OMEROMetadataStoreClient (omero-blitz 5.5.3 API)

java.lang.Object
- ome.formats.OMEROMetadataStoreClient

All Implemented Interfaces:

loci.formats.meta.IMinMaxStore, IObjectContainerStore, ome.xml.meta.BaseMetadata, ome.xml.meta.MetadataStore
```
public class OMEROMetadataStoreClient
extends java.lang.Object
implements loci.formats.meta.MetadataStore, loci.formats.meta.IMinMaxStore, IObjectContainerStore
```
Client side implementation of the Bio-Formats MetadataStore. It is responsible for handling metadata from Bio-Formats and maintaining communication with an OMERO server.

Field Summary

Fields
Modifier and Type	Field and Description
`static java.lang.String`	`OMERO_EMISSION_FILTER_SUFFIX` Emission filter LSID suffix.
`static java.lang.String`	`OMERO_EXCITATION_FILTER_SUFFIX` Excitation filter LSID suffix.

Constructor Summary

Constructors
Constructor and Description

OMEROMetadataStoreClient()

Constructors
Constructor and Description
`OMEROMetadataStoreClient()`

Method Summary

All Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method and Description
`Dataset`	`addDataset(java.lang.String datasetName, java.lang.String datasetDescription, Project project)`
`boolean`	`addModelProcessor(ModelProcessor processor)` Adds a model processor to the end of the processing chain.
`Project`	`addProject(java.lang.String projectName, java.lang.String projectDescription)`
`void`	`addReference(ome.util.LSID source, ome.util.LSID target)` Adds a reference to the reference cache.
`Screen`	`addScreen(java.lang.String screenName, java.lang.String screenDescription)`
`void`	`closeServices()` Closes all stateful services.
`int`	`countCachedContainers(java.lang.Class<? extends IObject> klass, int... indexes)` Counts the number of containers the MetadataStore has of a given class and at a given index of the hierarchy if specified.
`int`	`countCachedReferences(java.lang.Class<? extends IObject> source, java.lang.Class<? extends IObject> target)` Counts the number of references the MetadataStore has between objects of two classes.
`void`	`createRoot()`
`void`	`finalizePixelStore()` Closes the active raw pixels store.
`java.util.Map<java.lang.Class<? extends IObject>,java.util.Map<java.lang.String,IObjectContainer>>`	`getAuthoritativeContainerCache()` Returns the current authoritative LSID container cache.
`Channel`	`getChannel(int imageIndex, int channelIndex)`
`java.lang.String`	`getConfigValue(java.lang.String key)` Retrieves a configuration value from the `IConfig` service.
`java.util.Map<ome.util.LSID,IObjectContainer>`	`getContainerCache()` Returns the current container cache.
`java.util.List<Dataset>`	`getDatasets(Project p)`
`java.util.List<Dataset>`	`getDatasetsWithoutProjects()`
`int`	`getDefaultBatchSize()`
`int`	`getDefaultBlockSize()`
`int`	`getDefaultGroupLevel()` Deprecated.
`java.lang.String`	`getDefaultGroupName()` Retrieve the default group's name
`Detector`	`getDetector(int instrumentIndex, int detectorIndex)`
`EnumerationProvider`	`getEnumerationProvider()` Retrieves the active enumeration provider.
`long`	`getExperimenterID()`
`Filament`	`getFilament(int instrumentIndex, int lightSourceIndex)`
`FilterSet`	`getFilterSet(int instrumentIndex, int filterSetIndex)`
`ImagingEnvironment`	`getImagingEnvironment(int imageIndex)`
`InstanceProvider`	`getInstanceProvider()` Retrieves the active instance provider.
`IObjectContainer`	`getIObjectContainer(java.lang.Class<? extends IObject> klass, java.util.LinkedHashMap<Index,java.lang.Integer> indexes)` Retrieves an IObject container for a given class and location within the OME-XML data model.
`java.util.List<IObjectContainer>`	`getIObjectContainers(java.lang.Class<? extends IObject> klass)` Retrieves all IObject containers of a given class.
`IQueryPrx`	`getIQuery()`
`ClientKeepAlive`	`getKeepAlive()` Returns clientKeepAlive created in store
`Laser`	`getLaser(int instrumentIndex, int lightSourceIndex)`
`LightEmittingDiode`	`getLightEmittingDiode(int instrumentIndex, int lightSourceIndex)`
`Line`	`getLine(int ROIIndex, int shapeIndex)`
`ListAnnotation`	`getListAnnotation(int listAnnotationIndex)`
`LongAnnotation`	`getLongAnnotation(int longAnnotationIndex)`
`Mask`	`getMask(int ROIIndex, int shapeIndex)`
`MicrobeamManipulation`	`getMicrobeamManipulation(int experimentIndex, int microbeamManipulationIndex)`
`LightSettings`	`getMicrobeamManipulationLightSourceSettings(int experimentIndex, int microbeamManipulationIndex, int lightSourceSettingsIndex)`
`java.util.List<ModelProcessor>`	`getModelProcessors()` Retrieves the current list of model processors the metadata store is using.
`Objective`	`getObjective(int instrumentIndex, int objectiveIndex)`
`ObjectiveSettings`	`getObjectiveSettings(int imageIndex)`
`Project`	`getProject(long projectId)`
`java.util.List<Project>`	`getProjects()`
`loci.formats.IFormatReader`	`getReader()` Returns the current Bio-Formats reader that has been used to populate the container store.
`java.util.Map<ome.util.LSID,java.util.List<ome.util.LSID>>`	`getReferenceCache()` Returns the current reference cache.
`java.util.Map<java.lang.String,java.lang.String[]>`	`getReferenceStringCache()` Returns the current string based reference cache.
`long`	`getRepositorySpace()`
`ome.xml.meta.MetadataRoot`	`getRoot()`
`java.util.List<Screen>`	`getScreens()`
`ServiceFactoryPrx`	`getServiceFactory()` Returns the currently active service factory.
`IObject`	`getSourceObject(ome.util.LSID LSID)` Retrieves an OMERO Blitz source object for a given LSID.
`<T extends IObject> java.util.List<T>`	`getSourceObjects(java.lang.Class<T> klass)` Retrieves all OMERO Blitz source objects of a given class.
`<T extends IObject> T`	`getTarget(java.lang.Class<T> klass, long id)` Helper method to retrieve an object from iQuery
`int[]`	`getTileSize(java.lang.Long pixId)` Retrieves the suggested tile size for a pixels set.
`java.util.List<Annotation>`	`getUserSpecifiedAnnotations()` Returns the user specified annotations.
`java.lang.String`	`getUserSpecifiedDescription()` Returns the user specified image/plate description.
`java.lang.String`	`getUserSpecifiedImageName()`
`java.lang.String`	`getUserSpecifiedName()` Returns the user specified image/plate name.
`java.lang.Double[]`	`getUserSpecifiedPhysicalPixelSizes()` Returns the user specified physical pixel sizes.
`IObject`	`getUserSpecifiedTarget()` Returns the user-specified linkage target (usually a Dataset for Images) and a Screen for Plates).
`boolean`	`hasReference(ome.util.LSID source, ome.util.LSID target)` Checks to see if there is currently an active reference for two LSIDs.
`protected void`	`ignoreAnnotator(java.lang.String method, java.lang.Object... args)` For all cases of an annotator being ignore (WARN).
`protected void`	`ignoreInsecure(java.lang.String method, java.lang.Object... args)` Called when saving a property to OMERO would result in a SecurityViolation (DEBUG).
`protected void`	`ignoreMissing(java.lang.String method, java.lang.Object... args)` Called when a property is missing from the OMERO model (WARN).
`protected void`	`ignoreUnneeded(java.lang.String method, java.lang.Object... args)` Called when a property is not needed in OMERO since the data can be gotten elsewhere, as in directly from the file itself (DEBUG).
`protected void`	`ignoreUnsupported(java.lang.String method, java.lang.Object... args)` Called when a property is not expected in a file to be imported.
`void`	`initialize(client c)` Initializes the MetadataStore with an already logged in, ready to go service factory.
`void`	`initialize(ServiceFactoryPrx serviceFactory)` Initializes the MetadataStore with an already logged in, ready to go service factory.
`void`	`initialize(java.lang.String server, int port, java.lang.String sessionKey)` Initializes the MetadataStore by joining an existing session.
`void`	`initialize(java.lang.String server, int port, java.lang.String sessionKey, boolean isSecure)` Initializes the MetadataStore by joining an existing session.
`void`	`initialize(java.lang.String username, java.lang.String password, java.lang.String server, int port)` Initializes the MetadataStore taking string parameters to feed to the OMERO Blitz client object.
`void`	`initialize(java.lang.String username, java.lang.String password, java.lang.String server, int port, boolean isSecure)` Initializes the MetadataStore taking string parameters to feed to the OMERO Blitz client object.
`void`	`initialize(java.lang.String username, java.lang.String password, java.lang.String server, int port, java.lang.Long group, boolean isSecure)` Initializes the MetadataStore taking string parameters to feed to the OMERO Blitz client object.
`boolean`	`isEncryptedConnection()`
`java.util.List<InteractiveProcessorPrx>`	`launchProcessing()`
`void`	`logout()` Destroys the sessionFactory and closes the client.
`void`	`logVersionInfo(java.lang.String clientVersion)`
`java.util.Map<java.lang.Long,java.lang.String>`	`mapUserGroups()` Maps the user's groups for use by ScreenLogin.registerGroup() Also strips system groups from this map
`void`	`ping()` Pings all registered OMERO Blitz proxies.
`void`	`populateMinMax()` Sends all the minimums and maximums for all images processed so far to the server.
`void`	`postProcess()` Post processes the internal structure of the client side MetadataStore.
`void`	`prepare(java.util.Map<java.lang.Integer,Image> existingMetadata)` Prepares the metadata store using existing metadata that has been pre-registered by OMERO.fs.
`void`	`preparePixelsStore(java.util.List<java.lang.Long> pixelsIds)` Prepares the server side RawPixelsStore.
`void`	`removeIObjectContainer(ome.util.LSID lsid)` Removes an IObject container from within the OME-XML data model store.
`void`	`removeModelProcessor(ModelProcessor processor)` Removes a model processor from use.
`void`	`resetDefaultsAndGenerateThumbnails(java.util.List<java.lang.Long> plateIds, java.util.List<java.lang.Long> pixelsIds)` Resets the defaults and generates thumbnails for a given set of Pixels IDs.
`java.util.Map<java.lang.String,java.util.List<IObject>>`	`saveToDB(FilesetJobLink link)` Updates the server side MetadataStore with a list of our objects and references and saves them into the database.
`void`	`setArcAnnotationRef(java.lang.String annotation, int instrumentIndex, int lightSourceIndex, int annotationRefIndex)`
`void`	`setArcID(java.lang.String id, int instrumentIndex, int lightSourceIndex)`
`void`	`setArcLotNumber(java.lang.String lotNumber, int instrumentIndex, int lightSourceIndex)`
`void`	`setArcManufacturer(java.lang.String manufacturer, int instrumentIndex, int lightSourceIndex)`
`void`	`setArcModel(java.lang.String model, int instrumentIndex, int lightSourceIndex)`
`void`	`setArcPower(ome.units.quantity.Power power, int instrumentIndex, int lightSourceIndex)`
`void`	`setArcSerialNumber(java.lang.String serialNumber, int instrumentIndex, int lightSourceIndex)`
`void`	`setArcType(ome.xml.model.enums.ArcType type, int instrumentIndex, int lightSourceIndex)`
`void`	`setBinaryFileBinData(byte[] binData, int fileAnnotationIndex)`
`void`	`setBinaryFileBinDataBigEndian(java.lang.Boolean isBigEndian, int fileAnnotationIndex)`
`void`	`setBinaryFileBinDataCompression(ome.xml.model.enums.Compression compression, int fileAnnotationIndex)`
`void`	`setBinaryFileBinDataLength(ome.xml.model.primitives.NonNegativeLong length, int fileAnnotationIndex)`
`void`	`setBinaryFileFileName(java.lang.String fileName, int fileAnnotationIndex)`
`void`	`setBinaryFileMIMEType(java.lang.String mimeType, int fileAnnotationIndex)`
`void`	`setBinaryFileSize(ome.xml.model.primitives.NonNegativeLong size, int fileAnnotationIndex)`
`void`	`setBinaryOnlyMetadataFile(java.lang.String metadataFile)`
`void`	`setBinaryOnlyUUID(java.lang.String uuid)`
`void`	`setBooleanAnnotationAnnotationRef(java.lang.String annotation, int booleanAnnotationIndex, int annotationRefIndex)`
`void`	`setBooleanAnnotationAnnotator(java.lang.String value, int index)`
`void`	`setBooleanAnnotationDescription(java.lang.String description, int booleanAnnotationIndex)`
`void`	`setBooleanAnnotationID(java.lang.String id, int booleanAnnotationIndex)`
`void`	`setBooleanAnnotationNamespace(java.lang.String namespace, int booleanAnnotationIndex)`
`void`	`setBooleanAnnotationValue(java.lang.Boolean value, int booleanAnnotationIndex)`
`void`	`setChannelAcquisitionMode(ome.xml.model.enums.AcquisitionMode acquisitionMode, int imageIndex, int channelIndex)`
`void`	`setChannelAnnotationRef(java.lang.String annotation, int imageIndex, int channelIndex, int annotationRefIndex)`
`void`	`setChannelColor(ome.xml.model.primitives.Color color, int imageIndex, int channelIndex)`
`void`	`setChannelContrastMethod(ome.xml.model.enums.ContrastMethod contrastMethod, int imageIndex, int channelIndex)`
`void`	`setChannelEmissionWavelength(ome.units.quantity.Length emissionWavelength, int imageIndex, int channelIndex)`
`void`	`setChannelExcitationWavelength(ome.units.quantity.Length excitationWavelength, int imageIndex, int channelIndex)`
`void`	`setChannelFilterSetRef(java.lang.String filterSet, int imageIndex, int channelIndex)`
`void`	`setChannelFluor(java.lang.String fluor, int imageIndex, int channelIndex)`
`void`	`setChannelGlobalMinMax(int channel, double minimum, double maximum, int series)`
`void`	`setChannelID(java.lang.String id, int imageIndex, int channelIndex)`
`void`	`setChannelIlluminationType(ome.xml.model.enums.IlluminationType illuminationType, int imageIndex, int channelIndex)`
`void`	`setChannelLightSourceSettingsAttenuation(ome.xml.model.primitives.PercentFraction attenuation, int imageIndex, int channelIndex)`
`void`	`setChannelLightSourceSettingsID(java.lang.String id, int imageIndex, int channelIndex)`
`void`	`setChannelLightSourceSettingsWavelength(ome.units.quantity.Length wavelength, int imageIndex, int channelIndex)`
`void`	`setChannelName(java.lang.String name, int imageIndex, int channelIndex)`
`void`	`setChannelNDFilter(java.lang.Double ndfilter, int imageIndex, int channelIndex)`
`void`	`setChannelPinholeSize(ome.units.quantity.Length pinholeSize, int imageIndex, int channelIndex)`
`void`	`setChannelPockelCellSetting(java.lang.Integer pockelCellSetting, int imageIndex, int channelIndex)`
`void`	`setChannelSamplesPerPixel(ome.xml.model.primitives.PositiveInteger samplesPerPixel, int imageIndex, int channelIndex)`
`void`	`setCommentAnnotationAnnotationRef(java.lang.String annotation, int commentAnnotationIndex, int annotationRefIndex)`
`void`	`setCommentAnnotationAnnotator(java.lang.String value, int index)`
`void`	`setCommentAnnotationDescription(java.lang.String description, int commentAnnotationIndex)`
`void`	`setCommentAnnotationID(java.lang.String id, int commentAnnotationIndex)`
`void`	`setCommentAnnotationNamespace(java.lang.String namespace, int commentAnnotationIndex)`
`void`	`setCommentAnnotationValue(java.lang.String value, int commentAnnotationIndex)`
`void`	`setCurrentGroup(long groupID)` Changes the default group of the currently logged in user.
`void`	`setCurrentLogFile(java.lang.String logFilename, java.lang.String token)`
`void`	`setDatasetAnnotationRef(java.lang.String annotation, int datasetIndex, int annotationRefIndex)`
`void`	`setDatasetDescription(java.lang.String description, int datasetIndex)`
`void`	`setDatasetExperimenterGroupRef(java.lang.String group, int datasetIndex)`
`void`	`setDatasetExperimenterRef(java.lang.String experimenter, int datasetIndex)`
`void`	`setDatasetID(java.lang.String id, int datasetIndex)`
`void`	`setDatasetImageRef(java.lang.String image, int datasetIndex, int imageRefIndex)`
`void`	`setDatasetName(java.lang.String name, int datasetIndex)`
`void`	`setDetectorAmplificationGain(java.lang.Double amplificationGain, int instrumentIndex, int detectorIndex)`
`void`	`setDetectorAnnotationRef(java.lang.String annotation, int instrumentIndex, int detectorIndex, int annotationRefIndex)`
`void`	`setDetectorGain(java.lang.Double gain, int instrumentIndex, int detectorIndex)`
`void`	`setDetectorID(java.lang.String id, int instrumentIndex, int detectorIndex)`
`void`	`setDetectorLotNumber(java.lang.String lotNumber, int instrumentIndex, int detectorIndex)`
`void`	`setDetectorManufacturer(java.lang.String manufacturer, int instrumentIndex, int detectorIndex)`
`void`	`setDetectorModel(java.lang.String model, int instrumentIndex, int detectorIndex)`
`void`	`setDetectorOffset(java.lang.Double offset, int instrumentIndex, int detectorIndex)`
`void`	`setDetectorSerialNumber(java.lang.String serialNumber, int instrumentIndex, int detectorIndex)`
`void`	`setDetectorSettingsBinning(ome.xml.model.enums.Binning binning, int imageIndex, int channelIndex)`
`void`	`setDetectorSettingsGain(java.lang.Double gain, int imageIndex, int channelIndex)`
`void`	`setDetectorSettingsID(java.lang.String id, int imageIndex, int channelIndex)`
`void`	`setDetectorSettingsIntegration(ome.xml.model.primitives.PositiveInteger integration, int imageIndex, int channelIndex)`
`void`	`setDetectorSettingsOffset(java.lang.Double offset, int imageIndex, int channelIndex)`
`void`	`setDetectorSettingsReadOutRate(ome.units.quantity.Frequency readOutRate, int imageIndex, int channelIndex)`
`void`	`setDetectorSettingsVoltage(ome.units.quantity.ElectricPotential voltage, int imageIndex, int channelIndex)`
`void`	`setDetectorSettingsZoom(java.lang.Double zoom, int imageIndex, int channelIndex)`
`void`	`setDetectorType(ome.xml.model.enums.DetectorType type, int instrumentIndex, int detectorIndex)`
`void`	`setDetectorVoltage(ome.units.quantity.ElectricPotential voltage, int instrumentIndex, int detectorIndex)`
`void`	`setDetectorZoom(java.lang.Double zoom, int instrumentIndex, int detectorIndex)`
`void`	`setDichroicAnnotationRef(java.lang.String annotation, int instrumentIndex, int dichroicIndex, int annotationRefIndex)`
`void`	`setDichroicID(java.lang.String id, int instrumentIndex, int dichroicIndex)`
`void`	`setDichroicLotNumber(java.lang.String lotNumber, int instrumentIndex, int dichroicIndex)`
`void`	`setDichroicManufacturer(java.lang.String manufacturer, int instrumentIndex, int dichroicIndex)`
`void`	`setDichroicModel(java.lang.String model, int instrumentIndex, int dichroicIndex)`
`void`	`setDichroicSerialNumber(java.lang.String serialNumber, int instrumentIndex, int dichroicIndex)`
`void`	`setDoubleAnnotationAnnotationRef(java.lang.String annotation, int doubleAnnotationIndex, int annotationRefIndex)`
`void`	`setDoubleAnnotationAnnotator(java.lang.String value, int index)`
`void`	`setDoubleAnnotationDescription(java.lang.String description, int doubleAnnotationIndex)`
`void`	`setDoubleAnnotationID(java.lang.String id, int doubleAnnotationIndex)`
`void`	`setDoubleAnnotationNamespace(java.lang.String namespace, int doubleAnnotationIndex)`
`void`	`setDoubleAnnotationValue(java.lang.Double value, int doubleAnnotationIndex)`
`void`	`setEllipseAnnotationRef(java.lang.String annotation, int ROIIndex, int shapeIndex, int annotationRefIndex)`
`void`	`setEllipseFillColor(ome.xml.model.primitives.Color fill, int ROIIndex, int shapeIndex)`
`void`	`setEllipseFillRule(ome.xml.model.enums.FillRule fillRule, int ROIIndex, int shapeIndex)`
`void`	`setEllipseFontFamily(ome.xml.model.enums.FontFamily fontFamily, int ROIIndex, int shapeIndex)`
`void`	`setEllipseFontSize(ome.units.quantity.Length fontSize, int ROIIndex, int shapeIndex)`
`void`	`setEllipseFontStyle(ome.xml.model.enums.FontStyle fontStyle, int ROIIndex, int shapeIndex)`
`void`	`setEllipseID(java.lang.String id, int ROIIndex, int shapeIndex)`
`void`	`setEllipseLocked(java.lang.Boolean locked, int ROIIndex, int shapeIndex)`
`void`	`setEllipseRadiusX(java.lang.Double radiusX, int ROIIndex, int shapeIndex)`
`void`	`setEllipseRadiusY(java.lang.Double radiusY, int ROIIndex, int shapeIndex)`
`void`	`setEllipseStrokeColor(ome.xml.model.primitives.Color stroke, int ROIIndex, int shapeIndex)`
`void`	`setEllipseStrokeDashArray(java.lang.String strokeDashArray, int ROIIndex, int shapeIndex)`
`void`	`setEllipseStrokeWidth(ome.units.quantity.Length strokeWidth, int ROIIndex, int shapeIndex)`
`void`	`setEllipseText(java.lang.String text, int ROIIndex, int shapeIndex)`
`void`	`setEllipseTheC(ome.xml.model.primitives.NonNegativeInteger theC, int ROIIndex, int shapeIndex)`
`void`	`setEllipseTheT(ome.xml.model.primitives.NonNegativeInteger theT, int ROIIndex, int shapeIndex)`
`void`	`setEllipseTheZ(ome.xml.model.primitives.NonNegativeInteger theZ, int ROIIndex, int shapeIndex)`
`void`	`setEllipseTransform(ome.xml.model.AffineTransform transform, int ROIIndex, int shapeIndex)`
`void`	`setEllipseX(java.lang.Double x, int ROIIndex, int shapeIndex)`
`void`	`setEllipseY(java.lang.Double y, int ROIIndex, int shapeIndex)`
`void`	`setEncryptedConnection(boolean encryptedConnection)`
`void`	`setEnumerationProvider(EnumerationProvider enumProvider)` Sets the active enumeration provider.
`void`	`setExperimentDescription(java.lang.String description, int experimentIndex)`
`void`	`setExperimenterAnnotationRef(java.lang.String annotation, int experimenterIndex, int annotationRefIndex)`
`void`	`setExperimenterEmail(java.lang.String email, int experimenterIndex)`
`void`	`setExperimenterFirstName(java.lang.String firstName, int experimenterIndex)`
`void`	`setExperimenterGroupAnnotationRef(java.lang.String annotation, int experimenterGroupIndex, int annotationRefIndex)`
`void`	`setExperimenterGroupDescription(java.lang.String description, int groupIndex)`
`void`	`setExperimenterGroupExperimenterRef(java.lang.String experimenter, int experimenterGroupIndex, int experimenterRefIndex)`
`void`	`setExperimenterGroupID(java.lang.String id, int groupIndex)`
`void`	`setExperimenterGroupLeader(java.lang.String leader, int groupIndex, int leaderIndex)`
`void`	`setExperimenterGroupName(java.lang.String name, int groupIndex)`
`void`	`setExperimenterID(java.lang.String id, int experimenterIndex)`
`void`	`setExperimenterInstitution(java.lang.String institution, int experimenterIndex)`
`void`	`setExperimenterLastName(java.lang.String lastName, int experimenterIndex)`
`void`	`setExperimenterMiddleName(java.lang.String middleName, int experimenterIndex)`
`void`	`setExperimenterUserName(java.lang.String userName, int experimenterIndex)`
`void`	`setExperimentExperimenterRef(java.lang.String experimenter, int experimentIndex)`
`void`	`setExperimentID(java.lang.String id, int experimentIndex)`
`void`	`setExperimentType(ome.xml.model.enums.ExperimentType type, int experimentIndex)`
`void`	`setFilamentAnnotationRef(java.lang.String annotation, int instrumentIndex, int lightSourceIndex, int annotationRefIndex)`
`void`	`setFilamentID(java.lang.String id, int instrumentIndex, int lightSourceIndex)`
`void`	`setFilamentLotNumber(java.lang.String lotNumber, int instrumentIndex, int lightSourceIndex)`
`void`	`setFilamentManufacturer(java.lang.String manufacturer, int instrumentIndex, int lightSourceIndex)`
`void`	`setFilamentModel(java.lang.String model, int instrumentIndex, int lightSourceIndex)`
`void`	`setFilamentPower(ome.units.quantity.Power power, int instrumentIndex, int lightSourceIndex)`
`void`	`setFilamentSerialNumber(java.lang.String serialNumber, int instrumentIndex, int lightSourceIndex)`
`void`	`setFilamentType(ome.xml.model.enums.FilamentType type, int instrumentIndex, int lightSourceIndex)`
`void`	`setFileAnnotationAnnotationRef(java.lang.String annotation, int fileAnnotationIndex, int annotationRefIndex)`
`void`	`setFileAnnotationAnnotator(java.lang.String value, int index)`
`void`	`setFileAnnotationDescription(java.lang.String description, int fileAnnotationIndex)`
`void`	`setFileAnnotationID(java.lang.String id, int fileAnnotationIndex)`
`void`	`setFileAnnotationNamespace(java.lang.String namespace, int fileAnnotationIndex)`
`void`	`setFilterAnnotationRef(java.lang.String annotation, int instrumentIndex, int filterIndex, int annotationRefIndex)`
`void`	`setFilterFilterWheel(java.lang.String filterWheel, int instrumentIndex, int filterIndex)`
`void`	`setFilterID(java.lang.String id, int instrumentIndex, int filterIndex)`
`void`	`setFilterLotNumber(java.lang.String lotNumber, int instrumentIndex, int filterIndex)`
`void`	`setFilterManufacturer(java.lang.String manufacturer, int instrumentIndex, int filterIndex)`
`void`	`setFilterModel(java.lang.String model, int instrumentIndex, int filterIndex)`
`void`	`setFilterSerialNumber(java.lang.String serialNumber, int instrumentIndex, int filterIndex)`
`void`	`setFilterSetDichroicRef(java.lang.String dichroic, int instrumentIndex, int filterSetIndex)`
`void`	`setFilterSetEmissionFilterRef(java.lang.String emissionFilter, int instrumentIndex, int filterSetIndex, int emissionFilterRefIndex)`
`void`	`setFilterSetExcitationFilterRef(java.lang.String excitationFilter, int instrumentIndex, int filterSetIndex, int excitationFilterRefIndex)`
`void`	`setFilterSetID(java.lang.String id, int instrumentIndex, int filterSetIndex)`
`void`	`setFilterSetLotNumber(java.lang.String lotNumber, int instrumentIndex, int filterSetIndex)`
`void`	`setFilterSetManufacturer(java.lang.String manufacturer, int instrumentIndex, int filterSetIndex)`
`void`	`setFilterSetModel(java.lang.String model, int instrumentIndex, int filterSetIndex)`
`void`	`setFilterSetSerialNumber(java.lang.String serialNumber, int instrumentIndex, int filterSetIndex)`
`void`	`setFilterType(ome.xml.model.enums.FilterType type, int instrumentIndex, int filterIndex)`
`void`	`setFolderAnnotationRef(java.lang.String annotation, int folderIndex, int annotationRefIndex)`
`void`	`setFolderDescription(java.lang.String description, int folderIndex)`
`void`	`setFolderFolderRef(java.lang.String folder, int folderIndex, int folderRefIndex)`
`void`	`setFolderID(java.lang.String id, int folderIndex)`
`void`	`setFolderImageRef(java.lang.String image, int folderIndex, int imageRefIndex)`
`void`	`setFolderName(java.lang.String name, int folderIndex)`
`void`	`setFolderROIRef(java.lang.String roi, int folderIndex, int ROIRefIndex)`
`void`	`setGenericExcitationSourceAnnotationRef(java.lang.String annotation, int instrumentIndex, int lightSourceIndex, int annotationRefIndex)`
`void`	`setGenericExcitationSourceID(java.lang.String id, int instrumentIndex, int lightSourceIndex)`
`void`	`setGenericExcitationSourceLotNumber(java.lang.String lotNumber, int instrumentIndex, int lightSourceIndex)`
`void`	`setGenericExcitationSourceManufacturer(java.lang.String manufacturer, int instrumentIndex, int lightSourceIndex)`
`void`	`setGenericExcitationSourceMap(java.util.List<ome.xml.model.MapPair> map, int instrumentIndex, int lightSourceIndex)`
`void`	`setGenericExcitationSourceModel(java.lang.String model, int instrumentIndex, int lightSourceIndex)`
`void`	`setGenericExcitationSourcePower(ome.units.quantity.Power power, int instrumentIndex, int lightSourceIndex)`
`void`	`setGenericExcitationSourceSerialNumber(java.lang.String serialNumber, int instrumentIndex, int lightSourceIndex)`
`java.lang.Long`	`setGroup(java.lang.Long groupID)` Sets the id which will be used to set the call context for all services.
`void`	`setImageAcquisitionDate(ome.xml.model.primitives.Timestamp acquiredDate, int imageIndex)`
`void`	`setImageAnnotationRef(java.lang.String annotation, int imageIndex, int annotationRefIndex)`
`void`	`setImageDescription(java.lang.String description, int imageIndex)`
`void`	`setImageExperimenterGroupRef(java.lang.String group, int imageIndex)`
`void`	`setImageExperimenterRef(java.lang.String experimenter, int imageIndex)`
`void`	`setImageExperimentRef(java.lang.String experiment, int imageIndex)`
`void`	`setImageID(java.lang.String id, int imageIndex)`
`void`	`setImageInstrumentRef(java.lang.String instrument, int imageIndex)`
`void`	`setImageMicrobeamManipulationRef(java.lang.String microbeamManipulation, int imageIndex, int microbeamManipulationRefIndex)`
`void`	`setImageName(java.lang.String name, int imageIndex)`
`void`	`setImageROIRef(java.lang.String roi, int imageIndex, int ROIRefIndex)`
`void`	`setImagingEnvironmentAirPressure(ome.units.quantity.Pressure airPressure, int imageIndex)`
`void`	`setImagingEnvironmentCO2Percent(ome.xml.model.primitives.PercentFraction co2percent, int imageIndex)`
`void`	`setImagingEnvironmentHumidity(ome.xml.model.primitives.PercentFraction humidity, int imageIndex)`
`void`	`setImagingEnvironmentMap(java.util.List<ome.xml.model.MapPair> map, int imageIndex)`
`void`	`setImagingEnvironmentTemperature(ome.units.quantity.Temperature temperature, int imageIndex)`
`void`	`setInstanceProvider(InstanceProvider instanceProvider)` Sets the active instance provider.
`void`	`setInstrumentAnnotationRef(java.lang.String annotation, int instrumentIndex, int annotationRefIndex)`
`void`	`setInstrumentID(java.lang.String id, int instrumentIndex)`
`void`	`setLabelAnnotationRef(java.lang.String annotation, int ROIIndex, int shapeIndex, int annotationRefIndex)`
`void`	`setLabelFillColor(ome.xml.model.primitives.Color fill, int ROIIndex, int shapeIndex)`
`void`	`setLabelFillRule(ome.xml.model.enums.FillRule fillRule, int ROIIndex, int shapeIndex)`
`void`	`setLabelFontFamily(ome.xml.model.enums.FontFamily fontFamily, int ROIIndex, int shapeIndex)`
`void`	`setLabelFontSize(ome.units.quantity.Length fontSize, int ROIIndex, int shapeIndex)`
`void`	`setLabelFontStyle(ome.xml.model.enums.FontStyle fontStyle, int ROIIndex, int shapeIndex)`
`void`	`setLabelID(java.lang.String id, int ROIIndex, int shapeIndex)`
`void`	`setLabelLocked(java.lang.Boolean locked, int ROIIndex, int shapeIndex)`
`void`	`setLabelStrokeColor(ome.xml.model.primitives.Color stroke, int ROIIndex, int shapeIndex)`
`void`	`setLabelStrokeDashArray(java.lang.String strokeDashArray, int ROIIndex, int shapeIndex)`
`void`	`setLabelStrokeWidth(ome.units.quantity.Length strokeWidth, int ROIIndex, int shapeIndex)`
`void`	`setLabelText(java.lang.String text, int ROIIndex, int shapeIndex)`
`void`	`setLabelTheC(ome.xml.model.primitives.NonNegativeInteger theC, int ROIIndex, int shapeIndex)`
`void`	`setLabelTheT(ome.xml.model.primitives.NonNegativeInteger theT, int ROIIndex, int shapeIndex)`
`void`	`setLabelTheZ(ome.xml.model.primitives.NonNegativeInteger theZ, int ROIIndex, int shapeIndex)`
`void`	`setLabelTransform(ome.xml.model.AffineTransform transform, int ROIIndex, int shapeIndex)`
`void`	`setLabelX(java.lang.Double x, int ROIIndex, int shapeIndex)`
`void`	`setLabelY(java.lang.Double y, int ROIIndex, int shapeIndex)`
`void`	`setLaserAnnotationRef(java.lang.String annotation, int instrumentIndex, int lightSourceIndex, int annotationRefIndex)`
`void`	`setLaserFrequencyMultiplication(ome.xml.model.primitives.PositiveInteger frequencyMultiplication, int instrumentIndex, int lightSourceIndex)`
`void`	`setLaserID(java.lang.String id, int instrumentIndex, int lightSourceIndex)`
`void`	`setLaserLaserMedium(ome.xml.model.enums.LaserMedium laserMedium, int instrumentIndex, int lightSourceIndex)`
`void`	`setLaserLotNumber(java.lang.String lotNumber, int instrumentIndex, int lightSourceIndex)`
`void`	`setLaserManufacturer(java.lang.String manufacturer, int instrumentIndex, int lightSourceIndex)`
`void`	`setLaserModel(java.lang.String model, int instrumentIndex, int lightSourceIndex)`
`void`	`setLaserPockelCell(java.lang.Boolean pockelCell, int instrumentIndex, int lightSourceIndex)`
`void`	`setLaserPower(ome.units.quantity.Power power, int instrumentIndex, int lightSourceIndex)`
`void`	`setLaserPulse(ome.xml.model.enums.Pulse pulse, int instrumentIndex, int lightSourceIndex)`
`void`	`setLaserPump(java.lang.String pump, int instrumentIndex, int lightSourceIndex)`
`void`	`setLaserRepetitionRate(ome.units.quantity.Frequency repetitionRate, int instrumentIndex, int lightSourceIndex)`
`void`	`setLaserSerialNumber(java.lang.String serialNumber, int instrumentIndex, int lightSourceIndex)`
`void`	`setLaserTuneable(java.lang.Boolean tuneable, int instrumentIndex, int lightSourceIndex)`
`void`	`setLaserType(ome.xml.model.enums.LaserType type, int instrumentIndex, int lightSourceIndex)`
`void`	`setLaserWavelength(ome.units.quantity.Length wavelength, int instrumentIndex, int lightSourceIndex)`
`void`	`setLightEmittingDiodeAnnotationRef(java.lang.String annotation, int instrumentIndex, int lightSourceIndex, int annotationRefIndex)`
`void`	`setLightEmittingDiodeID(java.lang.String id, int instrumentIndex, int lightSourceIndex)`
`void`	`setLightEmittingDiodeLotNumber(java.lang.String lotNumber, int instrumentIndex, int lightSourceIndex)`
`void`	`setLightEmittingDiodeManufacturer(java.lang.String manufacturer, int instrumentIndex, int lightSourceIndex)`
`void`	`setLightEmittingDiodeModel(java.lang.String model, int instrumentIndex, int lightSourceIndex)`
