Index (omero-gateway 5.5.3 API)

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

A

accept(File) - Method in class omero.gateway.util.TIFFFilter: Accepts or not the file with the declared file extensions.
accept(String) - Method in class omero.gateway.util.TIFFFilter: Accepts or not the file identified by its name.
addAdminPrivileges(SecurityContext, ExperimenterData, Collection<String>) - Method in class omero.gateway.facility.AdminFacility: Grant an user additional admin privileges.
addArray(int[][], int, int, int) - Method in class omero.gateway.util.UploadMask: Adds a Mask Shape to the appropriate ROIClass, creating one if necessary.
addElement(int, Object, Object) - Method in interface omero.gateway.cache.CacheService: Adds the specified element to the selected cache.
addImage(byte[], int, int, int) - Method in class omero.gateway.util.UploadMask: Adds a Mask Shape to the appropriate ROIClass, creating one if necessary.
addImagesToDataset(SecurityContext, Collection<ImageData>, DatasetData) - Method in class omero.gateway.facility.DataManagerFacility: Adds the ImageDatas to the given DatasetData
addImageToDataset(SecurityContext, ImageData, DatasetData) - Method in class omero.gateway.facility.DataManagerFacility: Adds the ImageData to the given DatasetData
addMasks(Map<Integer, MaskData>) - Method in class omero.gateway.util.ROIComponent: Adds the Masks in the maskSet to the component.
addPropertyChangeListener(PropertyChangeListener) - Method in class omero.gateway.facility.Facility: Adds a PropertyChangeListener
addPropertyChangeListener(PropertyChangeListener) - Method in class omero.gateway.Gateway: Adds a PropertyChangeListener
addRoisToFolders(SecurityContext, long, Collection<ROIData>, Collection<FolderData>) - Method in class omero.gateway.facility.ROIFacility: Adds ROIs to Folders
addRoisToFolders(SecurityContext, long, Collection<ROIData>, Collection<FolderData>, boolean) - Method in class omero.gateway.facility.ROIFacility: Adds ROIs to Folders
addShapeData(ShapeData) - Method in class omero.gateway.model.ROIData: Adds ShapeData object to ROIData.
addTable(SecurityContext, DataObject, String, TableData) - Method in class omero.gateway.facility.TablesFacility: Adds a new table with the provided data
AdminFacility - Class in omero.gateway.facility: Facility for handling admin issues, e.g.
ALL_GROUPS_ID - Static variable in class omero.gateway.model.SearchParameters: The ID for searching across all groups
ALL_SCOPE - Static variable in class omero.gateway.model.SearchParameters
ALL_TYPES - Static variable in class omero.gateway.model.SearchParameters
AnnotationData - Class in omero.gateway.model: Holds a textual annotation of a given data object and a reference to the Experimenter that wrote it.
AnnotationData(Class<? extends Annotation>) - Constructor for class omero.gateway.model.AnnotationData: Creates a new instance.
AnnotationData(A) - Constructor for class omero.gateway.model.AnnotationData: Creates a new instance.
ANNOTATIONS - Static variable in class omero.gateway.model.ChannelData: Identifies the Channel.ANNOTATIONLINKS field.
ANNOTATIONS - Static variable in class omero.gateway.model.DatasetData: Identifies the DatasetI.ANNOTATIONLINKS field.
ANNOTATIONS - Static variable in class omero.gateway.model.ImageData: Identifies the ImageI.ANNOTATIONLINKS field.
ANNOTATIONS - Static variable in class omero.gateway.model.PlateData: Identifies the PlateI.ANNOTATIONLINKS field.
ARC - Static variable in class omero.gateway.model.LightSourceData: Indicates that the light source is a arc.
asAnnotation() - Method in class omero.gateway.model.DataObject: Returns the hosted IObject as an Annotation.
asCastedDataObjects(List) - Static method in class omero.gateway.util.PojoMapper: Converts each element of the collection into its corresponding DataObject.
ASCENDING_LETTER - Static variable in class omero.gateway.model.PlateData: Indicates that the column or row is a letter starting from A.
ASCENDING_NUMBER - Static variable in class omero.gateway.model.PlateData: Indicates that the column or row is a number starting from 1.
asChannel() - Method in class omero.gateway.model.DataObject: Returns the hosted IObject as a Well.
asDataObject(IObject) - Static method in class omero.gateway.util.PojoMapper: Converts the specified IObject into its corresponding DataObject.
asDataObjectMap(Class<K>, Class<V>, String, List) - Static method in class omero.gateway.util.PojoMapper: Converts each element of the list to a pair (key, value) in the map.
asDataObjects(Map) - Static method in class omero.gateway.util.PojoMapper: Converts each pair (key, value) of the map.
asDataset() - Method in class omero.gateway.model.DataObject: Returns the hosted IObject as a Dataset.
asExperimenter() - Method in class omero.gateway.model.DataObject: Returns the hosted IObject as an Experimenter.
asFolder() - Method in class omero.gateway.model.DataObject: Returns the hosted IObject as a Folder.
asGroup() - Method in class omero.gateway.model.DataObject: Returns the hosted IObject as an Experimenter Group.
asIAnnotated() - Method in class omero.gateway.model.DataObject: not null; may throw class-cast exception
asImage() - Method in class omero.gateway.model.DataObject: Returns the hosted IObject as an Image.
asIObject() - Method in class omero.gateway.model.DataObject: not null; no exceptions.
asPixels() - Method in class omero.gateway.model.DataObject: Returns the hosted IObject as a Pixels.
asPlate() - Method in class omero.gateway.model.DataObject: Returns the hosted IObject as a Plate.
asPojo(IObject) - Static method in class omero.gateway.model.DataObject: Converts the passed IObject into its corresponding Pojo object.
asPojos(Collection) - Static method in class omero.gateway.model.DataObject: Converts the collection of IObjects into the corresponding DataObjects
asPojos(Map) - Static method in class omero.gateway.model.DataObject: Converts the map of IObjects into the corresponding DataObjects
asProject() - Method in class omero.gateway.model.DataObject: Returns the hosted IObject as a Project.
asScreen() - Method in class omero.gateway.model.DataObject: Returns the hosted IObject as a Screen.
asWell() - Method in class omero.gateway.model.DataObject: Returns the hosted IObject as a Well.
asWellSample() - Method in class omero.gateway.model.DataObject: Returns the hosted IObject as a Well.
attachAnnotation(SecurityContext, T, DataObject) - Method in class omero.gateway.facility.DataManagerFacility: Create/attach an AnnotationData to a given DataObject
attachFile(SecurityContext, File, String, String, String, DataObject) - Method in class omero.gateway.facility.DataManagerFacility: Attaches a File to a DataObject

B

BooleanAnnotationData - Class in omero.gateway.model: Boolean annotation.
BooleanAnnotationData() - Constructor for class omero.gateway.model.BooleanAnnotationData: Creates a new instance.
BooleanAnnotationData(boolean) - Constructor for class omero.gateway.model.BooleanAnnotationData: Creates a new instance.
BooleanAnnotationData(BooleanAnnotation) - Constructor for class omero.gateway.model.BooleanAnnotationData: Creates a new instance.
BrowseFacility - Class in omero.gateway.facility: A Facility for browsing the data hierarchy and retrieving ProjectData, DatasetData, etc.
BTF - Static variable in class omero.gateway.util.TIFFFilter: Possible file extension.
BULK_ANNOTATIONS_NS - Static variable in class omero.gateway.model.FileAnnotationData: The name space used to indicate that the FileAnnotation is a Bulk Annotations file.

C

CACHE_SIZE - Static variable in interface omero.gateway.cache.CacheService: The default size of a cache.
CacheService - Interface in omero.gateway.cache: Defines the caching service interface.
canAnnotate() - Method in class omero.gateway.model.DataObject: Returns true if the object can be annotated false otherwise, depending on permissions level.
canChgrp() - Method in class omero.gateway.model.DataObject: Returns true if the object can be moved by the user currently logged in, false otherwise, depending on permissions level.
canChown() - Method in class omero.gateway.model.DataObject: Returns true if the object can be given by the user currently logged in, false otherwise, depending on permissions level.
canCreate(SecurityContext) - Method in class omero.gateway.Gateway: Get the read-only status of the server.
canDelete() - Method in class omero.gateway.model.DataObject: Returns true if the object can be deleted by the user currently logged in, false otherwise, depending on permissions level.
canEdit() - Method in class omero.gateway.model.DataObject: Returns true if the object can be edited by the user currently logged in false otherwise, depending on permissions level.
canLink() - Method in class omero.gateway.model.DataObject: Returns true if the object can be linked e.g.
changeGroup(SecurityContext, List<? extends DataObject>, long) - Method in class omero.gateway.facility.DataManagerFacility: Move the given objects into another group
ChannelAcquisitionData - Class in omero.gateway.model: Object hosting the acquisition related to a logical channel.
ChannelAcquisitionData(LogicalChannel) - Constructor for class omero.gateway.model.ChannelAcquisitionData: Creates a new instance.
ChannelData - Class in omero.gateway.model: The data that makes up an OME Channel along with links to its logical channel.
ChannelData(int) - Constructor for class omero.gateway.model.ChannelData: Creates a new instance.
ChannelData(int, Channel) - Constructor for class omero.gateway.model.ChannelData: Creates a new instance.
chgrp() - Static method in class omero.gateway.util.Requests
Chgrp2Builder() - Constructor for class omero.gateway.util.Requests.Chgrp2Builder: Instantiate a new Chgrp2.
childType(Iterable<String>) - Method in class omero.gateway.util.Requests.FindChildrenBuilder
childType(Class<? extends IObject>...) - Method in class omero.gateway.util.Requests.FindChildrenBuilder
childType(String...) - Method in class omero.gateway.util.Requests.FindChildrenBuilder
chmod() - Static method in class omero.gateway.util.Requests
Chmod2Builder() - Constructor for class omero.gateway.util.Requests.Chmod2Builder: Instantiate a new Chmod2.
chown() - Static method in class omero.gateway.util.Requests
Chown2Builder() - Constructor for class omero.gateway.util.Requests.Chown2Builder: Instantiate a new Chown2 and initialize its collection containers.
clear() - Static method in class omero.gateway.facility.Facility: Clears the Facility object cache
clear() - Method in class omero.gateway.model.SearchResultCollection
clearAllCaches() - Method in interface omero.gateway.cache.CacheService: Clears all the caches.
clearCache(int) - Method in interface omero.gateway.cache.CacheService: Clears the specified cache.
close() - Method in class omero.gateway.facility.RawDataFacility
close() - Method in class omero.gateway.Gateway
close() - Method in class omero.gateway.rnd.DataSink
closeConnector(SecurityContext) - Method in class omero.gateway.Gateway: Close a connector for a certain SecurityContext
closeImport(SecurityContext, String) - Method in class omero.gateway.Gateway: Close Import for a certain user
closeService(SecurityContext, StatefulServiceInterfacePrx) - Method in class omero.gateway.Gateway: Close a service
closeSessionOnExit(SecurityContext, boolean) - Method in class omero.gateway.Gateway: By default the session is closed if it was initialized by the gateway.
COMPANION_FILE_NS - Static variable in class omero.gateway.model.FileAnnotationData: The name space used to indicate that the FileAnnotation is a companion file.
compare(Object, Object) - Method in class omero.gateway.model.ROICoordinate: Implemented as specified by the Comparator I/F.
COMPLEX_TYPE - Static variable in class omero.gateway.model.PixelsData: Identifies the type used to store pixel values.
connect(LoginCredentials) - Method in class omero.gateway.Gateway: Connect to the server
CONNECTION - Static variable in exception omero.gateway.exception.RenderingServiceException: Indicates that the error occurred due to a connection failure.
ConnectionStatus - Enum in omero.gateway.exception: The various connections status.
consolidate() - Method in class omero.gateway.model.SearchResultCollection: Removes results which DataObjects are not set
contains(Object) - Method in class omero.gateway.model.SearchResultCollection
convertRTypeToJava(RType) - Static method in class omero.gateway.util.ModelMapper: Converts the passed OMERO type into its corresponding Java type.
convertToDataObjects(Collection) - Static method in class omero.gateway.util.PojoMapper: Converts each element of the collection into its corresponding DataObject.
convertTypeForSearch(Class) - Static method in class omero.gateway.util.PojoMapper: Converts the specified type to its corresponding type for search.
copy() - Method in class omero.gateway.SecurityContext: Returns a copy of the security context.
copyAnnotationLinks() - Method in class omero.gateway.model.FolderData: Copy the list of annotation links, see Folder.copyAnnotationLinks()
copyChildFolders() - Method in class omero.gateway.model.FolderData: Copy the list of child folders, see Folder.copyChildFolders()
copyImageLinks() - Method in class omero.gateway.model.FolderData: Copy the list of image links, see Folder.copyImageLinks()
copyROILinks() - Method in class omero.gateway.model.FolderData: Copy the list of roi links, see Folder.copyRoiLinks()
createAnnotation(AnnotationData) - Static method in class omero.gateway.util.ModelMapper: Creates a new annotation IObject.
createAnnotationAndLink(IObject, AnnotationData) - Static method in class omero.gateway.util.ModelMapper: Creates a new annotation IObject.
createCache() - Method in interface omero.gateway.cache.CacheService: Creates a default cache.
createCache(int, int) - Method in interface omero.gateway.cache.CacheService: Creates a cache of a given type.
createCache(int) - Method in interface omero.gateway.cache.CacheService: Creates a cache of a given type.
createCroppedMask(int[][]) - Static method in class omero.gateway.util.Mask: Creates a mask ROI; automatically crop to its bounding box.
createCroppedMask(boolean[][]) - Static method in class omero.gateway.util.Mask: Creates a mask ROI; automatically crop to its bounding box.
createCroppedMasks(int[][]) - Static method in class omero.gateway.util.Mask: Creates mask ROIs from the given integer array where each single mask ROI is specified by a specific integer.
createCroppedMasks(int[], int) - Static method in class omero.gateway.util.Mask: Creates mask ROIs from the given integer array where each single mask ROI is specified by a specific integer.
createDataset(SecurityContext, DatasetData, ProjectData) - Method in class omero.gateway.facility.DataManagerFacility: Creates the DatasetData on the server and attaches it to the ProjectData (if not null) (if the project doesn't exist on the server yet, it will be created, too)
createExperimenter(SecurityContext, ExperimenterData, String, String, List<GroupData>, boolean, boolean) - Method in class omero.gateway.facility.AdminFacility: Creates an experimenter and returns it.
createExperimenter(SecurityContext, ExperimenterData, String, String, List<GroupData>, boolean, boolean, List<String>) - Method in class omero.gateway.facility.AdminFacility: Creates an experimenter and returns it.
createGroup(SecurityContext, GroupData, ExperimenterData, int) - Method in class omero.gateway.facility.AdminFacility: Creates a group and returns it.
createIObject(DataObject) - Static method in class omero.gateway.util.ModelMapper: Converts the specified DataObject into its corresponding IObject.
createIObject(DataObject, DataObject) - Static method in class omero.gateway.util.ModelMapper: Converts the specified DataObject into its corresponding IObject.
createPixelsStore(SecurityContext) - Method in class omero.gateway.Gateway: Create a RawPixelsStorePrx
createTableResult(TablePrx, String, long) - Static method in class omero.gateway.util.PyTablesUtils: Transforms the passed table data for a given image.
createTableResult(TablePrx, long[]) - Static method in class omero.gateway.util.PyTablesUtils: Transforms a set of rows for the passed table.
createThumbnailStore(SecurityContext) - Method in class omero.gateway.Gateway: Create a ThumbnailStorePrx
CSV - Static variable in class omero.gateway.model.FileAnnotationData: Identifies the CSV file formats.

D

DataManagerFacility - Class in omero.gateway.facility: A Facility for saving, deleting and updating data objects
DataObject - Class in omero.gateway.model: Abstract superclass for objects that hold OMEDS data.
DataObject() - Constructor for class omero.gateway.model.DataObject
DATASET_LINKS - Static variable in class omero.gateway.model.ImageData: Identifies the ImageI.DATASETLINKS field.
DATASET_LINKS - Static variable in class omero.gateway.model.ProjectData: Identifies the ProjectI.DATASETLINKS field.
DatasetData - Class in omero.gateway.model: The data that makes up an OME Dataset along with links to its contained Images and enclosing Project as well as the Experimenter that owns this Dataset.
DatasetData() - Constructor for class omero.gateway.model.DatasetData: Creates a new instance.
DatasetData(Dataset) - Constructor for class omero.gateway.model.DatasetData: Creates a new instance.
DataSink - Class in omero.gateway.rnd: Encapsulates access to the image raw data.
DataSink(SecurityContext, PixelsData, Gateway) - Constructor for class omero.gateway.rnd.DataSink: Creates a new instance.
DataSourceException - Exception in omero.gateway.exception: Reports an error occurred while trying to pull out data from the pixels data repository.
DataSourceException() - Constructor for exception omero.gateway.exception.DataSourceException: Creates a new exception.
DataSourceException(String) - Constructor for exception omero.gateway.exception.DataSourceException: Constructs a new exception with the specified detail message.
DataSourceException(Throwable) - Constructor for exception omero.gateway.exception.DataSourceException: Constructs a new exception with the specified cause.
DataSourceException(String, Throwable) - Constructor for exception omero.gateway.exception.DataSourceException: Constructs a new exception with the specified detail message and cause.
DATE_ACQUISITION - Static variable in class omero.gateway.model.SearchParameters: Indicates that the date has to be interpreted as acquisition date
DATE_IMPORT - Static variable in class omero.gateway.model.SearchParameters: Indicates that the date has to be interpreted as import date
DEFAULT - Static variable in interface omero.gateway.cache.CacheService: Indicates to create a default cache.
DEFAULT - Static variable in class omero.gateway.model.GroupData: Identifies the default group.
DEFAULT_FILL_COLOUR - Static variable in class omero.gateway.model.ShapeSettingsData: The default fill color.
DEFAULT_FILL_COLOUR_ALPHA - Static variable in class omero.gateway.model.ShapeSettingsData: The default fill color.
DEFAULT_FONT_FAMILY - Static variable in class omero.gateway.model.ShapeSettingsData: The default font family.
DEFAULT_FONT_SIZE - Static variable in class omero.gateway.model.ShapeSettingsData: The default font size in "pt".
DEFAULT_MAX_ROWS_TO_FETCH - Static variable in class omero.gateway.facility.TablesFacility: Maximum number of rows to fetch if not specified otherwise
DEFAULT_STROKE_COLOUR - Static variable in class omero.gateway.model.ShapeSettingsData: The default stroke color.
DEFAULT_STROKE_WIDTH - Static variable in class omero.gateway.model.ShapeSettingsData: The default stroke width.
delete(SecurityContext, IObject) - Method in class omero.gateway.facility.DataManagerFacility: Deletes the specified object asynchronously
delete(SecurityContext, List<IObject>) - Method in class omero.gateway.facility.DataManagerFacility: Deletes the specified objects asynchronously
delete() - Static method in class omero.gateway.util.Requests
Delete2Builder() - Constructor for class omero.gateway.util.Requests.Delete2Builder: Instantiate a new Delete2.
deleteFolders(SecurityContext, Collection<FolderData>, boolean, boolean) - Method in class omero.gateway.facility.DataManagerFacility: Delete Folders (asynchronous)
DESCENDING_LETTER - Static variable in class omero.gateway.model.PlateData: Indicates that the column or row is a letter starting from Z or P.
DESCENDING_NUMBER - Static variable in class omero.gateway.model.PlateData: Indicates that the column or row is a letter starting from 26 or 16.
DESCRIPTION - Static variable in class omero.gateway.model.DatasetData: Identifies the DatasetI.DESCRIPTION field.
DESCRIPTION - Static variable in class omero.gateway.model.GroupData: Identifies the ExperimenterGroupI.DESCRIPTION field.
DESCRIPTION - Static variable in class omero.gateway.model.ImageData: Identifies the ImageI.DESCRIPTION field.
DESCRIPTION - Static variable in class omero.gateway.model.PlateData: Identifies the PlateI.DESCRIPTION field.
DESCRIPTION - Static variable in class omero.gateway.model.ProjectData: Identifies the ProjectI.DESCRIPTION field.
DESCRIPTION - Static variable in class omero.gateway.model.ScreenData: Identifies the ScreenI.DESCRIPTION field.
DetectorData - Class in omero.gateway.model: Hosts a detector.
DetectorData(Detector) - Constructor for class omero.gateway.model.DetectorData: Creates a new instance.
DichroicData - Class in omero.gateway.model: Hosts the dichroic.
DichroicData(Dichroic) - Constructor for class omero.gateway.model.DichroicData: Creates a new instance.
disconnect() - Method in class omero.gateway.Gateway: Disconnects from the server
diskUsage() - Static method in class omero.gateway.util.Requests
DOUBLE - Static variable in class omero.gateway.rnd.DataSink: Identifies the type used to store pixel values.
DOUBLE_COMPLEX_TYPE - Static variable in class omero.gateway.model.PixelsData: Identifies the type used to store pixel values.
DOUBLE_TYPE - Static variable in class omero.gateway.model.PixelsData: Identifies the type used to store pixel values.
DoubleAnnotationData - Class in omero.gateway.model: Wraps a double annotation.
DoubleAnnotationData(double) - Constructor for class omero.gateway.model.DoubleAnnotationData: Creates a new instance.
DoubleAnnotationData() - Constructor for class omero.gateway.model.DoubleAnnotationData: Creates a new instance.
DoubleAnnotationData(DoubleAnnotation) - Constructor for class omero.gateway.model.DoubleAnnotationData: Creates a new instance.
DoubleConverter - Class in omero.gateway.rnd: Packs a sequence of bytes representing a big-endian double into a double value of appropriate integer type.
DoubleConverter() - Constructor for class omero.gateway.rnd.DoubleConverter
downloadImage(SecurityContext, String, long) - Method in class omero.gateway.facility.TransferFacility: Downloads the original file of an image from the server.
DSAccessException - Exception in omero.gateway.exception: Reports an error occurred while trying to pull out data from the server.
DSAccessException(String) - Constructor for exception omero.gateway.exception.DSAccessException: Constructs a new exception with the specified detail message.
DSAccessException(String, Throwable) - Constructor for exception omero.gateway.exception.DSAccessException: Constructs a new exception with the specified detail message and cause.
DSOutOfServiceException - Exception in omero.gateway.exception: Reports an error occurred while trying to access the OMERO service.
DSOutOfServiceException(String) - Constructor for exception omero.gateway.exception.DSOutOfServiceException: Constructs a new exception with the specified detail message.
DSOutOfServiceException(String, ConnectionStatus) - Constructor for exception omero.gateway.exception.DSOutOfServiceException: Constructs a new exception with the specified detail message.
DSOutOfServiceException(String, Throwable) - Constructor for exception omero.gateway.exception.DSOutOfServiceException: Constructs a new exception with the specified detail message and cause.
DSOutOfServiceException(String, Throwable, ConnectionStatus) - Constructor for exception omero.gateway.exception.DSOutOfServiceException: Constructs a new exception with the specified detail message and cause.
duplicate() - Static method in class omero.gateway.util.Requests
DuplicateBuilder() - Constructor for class omero.gateway.util.Requests.DuplicateBuilder: Instantiate a new Duplicate and initialize its collection containers.
duplicateType(Iterable<String>) - Method in class omero.gateway.util.Requests.DuplicateBuilder
duplicateType(Class<? extends IObject>...) - Method in class omero.gateway.util.Requests.DuplicateBuilder
duplicateType(String...) - Method in class omero.gateway.util.Requests.DuplicateBuilder

