gateway.facility
Facility which provides data transfer functionality, i.e. download files and upload/import files.
TransferFacilityHelper - Class in omero.gateway.facility
Encapsulates some functionality needed by the TransferFacility
TransferState - Class in ome.formats.importer.transfers
Non-thread-safe argument holder for FileTransfer implementations.
TransferState(File, int, int, ImportProcessPrx, ImportLibrary, TimeEstimator, ChecksumProvider, byte[]) - Constructor for class ome.formats.importer.transfers.TransferState
State of the current file transfer.
transform(Function<String, String>) - Method in class ome.services.blitz.repo.path.FsFile
Transform each path component with the given transformer.
transformationMap - Variable in class ome.services.blitz.repo.path.FilePathRestrictions
 
transformationMatrix - Variable in class ome.services.blitz.repo.path.FilePathRestrictions
 
transformAwtShape(Shape, AffineTransform) - Static method in class omero.model.SmartShape.Util
 
TransmittanceRange_CutIn - Static variable in class ome.formats.model.UnitsFactory
 
TransmittanceRange_CutInTolerance - Static variable in class ome.formats.model.UnitsFactory
 
TransmittanceRange_CutOut - Static variable in class ome.formats.model.UnitsFactory
 
TransmittanceRange_CutOutTolerance - Static variable in class ome.formats.model.UnitsFactory
 
treeList(String, Current) - Method in class ome.services.blitz.repo.PublicRepositoryI
 
treeList(String, CheckedPath, Current) - Method in interface ome.services.blitz.repo.RepositoryDao
 
treeList(String, CheckedPath, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
 
trimPaths(FsFile, List<FsFile>, Class<? extends FormatReader>) - Method in class ome.services.blitz.repo.ManagedRepositoryI
Trim off the start of long client-side paths.
truncate_async(AMD_RawFileStore_truncate, long, Current) - Method in class ome.services.blitz.impl.RawFileStoreI
 
tryClass(String) - Method in class ome.formats.importer.targets.TargetBuilder
 
tSize - Variable in class ome.formats.importer.ImportSize
 
type(Iterable<String>) - Method in class omero.gateway.util.Requests.DiskUsageBuilder
 
type(Class<? extends IObject>...) - Method in class omero.gateway.util.Requests.DiskUsageBuilder
 
type(String...) - Method in class omero.gateway.util.Requests.DiskUsageBuilder
 
type() - Method in interface omero.rtypes.Conversion
Specifies the type that can be expected from the rtypes.Conversion.convert(IceMapper) method.
TypesI - Class in ome.services.blitz.impl
Implementation of the ITypes service.
TypesI(ITypes, BlitzExecutor) - Constructor for class ome.services.blitz.impl.TypesI
 

U

UINT16_TYPE - Static variable in class omero.gateway.model.PixelsData
Identifies the type used to store pixel values.
UINT32_TYPE - Static variable in class omero.gateway.model.PixelsData
Identifies the type used to store pixel values.
UINT8_TYPE - Static variable in class omero.gateway.model.PixelsData
Identifies the type used to store pixel values.
UINT_16 - Static variable in class omero.gateway.rnd.DataSink
Identifies the type used to store pixel values.
UINT_32 - Static variable in class omero.gateway.rnd.DataSink
Identifies the type used to store pixel values.
UINT_8 - Static variable in class omero.gateway.rnd.DataSink
Identifies the type used to store pixel values.
UintConverter - Class in omero.gateway.rnd
Packs a sequence of bytes representing an unsigned big-endian integer into an integer value of appropriate integer type.
UintConverter() - Constructor for class omero.gateway.rnd.UintConverter
 
unique() - Method in class omero.sys.ParametersI
 
UnitsFactory - Class in ome.formats.model
Utility class to generate and convert unit objects.
UnitsFactory() - Constructor for class ome.formats.model.UnitsFactory
 
UNKNOWN - Static variable in class omero.gateway.model.FileAnnotationData
Indicates that the format is not recognized.
UNKNOWN_FORMAT(String, Exception, Object) - Constructor for class ome.formats.importer.util.ErrorHandler.UNKNOWN_FORMAT
 
unlink_async(AMD_IContainer_unlink, List<IObject>, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI
 
unload(Current) - Method in class omero.model.DetailsI
 
unload(Current) - Method in class omero.model.PermissionsI
 
unloadCollections(IObject) - Static method in class omero.gateway.util.ModelMapper
Unlinks the collections linked to the specified IObject.
UnloadedCollectionException - Exception in omero
 