`void`	`setLightEmittingDiodePower(ome.units.quantity.Power power, int instrumentIndex, int lightSourceIndex)`
`void`	`setLightEmittingDiodeSerialNumber(java.lang.String serialNumber, int instrumentIndex, int lightSourceIndex)`
`void`	`setLightPathAnnotationRef(java.lang.String annotation, int imageIndex, int channelIndex, int annotationRefIndex)`
`void`	`setLightPathDichroicRef(java.lang.String dichroic, int imageIndex, int channelIndex)`
`void`	`setLightPathEmissionFilterRef(java.lang.String emissionFilter, int imageIndex, int channelIndex, int emissionFilterRefIndex)`
`void`	`setLightPathExcitationFilterRef(java.lang.String excitationFilter, int imageIndex, int channelIndex, int excitationFilterRefIndex)`
`void`	`setLineAnnotationRef(java.lang.String annotation, int ROIIndex, int shapeIndex, int annotationRefIndex)`
`void`	`setLineFillColor(ome.xml.model.primitives.Color fill, int ROIIndex, int shapeIndex)`
`void`	`setLineFillRule(ome.xml.model.enums.FillRule fillRule, int ROIIndex, int shapeIndex)`
`void`	`setLineFontFamily(ome.xml.model.enums.FontFamily fontFamily, int ROIIndex, int shapeIndex)`
`void`	`setLineFontSize(ome.units.quantity.Length fontSize, int ROIIndex, int shapeIndex)`
`void`	`setLineFontStyle(ome.xml.model.enums.FontStyle fontStyle, int ROIIndex, int shapeIndex)`
`void`	`setLineID(java.lang.String id, int ROIIndex, int shapeIndex)`
`void`	`setLineLocked(java.lang.Boolean locked, int ROIIndex, int shapeIndex)`
`void`	`setLineMarkerEnd(ome.xml.model.enums.Marker markerEnd, int ROIIndex, int shapeIndex)`
`void`	`setLineMarkerStart(ome.xml.model.enums.Marker markerStart, int ROIIndex, int shapeIndex)`
`void`	`setLineStrokeColor(ome.xml.model.primitives.Color stroke, int ROIIndex, int shapeIndex)`
`void`	`setLineStrokeDashArray(java.lang.String strokeDashArray, int ROIIndex, int shapeIndex)`
`void`	`setLineStrokeWidth(ome.units.quantity.Length strokeWidth, int ROIIndex, int shapeIndex)`
`void`	`setLineText(java.lang.String text, int ROIIndex, int shapeIndex)`
`void`	`setLineTheC(ome.xml.model.primitives.NonNegativeInteger theC, int ROIIndex, int shapeIndex)`
`void`	`setLineTheT(ome.xml.model.primitives.NonNegativeInteger theT, int ROIIndex, int shapeIndex)`
`void`	`setLineTheZ(ome.xml.model.primitives.NonNegativeInteger theZ, int ROIIndex, int shapeIndex)`
`void`	`setLineTransform(ome.xml.model.AffineTransform transform, int ROIIndex, int shapeIndex)`
`void`	`setLineX1(java.lang.Double x1, int ROIIndex, int shapeIndex)`
`void`	`setLineX2(java.lang.Double x2, int ROIIndex, int shapeIndex)`
`void`	`setLineY1(java.lang.Double y1, int ROIIndex, int shapeIndex)`
`void`	`setLineY2(java.lang.Double y2, int ROIIndex, int shapeIndex)`
`void`	`setListAnnotationAnnotationRef(java.lang.String annotation, int listAnnotationIndex, int annotationRefIndex)`
`void`	`setListAnnotationAnnotator(java.lang.String value, int index)`
`void`	`setListAnnotationDescription(java.lang.String description, int listAnnotationIndex)`
`void`	`setListAnnotationID(java.lang.String id, int listAnnotationIndex)`
`void`	`setListAnnotationNamespace(java.lang.String namespace, int listAnnotationIndex)`
`void`	`setLongAnnotationAnnotationRef(java.lang.String annotation, int longAnnotationIndex, int annotationRefIndex)`
`void`	`setLongAnnotationAnnotator(java.lang.String value, int XMLAnnotationIndex)`
`void`	`setLongAnnotationDescription(java.lang.String description, int longAnnotationIndex)`
`void`	`setLongAnnotationID(java.lang.String id, int longAnnotationIndex)`
`void`	`setLongAnnotationNamespace(java.lang.String namespace, int longAnnotationIndex)`
`void`	`setLongAnnotationValue(java.lang.Long value, int longAnnotationIndex)`
`void`	`setMapAnnotationAnnotationRef(java.lang.String annotation, int mapAnnotationIndex, int annotationRefIndex)`
`void`	`setMapAnnotationAnnotator(java.lang.String annotator, int mapAnnotationIndex)`
`void`	`setMapAnnotationDescription(java.lang.String description, int mapAnnotationIndex)`
`void`	`setMapAnnotationID(java.lang.String id, int mapAnnotationIndex)`
`void`	`setMapAnnotationNamespace(java.lang.String namespace, int mapAnnotationIndex)`
`void`	`setMapAnnotationValue(java.util.List<ome.xml.model.MapPair> value, int mapAnnotationIndex)`
`void`	`setMaskAnnotationRef(java.lang.String annotation, int ROIIndex, int shapeIndex, int annotationRefIndex)`
`void`	`setMaskBinData(byte[] binData, int roiIndex, int shapeIndex)`
`void`	`setMaskBinDataBigEndian(java.lang.Boolean isBigEndian, int roiIndex, int shapeIndex)`
`void`	`setMaskBinDataCompression(ome.xml.model.enums.Compression compression, int roiIndex, int shapeIndex)`
`void`	`setMaskBinDataLength(ome.xml.model.primitives.NonNegativeLong length, int roiIndex, int shapeIndex)`
`void`	`setMaskFillColor(ome.xml.model.primitives.Color fill, int ROIIndex, int shapeIndex)`
`void`	`setMaskFillRule(ome.xml.model.enums.FillRule fillRule, int ROIIndex, int shapeIndex)`
`void`	`setMaskFontFamily(ome.xml.model.enums.FontFamily fontFamily, int ROIIndex, int shapeIndex)`
`void`	`setMaskFontSize(ome.units.quantity.Length fontSize, int ROIIndex, int shapeIndex)`
`void`	`setMaskFontStyle(ome.xml.model.enums.FontStyle fontStyle, int ROIIndex, int shapeIndex)`
`void`	`setMaskHeight(java.lang.Double height, int ROIIndex, int shapeIndex)`
`void`	`setMaskID(java.lang.String id, int ROIIndex, int shapeIndex)`
`void`	`setMaskLocked(java.lang.Boolean locked, int ROIIndex, int shapeIndex)`
`void`	`setMaskStrokeColor(ome.xml.model.primitives.Color stroke, int ROIIndex, int shapeIndex)`
`void`	`setMaskStrokeDashArray(java.lang.String strokeDashArray, int ROIIndex, int shapeIndex)`
`void`	`setMaskStrokeWidth(ome.units.quantity.Length strokeWidth, int ROIIndex, int shapeIndex)`
`void`	`setMaskText(java.lang.String description, int ROIIndex, int shapeIndex)`
`void`	`setMaskTheC(ome.xml.model.primitives.NonNegativeInteger theC, int ROIIndex, int shapeIndex)`
`void`	`setMaskTheT(ome.xml.model.primitives.NonNegativeInteger theT, int ROIIndex, int shapeIndex)`
`void`	`setMaskTheZ(ome.xml.model.primitives.NonNegativeInteger theZ, int ROIIndex, int shapeIndex)`
`void`	`setMaskTransform(ome.xml.model.AffineTransform transform, int ROIIndex, int shapeIndex)`
`void`	`setMaskWidth(java.lang.Double width, int ROIIndex, int shapeIndex)`
`void`	`setMaskX(java.lang.Double x, int ROIIndex, int shapeIndex)`
`void`	`setMaskY(java.lang.Double y, int ROIIndex, int shapeIndex)`
`void`	`setMicrobeamManipulationDescription(java.lang.String description, int experimentIndex, int microbeamManipulationIndex)`
`void`	`setMicrobeamManipulationExperimenterRef(java.lang.String experimenter, int experimentIndex, int microbeamManipulationIndex)`
`void`	`setMicrobeamManipulationID(java.lang.String id, int experimentIndex, int microbeamManipulationIndex)`
`void`	`setMicrobeamManipulationLightSourceSettingsAttenuation(ome.xml.model.primitives.PercentFraction attenuation, int experimentIndex, int microbeamManipulationIndex, int lightSourceSettingsIndex)`
`void`	`setMicrobeamManipulationLightSourceSettingsID(java.lang.String id, int experimentIndex, int microbeamManipulationIndex, int lightSourceSettingsIndex)`
`void`	`setMicrobeamManipulationLightSourceSettingsWavelength(ome.units.quantity.Length wavelength, int experimentIndex, int microbeamManipulationIndex, int lightSourceSettingsIndex)`
`void`	`setMicrobeamManipulationROIRef(java.lang.String roi, int experimentIndex, int microbeamManipulationIndex, int ROIRefIndex)`
`void`	`setMicrobeamManipulationType(ome.xml.model.enums.MicrobeamManipulationType type, int experimentIndex, int microbeamManipulationIndex)`
`void`	`setMicroscopeLotNumber(java.lang.String lotNumber, int instrumentIndex)`
`void`	`setMicroscopeManufacturer(java.lang.String manufacturer, int instrumentIndex)`
`void`	`setMicroscopeModel(java.lang.String model, int instrumentIndex)`
`void`	`setMicroscopeSerialNumber(java.lang.String serialNumber, int instrumentIndex)`
`void`	`setMicroscopeType(ome.xml.model.enums.MicroscopeType type, int instrumentIndex)`
`void`	`setModelProcessors(java.util.List<ModelProcessor> modelProcessors)` Sets the current set of model processors.
`void`	`setObjectiveAnnotationRef(java.lang.String annotation, int instrumentIndex, int objectiveIndex, int annotationRefIndex)`
`void`	`setObjectiveCalibratedMagnification(java.lang.Double calibratedMagnification, int instrumentIndex, int objectiveIndex)`
`void`	`setObjectiveCorrection(ome.xml.model.enums.Correction correction, int instrumentIndex, int objectiveIndex)`
`void`	`setObjectiveID(java.lang.String id, int instrumentIndex, int objectiveIndex)`
`void`	`setObjectiveImmersion(ome.xml.model.enums.Immersion immersion, int instrumentIndex, int objectiveIndex)`
`void`	`setObjectiveIris(java.lang.Boolean iris, int instrumentIndex, int objectiveIndex)`
`void`	`setObjectiveLensNA(java.lang.Double lensNA, int instrumentIndex, int objectiveIndex)`
`void`	`setObjectiveLotNumber(java.lang.String lotNumber, int instrumentIndex, int objectiveIndex)`
`void`	`setObjectiveManufacturer(java.lang.String manufacturer, int instrumentIndex, int objectiveIndex)`
`void`	`setObjectiveModel(java.lang.String model, int instrumentIndex, int objectiveIndex)`
`void`	`setObjectiveNominalMagnification(java.lang.Double nominalMagnification, int instrumentIndex, int objectiveIndex)`
`void`	`setObjectiveSerialNumber(java.lang.String serialNumber, int instrumentIndex, int objectiveIndex)`
`void`	`setObjectiveSettingsCorrectionCollar(java.lang.Double correctionCollar, int imageIndex)`
`void`	`setObjectiveSettingsID(java.lang.String id, int imageIndex)`
`void`	`setObjectiveSettingsMedium(ome.xml.model.enums.Medium medium, int imageIndex)`
`void`	`setObjectiveSettingsRefractiveIndex(java.lang.Double refractiveIndex, int imageIndex)`
`void`	`setObjectiveWorkingDistance(ome.units.quantity.Length workingDistance, int instrumentIndex, int objectiveIndex)`
`void`	`setPixelsBigEndian(java.lang.Boolean value, int index)`
`void`	`setPixelsBinData(byte[] binData, int imageIndex, int binDataIndex)`
`void`	`setPixelsBinDataBigEndian(java.lang.Boolean bigEndian, int imageIndex, int binDataIndex)`
`void`	`setPixelsBinDataCompression(ome.xml.model.enums.Compression compression, int imageIndex, int binDataIndex)`
`void`	`setPixelsBinDataLength(ome.xml.model.primitives.NonNegativeLong length, int imageIndex, int binDataIndex)`
`void`	`setPixelsDimensionOrder(ome.xml.model.enums.DimensionOrder dimensionOrder, int imageIndex)`
`void`	`setPixelsFile(long pixelsId, java.lang.String file, java.lang.String repo)` Sets the path, name and repo in the pixels table.
`void`	`setPixelsID(java.lang.String id, int imageIndex)`
`void`	`setPixelsInterleaved(java.lang.Boolean value, int index)`
`void`	`setPixelsPhysicalSizeX(ome.units.quantity.Length physicalSizeX, int imageIndex)`
`void`	`setPixelsPhysicalSizeY(ome.units.quantity.Length physicalSizeY, int imageIndex)`
`void`	`setPixelsPhysicalSizeZ(ome.units.quantity.Length physicalSizeZ, int imageIndex)`
`void`	`setPixelsSignificantBits(ome.xml.model.primitives.PositiveInteger value, int imageIndex)`
`void`	`setPixelsSizeC(ome.xml.model.primitives.PositiveInteger sizeC, int imageIndex)`
`void`	`setPixelsSizeT(ome.xml.model.primitives.PositiveInteger sizeT, int imageIndex)`
`void`	`setPixelsSizeX(ome.xml.model.primitives.PositiveInteger sizeX, int imageIndex)`
`void`	`setPixelsSizeY(ome.xml.model.primitives.PositiveInteger sizeY, int imageIndex)`
`void`	`setPixelsSizeZ(ome.xml.model.primitives.PositiveInteger sizeZ, int imageIndex)`
`void`	`setPixelsTimeIncrement(ome.units.quantity.Time timeIncrement, int imageIndex)`
`void`	`setPixelsType(ome.xml.model.enums.PixelType type, int imageIndex)`
`void`	`setPlane(java.lang.Long pixId, byte[] arrayBuf, int z, int c, int t)` Writes a plane to the server.
`void`	`setPlaneAnnotationRef(java.lang.String annotation, int imageIndex, int planeIndex, int annotationRefIndex)`
`void`	`setPlaneDeltaT(ome.units.quantity.Time deltaT, int imageIndex, int planeIndex)`
`void`	`setPlaneExposureTime(ome.units.quantity.Time exposureTime, int imageIndex, int planeIndex)`
`void`	`setPlaneHashSHA1(java.lang.String hashSHA1, int imageIndex, int planeIndex)`
`void`	`setPlanePositionX(ome.units.quantity.Length positionX, int imageIndex, int planeIndex)`
`void`	`setPlanePositionY(ome.units.quantity.Length positionY, int imageIndex, int planeIndex)`
`void`	`setPlanePositionZ(ome.units.quantity.Length positionZ, int imageIndex, int planeIndex)`
`void`	`setPlaneTheC(ome.xml.model.primitives.NonNegativeInteger theC, int imageIndex, int planeIndex)`
`void`	`setPlaneTheT(ome.xml.model.primitives.NonNegativeInteger theT, int imageIndex, int planeIndex)`
`void`	`setPlaneTheZ(ome.xml.model.primitives.NonNegativeInteger theZ, int imageIndex, int planeIndex)`
`void`	`setPlateAcquisitionAnnotationRef(java.lang.String annotation, int plateIndex, int plateAcquisitionIndex, int annotationRefIndex)`
`void`	`setPlateAcquisitionDescription(java.lang.String description, int plateIndex, int plateAcquisitionIndex)`
`void`	`setPlateAcquisitionEndTime(ome.xml.model.primitives.Timestamp endTime, int plateIndex, int plateAcquisitionIndex)`
`void`	`setPlateAcquisitionID(java.lang.String id, int plateIndex, int plateAcquisitionIndex)`
`void`	`setPlateAcquisitionMaximumFieldCount(ome.xml.model.primitives.PositiveInteger maximumFieldCount, int plateIndex, int plateAcquisitionIndex)`
`void`	`setPlateAcquisitionName(java.lang.String name, int plateIndex, int plateAcquisitionIndex)`
`void`	`setPlateAcquisitionStartTime(ome.xml.model.primitives.Timestamp startTime, int plateIndex, int plateAcquisitionIndex)`
`void`	`setPlateAcquisitionWellSampleRef(java.lang.String wellSample, int plateIndex, int plateAcquisitionIndex, int wellSampleRefIndex)`
`void`	`setPlateAnnotationRef(java.lang.String annotation, int plateIndex, int annotationRefIndex)`
`void`	`setPlateColumnNamingConvention(ome.xml.model.enums.NamingConvention columnNamingConvention, int plateIndex)`
`void`	`setPlateColumns(ome.xml.model.primitives.PositiveInteger columns, int plateIndex)`
`void`	`setPlateDescription(java.lang.String description, int plateIndex)`
`void`	`setPlateExternalIdentifier(java.lang.String externalIdentifier, int plateIndex)`
`void`	`setPlateFieldIndex(ome.xml.model.primitives.NonNegativeInteger fieldIndex, int plateIndex)`
`void`	`setPlateID(java.lang.String id, int plateIndex)`
`void`	`setPlateName(java.lang.String name, int plateIndex)`
`void`	`setPlateRowNamingConvention(ome.xml.model.enums.NamingConvention rowNamingConvention, int plateIndex)`
`void`	`setPlateRows(ome.xml.model.primitives.PositiveInteger rows, int plateIndex)`
`void`	`setPlateStatus(java.lang.String status, int plateIndex)`
`void`	`setPlateWellOriginX(ome.units.quantity.Length wellOriginX, int plateIndex)`
`void`	`setPlateWellOriginY(ome.units.quantity.Length wellOriginY, int plateIndex)`
`void`	`setPointAnnotationRef(java.lang.String annotation, int ROIIndex, int shapeIndex, int annotationRefIndex)`
`void`	`setPointFillColor(ome.xml.model.primitives.Color fill, int ROIIndex, int shapeIndex)`
`void`	`setPointFillRule(ome.xml.model.enums.FillRule fillRule, int ROIIndex, int shapeIndex)`
`void`	`setPointFontFamily(ome.xml.model.enums.FontFamily fontFamily, int ROIIndex, int shapeIndex)`
`void`	`setPointFontSize(ome.units.quantity.Length fontSize, int ROIIndex, int shapeIndex)`
`void`	`setPointFontStyle(ome.xml.model.enums.FontStyle fontStyle, int ROIIndex, int shapeIndex)`
`void`	`setPointID(java.lang.String id, int ROIIndex, int shapeIndex)`
`void`	`setPointLocked(java.lang.Boolean locked, int ROIIndex, int shapeIndex)`
`void`	`setPointStrokeColor(ome.xml.model.primitives.Color stroke, int ROIIndex, int shapeIndex)`
`void`	`setPointStrokeDashArray(java.lang.String strokeDashArray, int ROIIndex, int shapeIndex)`
`void`	`setPointStrokeWidth(ome.units.quantity.Length strokeWidth, int ROIIndex, int shapeIndex)`
`void`	`setPointText(java.lang.String text, int ROIIndex, int shapeIndex)`
`void`	`setPointTheC(ome.xml.model.primitives.NonNegativeInteger theC, int ROIIndex, int shapeIndex)`
`void`	`setPointTheT(ome.xml.model.primitives.NonNegativeInteger theT, int ROIIndex, int shapeIndex)`
`void`	`setPointTheZ(ome.xml.model.primitives.NonNegativeInteger theZ, int ROIIndex, int shapeIndex)`
`void`	`setPointTransform(ome.xml.model.AffineTransform transform, int ROIIndex, int shapeIndex)`
`void`	`setPointX(java.lang.Double x, int ROIIndex, int shapeIndex)`
`void`	`setPointY(java.lang.Double y, int ROIIndex, int shapeIndex)`
`void`	`setPolygonAnnotationRef(java.lang.String annotation, int ROIIndex, int shapeIndex, int annotationRefIndex)`
`void`	`setPolygonFillColor(ome.xml.model.primitives.Color fillColor, int ROIIndex, int shapeIndex)`
`void`	`setPolygonFillRule(ome.xml.model.enums.FillRule fillRule, int ROIIndex, int shapeIndex)`
`void`	`setPolygonFontFamily(ome.xml.model.enums.FontFamily fontFamily, int ROIIndex, int shapeIndex)`
`void`	`setPolygonFontSize(ome.units.quantity.Length fontSize, int ROIIndex, int shapeIndex)`
`void`	`setPolygonFontStyle(ome.xml.model.enums.FontStyle fontStyle, int ROIIndex, int shapeIndex)`
`void`	`setPolygonID(java.lang.String id, int ROIIndex, int shapeIndex)`
`void`	`setPolygonLocked(java.lang.Boolean locked, int ROIIndex, int shapeIndex)`
`void`	`setPolygonPoints(java.lang.String points, int ROIIndex, int shapeIndex)`
`void`	`setPolygonStrokeColor(ome.xml.model.primitives.Color strokeColor, int ROIIndex, int shapeIndex)`
`void`	`setPolygonStrokeDashArray(java.lang.String strokeDashArray, int ROIIndex, int shapeIndex)`
`void`	`setPolygonStrokeWidth(ome.units.quantity.Length strokeWidth, int ROIIndex, int shapeIndex)`
`void`	`setPolygonText(java.lang.String text, int ROIIndex, int shapeIndex)`
`void`	`setPolygonTheC(ome.xml.model.primitives.NonNegativeInteger theC, int ROIIndex, int shapeIndex)`
`void`	`setPolygonTheT(ome.xml.model.primitives.NonNegativeInteger theT, int ROIIndex, int shapeIndex)`
`void`	`setPolygonTheZ(ome.xml.model.primitives.NonNegativeInteger theZ, int ROIIndex, int shapeIndex)`
`void`	`setPolygonTransform(ome.xml.model.AffineTransform transform, int ROIIndex, int shapeIndex)`
`void`	`setPolylineAnnotationRef(java.lang.String annotation, int ROIIndex, int shapeIndex, int annotationRefIndex)`
`void`	`setPolylineFillColor(ome.xml.model.primitives.Color fill, int ROIIndex, int shapeIndex)`
`void`	`setPolylineFillRule(ome.xml.model.enums.FillRule fillRule, int ROIIndex, int shapeIndex)`
`void`	`setPolylineFontFamily(ome.xml.model.enums.FontFamily fontFamily, int ROIIndex, int shapeIndex)`
`void`	`setPolylineFontSize(ome.units.quantity.Length fontSize, int ROIIndex, int shapeIndex)`
`void`	`setPolylineFontStyle(ome.xml.model.enums.FontStyle fontStyle, int ROIIndex, int shapeIndex)`
`void`	`setPolylineID(java.lang.String id, int ROIIndex, int shapeIndex)`
`void`	`setPolylineLocked(java.lang.Boolean locked, int ROIIndex, int shapeIndex)`
`void`	`setPolylineMarkerEnd(ome.xml.model.enums.Marker markerEnd, int ROIIndex, int shapeIndex)`
`void`	`setPolylineMarkerStart(ome.xml.model.enums.Marker markerStart, int ROIIndex, int shapeIndex)`
`void`	`setPolylinePoints(java.lang.String points, int ROIIndex, int shapeIndex)`
`void`	`setPolylineStrokeColor(ome.xml.model.primitives.Color stroke, int ROIIndex, int shapeIndex)`
`void`	`setPolylineStrokeDashArray(java.lang.String strokeDashArray, int ROIIndex, int shapeIndex)`
`void`	`setPolylineStrokeWidth(ome.units.quantity.Length strokeWidth, int ROIIndex, int shapeIndex)`
`void`	`setPolylineText(java.lang.String text, int ROIIndex, int shapeIndex)`
`void`	`setPolylineTheC(ome.xml.model.primitives.NonNegativeInteger theC, int ROIIndex, int shapeIndex)`
`void`	`setPolylineTheT(ome.xml.model.primitives.NonNegativeInteger theT, int ROIIndex, int shapeIndex)`
`void`	`setPolylineTheZ(ome.xml.model.primitives.NonNegativeInteger theZ, int ROIIndex, int shapeIndex)`
`void`	`setPolylineTransform(ome.xml.model.AffineTransform transform, int ROIIndex, int shapeIndex)`
`void`	`setProjectAnnotationRef(java.lang.String annotation, int projectIndex, int annotationRefIndex)`
`void`	`setProjectDatasetRef(java.lang.String dataset, int projectIndex, int datasetRefIndex)`
`void`	`setProjectDescription(java.lang.String description, int projectIndex)`
`void`	`setProjectExperimenterGroupRef(java.lang.String group, int projectIndex)`
`void`	`setProjectExperimenterRef(java.lang.String experimenter, int projectIndex)`
`void`	`setProjectID(java.lang.String id, int projectIndex)`
`void`	`setProjectName(java.lang.String name, int projectIndex)`
`void`	`setReader(loci.formats.IFormatReader reader)` Sets the Bio-Formats reader that will be used to populate the container store.
`void`	`setReagentAnnotationRef(java.lang.String annotation, int screenIndex, int reagentIndex, int annotationRefIndex)`
`void`	`setReagentDescription(java.lang.String description, int screenIndex, int reagentIndex)`
`void`	`setReagentID(java.lang.String id, int screenIndex, int reagentIndex)`
`void`	`setReagentName(java.lang.String name, int screenIndex, int reagentIndex)`
`void`	`setReagentReagentIdentifier(java.lang.String reagentIdentifier, int screenIndex, int reagentIndex)`
`void`	`setRectangleAnnotationRef(java.lang.String annotation, int ROIIndex, int shapeIndex, int annotationRefIndex)`
`void`	`setRectangleFillColor(ome.xml.model.primitives.Color fill, int ROIIndex, int shapeIndex)`
`void`	`setRectangleFillRule(ome.xml.model.enums.FillRule fillRule, int ROIIndex, int shapeIndex)`
`void`	`setRectangleFontFamily(ome.xml.model.enums.FontFamily fontFamily, int ROIIndex, int shapeIndex)`
`void`	`setRectangleFontSize(ome.units.quantity.Length fontSize, int ROIIndex, int shapeIndex)`
`void`	`setRectangleFontStyle(ome.xml.model.enums.FontStyle fontStyle, int ROIIndex, int shapeIndex)`
`void`	`setRectangleHeight(java.lang.Double height, int ROIIndex, int shapeIndex)`
`void`	`setRectangleID(java.lang.String id, int ROIIndex, int shapeIndex)`
`void`	`setRectangleLocked(java.lang.Boolean locked, int ROIIndex, int shapeIndex)`
`void`	`setRectangleStrokeColor(ome.xml.model.primitives.Color stroke, int ROIIndex, int shapeIndex)`
`void`	`setRectangleStrokeDashArray(java.lang.String strokeDashArray, int ROIIndex, int shapeIndex)`
`void`	`setRectangleStrokeWidth(ome.units.quantity.Length strokeWidth, int ROIIndex, int shapeIndex)`
`void`	`setRectangleText(java.lang.String description, int ROIIndex, int shapeIndex)`
`void`	`setRectangleTheC(ome.xml.model.primitives.NonNegativeInteger theC, int ROIIndex, int shapeIndex)`
`void`	`setRectangleTheT(ome.xml.model.primitives.NonNegativeInteger theT, int ROIIndex, int shapeIndex)`
`void`	`setRectangleTheZ(ome.xml.model.primitives.NonNegativeInteger theZ, int ROIIndex, int shapeIndex)`
`void`	`setRectangleTransform(ome.xml.model.AffineTransform transform, int ROIIndex, int shapeIndex)`
`void`	`setRectangleWidth(java.lang.Double width, int ROIIndex, int shapeIndex)`
`void`	`setRectangleX(java.lang.Double x, int ROIIndex, int shapeIndex)`
`void`	`setRectangleY(java.lang.Double y, int ROIIndex, int shapeIndex)`
`void`	`setReferenceStringCache(java.util.Map<java.lang.String,java.lang.String[]> referenceStringCache)` Sets the string based reference cache for this container store.
`void`	`setRightsRightsHeld(java.lang.String value)`
`void`	`setRightsRightsHolder(java.lang.String value)`
`void`	`setROIAnnotationRef(java.lang.String annotation, int ROIIndex, int annotationRefIndex)`
`void`	`setROIDescription(java.lang.String description, int ROIIndex)`
`void`	`setROIID(java.lang.String id, int ROIIndex)`
`void`	`setROIName(java.lang.String name, int ROIIndex)`
`void`	`setRoot(ome.xml.meta.MetadataRoot root)`
`void`	`setScreenAnnotationRef(java.lang.String annotation, int screenIndex, int annotationRefIndex)`
`void`	`setScreenDescription(java.lang.String description, int screenIndex)`
`void`	`setScreenID(java.lang.String id, int screenIndex)`
`void`	`setScreenName(java.lang.String name, int screenIndex)`
`void`	`setScreenPlateRef(java.lang.String plate, int screenIndex, int plateRefIndex)`
`void`	`setScreenProtocolDescription(java.lang.String protocolDescription, int screenIndex)`
`void`	`setScreenProtocolIdentifier(java.lang.String protocolIdentifier, int screenIndex)`
`void`	`setScreenReagentSetDescription(java.lang.String reagentSetDescription, int screenIndex)`
`void`	`setScreenReagentSetIdentifier(java.lang.String reagentSetIdentifier, int screenIndex)`
`void`	`setScreenType(java.lang.String type, int screenIndex)`
`void`	`setStageLabelName(java.lang.String name, int imageIndex)`
`void`	`setStageLabelX(ome.units.quantity.Length x, int imageIndex)`
`void`	`setStageLabelY(ome.units.quantity.Length y, int imageIndex)`
`void`	`setStageLabelZ(ome.units.quantity.Length z, int imageIndex)`
`void`	`setTagAnnotationAnnotationRef(java.lang.String annotation, int tagAnnotationIndex, int annotationRefIndex)`
`void`	`setTagAnnotationAnnotator(java.lang.String value, int index)`
`void`	`setTagAnnotationDescription(java.lang.String description, int tagAnnotationIndex)`
`void`	`setTagAnnotationID(java.lang.String id, int tagAnnotationIndex)`
`void`	`setTagAnnotationNamespace(java.lang.String namespace, int tagAnnotationIndex)`
`void`	`setTagAnnotationValue(java.lang.String value, int tagAnnotationIndex)`
`void`	`setTermAnnotationAnnotationRef(java.lang.String annotation, int termAnnotationIndex, int annotationRefIndex)`
`void`	`setTermAnnotationAnnotator(java.lang.String value, int index)`
`void`	`setTermAnnotationDescription(java.lang.String description, int termAnnotationIndex)`
`void`	`setTermAnnotationID(java.lang.String id, int termAnnotationIndex)`
`void`	`setTermAnnotationNamespace(java.lang.String namespace, int termAnnotationIndex)`
`void`	`setTermAnnotationValue(java.lang.String value, int termAnnotationIndex)`
`void`	`setTiffDataFirstC(ome.xml.model.primitives.NonNegativeInteger firstC, int imageIndex, int tiffDataIndex)`
`void`	`setTiffDataFirstT(ome.xml.model.primitives.NonNegativeInteger firstT, int imageIndex, int tiffDataIndex)`
`void`	`setTiffDataFirstZ(ome.xml.model.primitives.NonNegativeInteger firstZ, int imageIndex, int tiffDataIndex)`
`void`	`setTiffDataIFD(ome.xml.model.primitives.NonNegativeInteger ifd, int imageIndex, int tiffDataIndex)`
`void`	`setTiffDataPlaneCount(ome.xml.model.primitives.NonNegativeInteger planeCount, int imageIndex, int tiffDataIndex)`
`void`	`setTile(java.lang.Long pixId, byte[] arrayBuf, int z, int c, int t, int x, int y, int w, int h)` Writes a tile of pixels to the server.
`void`	`setTimestampAnnotationAnnotationRef(java.lang.String annotation, int timestampAnnotationIndex, int annotationRefIndex)`
`void`	`setTimestampAnnotationAnnotator(java.lang.String value, int index)`
`void`	`setTimestampAnnotationDescription(java.lang.String description, int timestampAnnotationIndex)`
`void`	`setTimestampAnnotationID(java.lang.String id, int timestampAnnotationIndex)`
`void`	`setTimestampAnnotationNamespace(java.lang.String namespace, int timestampAnnotationIndex)`
`void`	`setTimestampAnnotationValue(ome.xml.model.primitives.Timestamp value, int timestampAnnotationIndex)`
`void`	`setTransmittanceRangeCutIn(ome.units.quantity.Length cutIn, int instrumentIndex, int filterIndex)`
`void`	`setTransmittanceRangeCutInTolerance(ome.units.quantity.Length cutInTolerance, int instrumentIndex, int filterIndex)`
`void`	`setTransmittanceRangeCutOut(ome.units.quantity.Length cutOut, int instrumentIndex, int filterIndex)`
`void`	`setTransmittanceRangeCutOutTolerance(ome.units.quantity.Length cutOutTolerance, int instrumentIndex, int filterIndex)`
`void`	`setTransmittanceRangeTransmittance(ome.xml.model.primitives.PercentFraction transmittance, int instrumentIndex, int filterIndex)`
`void`	`setUserSpecifiedAnnotations(java.util.List<Annotation> annotations)` Sets the user specified image annotations.
`void`	`setUserSpecifiedDescription(java.lang.String description)` Sets the user specified image/plate description.
`void`	`setUserSpecifiedName(java.lang.String name)` Sets the user specified image/plate name.
`void`	`setUserSpecifiedPhysicalPixelSizes(java.lang.Double physicalSizeX, java.lang.Double physicalSizeY, java.lang.Double physicalSizeZ)` Sets the user specified physical pixel sizes.
`void`	`setUserSpecifiedTarget(IObject target)` Sets the user-specified linkage target (usually a Dataset for Images) and a Screen for Plates).
`void`	`setUUID(java.lang.String uuid)`
`void`	`setUUIDFileName(java.lang.String fileName, int imageIndex, int tiffDataIndex)`
`void`	`setUUIDValue(java.lang.String fileName, int imageIndex, int tiffDataIndex)`
`void`	`setWellAnnotationRef(java.lang.String annotation, int plateIndex, int wellIndex, int annotationRefIndex)`
`void`	`setWellColor(ome.xml.model.primitives.Color color, int plateIndex, int wellIndex)`
`void`	`setWellColumn(ome.xml.model.primitives.NonNegativeInteger column, int plateIndex, int wellIndex)`
`void`	`setWellExternalDescription(java.lang.String externalDescription, int plateIndex, int wellIndex)`
`void`	`setWellExternalIdentifier(java.lang.String externalIdentifier, int plateIndex, int wellIndex)`
`void`	`setWellID(java.lang.String id, int plateIndex, int wellIndex)`
`void`	`setWellReagentRef(java.lang.String reagent, int plateIndex, int wellIndex)`
`void`	`setWellRow(ome.xml.model.primitives.NonNegativeInteger row, int plateIndex, int wellIndex)`
`void`	`setWellSampleID(java.lang.String id, int plateIndex, int wellIndex, int wellSampleIndex)`
`void`	`setWellSampleImageRef(java.lang.String image, int plateIndex, int wellIndex, int wellSampleIndex)`
`void`	`setWellSampleIndex(ome.xml.model.primitives.NonNegativeInteger index, int plateIndex, int wellIndex, int wellSampleIndex)`
`void`	`setWellSamplePositionX(ome.units.quantity.Length positionX, int plateIndex, int wellIndex, int wellSampleIndex)`
`void`	`setWellSamplePositionY(ome.units.quantity.Length positionY, int plateIndex, int wellIndex, int wellSampleIndex)`
`void`	`setWellSampleTimepoint(ome.xml.model.primitives.Timestamp timepoint, int plateIndex, int wellIndex, int wellSampleIndex)`
`void`	`setWellType(java.lang.String type, int plateIndex, int wellIndex)`
`void`	`setXMLAnnotationAnnotationRef(java.lang.String annotation, int XMLAnnotationIndex, int annotationRefIndex)`
`void`	`setXMLAnnotationAnnotator(java.lang.String value, int index)`
`void`	`setXMLAnnotationDescription(java.lang.String description, int XMLAnnotationIndex)`
`void`	`setXMLAnnotationID(java.lang.String id, int XMLAnnotationIndex)`
`void`	`setXMLAnnotationNamespace(java.lang.String namespace, int XMLAnnotationIndex)`
`void`	`setXMLAnnotationValue(java.lang.String value, int XMLAnnotationIndex)`
`AffineTransform`	`toRType(ome.xml.model.AffineTransform schemaTransform)` Transforms a Java type into the corresponding OMERO RType.
`RBool`	`toRType(java.lang.Boolean value)` Transforms a Java type into the corresponding OMERO RType.
`RInt`	`toRType(ome.xml.model.primitives.Color value)` Transforms a Java type into the corresponding OMERO RType.
`RDouble`	`toRType(java.lang.Double value)` Transforms a Java type into the corresponding OMERO RType.
`RDouble`	`toRType(java.lang.Float value)` Transforms a Java type into the corresponding OMERO RType.
`RInt`	`toRType(java.lang.Integer value)` Transforms a Java type into the corresponding OMERO RType.
`RLong`	`toRType(java.lang.Long value)` Transforms a Java type into the corresponding OMERO RType.
`RString`	`toRType(ome.xml.model.enums.NamingConvention value)` Transforms a Java type into the corresponding OMERO RType.
`RInt`	`toRType(ome.xml.model.primitives.NonNegativeInteger value)` Transforms a Java type into the corresponding OMERO RType.
`RLong`	`toRType(ome.xml.model.primitives.NonNegativeLong value)` Transforms a Java type into the corresponding OMERO RType.
`RDouble`	`toRType(ome.xml.model.primitives.PercentFraction value)` Transforms a Java type into the corresponding OMERO RType.
`RDouble`	`toRType(ome.xml.model.primitives.PositiveFloat value)` Transforms a Java type into the corresponding OMERO RType.
`RString`	`toRType(java.lang.String value)` Transforms a Java type into the corresponding OMERO RType.
`RTime`	`toRType(ome.xml.model.primitives.Timestamp value)` Transforms a Java type into the corresponding OMERO RType.
`void`	`updateFileSize(OriginalFile file, long size)`
`void`	`updatePixels(java.util.List<Pixels> pixelsList)` Updates a list of Pixels.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail
- OMERO_EMISSION_FILTER_SUFFIX
```
public static final java.lang.String OMERO_EMISSION_FILTER_SUFFIX
```
  Emission filter LSID suffix. See setFilterSetEmissionFilterRef(String, int, int, int) for an explanation of its usage.
  