E

EllipseData - Class in omero.gateway.model: Represents an ellipse in the Euclidean space R².
EllipseData(Shape) - Constructor for class omero.gateway.model.EllipseData: Creates a new instance of Ellipse data from an existing shape.
EllipseData() - Constructor for class omero.gateway.model.EllipseData: Creates a new instance of EllipseData.
EllipseData(double, double, double, double) - Constructor for class omero.gateway.model.EllipseData: Creates a new instance of the EllipseData.
EMAIL - Static variable in class omero.gateway.model.ExperimenterData: Identifies the ExperimenterI.EMAIL field.
equals(Object) - Method in class omero.gateway.model.ROICoordinate: Overridden to control if the passed object equals the current one.
equals(Object) - Method in class omero.gateway.model.TableData
equals(Object) - Method in class omero.gateway.model.TableDataColumn
equals(Object) - Method in class omero.gateway.SecurityContext: Overridden to control if the passed object equals the current one.
equals(Object) - Method in class omero.gateway.ServerInformation
excludeNs(Iterable<String>) - Method in class omero.gateway.util.Requests.ChildOptionBuilder
excludeNs(String...) - Method in class omero.gateway.util.Requests.ChildOptionBuilder
excludeType(Iterable<String>) - Method in class omero.gateway.util.Requests.ChildOptionBuilder
excludeType(Class<? extends IObject>...) - Method in class omero.gateway.util.Requests.ChildOptionBuilder
excludeType(String...) - Method in class omero.gateway.util.Requests.ChildOptionBuilder
EXPERIMENTER_PHOTO_NS - Static variable in class omero.gateway.model.FileAnnotationData: The name space used to identify the experimenter photo.
ExperimenterData - Class in omero.gateway.model: The data that makes up an OME Experimenter along with information about the Group the Experimenter belongs in.
ExperimenterData() - Constructor for class omero.gateway.model.ExperimenterData: Creates a new instance.
ExperimenterData(Experimenter) - Constructor for class omero.gateway.model.ExperimenterData: Creates a new instance.
extensions - Static variable in class omero.gateway.util.TIFFFilter: The possible extensions.
extractIds(Collection<? extends DataObject>) - Static method in class omero.gateway.util.Pojos: Extract the (distinct) ids from a collection of DataObjects

F

Facility - Class in omero.gateway.facility: A Facility encapsulates a certain set of functionality for dealing with an OMERO server
FILAMENT - Static variable in class omero.gateway.model.LightSourceData: Indicates that the light source is a filament.
FILE_TRANSFER_NS - Static variable in class omero.gateway.model.AnnotationData: The name space used to identify the file transfer type.
FileAnnotationData - Class in omero.gateway.model: Annotation to upload files to the server.
FileAnnotationData(File) - Constructor for class omero.gateway.model.FileAnnotationData: Creates a new instance.
FileAnnotationData(FileAnnotation) - Constructor for class omero.gateway.model.FileAnnotationData: Creates a new instance.
FileData - Class in omero.gateway.model: DataObject used to handle the file visible via FS.
FileData(OriginalFile) - Constructor for class omero.gateway.model.FileData: Creates a new instance.
FileData(OriginalFile, boolean) - Constructor for class omero.gateway.model.FileData: Creates a new instance.
FileData(OriginalFile, boolean, boolean) - Constructor for class omero.gateway.model.FileData: Creates a new instance.
FilesetData - Class in omero.gateway.model: Wraps a file set object.
FilesetData(Fileset) - Constructor for class omero.gateway.model.FilesetData: Creates a new instance.
fillIObject(IObject, IObject) - Static method in class omero.gateway.util.ModelMapper: Fills the new IObject with data from the old one.
FilterData - Class in omero.gateway.model: Object hosting a filter.
FilterData(Filter) - Constructor for class omero.gateway.model.FilterData: Creates a new instance.
FilterSetData - Class in omero.gateway.model: Object hosting a filterSet.
FilterSetData(FilterSet) - Constructor for class omero.gateway.model.FilterSetData: Creates a new instance.
findChildren() - Static method in class omero.gateway.util.Requests
FindChildrenBuilder() - Constructor for class omero.gateway.util.Requests.FindChildrenBuilder: Instantiate a new FindChildren and initialize its collection containers.
findIObject(SecurityContext, String, long) - Method in class omero.gateway.facility.BrowseFacility: Retrieves an updated version of the specified object.
findIObject(SecurityContext, String, long, boolean) - Method in class omero.gateway.facility.BrowseFacility: Retrieves an updated version of the specified object.
findIObject(SecurityContext, IObject) - Method in class omero.gateway.facility.BrowseFacility: Retrieves an updated version of the specified object.
findObject(SecurityContext, Class<T>, long) - Method in class omero.gateway.facility.BrowseFacility: Retrieves an updated version of the specified object.
findObject(SecurityContext, Class<T>, long, boolean) - Method in class omero.gateway.facility.BrowseFacility: Retrieves an updated version of the specified object.
findObject(SecurityContext, String, long) - Method in class omero.gateway.facility.BrowseFacility: Retrieves an updated version of the specified object.
findObject(SecurityContext, String, long, boolean) - Method in class omero.gateway.facility.BrowseFacility: Retrieves an updated version of the specified object.
findParents() - Static method in class omero.gateway.util.Requests
FindParentsBuilder() - Constructor for class omero.gateway.util.Requests.FindParentsBuilder: Instantiate a new FindParents and initialize its collection containers.
firePropertyChanged(PropertyChangeEvent) - Method in class omero.gateway.facility.Facility: Fires a PropertyChangeEvent
firePropertyChanged(String, Object, Object) - Method in class omero.gateway.facility.Facility: Fires a PropertyChangeEvent
FIRSTNAME - Static variable in class omero.gateway.model.ExperimenterData: Identifies the ExperimenterI.FIRSTNAME field.
firstPlane() - Method in class omero.gateway.model.ROIData: Deprecated.
Will be removed in future. Does not work as expected if the ROI contains shapes which are associated with all planes (Z, C, T == -1)
FLIM_NS - Static variable in class omero.gateway.model.FileAnnotationData: Identifies the FLIM namespace.
FLOAT - Static variable in class omero.gateway.rnd.DataSink: Identifies the type used to store pixel values.
FLOAT_TYPE - Static variable in class omero.gateway.model.PixelsData: Identifies the type used to store pixel values.
FloatConverter - Class in omero.gateway.rnd: Packs a sequence of bytes representing a big-endian float into a double value of appropriate integer type.
FloatConverter() - Constructor for class omero.gateway.rnd.FloatConverter
fold(int[], int) - Static method in class omero.gateway.util.Mask: Breaks a one-dimensional array into 'length' chunks, forming a two-dimensional array, e.g.
FolderData - Class in omero.gateway.model: Pojo wrapper for an OME Folder.
FolderData() - Constructor for class omero.gateway.model.FolderData: Creates a new instance.
FolderData(Folder) - Constructor for class omero.gateway.model.FolderData: Creates a new instance.
FONT_BOLD - Static variable in class omero.gateway.model.ShapeSettingsData: Set if font bold.
FONT_BOLD_ITALIC - Static variable in class omero.gateway.model.ShapeSettingsData: Set if font bold.
FONT_ITALIC - Static variable in class omero.gateway.model.ShapeSettingsData: Set if font italic.
FONT_REGULAR - Static variable in class omero.gateway.model.ShapeSettingsData: Set if font bold.
fromEnum(Collection<E>) - Static method in class omero.gateway.util.Utils: Convert a list of omero.model.enums instances to their corresponding String values.
fromPoints(String) - Method in class omero.gateway.model.ShapeData: Parses out the type from the points string.