UnloadedCollectionException(String) - Constructor for exception omero.UnloadedCollectionException
 
UnloadedEntityException - Exception in omero
 
UnloadedEntityException(String) - Constructor for exception omero.UnloadedEntityException
 
UNMAPPED - Static variable in class omero.util.IceMapper
Specifies a return type which should not be parsed.
unordered_async(AMD_Search_unordered, Current) - Method in class ome.services.blitz.impl.SearchI
 
UNREADABLE_FILE(String, Exception, Object) - Constructor for class ome.formats.importer.util.ErrorHandler.UNREADABLE_FILE
 
unregister(String, ObjectPrx) - Method in class ome.services.blitz.fire.TopicManager.Impl
 
unregister(String, ObjectPrx) - Method in interface ome.services.blitz.fire.TopicManager
 
unregisterCallback(ProcessCallbackPrx, Current) - Method in class ome.services.blitz.impl.ScriptProcessI
 
unregisterServant(Identity) - Method in class omero.cmd.SessionI
unregisterServant(Identity, ObjectAdapter, ServantHolder) - Static method in class omero.cmd.SessionI
Reverts all the additions made by SessionI.registerServant(Ice.Identity, Ice.Object) Now called by SessionManagerI in response to an UnregisterServantMessage.
UnregisterServantMessage - Class in ome.services.blitz.util
InternalMessage raised when a servant should be removed from the adapter.
UnregisterServantMessage(Object, Current, ServantHolder) - Constructor for class ome.services.blitz.util.UnregisterServantMessage
 
unsafeNames - Variable in class ome.services.blitz.repo.path.FilePathRestrictions
 
unsafePrefixes - Variable in class ome.services.blitz.repo.path.FilePathRestrictions
 
unsafeSuffixes - Variable in class ome.services.blitz.repo.path.FilePathRestrictions
 
unsetGroupOwner_async(AMD_IAdmin_unsetGroupOwner, ExperimenterGroup, Experimenter, Current) - Method in class ome.services.blitz.impl.AdminI
 
unwrap(RType) - Static method in class omero.rtypes
Descends into data structures unwrapping all RType objects as it goes.
unwrap(RType, Map<RType, Object>) - Static method in class omero.rtypes
Descends into data structures wrapping all elements as it goes.
unwrapCollection(Collection<RType>, Collection<Object>, Map<RType, Object>) - Static method in class omero.rtypes
 
unwrapRawFileBean(RawFileStore) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
Loads
update(IObservable, ImportEvent) - Method in class ome.formats.importer.cli.LoggingImportMonitor
 
update(IObservable, ImportEvent) - Method in interface ome.formats.importer.IObserver
Update observable on event
update(IObservable, ImportEvent) - Method in class ome.formats.importer.util.ErrorHandler
 
update - Variable in class omero.cmd.admin.UpdateSessionTimeoutRequestI
 
updateCodomainMap_async(AMD_RenderingEngine_updateCodomainMap, CodomainMapContext, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
updateCollection(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
updated - Variable in class omero.cmd.admin.UpdateSessionTimeoutRequestI
 
updateDataObject_async(AMD_IContainer_updateDataObject, IObject, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI
 
updateDataObjects_async(AMD_IContainer_updateDataObjects, List<IObject>, Parameters, Current) - Method in class ome.services.blitz.impl.ContainerI
 
updateEntity(String) - Method in class org.hibernate.stat.ConcurrentStatisticsImpl
 
updateEnumeration_async(AMD_ITypes_updateEnumeration, IObject, Current) - Method in class ome.services.blitz.impl.TypesI
 
updateEnumerations_async(AMD_ITypes_updateEnumerations, List<IObject>, Current) - Method in class ome.services.blitz.impl.TypesI
 
updateExperimenter_async(AMD_IAdmin_updateExperimenter, Experimenter, Current) - Method in class ome.services.blitz.impl.AdminI
 