  See Also:
  
  Constant Field Values
- OMERO_EXCITATION_FILTER_SUFFIX
```
public static final java.lang.String OMERO_EXCITATION_FILTER_SUFFIX
```
  Excitation filter LSID suffix. See setFilterSetExcitationFilterRef(String, int, int, int) for an explanation of its usage.
  
  See Also:
  
  Constant Field Values

Constructor Detail
- OMEROMetadataStoreClient
```
public OMEROMetadataStoreClient()
```

Method Detail

getKeepAlive
```
public ClientKeepAlive getKeepAlive()
```
Returns clientKeepAlive created in store

Returns:

current ClientKeepAlive

logVersionInfo

public void logVersionInfo(java.lang.String clientVersion)
                    throws ServerError

Throws:: ServerError

getDefaultBatchSize
```
public int getDefaultBatchSize()
```
Returns:

user-configured "omero.batch_size" or DEFAULTBATCHSIZE if none is set.

getDefaultBlockSize
```
public int getDefaultBlockSize()
```
Returns:

user-configured "omero.block_size" or DEFAULTBLOCKSIZE if none is set.

getIQuery
```
public IQueryPrx getIQuery()
```
Returns:

IQuery proxy

setEncryptedConnection

public void setEncryptedConnection(boolean encryptedConnection)

isEncryptedConnection

public boolean isEncryptedConnection()

setGroup
```
public java.lang.Long setGroup(java.lang.Long groupID)
```
Sets the id which will be used to set the call context for all services. If null, the call context will be left which will then use the context of the session.

Parameters:

groupID - the group ID to use for call contexts

Returns:

the previous group ID, may be null

initialize
```
public void initialize(ServiceFactoryPrx serviceFactory)
                throws ServerError
```
Initializes the MetadataStore with an already logged in, ready to go service factory. When finished with this instance, close stateful services via closeServices().

Parameters:

serviceFactory - The factory. Mustn't be null.

Throws:

ServerError - if the services could not be initialized

initialize
```
public void initialize(client c)
                throws ServerError
```
Initializes the MetadataStore with an already logged in, ready to go service factory. When finished with this instance, close stateful services via closeServices().

Parameters:

c - The client. Mustn't be null.

Throws:

ServerError - if the services could not be initialized

initialize
```
public void initialize(java.lang.String username,
                       java.lang.String password,
                       java.lang.String server,
                       int port)
                throws Glacier2.CannotCreateSessionException,
                       Glacier2.PermissionDeniedException,
                       ServerError
```
Initializes the MetadataStore taking string parameters to feed to the OMERO Blitz client object. Using this method creates an unsecure session. When finished with this instance, close all resources via logout()

Parameters:

username - User's omename.

password - User's password.

server - Server hostname.

port - Server port.

Throws:

Glacier2.CannotCreateSessionException - If there is a session error when creating the OMERO Blitz client object.

Glacier2.PermissionDeniedException - If there is a problem logging the user in.

ServerError - If there is a critical error communicating with the server.

initialize
```
public void initialize(java.lang.String username,
                       java.lang.String password,
                       java.lang.String server,
                       int port,
                       boolean isSecure)
                throws Glacier2.CannotCreateSessionException,
                       Glacier2.PermissionDeniedException,
                       ServerError
```
Initializes the MetadataStore taking string parameters to feed to the OMERO Blitz client object. Using this method to create either secure or unsecure sessions. When finished with this instance, close all resources via logout()

Parameters:

username - User's omename.

password - User's password.

server - Server hostname.

port - Server port.

isSecure - is this session secure

Throws:

Glacier2.CannotCreateSessionException - If there is a session error when creating the OMERO Blitz client object.

Glacier2.PermissionDeniedException - If there is a problem logging the user in.

ServerError - If there is a critical error communicating with the server.

initialize
```
public void initialize(java.lang.String username,
                       java.lang.String password,
                       java.lang.String server,
                       int port,
                       java.lang.Long group,
                       boolean isSecure)
                throws Glacier2.CannotCreateSessionException,
                       Glacier2.PermissionDeniedException,
                       ServerError
```
Initializes the MetadataStore taking string parameters to feed to the OMERO Blitz client object. Using this method to create either secure or unsecure sessions and sets the user's group to supplied group. When finished with this instance, close all resources via logout()

Parameters:

username - User's omename.

password - User's password.

server - Server hostname.

port - Server port.

group - User's current group.

isSecure - is this session secure

Throws:

Glacier2.CannotCreateSessionException - If there is a session error when creating the OMERO Blitz client object.

Glacier2.PermissionDeniedException - If there is a problem logging the user in.

ServerError - If there is a critical error communicating with the server.

initialize
```
public void initialize(java.lang.String server,
                       int port,
                       java.lang.String sessionKey)
                throws Glacier2.CannotCreateSessionException,
                       Glacier2.PermissionDeniedException,
                       ServerError
```
Initializes the MetadataStore by joining an existing session. Use this method only with unsecure sessions. When finished with this instance, close all resources via logout()

Parameters:

server - Server hostname.

port - Server port.

sessionKey - Bind session key.

Throws:

Glacier2.CannotCreateSessionException - if a session could not be created

Glacier2.PermissionDeniedException - if the services may not be initialized

ServerError - if the services could not be initialized

initialize
```
public void initialize(java.lang.String server,
                       int port,
                       java.lang.String sessionKey,
                       boolean isSecure)
                throws Glacier2.CannotCreateSessionException,
                       Glacier2.PermissionDeniedException,
                       ServerError
```
Initializes the MetadataStore by joining an existing session. Use this method only with unsecure sessions. When finished with this instance, close all resources via logout()

Parameters:

server - Server hostname.

port - Server port.

sessionKey - Bind session key.

isSecure - if a secure session should be created

Throws:

Glacier2.CannotCreateSessionException - if a session could not be created

Glacier2.PermissionDeniedException - if the services may not be initialized

ServerError - if the services could not be initialized

getServiceFactory
```
public ServiceFactoryPrx getServiceFactory()
```
Returns the currently active service factory.

Returns:

See above.

ping
```
public void ping()
```
Pings all registered OMERO Blitz proxies.

setCurrentLogFile

public void setCurrentLogFile(java.lang.String logFilename,
                              java.lang.String token)

updateFileSize

public void updateFileSize(OriginalFile file,
                           long size)
                    throws ServerError

Throws:: ServerError

setEnumerationProvider
```
public void setEnumerationProvider(EnumerationProvider enumProvider)
```
Sets the active enumeration provider.

Parameters:

enumProvider - Enumeration provider to use.

getEnumerationProvider
```
public EnumerationProvider getEnumerationProvider()
```
Retrieves the active enumeration provider.

Returns:

See above.

setInstanceProvider
```
public void setInstanceProvider(InstanceProvider instanceProvider)
```
Sets the active instance provider.

Parameters:

instanceProvider - the instance provider to use

getInstanceProvider
```
public InstanceProvider getInstanceProvider()
```
Retrieves the active instance provider.

Returns:

See above.

toRType
```
public RInt toRType(java.lang.Integer value)
```
Transforms a Java type into the corresponding OMERO RType.

Parameters:

value - Java concrete type value.

Returns:

RType or null if value is null.

toRType
```
public RInt toRType(ome.xml.model.primitives.NonNegativeInteger value)
```
Transforms a Java type into the corresponding OMERO RType.

Parameters:

value - Java concrete type value.

Returns:

RType or null if value is null.

toRType
```
public RLong toRType(ome.xml.model.primitives.NonNegativeLong value)
```
Transforms a Java type into the corresponding OMERO RType.

Parameters:

value - Java concrete type value.

Returns:

RType or null if value is null.

toRType
```
public RDouble toRType(ome.xml.model.primitives.PositiveFloat value)
```
Transforms a Java type into the corresponding OMERO RType.

Parameters:

value - Java concrete type value.

Returns:

RType or null if value is null.

toRType
```
public RDouble toRType(ome.xml.model.primitives.PercentFraction value)
```
Transforms a Java type into the corresponding OMERO RType.

Parameters:

value - Java concrete type value.

Returns:

RType or null if value is null.

toRType
```
public RLong toRType(java.lang.Long value)
```
Transforms a Java type into the corresponding OMERO RType.

Parameters:

value - Java concrete type value.

Returns:

RType or null if value is null.

toRType
```
public RString toRType(java.lang.String value)
```
Transforms a Java type into the corresponding OMERO RType.

Parameters:

value - Java concrete type value.

Returns:

RType or null if value is null.

toRType
```
public RBool toRType(java.lang.Boolean value)
```
Transforms a Java type into the corresponding OMERO RType.

Parameters:

value - Java concrete type value.

Returns:

RType or null if value is null.

toRType
```
public RDouble toRType(java.lang.Double value)
```
Transforms a Java type into the corresponding OMERO RType.

Parameters:

value - Java concrete type value.

Returns:

RType or null if value is null.

toRType
```
public RDouble toRType(java.lang.Float value)
```
Transforms a Java type into the corresponding OMERO RType.

Parameters:

value - Java concrete type value.

Returns:

RType or null if value is null.

toRType
```
public RTime toRType(ome.xml.model.primitives.Timestamp value)
```
Transforms a Java type into the corresponding OMERO RType.

Parameters:

value - Java concrete type value.

Returns:

RType or null if value is null.

toRType
```
public RString toRType(ome.xml.model.enums.NamingConvention value)
```
Transforms a Java type into the corresponding OMERO RType.

Parameters:

value - Java concrete type value.

Returns:

RType or null if value is null.

toRType
```
public AffineTransform toRType(ome.xml.model.AffineTransform schemaTransform)
```
Transforms a Java type into the corresponding OMERO RType.

Parameters:

schemaTransform - Java concrete type value.

Returns:

RType or null if value is null.

toRType
```
public RInt toRType(ome.xml.model.primitives.Color value)
```
Transforms a Java type into the corresponding OMERO RType.

Parameters:

value - Java concrete type value.

Returns:

RType or null if value is null.

closeServices
```
public void closeServices()
```
Closes all stateful services. This method should be preferred over logout() when initialized via an client or a ServiceFactoryPrx instance.

See Also:

initialize(client), initialize(ServiceFactoryPrx)

logout
```
public void logout()
```
Destroys the sessionFactory and closes the client. This method should not be called when initialized via an client or a ServiceFactoryPrx instance. * @see #initialize(client)

See Also:

initialize(ServiceFactoryPrx), closeServices()

prepare
```
public void prepare(java.util.Map<java.lang.Integer,Image> existingMetadata)
```
Prepares the metadata store using existing metadata that has been pre-registered by OMERO.fs. The expected graph should be fully loaded:
- Image
- Pixels
NOTE: An execution of prepare() is only valid for a SINGLE importImage() execution. Following importImage() the existing metadata map will be reset regardless of success or failure.
Parameters:

existingMetadata - Map of imageIndex or series vs. populated Image source graph with the fetched objects defined above.

createRoot
```
public void createRoot()
```
Specified by:

createRoot in interface ome.xml.meta.MetadataStore

getRoot
```
public ome.xml.meta.MetadataRoot getRoot()
```
Specified by:

getRoot in interface ome.xml.meta.MetadataStore

getReader
```
public loci.formats.IFormatReader getReader()
```
Description copied from interface: IObjectContainerStore

Returns the current Bio-Formats reader that has been used to populate the container store.