G

Gateway - Class in omero.gateway: A Gateway for simplifying access to an OMERO server
Gateway(Logger) - Constructor for class omero.gateway.Gateway: Creates a new Gateway instance
Gateway(Logger, CacheService) - Constructor for class omero.gateway.Gateway: Creates a new Gateway instance
Gateway(Logger, CacheService, ExecutorService, boolean) - Constructor for class omero.gateway.Gateway: Creates a new Gateway instance
GENERAL_ERROR - Static variable in class omero.gateway.model.SearchResultCollection: Some other error
getAbsolutePath() - Method in class omero.gateway.model.FileData: Returns the absolute path.
getAbsolutePaths() - Method in class omero.gateway.model.FilesetData: Returns the collections of absolute paths.
getAcquisitionDate() - Method in class omero.gateway.model.ImageData: Returns the acquisition date.
getAdminPrivileges(SecurityContext) - Method in class omero.gateway.facility.AdminFacility: Get the logged in user's admin privileges (see omero.model.enums)
getAdminPrivileges(SecurityContext, ExperimenterData) - Method in class omero.gateway.facility.AdminFacility: Get the admin privileges of a certain user (see omero.model.enums)
getAdminService(SecurityContext) - Method in class omero.gateway.Gateway: Returns the IAdminPrx service.
getAdminService(SecurityContext, boolean) - Method in class omero.gateway.Gateway: Returns the IAdminPrx service.
getAirPressure(UnitsPressure) - Method in class omero.gateway.model.ImageAcquisitionData: Returns the air pressure.
getAllPixels() - Method in class omero.gateway.model.ImageData: Returns all the sets of pixels related to this image.
getAlpha() - Method in class omero.gateway.model.WellData: Returns the alpha component of the color associated to the well, or -1.
getAmplificationGain() - Method in class omero.gateway.model.DetectorData: Returns the amplification gain of the detector.
getAnnotatedObject(IObject) - Static method in class omero.gateway.util.ModelMapper: Returns the annotated IObject related to the specified annotation.
getAnnotationObject(IObject) - Static method in class omero.gateway.util.ModelMapper: Returns the annotation represented by the specified link
getAnnotations(SecurityContext, DataObject) - Method in class omero.gateway.facility.MetadataFacility: Get all annotations for the given DataObject
getAnnotations(SecurityContext, DataObject, List<Class<? extends AnnotationData>>, List<Long>) - Method in class omero.gateway.facility.MetadataFacility: Get the annotations for the given DataObject
getAnnotations(SecurityContext, List<? extends DataObject>, List<Class<? extends AnnotationData>>, List<Long>) - Method in class omero.gateway.facility.MetadataFacility: Get the annotations for the given DataObjects
getAnnotations() - Method in class omero.gateway.model.DatasetData: Returns the annotations related to this dataset.
getAnnotations() - Method in class omero.gateway.model.ImageData: Returns the annotations
getAnnotationsCounts() - Method in class omero.gateway.model.DatasetData: Returns the number of annotations linked to the object, key: id of the user, value: number of annotation.
getAnnotationsCounts() - Method in class omero.gateway.model.ImageData: Returns the number of annotations linked to the object, key: id of the user, value: number of annotation.
getAnnotationsCounts() - Method in class omero.gateway.model.PlateAcquisitionData: Returns the number of annotations linked to the object, key: id of the user, value: number of annotation.
getAnnotationsCounts() - Method in class omero.gateway.model.PlateData: Returns the number of annotations linked to the object, key: id of the user, value: number of annotation.
getAnnotationsCounts() - Method in class omero.gateway.model.ProjectData: Returns the number of annotations linked to the object, key: id of the user, value: number of annotation.
getAnnotationsCounts() - Method in class omero.gateway.model.ScreenData: Returns the number of annotations linked to the object, key: id of the user, value: number of annotation.
getAnnotationsCounts() - Method in class omero.gateway.model.WellData: Returns the number of annotations linked to the object, key: id of the user, value: number of annotation.
getApplicationName() - Method in class omero.gateway.LoginCredentials
getArguments() - Method in class omero.gateway.LoginCredentials: Returns the arguments if set as a read-only list.
getAttachedFile() - Method in class omero.gateway.model.FileAnnotationData: Returns the file to upload to the server.
getAvailableAdminPrivileges(SecurityContext) - Method in class omero.gateway.facility.AdminFacility: Get all available admin privileges
getAvailableGroups(SecurityContext, ExperimenterData) - Method in class omero.gateway.facility.BrowseFacility: Retrieves the groups visible by the current experimenter.
getAvailableTables(SecurityContext, DataObject) - Method in class omero.gateway.facility.TablesFacility: Get all available tables for a the specified object
getBit(byte[], int) - Method in class omero.gateway.model.MaskData: Sets the bit value in a byte array at position bit to be the value value.
getBlue() - Method in class omero.gateway.model.WellData: Returns the blue component of the color associated to the well, or -1.
getByGroup() - Method in class omero.gateway.model.SearchResultCollection: Get a perGroup map representation of the results
getByGroup(Class<? extends DataObject>) - Method in class omero.gateway.model.SearchResultCollection: Get a perGroup map representation of the results, filtered by type
getC() - Method in class omero.gateway.model.ShapeData: Returns the channel.
getCacheService() - Method in class omero.gateway.Gateway: Provides access to the CacheService
getCalibratedMagnification() - Method in class omero.gateway.model.ObjectiveData: Returns the objective's calibrated magnification factor.
getChannelData(SecurityContext, long) - Method in class omero.gateway.facility.MetadataFacility: Get the ChannelData for a specific image
getChannelLabeling() - Method in class omero.gateway.model.ChannelData: Returns the label of the channel.
getCheckVersion() - Method in class omero.gateway.LoginCredentials: Returns whether the version check is enabled
getChildFromLink(IObject) - Static method in class omero.gateway.util.ModelMapper: Returns the child from the passed link.
getCo2Percent() - Method in class omero.gateway.model.ImageAcquisitionData: Returns the Co2 level, this is a percent value in the interval [0, 1].
getColor(int) - Static method in class omero.gateway.model.ShapeSettingsData: Creates a Color object from an RGBA integer value
getColumn() - Method in class omero.gateway.model.WellData: Returns the column used to indicate the location of the well on the grid.
getColumnIndex(Integer) - Method in class omero.gateway.model.TableResult: Returns the index of the column corresponding to the specified value.
getColumns() - Method in class omero.gateway.model.TableData: Get the headers
getColumnSequenceIndex() - Method in class omero.gateway.model.PlateData: Returns the index indicating how to label a column.
getCompression() - Method in class omero.gateway.LoginCredentials: Returns the compression level.
getCompression() - Method in class omero.gateway.SecurityContext: Get the compression level (A percentage compression level from 1.00 (100%) to 0.01 (1%) (the default is 85%))
getConfigService(SecurityContext) - Method in class omero.gateway.Gateway: Returns the IConfigPrx service.
getConnectionStatus() - Method in exception omero.gateway.exception.DSOutOfServiceException: Gets the ConnectionStatus
getConnector(SecurityContext) - Method in class omero.gateway.Gateway: Get a connector for a certain SecurityContext
getConnector(SecurityContext, boolean, boolean) - Method in class omero.gateway.Gateway: Returns the connector corresponding to the passed context.
getContent() - Method in class omero.gateway.model.AnnotationData: Returns the content of the annotation.
getContent() - Method in class omero.gateway.model.BooleanAnnotationData: Returns the textual content of the annotation.
getContent() - Method in class omero.gateway.model.DoubleAnnotationData: Returns the value.
getContent() - Method in class omero.gateway.model.FileAnnotationData: Returns the original file.
getContent() - Method in class omero.gateway.model.LongAnnotationData: Returns the rating value.
getContent() - Method in class omero.gateway.model.MapAnnotationData
getContent() - Method in class omero.gateway.model.RatingAnnotationData: Returns the rating value.
getContent() - Method in class omero.gateway.model.TagAnnotationData: Returns the textual content of the annotation.
getContent() - Method in class omero.gateway.model.TermAnnotationData: Returns the textual content of the annotation.
getContent() - Method in class omero.gateway.model.TextualAnnotationData: Returns the textual content of the annotation.
getContent() - Method in class omero.gateway.model.TimeAnnotationData: Returns the timestamp of the annotation.
getContent() - Method in class omero.gateway.model.XMLAnnotationData: Returns the content of the annotation.
getContentAsString() - Method in class omero.gateway.model.AnnotationData: Returns the content of the annotation as a String, which is parsed on a Class-by-Class basis.
getContentAsString() - Method in class omero.gateway.model.BooleanAnnotationData: Returns the textual content of the annotation.
getContentAsString() - Method in class omero.gateway.model.DoubleAnnotationData: Returns the value as a string.
getContentAsString() - Method in class omero.gateway.model.FileAnnotationData: Returns the absolute path to the file
getContentAsString() - Method in class omero.gateway.model.LongAnnotationData: Returns the value as a string.
getContentAsString() - Method in class omero.gateway.model.MapAnnotationData
getContentAsString() - Method in class omero.gateway.model.RatingAnnotationData: Returns the rating value as a string.
getContentAsString() - Method in class omero.gateway.model.TagAnnotationData: Returns the textual content of the annotation.
getContentAsString() - Method in class omero.gateway.model.TermAnnotationData: Returns the textual content of the annotation.
getContentAsString() - Method in class omero.gateway.model.TextualAnnotationData: Returns the textual content of the annotation.
getContentAsString() - Method in class omero.gateway.model.TimeAnnotationData: Returns the time as a string.
getContentAsString() - Method in class omero.gateway.model.XMLAnnotationData: Returns the textual content of the annotation.
getContrastMethod() - Method in class omero.gateway.model.ChannelAcquisitionData: Returns the contrast method.
getContrastMethod() - Method in class omero.gateway.model.ChannelData: Returns the contrast method.
getContrastMethodAsEnum() - Method in class omero.gateway.model.ChannelData: Returns the contrast method enumeration value.
getCorrection() - Method in class omero.gateway.model.ObjectiveData: Returns the correction value of the objective.
getCorrectionCollar() - Method in class omero.gateway.model.ImageAcquisitionData: Returns the correction collar of the objective.
getCreated() - Method in class omero.gateway.model.DataObject: Returns the creation time of the object.
getCutIn(UnitsLength) - Method in class omero.gateway.model.FilterData: Returns the cut in value or null.
getCutInTolerance(UnitsLength) - Method in class omero.gateway.model.FilterData: Returns the cut in tolerance value or null.
getCutOut(UnitsLength) - Method in class omero.gateway.model.FilterData: Returns the cut out value or null.
getCutOutTolerance(UnitsLength) - Method in class omero.gateway.model.FilterData: Returns the cut out tolerance value or null.
getData() - Method in class omero.gateway.model.TableData: Get the data in form Object['column index']['row data']
getData() - Method in class omero.gateway.model.TableResult: Returns the data.
getDataObjects(int, Class<? extends DataObject>) - Method in class omero.gateway.model.SearchResultCollection: Get DataObjects filtered by scope and type
getDataObjects() - Method in class omero.gateway.model.TagAnnotationData: Returns the collection of data objects related to this tag.
getDatasets(SecurityContext) - Method in class omero.gateway.facility.BrowseFacility: Loads all datasets
getDatasets(SecurityContext, Collection<Long>) - Method in class omero.gateway.facility.BrowseFacility: Loads the datasets with the given ids
getDatasets(SecurityContext, long) - Method in class omero.gateway.facility.BrowseFacility: Loads the datasets for a particular user
getDatasets(SecurityContext, long, Collection<Long>) - Method in class omero.gateway.facility.BrowseFacility: Loads the datasets with the given ids which belong to a particular user
getDatasets(SecurityContext, String) - Method in class omero.gateway.facility.BrowseFacility: Load dataset by name
getDatasets() - Method in class omero.gateway.model.ImageData: Returns the datasets containing this image.
getDatasets() - Method in class omero.gateway.model.ProjectData: Returns the datasets contained in this project.
getDataValue() - Method in class omero.gateway.model.DoubleAnnotationData: Returns the value.
getDataValue() - Method in class omero.gateway.model.LongAnnotationData: Returns the value.
getDateType() - Method in class omero.gateway.model.SearchParameters
getDefaultGroup() - Method in class omero.gateway.model.ExperimenterData: Returns the default Group for this Experimenter
getDefaultPixels() - Method in class omero.gateway.model.ImageData: Returns the default set of pixels.
getDefaultSample() - Method in class omero.gateway.model.PlateData: Returns the currently selected field or 0.
getDescription() - Method in class omero.gateway.model.AnnotationData: Retrieves the description of the underlying Annotation instance.
getDescription() - Method in class omero.gateway.model.DatasetData: Returns the description of the dataset.
getDescription() - Method in class omero.gateway.model.FileAnnotationData: Returns the description of the annotation.
getDescription() - Method in class omero.gateway.model.FileData: Returns the description of the file.
getDescription() - Method in class omero.gateway.model.FolderData: Get the description of the Folder
getDescription() - Method in class omero.gateway.model.GroupData: Returns the description of the group.
getDescription() - Method in class omero.gateway.model.ImageData: Returns the description of the image.
getDescription() - Method in class omero.gateway.model.PlateAcquisitionData: Returns the description of the plate acquisition.
getDescription() - Method in class omero.gateway.model.PlateData: Returns the description of the plate.
getDescription() - Method in class omero.gateway.model.ProjectData: Returns the description of the project.
getDescription() - Method in class omero.gateway.model.ScreenData: Returns the description of the screen.
getDescription() - Method in class omero.gateway.model.TableDataColumn: Get the description
getDescription() - Method in class omero.gateway.model.XMLAnnotationData: Returns the description of the annotation.
getDescription() - Method in class omero.gateway.util.TIFFFilter: Returns the description of the filter.
getDetails() - Method in class omero.gateway.model.DataObject: Returns the details of the object.
getDetector() - Method in class omero.gateway.model.ChannelAcquisitionData: Returns the detector used for that channel.
getDetectorBinningAsEnum() - Method in class omero.gateway.model.ChannelAcquisitionData: Returns the binning enumeration value.
getDetectors() - Method in class omero.gateway.model.InstrumentData: Returns the collection of detectors.
getDetectorSettingsBinning() - Method in class omero.gateway.model.ChannelAcquisitionData: Returns the Binning factor.
getDetectorSettingsGain() - Method in class omero.gateway.model.ChannelAcquisitionData: Returns the gain set on the detector.
getDetectorSettingsOffset() - Method in class omero.gateway.model.ChannelAcquisitionData: Returns the offset set on the detector.
getDetectorSettingsReadOutRate(UnitsFrequency) - Method in class omero.gateway.model.ChannelAcquisitionData: Returns the Read out rate set on the detector.
getDetectorSettingsVoltage(UnitsElectricPotential) - Method in class omero.gateway.model.ChannelAcquisitionData: Returns the voltage set on the detector.
getDichroic() - Method in class omero.gateway.model.FilterSetData: Returns the dichroic if any.
getDichroic() - Method in class omero.gateway.model.LightPathData: Returns the dichroic if any.
getDichroics() - Method in class omero.gateway.model.InstrumentData: Returns the collection of dichroics.
getDisplayedFileName(String, Integer) - Static method in class omero.gateway.util.Utils: Returns the name to display for a file.
getElement(int, Object) - Method in interface omero.gateway.cache.CacheService: Adds the specified element to the selected cache.
getEmail() - Method in class omero.gateway.model.ExperimenterData: Returns the e-mail of the experimenter.
getEmissionFilters() - Method in class omero.gateway.model.FilterSetData: Returns the collections of emission filters if any.
getEmissionFilters() - Method in class omero.gateway.model.LightPathData: Returns the collections of emission filters if any.
getEmissionWavelength(UnitsLength) - Method in class omero.gateway.model.ChannelData: Returns the emission wavelength of the channel.
getEnd() - Method in class omero.gateway.model.SearchParameters: Returns the upper bound of the time interval.
getEndTime() - Method in class omero.gateway.model.PlateAcquisitionData: Returns the time when the last image was collected.
getError() - Method in class omero.gateway.model.SearchResultCollection: Get the error code
getExcitationFilters() - Method in class omero.gateway.model.FilterSetData: Returns the collections of excitation filters if any.
getExcitationFilters() - Method in class omero.gateway.model.LightPathData: Returns the collections of excitation filters if any.
getExcitationWavelength(UnitsLength) - Method in class omero.gateway.model.ChannelData: Returns the excitation wavelength of the channel.
getExperimenter() - Method in class omero.gateway.SecurityContext: Returns the id of the experimenter.
getExperimenterData() - Method in class omero.gateway.SecurityContext: Returns the experimenter.
getExperimenters() - Method in class omero.gateway.model.GroupData: Returns the experimenters contained in this group.
getExporterService(SecurityContext) - Method in class omero.gateway.Gateway: Returns the ExporterPrx service.
getExtendedMessage() - Method in exception omero.gateway.exception.RenderingServiceException: Prints the stack trace and returns it as a string.
getExtension() - Method in class omero.gateway.util.TIFFFilter: Returns the extension of the filter.
getExternalDescription() - Method in class omero.gateway.model.WellData: Returns the external description of the well.
getExternalIdentifier() - Method in class omero.gateway.model.PlateData: Returns the external identifier of the plate.
getFacility(Class<T>, Gateway) - Static method in class omero.gateway.facility.Facility: Get a reference to a certain Facility
getFacility(Class<T>) - Method in class omero.gateway.Gateway: Get a Facility to perform further operations with the server
getFileFormat() - Method in class omero.gateway.model.FileAnnotationData: Returns the format of the uploaded file.
getFileID() - Method in class omero.gateway.model.FileAnnotationData: Returns the id of the file.
getFileID() - Method in class omero.gateway.model.ROIResult: Returns the id of the file.
getFileKind() - Method in class omero.gateway.model.FileAnnotationData: Returns a user readable description of the file.
getFileName() - Method in class omero.gateway.model.FileAnnotationData: Returns the name of the file.
getFilePath() - Method in class omero.gateway.model.FileAnnotationData: Returns the absolute path to the file.
getFilesetId() - Method in class omero.gateway.model.ImageData: Returns the ID of the fileset to which this image belongs.
getFileSize() - Method in class omero.gateway.model.FileAnnotationData: Returns the size of the file.
getFill() - Method in class omero.gateway.model.ShapeSettingsData: Returns the fill color.
getFillRule() - Method in class omero.gateway.model.ShapeSettingsData: Returns the fill rule.
getFilters() - Method in class omero.gateway.model.InstrumentData: Returns the collection of filters.
getFilterSet() - Method in class omero.gateway.model.ChannelAcquisitionData: Returns the filter set or null.
getFilterSet() - Method in class omero.gateway.model.OTFData: Returns the associated filter set.
getFilterSets() - Method in class omero.gateway.model.InstrumentData: Returns the collection of filter sets.
getFilterWheel() - Method in class omero.gateway.model.FilterData: Returns the wheel.
getFirstName() - Method in class omero.gateway.model.ExperimenterData: Returns the first name of the experimenter.
getFluor() - Method in class omero.gateway.model.ChannelData: Returns the Fluorophore used.
getFolderAsContainerName(File) - Static method in class omero.gateway.util.Utils: Returns the name as container if option is on.
getFolderPathString() - Method in class omero.gateway.model.FolderData: Returns the folder path as string
getFolderPathString(char) - Method in class omero.gateway.model.FolderData: Returns the folder path as string using a custom path separator
getFolders(SecurityContext) - Method in class omero.gateway.facility.BrowseFacility: Get all folders the logged in user has access to.
getFolders(SecurityContext, Collection<Long>) - Method in class omero.gateway.facility.BrowseFacility: Get the folders for the given folder ids.
getFolders(SecurityContext, long) - Method in class omero.gateway.facility.BrowseFacility: Get the folders which belong to the given user.
getFolders() - Method in class omero.gateway.model.ROIData: Get the folders this ROI is part of
getFolders() - Method in class omero.gateway.model.ROIResult: Get the available folders
getFont() - Method in class omero.gateway.model.ShapeSettingsData: Get the style of the font for Shape.
getFontFamily() - Method in class omero.gateway.model.ShapeSettingsData: Returns the stroke.
getFontSize(UnitsLength) - Method in class omero.gateway.model.ShapeSettingsData: Returns the stroke.
getFontStyle() - Method in class omero.gateway.model.ShapeSettingsData: Returns the font style.
getFormat() - Method in class omero.gateway.model.ImageData: Returns the format of the image.
getGain() - Method in class omero.gateway.model.DetectorData: Returns the gain of the detector.
getGlobalMax() - Method in class omero.gateway.model.ChannelData: Returns the global maximum of the channel i.e.
getGlobalMin() - Method in class omero.gateway.model.ChannelData: Returns the global minimum of the channel i.e.
getGraphType(Class<? extends DataObject>) - Static method in class omero.gateway.util.PojoMapper: Returns the name of the data type which has to used for Graph actions, see Requests
getGreen() - Method in class omero.gateway.model.WellData: Returns the green component of the color associated to the well, or -1.
getGridColumns() - Method in class omero.gateway.facility.TablesFacilityHelper: Get the grid columns; (TablesFacilityHelper.parseTableData(TableData) needs to be called first)
getGroupID() - Method in class omero.gateway.LoginCredentials: Returns the OMERO group identifier.
getGroupId() - Method in class omero.gateway.model.DataObject: Returns the id of the group.
getGroupId() - Method in class omero.gateway.model.ExperimenterData: Overridden to return the id of the default group.
getGroupId() - Method in class omero.gateway.model.GroupData: Overridden to return the id of the object.
getGroupId() - Method in class omero.gateway.model.SearchParameters
getGroupId() - Method in class omero.gateway.model.SearchResult: Get the group id of the object
getGroupID() - Method in class omero.gateway.SecurityContext: Returns the identifier of the group.
getGroups() - Method in class omero.gateway.model.ExperimenterData: Returns the groups the experimenter is a member of.
getHeaders() - Method in class omero.gateway.model.TableResult: Returns the name of the columns.
getHeadersDescription() - Method in class omero.gateway.model.TableResult: Returns the name of the columns.
getHeight() - Method in class omero.gateway.model.MaskData: Returns the height of the mask.
getHeight() - Method in class omero.gateway.model.RectangleData: Returns the height untransformed rectangle.
getHierarchy(SecurityContext, Class, long) - Method in class omero.gateway.facility.BrowseFacility: Retrieves hierarchy trees rooted by a given node.
getHierarchy(SecurityContext, Class, List<Long>, Parameters) - Method in class omero.gateway.facility.BrowseFacility: Retrieves hierarchy trees rooted by a given node i.e.
getHistogram(SecurityContext, PixelsData, int[], int, int) - Method in class omero.gateway.facility.RawDataFacility: Get the histogram data for the given image, using default 256 bins and the channels global min/max for the histogram range.
getHistogram(SecurityContext, PixelsData, int[], int, boolean, PlaneDef) - Method in class omero.gateway.facility.RawDataFacility: Get the histogram data for the given image.
getHistogram(int[], int, boolean, PlaneDef) - Method in class omero.gateway.rnd.DataSink: Get the histogram data for the given image.
getHostname() - Method in class omero.gateway.ServerInformation: Return the hostname.
getHQLEntityName(Class<? extends IObject>) - Static method in class omero.gateway.util.PojoMapper: Gets the type of an IObject class as String which can be used in HQL queries.
getHumidity() - Method in class omero.gateway.model.ImageAcquisitionData: Returns the humidity level, this is a value in the interval [0, 1].
getId() - Method in class omero.gateway.model.DataObject: Returns the database id of the IObject or -1 if null
getIllumination() - Method in class omero.gateway.model.ChannelAcquisitionData: Returns the illumination.
getIllumination() - Method in class omero.gateway.model.ChannelData: Returns the illumination.
getIlluminationAsEnum() - Method in class omero.gateway.model.ChannelData: Returns the illumination enumeration value.
getImage(SecurityContext, long) - Method in class omero.gateway.facility.BrowseFacility: Loads a image
getImage(SecurityContext, long, ParametersI) - Method in class omero.gateway.facility.BrowseFacility: Loads a image
getImage() - Method in class omero.gateway.model.PixelsData: Returns the image linked to this pixels' set.
getImage() - Method in class omero.gateway.model.ROIData: Returns the image for the ROI.
getImage() - Method in class omero.gateway.model.WellSampleData: Returns the image related to that sample if any.
getImageAcquisitionData(SecurityContext, long) - Method in class omero.gateway.facility.MetadataFacility: Loads the ImageAcquisitionData for a specific image
getImageIds() - Method in class omero.gateway.model.FilesetData: Returns the collection of images related to the file set.
getImages(SecurityContext, Collection<Long>) - Method in class omero.gateway.facility.BrowseFacility: Loads the images with the given ids
getImages(SecurityContext, Collection<Long>, ParametersI) - Method in class omero.gateway.facility.BrowseFacility: Loads the images with the given ids
getImages(SecurityContext, long, Collection<Long>) - Method in class omero.gateway.facility.BrowseFacility: Loads the images for a particular user
getImages(SecurityContext, String) - Method in class omero.gateway.facility.BrowseFacility: Load image by name
getImages() - Method in class omero.gateway.model.DatasetData: Returns a set of images contained in the dataset.
getImagesForDatasets(SecurityContext, Collection<Long>) - Method in class omero.gateway.facility.BrowseFacility: Load all images belonging to particular datasets
getImagesForProjects(SecurityContext, Collection<Long>) - Method in class omero.gateway.facility.BrowseFacility: Load all images belonging to particular projects
getImagingEnvironmentId() - Method in class omero.gateway.model.ImageAcquisitionData: Returns the id of the StageLabel or -1 if not already linked to the image.
getImmersion() - Method in class omero.gateway.model.ObjectiveData: Returns the immersion value of the objective.
getImportStore(SecurityContext) - Method in class omero.gateway.Gateway: Creates or recycles the import store.
getImportStore(SecurityContext, String) - Method in class omero.gateway.Gateway: Creates or recycles the import store.
getIndex() - Method in exception omero.gateway.exception.RenderingServiceException: Returns the index.
getIndex() - Method in class omero.gateway.model.ChannelData: Returns the channel's index.
getIndex() - Method in class omero.gateway.model.ImageData: Returns the index of the image within the multi-images file.
getIndex() - Method in class omero.gateway.model.TableDataColumn: Get the index
getInserted() - Method in class omero.gateway.model.ImageData: Returns the insertion time of the image.
getInstitution() - Method in class omero.gateway.model.ExperimenterData: Returns the institution where the experimenter works.
getInstrumentId() - Method in class omero.gateway.model.ImageData: Returns the id of the instrument if any.
getIterator() - Method in class omero.gateway.model.ROIData: Returns the iterator of the collection of the map.
getKind() - Method in class omero.gateway.model.LightSourceData: Returns the kind of light source.
getLabel() - Method in class omero.gateway.model.PlateAcquisitionData: Returns the label associated to the plate acquisition.
getLabelName() - Method in class omero.gateway.model.ImageAcquisitionData: Returns the name of the stage label.
getLaserFrequencyMultiplication() - Method in class omero.gateway.model.LightSourceData: Returns the frequency multiplication of the laser.
getLaserMedium() - Method in class omero.gateway.model.LightSourceData: Returns the laser's medium.
getLaserPockelCell() - Method in class omero.gateway.model.LightSourceData: Returns the pockel cell flag of the laser.
getLaserPulse() - Method in class omero.gateway.model.LightSourceData: Returns the pulse of the laser.
getLaserPump() - Method in class omero.gateway.model.LightSourceData: Returns the pump.
getLaserRepetitionRate(UnitsFrequency) - Method in class omero.gateway.model.LightSourceData: Returns the repetition rate (Hz) if the laser is repetitive.
getLaserTuneable() - Method in class omero.gateway.model.LightSourceData: Returns the value of the tuneable field or null if no value set.
getLaserWavelength(UnitsLength) - Method in class omero.gateway.model.LightSourceData: Returns the laser's wavelength.
getLastModified() - Method in class omero.gateway.model.AnnotationData: Returns the time when the annotation was last modified.
getLastName() - Method in class omero.gateway.model.ExperimenterData: Returns the last name of the experimenter.
getLeaders() - Method in class omero.gateway.model.GroupData: Returns the experimenters contained in this group.
getLensNA() - Method in class omero.gateway.model.ObjectiveData: Returns the objective's LensNA.
getLightPath() - Method in class omero.gateway.model.ChannelAcquisitionData: Returns the light path or null.
getLightSettingsAttenuation() - Method in class omero.gateway.model.ChannelAcquisitionData: Returns the attenuation of the light source, percent value between 0 and 1.
getLightSettingsWavelength(UnitsLength) - Method in class omero.gateway.model.ChannelAcquisitionData: Returns the wavelength of the light source.
getLightSource() - Method in class omero.gateway.model.ChannelAcquisitionData: Returns the source of light.
getLightSourceModel() - Method in class omero.gateway.model.LightSourceData: Returns the model of the light source.
getLightSources() - Method in class omero.gateway.model.InstrumentData: Returns the collection of light sources.
getLinkClass(Class<? extends DataObject>, Class<? extends DataObject>) - Static method in class omero.gateway.util.Links: Get the Link class for a certain child parent combination, e.g.
getLoggedInUser() - Method in class omero.gateway.Gateway: Get the currently logged in user
getLogger() - Method in class omero.gateway.Gateway: Provides access to the Logger
getLookupTables(SecurityContext) - Method in class omero.gateway.facility.BrowseFacility: Get the available lookup tables
getLotNumber() - Method in class omero.gateway.model.DetectorData: Returns the lot number of the detector.
getLotNumber() - Method in class omero.gateway.model.DichroicData: Returns the lot number.