updateExperimenterWithPassword_async(AMD_IAdmin_updateExperimenterWithPassword, Experimenter, RString, Current) - Method in class ome.services.blitz.impl.AdminI
 
updateField(Session, String, RLong, boolean) - Method in class omero.cmd.admin.UpdateSessionTimeoutRequestI
 
updateFileSize(OriginalFile, long) - Method in class ome.formats.OMEROMetadataStoreClient
 
updateFlexReaderServerMaps() - Method in class ome.formats.importer.util.IniFileLoader
Updates the Flex reader server maps from the configuration file.
updateGroup_async(AMD_IAdmin_updateGroup, ExperimenterGroup, Current) - Method in class ome.services.blitz.impl.AdminI
 
UpdateI - Class in ome.services.blitz.impl
Implementation of the IUpdate service.
UpdateI(IUpdate, BlitzExecutor) - Constructor for class ome.services.blitz.impl.UpdateI
 
updateJob(Job, String, String, Current) - Method in interface ome.services.blitz.repo.RepositoryDao
Set both the message and the status of the given job.
updateJob(Job, String, String, Current) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
 
updateMinMax(int, byte[], int) - Method in class ome.formats.importer.OMEROWrapper
 
updateObject(SecurityContext, IObject, Parameters) - Method in class omero.gateway.facility.DataManagerFacility
Updates the specified object.
updateObjects(SecurityContext, List<IObject>, Parameters) - Method in class omero.gateway.facility.DataManagerFacility
Updates the specified IObjects and returned the updated IObjects.
updateObjects_async(AMD_MetadataStore_updateObjects, IObjectContainer[], Current) - Method in class ome.services.blitz.impl.MetadataStoreI
 
updatePixels(List<Pixels>) - Method in class ome.formats.OMEROMetadataStoreClient
Updates a list of Pixels.
updateReferences_async(AMD_MetadataStore_updateReferences, Map<String, String[]>, Current) - Method in class ome.services.blitz.impl.MetadataStoreI
 
updateSelf_async(AMD_IAdmin_updateSelf, Experimenter, Current) - Method in class ome.services.blitz.impl.AdminI
 
updateSession() - Method in class omero.cmd.admin.UpdateSessionTimeoutRequestI
 
UpdateSessionTimeoutRequestI - Class in omero.cmd.admin
 
UpdateSessionTimeoutRequestI(CurrentDetails, SessionManager, SecuritySystem) - Constructor for class omero.cmd.admin.UpdateSessionTimeoutRequestI
 
UpdateSessionTimeoutRequestI.Factory - Class in omero.cmd.admin
 
updateSettings_async(AMD_RenderingEngine_updateSettings, RenderingDef, Current) - Method in class ome.services.blitz.impl.RenderingEngineI
 
updateTable(SecurityContext, TableData) - Method in class omero.gateway.facility.TablesFacility
Saves the (modified) TableData back to the server.
updateUsedFilesTotalSize() - Method in class ome.formats.importer.ImportContainer
 
upload(File) - Method in class omero.client
 
upload(File, OriginalFile) - Method in class omero.client
 
upload(File, OriginalFile, Integer) - Method in class omero.client
Utility method to upload a file to the server
uploadBytes(long) - Method in class ome.formats.importer.transfers.TransferState
Raise the ImportEvent.FILE_UPLOAD_BYTES event to all observers.
uploadComplete(long) - Method in class ome.formats.importer.transfers.TransferState
Raise the ImportEvent.FILE_UPLOAD_COMPLETE event to all observers.
uploadedBytes - Variable in class ome.formats.importer.ImportEvent.FILE_UPLOAD_EVENT
 
uploadFile(ImportProcessPrx, String[], int, TimeEstimator) - Method in class ome.formats.importer.ImportLibrary
 
uploadFile(ImportProcessPrx, String[], int, ChecksumProviderFactory, TimeEstimator, byte[]) - Method in class ome.formats.importer.ImportLibrary
 
uploadFile(ErrorContainer) - Method in class ome.formats.importer.util.ErrorHandler
Upload a single ErrorContainer.
uploadFiles(String, int, ErrorContainer) - Method in class ome.formats.importer.util.FileUploader
Upload files from error container to url
uploadFileset(Fileset, ImportSettings, Current) - Method in class ome.services.blitz.repo.ManagedRepositoryI
Return a template based directory path.
uploadFilesToRepository(String[], ImportProcessPrx) - Method in class ome.formats.importer.ImportLibrary
Upload files to the managed repository.
UploadFileTransfer - Class in ome.formats.importer.transfers
Traditional file transfer mechanism which uploads files using the API.
UploadFileTransfer() - Constructor for class ome.formats.importer.transfers.UploadFileTransfer
 