Specified by:

getReader in interface IObjectContainerStore

Returns:

See above.

setReader
```
public void setReader(loci.formats.IFormatReader reader)
```
Description copied from interface: IObjectContainerStore

Sets the Bio-Formats reader that will be used to populate the container store.

Specified by:

setReader in interface IObjectContainerStore

Parameters:

reader - Bio-Formats reader.

getUserSpecifiedAnnotations
```
public java.util.List<Annotation> getUserSpecifiedAnnotations()
```
Description copied from interface: IObjectContainerStore

Returns the user specified annotations.

Specified by:

getUserSpecifiedAnnotations in interface IObjectContainerStore

Returns:

See above.

setUserSpecifiedAnnotations
```
public void setUserSpecifiedAnnotations(java.util.List<Annotation> annotations)
```
Description copied from interface: IObjectContainerStore

Sets the user specified image annotations.

Specified by:

setUserSpecifiedAnnotations in interface IObjectContainerStore

Parameters:

annotations - user specified annotations

getUserSpecifiedName
```
public java.lang.String getUserSpecifiedName()
```
Description copied from interface: IObjectContainerStore

Returns the user specified image/plate name.

Specified by:

getUserSpecifiedName in interface IObjectContainerStore

Returns:

See above.

getUserSpecifiedImageName

public java.lang.String getUserSpecifiedImageName()

setUserSpecifiedName
```
public void setUserSpecifiedName(java.lang.String name)
```
Description copied from interface: IObjectContainerStore

Sets the user specified image/plate name.

Specified by:

setUserSpecifiedName in interface IObjectContainerStore

Parameters:

name - user specified image/plate name

getUserSpecifiedDescription
```
public java.lang.String getUserSpecifiedDescription()
```
Description copied from interface: IObjectContainerStore

Returns the user specified image/plate description.

Specified by:

getUserSpecifiedDescription in interface IObjectContainerStore

Returns:

See above.

setUserSpecifiedDescription
```
public void setUserSpecifiedDescription(java.lang.String description)
```
Description copied from interface: IObjectContainerStore

Sets the user specified image/plate description.

Specified by:

setUserSpecifiedDescription in interface IObjectContainerStore

Parameters:

description - user-specified image/plate description

getUserSpecifiedTarget
```
public IObject getUserSpecifiedTarget()
```
Description copied from interface: IObjectContainerStore

Returns the user-specified linkage target (usually a Dataset for Images) and a Screen for Plates).

Specified by:

getUserSpecifiedTarget in interface IObjectContainerStore

Returns:

See above.

setUserSpecifiedTarget
```
public void setUserSpecifiedTarget(IObject target)
```
Description copied from interface: IObjectContainerStore

Sets the user-specified linkage target (usually a Dataset for Images) and a Screen for Plates).

Specified by:

setUserSpecifiedTarget in interface IObjectContainerStore

Parameters:

target - user-specified linkage target

getUserSpecifiedPhysicalPixelSizes
```
public java.lang.Double[] getUserSpecifiedPhysicalPixelSizes()
```
Description copied from interface: IObjectContainerStore

Returns the user specified physical pixel sizes.

Specified by:

getUserSpecifiedPhysicalPixelSizes in interface IObjectContainerStore

Returns:

An array of double[] { physicalSizeX, physicalSizeY, physicalSizeZ } as specified by the user. A value of null for any one index states the user has not made a choice for the size of that particular dimension.

setUserSpecifiedPhysicalPixelSizes
```
public void setUserSpecifiedPhysicalPixelSizes(java.lang.Double physicalSizeX,
                                               java.lang.Double physicalSizeY,
                                               java.lang.Double physicalSizeZ)
```
Description copied from interface: IObjectContainerStore

Sets the user specified physical pixel sizes. A value of null states the original file physical size for that dimension should be used.

Specified by:

setUserSpecifiedPhysicalPixelSizes in interface IObjectContainerStore

Parameters:

physicalSizeX - Physical pixel size width.

physicalSizeY - Physical pixel height.

physicalSizeZ - Physical pixel depth.

getModelProcessors
```
public java.util.List<ModelProcessor> getModelProcessors()
```
Retrieves the current list of model processors the metadata store is using.

Returns:

See above.

setModelProcessors
```
public void setModelProcessors(java.util.List<ModelProcessor> modelProcessors)
```
Sets the current set of model processors.

Parameters:

modelProcessors - List of model processors to use.

removeModelProcessor
```
public void removeModelProcessor(ModelProcessor processor)
```
Removes a model processor from use.

Parameters:

processor - Model processor to remove.

addModelProcessor
```
public boolean addModelProcessor(ModelProcessor processor)
```
Adds a model processor to the end of the processing chain.

Parameters:

processor - Model processor to add.

Returns:

true as specified by Collection.add(Object)

getContainerCache
```
public java.util.Map<ome.util.LSID,IObjectContainer> getContainerCache()
```
Description copied from interface: IObjectContainerStore

Returns the current container cache.

Specified by:

getContainerCache in interface IObjectContainerStore

Returns:

See above.

getReferenceCache
```
public java.util.Map<ome.util.LSID,java.util.List<ome.util.LSID>> getReferenceCache()
```
Description copied from interface: IObjectContainerStore

Returns the current reference cache.

Specified by:

getReferenceCache in interface IObjectContainerStore

Returns:

See above.

getAuthoritativeContainerCache
```
public java.util.Map<java.lang.Class<? extends IObject>,java.util.Map<java.lang.String,IObjectContainer>> getAuthoritativeContainerCache()
```
Description copied from interface: IObjectContainerStore

Returns the current authoritative LSID container cache. This container cache records the explicitly set LSID to container references.

Specified by:

getAuthoritativeContainerCache in interface IObjectContainerStore

Returns:

See above.

addReference
```
public void addReference(ome.util.LSID source,
                         ome.util.LSID target)
```
Adds a reference to the reference cache.

Specified by:

addReference in interface IObjectContainerStore

Parameters:

source - Source LSID to add.

target - Target LSID to add.

getReferenceStringCache
```
public java.util.Map<java.lang.String,java.lang.String[]> getReferenceStringCache()
```
Description copied from interface: IObjectContainerStore

Returns the current string based reference cache. This is usually populated by a ReferenceProcessor instance.

Specified by:

getReferenceStringCache in interface IObjectContainerStore

Returns:

See above.

setReferenceStringCache
```
public void setReferenceStringCache(java.util.Map<java.lang.String,java.lang.String[]> referenceStringCache)
```
Description copied from interface: IObjectContainerStore

Sets the string based reference cache for this container store. This is usually called by a ReferenceProcessor instance.

Specified by:

setReferenceStringCache in interface IObjectContainerStore

Parameters:

referenceStringCache - String based reference cache to use.

getSourceObject
```
public IObject getSourceObject(ome.util.LSID LSID)
```
Description copied from interface: IObjectContainerStore

Retrieves an OMERO Blitz source object for a given LSID.

Specified by:

getSourceObject in interface IObjectContainerStore

Parameters:

LSID - LSID to retrieve a source object for.

Returns:

See above.

getSourceObjects
```
public <T extends IObject> java.util.List<T> getSourceObjects(java.lang.Class<T> klass)
```
Description copied from interface: IObjectContainerStore

Retrieves all OMERO Blitz source objects of a given class.

Specified by:

getSourceObjects in interface IObjectContainerStore

Parameters:

klass - Class to retrieve source objects for.

Returns:

See above.

hasReference
```
public boolean hasReference(ome.util.LSID source,
                            ome.util.LSID target)
```
Description copied from interface: IObjectContainerStore

Checks to see if there is currently an active reference for two LSIDs.

Specified by:

hasReference in interface IObjectContainerStore

Parameters:

source - LSID of the source object.

target - LSID of the target object.

Returns:

true if a reference exists, false otherwise.

setPixelsFile
```
public void setPixelsFile(long pixelsId,
                          java.lang.String file,
                          java.lang.String repo)
                   throws ServerError
```
Sets the path, name and repo in the pixels table.

Parameters:

pixelsId - the ID of the Pixels object

file - the file's filename, with path in the repository

repo - the file's repository's UUID

Throws:

ServerError - in the event of a server error

setCurrentGroup
```
public void setCurrentGroup(long groupID)
                     throws ServerError
```
Changes the default group of the currently logged in user.

Parameters:

groupID - The id of the group.

Throws:

ServerError - if the group could not be set or the services initialized accordingly

mapUserGroups
```
public java.util.Map<java.lang.Long,java.lang.String> mapUserGroups()
                                                             throws ServerError
```
Maps the user's groups for use by ScreenLogin.registerGroup() Also strips system groups from this map

Returns:

map of group id and name

Throws:

ServerError - if the groups could not be mapped

getDefaultGroupName
```
public java.lang.String getDefaultGroupName()
                                     throws ServerError
```
Retrieve the default group's name

Returns:

the name of the default group

Throws:

ServerError - if the default group could not be retrieved

getDefaultGroupLevel
```
@Deprecated
public int getDefaultGroupLevel()
                                     throws ServerError
```
Deprecated.

Retrieve the default group's permission 'level'.

Returns:

ImportEvent's group level

Throws:

ServerError - if the default group could not be retrieved

getRepositorySpace
```
public long getRepositorySpace()
```
Returns:

repository space as a long

postProcess
```
public void postProcess()
```
Post processes the internal structure of the client side MetadataStore. Should be called before saveToDB(FilesetJobLink).

saveToDB
```
public java.util.Map<java.lang.String,java.util.List<IObject>> saveToDB(FilesetJobLink link)
```
Updates the server side MetadataStore with a list of our objects and references and saves them into the database.

Parameters:

link - the link to save to the database

Returns:

List of Pixels after database commit.

launchProcessing

public java.util.List<InteractiveProcessorPrx> launchProcessing()

getTarget
```
public <T extends IObject> T getTarget(java.lang.Class<T> klass,
                                       long id)
```
Helper method to retrieve an object from iQuery

Type Parameters:

T - the kind of model object to retrieve

Parameters:

klass - the class of the model object

id - the ID of the model object

Returns:

the model object

getProject
```
public Project getProject(long projectId)
```
Parameters:

projectId -

Returns:

project with given id

addDataset

public Dataset addDataset(java.lang.String datasetName,
                          java.lang.String datasetDescription,
                          Project project)

Parameters:: datasetName - the name of the dataset; datasetDescription - the description of the dataset; project - the project in which the dataset is (if any)
Returns:: the newly persisted dataset

getExperimenterID
```
public long getExperimenterID()
```
Returns:

- experimenter id

getConfigValue
```
public java.lang.String getConfigValue(java.lang.String key)
```
Retrieves a configuration value from the IConfig service.

Parameters:

key - Key for the string encoded value.

Returns:

String encoded configuration value.

getScreens

public java.util.List<Screen> getScreens()

Returns:: the screens

getProjects

public java.util.List<Project> getProjects()

Returns:: the projects

getDatasets
```
public java.util.List<Dataset> getDatasets(Project p)
```
Parameters:

p - the project whose datasets to get (null for orphaned datasets)

Returns:

the datasets

getDatasetsWithoutProjects

public java.util.List<Dataset> getDatasetsWithoutProjects()

Returns:: the orphaned datasets

addProject
```
public Project addProject(java.lang.String projectName,
                          java.lang.String projectDescription)
```
Parameters:

projectName - the name of the project

projectDescription - the description of the project

Returns:

the newly persisted project

addScreen
```
public Screen addScreen(java.lang.String screenName,
                        java.lang.String screenDescription)
```
Parameters:

screenName - the name of the screen

screenDescription - the description of the screen

Returns:

the newly persisted screen

preparePixelsStore
```
public void preparePixelsStore(java.util.List<java.lang.Long> pixelsIds)
```
Prepares the server side RawPixelsStore.

Parameters:

pixelsIds - List of Pixels IDs we'll be populating.

finalizePixelStore
```
public void finalizePixelStore()
                        throws ServerError
```
Closes the active raw pixels store. Finalizing any open server side resources. The call to close on the RawPixelsStorePrx may throw, in which case the current import should be considered failed, since the saving of the pixels server-side will have not completed successfully.

Throws:

ServerError - if the pixel store could not be finalized or a new one created

See Also:

Trac ticket #5594

getTileSize
```
public int[] getTileSize(java.lang.Long pixId)
                  throws ServerError
```
Retrieves the suggested tile size for a pixels set.

Parameters:

pixId - Pixels set to write to.

Returns:

Width and height of the tile as an array.

Throws:

ServerError - If there is an error writing this tile to the server.

setTile
```
public void setTile(java.lang.Long pixId,
                    byte[] arrayBuf,
                    int z,
                    int c,
                    int t,
                    int x,
                    int y,
                    int w,
                    int h)
             throws ServerError
```
Writes a tile of pixels to the server.

Parameters:

pixId - Pixels set to write to.

arrayBuf - Byte array containing all pixels for this plane.

z - Z offset within the Pixels set.

c - Channel offset within the Pixels set.

t - Timepoint offset within the Pixels set.

x - X offset of the tile.

y - Y offset of the tile.

w - Width of the tile.

h - Height of the tile.

Throws:

ServerError - If there is an error writing this tile to the server.

See Also:

setPlane(Long, byte[], int, int, int)

setPlane
```
public void setPlane(java.lang.Long pixId,
                     byte[] arrayBuf,
                     int z,
                     int c,
                     int t)
              throws ServerError
```
Writes a plane to the server.

Parameters:

pixId - Pixels set to write to.

arrayBuf - Byte array containing all pixels for this plane.

z - Z offset within the Pixels set.

c - Channel offset within the Pixels set.

t - Timepoint offset within the Pixels set.

Throws:

ServerError - If there is an error writing this plane to the server.

setChannelGlobalMinMax

public void setChannelGlobalMinMax(int channel,
                                   double minimum,
                                   double maximum,
                                   int series)

Specified by:: setChannelGlobalMinMax in interface loci.formats.meta.IMinMaxStore

updatePixels
```
public void updatePixels(java.util.List<Pixels> pixelsList)
```
Updates a list of Pixels.

Parameters:

pixelsList - List of Pixels to update.

populateMinMax
```
public void populateMinMax()
```
Sends all the minimums and maximums for all images processed so far to the server.

resetDefaultsAndGenerateThumbnails
```
public void resetDefaultsAndGenerateThumbnails(java.util.List<java.lang.Long> plateIds,
                                               java.util.List<java.lang.Long> pixelsIds)
```
Resets the defaults and generates thumbnails for a given set of Pixels IDs.

Parameters:

plateIds - Set of Plate IDs to reset defaults and thumbnails for.

pixelsIds - Set of Pixels IDs to reset defaults and thumbnails for.

getIObjectContainer
```
public IObjectContainer getIObjectContainer(java.lang.Class<? extends IObject> klass,
                                            java.util.LinkedHashMap<Index,java.lang.Integer> indexes)
```
Description copied from interface: IObjectContainerStore

Retrieves an IObject container for a given class and location within the OME-XML data model. NOTE: The container will be created if it does not already exist.

Specified by:

getIObjectContainer in interface IObjectContainerStore

Parameters:

klass - Class to retrieve a container for.

indexes - Indexes into the OME-XML data model.

Returns:

See above.

removeIObjectContainer
```
public void removeIObjectContainer(ome.util.LSID lsid)
```
Description copied from interface: IObjectContainerStore

Removes an IObject container from within the OME-XML data model store.

Specified by:

removeIObjectContainer in interface IObjectContainerStore

Parameters:

lsid - LSID of the container to remove.

getIObjectContainers
```
public java.util.List<IObjectContainer> getIObjectContainers(java.lang.Class<? extends IObject> klass)
```
Description copied from interface: IObjectContainerStore

Retrieves all IObject containers of a given class. NOTE: this will only return existing containers.

Specified by:

getIObjectContainers in interface IObjectContainerStore

Parameters:

klass - Class to retrieve containers for.

Returns:

See above.

countCachedContainers
```
public int countCachedContainers(java.lang.Class<? extends IObject> klass,
                                 int... indexes)
```
Description copied from interface: IObjectContainerStore

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

Specified by:

countCachedContainers in interface IObjectContainerStore

Parameters:

klass - Class to count containers of.

indexes - Indexes to use in the container count. For example, if klass is Image and indexes is int[] { 0 }; only containers that have an LSID of type Image and a first index of 0 will be counted.

Returns:

See above.

countCachedReferences
```
public int countCachedReferences(java.lang.Class<? extends IObject> source,
                                 java.lang.Class<? extends IObject> target)
```
Description copied from interface: IObjectContainerStore

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

Specified by:

countCachedReferences in interface IObjectContainerStore

Parameters:

source - Class of the source object. If null it is treated as a wild card, all references whose target match target will be counted.

target - Class of the target object. If null it is treated as a wild card, all references whose source match source will be counted.

Returns:

See above.

setArcID

public void setArcID(java.lang.String id,
                     int instrumentIndex,
                     int lightSourceIndex)

Specified by:: setArcID in interface ome.xml.meta.MetadataStore

setArcLotNumber

public void setArcLotNumber(java.lang.String lotNumber,
                            int instrumentIndex,
                            int lightSourceIndex)

Specified by:: setArcLotNumber in interface ome.xml.meta.MetadataStore

setArcManufacturer

public void setArcManufacturer(java.lang.String manufacturer,
                               int instrumentIndex,
                               int lightSourceIndex)

Specified by:: setArcManufacturer in interface ome.xml.meta.MetadataStore

setArcModel

public void setArcModel(java.lang.String model,
                        int instrumentIndex,
                        int lightSourceIndex)

Specified by:: setArcModel in interface ome.xml.meta.MetadataStore

setArcPower

public void setArcPower(ome.units.quantity.Power power,
                        int instrumentIndex,
                        int lightSourceIndex)

Specified by:: setArcPower in interface ome.xml.meta.MetadataStore

setArcSerialNumber

public void setArcSerialNumber(java.lang.String serialNumber,
                               int instrumentIndex,
                               int lightSourceIndex)

Specified by:: setArcSerialNumber in interface ome.xml.meta.MetadataStore

setArcType

public void setArcType(ome.xml.model.enums.ArcType type,
                       int instrumentIndex,
                       int lightSourceIndex)

Specified by:: setArcType in interface ome.xml.meta.MetadataStore

setArcAnnotationRef

public void setArcAnnotationRef(java.lang.String annotation,
                                int instrumentIndex,
                                int lightSourceIndex,
                                int annotationRefIndex)

Specified by:: setArcAnnotationRef in interface ome.xml.meta.MetadataStore

setBooleanAnnotationID

public void setBooleanAnnotationID(java.lang.String id,
                                   int booleanAnnotationIndex)

Specified by:: setBooleanAnnotationID in interface ome.xml.meta.MetadataStore

setBooleanAnnotationNamespace

public void setBooleanAnnotationNamespace(java.lang.String namespace,
                                          int booleanAnnotationIndex)

Specified by:: setBooleanAnnotationNamespace in interface ome.xml.meta.MetadataStore

setBooleanAnnotationValue

public void setBooleanAnnotationValue(java.lang.Boolean value,
                                      int booleanAnnotationIndex)

Specified by:: setBooleanAnnotationValue in interface ome.xml.meta.MetadataStore

setBinaryOnlyUUID
```
public void setBinaryOnlyUUID(java.lang.String uuid)
```
Specified by:

setBinaryOnlyUUID in interface ome.xml.meta.MetadataStore

setBinaryOnlyMetadataFile
```
public void setBinaryOnlyMetadataFile(java.lang.String metadataFile)
```
Specified by:

setBinaryOnlyMetadataFile in interface ome.xml.meta.MetadataStore

getChannel

public Channel getChannel(int imageIndex,
                          int channelIndex)

setChannelID

public void setChannelID(java.lang.String id,
                         int imageIndex,
                         int channelIndex)

Specified by:: setChannelID in interface ome.xml.meta.MetadataStore

setChannelAcquisitionMode

public void setChannelAcquisitionMode(ome.xml.model.enums.AcquisitionMode acquisitionMode,
                                      int imageIndex,
                                      int channelIndex)

Specified by:: setChannelAcquisitionMode in interface ome.xml.meta.MetadataStore

setChannelColor

public void setChannelColor(ome.xml.model.primitives.Color color,
                            int imageIndex,
                            int channelIndex)

Specified by:: setChannelColor in interface ome.xml.meta.MetadataStore

setChannelContrastMethod

public void setChannelContrastMethod(ome.xml.model.enums.ContrastMethod contrastMethod,
                                     int imageIndex,
                                     int channelIndex)

Specified by:: setChannelContrastMethod in interface ome.xml.meta.MetadataStore

setChannelEmissionWavelength

public void setChannelEmissionWavelength(ome.units.quantity.Length emissionWavelength,
                                         int imageIndex,
                                         int channelIndex)

Specified by:: setChannelEmissionWavelength in interface ome.xml.meta.MetadataStore

setChannelExcitationWavelength

public void setChannelExcitationWavelength(ome.units.quantity.Length excitationWavelength,
                                           int imageIndex,
                                           int channelIndex)

Specified by:: setChannelExcitationWavelength in interface ome.xml.meta.MetadataStore
See Also:: MetadataStore.setChannelExcitationWavelength(Length, int, int)

setChannelFilterSetRef

public void setChannelFilterSetRef(java.lang.String filterSet,
                                   int imageIndex,
                                   int channelIndex)

Specified by:: setChannelFilterSetRef in interface ome.xml.meta.MetadataStore

setChannelFluor

public void setChannelFluor(java.lang.String fluor,
                            int imageIndex,
                            int channelIndex)

Specified by:: setChannelFluor in interface ome.xml.meta.MetadataStore

setChannelIlluminationType

public void setChannelIlluminationType(ome.xml.model.enums.IlluminationType illuminationType,
                                       int imageIndex,
                                       int channelIndex)

Specified by:: setChannelIlluminationType in interface ome.xml.meta.MetadataStore

setChannelNDFilter

public void setChannelNDFilter(java.lang.Double ndfilter,
                               int imageIndex,
                               int channelIndex)

Specified by:: setChannelNDFilter in interface ome.xml.meta.MetadataStore

setChannelName

public void setChannelName(java.lang.String name,
                           int imageIndex,
                           int channelIndex)

Specified by:: setChannelName in interface ome.xml.meta.MetadataStore

setChannelPinholeSize

public void setChannelPinholeSize(ome.units.quantity.Length pinholeSize,
                                  int imageIndex,
                                  int channelIndex)

Specified by:: setChannelPinholeSize in interface ome.xml.meta.MetadataStore

setChannelPockelCellSetting

public void setChannelPockelCellSetting(java.lang.Integer pockelCellSetting,
                                        int imageIndex,
                                        int channelIndex)

Specified by:: setChannelPockelCellSetting in interface ome.xml.meta.MetadataStore

setChannelSamplesPerPixel

public void setChannelSamplesPerPixel(ome.xml.model.primitives.PositiveInteger samplesPerPixel,
                                      int imageIndex,
                                      int channelIndex)

Specified by:: setChannelSamplesPerPixel in interface ome.xml.meta.MetadataStore

setChannelAnnotationRef

public void setChannelAnnotationRef(java.lang.String annotation,
                                    int imageIndex,
                                    int channelIndex,
                                    int annotationRefIndex)

Specified by:: setChannelAnnotationRef in interface ome.xml.meta.MetadataStore

setChannelLightSourceSettingsID

public void setChannelLightSourceSettingsID(java.lang.String id,
                                            int imageIndex,
                                            int channelIndex)

Specified by:: setChannelLightSourceSettingsID in interface ome.xml.meta.MetadataStore

setChannelLightSourceSettingsAttenuation

public void setChannelLightSourceSettingsAttenuation(ome.xml.model.primitives.PercentFraction attenuation,
                                                     int imageIndex,
                                                     int channelIndex)

Specified by:: setChannelLightSourceSettingsAttenuation in interface ome.xml.meta.MetadataStore

setChannelLightSourceSettingsWavelength

public void setChannelLightSourceSettingsWavelength(ome.units.quantity.Length wavelength,
                                                    int imageIndex,
                                                    int channelIndex)

Specified by:: setChannelLightSourceSettingsWavelength in interface ome.xml.meta.MetadataStore

setDatasetID

public void setDatasetID(java.lang.String id,
                         int datasetIndex)

Specified by:: setDatasetID in interface ome.xml.meta.MetadataStore

setDatasetAnnotationRef

public void setDatasetAnnotationRef(java.lang.String annotation,
                                    int datasetIndex,
                                    int annotationRefIndex)

Specified by:: setDatasetAnnotationRef in interface ome.xml.meta.MetadataStore

setDatasetDescription

public void setDatasetDescription(java.lang.String description,
                                  int datasetIndex)

Specified by:: setDatasetDescription in interface ome.xml.meta.MetadataStore

setDatasetExperimenterRef

public void setDatasetExperimenterRef(java.lang.String experimenter,
                                      int datasetIndex)

Specified by:: setDatasetExperimenterRef in interface ome.xml.meta.MetadataStore

setDatasetExperimenterGroupRef

public void setDatasetExperimenterGroupRef(java.lang.String group,
                                           int datasetIndex)

Specified by:: setDatasetExperimenterGroupRef in interface ome.xml.meta.MetadataStore

setDatasetName

public void setDatasetName(java.lang.String name,
                           int datasetIndex)

Specified by:: setDatasetName in interface ome.xml.meta.MetadataStore

getDetector
```
public Detector getDetector(int instrumentIndex,
                            int detectorIndex)
```
Parameters:

instrumentIndex - the instrument index

detectorIndex - the detector index within the instrument

Returns:

the detector

setDetectorID

public void setDetectorID(java.lang.String id,
                          int instrumentIndex,
                          int detectorIndex)

Specified by:: setDetectorID in interface ome.xml.meta.MetadataStore

setDetectorAmplificationGain

public void setDetectorAmplificationGain(java.lang.Double amplificationGain,
                                         int instrumentIndex,
                                         int detectorIndex)

Specified by:: setDetectorAmplificationGain in interface ome.xml.meta.MetadataStore

setDetectorGain

public void setDetectorGain(java.lang.Double gain,
                            int instrumentIndex,
                            int detectorIndex)

Specified by:: setDetectorGain in interface ome.xml.meta.MetadataStore

setDetectorLotNumber

public void setDetectorLotNumber(java.lang.String lotNumber,
                                 int instrumentIndex,
                                 int detectorIndex)

Specified by:: setDetectorLotNumber in interface ome.xml.meta.MetadataStore

setDetectorManufacturer

public void setDetectorManufacturer(java.lang.String manufacturer,
                                    int instrumentIndex,
                                    int detectorIndex)

Specified by:: setDetectorManufacturer in interface ome.xml.meta.MetadataStore

setDetectorModel

public void setDetectorModel(java.lang.String model,
                             int instrumentIndex,
                             int detectorIndex)

Specified by:: setDetectorModel in interface ome.xml.meta.MetadataStore

setDetectorOffset

public void setDetectorOffset(java.lang.Double offset,
                              int instrumentIndex,
                              int detectorIndex)

Specified by:: setDetectorOffset in interface ome.xml.meta.MetadataStore

setDetectorSerialNumber

public void setDetectorSerialNumber(java.lang.String serialNumber,
                                    int instrumentIndex,
                                    int detectorIndex)

Specified by:: setDetectorSerialNumber in interface ome.xml.meta.MetadataStore

setDetectorType

public void setDetectorType(ome.xml.model.enums.DetectorType type,
                            int instrumentIndex,
                            int detectorIndex)

Specified by:: setDetectorType in interface ome.xml.meta.MetadataStore

setDetectorVoltage

public void setDetectorVoltage(ome.units.quantity.ElectricPotential voltage,
                               int instrumentIndex,
                               int detectorIndex)

Specified by:: setDetectorVoltage in interface ome.xml.meta.MetadataStore

setDetectorZoom

public void setDetectorZoom(java.lang.Double zoom,
                            int instrumentIndex,
                            int detectorIndex)

Specified by:: setDetectorZoom in interface ome.xml.meta.MetadataStore

setDetectorSettingsID

public void setDetectorSettingsID(java.lang.String id,
                                  int imageIndex,
                                  int channelIndex)

Specified by:: setDetectorSettingsID in interface ome.xml.meta.MetadataStore

setDetectorSettingsBinning

public void setDetectorSettingsBinning(ome.xml.model.enums.Binning binning,
                                       int imageIndex,
                                       int channelIndex)

Specified by:: setDetectorSettingsBinning in interface ome.xml.meta.MetadataStore

setDetectorSettingsGain

public void setDetectorSettingsGain(java.lang.Double gain,
                                    int imageIndex,
                                    int channelIndex)

Specified by:: setDetectorSettingsGain in interface ome.xml.meta.MetadataStore

setDetectorSettingsIntegration

public void setDetectorSettingsIntegration(ome.xml.model.primitives.PositiveInteger integration,
                                           int imageIndex,
                                           int channelIndex)