getLotNumber() - Method in class omero.gateway.model.FilterData: Returns the lot number.
getLotNumber() - Method in class omero.gateway.model.FilterSetData: Returns the lot number.
getLotNumber() - Method in class omero.gateway.model.LightSourceData: Returns the lot of number the light source.
getLotNumber() - Method in class omero.gateway.model.ObjectiveData: Returns the lot number of the detector.
getManagedRepositoriesPaths(SecurityContext, ImageData) - Method in class omero.gateway.facility.MetadataFacility: Get the file paths of the image in the managed repository
getManufacturer() - Method in class omero.gateway.model.DetectorData: Returns the manufacturer of the detector.
getManufacturer() - Method in class omero.gateway.model.DichroicData: Returns the manufacturer.
getManufacturer() - Method in class omero.gateway.model.FilterData: Returns the manufacturer.
getManufacturer() - Method in class omero.gateway.model.FilterSetData: Returns the manufacturer.
getManufacturer() - Method in class omero.gateway.model.LightSourceData: Returns the manufacturer of the light source.
getManufacturer() - Method in class omero.gateway.model.ObjectiveData: Returns the manufacturer of the detector.
getMarkerEnd() - Method in class omero.gateway.model.ShapeSettingsData: Returns the marker end.
getMarkerStart() - Method in class omero.gateway.model.ShapeSettingsData: Returns the marker start.
getMask() - Method in class omero.gateway.model.MaskData: Returns the mask as a byte array.
getMaskAsBinaryArray() - Method in class omero.gateway.model.MaskData: Returns the mask image.
getMaskAsBufferedImage() - Method in class omero.gateway.model.MaskData: Returns the mask image.
getMaskPoints() - Method in class omero.gateway.model.PolygonData: Returns the points in the polygon.
getMaximumFieldCount() - Method in class omero.gateway.model.PlateAcquisitionData: Returns the maximum number of fields in any well.
getMedium() - Method in class omero.gateway.model.ImageAcquisitionData: Returns the medium of the objective.
getMediumAsEnum() - Method in class omero.gateway.model.ImageAcquisitionData: Returns the medium enumeration value.
getMembersOnly() - Method in class omero.gateway.model.GroupData: Returns the list of experimenters that are not owners of the group.
getMetadataService(SecurityContext) - Method in class omero.gateway.Gateway: Returns the IMetadataPrx service.
getMicroscopeLotNumber() - Method in class omero.gateway.model.InstrumentData: Returns the lot number of the microscope.
getMicroscopeManufacturer() - Method in class omero.gateway.model.InstrumentData: Returns the model of the microscope.
getMicroscopeModel() - Method in class omero.gateway.model.InstrumentData: Returns the model of the microscope.
getMicroscopeSerialNumber() - Method in class omero.gateway.model.InstrumentData: Returns the serial number of the microscope.
getMicroscopeType() - Method in class omero.gateway.model.InstrumentData: Returns the type of microscope.
getMiddleName() - Method in class omero.gateway.model.ExperimenterData: Returns the middle name of the experimenter.
getMIMEType() - Method in class omero.gateway.util.TIFFFilter: Returns the MIME type.
getMode() - Method in class omero.gateway.model.ChannelAcquisitionData: Returns the mode.
getMode() - Method in class omero.gateway.model.ChannelData: Returns the mode.
getModeAsEnum() - Method in class omero.gateway.model.ChannelData: Returns the acquisition enumeration value.
getModel() - Method in class omero.gateway.model.DetectorData: Returns the manufacturer of the detector.
getModel() - Method in class omero.gateway.model.DichroicData: Returns the model.
getModel() - Method in class omero.gateway.model.FilterData: Returns the model.
getModel() - Method in class omero.gateway.model.FilterSetData: Returns the model.
getModel() - Method in class omero.gateway.model.ObjectiveData: Returns the model of the objective.
getModelType(String) - Static method in class omero.gateway.util.PojoMapper: Converts the specified POJO into the corresponding model class, see PojoMapper.getModelType(Class)
getModelType(Class<? extends DataObject>) - Static method in class omero.gateway.util.PojoMapper: Converts the specified POJO into the corresponding model class.
getName() - Method in class omero.gateway.model.ChannelData: Returns the name of the channel.
getName() - Method in class omero.gateway.model.DatasetData: Returns the name of the dataset.
getName() - Method in class omero.gateway.model.FileData: Returns the name of the file.
getName() - Method in class omero.gateway.model.FolderData: Get the name of the Folder
getName() - Method in class omero.gateway.model.GroupData: Returns the name of the group.
getName() - Method in class omero.gateway.model.ImageData: Returns the name of the image.
getName() - Method in class omero.gateway.model.PlateAcquisitionData: Returns the name of the plate acquisition.
getName() - Method in class omero.gateway.model.PlateData: Returns the name of the plate.
getName() - Method in class omero.gateway.model.ProjectData: Returns the name of the project.
getName() - Method in class omero.gateway.model.ScreenData: Returns the name of the screen.
getName() - Method in class omero.gateway.model.TableDataColumn: Get the header
getNameSpace() - Method in class omero.gateway.model.AnnotationData: Retrieves the nameSpace of the underlying Annotation instance.
getNDFilter() - Method in class omero.gateway.model.ChannelData: Returns the ND filter wavelength of the channel.
getNominalMagnification() - Method in class omero.gateway.model.ObjectiveData: Returns the objective's nominal magnification factor.
getNumberOfRows() - Method in class omero.gateway.model.TableData
getObject() - Method in class omero.gateway.model.SearchResult: Get the found object
getObjectId() - Method in class omero.gateway.model.SearchResult: Get the Id of the found object
getObjective() - Method in class omero.gateway.model.ImageAcquisitionData: Returns the objective used to capture the image.
getObjective() - Method in class omero.gateway.model.OTFData: Returns the associated objective.
getObjectives() - Method in class omero.gateway.model.InstrumentData: Returns the collection of objectives.
getObjectiveSettingsId() - Method in class omero.gateway.model.ImageAcquisitionData: Returns the id of the Objective settings or -1 if not already linked to the image.
getOffset() - Method in class omero.gateway.model.DetectorData: Returns the offset of the detector.
getOffset() - Method in class omero.gateway.model.TableData: Get the row offset (if this TableData represents only a subset of the original table)
getOriginalFileId() - Method in class omero.gateway.model.TableData: Get the original file id
getOriginalMimetype() - Method in class omero.gateway.model.FileAnnotationData: Returns the format of the original file.
getOriginalPaths(SecurityContext, ImageData) - Method in class omero.gateway.facility.MetadataFacility: Get the original file paths where the image was imported from.
getOrphanedImages(SecurityContext, long) - Method in class omero.gateway.facility.BrowseFacility: Get orphaned images for a certain user
getOTF() - Method in class omero.gateway.model.ChannelAcquisitionData: Returns the OTF used for that channel.
getOTF() - Method in class omero.gateway.model.InstrumentData: Returns the collection of OTFs.
getOwner() - Method in class omero.gateway.model.DataObject: Returns the owner of the object.
getParentFilePath() - Method in class omero.gateway.model.ImageData: Returns the path to the file hosting the image.
getParentFolder() - Method in class omero.gateway.model.FolderData: Get the the parent folder
getParentFromLink(IObject) - Static method in class omero.gateway.util.ModelMapper: Returns the child from the passed link.
getPassword() - Method in class omero.gateway.UserCredentials: Returns the password.
getPath() - Method in class omero.gateway.model.FileData: Returns the (relative) path of the file.
getPath() - Method in class omero.gateway.model.OTFData: Returns the path.
getPathToFile() - Method in class omero.gateway.model.ImageData: Returns the path to the file.
getPermissions() - Method in class omero.gateway.model.DataObject: Returns the permission of the object.
getPermissionsLevel() - Method in class omero.gateway.model.PermissionData: Returns the permissions level.
getPinholeSize(UnitsLength) - Method in class omero.gateway.model.ChannelData: Returns the pin hole size of the channel.
getPixelSizeX(UnitsLength) - Method in class omero.gateway.model.PixelsData: Returns the dimension of a pixel along the X-axis.
getPixelSizeY(UnitsLength) - Method in class omero.gateway.model.PixelsData: Returns the dimension of a pixel along the Y-axis.
getPixelSizeZ(UnitsLength) - Method in class omero.gateway.model.PixelsData: Returns the dimension of a pixel along the Z-axis Note: Do not use the returned Length object to modify the pixel size, use the setPixelSizeZ method instead.
getPixelsService(SecurityContext) - Method in class omero.gateway.Gateway: Returns the IPixelsPrx service.
getPixelsStore(SecurityContext) - Method in class omero.gateway.Gateway: Returns the RawPixelsStorePrx service.
getPixelsType() - Method in class omero.gateway.model.OTFData: Returns the pixels type.
getPixelType() - Method in class omero.gateway.model.PixelsData: Returns the pixels type.
getPixelValue(int, int) - Method in class omero.gateway.rnd.Plane2D: Returns the pixels value at the point specified by the x-coordinate and y-coordinate.
getPixelValues() - Method in class omero.gateway.rnd.Plane2D: Returns the pixels values
getPlane(SecurityContext, PixelsData, int, int, int) - Method in class omero.gateway.facility.RawDataFacility: Extracts a 2D plane from the pixels set.
getPlane(int, int, int) - Method in class omero.gateway.rnd.DataSink: Extracts a 2D plane from the pixels set this object is working for.
getPlaneCount() - Method in class omero.gateway.model.ROIData: Deprecated.
Will be removed in future. Does not work as expected if the ROI contains shapes which are associated with all planes (Z, C, T == -1)
getPlate() - Method in class omero.gateway.model.WellData: Returns the plate containing this Well.
getPlateAcquisitions() - Method in class omero.gateway.model.PlateData: Returns the plate acquisitions related to this plate.
getPlates(SecurityContext) - Method in class omero.gateway.facility.BrowseFacility: Loads all plates
getPlates(SecurityContext, Collection<Long>) - Method in class omero.gateway.facility.BrowseFacility: Loads the plates with the given ids
getPlates(SecurityContext, long) - Method in class omero.gateway.facility.BrowseFacility: Loads the plates for a particular user
getPlates(SecurityContext, long, Collection<Long>) - Method in class omero.gateway.facility.BrowseFacility: Loads the plates with the given ids which belong to a particular user
getPlates(SecurityContext, String) - Method in class omero.gateway.facility.BrowseFacility: Load plate by name
getPlates() - Method in class omero.gateway.model.ScreenData: Returns the plates contained in this screen.
getPlateType() - Method in class omero.gateway.model.PlateData: Returns the type of plate e.g.
getPockelCell() - Method in class omero.gateway.model.ChannelData: Returns the Pockel cell settings.
getPoints() - Method in class omero.gateway.model.PolygonData: Returns the points in the polygon.
getPoints() - Method in class omero.gateway.model.PolylineData: Returns the points in the Polyline.
getPojosService(SecurityContext) - Method in class omero.gateway.Gateway: Returns the IContainerPrx service.
getPojoType(Class<? extends IObject>) - Static method in class omero.gateway.util.PojoMapper: Get the pojo type for a an IObject class (Reverse of PojoMapper.getModelType(Class))
getPort() - Method in class omero.gateway.ServerInformation: Return the port
getPositionX(UnitsLength) - Method in class omero.gateway.model.ImageAcquisitionData: Returns the x-coordinate in the frame microscope.
getPositionX(UnitsLength) - Method in class omero.gateway.model.WellSampleData: Returns the position X.
getPositionY(UnitsLength) - Method in class omero.gateway.model.ImageAcquisitionData: Returns the y-coordinate in the frame microscope.
getPositionY(UnitsLength) - Method in class omero.gateway.model.WellSampleData: Returns the position Y.
getPositionZ(UnitsLength) - Method in class omero.gateway.model.ImageAcquisitionData: Returns the z-coordinate in the frame microscope.
getPower(UnitsPower) - Method in class omero.gateway.model.LightSourceData: Returns the power of the light source.
getProjectionService(SecurityContext) - Method in class omero.gateway.Gateway: Returns the IProjectionPrx service.
getProjects(SecurityContext) - Method in class omero.gateway.facility.BrowseFacility: Get all projects
getProjects(SecurityContext, Collection<Long>) - Method in class omero.gateway.facility.BrowseFacility: Get the projects for the given project ids
getProjects(SecurityContext, long) - Method in class omero.gateway.facility.BrowseFacility: Get the projects of a certain user
getProjects(SecurityContext, long, Collection<Long>) - Method in class omero.gateway.facility.BrowseFacility: Get the projects for the given project ids which belong to a certain user
getProjects(SecurityContext, String) - Method in class omero.gateway.facility.BrowseFacility: Load project by name
getProjects() - Method in class omero.gateway.model.DatasetData: Returns a set of projects containing the dataset.
getPropertyChangeListeners() - Method in class omero.gateway.Gateway: Get the PropertyChangeListeners
getProtocolDescription() - Method in class omero.gateway.model.ScreenData: Returns the description of the protocol.
getProtocolIdentifier() - Method in class omero.gateway.model.ScreenData: Returns the identifier of the protocol.
getQuery() - Method in class omero.gateway.model.SearchParameters: Returns the query terms to search for
getQueryService(SecurityContext) - Method in class omero.gateway.Gateway: Returns the IQueryPrx service.
getRadiusX() - Method in class omero.gateway.model.EllipseData: Returns the radius along the X-axis.
getRadiusY() - Method in class omero.gateway.model.EllipseData: Returns the radius along the Y-axis.
getRating() - Method in class omero.gateway.model.RatingAnnotationData: Returns the rating value.
getRawFileService(SecurityContext) - Method in class omero.gateway.Gateway: Returns the RawFileStorePrx service.
getRawValue(int) - Method in class omero.gateway.rnd.Plane2D: Returns the raw data value at the given offset
getReagentsCounts() - Method in class omero.gateway.model.WellData: Returns the number of reagents linked to the object, key: id of the user, value: number of annotation.
getReagentSetDescripion() - Method in class omero.gateway.model.ScreenData: Returns the description of the reagent set.
getReagentSetIdentifier() - Method in class omero.gateway.model.ScreenData: Returns the identifier of the Reagent set.
getRed() - Method in class omero.gateway.model.WellData: Returns the red component of the color associated to the well, or -1.
getReference() - Method in class omero.gateway.model.ImageData: Returns the reference to the file to register.
getRefPlateId() - Method in class omero.gateway.model.PlateAcquisitionData: Returns the id of the plate of reference.
getRefractiveIndex() - Method in class omero.gateway.model.ImageAcquisitionData: Returns the refractive index of the objective.
getRenderingEngines() - Method in class omero.gateway.Gateway: Returns the rendering engines to re-activate.
getRenderingService(SecurityContext, long) - Method in class omero.gateway.Gateway: Returns the Rendering service.
getRenderingSettingsService(SecurityContext) - Method in class omero.gateway.Gateway: Returns the IRenderingSettingsPrx service.
getRepositoryService(SecurityContext) - Method in class omero.gateway.Gateway: Returns the IRepositoryInfoPrx service.
getResult() - Method in class omero.gateway.model.ROIResult: Returns the result.
getResults(int, Class<? extends DataObject>) - Method in class omero.gateway.model.SearchResultCollection: Get all results of a certain scope and/or type
getRGBA(Color) - Static method in class omero.gateway.model.ShapeSettingsData: Returns the Color's RGBA value as integer
getROI() - Method in class omero.gateway.util.ROIComponent: Returns all the ROI in the component as a list.
getROI() - Method in class omero.gateway.util.UploadMask: Returns the ROIs created from uploading the images.
getROICoordinate() - Method in class omero.gateway.model.ShapeData: Returns the ROICoordinate for the ShapeData.
getROICount(SecurityContext, long) - Method in class omero.gateway.facility.ROIFacility: Get the number of ROIs for an image (-1 in case of error)
getROIFolders(SecurityContext, long) - Method in class omero.gateway.facility.ROIFacility: Get all ROI folders for a certain image
getROIs() - Method in class omero.gateway.model.ROIResult: Returns the collection of ROIs.
getROIService(SecurityContext) - Method in class omero.gateway.Gateway: Returns the IRoiPrx service.
getRow() - Method in class omero.gateway.model.WellData: Returns the row used to indicate the location of the well on the grid.
getRowSequenceIndex() - Method in class omero.gateway.model.PlateData: Returns the index indicating how to label a row.
getScope() - Method in class omero.gateway.model.SearchParameters: Returns the scope of the search.
getScopeId() - Method in class omero.gateway.model.SearchResult: The Id of the search scope, e.g.
getScreens(SecurityContext) - Method in class omero.gateway.facility.BrowseFacility: Loads all screens
getScreens(SecurityContext, Collection<Long>) - Method in class omero.gateway.facility.BrowseFacility: Loads the screens with the given ids
getScreens(SecurityContext, long) - Method in class omero.gateway.facility.BrowseFacility: Loads the screens for a particular user
getScreens(SecurityContext, long, Collection<Long>) - Method in class omero.gateway.facility.BrowseFacility: Loads the screens with the given ids which belong to a particular user
getScreens(SecurityContext, String) - Method in class omero.gateway.facility.BrowseFacility: Load screen by name
getScreens() - Method in class omero.gateway.model.PlateData: Returns a set of screens containing the plate.
getScriptService(SecurityContext) - Method in class omero.gateway.Gateway: Returns the IScriptPrx service.
getSearchService(SecurityContext) - Method in class omero.gateway.Gateway: Returns the SearchPrx service.
getSerialNumber() - Method in class omero.gateway.model.DetectorData: Returns the serial number of the detector.
getSerialNumber() - Method in class omero.gateway.model.DichroicData: Returns the serial number.
getSerialNumber() - Method in class omero.gateway.model.FilterData: Returns the serial number.
getSerialNumber() - Method in class omero.gateway.model.FilterSetData: Returns the serial number.
getSerialNumber() - Method in class omero.gateway.model.LightSourceData: Returns the serial number of the light source.
getSerialNumber() - Method in class omero.gateway.model.ObjectiveData: Returns the serial number of the objective.
getSeries() - Method in class omero.gateway.model.ImageData: Returns the series.
getServer() - Method in class omero.gateway.LoginCredentials: Returns the server information.
getServerFileMimetype() - Method in class omero.gateway.model.FileAnnotationData: Returns the file format as defined by the specification, corresponding to the file extension.
getServerInformation() - Method in class omero.gateway.SecurityContext
getServerVersion() - Method in class omero.gateway.Gateway: Get the version of the server the Gateway is connected to
getSessionId(ExperimenterData) - Method in class omero.gateway.Gateway: Get the ID of the current session
getShapeCount() - Method in class omero.gateway.model.ROIData: Returns the number of shapes in the ROI.
getShapes() - Method in class omero.gateway.model.ROIData: Returns a list of all shapes.
getShapes(int, int) - Method in class omero.gateway.model.ROIData: Returns a list of shapes on a given plane, including shapes which are not specifically attached to the plane (span over all z planes and/or timepoints).
getShapes(int, int, boolean) - Method in class omero.gateway.model.ROIData: Returns a list of shapes on a given plane.
getShapeSettings() - Method in class omero.gateway.model.ShapeData: Returns the settings associated to the shape.
getShapesInRange(ROICoordinate, ROICoordinate) - Method in class omero.gateway.model.ROIData: Deprecated.
Will be removed in future. Does not work as expected if the ROI contains shapes which are associated with all planes (Z, C, T == -1)
getSharedResources(SecurityContext) - Method in class omero.gateway.Gateway: Returns the SharedResourcesPrx service.
getSizeC() - Method in class omero.gateway.model.PixelsData: Returns the number of channels.
getSizeT() - Method in class omero.gateway.model.PixelsData: Returns the number of time-points.
getSizeX() - Method in class omero.gateway.model.OTFData: Returns the size along the X-axis.
getSizeX() - Method in class omero.gateway.model.PixelsData: Returns the number of pixels along the X-axis.
getSizeY() - Method in class omero.gateway.model.OTFData: Returns the size along the Y-axis.
getSizeY() - Method in class omero.gateway.model.PixelsData: Returns the number of pixels along the Y-axis.
getSizeZ() - Method in class omero.gateway.model.PixelsData: Returns the number of pixels along the Z-axis.
getStageLabelId() - Method in class omero.gateway.model.ImageAcquisitionData: Returns the id of the StageLabel or -1 if not already linked to the image.
getStart() - Method in class omero.gateway.model.SearchParameters: Returns the lower bound of the time interval.
getStartTime() - Method in class omero.gateway.model.PlateAcquisitionData: Returns the time when the first image was collected.
getStartTime() - Method in class omero.gateway.model.WellSampleData: Returns the time at which the field was acquired.
getStatus() - Method in class omero.gateway.model.PlateData: Returns the status of the plate.
getStatus() - Method in class omero.gateway.model.WellData: Returns the status of the well.
getStringRepresentation() - Method in enum omero.gateway.model.SearchScope: Get a String representation of this scope which can be used in a lucene search
getStringRepresentation(Collection<SearchScope>) - Static method in enum omero.gateway.model.SearchScope: Get a String representation of the given scopes which can be used in a lucence search
getStringSeparator(String) - Static method in class omero.gateway.util.Utils: Returns the separator or null.
getStroke() - Method in class omero.gateway.model.ShapeSettingsData: Returns the color of the stroke.
getStrokeDashArray() - Method in class omero.gateway.model.ShapeSettingsData: Returns the stroke dashes.
getStrokeWidth(UnitsLength) - Method in class omero.gateway.model.ShapeSettingsData: Returns the stroke's width (or 1 px if it's not set or less than or equals to 0)
getT() - Method in class omero.gateway.model.ShapeData: Returns the time-point.
getTable(SecurityContext, long) - Method in class omero.gateway.facility.TablesFacility: Load the data from a table (Note: limited to TablesFacility.DEFAULT_MAX_ROWS_TO_FETCH number of rows)
getTable(SecurityContext, long, long, long, int...) - Method in class omero.gateway.facility.TablesFacility: Load data from a table
getTable(SecurityContext, long, List<Long>) - Method in class omero.gateway.facility.TablesFacility: Load data from a table
getTable(SecurityContext, long, long...) - Method in class omero.gateway.facility.TablesFacility: Load data from a table
getTable(SecurityContext, long, long, long, long...) - Method in class omero.gateway.facility.TablesFacility: Load data from a table
getTableID() - Method in class omero.gateway.model.TableResult: Returns the id of the table.
getTableInfo(SecurityContext, long) - Method in class omero.gateway.facility.TablesFacility: Get basic information about a table.
getTagDescription() - Method in class omero.gateway.model.TagAnnotationData: Returns the description of the tag.
getTagDescriptions() - Method in class omero.gateway.model.TagAnnotationData: Returns the descriptions linked to that tag.
getTags() - Method in class omero.gateway.model.TagAnnotationData: Returns the collection of tags related to this tag.
getTagValue() - Method in class omero.gateway.model.TagAnnotationData: Returns the text of the tag.
getTemperature(UnitsTemperature) - Method in class omero.gateway.model.ImageAcquisitionData: Returns the temperature.
getTerm() - Method in class omero.gateway.model.TermAnnotationData: Returns the term.
getTermDescription() - Method in class omero.gateway.model.TermAnnotationData: Returns the description of the term.
getText() - Method in class omero.gateway.model.EllipseData: Returns the text of the shape.
getText() - Method in class omero.gateway.model.LineData: Returns the text of the shape.
getText() - Method in class omero.gateway.model.MaskData: Returns the text of the shape.
getText() - Method in class omero.gateway.model.PointData: Returns the text of the shape.
getText() - Method in class omero.gateway.model.PolygonData: Returns the text of the shape.
getText() - Method in class omero.gateway.model.PolylineData: Returns the text of the shape.
getText() - Method in class omero.gateway.model.RectangleData: Returns the text of the shape.
getText() - Method in class omero.gateway.model.TextData: Returns the text of the shape.
getText() - Method in class omero.gateway.model.TextualAnnotationData: Returns the text of this annotation.
getText() - Method in class omero.gateway.model.XMLAnnotationData: Returns the text of this annotation.
getThumbnailService(SecurityContext) - Method in class omero.gateway.Gateway: Returns the ThumbnailStorePrx service.
getTile(SecurityContext, PixelsData, int, int, int, int, int, int, int) - Method in class omero.gateway.facility.RawDataFacility: Extracts a 2D tile from the pixels set
getTile(int, int, int, int, int, int, int) - Method in class omero.gateway.rnd.DataSink: Extracts a 2D tile from the pixels set this object is working for.
getTime() - Method in class omero.gateway.model.TimeAnnotationData: Returns the time value.
getTimePoint() - Method in class omero.gateway.model.ROICoordinate: Returns the timepoint.
getTransform() - Method in class omero.gateway.model.ShapeData: Returns the transformation.
getTransmittance() - Method in class omero.gateway.model.FilterData: Returns the cut out tolerance value or -1.
getType() - Method in class omero.gateway.model.DetectorData: Returns the type of the detector.
getType() - Method in class omero.gateway.model.FilterData: Returns the type.
getType() - Method in class omero.gateway.model.LightSourceData: Returns the type of light.
getType() - Method in class omero.gateway.model.SearchResult: Get the type (class) of objects to search for see DataObject
getType() - Method in class omero.gateway.model.TableDataColumn: Get the data type
getTypes() - Method in class omero.gateway.model.SearchParameters: Returns the types to search on.
getTypesService(SecurityContext) - Method in class omero.gateway.Gateway: Returns the ITypesPrx service.
getUpdated() - Method in class omero.gateway.model.DataObject: Returns the updated time of the object.
getUpdateService(SecurityContext) - Method in class omero.gateway.Gateway: Returns the IUpdatePrx service.
getUpdateService(SecurityContext, String) - Method in class omero.gateway.Gateway: Returns the IUpdatePrx service.
getUsedFilePaths() - Method in class omero.gateway.model.FilesetData: Returns the collection of file paths used for importing the files (in case of in-place imports these are the targets of the (sym)links)
getUser() - Method in class omero.gateway.LoginCredentials: Returns the credentials.
getUserDetails(SecurityContext, String) - Method in class omero.gateway.Gateway: Get the user details of a certain user
getUserId() - Method in class omero.gateway.model.SearchParameters
getUserImages(SecurityContext) - Method in class omero.gateway.facility.BrowseFacility: Loads all images of the logged in user
getUserName() - Method in class omero.gateway.model.ExperimenterData: Returns the last name of the experimenter.
getUsername() - Method in class omero.gateway.UserCredentials: Returns the user name (or session ID, if it was set before instead of an username)
getUuid() - Method in class omero.gateway.model.ROIData: Get the UUID
getValue() - Method in class omero.gateway.model.BooleanAnnotationData: Returns the text of this annotation.
getVersion() - Method in class omero.gateway.model.DataObject: Returns the version of the object if the object is immutable, false otherwise.
getVoltage(UnitsElectricPotential) - Method in class omero.gateway.model.DetectorData: Returns the voltage of the detector.
getWellOriginX(UnitsLength) - Method in class omero.gateway.model.PlateData: Returns the x-coordinate in 2D-space of the well.
getWellOriginY(UnitsLength) - Method in class omero.gateway.model.PlateData: Returns the y-coordinate in 2D-space of the well.
getWells(SecurityContext, Collection<Long>) - Method in class omero.gateway.facility.BrowseFacility: Loads the wells
getWells(SecurityContext, long) - Method in class omero.gateway.facility.BrowseFacility: Loads the wells for a given plate
getWellSamples() - Method in class omero.gateway.model.WellData: Returns the well samples linked to the well.
getWellType() - Method in class omero.gateway.model.WellData: Returns a human readable identifier for the screening status e.g.
getWidth() - Method in class omero.gateway.model.MaskData: Returns the width of the mask.
getWidth() - Method in class omero.gateway.model.RectangleData: Returns the width untransformed rectangle.
getWorkingDistance(UnitsLength) - Method in class omero.gateway.model.ObjectiveData: Returns the working distance.
getX() - Method in class omero.gateway.model.EllipseData: Returns the x-coordinate of the center of the ellipse.
getX() - Method in class omero.gateway.model.MaskData: Returns the x-coordinate of the top-left corner of the mask.
getX() - Method in class omero.gateway.model.PointData: Returns the x-coordinate of the shape.
getX() - Method in class omero.gateway.model.RectangleData: Returns the x-coordinate of the top-left corner of an untransformed rectangle.
getX() - Method in class omero.gateway.model.TextData: Returns the x-coordinate text field.
getX1() - Method in class omero.gateway.model.LineData: Returns the x-coordinate of the starting point of an untransformed line.
getX2() - Method in class omero.gateway.model.LineData: Returns the x-coordinate of the end point of an untransformed line.
getY() - Method in class omero.gateway.model.EllipseData: Returns the y-coordinate of the center of the ellipse.
getY() - Method in class omero.gateway.model.MaskData: Returns the y-coordinate of the top-left corner of the mask.
getY() - Method in class omero.gateway.model.PointData: Returns the y coordinate of the shape.
getY() - Method in class omero.gateway.model.RectangleData: Returns the y-coordinate of the top-left corner of an untransformed rectangle.
getY() - Method in class omero.gateway.model.TextData: Returns the y-coordinate text field.
getY1() - Method in class omero.gateway.model.LineData: Returns the y-coordinate of the starting point of an untransformed line.
getY2() - Method in class omero.gateway.model.LineData: Returns the y-coordinate of the end point of an untransformed line.
getZ() - Method in class omero.gateway.model.ShapeData: Returns the z-section.
getZoom() - Method in class omero.gateway.model.DetectorData: Returns the offset of the detector.
getZSection() - Method in class omero.gateway.model.ROICoordinate: Returns the z-section.
GROUP_EXPERIMENTER_MAP - Static variable in class omero.gateway.model.ExperimenterData: Identifies the ExperimenterI.GROUPEXPERIMENTERMAP field.
GROUP_EXPERIMENTER_MAP - Static variable in class omero.gateway.model.GroupData: Identifies the ExperimenterGroupI.GROUPEXPERIMENTERMAP field.
GroupData - Class in omero.gateway.model: The data that makes up an OME Group along with the various members of the Group
GroupData() - Constructor for class omero.gateway.model.GroupData: Creates a new instance.
GroupData(ExperimenterGroup) - Constructor for class omero.gateway.model.GroupData: Creates a new instance.
GUEST - Static variable in class omero.gateway.model.GroupData: Identifies the Guest group.