UploadMask - Class in omero.gateway.util
Uploaded for masks.
UploadMask(long) - Constructor for class omero.gateway.util.UploadMask
Creates a new instance.
uploadMask_async(AMD_IRoi_uploadMask, long, int, int, byte[], Current) - Method in class ome.services.blitz.impl.RoiI
 
uploadMyUserPhoto_async(AMD_IAdmin_uploadMyUserPhoto, String, String, byte[], Current) - Method in class ome.services.blitz.impl.AdminI
 
uploadOfficialScript_async(AMD_IScript_uploadOfficialScript, String, String, Current) - Method in class ome.services.blitz.impl.ScriptI
 
UploadRmFileTransfer - Class in ome.formats.importer.transfers
Version of the default UploadFileTransfer which deletes all files in a transfer set if the upload is successful.
UploadRmFileTransfer() - Constructor for class ome.formats.importer.transfers.UploadRmFileTransfer
 
uploadScript_async(AMD_IScript_uploadScript, String, String, Current) - Method in class ome.services.blitz.impl.ScriptI
Upload script to the server.
uploadStarted() - Method in class ome.formats.importer.transfers.TransferState
Raise the ImportEvent.FILE_UPLOAD_STARTED event to all observers.
usage() - Static method in class ome.formats.importer.cli.CommandLineImporter
Prints usage to STDERR and exits with return code 1.
useCustomImageNaming - Variable in class ome.formats.importer.ImportConfig
 
usedFiles - Variable in class ome.formats.importer.util.ErrorHandler.FILE_EXCEPTION
 
usedFiles - Variable in class ome.formats.importer.util.ErrorHandler.INTERNAL_EXCEPTION
 
UsedFilesRequestI - Class in omero.cmd.fs
Lists the IDs of the original files associated with an image.
UsedFilesRequestI(PixelsService) - Constructor for class omero.cmd.fs.UsedFilesRequestI
Construct a new used files request.
useFirstAcceptable() - Method in class ome.services.blitz.repo.path.MakeNextDirectory
Use the first acceptable path (that with the lowest index for MakeNextDirectory.getPathFor(long)) and return the corresponding subdirectories.
useFullPath - Variable in class ome.formats.importer.ImportConfig
Deprecated.
usePath(List<String>) - Method in class ome.services.blitz.repo.path.MakeNextDirectory
Actually use the path.
USER - Static variable in class omero.gateway.model.GroupData
Identifies the User group.
UserCredentials - Class in omero.gateway
Holds username and password of a user
UserCredentials() - Constructor for class omero.gateway.UserCredentials
Creates an empty instance
UserCredentials(String, String) - Constructor for class omero.gateway.UserCredentials
Creates a new instance
username - Variable in class loci.ome.io.OMECredentials
Deprecated.
 
username - Variable in class ome.formats.importer.ImportConfig
 
username() - Method in class omero.util.TempFileManager
Returns the current OS-user's name.
userPixels - Variable in class ome.formats.importer.ImportConfig
 
userSpecifiedDescription - Variable in class ome.formats.importer.ImportConfig
 
userSpecifiedName - Variable in class ome.formats.importer.ImportConfig
 
Util() - Constructor for class omero.model.SmartShape.Util
 
Utils - Class in omero.gateway.util
Collection of methods used to set the name of files to import and to handle enumerations.
Utils() - Constructor for class omero.gateway.util.Utils
 
uuid - Variable in class ome.services.blitz.fire.Ring
UUID for this cluster node.
uuid() - Method in class ome.services.blitz.fire.Ring
 
uuid() - Method in interface ome.services.blitz.redirect.Redirector.Context
The UUID for the local node which will be used as the redirect lookup string for this Redirector.Context.
uuid - Variable in class ome.services.roi.GeomTool
 