Specified by:: setDetectorSettingsIntegration in interface ome.xml.meta.MetadataStore

setDetectorSettingsOffset

public void setDetectorSettingsOffset(java.lang.Double offset,
                                      int imageIndex,
                                      int channelIndex)

Specified by:: setDetectorSettingsOffset in interface ome.xml.meta.MetadataStore

setDetectorSettingsReadOutRate

public void setDetectorSettingsReadOutRate(ome.units.quantity.Frequency readOutRate,
                                           int imageIndex,
                                           int channelIndex)

Specified by:: setDetectorSettingsReadOutRate in interface ome.xml.meta.MetadataStore

setDetectorSettingsVoltage

public void setDetectorSettingsVoltage(ome.units.quantity.ElectricPotential voltage,
                                       int imageIndex,
                                       int channelIndex)

Specified by:: setDetectorSettingsVoltage in interface ome.xml.meta.MetadataStore

setDetectorSettingsZoom

public void setDetectorSettingsZoom(java.lang.Double zoom,
                                    int imageIndex,
                                    int channelIndex)

Specified by:: setDetectorSettingsZoom in interface ome.xml.meta.MetadataStore

setDichroicID

public void setDichroicID(java.lang.String id,
                          int instrumentIndex,
                          int dichroicIndex)

Specified by:: setDichroicID in interface ome.xml.meta.MetadataStore

setDichroicLotNumber

public void setDichroicLotNumber(java.lang.String lotNumber,
                                 int instrumentIndex,
                                 int dichroicIndex)

Specified by:: setDichroicLotNumber in interface ome.xml.meta.MetadataStore

setDichroicManufacturer

public void setDichroicManufacturer(java.lang.String manufacturer,
                                    int instrumentIndex,
                                    int dichroicIndex)

Specified by:: setDichroicManufacturer in interface ome.xml.meta.MetadataStore

setDichroicModel

public void setDichroicModel(java.lang.String model,
                             int instrumentIndex,
                             int dichroicIndex)

Specified by:: setDichroicModel in interface ome.xml.meta.MetadataStore

setDichroicSerialNumber

public void setDichroicSerialNumber(java.lang.String serialNumber,
                                    int instrumentIndex,
                                    int dichroicIndex)

Specified by:: setDichroicSerialNumber in interface ome.xml.meta.MetadataStore

setDoubleAnnotationID

public void setDoubleAnnotationID(java.lang.String id,
                                  int doubleAnnotationIndex)

Specified by:: setDoubleAnnotationID in interface ome.xml.meta.MetadataStore

setDoubleAnnotationNamespace

public void setDoubleAnnotationNamespace(java.lang.String namespace,
                                         int doubleAnnotationIndex)

Specified by:: setDoubleAnnotationNamespace in interface ome.xml.meta.MetadataStore

setDoubleAnnotationValue

public void setDoubleAnnotationValue(java.lang.Double value,
                                     int doubleAnnotationIndex)

Specified by:: setDoubleAnnotationValue in interface ome.xml.meta.MetadataStore

setEllipseID

public void setEllipseID(java.lang.String id,
                         int ROIIndex,
                         int shapeIndex)

Specified by:: setEllipseID in interface ome.xml.meta.MetadataStore

setEllipseFillColor

public void setEllipseFillColor(ome.xml.model.primitives.Color fill,
                                int ROIIndex,
                                int shapeIndex)

Specified by:: setEllipseFillColor in interface ome.xml.meta.MetadataStore

setEllipseFontSize

public void setEllipseFontSize(ome.units.quantity.Length fontSize,
                               int ROIIndex,
                               int shapeIndex)

Specified by:: setEllipseFontSize in interface ome.xml.meta.MetadataStore

setEllipseText

public void setEllipseText(java.lang.String text,
                           int ROIIndex,
                           int shapeIndex)

Specified by:: setEllipseText in interface ome.xml.meta.MetadataStore

setEllipseRadiusX

public void setEllipseRadiusX(java.lang.Double radiusX,
                              int ROIIndex,
                              int shapeIndex)

Specified by:: setEllipseRadiusX in interface ome.xml.meta.MetadataStore

setEllipseRadiusY

public void setEllipseRadiusY(java.lang.Double radiusY,
                              int ROIIndex,
                              int shapeIndex)

Specified by:: setEllipseRadiusY in interface ome.xml.meta.MetadataStore

setEllipseStrokeColor

public void setEllipseStrokeColor(ome.xml.model.primitives.Color stroke,
                                  int ROIIndex,
                                  int shapeIndex)

Specified by:: setEllipseStrokeColor in interface ome.xml.meta.MetadataStore

setEllipseStrokeDashArray

public void setEllipseStrokeDashArray(java.lang.String strokeDashArray,
                                      int ROIIndex,
                                      int shapeIndex)

Specified by:: setEllipseStrokeDashArray in interface ome.xml.meta.MetadataStore

setEllipseStrokeWidth

public void setEllipseStrokeWidth(ome.units.quantity.Length strokeWidth,
                                  int ROIIndex,
                                  int shapeIndex)

Specified by:: setEllipseStrokeWidth in interface ome.xml.meta.MetadataStore

setEllipseTheC

public void setEllipseTheC(ome.xml.model.primitives.NonNegativeInteger theC,
                           int ROIIndex,
                           int shapeIndex)

Specified by:: setEllipseTheC in interface ome.xml.meta.MetadataStore

setEllipseTheT

public void setEllipseTheT(ome.xml.model.primitives.NonNegativeInteger theT,
                           int ROIIndex,
                           int shapeIndex)

Specified by:: setEllipseTheT in interface ome.xml.meta.MetadataStore

setEllipseTheZ

public void setEllipseTheZ(ome.xml.model.primitives.NonNegativeInteger theZ,
                           int ROIIndex,
                           int shapeIndex)

Specified by:: setEllipseTheZ in interface ome.xml.meta.MetadataStore

setEllipseTransform

public void setEllipseTransform(ome.xml.model.AffineTransform transform,
                                int ROIIndex,
                                int shapeIndex)

Specified by:: setEllipseTransform in interface ome.xml.meta.MetadataStore

setEllipseX

public void setEllipseX(java.lang.Double x,
                        int ROIIndex,
                        int shapeIndex)

Specified by:: setEllipseX in interface ome.xml.meta.MetadataStore

setEllipseY

public void setEllipseY(java.lang.Double y,
                        int ROIIndex,
                        int shapeIndex)

Specified by:: setEllipseY in interface ome.xml.meta.MetadataStore

setExperimentID

public void setExperimentID(java.lang.String id,
                            int experimentIndex)

Specified by:: setExperimentID in interface ome.xml.meta.MetadataStore

setExperimentDescription

public void setExperimentDescription(java.lang.String description,
                                     int experimentIndex)

Specified by:: setExperimentDescription in interface ome.xml.meta.MetadataStore

setExperimentExperimenterRef

public void setExperimentExperimenterRef(java.lang.String experimenter,
                                         int experimentIndex)

Specified by:: setExperimentExperimenterRef in interface ome.xml.meta.MetadataStore

setExperimentType

public void setExperimentType(ome.xml.model.enums.ExperimentType type,
                              int experimentIndex)

Specified by:: setExperimentType in interface ome.xml.meta.MetadataStore

setExperimenterID

public void setExperimenterID(java.lang.String id,
                              int experimenterIndex)

Specified by:: setExperimenterID in interface ome.xml.meta.MetadataStore

setExperimenterAnnotationRef

public void setExperimenterAnnotationRef(java.lang.String annotation,
                                         int experimenterIndex,
                                         int annotationRefIndex)

Specified by:: setExperimenterAnnotationRef in interface ome.xml.meta.MetadataStore

setExperimenterEmail

public void setExperimenterEmail(java.lang.String email,
                                 int experimenterIndex)

Specified by:: setExperimenterEmail in interface ome.xml.meta.MetadataStore

setExperimenterFirstName

public void setExperimenterFirstName(java.lang.String firstName,
                                     int experimenterIndex)

Specified by:: setExperimenterFirstName in interface ome.xml.meta.MetadataStore

setExperimenterInstitution

public void setExperimenterInstitution(java.lang.String institution,
                                       int experimenterIndex)

Specified by:: setExperimenterInstitution in interface ome.xml.meta.MetadataStore

setExperimenterLastName

public void setExperimenterLastName(java.lang.String lastName,
                                    int experimenterIndex)

Specified by:: setExperimenterLastName in interface ome.xml.meta.MetadataStore

setExperimenterMiddleName

public void setExperimenterMiddleName(java.lang.String middleName,
                                      int experimenterIndex)

Specified by:: setExperimenterMiddleName in interface ome.xml.meta.MetadataStore

setExperimenterUserName

public void setExperimenterUserName(java.lang.String userName,
                                    int experimenterIndex)

Specified by:: setExperimenterUserName in interface ome.xml.meta.MetadataStore

getFilament

public Filament getFilament(int instrumentIndex,
                            int lightSourceIndex)

setFilamentID

public void setFilamentID(java.lang.String id,
                          int instrumentIndex,
                          int lightSourceIndex)

Specified by:: setFilamentID in interface ome.xml.meta.MetadataStore

setFilamentLotNumber

public void setFilamentLotNumber(java.lang.String lotNumber,
                                 int instrumentIndex,
                                 int lightSourceIndex)

Specified by:: setFilamentLotNumber in interface ome.xml.meta.MetadataStore

setFilamentManufacturer

public void setFilamentManufacturer(java.lang.String manufacturer,
                                    int instrumentIndex,
                                    int lightSourceIndex)

Specified by:: setFilamentManufacturer in interface ome.xml.meta.MetadataStore

setFilamentModel

public void setFilamentModel(java.lang.String model,
                             int instrumentIndex,
                             int lightSourceIndex)

Specified by:: setFilamentModel in interface ome.xml.meta.MetadataStore

setFilamentPower

public void setFilamentPower(ome.units.quantity.Power power,
                             int instrumentIndex,
                             int lightSourceIndex)

Specified by:: setFilamentPower in interface ome.xml.meta.MetadataStore

setFilamentSerialNumber

public void setFilamentSerialNumber(java.lang.String serialNumber,
                                    int instrumentIndex,
                                    int lightSourceIndex)

Specified by:: setFilamentSerialNumber in interface ome.xml.meta.MetadataStore

setFilamentType

public void setFilamentType(ome.xml.model.enums.FilamentType type,
                            int instrumentIndex,
                            int lightSourceIndex)

Specified by:: setFilamentType in interface ome.xml.meta.MetadataStore

setFileAnnotationID

public void setFileAnnotationID(java.lang.String id,
                                int fileAnnotationIndex)

Specified by:: setFileAnnotationID in interface ome.xml.meta.MetadataStore

setFileAnnotationNamespace

public void setFileAnnotationNamespace(java.lang.String namespace,
                                       int fileAnnotationIndex)

Specified by:: setFileAnnotationNamespace in interface ome.xml.meta.MetadataStore

setFilterID

public void setFilterID(java.lang.String id,
                        int instrumentIndex,
                        int filterIndex)

Specified by:: setFilterID in interface ome.xml.meta.MetadataStore

setFilterFilterWheel

public void setFilterFilterWheel(java.lang.String filterWheel,
                                 int instrumentIndex,
                                 int filterIndex)

Specified by:: setFilterFilterWheel in interface ome.xml.meta.MetadataStore

setFilterLotNumber

public void setFilterLotNumber(java.lang.String lotNumber,
                               int instrumentIndex,
                               int filterIndex)

Specified by:: setFilterLotNumber in interface ome.xml.meta.MetadataStore

setFilterManufacturer

public void setFilterManufacturer(java.lang.String manufacturer,
                                  int instrumentIndex,
                                  int filterIndex)

Specified by:: setFilterManufacturer in interface ome.xml.meta.MetadataStore

setFilterModel

public void setFilterModel(java.lang.String model,
                           int instrumentIndex,
                           int filterIndex)

Specified by:: setFilterModel in interface ome.xml.meta.MetadataStore

setFilterSerialNumber

public void setFilterSerialNumber(java.lang.String serialNumber,
                                  int instrumentIndex,
                                  int filterIndex)

Specified by:: setFilterSerialNumber in interface ome.xml.meta.MetadataStore

setFilterType

public void setFilterType(ome.xml.model.enums.FilterType type,
                          int instrumentIndex,
                          int filterIndex)

Specified by:: setFilterType in interface ome.xml.meta.MetadataStore

getFilterSet

public FilterSet getFilterSet(int instrumentIndex,
                              int filterSetIndex)

setFilterSetID

public void setFilterSetID(java.lang.String id,
                           int instrumentIndex,
                           int filterSetIndex)

Specified by:: setFilterSetID in interface ome.xml.meta.MetadataStore

setFilterSetDichroicRef

public void setFilterSetDichroicRef(java.lang.String dichroic,
                                    int instrumentIndex,
                                    int filterSetIndex)

Specified by:: setFilterSetDichroicRef in interface ome.xml.meta.MetadataStore

setFilterSetEmissionFilterRef

public void setFilterSetEmissionFilterRef(java.lang.String emissionFilter,
                                          int instrumentIndex,
                                          int filterSetIndex,
                                          int emissionFilterRefIndex)

Specified by:: setFilterSetEmissionFilterRef in interface ome.xml.meta.MetadataStore

setFilterSetExcitationFilterRef

public void setFilterSetExcitationFilterRef(java.lang.String excitationFilter,
                                            int instrumentIndex,
                                            int filterSetIndex,
                                            int excitationFilterRefIndex)

Specified by:: setFilterSetExcitationFilterRef in interface ome.xml.meta.MetadataStore

setFilterSetLotNumber

public void setFilterSetLotNumber(java.lang.String lotNumber,
                                  int instrumentIndex,
                                  int filterSetIndex)

Specified by:: setFilterSetLotNumber in interface ome.xml.meta.MetadataStore

setFilterSetManufacturer

public void setFilterSetManufacturer(java.lang.String manufacturer,
                                     int instrumentIndex,
                                     int filterSetIndex)

Specified by:: setFilterSetManufacturer in interface ome.xml.meta.MetadataStore

setFilterSetModel

public void setFilterSetModel(java.lang.String model,
                              int instrumentIndex,
                              int filterSetIndex)

Specified by:: setFilterSetModel in interface ome.xml.meta.MetadataStore

setFilterSetSerialNumber

public void setFilterSetSerialNumber(java.lang.String serialNumber,
                                     int instrumentIndex,
                                     int filterSetIndex)

Specified by:: setFilterSetSerialNumber in interface ome.xml.meta.MetadataStore

setFolderAnnotationRef

public void setFolderAnnotationRef(java.lang.String annotation,
                                   int folderIndex,
                                   int annotationRefIndex)

Specified by:: setFolderAnnotationRef in interface ome.xml.meta.MetadataStore

setFolderDescription

public void setFolderDescription(java.lang.String description,
                                 int folderIndex)

Specified by:: setFolderDescription in interface ome.xml.meta.MetadataStore

setFolderFolderRef

public void setFolderFolderRef(java.lang.String folder,
                               int folderIndex,
                               int folderRefIndex)

Specified by:: setFolderFolderRef in interface ome.xml.meta.MetadataStore

setFolderID

public void setFolderID(java.lang.String id,
                        int folderIndex)

Specified by:: setFolderID in interface ome.xml.meta.MetadataStore

setFolderImageRef

public void setFolderImageRef(java.lang.String image,
                              int folderIndex,
                              int imageRefIndex)

Specified by:: setFolderImageRef in interface ome.xml.meta.MetadataStore

setFolderName

public void setFolderName(java.lang.String name,
                          int folderIndex)

Specified by:: setFolderName in interface ome.xml.meta.MetadataStore

setFolderROIRef

public void setFolderROIRef(java.lang.String roi,
                            int folderIndex,
                            int ROIRefIndex)

Specified by:: setFolderROIRef in interface ome.xml.meta.MetadataStore

setGenericExcitationSourceID

public void setGenericExcitationSourceID(java.lang.String id,
                                         int instrumentIndex,
                                         int lightSourceIndex)

Specified by:: setGenericExcitationSourceID in interface ome.xml.meta.MetadataStore

setGenericExcitationSourceLotNumber

public void setGenericExcitationSourceLotNumber(java.lang.String lotNumber,
                                                int instrumentIndex,
                                                int lightSourceIndex)

Specified by:: setGenericExcitationSourceLotNumber in interface ome.xml.meta.MetadataStore

setGenericExcitationSourceMap

public void setGenericExcitationSourceMap(java.util.List<ome.xml.model.MapPair> map,
                                          int instrumentIndex,
                                          int lightSourceIndex)

Specified by:: setGenericExcitationSourceMap in interface ome.xml.meta.MetadataStore

setGenericExcitationSourceManufacturer

public void setGenericExcitationSourceManufacturer(java.lang.String manufacturer,
                                                   int instrumentIndex,
                                                   int lightSourceIndex)

Specified by:: setGenericExcitationSourceManufacturer in interface ome.xml.meta.MetadataStore

setGenericExcitationSourceModel

public void setGenericExcitationSourceModel(java.lang.String model,
                                            int instrumentIndex,
                                            int lightSourceIndex)

Specified by:: setGenericExcitationSourceModel in interface ome.xml.meta.MetadataStore

setGenericExcitationSourcePower

public void setGenericExcitationSourcePower(ome.units.quantity.Power power,
                                            int instrumentIndex,
                                            int lightSourceIndex)

Specified by:: setGenericExcitationSourcePower in interface ome.xml.meta.MetadataStore

setGenericExcitationSourceSerialNumber

public void setGenericExcitationSourceSerialNumber(java.lang.String serialNumber,
                                                   int instrumentIndex,
                                                   int lightSourceIndex)

Specified by:: setGenericExcitationSourceSerialNumber in interface ome.xml.meta.MetadataStore

setExperimenterGroupID

public void setExperimenterGroupID(java.lang.String id,
                                   int groupIndex)

Specified by:: setExperimenterGroupID in interface ome.xml.meta.MetadataStore

setExperimenterGroupDescription

public void setExperimenterGroupDescription(java.lang.String description,
                                            int groupIndex)

Specified by:: setExperimenterGroupDescription in interface ome.xml.meta.MetadataStore

setExperimenterGroupLeader

public void setExperimenterGroupLeader(java.lang.String leader,
                                       int groupIndex,
                                       int leaderIndex)

Specified by:: setExperimenterGroupLeader in interface ome.xml.meta.MetadataStore

setExperimenterGroupName

public void setExperimenterGroupName(java.lang.String name,
                                     int groupIndex)

Specified by:: setExperimenterGroupName in interface ome.xml.meta.MetadataStore

setImageID

public void setImageID(java.lang.String id,
                       int imageIndex)

Specified by:: setImageID in interface ome.xml.meta.MetadataStore

setImageAcquisitionDate

public void setImageAcquisitionDate(ome.xml.model.primitives.Timestamp acquiredDate,
                                    int imageIndex)

Specified by:: setImageAcquisitionDate in interface ome.xml.meta.MetadataStore

setImageAnnotationRef

public void setImageAnnotationRef(java.lang.String annotation,
                                  int imageIndex,
                                  int annotationRefIndex)

Specified by:: setImageAnnotationRef in interface ome.xml.meta.MetadataStore

setImageDescription

public void setImageDescription(java.lang.String description,
                                int imageIndex)

Specified by:: setImageDescription in interface ome.xml.meta.MetadataStore

setImageExperimentRef

public void setImageExperimentRef(java.lang.String experiment,
                                  int imageIndex)

Specified by:: setImageExperimentRef in interface ome.xml.meta.MetadataStore

setImageExperimenterRef

public void setImageExperimenterRef(java.lang.String experimenter,
                                    int imageIndex)

Specified by:: setImageExperimenterRef in interface ome.xml.meta.MetadataStore

setImageExperimenterGroupRef

public void setImageExperimenterGroupRef(java.lang.String group,
                                         int imageIndex)

Specified by:: setImageExperimenterGroupRef in interface ome.xml.meta.MetadataStore

setImageInstrumentRef

public void setImageInstrumentRef(java.lang.String instrument,
                                  int imageIndex)

Specified by:: setImageInstrumentRef in interface ome.xml.meta.MetadataStore

setImageMicrobeamManipulationRef

public void setImageMicrobeamManipulationRef(java.lang.String microbeamManipulation,
                                             int imageIndex,
                                             int microbeamManipulationRefIndex)

Specified by:: setImageMicrobeamManipulationRef in interface ome.xml.meta.MetadataStore

setImageName

public void setImageName(java.lang.String name,
                         int imageIndex)

Specified by:: setImageName in interface ome.xml.meta.MetadataStore

setImageROIRef

public void setImageROIRef(java.lang.String roi,
                           int imageIndex,
                           int ROIRefIndex)

Specified by:: setImageROIRef in interface ome.xml.meta.MetadataStore

getObjectiveSettings

public ObjectiveSettings getObjectiveSettings(int imageIndex)

setObjectiveSettingsID

public void setObjectiveSettingsID(java.lang.String id,
                                   int imageIndex)

Specified by:: setObjectiveSettingsID in interface ome.xml.meta.MetadataStore

setObjectiveSettingsCorrectionCollar

public void setObjectiveSettingsCorrectionCollar(java.lang.Double correctionCollar,
                                                 int imageIndex)

Specified by:: setObjectiveSettingsCorrectionCollar in interface ome.xml.meta.MetadataStore

setObjectiveSettingsMedium

public void setObjectiveSettingsMedium(ome.xml.model.enums.Medium medium,
                                       int imageIndex)

Specified by:: setObjectiveSettingsMedium in interface ome.xml.meta.MetadataStore

setObjectiveSettingsRefractiveIndex

public void setObjectiveSettingsRefractiveIndex(java.lang.Double refractiveIndex,
                                                int imageIndex)

Specified by:: setObjectiveSettingsRefractiveIndex in interface ome.xml.meta.MetadataStore

getImagingEnvironment

public ImagingEnvironment getImagingEnvironment(int imageIndex)

setImagingEnvironmentAirPressure

public void setImagingEnvironmentAirPressure(ome.units.quantity.Pressure airPressure,
                                             int imageIndex)

Specified by:: setImagingEnvironmentAirPressure in interface ome.xml.meta.MetadataStore

setImagingEnvironmentCO2Percent

public void setImagingEnvironmentCO2Percent(ome.xml.model.primitives.PercentFraction co2percent,
                                            int imageIndex)

Specified by:: setImagingEnvironmentCO2Percent in interface ome.xml.meta.MetadataStore

setImagingEnvironmentHumidity

public void setImagingEnvironmentHumidity(ome.xml.model.primitives.PercentFraction humidity,
                                          int imageIndex)

Specified by:: setImagingEnvironmentHumidity in interface ome.xml.meta.MetadataStore

setImagingEnvironmentMap

public void setImagingEnvironmentMap(java.util.List<ome.xml.model.MapPair> map,
                                     int imageIndex)

Specified by:: setImagingEnvironmentMap in interface ome.xml.meta.MetadataStore

setImagingEnvironmentTemperature

public void setImagingEnvironmentTemperature(ome.units.quantity.Temperature temperature,
                                             int imageIndex)

Specified by:: setImagingEnvironmentTemperature in interface ome.xml.meta.MetadataStore

setInstrumentID

public void setInstrumentID(java.lang.String id,
                            int instrumentIndex)

Specified by:: setInstrumentID in interface ome.xml.meta.MetadataStore

getLaser

public Laser getLaser(int instrumentIndex,
                      int lightSourceIndex)

setLaserID

public void setLaserID(java.lang.String id,
                       int instrumentIndex,
                       int lightSourceIndex)

Specified by:: setLaserID in interface ome.xml.meta.MetadataStore

setLaserFrequencyMultiplication

public void setLaserFrequencyMultiplication(ome.xml.model.primitives.PositiveInteger frequencyMultiplication,
                                            int instrumentIndex,
                                            int lightSourceIndex)

Specified by:: setLaserFrequencyMultiplication in interface ome.xml.meta.MetadataStore

setLaserLaserMedium

public void setLaserLaserMedium(ome.xml.model.enums.LaserMedium laserMedium,
                                int instrumentIndex,
                                int lightSourceIndex)

Specified by:: setLaserLaserMedium in interface ome.xml.meta.MetadataStore

setLaserLotNumber

public void setLaserLotNumber(java.lang.String lotNumber,
                              int instrumentIndex,
                              int lightSourceIndex)

Specified by:: setLaserLotNumber in interface ome.xml.meta.MetadataStore

setLaserManufacturer

public void setLaserManufacturer(java.lang.String manufacturer,
                                 int instrumentIndex,
                                 int lightSourceIndex)

Specified by:: setLaserManufacturer in interface ome.xml.meta.MetadataStore

setLaserModel

public void setLaserModel(java.lang.String model,
                          int instrumentIndex,
                          int lightSourceIndex)

Specified by:: setLaserModel in interface ome.xml.meta.MetadataStore

setLaserPockelCell

public void setLaserPockelCell(java.lang.Boolean pockelCell,
                               int instrumentIndex,
                               int lightSourceIndex)

Specified by:: setLaserPockelCell in interface ome.xml.meta.MetadataStore

setLaserPower

public void setLaserPower(ome.units.quantity.Power power,
                          int instrumentIndex,
                          int lightSourceIndex)

Specified by:: setLaserPower in interface ome.xml.meta.MetadataStore

setLaserPulse

public void setLaserPulse(ome.xml.model.enums.Pulse pulse,
                          int instrumentIndex,
                          int lightSourceIndex)

Specified by:: setLaserPulse in interface ome.xml.meta.MetadataStore

setLaserPump

public void setLaserPump(java.lang.String pump,
                         int instrumentIndex,
                         int lightSourceIndex)

Specified by:: setLaserPump in interface ome.xml.meta.MetadataStore

setLaserRepetitionRate

public void setLaserRepetitionRate(ome.units.quantity.Frequency repetitionRate,
                                   int instrumentIndex,
                                   int lightSourceIndex)

Specified by:: setLaserRepetitionRate in interface ome.xml.meta.MetadataStore

setLaserSerialNumber

public void setLaserSerialNumber(java.lang.String serialNumber,
                                 int instrumentIndex,
                                 int lightSourceIndex)

Specified by:: setLaserSerialNumber in interface ome.xml.meta.MetadataStore

setLaserTuneable

public void setLaserTuneable(java.lang.Boolean tuneable,
                             int instrumentIndex,
                             int lightSourceIndex)

Specified by:: setLaserTuneable in interface ome.xml.meta.MetadataStore

setLaserType

public void setLaserType(ome.xml.model.enums.LaserType type,
                         int instrumentIndex,
                         int lightSourceIndex)

Specified by:: setLaserType in interface ome.xml.meta.MetadataStore

setLaserWavelength

public void setLaserWavelength(ome.units.quantity.Length wavelength,
                               int instrumentIndex,
                               int lightSourceIndex)

Specified by:: setLaserWavelength in interface ome.xml.meta.MetadataStore

getLightEmittingDiode

public LightEmittingDiode getLightEmittingDiode(int instrumentIndex,
                                                int lightSourceIndex)

setLightEmittingDiodeID

public void setLightEmittingDiodeID(java.lang.String id,
                                    int instrumentIndex,
                                    int lightSourceIndex)

Specified by:: setLightEmittingDiodeID in interface ome.xml.meta.MetadataStore

setLightEmittingDiodeLotNumber

public void setLightEmittingDiodeLotNumber(java.lang.String lotNumber,
                                           int instrumentIndex,
                                           int lightSourceIndex)

Specified by:: setLightEmittingDiodeLotNumber in interface ome.xml.meta.MetadataStore

setLightEmittingDiodeManufacturer

public void setLightEmittingDiodeManufacturer(java.lang.String manufacturer,
                                              int instrumentIndex,
                                              int lightSourceIndex)

Specified by:: setLightEmittingDiodeManufacturer in interface ome.xml.meta.MetadataStore

setLightEmittingDiodeModel

public void setLightEmittingDiodeModel(java.lang.String model,
                                       int instrumentIndex,
                                       int lightSourceIndex)

Specified by:: setLightEmittingDiodeModel in interface ome.xml.meta.MetadataStore

setLightEmittingDiodePower

public void setLightEmittingDiodePower(ome.units.quantity.Power power,
                                       int instrumentIndex,
                                       int lightSourceIndex)

Specified by:: setLightEmittingDiodePower in interface ome.xml.meta.MetadataStore

setLightEmittingDiodeSerialNumber

public void setLightEmittingDiodeSerialNumber(java.lang.String serialNumber,
                                              int instrumentIndex,
                                              int lightSourceIndex)