H

hasDectector() - Method in class omero.gateway.model.ChannelAcquisitionData: Returns true if there is a detector for that channel, false otherwise.
hasFilter() - Method in class omero.gateway.model.ChannelAcquisitionData: Returns true if there is a filter set linked to the channel false otherwise.
hashCode() - Method in class omero.gateway.model.ROICoordinate: Calculate the hashCode for the data, The hashcode is generated by bitshifting z by ZTBITSPLIT bits and adding t.
hashCode() - Method in class omero.gateway.model.TableData
hashCode() - Method in class omero.gateway.model.TableDataColumn
hashCode() - Method in class omero.gateway.SecurityContext: Calculate the hashCode for the data.
hashCode() - Method in class omero.gateway.ServerInformation
hasID(DataObject) - Static method in class omero.gateway.util.Pojos: Checks if a DataObject Pojo is not null and has an ID
hasIris() - Method in class omero.gateway.model.ObjectiveData: Returns a boolean flag if the value has been set, null otherwise.
hasLightPath() - Method in class omero.gateway.model.ChannelAcquisitionData: Returns true if there is a light path described for that channel, false otherwise.
hasOpticalAxisAveraged() - Method in class omero.gateway.model.OTFData: Returns a boolean flag if the value has been set
hasPump() - Method in class omero.gateway.model.LightSourceData: Returns true if the light source is a laser with a pump, false otherwise.
hasStats() - Method in class omero.gateway.model.ChannelData: Returns true if the channel has some channel information false otherwise.
hasTextToSearch() - Method in class omero.gateway.model.SearchParameters: Returns true if text to search for, false otherwise.
HTM - Static variable in class omero.gateway.model.FileAnnotationData: Identifies the HTM file formats.
HTML - Static variable in class omero.gateway.model.FileAnnotationData: Identifies the HTML file formats.

I

ignoreType(Iterable<String>) - Method in class omero.gateway.util.Requests.DuplicateBuilder
ignoreType(Class<? extends IObject>...) - Method in class omero.gateway.util.Requests.DuplicateBuilder
ignoreType(String...) - Method in class omero.gateway.util.Requests.DuplicateBuilder
IMAGE - Static variable in class omero.gateway.model.PixelsData: Identifies the PixelsI.IMAGE field.
IMAGE_COLUMN_INDEX - Static variable in class omero.gateway.model.TableResult: Identifies the index of the Image column.
IMAGE_LINKS - Static variable in class omero.gateway.model.DatasetData: Identifies the DatasetI.IMAGELINKS field.
ImageAcquisitionData - Class in omero.gateway.model: Object hosting the acquisition metadata.
ImageAcquisitionData(Image) - Constructor for class omero.gateway.model.ImageAcquisitionData: Creates a new instance.
imageCount() - Method in class omero.gateway.model.FolderData: Get the number of images linked to this folder
ImageData - Class in omero.gateway.model: The data that makes up an OME Image along with links to its Pixels, enclosing Datasets, and the Experimenter that owns this Image.
ImageData() - Constructor for class omero.gateway.model.ImageData: Creates a new instance.
ImageData(Image) - Constructor for class omero.gateway.model.ImageData: Creates a new instance.
IN_MEMORY - Static variable in interface omero.gateway.cache.CacheService: Indicates to cache data in memory only.
includeNs(Iterable<String>) - Method in class omero.gateway.util.Requests.ChildOptionBuilder
includeNs(String...) - Method in class omero.gateway.util.Requests.ChildOptionBuilder
includeType(Iterable<String>) - Method in class omero.gateway.util.Requests.ChildOptionBuilder
includeType(Class<? extends IObject>...) - Method in class omero.gateway.util.Requests.ChildOptionBuilder
includeType(String...) - Method in class omero.gateway.util.Requests.ChildOptionBuilder
INSIGHT_PUBLISHED_NS - Static variable in class omero.gateway.model.BooleanAnnotationData: The name space used to indicate that the tag is used a tag set.
INSIGHT_RATING_NS - Static variable in class omero.gateway.model.RatingAnnotationData: The name space used to identify the archived annotation linked to a set of pixels.
INSIGHT_TAGSET_NS - Static variable in class omero.gateway.model.TagAnnotationData: The name space used to indicate that the tag is used a tag set.
INSTITUTION - Static variable in class omero.gateway.model.ExperimenterData: Identifies the ExperimenterI.INSTITUTION field.
InstrumentData - Class in omero.gateway.model: Hosts the instrument used to capture an image.
InstrumentData(Instrument) - Constructor for class omero.gateway.model.InstrumentData: Creates a new instance.
INT16_TYPE - Static variable in class omero.gateway.model.PixelsData: Identifies the type used to store pixel values.
INT32_TYPE - Static variable in class omero.gateway.model.PixelsData: Identifies the type used to store pixel values.
INT8_TYPE - Static variable in class omero.gateway.model.PixelsData: Identifies the type used to store pixel values.
INT_16 - Static variable in class omero.gateway.rnd.DataSink: Identifies the type used to store pixel values.
INT_32 - Static variable in class omero.gateway.rnd.DataSink: Identifies the type used to store pixel values.
INT_8 - Static variable in class omero.gateway.rnd.DataSink: Identifies the type used to store pixel values.
IntConverter - Class in omero.gateway.rnd: Packs a sequence of bytes representing a signed (2's complement) big-endian integer into an integer value of appropriate integer value.
IntConverter() - Constructor for class omero.gateway.rnd.IntConverter
isActive() - Method in class omero.gateway.model.ExperimenterData: Returns true if the experimenter is active, false otherwise.
isAlive(SecurityContext) - Method in class omero.gateway.Gateway: Checks if there is a Connector for a particular SecurityContext
isArchived() - Method in class omero.gateway.model.ImageData: Returns true if the image has been archived, false otherwise.
isAvailable() - Method in class omero.gateway.util.NetworkChecker: Checks the network is available or not.
isCheckNetwork() - Method in class omero.gateway.LoginCredentials
isClientObject() - Method in class omero.gateway.model.ShapeData: Returns true if the object one that has been created client side.
isClientSide() - Method in class omero.gateway.model.ROIData: Returns true if the object a client-side object, false otherwise.
isCompleted() - Method in class omero.gateway.model.TableData
isConnected() - Method in class omero.gateway.Gateway: Check if the Gateway is still connected to the server
isDetectorSettingsDirty() - Method in class omero.gateway.model.ChannelAcquisitionData: Returns true if the detector settings has been updated, false otherwise.
isDirectory() - Method in class omero.gateway.model.FileData: Returns true if the file is a directory, false otherwise.
isDirty() - Method in class omero.gateway.model.DataObject: Returns true if setter value has modified the value of the stored IObject, false otherwise.
isEmpty() - Method in class omero.gateway.model.TableData
isEncryption() - Method in class omero.gateway.LoginCredentials
isError() - Method in class omero.gateway.model.SearchResultCollection
isFontBold() - Method in class omero.gateway.model.ShapeSettingsData: Returns true if it is bold, false otherwise.
isFontItalic() - Method in class omero.gateway.model.ShapeSettingsData: Returns true if it is italic, false otherwise.
isFSImage() - Method in class omero.gateway.model.ImageData: Returns true is the image has been imported the new import strategy known as FS import, false if imported using the previous import approach (data duplication).
isFullAdmin(SecurityContext) - Method in class omero.gateway.facility.AdminFacility: Checks if the currently logged in user has full admin privileges
isFullAdmin(SecurityContext, ExperimenterData) - Method in class omero.gateway.facility.AdminFacility: Checks if a user has full admin privileges
isGroupAnnotate() - Method in class omero.gateway.model.PermissionData: Returns true if the group has annotate access i.e.
isGroupRead() - Method in class omero.gateway.model.PermissionData: Returns true if the group has read access i.e.
isGroupWrite() - Method in class omero.gateway.model.PermissionData: Returns true if the group has write access i.e.
isHidden() - Method in class omero.gateway.model.FileData: Returns true if the file is hidden, false otherwise.
isIdMatch() - Method in class omero.gateway.model.SearchResult: Indicates if this result is an ID match
isImagingEnvironmentDirty() - Method in class omero.gateway.model.ImageAcquisitionData: Returns true if the StageLabel has been updated, false otherwise.
isLDAP() - Method in class omero.gateway.model.ExperimenterData: Returns true if the user is connected via LDAP.
isLifetime() - Method in class omero.gateway.model.ImageData: Returns true if the image is a lifetime image, false otherwise.
isLightSourceSettingsDirty() - Method in class omero.gateway.model.ChannelAcquisitionData: Returns true if the light source settings has been updated, false otherwise.
isLoaded() - Method in class omero.gateway.model.DataObject: Returns true if the object is loaded, false otherwise.
isMemberOfGroup(long) - Method in class omero.gateway.model.ExperimenterData: Checks if supplied group id matches any group to which the current experimenter belongs to.
isMovieFile() - Method in class omero.gateway.model.FileAnnotationData: Returns true if it is a movie file.
isNetworkUp(boolean) - Method in class omero.gateway.Gateway: Checks if the network interface is up.
isNetworkup(boolean) - Method in class omero.gateway.util.NetworkChecker: Returns true if the network is still up, otherwise throws an UnknownHostException.
isObjectiveSettingsDirty() - Method in class omero.gateway.model.ImageAcquisitionData: Returns true if the objective settings has been updated, false otherwise.
isReadOnly() - Method in class omero.gateway.model.ShapeData: Returns true if the object a read-only object, false otherwise.
isSame(long) - Method in class omero.gateway.rnd.DataSink: Returns true if a data source has already been created for the specified pixels set, false otherwise.
isStageLabelDirty() - Method in class omero.gateway.model.ImageAcquisitionData: Returns true if the position has been updated, false otherwise.
isSudo() - Method in class omero.gateway.SecurityContext: Returns true if a session has to be created for another user, false otherwise.
isUserRead() - Method in class omero.gateway.model.PermissionData: Returns true if the user has read access, false otherwise.
isUserWrite() - Method in class omero.gateway.model.PermissionData: Returns true if the user has write access, false otherwise.
isValid() - Method in class omero.gateway.model.SearchParameters: Returns true if the context of the search is valid i.e.
isWorldRead() - Method in class omero.gateway.model.PermissionData: Returns true if the world has read access, false otherwise.
isWorldWrite() - Method in class omero.gateway.model.PermissionData: Returns true if the world has write access, false otherwise.