V

validateFilePathNaming(FsFile) - Method in class ome.services.blitz.repo.path.FilePathNamingValidator
Validate the given FS file.
validateFilePathNaming(String) - Method in class ome.services.blitz.repo.path.FilePathNamingValidator
Validate the given file path.
validateScript_async(AMD_IScript_validateScript, Job, List<IObject>, Current) - Method in class ome.services.blitz.impl.ScriptI
 
valueOf(String) - Static method in enum ome.formats.importer.exclusions.AbstractFileExclusion.Exclusion
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ome.formats.importer.ImportConfig.VersionInfo
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ome.formats.importer.transfers.AbstractFileTransfer.Transfers
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ome.formats.Index
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ome.services.blitz.repo.path.FilePathRestrictionInstance
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum omero.gateway.exception.ConnectionStatus
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum omero.gateway.model.SearchScope
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum omero.grid.ProcessCallbackI.Action
Returns the enum constant of this type with the specified name.
values() - Static method in enum ome.formats.importer.exclusions.AbstractFileExclusion.Exclusion
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Method in class ome.formats.importer.ImportConfig
 
values() - Static method in enum ome.formats.importer.ImportConfig.VersionInfo
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ome.formats.importer.transfers.AbstractFileTransfer.Transfers
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ome.formats.Index
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ome.services.blitz.repo.path.FilePathRestrictionInstance
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum omero.gateway.exception.ConnectionStatus
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum omero.gateway.model.SearchScope
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum omero.grid.ProcessCallbackI.Action
Returns an array containing the constants of this enum type, in the order they are declared.
verifyChecksums(List<Long>, Current) - Method in class ome.services.blitz.repo.ManagedRepositoryI
 
verifyUpload(List<String>, Current) - Method in class ome.services.blitz.repo.ManagedImportProcessI
 
Version - Class in ome.formats.importer
Deprecated.
As of release 5.3.2
Version() - Constructor for class ome.formats.importer.Version
Deprecated.
 
versionNote - Static variable in class ome.formats.importer.Version
Deprecated.
 
VOID - Static variable in class omero.util.IceMapper
 

W

waitCompleted(ImportConfig) - Static method in class ome.formats.importer.cli.CommandLineImporter
Look for all ImportProcessPrx in the current session and close them if they return a non-null Response (i.e. they are done).
waitOnFinishedDone() - Method in class omero.cmd.CmdCallbackI
 
waitOnInitialization() - Method in class omero.cmd.CmdCallbackI
Subclasses which must perform their own initialization before CmdCallbackI.onFinished(Response, Status, Current) is called should call CmdCallbackI.waitOnInitialization() before accessing any initialized state.
warn(String, Object...) - Method in class omero.cmd.Helper
 
warn(Object, String) - Method in interface omero.log.Logger
Logs a warn message.
warn(Object, LogMessage) - Method in interface omero.log.Logger
Logs a warn message.
warn(Object, String) - Method in class omero.log.NullLogger
 
warn(Object, LogMessage) - Method in class omero.log.NullLogger
 
warn(Object, String) - Method in class omero.log.SimpleLogger
 
warn(Object, LogMessage) - Method in class omero.log.SimpleLogger
 
wasCancelled() - Method in class ome.formats.importer.ImportCandidates
 
WELL_COLUMN_INDEX - Static variable in class omero.gateway.model.TableResult
Identifies the index of the Well column.
WellData - Class in omero.gateway.model
The data that makes up an OME Well and the Experimenter that owns this Well.
WellData() - Constructor for class omero.gateway.model.WellData
Creates a new instance.
WellData(Well) - Constructor for class omero.gateway.model.WellData
Creates a new instance.
WellProcessor - Class in ome.formats.model
Processes the Wells of an IObjectContainerStore and ensures that the Plate has been populated and that it is validated and that if any PlateAcquisition objects are in the hierarchy that they have a name.
WellProcessor() - Constructor for class ome.formats.model.WellProcessor
 
WELLS - Static variable in class omero.gateway.model.PlateData
Identifies the PlateI.WELLS field.
WellSample_PositionX - Static variable in class ome.formats.model.UnitsFactory
 