Specified by:: setLightEmittingDiodeSerialNumber in interface ome.xml.meta.MetadataStore

setLightPathDichroicRef

public void setLightPathDichroicRef(java.lang.String dichroic,
                                    int imageIndex,
                                    int channelIndex)

Specified by:: setLightPathDichroicRef in interface ome.xml.meta.MetadataStore

setLightPathEmissionFilterRef

public void setLightPathEmissionFilterRef(java.lang.String emissionFilter,
                                          int imageIndex,
                                          int channelIndex,
                                          int emissionFilterRefIndex)

Specified by:: setLightPathEmissionFilterRef in interface ome.xml.meta.MetadataStore

setLightPathExcitationFilterRef

public void setLightPathExcitationFilterRef(java.lang.String excitationFilter,
                                            int imageIndex,
                                            int channelIndex,
                                            int excitationFilterRefIndex)

Specified by:: setLightPathExcitationFilterRef in interface ome.xml.meta.MetadataStore

getLine

public Line getLine(int ROIIndex,
                    int shapeIndex)

setLineID

public void setLineID(java.lang.String id,
                      int ROIIndex,
                      int shapeIndex)

Specified by:: setLineID in interface ome.xml.meta.MetadataStore

setLineText

public void setLineText(java.lang.String text,
                        int ROIIndex,
                        int shapeIndex)

Specified by:: setLineText in interface ome.xml.meta.MetadataStore

setLineFillColor

public void setLineFillColor(ome.xml.model.primitives.Color fill,
                             int ROIIndex,
                             int shapeIndex)

Specified by:: setLineFillColor in interface ome.xml.meta.MetadataStore

setLineFontSize

public void setLineFontSize(ome.units.quantity.Length fontSize,
                            int ROIIndex,
                            int shapeIndex)

Specified by:: setLineFontSize in interface ome.xml.meta.MetadataStore

setLineStrokeColor

public void setLineStrokeColor(ome.xml.model.primitives.Color stroke,
                               int ROIIndex,
                               int shapeIndex)

Specified by:: setLineStrokeColor in interface ome.xml.meta.MetadataStore

setLineStrokeDashArray

public void setLineStrokeDashArray(java.lang.String strokeDashArray,
                                   int ROIIndex,
                                   int shapeIndex)

Specified by:: setLineStrokeDashArray in interface ome.xml.meta.MetadataStore

setLineStrokeWidth

public void setLineStrokeWidth(ome.units.quantity.Length strokeWidth,
                               int ROIIndex,
                               int shapeIndex)

Specified by:: setLineStrokeWidth in interface ome.xml.meta.MetadataStore

setLineTheC

public void setLineTheC(ome.xml.model.primitives.NonNegativeInteger theC,
                        int ROIIndex,
                        int shapeIndex)

Specified by:: setLineTheC in interface ome.xml.meta.MetadataStore

setLineTheT

public void setLineTheT(ome.xml.model.primitives.NonNegativeInteger theT,
                        int ROIIndex,
                        int shapeIndex)

Specified by:: setLineTheT in interface ome.xml.meta.MetadataStore

setLineTheZ

public void setLineTheZ(ome.xml.model.primitives.NonNegativeInteger theZ,
                        int ROIIndex,
                        int shapeIndex)

Specified by:: setLineTheZ in interface ome.xml.meta.MetadataStore

setLineTransform

public void setLineTransform(ome.xml.model.AffineTransform transform,
                             int ROIIndex,
                             int shapeIndex)

Specified by:: setLineTransform in interface ome.xml.meta.MetadataStore

setLineX1

public void setLineX1(java.lang.Double x1,
                      int ROIIndex,
                      int shapeIndex)

Specified by:: setLineX1 in interface ome.xml.meta.MetadataStore

setLineX2

public void setLineX2(java.lang.Double x2,
                      int ROIIndex,
                      int shapeIndex)

Specified by:: setLineX2 in interface ome.xml.meta.MetadataStore

setLineY1

public void setLineY1(java.lang.Double y1,
                      int ROIIndex,
                      int shapeIndex)

Specified by:: setLineY1 in interface ome.xml.meta.MetadataStore

setLineY2

public void setLineY2(java.lang.Double y2,
                      int ROIIndex,
                      int shapeIndex)

Specified by:: setLineY2 in interface ome.xml.meta.MetadataStore

getListAnnotation

public ListAnnotation getListAnnotation(int listAnnotationIndex)

setListAnnotationID

public void setListAnnotationID(java.lang.String id,
                                int listAnnotationIndex)

Specified by:: setListAnnotationID in interface ome.xml.meta.MetadataStore

setListAnnotationAnnotationRef

public void setListAnnotationAnnotationRef(java.lang.String annotation,
                                           int listAnnotationIndex,
                                           int annotationRefIndex)

Specified by:: setListAnnotationAnnotationRef in interface ome.xml.meta.MetadataStore

setListAnnotationNamespace

public void setListAnnotationNamespace(java.lang.String namespace,
                                       int listAnnotationIndex)

Specified by:: setListAnnotationNamespace in interface ome.xml.meta.MetadataStore

getLongAnnotation

public LongAnnotation getLongAnnotation(int longAnnotationIndex)

setLongAnnotationID

public void setLongAnnotationID(java.lang.String id,
                                int longAnnotationIndex)

Specified by:: setLongAnnotationID in interface ome.xml.meta.MetadataStore

setLongAnnotationNamespace

public void setLongAnnotationNamespace(java.lang.String namespace,
                                       int longAnnotationIndex)

Specified by:: setLongAnnotationNamespace in interface ome.xml.meta.MetadataStore

setLongAnnotationValue

public void setLongAnnotationValue(java.lang.Long value,
                                   int longAnnotationIndex)

Specified by:: setLongAnnotationValue in interface ome.xml.meta.MetadataStore

getMask

public Mask getMask(int ROIIndex,
                    int shapeIndex)

setMaskBinData

public void setMaskBinData(byte[] binData,
                           int roiIndex,
                           int shapeIndex)

Specified by:: setMaskBinData in interface ome.xml.meta.MetadataStore

setMaskBinDataBigEndian

public void setMaskBinDataBigEndian(java.lang.Boolean isBigEndian,
                                    int roiIndex,
                                    int shapeIndex)

Specified by:: setMaskBinDataBigEndian in interface ome.xml.meta.MetadataStore

setMaskBinDataCompression

public void setMaskBinDataCompression(ome.xml.model.enums.Compression compression,
                                      int roiIndex,
                                      int shapeIndex)

Specified by:: setMaskBinDataCompression in interface ome.xml.meta.MetadataStore

setMaskBinDataLength

public void setMaskBinDataLength(ome.xml.model.primitives.NonNegativeLong length,
                                 int roiIndex,
                                 int shapeIndex)

Specified by:: setMaskBinDataLength in interface ome.xml.meta.MetadataStore

setMaskText

public void setMaskText(java.lang.String description,
                        int ROIIndex,
                        int shapeIndex)

Specified by:: setMaskText in interface ome.xml.meta.MetadataStore

setMaskFillColor

public void setMaskFillColor(ome.xml.model.primitives.Color fill,
                             int ROIIndex,
                             int shapeIndex)

Specified by:: setMaskFillColor in interface ome.xml.meta.MetadataStore

setMaskFontSize

public void setMaskFontSize(ome.units.quantity.Length fontSize,
                            int ROIIndex,
                            int shapeIndex)

Specified by:: setMaskFontSize in interface ome.xml.meta.MetadataStore

setMaskID

public void setMaskID(java.lang.String id,
                      int ROIIndex,
                      int shapeIndex)

Specified by:: setMaskID in interface ome.xml.meta.MetadataStore

setMaskStrokeColor

public void setMaskStrokeColor(ome.xml.model.primitives.Color stroke,
                               int ROIIndex,
                               int shapeIndex)

Specified by:: setMaskStrokeColor in interface ome.xml.meta.MetadataStore

setMaskStrokeDashArray

public void setMaskStrokeDashArray(java.lang.String strokeDashArray,
                                   int ROIIndex,
                                   int shapeIndex)

Specified by:: setMaskStrokeDashArray in interface ome.xml.meta.MetadataStore

setMaskStrokeWidth

public void setMaskStrokeWidth(ome.units.quantity.Length strokeWidth,
                               int ROIIndex,
                               int shapeIndex)

Specified by:: setMaskStrokeWidth in interface ome.xml.meta.MetadataStore

setMaskTheC

public void setMaskTheC(ome.xml.model.primitives.NonNegativeInteger theC,
                        int ROIIndex,
                        int shapeIndex)

Specified by:: setMaskTheC in interface ome.xml.meta.MetadataStore

setMaskTheT

public void setMaskTheT(ome.xml.model.primitives.NonNegativeInteger theT,
                        int ROIIndex,
                        int shapeIndex)

Specified by:: setMaskTheT in interface ome.xml.meta.MetadataStore

setMaskTheZ

public void setMaskTheZ(ome.xml.model.primitives.NonNegativeInteger theZ,
                        int ROIIndex,
                        int shapeIndex)

Specified by:: setMaskTheZ in interface ome.xml.meta.MetadataStore

setMaskTransform

public void setMaskTransform(ome.xml.model.AffineTransform transform,
                             int ROIIndex,
                             int shapeIndex)

Specified by:: setMaskTransform in interface ome.xml.meta.MetadataStore

setMaskX

public void setMaskX(java.lang.Double x,
                     int ROIIndex,
                     int shapeIndex)

Specified by:: setMaskX in interface ome.xml.meta.MetadataStore

setMaskY

public void setMaskY(java.lang.Double y,
                     int ROIIndex,
                     int shapeIndex)

Specified by:: setMaskY in interface ome.xml.meta.MetadataStore

setMaskHeight

public void setMaskHeight(java.lang.Double height,
                          int ROIIndex,
                          int shapeIndex)

Specified by:: setMaskHeight in interface ome.xml.meta.MetadataStore

setMaskWidth

public void setMaskWidth(java.lang.Double width,
                         int ROIIndex,
                         int shapeIndex)

Specified by:: setMaskWidth in interface ome.xml.meta.MetadataStore

getMicrobeamManipulation

public MicrobeamManipulation getMicrobeamManipulation(int experimentIndex,
                                                      int microbeamManipulationIndex)

setMicrobeamManipulationID

public void setMicrobeamManipulationID(java.lang.String id,
                                       int experimentIndex,
                                       int microbeamManipulationIndex)

Specified by:: setMicrobeamManipulationID in interface ome.xml.meta.MetadataStore

setMicrobeamManipulationDescription

public void setMicrobeamManipulationDescription(java.lang.String description,
                                                int experimentIndex,
                                                int microbeamManipulationIndex)

Specified by:: setMicrobeamManipulationDescription in interface ome.xml.meta.MetadataStore

setMicrobeamManipulationExperimenterRef

public void setMicrobeamManipulationExperimenterRef(java.lang.String experimenter,
                                                    int experimentIndex,
                                                    int microbeamManipulationIndex)

Specified by:: setMicrobeamManipulationExperimenterRef in interface ome.xml.meta.MetadataStore

setMicrobeamManipulationROIRef

public void setMicrobeamManipulationROIRef(java.lang.String roi,
                                           int experimentIndex,
                                           int microbeamManipulationIndex,
                                           int ROIRefIndex)

Specified by:: setMicrobeamManipulationROIRef in interface ome.xml.meta.MetadataStore

setMicrobeamManipulationType

public void setMicrobeamManipulationType(ome.xml.model.enums.MicrobeamManipulationType type,
                                         int experimentIndex,
                                         int microbeamManipulationIndex)

Specified by:: setMicrobeamManipulationType in interface ome.xml.meta.MetadataStore

getMicrobeamManipulationLightSourceSettings

public LightSettings getMicrobeamManipulationLightSourceSettings(int experimentIndex,
                                                                 int microbeamManipulationIndex,
                                                                 int lightSourceSettingsIndex)

setMicrobeamManipulationLightSourceSettingsID

public void setMicrobeamManipulationLightSourceSettingsID(java.lang.String id,
                                                          int experimentIndex,
                                                          int microbeamManipulationIndex,
                                                          int lightSourceSettingsIndex)

Specified by:: setMicrobeamManipulationLightSourceSettingsID in interface ome.xml.meta.MetadataStore

setMicrobeamManipulationLightSourceSettingsAttenuation

public void setMicrobeamManipulationLightSourceSettingsAttenuation(ome.xml.model.primitives.PercentFraction attenuation,
                                                                   int experimentIndex,
                                                                   int microbeamManipulationIndex,
                                                                   int lightSourceSettingsIndex)

Specified by:: setMicrobeamManipulationLightSourceSettingsAttenuation in interface ome.xml.meta.MetadataStore

setMicrobeamManipulationLightSourceSettingsWavelength

public void setMicrobeamManipulationLightSourceSettingsWavelength(ome.units.quantity.Length wavelength,
                                                                  int experimentIndex,
                                                                  int microbeamManipulationIndex,
                                                                  int lightSourceSettingsIndex)

Specified by:: setMicrobeamManipulationLightSourceSettingsWavelength in interface ome.xml.meta.MetadataStore

setMicroscopeLotNumber

public void setMicroscopeLotNumber(java.lang.String lotNumber,
                                   int instrumentIndex)

Specified by:: setMicroscopeLotNumber in interface ome.xml.meta.MetadataStore

setMicroscopeManufacturer

public void setMicroscopeManufacturer(java.lang.String manufacturer,
                                      int instrumentIndex)

Specified by:: setMicroscopeManufacturer in interface ome.xml.meta.MetadataStore

setMicroscopeModel

public void setMicroscopeModel(java.lang.String model,
                               int instrumentIndex)

Specified by:: setMicroscopeModel in interface ome.xml.meta.MetadataStore

setMicroscopeSerialNumber

public void setMicroscopeSerialNumber(java.lang.String serialNumber,
                                      int instrumentIndex)

Specified by:: setMicroscopeSerialNumber in interface ome.xml.meta.MetadataStore

setMicroscopeType

public void setMicroscopeType(ome.xml.model.enums.MicroscopeType type,
                              int instrumentIndex)

Specified by:: setMicroscopeType in interface ome.xml.meta.MetadataStore

getObjective

public Objective getObjective(int instrumentIndex,
                              int objectiveIndex)

setObjectiveCalibratedMagnification

public void setObjectiveCalibratedMagnification(java.lang.Double calibratedMagnification,
                                                int instrumentIndex,
                                                int objectiveIndex)

Specified by:: setObjectiveCalibratedMagnification in interface ome.xml.meta.MetadataStore

setObjectiveCorrection

public void setObjectiveCorrection(ome.xml.model.enums.Correction correction,
                                   int instrumentIndex,
                                   int objectiveIndex)

Specified by:: setObjectiveCorrection in interface ome.xml.meta.MetadataStore

setObjectiveID

public void setObjectiveID(java.lang.String id,
                           int instrumentIndex,
                           int objectiveIndex)

Specified by:: setObjectiveID in interface ome.xml.meta.MetadataStore

setObjectiveImmersion

public void setObjectiveImmersion(ome.xml.model.enums.Immersion immersion,
                                  int instrumentIndex,
                                  int objectiveIndex)

Specified by:: setObjectiveImmersion in interface ome.xml.meta.MetadataStore

setObjectiveIris

public void setObjectiveIris(java.lang.Boolean iris,
                             int instrumentIndex,
                             int objectiveIndex)

Specified by:: setObjectiveIris in interface ome.xml.meta.MetadataStore

setObjectiveLensNA

public void setObjectiveLensNA(java.lang.Double lensNA,
                               int instrumentIndex,
                               int objectiveIndex)

Specified by:: setObjectiveLensNA in interface ome.xml.meta.MetadataStore

setObjectiveLotNumber

public void setObjectiveLotNumber(java.lang.String lotNumber,
                                  int instrumentIndex,
                                  int objectiveIndex)

Specified by:: setObjectiveLotNumber in interface ome.xml.meta.MetadataStore

setObjectiveManufacturer

public void setObjectiveManufacturer(java.lang.String manufacturer,
                                     int instrumentIndex,
                                     int objectiveIndex)

Specified by:: setObjectiveManufacturer in interface ome.xml.meta.MetadataStore

setObjectiveModel

public void setObjectiveModel(java.lang.String model,
                              int instrumentIndex,
                              int objectiveIndex)

Specified by:: setObjectiveModel in interface ome.xml.meta.MetadataStore

setObjectiveNominalMagnification

public void setObjectiveNominalMagnification(java.lang.Double nominalMagnification,
                                             int instrumentIndex,
                                             int objectiveIndex)

Specified by:: setObjectiveNominalMagnification in interface ome.xml.meta.MetadataStore

setObjectiveSerialNumber

public void setObjectiveSerialNumber(java.lang.String serialNumber,
                                     int instrumentIndex,
                                     int objectiveIndex)

Specified by:: setObjectiveSerialNumber in interface ome.xml.meta.MetadataStore

setObjectiveWorkingDistance

public void setObjectiveWorkingDistance(ome.units.quantity.Length workingDistance,
                                        int instrumentIndex,
                                        int objectiveIndex)

Specified by:: setObjectiveWorkingDistance in interface ome.xml.meta.MetadataStore

setPixelsID

public void setPixelsID(java.lang.String id,
                        int imageIndex)

Specified by:: setPixelsID in interface ome.xml.meta.MetadataStore

setPixelsBigEndian

public void setPixelsBigEndian(java.lang.Boolean value,
                               int index)

Specified by:: setPixelsBigEndian in interface ome.xml.meta.MetadataStore

setPixelsBinData

public void setPixelsBinData(byte[] binData,
                             int imageIndex,
                             int binDataIndex)

Specified by:: setPixelsBinData in interface ome.xml.meta.MetadataStore

setPixelsBinDataBigEndian

public void setPixelsBinDataBigEndian(java.lang.Boolean bigEndian,
                                      int imageIndex,
                                      int binDataIndex)

Specified by:: setPixelsBinDataBigEndian in interface ome.xml.meta.MetadataStore

setPixelsBinDataCompression

public void setPixelsBinDataCompression(ome.xml.model.enums.Compression compression,
                                        int imageIndex,
                                        int binDataIndex)

Specified by:: setPixelsBinDataCompression in interface ome.xml.meta.MetadataStore

setPixelsBinDataLength

public void setPixelsBinDataLength(ome.xml.model.primitives.NonNegativeLong length,
                                   int imageIndex,
                                   int binDataIndex)

Specified by:: setPixelsBinDataLength in interface ome.xml.meta.MetadataStore

setPixelsDimensionOrder

public void setPixelsDimensionOrder(ome.xml.model.enums.DimensionOrder dimensionOrder,
                                    int imageIndex)

Specified by:: setPixelsDimensionOrder in interface ome.xml.meta.MetadataStore

setPixelsInterleaved

public void setPixelsInterleaved(java.lang.Boolean value,
                                 int index)

Specified by:: setPixelsInterleaved in interface ome.xml.meta.MetadataStore

setPixelsPhysicalSizeX

public void setPixelsPhysicalSizeX(ome.units.quantity.Length physicalSizeX,
                                   int imageIndex)

Specified by:: setPixelsPhysicalSizeX in interface ome.xml.meta.MetadataStore

setPixelsPhysicalSizeY

public void setPixelsPhysicalSizeY(ome.units.quantity.Length physicalSizeY,
                                   int imageIndex)

Specified by:: setPixelsPhysicalSizeY in interface ome.xml.meta.MetadataStore

setPixelsPhysicalSizeZ

public void setPixelsPhysicalSizeZ(ome.units.quantity.Length physicalSizeZ,
                                   int imageIndex)

Specified by:: setPixelsPhysicalSizeZ in interface ome.xml.meta.MetadataStore

setPixelsSignificantBits

public void setPixelsSignificantBits(ome.xml.model.primitives.PositiveInteger value,
                                     int imageIndex)

Specified by:: setPixelsSignificantBits in interface ome.xml.meta.MetadataStore

setPixelsSizeC

public void setPixelsSizeC(ome.xml.model.primitives.PositiveInteger sizeC,
                           int imageIndex)

Specified by:: setPixelsSizeC in interface ome.xml.meta.MetadataStore

setPixelsSizeT

public void setPixelsSizeT(ome.xml.model.primitives.PositiveInteger sizeT,
                           int imageIndex)

Specified by:: setPixelsSizeT in interface ome.xml.meta.MetadataStore

setPixelsSizeX

public void setPixelsSizeX(ome.xml.model.primitives.PositiveInteger sizeX,
                           int imageIndex)

Specified by:: setPixelsSizeX in interface ome.xml.meta.MetadataStore

setPixelsSizeY

public void setPixelsSizeY(ome.xml.model.primitives.PositiveInteger sizeY,
                           int imageIndex)

Specified by:: setPixelsSizeY in interface ome.xml.meta.MetadataStore

setPixelsSizeZ

public void setPixelsSizeZ(ome.xml.model.primitives.PositiveInteger sizeZ,
                           int imageIndex)

Specified by:: setPixelsSizeZ in interface ome.xml.meta.MetadataStore

setPixelsTimeIncrement

public void setPixelsTimeIncrement(ome.units.quantity.Time timeIncrement,
                                   int imageIndex)

Specified by:: setPixelsTimeIncrement in interface ome.xml.meta.MetadataStore

setPixelsType

public void setPixelsType(ome.xml.model.enums.PixelType type,
                          int imageIndex)

Specified by:: setPixelsType in interface ome.xml.meta.MetadataStore

setPlaneAnnotationRef

public void setPlaneAnnotationRef(java.lang.String annotation,
                                  int imageIndex,
                                  int planeIndex,
                                  int annotationRefIndex)

Specified by:: setPlaneAnnotationRef in interface ome.xml.meta.MetadataStore

setPlaneDeltaT

public void setPlaneDeltaT(ome.units.quantity.Time deltaT,
                           int imageIndex,
                           int planeIndex)

Specified by:: setPlaneDeltaT in interface ome.xml.meta.MetadataStore

setPlaneExposureTime

public void setPlaneExposureTime(ome.units.quantity.Time exposureTime,
                                 int imageIndex,
                                 int planeIndex)

Specified by:: setPlaneExposureTime in interface ome.xml.meta.MetadataStore

setPlaneHashSHA1

public void setPlaneHashSHA1(java.lang.String hashSHA1,
                             int imageIndex,
                             int planeIndex)

Specified by:: setPlaneHashSHA1 in interface ome.xml.meta.MetadataStore

setPlanePositionX

public void setPlanePositionX(ome.units.quantity.Length positionX,
                              int imageIndex,
                              int planeIndex)

Specified by:: setPlanePositionX in interface ome.xml.meta.MetadataStore

setPlanePositionY

public void setPlanePositionY(ome.units.quantity.Length positionY,
                              int imageIndex,
                              int planeIndex)

Specified by:: setPlanePositionY in interface ome.xml.meta.MetadataStore

setPlanePositionZ

public void setPlanePositionZ(ome.units.quantity.Length positionZ,
                              int imageIndex,
                              int planeIndex)

Specified by:: setPlanePositionZ in interface ome.xml.meta.MetadataStore

setPlaneTheC

public void setPlaneTheC(ome.xml.model.primitives.NonNegativeInteger theC,
                         int imageIndex,
                         int planeIndex)

Specified by:: setPlaneTheC in interface ome.xml.meta.MetadataStore

setPlaneTheT

public void setPlaneTheT(ome.xml.model.primitives.NonNegativeInteger theT,
                         int imageIndex,
                         int planeIndex)

Specified by:: setPlaneTheT in interface ome.xml.meta.MetadataStore

setPlaneTheZ

public void setPlaneTheZ(ome.xml.model.primitives.NonNegativeInteger theZ,
                         int imageIndex,
                         int planeIndex)

Specified by:: setPlaneTheZ in interface ome.xml.meta.MetadataStore

setPlateAcquisitionAnnotationRef

public void setPlateAcquisitionAnnotationRef(java.lang.String annotation,
                                             int plateIndex,
                                             int plateAcquisitionIndex,
                                             int annotationRefIndex)

Specified by:: setPlateAcquisitionAnnotationRef in interface ome.xml.meta.MetadataStore

setPlateAcquisitionDescription

public void setPlateAcquisitionDescription(java.lang.String description,
                                           int plateIndex,
                                           int plateAcquisitionIndex)

Specified by:: setPlateAcquisitionDescription in interface ome.xml.meta.MetadataStore

setPlateAcquisitionEndTime

public void setPlateAcquisitionEndTime(ome.xml.model.primitives.Timestamp endTime,
                                       int plateIndex,
                                       int plateAcquisitionIndex)

Specified by:: setPlateAcquisitionEndTime in interface ome.xml.meta.MetadataStore

setPlateAcquisitionID

public void setPlateAcquisitionID(java.lang.String id,
                                  int plateIndex,
                                  int plateAcquisitionIndex)

Specified by:: setPlateAcquisitionID in interface ome.xml.meta.MetadataStore

setPlateAcquisitionMaximumFieldCount

public void setPlateAcquisitionMaximumFieldCount(ome.xml.model.primitives.PositiveInteger maximumFieldCount,
                                                 int plateIndex,
                                                 int plateAcquisitionIndex)

Specified by:: setPlateAcquisitionMaximumFieldCount in interface ome.xml.meta.MetadataStore

setPlateAcquisitionName

public void setPlateAcquisitionName(java.lang.String name,
                                    int plateIndex,
                                    int plateAcquisitionIndex)

Specified by:: setPlateAcquisitionName in interface ome.xml.meta.MetadataStore

setPlateAcquisitionStartTime

public void setPlateAcquisitionStartTime(ome.xml.model.primitives.Timestamp startTime,
                                         int plateIndex,
                                         int plateAcquisitionIndex)

Specified by:: setPlateAcquisitionStartTime in interface ome.xml.meta.MetadataStore

setPlateAcquisitionWellSampleRef

public void setPlateAcquisitionWellSampleRef(java.lang.String wellSample,
                                             int plateIndex,
                                             int plateAcquisitionIndex,
                                             int wellSampleRefIndex)

Specified by:: setPlateAcquisitionWellSampleRef in interface ome.xml.meta.MetadataStore

setPlateAnnotationRef

public void setPlateAnnotationRef(java.lang.String annotation,
                                  int plateIndex,
                                  int annotationRefIndex)

Specified by:: setPlateAnnotationRef in interface ome.xml.meta.MetadataStore

setPlateColumnNamingConvention

public void setPlateColumnNamingConvention(ome.xml.model.enums.NamingConvention columnNamingConvention,
                                           int plateIndex)

Specified by:: setPlateColumnNamingConvention in interface ome.xml.meta.MetadataStore

setPlateColumns

public void setPlateColumns(ome.xml.model.primitives.PositiveInteger columns,
                            int plateIndex)

Specified by:: setPlateColumns in interface ome.xml.meta.MetadataStore

setPlateDescription

public void setPlateDescription(java.lang.String description,
                                int plateIndex)

Specified by:: setPlateDescription in interface ome.xml.meta.MetadataStore

setPlateExternalIdentifier

public void setPlateExternalIdentifier(java.lang.String externalIdentifier,
                                       int plateIndex)

Specified by:: setPlateExternalIdentifier in interface ome.xml.meta.MetadataStore

setPlateID

public void setPlateID(java.lang.String id,
                       int plateIndex)

Specified by:: setPlateID in interface ome.xml.meta.MetadataStore

setPlateName

public void setPlateName(java.lang.String name,
                         int plateIndex)

Specified by:: setPlateName in interface ome.xml.meta.MetadataStore

setPlateRowNamingConvention

public void setPlateRowNamingConvention(ome.xml.model.enums.NamingConvention rowNamingConvention,
                                        int plateIndex)

Specified by:: setPlateRowNamingConvention in interface ome.xml.meta.MetadataStore

setPlateRows

public void setPlateRows(ome.xml.model.primitives.PositiveInteger rows,
                         int plateIndex)

Specified by:: setPlateRows in interface ome.xml.meta.MetadataStore

setPlateStatus

public void setPlateStatus(java.lang.String status,
                           int plateIndex)

Specified by:: setPlateStatus in interface ome.xml.meta.MetadataStore

setPlateWellOriginX

public void setPlateWellOriginX(ome.units.quantity.Length wellOriginX,
                                int plateIndex)

Specified by:: setPlateWellOriginX in interface ome.xml.meta.MetadataStore

setPlateWellOriginY

public void setPlateWellOriginY(ome.units.quantity.Length wellOriginY,
                                int plateIndex)

Specified by:: setPlateWellOriginY in interface ome.xml.meta.MetadataStore

setPointText

public void setPointText(java.lang.String text,
                         int ROIIndex,
                         int shapeIndex)

Specified by:: setPointText in interface ome.xml.meta.MetadataStore

setPointFillColor

public void setPointFillColor(ome.xml.model.primitives.Color fill,
                              int ROIIndex,
                              int shapeIndex)