J

joinSession() - Method in class omero.gateway.Gateway: Deprecated.
This method will be removed in future (never used). Tries to rejoin the session.
JoinSessionCredentials - Class in omero.gateway: Holds all necessary information needed for joining an active OMERO server session
JoinSessionCredentials(String, String) - Constructor for class omero.gateway.JoinSessionCredentials: Creates a new instance
JoinSessionCredentials(String, String, int) - Constructor for class omero.gateway.JoinSessionCredentials: Creates a new instance

L

LASER - Static variable in class omero.gateway.model.LightSourceData: Indicates that the light source is a laser.
lastModified() - Method in class omero.gateway.model.FileData: Returns when the file was last modified.
LASTNAME - Static variable in class omero.gateway.model.ExperimenterData: Identifies the ExperimenterI.LASTNAME field.
lastPlane() - Method in class omero.gateway.model.ROIData: Deprecated.
Will be removed in future. Does not work as expected if the ROI contains shapes which are associated with all planes (Z, C, T == -1)
LEVEL_FIVE - Static variable in class omero.gateway.model.RatingAnnotationData: Indicates the object is rated with five stars.
LEVEL_FOUR - Static variable in class omero.gateway.model.RatingAnnotationData: Indicates the object is rated with four stars.
LEVEL_ONE - Static variable in class omero.gateway.model.RatingAnnotationData: Indicates the object is rated with one star.
LEVEL_THREE - Static variable in class omero.gateway.model.RatingAnnotationData: Indicates the object is rated with three stars.
LEVEL_TWO - Static variable in class omero.gateway.model.RatingAnnotationData: Indicates the object is rated with two stars.
LEVEL_ZERO - Static variable in class omero.gateway.model.RatingAnnotationData: Indicates the object is not rated.
LIGHT_EMITTING_DIODE - Static variable in class omero.gateway.model.LightSourceData: Indicates that the light source is a light emitting diode.
LightPathData - Class in omero.gateway.model: Object hosting a light path.
LightPathData(LightPath) - Constructor for class omero.gateway.model.LightPathData: Creates a new instance.
LightSourceData - Class in omero.gateway.model: Object hosting a light source: filament, arc, laser or light emitting diode
LightSourceData(LightSource) - Constructor for class omero.gateway.model.LightSourceData: Creates a new instance.
LineData - Class in omero.gateway.model: Represents a line in the Euclidean space R².
LineData(Shape) - Constructor for class omero.gateway.model.LineData: Creates a new instance.
LineData() - Constructor for class omero.gateway.model.LineData: Create a new instance of LineData, creating a new LineI Object.
LineData(double, double, double, double) - Constructor for class omero.gateway.model.LineData: Create a new instance of the LineData,
linkAnnotation(IObject, Annotation) - Static method in class omero.gateway.util.ModelMapper: Links the annotation to the passed object.
linkParentToChild(IObject, IObject) - Static method in class omero.gateway.util.ModelMapper: Links the child to its parent.
linkParentToNewChild(IObject, IObject) - Static method in class omero.gateway.util.ModelMapper: Links the newly created child to its parent.
Links - Class in omero.gateway.util: Some helper methods dealing with XXXYYYLinkI IObjects, e.g.
loadFolders(SecurityContext, Collection<Long>) - Method in class omero.gateway.facility.BrowseFacility: Loads the folders for the given Ids.
loadROI(SecurityContext, long) - Method in class omero.gateway.facility.ROIFacility: Loads the ROI
loadROIs(SecurityContext, long) - Method in class omero.gateway.facility.ROIFacility: Loads the ROI related to the specified image.
loadROIs(SecurityContext, long, List<Long>) - Method in class omero.gateway.facility.ROIFacility: Loads the ROI related to the specified image.
loadROIs(SecurityContext, long, List<Long>, long) - Method in class omero.gateway.facility.ROIFacility: Loads the ROI related to the specified image.
loadROIsByPlane(SecurityContext, long, int, int) - Method in class omero.gateway.facility.ROIFacility: Loads the ROI related to the specified image.
loadROIsForFolder(SecurityContext, long, long) - Method in class omero.gateway.facility.ROIFacility: Get all ROIs which are part of a certain folder
LOG_FILE_NS - Static variable in class omero.gateway.model.FileAnnotationData: The name space used to indicate that the FileAnnotation is an import log file.
logDebug(Object, String, Throwable) - Method in class omero.gateway.facility.Facility: Helper method to simplify logging
logError(Object, String, Throwable) - Method in class omero.gateway.facility.Facility: Helper method to simplify logging
LoginCredentials - Class in omero.gateway: Holds all necessary information needed for connecting to an OMERO server
LoginCredentials() - Constructor for class omero.gateway.LoginCredentials: Creates a new instance
LoginCredentials(String[]) - Constructor for class omero.gateway.LoginCredentials: Creates a new instance.
LoginCredentials(String, String, String) - Constructor for class omero.gateway.LoginCredentials: Creates a new instance with the given credentials and default port
LoginCredentials(String, String, String, int) - Constructor for class omero.gateway.LoginCredentials: Creates a new instance with the given credentials
logInfo(Object, String, Throwable) - Method in class omero.gateway.facility.Facility: Helper method to simplify logging
logWarn(Object, String, Throwable) - Method in class omero.gateway.facility.Facility: Helper method to simplify logging
LongAnnotationData - Class in omero.gateway.model: Wraps a long annotation.
LongAnnotationData(long) - Constructor for class omero.gateway.model.LongAnnotationData: Creates a new instance.
LongAnnotationData() - Constructor for class omero.gateway.model.LongAnnotationData: Creates a new instance.
LongAnnotationData(LongAnnotation) - Constructor for class omero.gateway.model.LongAnnotationData: Creates a new instance.
lookupExperimenter(SecurityContext, String) - Method in class omero.gateway.facility.AdminFacility: Returns the experimenter corresponding to the passed name or null.
lookupGroup(SecurityContext, String) - Method in class omero.gateway.facility.AdminFacility: Returns the group corresponding to the passed name or null.

M

MapAnnotationData - Class in omero.gateway.model
MapAnnotationData(MapAnnotation) - Constructor for class omero.gateway.model.MapAnnotationData
MapAnnotationData() - Constructor for class omero.gateway.model.MapAnnotationData
Mask - Class in omero.gateway.util: Provides some utility methods for dealing with mask ROIs.
MaskData - Class in omero.gateway.model: Represents an Mask in the Euclidean space R².
MaskData(Shape) - Constructor for class omero.gateway.model.MaskData: Creates a new instance.
MaskData() - Constructor for class omero.gateway.model.MaskData: Creates a new instance of MaskData.
MaskData(double, double, double, double, byte[]) - Constructor for class omero.gateway.model.MaskData: Creates a new instance of the MaskData.
MEASUREMENT_NS - Static variable in class omero.gateway.model.FileAnnotationData: The name space used to indicate that the FileAnnotation is a Measurement file.
MetadataFacility - Class in omero.gateway.facility: A Facility to access the metadata.
MIDDLENAME - Static variable in class omero.gateway.model.ExperimenterData: Identifies the ExperimenterI.MIDDLENAME field.
MIMETYPE - Static variable in class omero.gateway.util.TIFFFilter: The MIMEType associated to this type of file.
ModelMapper - Class in omero.gateway.util: Helper class to map DataObjects into their corresponding IObjects.
ModelMapper() - Constructor for class omero.gateway.util.ModelMapper
MODULO_NS - Static variable in class omero.gateway.model.XMLAnnotationData: The name space used to identify modulo concept.
move(SecurityContext, List<? extends DataObject>, DataObject, DataObject) - Method in class omero.gateway.facility.DataManagerFacility: Moves DataObjects from one object to another, i.e.
MOVIE_NS - Static variable in class omero.gateway.model.FileAnnotationData: The name space used to indicate that the FileAnnotation is a movie.
MS_EXCEL - Static variable in class omero.gateway.model.FileAnnotationData: Identifies the Excel file formats.
MS_POWER_POINT - Static variable in class omero.gateway.model.FileAnnotationData: Identifies the Power point file formats.
MS_POWER_POINT_SHOW - Static variable in class omero.gateway.model.FileAnnotationData: Identifies the Power point file formats.
MS_POWER_POINT_X - Static variable in class omero.gateway.model.FileAnnotationData: Identifies the Power point file formats.
MS_WORD - Static variable in class omero.gateway.model.FileAnnotationData: Identifies the Word file formats.
MS_WORD_X - Static variable in class omero.gateway.model.FileAnnotationData: Identifies the Word file formats.

N

NAME - Static variable in class omero.gateway.model.DatasetData: Identifies the DatasetI.NAME field.
NAME - Static variable in class omero.gateway.model.GroupData: Identifies the ExperimenterGroupI.NAME field.
NAME - Static variable in class omero.gateway.model.ImageData: Identifies the ImageI.NAME field.
NAME - Static variable in class omero.gateway.model.PlateData: Identifies the PlateI.NAME field.
NAME - Static variable in class omero.gateway.model.ProjectData: Identifies the ProjectI.NAME field.
NAME - Static variable in class omero.gateway.model.ScreenData: Identifies the ScreenI.NAME field.
NetworkChecker - Class in omero.gateway.util: Checks if the network is still up.
NetworkChecker(String, Logger) - Constructor for class omero.gateway.util.NetworkChecker: Creates a new instance.
NO_ERROR - Static variable in class omero.gateway.model.SearchResultCollection: No error
NS_CLIENT_CREATED - Static variable in class omero.gateway.model.MapAnnotationData: The name space used to identify MapAnnotations created be the user
nullDetails() - Method in class omero.gateway.model.DataObject: Returns true if the details are null otherwise false otherwise.
nullSafe(Integer) - Method in class omero.gateway.model.DataObject
nullSafe(RInt) - Method in class omero.gateway.model.DataObject
nullSafe(Long) - Method in class omero.gateway.model.DataObject
nullSafe(Double) - Method in class omero.gateway.model.DataObject
nullSafe(Float) - Method in class omero.gateway.model.DataObject
nullSafe(RFloat) - Method in class omero.gateway.model.DataObject
nullSafe(RDouble) - Method in class omero.gateway.model.DataObject
nullSafe(Length) - Method in class omero.gateway.model.DataObject

O

ObjectiveData - Class in omero.gateway.model: Hosts an objective used to capture an image.
ObjectiveData(Objective) - Constructor for class omero.gateway.model.ObjectiveData: Creates a new instance.
OMENAME - Static variable in class omero.gateway.model.ExperimenterData: Identifies the ExperimenterI.OMENAME field.
omero.gateway - package omero.gateway
omero.gateway.cache - package omero.gateway.cache
omero.gateway.exception - package omero.gateway.exception
omero.gateway.facility - package omero.gateway.facility
omero.gateway.model - package omero.gateway.model
omero.gateway.rnd - package omero.gateway.rnd
omero.gateway.util - package omero.gateway.util
OPERATION_NOT_SUPPORTED - Static variable in exception omero.gateway.exception.RenderingServiceException: Indicates that the error occurred due to an operation not being supported.
option() - Static method in class omero.gateway.util.Requests
ORIGINAL_METADATA_NAME - Static variable in class omero.gateway.model.FileAnnotationData: The default name for the original metadata file.
OTFData - Class in omero.gateway.model: Hosts an OTF.
OTFData(OTF) - Constructor for class omero.gateway.model.OTFData: Creates a new instance.

P

pack(ReadOnlyByteArray, int, int) - Method in class omero.gateway.rnd.DoubleConverter: Implemented as specified by BytesConverter
pack(ReadOnlyByteArray, int, int) - Method in class omero.gateway.rnd.FloatConverter: Implemented as specified by BytesConverter
pack(ReadOnlyByteArray, int, int) - Method in class omero.gateway.rnd.IntConverter: Implemented as specified by BytesConverter
pack(ReadOnlyByteArray, int, int) - Method in class omero.gateway.rnd.UintConverter: Implemented as specified by BytesConverter
parentType(Iterable<String>) - Method in class omero.gateway.util.Requests.FindParentsBuilder
parentType(Class<? extends IObject>...) - Method in class omero.gateway.util.Requests.FindParentsBuilder
parentType(String...) - Method in class omero.gateway.util.Requests.FindParentsBuilder
parsePointsToIntegerList(String) - Method in class omero.gateway.model.ShapeData: Parses the points list from the string to a list of integer objects.
parsePointsToPoint2DList(String) - Method in class omero.gateway.model.ShapeData: Parses the points list from the string to a list of point2d objects.
PDF - Static variable in class omero.gateway.model.FileAnnotationData: Identifies the PDF file formats.
PermissionData - Class in omero.gateway.model: Simple data object to wrap a Permissions instance.
PermissionData() - Constructor for class omero.gateway.model.PermissionData: Creates a new instance.
PermissionData(Permissions) - Constructor for class omero.gateway.model.PermissionData: Creates a new instance.
PERMISSIONS_GROUP_READ - Static variable in class omero.gateway.model.GroupData: Indicates that the group is Group i.e.
PERMISSIONS_GROUP_READ_LINK - Static variable in class omero.gateway.model.GroupData: Indicates that the group is Group i.e.
PERMISSIONS_GROUP_READ_LINK_SHORT_TEXT - Static variable in class omero.gateway.model.GroupData: Indicates that the group is Group i.e.
PERMISSIONS_GROUP_READ_LINK_TEXT - Static variable in class omero.gateway.model.GroupData: Indicates that the group is Group i.e.
PERMISSIONS_GROUP_READ_SHORT_TEXT - Static variable in class omero.gateway.model.GroupData: Indicates that the group is Group i.e.
PERMISSIONS_GROUP_READ_TEXT - Static variable in class omero.gateway.model.GroupData: Indicates that the group is Group i.e.
PERMISSIONS_GROUP_READ_WRITE - Static variable in class omero.gateway.model.GroupData: Indicates that the group is Group i.e.
PERMISSIONS_GROUP_READ_WRITE_SHORT_TEXT - Static variable in class omero.gateway.model.GroupData: Indicates that the group is Group i.e.
PERMISSIONS_GROUP_READ_WRITE_TEXT - Static variable in class omero.gateway.model.GroupData: Indicates that the group is Group i.e.
PERMISSIONS_PRIVATE - Static variable in class omero.gateway.model.GroupData: Indicates that the group is Private i.e.
PERMISSIONS_PRIVATE_TEXT - Static variable in class omero.gateway.model.GroupData: Indicates that the group is Private i.e.
PERMISSIONS_PUBLIC_READ - Static variable in class omero.gateway.model.GroupData: Indicates that the group is Public i.e.
PERMISSIONS_PUBLIC_READ_TEXT - Static variable in class omero.gateway.model.GroupData: Indicates that the group is Public i.e.
PERMISSIONS_PUBLIC_READ_WRITE - Static variable in class omero.gateway.model.GroupData: Indicates that the group is Public i.e.
PERMISSIONS_PUBLIC_READ_WRITE_TEXT - Static variable in class omero.gateway.model.GroupData: Indicates that the group is Public i.e.
PERSISTENCE_ON_DISK - Static variable in interface omero.gateway.cache.CacheService: Indicates to cache data on disk.
PIXELS - Static variable in class omero.gateway.model.ImageData: Identifies the ImageI.PIXELS field.
PixelsData - Class in omero.gateway.model: The data that makes up an OME Pixels object along with a back pointer to the Image that owns this Pixels.
PixelsData() - Constructor for class omero.gateway.model.PixelsData: Creates a new instance.
PixelsData(Pixels) - Constructor for class omero.gateway.model.PixelsData: Creates a new instance.
Plane2D - Class in omero.gateway.rnd: Holds structure used to mapped the raw pixels data.
Plane2D(ReadOnlyByteArray, int, int, int, BytesConverter) - Constructor for class omero.gateway.rnd.Plane2D: Creates a new instance.
PLATE_LINKS - Static variable in class omero.gateway.model.ScreenData: Identifies the ScreenI.PLATELINKS field.
PlateAcquisitionData - Class in omero.gateway.model: The data that makes up an OME PlateAcquisition.
PlateAcquisitionData() - Constructor for class omero.gateway.model.PlateAcquisitionData: Creates a new instance.
PlateAcquisitionData(PlateAcquisition) - Constructor for class omero.gateway.model.PlateAcquisitionData: Creates a new instance.
PlateData - Class in omero.gateway.model: The data that makes up an OME Plate along with links to its contained Well and enclosing Screen as well as the Experimenter that owns this Plate.
PlateData() - Constructor for class omero.gateway.model.PlateData: Creates a new instance.
PlateData(Plate) - Constructor for class omero.gateway.model.PlateData: Creates a new instance.
PointData - Class in omero.gateway.model: Represents a point in the Euclidean space R².
PointData(Shape) - Constructor for class omero.gateway.model.PointData: Creates a new instance.
PointData() - Constructor for class omero.gateway.model.PointData: Creates a new instance of PointData, creating a new pointI Object.
PointData(double, double) - Constructor for class omero.gateway.model.PointData: Create a new instance of the PointData,
PojoMapper - Class in omero.gateway.util: Helper methods to convert IObjects into their corresponding DataObjects.
PojoMapper() - Constructor for class omero.gateway.util.PojoMapper
Pojos - Class in omero.gateway.util: Utility methods for the Pojo DataObjects
Pojos() - Constructor for class omero.gateway.util.Pojos
PolygonData - Class in omero.gateway.model: Represents an Polygon shape in the Euclidean space R².
PolygonData(Shape) - Constructor for class omero.gateway.model.PolygonData: Creates a new instance.
PolygonData() - Constructor for class omero.gateway.model.PolygonData: Creates a new instance of PolygonData.
PolygonData(List<Point2D.Double>) - Constructor for class omero.gateway.model.PolygonData: Create a new instance of the PolylineData, set the points in the polyline.
PolylineData - Class in omero.gateway.model: Represents an Polyline shape in the Euclidean space R².
PolylineData(Shape) - Constructor for class omero.gateway.model.PolylineData: Creates a new instance.
PolylineData() - Constructor for class omero.gateway.model.PolylineData: Creates a new instance of polyline, creating a new PolylineI Object.
PolylineData(List<Point2D.Double>) - Constructor for class omero.gateway.model.PolylineData: Create a new instance of the PolylineData, set the points in the polyline.
PROJECT_LINKS - Static variable in class omero.gateway.model.DatasetData: Identifies the DatasetI.PROJECTLINKS field.
ProjectData - Class in omero.gateway.model: The data that makes up an OME Project along with links to its contained Datasets and the Experimenter that owns this Project.
ProjectData() - Constructor for class omero.gateway.model.ProjectData: Creates a new instance.
ProjectData(Project) - Constructor for class omero.gateway.model.ProjectData: Creates a new instance.
PROP_CONNECTOR_CLOSED - Static variable in class omero.gateway.Gateway: Property to indicate that a Connector has been closed
PROP_CONNECTOR_CREATED - Static variable in class omero.gateway.Gateway: Property to indicate that a Connector has been created
PROP_FACILITY_CLOSED - Static variable in class omero.gateway.Gateway: Property to indicate that a Facility has been closed
PROP_FACILITY_CREATED - Static variable in class omero.gateway.Gateway: Property to indicate that a Facility has been created
PROP_IMPORTSTORE_CLOSED - Static variable in class omero.gateway.Gateway: Property to indicate that an import store has been closed
PROP_IMPORTSTORE_CREATED - Static variable in class omero.gateway.Gateway: Property to indicate that an import store has been created
PROP_RENDERINGENGINE_CLOSED - Static variable in class omero.gateway.Gateway: Property to indicate that a rendering engine has been closed
PROP_RENDERINGENGINE_CREATED - Static variable in class omero.gateway.Gateway: Property to indicate that a rendering engine has been created
PROP_SESSION_CLOSED - Static variable in class omero.gateway.Gateway: Property to indicate that a session has been closed
PROP_SESSION_CREATED - Static variable in class omero.gateway.Gateway: Property to indicate that a session has been created
PROP_SESSION_DETACHED - Static variable in class omero.gateway.Gateway: Property to indicate that client got detached from a session
PROP_STATEFUL_SERVICE_CLOSED - Static variable in class omero.gateway.Gateway: Property to indicate that a stateful service has been closed
PROP_STATEFUL_SERVICE_CREATED - Static variable in class omero.gateway.Gateway: Property to indicate that a stateful service has been created
PROP_STATELESS_SERVICE_CREATED - Static variable in class omero.gateway.Gateway: Property to indicate that a stateless service has been created
PyTablesUtils - Class in omero.gateway.util: Collection of utility classes to convert OMERO tables.
PyTablesUtils() - Constructor for class omero.gateway.util.PyTablesUtils

Q

query(SecurityContext, long, String) - Method in class omero.gateway.facility.TablesFacility: Perform a query on the table
query(SecurityContext, long, String, long, long, long) - Method in class omero.gateway.facility.TablesFacility: Perform a query on the table