WellSample_PositionY - Static variable in class ome.formats.model.UnitsFactory
 
WellSampleData - Class in omero.gateway.model
The data that makes up an OME WellSample along with links to its images and the Experimenter that owns this WellSample.
WellSampleData() - Constructor for class omero.gateway.model.WellSampleData
Creates a new instance.
WellSampleData(WellSample) - Constructor for class omero.gateway.model.WellSampleData
Creates a new instance.
wrap(Hashtable<String, Object>) - Method in class omero.cmd.fs.OriginalMetadataRequestI
Use IceMapper to convert from Object instances in the given Hashtable to RType instances.
wrap(Object) - Static method in class omero.rtypes
Descends into data structures wrapping all elements as it goes.
wrap(Object, Map<Object, RType>) - Static method in class omero.rtypes
Descends into data structures wrapping all elements as it goes.
WrappableRequest<X> - Interface in omero.cmd.graphs
Requests that can be wrapped by a SkipHeadI request.
wrapSecurityViolation(SecurityViolation) - Method in class ome.services.blitz.repo.RepositoryDaoImpl
 
write_async(AMD_RawFileStore_write, byte[], long, int, Current) - Method in class ome.services.blitz.impl.RawFileStoreI
 
write_async(AMD_RawFileStore_write, byte[], long, int, Current) - Method in class ome.services.blitz.repo.RepoRawFileStoreI
 
writeLine(String) - Method in class ome.services.blitz.repo.FileMaker
 
wSize - Variable in class ome.formats.importer.ImportSize
 

X

XML - Static variable in class omero.gateway.model.FileAnnotationData
Identifies the XML file formats.
XMLAnnotationData - Class in omero.gateway.model
Defines an XML Annotation.
XMLAnnotationData() - Constructor for class omero.gateway.model.XMLAnnotationData
Creates a new instance.
XMLAnnotationData(String) - Constructor for class omero.gateway.model.XMLAnnotationData
Creates a new instance.
XMLAnnotationData(XmlAnnotation) - Constructor for class omero.gateway.model.XMLAnnotationData
Creates a new instance.
xmlElectricPotentialEnumToOMERO(Unit<ElectricPotential>) - Static method in class ome.formats.model.UnitsFactory
 
xmlElectricPotentialEnumToOMERO(String) - Static method in class ome.formats.model.UnitsFactory
 
xmlFrequencyEnumToOMERO(Unit<Frequency>) - Static method in class ome.formats.model.UnitsFactory
 
xmlFrequencyEnumToOMERO(String) - Static method in class ome.formats.model.UnitsFactory
 
xmlLengthEnumToOMERO(Unit<Length>) - Static method in class ome.formats.model.UnitsFactory
 
xmlLengthEnumToOMERO(String) - Static method in class ome.formats.model.UnitsFactory
 
xmlPowerEnumToOMERO(Unit<Power>) - Static method in class ome.formats.model.UnitsFactory
 
xmlPowerEnumToOMERO(String) - Static method in class ome.formats.model.UnitsFactory
 
xmlPressureEnumToOMERO(Unit<Pressure>) - Static method in class ome.formats.model.UnitsFactory
 
xmlPressureEnumToOMERO(String) - Static method in class ome.formats.model.UnitsFactory
 
xmlTemperatureEnumToOMERO(Unit<Temperature>) - Static method in class ome.formats.model.UnitsFactory
 
xmlTemperatureEnumToOMERO(String) - Static method in class ome.formats.model.UnitsFactory
 
xmlTimeEnumToOMERO(Unit<Time>) - Static method in class ome.formats.model.UnitsFactory
 
xmlTimeEnumToOMERO(String) - Static method in class ome.formats.model.UnitsFactory
 

Z

ZIP_EXTENSION - Static variable in class ome.formats.importer.util.FileUploader
The extension used for the zip.
zSize - Variable in class ome.formats.importer.ImportSize
 

_

__del__() - Method in class omero.client
Calls closeSession() and ignores any exceptions.
__redirect(long, _RawFileStoreTie, Current) - Method in class ome.services.blitz.impl.RawFileStoreI
 
_wait(Current) - Method in class ome.services.blitz.impl.ScriptProcessI
 
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