Specified by:: setPointFillColor in interface ome.xml.meta.MetadataStore

setPointFontSize

public void setPointFontSize(ome.units.quantity.Length fontSize,
                             int ROIIndex,
                             int shapeIndex)

Specified by:: setPointFontSize in interface ome.xml.meta.MetadataStore

setPointID

public void setPointID(java.lang.String id,
                       int ROIIndex,
                       int shapeIndex)

Specified by:: setPointID in interface ome.xml.meta.MetadataStore

setPointStrokeColor

public void setPointStrokeColor(ome.xml.model.primitives.Color stroke,
                                int ROIIndex,
                                int shapeIndex)

Specified by:: setPointStrokeColor in interface ome.xml.meta.MetadataStore

setPointStrokeDashArray

public void setPointStrokeDashArray(java.lang.String strokeDashArray,
                                    int ROIIndex,
                                    int shapeIndex)

Specified by:: setPointStrokeDashArray in interface ome.xml.meta.MetadataStore

setPointStrokeWidth

public void setPointStrokeWidth(ome.units.quantity.Length strokeWidth,
                                int ROIIndex,
                                int shapeIndex)

Specified by:: setPointStrokeWidth in interface ome.xml.meta.MetadataStore

setPointTheC

public void setPointTheC(ome.xml.model.primitives.NonNegativeInteger theC,
                         int ROIIndex,
                         int shapeIndex)

Specified by:: setPointTheC in interface ome.xml.meta.MetadataStore

setPointTheT

public void setPointTheT(ome.xml.model.primitives.NonNegativeInteger theT,
                         int ROIIndex,
                         int shapeIndex)

Specified by:: setPointTheT in interface ome.xml.meta.MetadataStore

setPointTheZ

public void setPointTheZ(ome.xml.model.primitives.NonNegativeInteger theZ,
                         int ROIIndex,
                         int shapeIndex)

Specified by:: setPointTheZ in interface ome.xml.meta.MetadataStore

setPointTransform

public void setPointTransform(ome.xml.model.AffineTransform transform,
                              int ROIIndex,
                              int shapeIndex)

Specified by:: setPointTransform in interface ome.xml.meta.MetadataStore

setPointX

public void setPointX(java.lang.Double x,
                      int ROIIndex,
                      int shapeIndex)

Specified by:: setPointX in interface ome.xml.meta.MetadataStore

setPointY

public void setPointY(java.lang.Double y,
                      int ROIIndex,
                      int shapeIndex)

Specified by:: setPointY in interface ome.xml.meta.MetadataStore

setPolylineID

public void setPolylineID(java.lang.String id,
                          int ROIIndex,
                          int shapeIndex)

Specified by:: setPolylineID in interface ome.xml.meta.MetadataStore

setPolylineText

public void setPolylineText(java.lang.String text,
                            int ROIIndex,
                            int shapeIndex)

Specified by:: setPolylineText in interface ome.xml.meta.MetadataStore

setPolylineFillColor

public void setPolylineFillColor(ome.xml.model.primitives.Color fill,
                                 int ROIIndex,
                                 int shapeIndex)

Specified by:: setPolylineFillColor in interface ome.xml.meta.MetadataStore

setPolylineFontSize

public void setPolylineFontSize(ome.units.quantity.Length fontSize,
                                int ROIIndex,
                                int shapeIndex)

Specified by:: setPolylineFontSize in interface ome.xml.meta.MetadataStore

setPolylinePoints

public void setPolylinePoints(java.lang.String points,
                              int ROIIndex,
                              int shapeIndex)

Specified by:: setPolylinePoints in interface ome.xml.meta.MetadataStore

setPolylineStrokeColor

public void setPolylineStrokeColor(ome.xml.model.primitives.Color stroke,
                                   int ROIIndex,
                                   int shapeIndex)

Specified by:: setPolylineStrokeColor in interface ome.xml.meta.MetadataStore

setPolylineStrokeDashArray

public void setPolylineStrokeDashArray(java.lang.String strokeDashArray,
                                       int ROIIndex,
                                       int shapeIndex)

Specified by:: setPolylineStrokeDashArray in interface ome.xml.meta.MetadataStore

setPolylineStrokeWidth

public void setPolylineStrokeWidth(ome.units.quantity.Length strokeWidth,
                                   int ROIIndex,
                                   int shapeIndex)

Specified by:: setPolylineStrokeWidth in interface ome.xml.meta.MetadataStore

setPolylineTheC

public void setPolylineTheC(ome.xml.model.primitives.NonNegativeInteger theC,
                            int ROIIndex,
                            int shapeIndex)

Specified by:: setPolylineTheC in interface ome.xml.meta.MetadataStore

setPolylineTheT

public void setPolylineTheT(ome.xml.model.primitives.NonNegativeInteger theT,
                            int ROIIndex,
                            int shapeIndex)

Specified by:: setPolylineTheT in interface ome.xml.meta.MetadataStore

setPolylineTheZ

public void setPolylineTheZ(ome.xml.model.primitives.NonNegativeInteger theZ,
                            int ROIIndex,
                            int shapeIndex)

Specified by:: setPolylineTheZ in interface ome.xml.meta.MetadataStore

setPolylineTransform

public void setPolylineTransform(ome.xml.model.AffineTransform transform,
                                 int ROIIndex,
                                 int shapeIndex)

Specified by:: setPolylineTransform in interface ome.xml.meta.MetadataStore

setProjectID

public void setProjectID(java.lang.String id,
                         int projectIndex)

Specified by:: setProjectID in interface ome.xml.meta.MetadataStore

setProjectAnnotationRef

public void setProjectAnnotationRef(java.lang.String annotation,
                                    int projectIndex,
                                    int annotationRefIndex)

Specified by:: setProjectAnnotationRef in interface ome.xml.meta.MetadataStore

setProjectDescription

public void setProjectDescription(java.lang.String description,
                                  int projectIndex)

Specified by:: setProjectDescription in interface ome.xml.meta.MetadataStore

setProjectExperimenterRef

public void setProjectExperimenterRef(java.lang.String experimenter,
                                      int projectIndex)

Specified by:: setProjectExperimenterRef in interface ome.xml.meta.MetadataStore

setProjectExperimenterGroupRef

public void setProjectExperimenterGroupRef(java.lang.String group,
                                           int projectIndex)

Specified by:: setProjectExperimenterGroupRef in interface ome.xml.meta.MetadataStore

setProjectName

public void setProjectName(java.lang.String name,
                           int projectIndex)

Specified by:: setProjectName in interface ome.xml.meta.MetadataStore

setROIID

public void setROIID(java.lang.String id,
                     int ROIIndex)

Specified by:: setROIID in interface ome.xml.meta.MetadataStore

setROIAnnotationRef

public void setROIAnnotationRef(java.lang.String annotation,
                                int ROIIndex,
                                int annotationRefIndex)

Specified by:: setROIAnnotationRef in interface ome.xml.meta.MetadataStore

setROIDescription

public void setROIDescription(java.lang.String description,
                              int ROIIndex)

Specified by:: setROIDescription in interface ome.xml.meta.MetadataStore

setROIName

public void setROIName(java.lang.String name,
                       int ROIIndex)

Specified by:: setROIName in interface ome.xml.meta.MetadataStore

setReagentID

public void setReagentID(java.lang.String id,
                         int screenIndex,
                         int reagentIndex)

Specified by:: setReagentID in interface ome.xml.meta.MetadataStore

setReagentAnnotationRef

public void setReagentAnnotationRef(java.lang.String annotation,
                                    int screenIndex,
                                    int reagentIndex,
                                    int annotationRefIndex)

Specified by:: setReagentAnnotationRef in interface ome.xml.meta.MetadataStore

setReagentDescription

public void setReagentDescription(java.lang.String description,
                                  int screenIndex,
                                  int reagentIndex)

Specified by:: setReagentDescription in interface ome.xml.meta.MetadataStore

setReagentName

public void setReagentName(java.lang.String name,
                           int screenIndex,
                           int reagentIndex)

Specified by:: setReagentName in interface ome.xml.meta.MetadataStore

setReagentReagentIdentifier

public void setReagentReagentIdentifier(java.lang.String reagentIdentifier,
                                        int screenIndex,
                                        int reagentIndex)

Specified by:: setReagentReagentIdentifier in interface ome.xml.meta.MetadataStore

setRectangleID

public void setRectangleID(java.lang.String id,
                           int ROIIndex,
                           int shapeIndex)

Specified by:: setRectangleID in interface ome.xml.meta.MetadataStore

setRectangleText

public void setRectangleText(java.lang.String description,
                             int ROIIndex,
                             int shapeIndex)

Specified by:: setRectangleText in interface ome.xml.meta.MetadataStore

setRectangleFillColor

public void setRectangleFillColor(ome.xml.model.primitives.Color fill,
                                  int ROIIndex,
                                  int shapeIndex)

Specified by:: setRectangleFillColor in interface ome.xml.meta.MetadataStore

setRectangleFontSize

public void setRectangleFontSize(ome.units.quantity.Length fontSize,
                                 int ROIIndex,
                                 int shapeIndex)

Specified by:: setRectangleFontSize in interface ome.xml.meta.MetadataStore

setRectangleHeight

public void setRectangleHeight(java.lang.Double height,
                               int ROIIndex,
                               int shapeIndex)

Specified by:: setRectangleHeight in interface ome.xml.meta.MetadataStore

setRectangleStrokeColor

public void setRectangleStrokeColor(ome.xml.model.primitives.Color stroke,
                                    int ROIIndex,
                                    int shapeIndex)

Specified by:: setRectangleStrokeColor in interface ome.xml.meta.MetadataStore

setRectangleStrokeDashArray

public void setRectangleStrokeDashArray(java.lang.String strokeDashArray,
                                        int ROIIndex,
                                        int shapeIndex)

Specified by:: setRectangleStrokeDashArray in interface ome.xml.meta.MetadataStore

setRectangleStrokeWidth

public void setRectangleStrokeWidth(ome.units.quantity.Length strokeWidth,
                                    int ROIIndex,
                                    int shapeIndex)

Specified by:: setRectangleStrokeWidth in interface ome.xml.meta.MetadataStore

setRectangleTheC

public void setRectangleTheC(ome.xml.model.primitives.NonNegativeInteger theC,
                             int ROIIndex,
                             int shapeIndex)

Specified by:: setRectangleTheC in interface ome.xml.meta.MetadataStore

setRectangleTheT

public void setRectangleTheT(ome.xml.model.primitives.NonNegativeInteger theT,
                             int ROIIndex,
                             int shapeIndex)

Specified by:: setRectangleTheT in interface ome.xml.meta.MetadataStore

setRectangleTheZ

public void setRectangleTheZ(ome.xml.model.primitives.NonNegativeInteger theZ,
                             int ROIIndex,
                             int shapeIndex)

Specified by:: setRectangleTheZ in interface ome.xml.meta.MetadataStore

setRectangleTransform

public void setRectangleTransform(ome.xml.model.AffineTransform transform,
                                  int ROIIndex,
                                  int shapeIndex)

Specified by:: setRectangleTransform in interface ome.xml.meta.MetadataStore

setRectangleWidth

public void setRectangleWidth(java.lang.Double width,
                              int ROIIndex,
                              int shapeIndex)

Specified by:: setRectangleWidth in interface ome.xml.meta.MetadataStore

setRectangleX

public void setRectangleX(java.lang.Double x,
                          int ROIIndex,
                          int shapeIndex)

Specified by:: setRectangleX in interface ome.xml.meta.MetadataStore

setRectangleY

public void setRectangleY(java.lang.Double y,
                          int ROIIndex,
                          int shapeIndex)

Specified by:: setRectangleY in interface ome.xml.meta.MetadataStore

setRoot
```
public void setRoot(ome.xml.meta.MetadataRoot root)
```
Specified by:

setRoot in interface ome.xml.meta.MetadataStore

setScreenID

public void setScreenID(java.lang.String id,
                        int screenIndex)

Specified by:: setScreenID in interface ome.xml.meta.MetadataStore

setScreenAnnotationRef

public void setScreenAnnotationRef(java.lang.String annotation,
                                   int screenIndex,
                                   int annotationRefIndex)

Specified by:: setScreenAnnotationRef in interface ome.xml.meta.MetadataStore

setScreenDescription

public void setScreenDescription(java.lang.String description,
                                 int screenIndex)

Specified by:: setScreenDescription in interface ome.xml.meta.MetadataStore

setScreenName

public void setScreenName(java.lang.String name,
                          int screenIndex)

Specified by:: setScreenName in interface ome.xml.meta.MetadataStore

setScreenPlateRef

public void setScreenPlateRef(java.lang.String plate,
                              int screenIndex,
                              int plateRefIndex)

Specified by:: setScreenPlateRef in interface ome.xml.meta.MetadataStore

setScreenProtocolDescription

public void setScreenProtocolDescription(java.lang.String protocolDescription,
                                         int screenIndex)

Specified by:: setScreenProtocolDescription in interface ome.xml.meta.MetadataStore

setScreenProtocolIdentifier

public void setScreenProtocolIdentifier(java.lang.String protocolIdentifier,
                                        int screenIndex)

Specified by:: setScreenProtocolIdentifier in interface ome.xml.meta.MetadataStore

setScreenReagentSetDescription

public void setScreenReagentSetDescription(java.lang.String reagentSetDescription,
                                           int screenIndex)

Specified by:: setScreenReagentSetDescription in interface ome.xml.meta.MetadataStore

setScreenReagentSetIdentifier

public void setScreenReagentSetIdentifier(java.lang.String reagentSetIdentifier,
                                          int screenIndex)

Specified by:: setScreenReagentSetIdentifier in interface ome.xml.meta.MetadataStore

setScreenType

public void setScreenType(java.lang.String type,
                          int screenIndex)

Specified by:: setScreenType in interface ome.xml.meta.MetadataStore

setStageLabelName

public void setStageLabelName(java.lang.String name,
                              int imageIndex)

Specified by:: setStageLabelName in interface ome.xml.meta.MetadataStore

setStageLabelX

public void setStageLabelX(ome.units.quantity.Length x,
                           int imageIndex)

Specified by:: setStageLabelX in interface ome.xml.meta.MetadataStore

setStageLabelY

public void setStageLabelY(ome.units.quantity.Length y,
                           int imageIndex)

Specified by:: setStageLabelY in interface ome.xml.meta.MetadataStore

setStageLabelZ

public void setStageLabelZ(ome.units.quantity.Length z,
                           int imageIndex)

Specified by:: setStageLabelZ in interface ome.xml.meta.MetadataStore

setCommentAnnotationID

public void setCommentAnnotationID(java.lang.String id,
                                   int commentAnnotationIndex)

Specified by:: setCommentAnnotationID in interface ome.xml.meta.MetadataStore

setCommentAnnotationNamespace

public void setCommentAnnotationNamespace(java.lang.String namespace,
                                          int commentAnnotationIndex)

Specified by:: setCommentAnnotationNamespace in interface ome.xml.meta.MetadataStore

setCommentAnnotationAnnotator

public void setCommentAnnotationAnnotator(java.lang.String value,
                                          int index)

Specified by:: setCommentAnnotationAnnotator in interface ome.xml.meta.MetadataStore

setCommentAnnotationValue

public void setCommentAnnotationValue(java.lang.String value,
                                      int commentAnnotationIndex)

Specified by:: setCommentAnnotationValue in interface ome.xml.meta.MetadataStore

setLabelID

public void setLabelID(java.lang.String id,
                       int ROIIndex,
                       int shapeIndex)

Specified by:: setLabelID in interface ome.xml.meta.MetadataStore

setLabelText

public void setLabelText(java.lang.String text,
                         int ROIIndex,
                         int shapeIndex)

Specified by:: setLabelText in interface ome.xml.meta.MetadataStore

setLabelFillColor

public void setLabelFillColor(ome.xml.model.primitives.Color fill,
                              int ROIIndex,
                              int shapeIndex)

Specified by:: setLabelFillColor in interface ome.xml.meta.MetadataStore

setLabelFontSize

public void setLabelFontSize(ome.units.quantity.Length fontSize,
                             int ROIIndex,
                             int shapeIndex)

Specified by:: setLabelFontSize in interface ome.xml.meta.MetadataStore

setLabelStrokeColor

public void setLabelStrokeColor(ome.xml.model.primitives.Color stroke,
                                int ROIIndex,
                                int shapeIndex)

Specified by:: setLabelStrokeColor in interface ome.xml.meta.MetadataStore

setLabelStrokeDashArray

public void setLabelStrokeDashArray(java.lang.String strokeDashArray,
                                    int ROIIndex,
                                    int shapeIndex)

Specified by:: setLabelStrokeDashArray in interface ome.xml.meta.MetadataStore

setLabelStrokeWidth

public void setLabelStrokeWidth(ome.units.quantity.Length strokeWidth,
                                int ROIIndex,
                                int shapeIndex)

Specified by:: setLabelStrokeWidth in interface ome.xml.meta.MetadataStore

setLabelTheC

public void setLabelTheC(ome.xml.model.primitives.NonNegativeInteger theC,
                         int ROIIndex,
                         int shapeIndex)

Specified by:: setLabelTheC in interface ome.xml.meta.MetadataStore

setLabelTheT

public void setLabelTheT(ome.xml.model.primitives.NonNegativeInteger theT,
                         int ROIIndex,
                         int shapeIndex)

Specified by:: setLabelTheT in interface ome.xml.meta.MetadataStore

setLabelTheZ

public void setLabelTheZ(ome.xml.model.primitives.NonNegativeInteger theZ,
                         int ROIIndex,
                         int shapeIndex)

Specified by:: setLabelTheZ in interface ome.xml.meta.MetadataStore

setLabelTransform

public void setLabelTransform(ome.xml.model.AffineTransform transform,
                              int ROIIndex,
                              int shapeIndex)

Specified by:: setLabelTransform in interface ome.xml.meta.MetadataStore

setLabelX

public void setLabelX(java.lang.Double x,
                      int ROIIndex,
                      int shapeIndex)

Specified by:: setLabelX in interface ome.xml.meta.MetadataStore

setLabelY

public void setLabelY(java.lang.Double y,
                      int ROIIndex,
                      int shapeIndex)

Specified by:: setLabelY in interface ome.xml.meta.MetadataStore

setTiffDataFirstC

public void setTiffDataFirstC(ome.xml.model.primitives.NonNegativeInteger firstC,
                              int imageIndex,
                              int tiffDataIndex)

Specified by:: setTiffDataFirstC in interface ome.xml.meta.MetadataStore

setTiffDataFirstT

public void setTiffDataFirstT(ome.xml.model.primitives.NonNegativeInteger firstT,
                              int imageIndex,
                              int tiffDataIndex)

Specified by:: setTiffDataFirstT in interface ome.xml.meta.MetadataStore

setTiffDataFirstZ

public void setTiffDataFirstZ(ome.xml.model.primitives.NonNegativeInteger firstZ,
                              int imageIndex,
                              int tiffDataIndex)

Specified by:: setTiffDataFirstZ in interface ome.xml.meta.MetadataStore

setTiffDataIFD

public void setTiffDataIFD(ome.xml.model.primitives.NonNegativeInteger ifd,
                           int imageIndex,
                           int tiffDataIndex)

Specified by:: setTiffDataIFD in interface ome.xml.meta.MetadataStore

setTiffDataPlaneCount

public void setTiffDataPlaneCount(ome.xml.model.primitives.NonNegativeInteger planeCount,
                                  int imageIndex,
                                  int tiffDataIndex)

Specified by:: setTiffDataPlaneCount in interface ome.xml.meta.MetadataStore

setTimestampAnnotationID

public void setTimestampAnnotationID(java.lang.String id,
                                     int timestampAnnotationIndex)

Specified by:: setTimestampAnnotationID in interface ome.xml.meta.MetadataStore

setTimestampAnnotationNamespace

public void setTimestampAnnotationNamespace(java.lang.String namespace,
                                            int timestampAnnotationIndex)

Specified by:: setTimestampAnnotationNamespace in interface ome.xml.meta.MetadataStore

setTimestampAnnotationValue

public void setTimestampAnnotationValue(ome.xml.model.primitives.Timestamp value,
                                        int timestampAnnotationIndex)

Specified by:: setTimestampAnnotationValue in interface ome.xml.meta.MetadataStore

setTransmittanceRangeCutIn

public void setTransmittanceRangeCutIn(ome.units.quantity.Length cutIn,
                                       int instrumentIndex,
                                       int filterIndex)

Specified by:: setTransmittanceRangeCutIn in interface ome.xml.meta.MetadataStore

setTransmittanceRangeCutInTolerance

public void setTransmittanceRangeCutInTolerance(ome.units.quantity.Length cutInTolerance,
                                                int instrumentIndex,
                                                int filterIndex)

Specified by:: setTransmittanceRangeCutInTolerance in interface ome.xml.meta.MetadataStore

setTransmittanceRangeCutOut

public void setTransmittanceRangeCutOut(ome.units.quantity.Length cutOut,
                                        int instrumentIndex,
                                        int filterIndex)

Specified by:: setTransmittanceRangeCutOut in interface ome.xml.meta.MetadataStore

setTransmittanceRangeCutOutTolerance

public void setTransmittanceRangeCutOutTolerance(ome.units.quantity.Length cutOutTolerance,
                                                 int instrumentIndex,
                                                 int filterIndex)

Specified by:: setTransmittanceRangeCutOutTolerance in interface ome.xml.meta.MetadataStore

setTransmittanceRangeTransmittance

public void setTransmittanceRangeTransmittance(ome.xml.model.primitives.PercentFraction transmittance,
                                               int instrumentIndex,
                                               int filterIndex)

Specified by:: setTransmittanceRangeTransmittance in interface ome.xml.meta.MetadataStore

setUUID
```
public void setUUID(java.lang.String uuid)
```
Specified by:

setUUID in interface ome.xml.meta.MetadataStore

setUUIDFileName

public void setUUIDFileName(java.lang.String fileName,
                            int imageIndex,
                            int tiffDataIndex)

Specified by:: setUUIDFileName in interface ome.xml.meta.MetadataStore

setUUIDValue

public void setUUIDValue(java.lang.String fileName,
                         int imageIndex,
                         int tiffDataIndex)

Specified by:: setUUIDValue in interface ome.xml.meta.MetadataStore

setWellID

public void setWellID(java.lang.String id,
                      int plateIndex,
                      int wellIndex)

Specified by:: setWellID in interface ome.xml.meta.MetadataStore

setWellAnnotationRef

public void setWellAnnotationRef(java.lang.String annotation,
                                 int plateIndex,
                                 int wellIndex,
                                 int annotationRefIndex)

Specified by:: setWellAnnotationRef in interface ome.xml.meta.MetadataStore

setWellColor

public void setWellColor(ome.xml.model.primitives.Color color,
                         int plateIndex,
                         int wellIndex)

Specified by:: setWellColor in interface ome.xml.meta.MetadataStore

setWellColumn

public void setWellColumn(ome.xml.model.primitives.NonNegativeInteger column,
                          int plateIndex,
                          int wellIndex)

Specified by:: setWellColumn in interface ome.xml.meta.MetadataStore

setWellExternalDescription

public void setWellExternalDescription(java.lang.String externalDescription,
                                       int plateIndex,
                                       int wellIndex)

Specified by:: setWellExternalDescription in interface ome.xml.meta.MetadataStore

setWellExternalIdentifier

public void setWellExternalIdentifier(java.lang.String externalIdentifier,
                                      int plateIndex,
                                      int wellIndex)

Specified by:: setWellExternalIdentifier in interface ome.xml.meta.MetadataStore

setWellReagentRef

public void setWellReagentRef(java.lang.String reagent,
                              int plateIndex,
                              int wellIndex)

Specified by:: setWellReagentRef in interface ome.xml.meta.MetadataStore

setWellRow

public void setWellRow(ome.xml.model.primitives.NonNegativeInteger row,
                       int plateIndex,
                       int wellIndex)

Specified by:: setWellRow in interface ome.xml.meta.MetadataStore

setWellSampleID

public void setWellSampleID(java.lang.String id,
                            int plateIndex,
                            int wellIndex,
                            int wellSampleIndex)

Specified by:: setWellSampleID in interface ome.xml.meta.MetadataStore

setWellSampleImageRef

public void setWellSampleImageRef(java.lang.String image,
                                  int plateIndex,
                                  int wellIndex,
                                  int wellSampleIndex)

Specified by:: setWellSampleImageRef in interface ome.xml.meta.MetadataStore

setWellSampleIndex

public void setWellSampleIndex(ome.xml.model.primitives.NonNegativeInteger index,
                               int plateIndex,
                               int wellIndex,
                               int wellSampleIndex)

Specified by:: setWellSampleIndex in interface ome.xml.meta.MetadataStore

setWellSamplePositionX

public void setWellSamplePositionX(ome.units.quantity.Length positionX,
                                   int plateIndex,
                                   int wellIndex,
                                   int wellSampleIndex)

Specified by:: setWellSamplePositionX in interface ome.xml.meta.MetadataStore

setWellSamplePositionY

public void setWellSamplePositionY(ome.units.quantity.Length positionY,
                                   int plateIndex,
                                   int wellIndex,
                                   int wellSampleIndex)

Specified by:: setWellSamplePositionY in interface ome.xml.meta.MetadataStore

setWellSampleTimepoint

public void setWellSampleTimepoint(ome.xml.model.primitives.Timestamp timepoint,
                                   int plateIndex,
                                   int wellIndex,
                                   int wellSampleIndex)

Specified by:: setWellSampleTimepoint in interface ome.xml.meta.MetadataStore

setXMLAnnotationID

public void setXMLAnnotationID(java.lang.String id,
                               int XMLAnnotationIndex)

Specified by:: setXMLAnnotationID in interface ome.xml.meta.MetadataStore

setXMLAnnotationNamespace

public void setXMLAnnotationNamespace(java.lang.String namespace,
                                      int XMLAnnotationIndex)

Specified by:: setXMLAnnotationNamespace in interface ome.xml.meta.MetadataStore

setXMLAnnotationValue

public void setXMLAnnotationValue(java.lang.String value,
                                  int XMLAnnotationIndex)

Specified by:: setXMLAnnotationValue in interface ome.xml.meta.MetadataStore

setXMLAnnotationAnnotator

public void setXMLAnnotationAnnotator(java.lang.String value,
                                      int index)

Specified by:: setXMLAnnotationAnnotator in interface ome.xml.meta.MetadataStore

setXMLAnnotationAnnotationRef

public void setXMLAnnotationAnnotationRef(java.lang.String annotation,
                                          int XMLAnnotationIndex,
                                          int annotationRefIndex)

Specified by:: setXMLAnnotationAnnotationRef in interface ome.xml.meta.MetadataStore

setXMLAnnotationDescription

public void setXMLAnnotationDescription(java.lang.String description,
                                        int XMLAnnotationIndex)

Specified by:: setXMLAnnotationDescription in interface ome.xml.meta.MetadataStore

setBooleanAnnotationAnnotationRef

public void setBooleanAnnotationAnnotationRef(java.lang.String annotation,
                                              int booleanAnnotationIndex,
                                              int annotationRefIndex)

Specified by:: setBooleanAnnotationAnnotationRef in interface ome.xml.meta.MetadataStore

setBooleanAnnotationDescription

public void setBooleanAnnotationDescription(java.lang.String description,
                                            int booleanAnnotationIndex)

Specified by:: setBooleanAnnotationDescription in interface ome.xml.meta.MetadataStore

setBooleanAnnotationAnnotator

public void setBooleanAnnotationAnnotator(java.lang.String value,
                                          int index)

Specified by:: setBooleanAnnotationAnnotator in interface ome.xml.meta.MetadataStore

setCommentAnnotationAnnotationRef

public void setCommentAnnotationAnnotationRef(java.lang.String annotation,
                                              int commentAnnotationIndex,
                                              int annotationRefIndex)

Specified by:: setCommentAnnotationAnnotationRef in interface ome.xml.meta.MetadataStore

setCommentAnnotationDescription

public void setCommentAnnotationDescription(java.lang.String description,
                                            int commentAnnotationIndex)

Specified by:: setCommentAnnotationDescription in interface ome.xml.meta.MetadataStore

setDoubleAnnotationAnnotationRef

public void setDoubleAnnotationAnnotationRef(java.lang.String annotation,
                                             int doubleAnnotationIndex,
                                             int annotationRefIndex)

Specified by:: setDoubleAnnotationAnnotationRef in interface ome.xml.meta.MetadataStore

setDoubleAnnotationDescription

public void setDoubleAnnotationDescription(java.lang.String description,
                                           int doubleAnnotationIndex)

Specified by:: setDoubleAnnotationDescription in interface ome.xml.meta.MetadataStore

setDoubleAnnotationAnnotator

public void setDoubleAnnotationAnnotator(java.lang.String value,
                                         int index)