R

RatingAnnotationData - Class in omero.gateway.model: Annotation used to rate an object.
RatingAnnotationData() - Constructor for class omero.gateway.model.RatingAnnotationData: Creates a new instance of value LEVEL_ZERO.
RatingAnnotationData(int) - Constructor for class omero.gateway.model.RatingAnnotationData: Creates a new instance.
RatingAnnotationData(LongAnnotation) - Constructor for class omero.gateway.model.RatingAnnotationData: Creates a new instance.
RawDataFacility - Class in omero.gateway.facility: A Facility for accessing raw data
READONLY_FLAG - Static variable in class omero.gateway.model.ShapeData: Flag stating that the ROI is read only.
RectangleData - Class in omero.gateway.model: Represents a rectangle in the Euclidean space R².
RectangleData(Shape) - Constructor for class omero.gateway.model.RectangleData: Creates a new instance.
RectangleData() - Constructor for class omero.gateway.model.RectangleData: Creates a new instance with a default rectangle.
RectangleData(double, double, double, double) - Constructor for class omero.gateway.model.RectangleData: Creates a new instance of the RectangleData.
referenceType(Iterable<String>) - Method in class omero.gateway.util.Requests.DuplicateBuilder
referenceType(Class<? extends IObject>...) - Method in class omero.gateway.util.Requests.DuplicateBuilder
referenceType(String...) - Method in class omero.gateway.util.Requests.DuplicateBuilder
relativeComplement(Collection<T>, Collection<T>) - Static method in class omero.gateway.util.Pojos: Get the relative complement of coll1 in coll2
removeAdminPrivileges(SecurityContext, ExperimenterData, Collection<String>) - Method in class omero.gateway.facility.AdminFacility: Revoke admin privileges for a user
removeCache(int) - Method in interface omero.gateway.cache.CacheService: Removes the cache corresponding to the passed id.
removeIObject(IObject, IObject) - Static method in class omero.gateway.util.ModelMapper: Unlinks the specified child and the parent and returns the updated child IObject.
removePropertyChangeListener(PropertyChangeListener) - Method in class omero.gateway.facility.Facility: Removes a PropertyChangeListener (Pass null to remove all PropertyChangeListeners)
removePropertyChangeListener(PropertyChangeListener) - Method in class omero.gateway.Gateway: Removes a PropertyChangeListener
removeRoisFromFolders(SecurityContext, long, Collection<ROIData>, Collection<FolderData>) - Method in class omero.gateway.facility.ROIFacility: Remove the ROIs from the folders
removeShapeData(ShapeData) - Method in class omero.gateway.model.ROIData: Removes the ShapeData object from ROIData.
RenderingServiceException - Exception in omero.gateway.exception: Reports an error occurred while trying to render a plane.
RenderingServiceException() - Constructor for exception omero.gateway.exception.RenderingServiceException: Creates a new exception.
RenderingServiceException(String) - Constructor for exception omero.gateway.exception.RenderingServiceException: Constructs a new exception with the specified detail message.
RenderingServiceException(Throwable) - Constructor for exception omero.gateway.exception.RenderingServiceException: Constructs a new exception with the specified cause.
RenderingServiceException(String, Throwable) - Constructor for exception omero.gateway.exception.RenderingServiceException: Constructs a new exception with the specified detail message and cause.
request(GraphModify2) - Method in class omero.gateway.util.Requests.SkipHeadBuilder
request(Class<? extends GraphModify2>) - Method in class omero.gateway.util.Requests.SkipHeadBuilder
Requests - Class in omero.gateway.util: A utility class of factory methods with various signatures for clients to use in generating requests for graph operations.
Requests() - Constructor for class omero.gateway.util.Requests
Requests.Chgrp2Builder - Class in omero.gateway.util: A builder for Chgrp2 instances.
Requests.ChildOptionBuilder - Class in omero.gateway.util: A builder for ChildOption instances.
Requests.Chmod2Builder - Class in omero.gateway.util: A builder for Chmod2 instances.
Requests.Chown2Builder - Class in omero.gateway.util: A builder for Chown2 instances.
Requests.Delete2Builder - Class in omero.gateway.util: A builder for Delete2 instances.
Requests.DiskUsageBuilder - Class in omero.gateway.util: A builder for DiskUsage2 instances.
Requests.DuplicateBuilder - Class in omero.gateway.util: A builder for Duplicate instances.
Requests.FindChildrenBuilder - Class in omero.gateway.util: A builder for FindChildren instances.
Requests.FindParentsBuilder - Class in omero.gateway.util: A builder for FindParents instances.
Requests.SkipHeadBuilder - Class in omero.gateway.util: A builder for SkipHead instances.
ROI_COLUMN_INDEX - Static variable in class omero.gateway.model.TableResult: Identifies the index of the ROI column.
ROIComponent - Class in omero.gateway.util: Component hosting the ROI.
ROIComponent(long) - Constructor for class omero.gateway.util.ROIComponent: Instantiate the ROIComponent.
ROICoordinate - Class in omero.gateway.model: Defines a plane.
ROICoordinate() - Constructor for class omero.gateway.model.ROICoordinate: Creates a default instance.
ROICoordinate(int, int) - Constructor for class omero.gateway.model.ROICoordinate: Creates a new instance.
roiCount() - Method in class omero.gateway.model.FolderData: Get the number of ROIs linked to this folder
ROIData - Class in omero.gateway.model: Converts the ROI object.
ROIData(Roi) - Constructor for class omero.gateway.model.ROIData: Creates a new instance.
ROIData() - Constructor for class omero.gateway.model.ROIData: Create a new instance of an ROIData object.
ROIFacility - Class in omero.gateway.facility: A Facility for ROI.
ROIResult - Class in omero.gateway.model: Hosts the results of a call loading the ROI.
ROIResult(Collection<ROIData>) - Constructor for class omero.gateway.model.ROIResult: Creates a new instance.
ROIResult(Collection<ROIData>, long) - Constructor for class omero.gateway.model.ROIResult: Creates a new instance.
ROIResult(Collection<ROIData>, long, Object) - Constructor for class omero.gateway.model.ROIResult: Creates a new instance.
RTF - Static variable in class omero.gateway.model.FileAnnotationData: Identifies the RTF file formats.
runScript(SecurityContext, long, Map<String, RType>) - Method in class omero.gateway.Gateway: Run a script on the server

S

saveAndReturnObject(SecurityContext, IObject, Map) - Method in class omero.gateway.facility.DataManagerFacility: Updates the specified object.
saveAndReturnObject(SecurityContext, DataObject) - Method in class omero.gateway.facility.DataManagerFacility: Updates the specified object.
saveAndReturnObject(SecurityContext, IObject) - Method in class omero.gateway.facility.DataManagerFacility: Updates the specified object.
saveAndReturnObject(SecurityContext, IObject, Map, String) - Method in class omero.gateway.facility.DataManagerFacility: Updates the specified object.
saveAndReturnObject(SecurityContext, DataObject, String) - Method in class omero.gateway.facility.DataManagerFacility: Updates the specified object.
saveAndReturnObject(SecurityContext, IObject, String) - Method in class omero.gateway.facility.DataManagerFacility: Updates the specified object.
saveAndReturnObject(SecurityContext, List<IObject>, Map, String) - Method in class omero.gateway.facility.DataManagerFacility: Updates the specified object.
saveROIs(SecurityContext, long, Collection<ROIData>) - Method in class omero.gateway.facility.ROIFacility: Save the ROI for the image to the server.
saveROIs(SecurityContext, long, long, Collection<ROIData>) - Method in class omero.gateway.facility.ROIFacility: Save the ROI for the image to the server.
SCREEN_LINKS - Static variable in class omero.gateway.model.PlateData: Identifies the PlateI.SCREENLINKS field.
ScreenData - Class in omero.gateway.model: The data that makes up an OME Screen along with links to its contained Plates and the Experimenter that owns this Screen.
ScreenData() - Constructor for class omero.gateway.model.ScreenData: Creates a new instance.
ScreenData(Screen) - Constructor for class omero.gateway.model.ScreenData: Creates a new instance.
search(SecurityContext, SearchParameters) - Method in class omero.gateway.facility.SearchFacility: Searches for data.
SearchFacility - Class in omero.gateway.facility: A Facility for performing searches
SearchParameters - Class in omero.gateway.model: Holds all parameters needed to perform a search operation; See SearchFacility.search(omero.gateway.SecurityContext, SearchParameters)
SearchParameters(Set<SearchScope>, List<Class<? extends DataObject>>, String) - Constructor for class omero.gateway.model.SearchParameters: Creates a new instance.
SearchResult - Class in omero.gateway.model: Encapsulates a single object found by a search together with the search scope (name, description, etc.) it was found with.
SearchResult() - Constructor for class omero.gateway.model.SearchResult: Create a new instance
SearchResult(int, Class<? extends DataObject>, long, long) - Constructor for class omero.gateway.model.SearchResult: Create a new instance
SearchResultCollection - Class in omero.gateway.model: Holds the results of a search; a collection of SearchResults
SearchResultCollection() - Constructor for class omero.gateway.model.SearchResultCollection
SearchScope - Enum in omero.gateway.model: Defines the scope of a search, i.e.
SecurityContext - Class in omero.gateway: Hosts information required to access correct connector.
SecurityContext(long) - Constructor for class omero.gateway.SecurityContext: Creates a new instance.
ServerInformation - Class in omero.gateway: Holds hostname and port of an OMERO server
ServerInformation() - Constructor for class omero.gateway.ServerInformation: Creates an empty instance
ServerInformation(String, int) - Constructor for class omero.gateway.ServerInformation: Creates a new instance
setAdminPrivileges(SecurityContext, ExperimenterData, Collection<String>) - Method in class omero.gateway.facility.AdminFacility: Set the admin privileges of a certain user (see omero.model.enums)
setAirPressure(Pressure) - Method in class omero.gateway.model.ImageAcquisitionData: Sets the air pressure.
setAllPixels(List<PixelsData>) - Method in class omero.gateway.model.ImageData: Sets the set of pixels related to this image.
setAlpha(Integer) - Method in class omero.gateway.model.WellData: Sets the alpha component of the color associated to the well.
setAnnotations(Set) - Method in class omero.gateway.model.DatasetData: Sets the annotations related to this dataset.
setAnnotations(Set) - Method in class omero.gateway.model.ImageData: Sets the image's annotations.
setApplicationName(String) - Method in class omero.gateway.LoginCredentials: Set the application name
setBit(byte[], int, int) - Method in class omero.gateway.model.MaskData: Sets the bit value in a byte array at position bit to be the value value.
setBlue(Integer) - Method in class omero.gateway.model.WellData: Sets the blue component of the color associated to the well.
setC(int) - Method in class omero.gateway.model.ShapeData: Sets the channel.
setCacheEntries(int, int) - Method in interface omero.gateway.cache.CacheService: Resets the number of items in memory of the cache, when a new cache is created or deleted.
setCheckNetwork(boolean) - Method in class omero.gateway.LoginCredentials: Enable/Disable network checks
setCheckVersion(boolean) - Method in class omero.gateway.LoginCredentials: Enable/Disable version check
setClientObject(boolean) - Method in class omero.gateway.model.ShapeData: Sets to true if the object one that has been created client side, false otherwise.
setClientSide(boolean) - Method in class omero.gateway.model.ROIData: Sets the flag indicating if the object is a client-side object or not.
setCo2Percent(double) - Method in class omero.gateway.model.ImageAcquisitionData: Sets the co2 level.
setCompleted() - Method in class omero.gateway.model.TableData: Manually set completed state (sets the TableData.numberOfRows to the last row in the TableData.data array)
setCompression(float) - Method in class omero.gateway.LoginCredentials: Sets the compression level
setCompression(float) - Method in class omero.gateway.SecurityContext: Set the compression level
setContent(Object) - Method in class omero.gateway.model.AnnotationData: Sets the annotation value.
setContent(Object) - Method in class omero.gateway.model.BooleanAnnotationData: Sets the text annotation.
setContent(Object) - Method in class omero.gateway.model.DoubleAnnotationData: Sets the text annotation.
setContent(Object) - Method in class omero.gateway.model.FileAnnotationData: Sets the text annotation.
setContent(Object) - Method in class omero.gateway.model.LongAnnotationData: Sets the text annotation.
setContent(Object) - Method in class omero.gateway.model.MapAnnotationData
setContent(Object) - Method in class omero.gateway.model.RatingAnnotationData: Sets the text annotation.
setContent(Object) - Method in class omero.gateway.model.TagAnnotationData: Sets the text annotation.
setContent(Object) - Method in class omero.gateway.model.TermAnnotationData: Sets the text annotation.
setContent(Object) - Method in class omero.gateway.model.TextualAnnotationData: Sets the text annotation.
setContent(Object) - Method in class omero.gateway.model.TimeAnnotationData: Sets the time annotation.
setContent(Object) - Method in class omero.gateway.model.XMLAnnotationData: Sets the annotation.
setContrastMethod(ContrastMethod) - Method in class omero.gateway.model.ChannelData: Sets the contrast method value.
setCorrectionCollar(double) - Method in class omero.gateway.model.ImageAcquisitionData: Sets the correction of the objective.
setDataObjects(Set<DataObject>) - Method in class omero.gateway.model.TagAnnotationData: Sets the collection of data objects related to that tag.
setDatasets(Set) - Method in class omero.gateway.model.ImageData: Sets the datasets containing the image.
setDatasets(Set<DatasetData>) - Method in class omero.gateway.model.ProjectData: Sets the datasets contained in this project.
setDataValue(double) - Method in class omero.gateway.model.DoubleAnnotationData: Sets the rating value.
setDataValue(long) - Method in class omero.gateway.model.LongAnnotationData: Sets the rating value.
setDateType(int) - Method in class omero.gateway.model.SearchParameters
setDefaultPixels(PixelsData) - Method in class omero.gateway.model.ImageData: Sets the default set of pixels.
setDefaultSample(int) - Method in class omero.gateway.model.PlateData: Sets the default sample.
setDescription(String) - Method in class omero.gateway.model.AnnotationData: Sets the description of the underlying Annotation instance.
setDescription(String) - Method in class omero.gateway.model.DatasetData: Sets the description of the dataset.
setDescription(String) - Method in class omero.gateway.model.FileAnnotationData: Sets the description of the annotation.
setDescription(String) - Method in class omero.gateway.model.FileData: Sets the description.
setDescription(String) - Method in class omero.gateway.model.FolderData: Set the description of the Folder
setDescription(String) - Method in class omero.gateway.model.GroupData: Sets the name of the group.
setDescription(String) - Method in class omero.gateway.model.ImageData: Sets the description of the image.
setDescription(String) - Method in class omero.gateway.model.PlateAcquisitionData: Sets the name of the acquisition.
setDescription(String) - Method in class omero.gateway.model.PlateData: Sets the description of the plate.
setDescription(String) - Method in class omero.gateway.model.ProjectData: Sets the description of the project.
setDescription(String) - Method in class omero.gateway.model.ScreenData: Sets the description of the screen.
setDescription(String) - Method in class omero.gateway.model.TableDataColumn: Set the description
setDescription(String) - Method in class omero.gateway.model.XMLAnnotationData: Sets the description of the annotation.
setDetectorSettingBinning(Binning) - Method in class omero.gateway.model.ChannelAcquisitionData: Sets the detector's binning.
setDetectorSettingOffset(double) - Method in class omero.gateway.model.ChannelAcquisitionData: Sets the detector's setting offset.
setDetectorSettingsGain(double) - Method in class omero.gateway.model.ChannelAcquisitionData: Sets the detector setting's gain.
setDetectorSettingsReadOutRate(Frequency) - Method in class omero.gateway.model.ChannelAcquisitionData: Sets the detector setting's read out rate.
setDetectorSettingsVoltage(ElectricPotential) - Method in class omero.gateway.model.ChannelAcquisitionData: Sets the detector setting's voltage.
setDirty(boolean) - Method in class omero.gateway.model.DataObject: Sets to true if the value has been modified, otherwise.
setDirty(boolean) - Method in class omero.gateway.model.ShapeData: Sets to true if the figure been changed from the server side version, false otherwise.
setEmail(String) - Method in class omero.gateway.model.ExperimenterData: Sets the e-mail of the experimenter.
setEmissionWavelength(Length) - Method in class omero.gateway.model.ChannelData: Sets the emission wavelength.
setEncryption(boolean) - Method in class omero.gateway.LoginCredentials: Enable/Disable encryption
setError(int) - Method in class omero.gateway.model.SearchResultCollection: Set the error state
setExcitationWavelength(Length) - Method in class omero.gateway.model.ChannelData: Sets the excitation wavelength.
setExperimenter(ExperimenterData) - Method in class omero.gateway.SecurityContext: Sets the experimenter
setExperimenters(Set<ExperimenterData>) - Method in class omero.gateway.model.GroupData: Sets the experimenters contained in this group.
setExternalDescription(String) - Method in class omero.gateway.model.WellData: Sets the external description of the well.
setExternalIdentifier(String) - Method in class omero.gateway.model.PlateData: Sets the external identifier.
setFill(Color) - Method in class omero.gateway.model.ShapeSettingsData: Set the fill color.
setFillRule(String) - Method in class omero.gateway.model.ShapeSettingsData: Set the fill rule.
setFirstName(String) - Method in class omero.gateway.model.ExperimenterData: Sets the first name of the experimenter.
setFluor(String) - Method in class omero.gateway.model.ChannelData: Sets the fluor.
setFolder(Folder) - Method in class omero.gateway.model.FolderData: Set the Folder
setFolders(Collection<FolderData>) - Method in class omero.gateway.model.ROIResult: Sets the available folders
setFontFamily(String) - Method in class omero.gateway.model.ShapeSettingsData: Returns the stroke.
setFontSize(Length) - Method in class omero.gateway.model.ShapeSettingsData: Set the size of the font.
setFontStyle(String) - Method in class omero.gateway.model.ShapeSettingsData: Sets the style of the font.
setGreen(Integer) - Method in class omero.gateway.model.WellData: Sets the green component of the color associated to the well.
setGroupAnnotate(boolean) - Method in class omero.gateway.model.PermissionData: Sets to true if the group has annotate access, false otherwise.
setGroupID(long) - Method in class omero.gateway.LoginCredentials: Sets the groupID to use for the connection
setGroupId(long) - Method in class omero.gateway.model.SearchParameters
setGroupId(long) - Method in class omero.gateway.model.SearchResult: Set the group id of the object
setGroupRead(boolean) - Method in class omero.gateway.model.PermissionData: Sets to true if the group has read access, false otherwise.
setGroups(List<GroupData>) - Method in class omero.gateway.model.ExperimenterData: Sets the groups the experimenter is a member of.
setGroupWrite(boolean) - Method in class omero.gateway.model.PermissionData: Sets to true if the group has write access, false otherwise.
setHeight(double) - Method in class omero.gateway.model.MaskData: Sets the height of an untransformed mask.
setHeight(double) - Method in class omero.gateway.model.RectangleData: Sets the height of an untransformed rectangle.
setHostname(String) - Method in class omero.gateway.ServerInformation: Set the hostname
setHumidity(double) - Method in class omero.gateway.model.ImageAcquisitionData: Sets the humidity.
setId(long) - Method in class omero.gateway.model.DataObject: Sets the database id.
setIdMatch(boolean) - Method in class omero.gateway.model.SearchResult: Set to true if this result is an ID match.
setIllumination(Illumination) - Method in class omero.gateway.model.ChannelData: Sets the illumination value.
setImage(ImageData) - Method in class omero.gateway.model.PixelsData: Sets the image linked to this pixels' set.
setImage(Image) - Method in class omero.gateway.model.ROIData: Sets the image for the ROI.
setImage(ImageData) - Method in class omero.gateway.model.WellSampleData: Sets the image linked to this well sample.
setImages(Set<ImageData>) - Method in class omero.gateway.model.DatasetData: Sets the images contained in this dataset.
setIndex(int) - Method in exception omero.gateway.exception.RenderingServiceException: Sets the index indicating if the error occurred due to a network failure.
setIndex(int) - Method in class omero.gateway.model.TableDataColumn: Set the index
setIndexes(Map<Integer, Integer>) - Method in class omero.gateway.model.TableResult: Sets the indexes.
setInstitution(String) - Method in class omero.gateway.model.ExperimenterData: Sets the institution where the experimenter works.
setLabelName(String) - Method in class omero.gateway.model.ImageAcquisitionData: Sets the name of the stage label.
setLastName(String) - Method in class omero.gateway.model.ExperimenterData: Sets the last name of the experimenter.
setLightSettingsAttenuation(double) - Method in class omero.gateway.model.ChannelAcquisitionData: Sets the attenuation of the light settings.
setLightSettingsWavelength(Length) - Method in class omero.gateway.model.ChannelAcquisitionData: Sets the wavelength of the light source.
setLightSource(LightSourceData) - Method in class omero.gateway.model.ChannelAcquisitionData: Sets the light source associated to the settings.
setMarkerEnd(String) - Method in class omero.gateway.model.ShapeSettingsData: Sets the marker end.
setMarkerStart(String) - Method in class omero.gateway.model.ShapeSettingsData: Sets the marker start.
setMask(byte[]) - Method in class omero.gateway.model.MaskData: Sets the mask image.
setMask(BufferedImage) - Method in class omero.gateway.model.MaskData: Sets the mask from the bufferedImage.
setMask(int[]) - Method in class omero.gateway.model.MaskData: Set the mask
setMask(int[][]) - Method in class omero.gateway.model.MaskData: Set the mask
setMask(boolean[]) - Method in class omero.gateway.model.MaskData: Set the mask
setMask(boolean[][]) - Method in class omero.gateway.model.MaskData: Set the mask
setMedium(Medium) - Method in class omero.gateway.model.ImageAcquisitionData: Sets the medium of the objective.
setMiddleName(String) - Method in class omero.gateway.model.ExperimenterData: Sets the middle name of the experimenter.
setMode(AcquisitionMode) - Method in class omero.gateway.model.ChannelData: Sets the acquisition mode value.
setName(String) - Method in class omero.gateway.model.ChannelData: Sets the name of the logical channel.
setName(String) - Method in class omero.gateway.model.DatasetData: Sets the name of the dataset.
setName(String) - Method in class omero.gateway.model.FolderData: Set the name of the Folder
setName(String) - Method in class omero.gateway.model.GroupData: Sets the name of the group.
setName(String) - Method in class omero.gateway.model.ImageData: Sets the name of the image.
setName(String) - Method in class omero.gateway.model.PlateAcquisitionData: Sets the name of the acquisition.
setName(String) - Method in class omero.gateway.model.PlateData: Sets the name of the plate.
setName(String) - Method in class omero.gateway.model.ProjectData: Sets the name of the project.
setName(String) - Method in class omero.gateway.model.ScreenData: Sets the name of the screen.
setName(String) - Method in class omero.gateway.model.TableDataColumn: Set the header
setNameSpace(String) - Method in class omero.gateway.model.AnnotationData: Sets the name space of the underlying Annotation instance.
setNDFilter(double) - Method in class omero.gateway.model.ChannelData: Sets the ND filter.
setNumberOfRows(long) - Method in class omero.gateway.model.TableData: Set the total number of rows in the original table
setObject(DataObject) - Method in class omero.gateway.model.SearchResult: Set the found object
setObjectId(long) - Method in class omero.gateway.model.SearchResult: Set the Id of the found object
setObjects(IObject, DataObject, DataObject) - Static method in class omero.gateway.util.Links: Set the parent, child or both of an existing link
setOffset(long) - Method in class omero.gateway.model.TableData: Set the row offset (if this TableData represents only a subset of the original table)
setOriginalFileId(long) - Method in class omero.gateway.model.TableData: Set the originalfile id
setParentFilePath(String, int) - Method in class omero.gateway.model.ImageData: Sets the path to the file hosting the image.
setParentFolder(Folder) - Method in class omero.gateway.model.FolderData: Set the the parent folder
setPassword(String) - Method in class omero.gateway.UserCredentials: Sets the password
setPathToFile(String) - Method in class omero.gateway.model.ImageData: Sets the path to the file.
setPinholeSize(Length) - Method in class omero.gateway.model.ChannelData: Sets the pinhole size.
setPixelSizeX(Length) - Method in class omero.gateway.model.PixelsData: Sets the dimension of a pixel along the X-axis
setPixelSizeY(Length) - Method in class omero.gateway.model.PixelsData: Sets the dimension of a pixel along the Y-axis.
setPixelSizeZ(Length) - Method in class omero.gateway.model.PixelsData: Sets the dimension of a pixel along the Z-axis
setPlateAcquisition(Set<PlateAcquisitionData>) - Method in class omero.gateway.model.PlateData: Sets the plate acquisition linked to the plate.
setPlates(Set<PlateData>) - Method in class omero.gateway.model.ScreenData: Sets the plates contained in this screen.
setPockelCell(int) - Method in class omero.gateway.model.ChannelData: Sets the pockel cell.
setPoints(List<Point2D.Double>) - Method in class omero.gateway.model.PolygonData: Sets the points in the polygon.
setPoints(List<Point2D.Double>) - Method in class omero.gateway.model.PolylineData: Sets the points in the polyline.
setPort(int) - Method in class omero.gateway.ServerInformation: Set the port
setPositionX(Length) - Method in class omero.gateway.model.ImageAcquisitionData: Sets the x-position.
setPositionY(Length) - Method in class omero.gateway.model.ImageAcquisitionData: Sets the y-position.
setPositionZ(Length) - Method in class omero.gateway.model.ImageAcquisitionData: Sets the z-position.
setProjects(Set<ProjectData>) - Method in class omero.gateway.model.DatasetData: Sets the projects containing the dataset.
setProtocolDescription(String) - Method in class omero.gateway.model.ScreenData: Sets the description of the protocol.
setProtocolIdentifier(String) - Method in class omero.gateway.model.ScreenData: Sets the identifier of the protocol.
setRadiusX(double) - Method in class omero.gateway.model.EllipseData: Sets the radius along the X-axis.
setRadiusY(double) - Method in class omero.gateway.model.EllipseData: Sets the radius along the Y-axis.
setRating(int) - Method in class omero.gateway.model.RatingAnnotationData: Sets the rating value.
setReadOnly(boolean) - Method in class omero.gateway.model.ShapeData: Sets to true if the object is a read-only object, false otherwise.
setReagentSetDescripion(String) - Method in class omero.gateway.model.ScreenData: Sets the identifier of the reagent.
setReagentSetIdentifier(String) - Method in class omero.gateway.model.ScreenData: Sets the identifier of the reagent.
setRed(Integer) - Method in class omero.gateway.model.WellData: Sets the red component of the color associated to the well.
setReference(OriginalFile) - Method in class omero.gateway.model.ImageData: Sets the reference to the file to register.
setRefPlateId(long) - Method in class omero.gateway.model.PlateAcquisitionData: Sets the id of the plate this plate acquisition is for.
setRefractiveIndex(double) - Method in class omero.gateway.model.ImageAcquisitionData: Sets the refractive index of the objective.
setRegisteredFile(OriginalFile) - Method in class omero.gateway.model.FileData: Sets the registered file.
setRegisteredFile(Image) - Method in class omero.gateway.model.ImageData: Sets the registered file.
setRepositoryPath(String) - Method in class omero.gateway.model.FileData: Sets the path to the parent.
setResult(Object) - Method in class omero.gateway.model.ROIResult: Sets the results.
setROICoordinate(ROICoordinate) - Method in class omero.gateway.model.ShapeData: Sets the ROICoordinate for the ShapeData.
setScopeId(int) - Method in class omero.gateway.model.SearchResult: Set the id of the search scope, e.g.
setScreens(Set<ScreenData>) - Method in class omero.gateway.model.PlateData: Sets the screens containing the plate.
setServerInformation(ServerInformation) - Method in class omero.gateway.SecurityContext: Sets the ServerInformation
setShapeSettings(Shape) - Method in class omero.gateway.model.ShapeData: Set the settings associated to the shape.
setSizeC(int) - Method in class omero.gateway.model.PixelsData: Sets the number of channels.
setSizeT(int) - Method in class omero.gateway.model.PixelsData: Sets the number of time-points.
setSizeX(int) - Method in class omero.gateway.model.PixelsData: Sets the number of pixels along the X-axis.
setSizeY(int) - Method in class omero.gateway.model.PixelsData: Sets the number of pixels along the Y-axis.
setSizeZ(int) - Method in class omero.gateway.model.PixelsData: Sets the number of pixels along the Z-axis.
setStatus(String) - Method in class omero.gateway.model.PlateData: Sets the status.
setStatus(String) - Method in class omero.gateway.model.WellData: Sets the status of the well.
setStroke(Color) - Method in class omero.gateway.model.ShapeSettingsData: Set the stroke color.
setStrokeDashArray(double[]) - Method in class omero.gateway.model.ShapeSettingsData: Set the stroke dashes.
setStrokeWidth(Length) - Method in class omero.gateway.model.ShapeSettingsData: Set the stroke width.
setT(int) - Method in class omero.gateway.model.ShapeData: Sets the time-point.
setTableID(long) - Method in class omero.gateway.model.TableResult: Sets the id of the table.
setTagDescription(String) - Method in class omero.gateway.model.TagAnnotationData: Sets the description of the tag.
setTagDescriptions(List<TextualAnnotationData>) - Method in class omero.gateway.model.TagAnnotationData: Sets the tag's descriptions.
setTagValue(String) - Method in class omero.gateway.model.TagAnnotationData: Sets the value of the tag.
setTemperature(Temperature) - Method in class omero.gateway.model.ImageAcquisitionData: Sets the temperature.
setTerm(String) - Method in class omero.gateway.model.TermAnnotationData: Sets the term.
setTermDescription(String) - Method in class omero.gateway.model.TermAnnotationData: Sets the description of the tag.
setText(String) - Method in class omero.gateway.model.EllipseData: Sets the text of the shape.
setText(String) - Method in class omero.gateway.model.LineData: Sets the text of the shape.
setText(String) - Method in class omero.gateway.model.MaskData: Sets the text of the shape.
setText(String) - Method in class omero.gateway.model.PointData: Sets the text of the shape.
setText(String) - Method in class omero.gateway.model.PolygonData: Sets the text of the shape.
setText(String) - Method in class omero.gateway.model.PolylineData: Sets the text of the shape.
setText(String) - Method in class omero.gateway.model.RectangleData: Sets the text of the shape.
setText(String) - Method in class omero.gateway.model.TextData: Sets the text of the shape.
setText(String) - Method in class omero.gateway.model.TextualAnnotationData: Sets the text.
setText(String) - Method in class omero.gateway.model.XMLAnnotationData: Sets the text value.
setTimeInterval(Timestamp, Timestamp, int) - Method in class omero.gateway.model.SearchParameters: Sets the time interval.
settings - Variable in class omero.gateway.model.ShapeData: The representation of the shape.
setTransform(AffineTransform) - Method in class omero.gateway.model.ShapeData: Sets the Affine transform of the shape.
setType(Class<? extends DataObject>) - Method in class omero.gateway.model.SearchResult: Set the type (class) of objects to search for see DataObject
setType(Class<?>) - Method in class omero.gateway.model.TableDataColumn: Set the data type
setUserId(long) - Method in class omero.gateway.model.SearchParameters
setUsername(String) - Method in class omero.gateway.UserCredentials: Sets the username (or session ID)
setUserRead(boolean) - Method in class omero.gateway.model.PermissionData: Sets to true if the user has read access, false otherwise.
setUserWrite(boolean) - Method in class omero.gateway.model.PermissionData: Sets to true if the user has write access, false otherwise.
setUuid(String) - Method in class omero.gateway.model.ROIData: Set the UUID
setValue(boolean) - Method in class omero.gateway.model.BooleanAnnotationData: Returns the text.
setValue(IObject) - Method in class omero.gateway.model.DataObject: Sets the IObject.
setVersion(int) - Method in class omero.gateway.model.DataObject: Sets the version of the object if it is immutable.
setWellSamples(List<WellSampleData>) - Method in class omero.gateway.model.WellData: Sets the well samples linked to the well.
setWellType(String) - Method in class omero.gateway.model.WellData: Sets a human readable identifier for the screening status e.g.
setWidth(double) - Method in class omero.gateway.model.MaskData: Sets the width of an untransformed mask.
setWidth(double) - Method in class omero.gateway.model.RectangleData: Sets width of an untransformed rectangle.
setWorldRead(boolean) - Method in class omero.gateway.model.PermissionData: Sets to true if the world has read access, false otherwise.
setWorldWrite(boolean) - Method in class omero.gateway.model.PermissionData: Sets to true if the world has write access, false otherwise.
setX(double) - Method in class omero.gateway.model.EllipseData: Sets the x-coordinate of the center of the ellipse.
setX(double) - Method in class omero.gateway.model.MaskData: Sets the x-coordinate top-left corner of an untransformed mask.
setX(double) - Method in class omero.gateway.model.PointData: set the x-coordinate of the shape.
setX(double) - Method in class omero.gateway.model.RectangleData: Sets the x-coordinate of the top-left corner of an untransformed rectangle.
setX(double) - Method in class omero.gateway.model.TextData: Sets the x-coordinate of the text field.
setX1(double) - Method in class omero.gateway.model.LineData: Set the x-coordinate of the starting point of an untransformed line.
setX2(double) - Method in class omero.gateway.model.LineData: Set the x-coordinate of the end point of an untransformed line.
setY(double) - Method in class omero.gateway.model.EllipseData: Sets the y-coordinate of the center of the ellipse.
setY(double) - Method in class omero.gateway.model.MaskData: Sets the y-coordinate top-left corner of an untransformed mask.
setY(double) - Method in class omero.gateway.model.PointData: set the y-coordinate of the shape.
setY(double) - Method in class omero.gateway.model.RectangleData: Sets the y-coordinate of the top-left corner of an untransformed rectangle.
setY(double) - Method in class omero.gateway.model.TextData: Sets the y-coordinate of the text field.
setY1(double) - Method in class omero.gateway.model.LineData: Set the y-coordinate of the starting point of an untransformed line.
setY2(double) - Method in class omero.gateway.model.LineData: Set the y-coordinate of the end point of an untransformed line.
setZ(int) - Method in class omero.gateway.model.ShapeData: Sets the z-section.
ShapeData - Class in omero.gateway.model: Hosts a shape.
ShapeData(Shape, boolean) - Constructor for class omero.gateway.model.ShapeData: Creates a new instance.
ShapeData(Shape) - Constructor for class omero.gateway.model.ShapeData: Creates a new instance.
ShapeSettingsData - Class in omero.gateway.model: Stores the settings related to a given shape.
shutDown() - Method in interface omero.gateway.cache.CacheService: Shuts the cache down.
shutDownDerivedConnector(SecurityContext) - Method in class omero.gateway.Gateway: Shuts down the connectors created while creating/importing data for other users.
shutdownRenderingEngine(SecurityContext, long) - Method in class omero.gateway.Gateway: Shuts down the rendering engine
skipHead() - Static method in class omero.gateway.util.Requests
SkipHeadBuilder() - Constructor for class omero.gateway.util.Requests.SkipHeadBuilder: Instantiate a new SkipHead and initialize its collection containers.
splitString(String) - Static method in class omero.gateway.util.Utils: Returns the partial name of the image's name
startFrom(Iterable<String>) - Method in class omero.gateway.util.Requests.SkipHeadBuilder
startFrom(Class<? extends IObject>...) - Method in class omero.gateway.util.Requests.SkipHeadBuilder
startFrom(String...) - Method in class omero.gateway.util.Requests.SkipHeadBuilder
stopBefore(Iterable<String>) - Method in class omero.gateway.util.Requests.FindChildrenBuilder
stopBefore(Class<? extends IObject>...) - Method in class omero.gateway.util.Requests.FindChildrenBuilder
stopBefore(String...) - Method in class omero.gateway.util.Requests.FindChildrenBuilder
stopBefore(Iterable<String>) - Method in class omero.gateway.util.Requests.FindParentsBuilder
stopBefore(Class<? extends IObject>...) - Method in class omero.gateway.util.Requests.FindParentsBuilder
stopBefore(String...) - Method in class omero.gateway.util.Requests.FindParentsBuilder
subfolderCount() - Method in class omero.gateway.model.FolderData: Get the number of sub folders
submit(Callable<T>) - Method in class omero.gateway.Gateway: Submits an async task
submit(SecurityContext, List<Request>, SecurityContext) - Method in class omero.gateway.Gateway: Executes the commands.
submit(SecurityContext, Request) - Method in class omero.gateway.Gateway: Directly submit a Request to the server
sudo() - Method in class omero.gateway.SecurityContext: Indicates to create a session for another user.
SYSTEM - Static variable in class omero.gateway.model.GroupData: Identifies the System group.