Specified by:: setDoubleAnnotationAnnotator in interface ome.xml.meta.MetadataStore

setFileAnnotationAnnotationRef

public void setFileAnnotationAnnotationRef(java.lang.String annotation,
                                           int fileAnnotationIndex,
                                           int annotationRefIndex)

Specified by:: setFileAnnotationAnnotationRef in interface ome.xml.meta.MetadataStore

setFileAnnotationDescription

public void setFileAnnotationDescription(java.lang.String description,
                                         int fileAnnotationIndex)

Specified by:: setFileAnnotationDescription in interface ome.xml.meta.MetadataStore

setFileAnnotationAnnotator

public void setFileAnnotationAnnotator(java.lang.String value,
                                       int index)

Specified by:: setFileAnnotationAnnotator in interface ome.xml.meta.MetadataStore

setListAnnotationDescription

public void setListAnnotationDescription(java.lang.String description,
                                         int listAnnotationIndex)

Specified by:: setListAnnotationDescription in interface ome.xml.meta.MetadataStore

setListAnnotationAnnotator

public void setListAnnotationAnnotator(java.lang.String value,
                                       int index)

Specified by:: setListAnnotationAnnotator in interface ome.xml.meta.MetadataStore

setLongAnnotationAnnotationRef

public void setLongAnnotationAnnotationRef(java.lang.String annotation,
                                           int longAnnotationIndex,
                                           int annotationRefIndex)

Specified by:: setLongAnnotationAnnotationRef in interface ome.xml.meta.MetadataStore

setLongAnnotationDescription

public void setLongAnnotationDescription(java.lang.String description,
                                         int longAnnotationIndex)

Specified by:: setLongAnnotationDescription in interface ome.xml.meta.MetadataStore

setLongAnnotationAnnotator

public void setLongAnnotationAnnotator(java.lang.String value,
                                       int XMLAnnotationIndex)

Specified by:: setLongAnnotationAnnotator in interface ome.xml.meta.MetadataStore

setMapAnnotationAnnotationRef

public void setMapAnnotationAnnotationRef(java.lang.String annotation,
                                          int mapAnnotationIndex,
                                          int annotationRefIndex)

Specified by:: setMapAnnotationAnnotationRef in interface ome.xml.meta.MetadataStore

setMapAnnotationAnnotator

public void setMapAnnotationAnnotator(java.lang.String annotator,
                                      int mapAnnotationIndex)

Specified by:: setMapAnnotationAnnotator in interface ome.xml.meta.MetadataStore

setMapAnnotationDescription

public void setMapAnnotationDescription(java.lang.String description,
                                        int mapAnnotationIndex)

Specified by:: setMapAnnotationDescription in interface ome.xml.meta.MetadataStore

setMapAnnotationID

public void setMapAnnotationID(java.lang.String id,
                               int mapAnnotationIndex)

Specified by:: setMapAnnotationID in interface ome.xml.meta.MetadataStore

setMapAnnotationNamespace

public void setMapAnnotationNamespace(java.lang.String namespace,
                                      int mapAnnotationIndex)

Specified by:: setMapAnnotationNamespace in interface ome.xml.meta.MetadataStore

setMapAnnotationValue

public void setMapAnnotationValue(java.util.List<ome.xml.model.MapPair> value,
                                  int mapAnnotationIndex)

Specified by:: setMapAnnotationValue in interface ome.xml.meta.MetadataStore

setTagAnnotationAnnotationRef

public void setTagAnnotationAnnotationRef(java.lang.String annotation,
                                          int tagAnnotationIndex,
                                          int annotationRefIndex)

Specified by:: setTagAnnotationAnnotationRef in interface ome.xml.meta.MetadataStore

setTagAnnotationDescription

public void setTagAnnotationDescription(java.lang.String description,
                                        int tagAnnotationIndex)

Specified by:: setTagAnnotationDescription in interface ome.xml.meta.MetadataStore

setTagAnnotationID

public void setTagAnnotationID(java.lang.String id,
                               int tagAnnotationIndex)

Specified by:: setTagAnnotationID in interface ome.xml.meta.MetadataStore

setTagAnnotationNamespace

public void setTagAnnotationNamespace(java.lang.String namespace,
                                      int tagAnnotationIndex)

Specified by:: setTagAnnotationNamespace in interface ome.xml.meta.MetadataStore

setTagAnnotationAnnotator

public void setTagAnnotationAnnotator(java.lang.String value,
                                      int index)

Specified by:: setTagAnnotationAnnotator in interface ome.xml.meta.MetadataStore

setTagAnnotationValue

public void setTagAnnotationValue(java.lang.String value,
                                  int tagAnnotationIndex)

Specified by:: setTagAnnotationValue in interface ome.xml.meta.MetadataStore

setTermAnnotationAnnotationRef

public void setTermAnnotationAnnotationRef(java.lang.String annotation,
                                           int termAnnotationIndex,
                                           int annotationRefIndex)

Specified by:: setTermAnnotationAnnotationRef in interface ome.xml.meta.MetadataStore

setTermAnnotationDescription

public void setTermAnnotationDescription(java.lang.String description,
                                         int termAnnotationIndex)

Specified by:: setTermAnnotationDescription in interface ome.xml.meta.MetadataStore

setTermAnnotationID

public void setTermAnnotationID(java.lang.String id,
                                int termAnnotationIndex)

Specified by:: setTermAnnotationID in interface ome.xml.meta.MetadataStore

setTermAnnotationNamespace

public void setTermAnnotationNamespace(java.lang.String namespace,
                                       int termAnnotationIndex)

Specified by:: setTermAnnotationNamespace in interface ome.xml.meta.MetadataStore

setTermAnnotationAnnotator

public void setTermAnnotationAnnotator(java.lang.String value,
                                       int index)

Specified by:: setTermAnnotationAnnotator in interface ome.xml.meta.MetadataStore

setTermAnnotationValue

public void setTermAnnotationValue(java.lang.String value,
                                   int termAnnotationIndex)

Specified by:: setTermAnnotationValue in interface ome.xml.meta.MetadataStore

setTimestampAnnotationAnnotationRef

public void setTimestampAnnotationAnnotationRef(java.lang.String annotation,
                                                int timestampAnnotationIndex,
                                                int annotationRefIndex)

Specified by:: setTimestampAnnotationAnnotationRef in interface ome.xml.meta.MetadataStore

setTimestampAnnotationDescription

public void setTimestampAnnotationDescription(java.lang.String description,
                                              int timestampAnnotationIndex)

Specified by:: setTimestampAnnotationDescription in interface ome.xml.meta.MetadataStore

setTimestampAnnotationAnnotator

public void setTimestampAnnotationAnnotator(java.lang.String value,
                                            int index)

Specified by:: setTimestampAnnotationAnnotator in interface ome.xml.meta.MetadataStore

setPlateFieldIndex

public void setPlateFieldIndex(ome.xml.model.primitives.NonNegativeInteger fieldIndex,
                               int plateIndex)

Specified by:: setPlateFieldIndex in interface ome.xml.meta.MetadataStore

setBinaryFileBinData

public void setBinaryFileBinData(byte[] binData,
                                 int fileAnnotationIndex)

Specified by:: setBinaryFileBinData in interface ome.xml.meta.MetadataStore

setBinaryFileBinDataBigEndian

public void setBinaryFileBinDataBigEndian(java.lang.Boolean isBigEndian,
                                          int fileAnnotationIndex)

Specified by:: setBinaryFileBinDataBigEndian in interface ome.xml.meta.MetadataStore

setBinaryFileBinDataCompression

public void setBinaryFileBinDataCompression(ome.xml.model.enums.Compression compression,
                                            int fileAnnotationIndex)

Specified by:: setBinaryFileBinDataCompression in interface ome.xml.meta.MetadataStore

setBinaryFileBinDataLength

public void setBinaryFileBinDataLength(ome.xml.model.primitives.NonNegativeLong length,
                                       int fileAnnotationIndex)

Specified by:: setBinaryFileBinDataLength in interface ome.xml.meta.MetadataStore

setBinaryFileFileName

public void setBinaryFileFileName(java.lang.String fileName,
                                  int fileAnnotationIndex)

Specified by:: setBinaryFileFileName in interface ome.xml.meta.MetadataStore

setBinaryFileMIMEType

public void setBinaryFileMIMEType(java.lang.String mimeType,
                                  int fileAnnotationIndex)

Specified by:: setBinaryFileMIMEType in interface ome.xml.meta.MetadataStore

setBinaryFileSize

public void setBinaryFileSize(ome.xml.model.primitives.NonNegativeLong size,
                              int fileAnnotationIndex)

Specified by:: setBinaryFileSize in interface ome.xml.meta.MetadataStore

setDatasetImageRef

public void setDatasetImageRef(java.lang.String image,
                               int datasetIndex,
                               int imageRefIndex)

Specified by:: setDatasetImageRef in interface ome.xml.meta.MetadataStore

setEllipseFillRule

public void setEllipseFillRule(ome.xml.model.enums.FillRule fillRule,
                               int ROIIndex,
                               int shapeIndex)

Specified by:: setEllipseFillRule in interface ome.xml.meta.MetadataStore

setEllipseFontFamily

public void setEllipseFontFamily(ome.xml.model.enums.FontFamily fontFamily,
                                 int ROIIndex,
                                 int shapeIndex)

Specified by:: setEllipseFontFamily in interface ome.xml.meta.MetadataStore

setEllipseFontStyle

public void setEllipseFontStyle(ome.xml.model.enums.FontStyle fontStyle,
                                int ROIIndex,
                                int shapeIndex)

Specified by:: setEllipseFontStyle in interface ome.xml.meta.MetadataStore

setEllipseLocked

public void setEllipseLocked(java.lang.Boolean locked,
                             int ROIIndex,
                             int shapeIndex)

Specified by:: setEllipseLocked in interface ome.xml.meta.MetadataStore

setExperimenterGroupAnnotationRef

public void setExperimenterGroupAnnotationRef(java.lang.String annotation,
                                              int experimenterGroupIndex,
                                              int annotationRefIndex)

Specified by:: setExperimenterGroupAnnotationRef in interface ome.xml.meta.MetadataStore

setExperimenterGroupExperimenterRef

public void setExperimenterGroupExperimenterRef(java.lang.String experimenter,
                                                int experimenterGroupIndex,
                                                int experimenterRefIndex)

Specified by:: setExperimenterGroupExperimenterRef in interface ome.xml.meta.MetadataStore

setLabelFillRule

public void setLabelFillRule(ome.xml.model.enums.FillRule fillRule,
                             int ROIIndex,
                             int shapeIndex)

Specified by:: setLabelFillRule in interface ome.xml.meta.MetadataStore

setLabelFontFamily

public void setLabelFontFamily(ome.xml.model.enums.FontFamily fontFamily,
                               int ROIIndex,
                               int shapeIndex)

Specified by:: setLabelFontFamily in interface ome.xml.meta.MetadataStore

setLabelFontStyle

public void setLabelFontStyle(ome.xml.model.enums.FontStyle fontStyle,
                              int ROIIndex,
                              int shapeIndex)

Specified by:: setLabelFontStyle in interface ome.xml.meta.MetadataStore

setLabelLocked

public void setLabelLocked(java.lang.Boolean locked,
                           int ROIIndex,
                           int shapeIndex)

Specified by:: setLabelLocked in interface ome.xml.meta.MetadataStore

setLineFillRule

public void setLineFillRule(ome.xml.model.enums.FillRule fillRule,
                            int ROIIndex,
                            int shapeIndex)

Specified by:: setLineFillRule in interface ome.xml.meta.MetadataStore

setLineFontFamily

public void setLineFontFamily(ome.xml.model.enums.FontFamily fontFamily,
                              int ROIIndex,
                              int shapeIndex)

Specified by:: setLineFontFamily in interface ome.xml.meta.MetadataStore

setLineFontStyle

public void setLineFontStyle(ome.xml.model.enums.FontStyle fontStyle,
                             int ROIIndex,
                             int shapeIndex)

Specified by:: setLineFontStyle in interface ome.xml.meta.MetadataStore

setLineLocked

public void setLineLocked(java.lang.Boolean locked,
                          int ROIIndex,
                          int shapeIndex)

Specified by:: setLineLocked in interface ome.xml.meta.MetadataStore

setLineMarkerEnd

public void setLineMarkerEnd(ome.xml.model.enums.Marker markerEnd,
                             int ROIIndex,
                             int shapeIndex)

Specified by:: setLineMarkerEnd in interface ome.xml.meta.MetadataStore

setLineMarkerStart

public void setLineMarkerStart(ome.xml.model.enums.Marker markerStart,
                               int ROIIndex,
                               int shapeIndex)

Specified by:: setLineMarkerStart in interface ome.xml.meta.MetadataStore

setMaskFillRule

public void setMaskFillRule(ome.xml.model.enums.FillRule fillRule,
                            int ROIIndex,
                            int shapeIndex)

Specified by:: setMaskFillRule in interface ome.xml.meta.MetadataStore

setMaskFontFamily

public void setMaskFontFamily(ome.xml.model.enums.FontFamily fontFamily,
                              int ROIIndex,
                              int shapeIndex)

Specified by:: setMaskFontFamily in interface ome.xml.meta.MetadataStore

setMaskFontStyle

public void setMaskFontStyle(ome.xml.model.enums.FontStyle fontStyle,
                             int ROIIndex,
                             int shapeIndex)

Specified by:: setMaskFontStyle in interface ome.xml.meta.MetadataStore

setMaskLocked

public void setMaskLocked(java.lang.Boolean locked,
                          int ROIIndex,
                          int shapeIndex)

Specified by:: setMaskLocked in interface ome.xml.meta.MetadataStore

setPointFillRule

public void setPointFillRule(ome.xml.model.enums.FillRule fillRule,
                             int ROIIndex,
                             int shapeIndex)

Specified by:: setPointFillRule in interface ome.xml.meta.MetadataStore

setPointFontFamily

public void setPointFontFamily(ome.xml.model.enums.FontFamily fontFamily,
                               int ROIIndex,
                               int shapeIndex)

Specified by:: setPointFontFamily in interface ome.xml.meta.MetadataStore

setPointFontStyle

public void setPointFontStyle(ome.xml.model.enums.FontStyle fontStyle,
                              int ROIIndex,
                              int shapeIndex)

Specified by:: setPointFontStyle in interface ome.xml.meta.MetadataStore

setPointLocked

public void setPointLocked(java.lang.Boolean locked,
                           int ROIIndex,
                           int shapeIndex)

Specified by:: setPointLocked in interface ome.xml.meta.MetadataStore

setPolygonFillColor

public void setPolygonFillColor(ome.xml.model.primitives.Color fillColor,
                                int ROIIndex,
                                int shapeIndex)

Specified by:: setPolygonFillColor in interface ome.xml.meta.MetadataStore

setPolygonFillRule

public void setPolygonFillRule(ome.xml.model.enums.FillRule fillRule,
                               int ROIIndex,
                               int shapeIndex)

Specified by:: setPolygonFillRule in interface ome.xml.meta.MetadataStore

setPolygonFontFamily

public void setPolygonFontFamily(ome.xml.model.enums.FontFamily fontFamily,
                                 int ROIIndex,
                                 int shapeIndex)

Specified by:: setPolygonFontFamily in interface ome.xml.meta.MetadataStore

setPolygonFontSize

public void setPolygonFontSize(ome.units.quantity.Length fontSize,
                               int ROIIndex,
                               int shapeIndex)

Specified by:: setPolygonFontSize in interface ome.xml.meta.MetadataStore

setPolygonFontStyle

public void setPolygonFontStyle(ome.xml.model.enums.FontStyle fontStyle,
                                int ROIIndex,
                                int shapeIndex)

Specified by:: setPolygonFontStyle in interface ome.xml.meta.MetadataStore

setPolygonID

public void setPolygonID(java.lang.String id,
                         int ROIIndex,
                         int shapeIndex)

Specified by:: setPolygonID in interface ome.xml.meta.MetadataStore

setPolygonLocked

public void setPolygonLocked(java.lang.Boolean locked,
                             int ROIIndex,
                             int shapeIndex)

Specified by:: setPolygonLocked in interface ome.xml.meta.MetadataStore

setPolygonStrokeColor

public void setPolygonStrokeColor(ome.xml.model.primitives.Color strokeColor,
                                  int ROIIndex,
                                  int shapeIndex)

Specified by:: setPolygonStrokeColor in interface ome.xml.meta.MetadataStore

setPolygonStrokeDashArray

public void setPolygonStrokeDashArray(java.lang.String strokeDashArray,
                                      int ROIIndex,
                                      int shapeIndex)

Specified by:: setPolygonStrokeDashArray in interface ome.xml.meta.MetadataStore

setPolygonStrokeWidth

public void setPolygonStrokeWidth(ome.units.quantity.Length strokeWidth,
                                  int ROIIndex,
                                  int shapeIndex)

Specified by:: setPolygonStrokeWidth in interface ome.xml.meta.MetadataStore

setPolygonText

public void setPolygonText(java.lang.String text,
                           int ROIIndex,
                           int shapeIndex)

Specified by:: setPolygonText in interface ome.xml.meta.MetadataStore

setPolygonTheC

public void setPolygonTheC(ome.xml.model.primitives.NonNegativeInteger theC,
                           int ROIIndex,
                           int shapeIndex)

Specified by:: setPolygonTheC in interface ome.xml.meta.MetadataStore

setPolygonTheT

public void setPolygonTheT(ome.xml.model.primitives.NonNegativeInteger theT,
                           int ROIIndex,
                           int shapeIndex)

Specified by:: setPolygonTheT in interface ome.xml.meta.MetadataStore

setPolygonTheZ

public void setPolygonTheZ(ome.xml.model.primitives.NonNegativeInteger theZ,
                           int ROIIndex,
                           int shapeIndex)

Specified by:: setPolygonTheZ in interface ome.xml.meta.MetadataStore

setPolygonTransform

public void setPolygonTransform(ome.xml.model.AffineTransform transform,
                                int ROIIndex,
                                int shapeIndex)

Specified by:: setPolygonTransform in interface ome.xml.meta.MetadataStore

setPolygonPoints

public void setPolygonPoints(java.lang.String points,
                             int ROIIndex,
                             int shapeIndex)

Specified by:: setPolygonPoints in interface ome.xml.meta.MetadataStore

setPolylineFillRule

public void setPolylineFillRule(ome.xml.model.enums.FillRule fillRule,
                                int ROIIndex,
                                int shapeIndex)

Specified by:: setPolylineFillRule in interface ome.xml.meta.MetadataStore

setPolylineFontFamily

public void setPolylineFontFamily(ome.xml.model.enums.FontFamily fontFamily,
                                  int ROIIndex,
                                  int shapeIndex)

Specified by:: setPolylineFontFamily in interface ome.xml.meta.MetadataStore

setPolylineFontStyle

public void setPolylineFontStyle(ome.xml.model.enums.FontStyle fontStyle,
                                 int ROIIndex,
                                 int shapeIndex)

Specified by:: setPolylineFontStyle in interface ome.xml.meta.MetadataStore

setPolylineLocked

public void setPolylineLocked(java.lang.Boolean locked,
                              int ROIIndex,
                              int shapeIndex)

Specified by:: setPolylineLocked in interface ome.xml.meta.MetadataStore

setPolylineMarkerEnd

public void setPolylineMarkerEnd(ome.xml.model.enums.Marker markerEnd,
                                 int ROIIndex,
                                 int shapeIndex)

Specified by:: setPolylineMarkerEnd in interface ome.xml.meta.MetadataStore

setPolylineMarkerStart

public void setPolylineMarkerStart(ome.xml.model.enums.Marker markerStart,
                                   int ROIIndex,
                                   int shapeIndex)

Specified by:: setPolylineMarkerStart in interface ome.xml.meta.MetadataStore

setProjectDatasetRef

public void setProjectDatasetRef(java.lang.String dataset,
                                 int projectIndex,
                                 int datasetRefIndex)

Specified by:: setProjectDatasetRef in interface ome.xml.meta.MetadataStore

setRectangleFillRule

public void setRectangleFillRule(ome.xml.model.enums.FillRule fillRule,
                                 int ROIIndex,
                                 int shapeIndex)

Specified by:: setRectangleFillRule in interface ome.xml.meta.MetadataStore

setRectangleFontFamily

public void setRectangleFontFamily(ome.xml.model.enums.FontFamily fontFamily,
                                   int ROIIndex,
                                   int shapeIndex)

Specified by:: setRectangleFontFamily in interface ome.xml.meta.MetadataStore

setRectangleFontStyle

public void setRectangleFontStyle(ome.xml.model.enums.FontStyle fontStyle,
                                  int ROIIndex,
                                  int shapeIndex)

Specified by:: setRectangleFontStyle in interface ome.xml.meta.MetadataStore

setRectangleLocked

public void setRectangleLocked(java.lang.Boolean locked,
                               int ROIIndex,
                               int shapeIndex)

Specified by:: setRectangleLocked in interface ome.xml.meta.MetadataStore

setWellType

public void setWellType(java.lang.String type,
                        int plateIndex,
                        int wellIndex)

Specified by:: setWellType in interface ome.xml.meta.MetadataStore

setRightsRightsHeld
```
public void setRightsRightsHeld(java.lang.String value)
```
Specified by:

setRightsRightsHeld in interface ome.xml.meta.MetadataStore

setRightsRightsHolder
```
public void setRightsRightsHolder(java.lang.String value)
```
Specified by:

setRightsRightsHolder in interface ome.xml.meta.MetadataStore

setDetectorAnnotationRef

public void setDetectorAnnotationRef(java.lang.String annotation,
                                     int instrumentIndex,
                                     int detectorIndex,
                                     int annotationRefIndex)

Specified by:: setDetectorAnnotationRef in interface ome.xml.meta.MetadataStore

setDichroicAnnotationRef

public void setDichroicAnnotationRef(java.lang.String annotation,
                                     int instrumentIndex,
                                     int dichroicIndex,
                                     int annotationRefIndex)

Specified by:: setDichroicAnnotationRef in interface ome.xml.meta.MetadataStore

setEllipseAnnotationRef

public void setEllipseAnnotationRef(java.lang.String annotation,
                                    int ROIIndex,
                                    int shapeIndex,
                                    int annotationRefIndex)

Specified by:: setEllipseAnnotationRef in interface ome.xml.meta.MetadataStore

setFilamentAnnotationRef

public void setFilamentAnnotationRef(java.lang.String annotation,
                                     int instrumentIndex,
                                     int lightSourceIndex,
                                     int annotationRefIndex)

Specified by:: setFilamentAnnotationRef in interface ome.xml.meta.MetadataStore

setFilterAnnotationRef

public void setFilterAnnotationRef(java.lang.String annotation,
                                   int instrumentIndex,
                                   int filterIndex,
                                   int annotationRefIndex)

Specified by:: setFilterAnnotationRef in interface ome.xml.meta.MetadataStore

setGenericExcitationSourceAnnotationRef

public void setGenericExcitationSourceAnnotationRef(java.lang.String annotation,
                                                    int instrumentIndex,
                                                    int lightSourceIndex,
                                                    int annotationRefIndex)

Specified by:: setGenericExcitationSourceAnnotationRef in interface ome.xml.meta.MetadataStore

setInstrumentAnnotationRef

public void setInstrumentAnnotationRef(java.lang.String annotation,
                                       int instrumentIndex,
                                       int annotationRefIndex)

Specified by:: setInstrumentAnnotationRef in interface ome.xml.meta.MetadataStore

setLabelAnnotationRef

public void setLabelAnnotationRef(java.lang.String annotation,
                                  int ROIIndex,
                                  int shapeIndex,
                                  int annotationRefIndex)

Specified by:: setLabelAnnotationRef in interface ome.xml.meta.MetadataStore

setLaserAnnotationRef

public void setLaserAnnotationRef(java.lang.String annotation,
                                  int instrumentIndex,
                                  int lightSourceIndex,
                                  int annotationRefIndex)

Specified by:: setLaserAnnotationRef in interface ome.xml.meta.MetadataStore

setLightEmittingDiodeAnnotationRef

public void setLightEmittingDiodeAnnotationRef(java.lang.String annotation,
                                               int instrumentIndex,
                                               int lightSourceIndex,
                                               int annotationRefIndex)

Specified by:: setLightEmittingDiodeAnnotationRef in interface ome.xml.meta.MetadataStore

setLightPathAnnotationRef

public void setLightPathAnnotationRef(java.lang.String annotation,
                                      int imageIndex,
                                      int channelIndex,
                                      int annotationRefIndex)

Specified by:: setLightPathAnnotationRef in interface ome.xml.meta.MetadataStore

setLineAnnotationRef

public void setLineAnnotationRef(java.lang.String annotation,
                                 int ROIIndex,
                                 int shapeIndex,
                                 int annotationRefIndex)

Specified by:: setLineAnnotationRef in interface ome.xml.meta.MetadataStore

setMaskAnnotationRef

public void setMaskAnnotationRef(java.lang.String annotation,
                                 int ROIIndex,
                                 int shapeIndex,
                                 int annotationRefIndex)

Specified by:: setMaskAnnotationRef in interface ome.xml.meta.MetadataStore

setObjectiveAnnotationRef

public void setObjectiveAnnotationRef(java.lang.String annotation,
                                      int instrumentIndex,
                                      int objectiveIndex,
                                      int annotationRefIndex)

Specified by:: setObjectiveAnnotationRef in interface ome.xml.meta.MetadataStore

setPointAnnotationRef

public void setPointAnnotationRef(java.lang.String annotation,
                                  int ROIIndex,
                                  int shapeIndex,
                                  int annotationRefIndex)

Specified by:: setPointAnnotationRef in interface ome.xml.meta.MetadataStore

setPolygonAnnotationRef

public void setPolygonAnnotationRef(java.lang.String annotation,
                                    int ROIIndex,
                                    int shapeIndex,
                                    int annotationRefIndex)

Specified by:: setPolygonAnnotationRef in interface ome.xml.meta.MetadataStore

setPolylineAnnotationRef

public void setPolylineAnnotationRef(java.lang.String annotation,
                                     int ROIIndex,
                                     int shapeIndex,
                                     int annotationRefIndex)

Specified by:: setPolylineAnnotationRef in interface ome.xml.meta.MetadataStore

setRectangleAnnotationRef

public void setRectangleAnnotationRef(java.lang.String annotation,
                                      int ROIIndex,
                                      int shapeIndex,
                                      int annotationRefIndex)

Specified by:: setRectangleAnnotationRef in interface ome.xml.meta.MetadataStore

ignoreMissing

protected void ignoreMissing(java.lang.String method,
                             java.lang.Object... args)

Called when a property is missing from the OMERO model (WARN).

ignoreUnneeded
```
protected void ignoreUnneeded(java.lang.String method,
                              java.lang.Object... args)
```
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
```
protected void ignoreUnsupported(java.lang.String method,
                                 java.lang.Object... args)
```
Called when a property is not expected in a file to be imported. log.warn is used to signal to the user that something is being missed (WARN).

ignoreInsecure
```
protected void ignoreInsecure(java.lang.String method,
                              java.lang.Object... args)
```
Called when saving a property to OMERO would result in a SecurityViolation (DEBUG). These are logged at debug since there's nothing the user need worry about.

ignoreAnnotator

protected void ignoreAnnotator(java.lang.String method,
                               java.lang.Object... args)

For all cases of an annotator being ignore (WARN).

Class OMEROMetadataStoreClient

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

OMERO_EMISSION_FILTER_SUFFIX

OMERO_EXCITATION_FILTER_SUFFIX

Constructor Detail

OMEROMetadataStoreClient

Method Detail

getKeepAlive

logVersionInfo

getDefaultBatchSize

getDefaultBlockSize

getIQuery

setEncryptedConnection

isEncryptedConnection

setGroup

initialize

initialize

initialize

initialize

initialize

initialize

initialize

getServiceFactory

ping

setCurrentLogFile

updateFileSize

setEnumerationProvider

getEnumerationProvider

setInstanceProvider

getInstanceProvider

toRType

toRType

toRType

toRType

toRType

toRType

toRType

toRType

toRType

toRType

toRType

toRType

toRType

toRType

closeServices

logout

prepare

createRoot

getRoot

getReader

setReader

getUserSpecifiedAnnotations

setUserSpecifiedAnnotations

getUserSpecifiedName

getUserSpecifiedImageName

setUserSpecifiedName

getUserSpecifiedDescription

setUserSpecifiedDescription

getUserSpecifiedTarget

setUserSpecifiedTarget

getUserSpecifiedPhysicalPixelSizes

setUserSpecifiedPhysicalPixelSizes

getModelProcessors

setModelProcessors

removeModelProcessor

addModelProcessor

getContainerCache

getReferenceCache

getAuthoritativeContainerCache

addReference

getReferenceStringCache

setReferenceStringCache

getSourceObject

getSourceObjects

hasReference

setPixelsFile