T

TableData - Class in omero.gateway.model: A simple data 'container' for an OMERO.table
TableData(List<TableDataColumn>, List<List<Object>>) - Constructor for class omero.gateway.model.TableData: Creates a new instance
TableData(TableDataColumn[], Object[][]) - Constructor for class omero.gateway.model.TableData: Creates a new instance
TableDataColumn - Class in omero.gateway.model: Defines a column for a TableData object
TableDataColumn(String, int, Class<?>) - Constructor for class omero.gateway.model.TableDataColumn: Creates a new instance
TableDataColumn(String, String, int, Class<?>) - Constructor for class omero.gateway.model.TableDataColumn: Creates a new instance
TableResult - Class in omero.gateway.model: Store the element of the py-tables.
TableResult(Object[][], String[]) - Constructor for class omero.gateway.model.TableResult: Creates a new instance.
TableResult(Object[][], String[], String[]) - Constructor for class omero.gateway.model.TableResult: Creates a new instance.
TABLES_MIMETYPE - Static variable in class omero.gateway.facility.TablesFacility: The mimetype of an omero tables file
TablesFacility - Class in omero.gateway.facility: Facility to interact with OMERO.tables
TablesFacilityHelper - Class in omero.gateway.facility: Helper class which deals with the various conversions from omero.grid objects into plain Java, respectively gateway.model objects
TagAnnotationData - Class in omero.gateway.model: A tag annotation can either be related to an image or a tag but not to both at the same time.
TagAnnotationData(String, boolean) - Constructor for class omero.gateway.model.TagAnnotationData: Creates a new instance.
TagAnnotationData(String) - Constructor for class omero.gateway.model.TagAnnotationData: Creates a new instance.
TagAnnotationData(String, String) - Constructor for class omero.gateway.model.TagAnnotationData: Creates a new instance.
TagAnnotationData(String, String, boolean) - Constructor for class omero.gateway.model.TagAnnotationData: Creates a new instance.
TagAnnotationData(TagAnnotation) - Constructor for class omero.gateway.model.TagAnnotationData: Creates a new instance.
TagAnnotationData(TagAnnotation, List<CommentAnnotation>) - Constructor for class omero.gateway.model.TagAnnotationData: Creates a new instance.
targetUsers(Iterable<Long>) - Method in class omero.gateway.util.Requests.Chown2Builder
targetUsers(RLong...) - Method in class omero.gateway.util.Requests.Chown2Builder
targetUsers(Long...) - Method in class omero.gateway.util.Requests.Chown2Builder
targetUsers(Experimenter) - Method in class omero.gateway.util.Requests.Chown2Builder
TermAnnotationData - Class in omero.gateway.model: Defines a Term Annotation.
TermAnnotationData(String) - Constructor for class omero.gateway.model.TermAnnotationData: Creates a new instance.
TermAnnotationData(TermAnnotation) - Constructor for class omero.gateway.model.TermAnnotationData: Creates a new instance.
TEXT - Static variable in class omero.gateway.model.FileAnnotationData: Identifies the Text file formats.
TextData - Class in omero.gateway.model: Represents a Text in the Euclidean space R².
TextData(Shape) - Constructor for class omero.gateway.model.TextData: Creates a new instance of Text data from an existing shape.
TextData() - Constructor for class omero.gateway.model.TextData: Creates a new instance of TextData, creating a new TextI Object.
TextData(String, double, double) - Constructor for class omero.gateway.model.TextData: Creates a new instance of the TextData, sets the centre and major, minor axes.
TextualAnnotationData - Class in omero.gateway.model: Basic textual annotation used to add comments to a given object.
TextualAnnotationData() - Constructor for class omero.gateway.model.TextualAnnotationData: Creates a new instance.
TextualAnnotationData(String) - Constructor for class omero.gateway.model.TextualAnnotationData: Creates a new instance.
TextualAnnotationData(CommentAnnotation) - Constructor for class omero.gateway.model.TextualAnnotationData: Creates a new instance.
TF_2 - Static variable in class omero.gateway.util.TIFFFilter: Possible file extension.
TF_8 - Static variable in class omero.gateway.util.TIFFFilter: Possible file extension.
TIF - Static variable in class omero.gateway.util.TIFFFilter: Possible file extension.
TIFF - Static variable in class omero.gateway.util.TIFFFilter: Possible file extension.
TIFFFilter - Class in omero.gateway.util: Methods to check if an image is a TIFF image.
TIFFFilter() - Constructor for class omero.gateway.util.TIFFFilter
TimeAnnotationData - Class in omero.gateway.model: Basic time annotation.
TimeAnnotationData() - Constructor for class omero.gateway.model.TimeAnnotationData: Creates a default instance.
TimeAnnotationData(TimestampAnnotation) - Constructor for class omero.gateway.model.TimeAnnotationData: Creates a new instance.
timeOfEvent(Event) - Method in class omero.gateway.model.DataObject
toEnum(Class<E>, Class<I>, Collection<String>) - Static method in class omero.gateway.util.Utils: Convert a list of String values to their corresponding omero.model.enums instances.
toGroup(long) - Method in class omero.gateway.util.Requests.Chgrp2Builder
toGroup(RLong) - Method in class omero.gateway.util.Requests.Chgrp2Builder
toGroup(ExperimenterGroup) - Method in class omero.gateway.util.Requests.Chgrp2Builder
toNumber(double) - Static method in class omero.gateway.model.ShapeData: Returns a double array as a number attribute value.
TOO_MANY_CLAUSES - Static variable in class omero.gateway.model.SearchResultCollection: The search has to many clauses, e.g.
TOO_MANY_RESULTS_ERROR - Static variable in class omero.gateway.model.SearchResultCollection: The search has to many results
toPerms(String) - Method in class omero.gateway.util.Requests.Chmod2Builder
toPoints(Point2D.Double[]) - Static method in class omero.gateway.model.ShapeData: Returns a Point2D.Double array as a Points attribute value.
toString() - Method in class omero.gateway.model.DataObject: Overridden to return the name of the class and the object id.
toString() - Method in class omero.gateway.model.FolderData
toString() - Method in class omero.gateway.model.MaskData
toString() - Method in class omero.gateway.model.PermissionData
toString() - Method in class omero.gateway.model.ROICoordinate: Returns the string of the coordinates.
toString() - Method in class omero.gateway.model.SearchResult
toString() - Method in class omero.gateway.model.SearchResultCollection
toString() - Method in class omero.gateway.model.TableData
toString() - Method in class omero.gateway.model.TableDataColumn
toString() - Method in class omero.gateway.SecurityContext
toString() - Method in class omero.gateway.ServerInformation
toString() - Method in class omero.gateway.UserCredentials: Formats user name and password.
toUser(long) - Method in class omero.gateway.util.Requests.Chown2Builder
toUser(RLong) - Method in class omero.gateway.util.Requests.Chown2Builder
toUser(Experimenter) - Method in class omero.gateway.util.Requests.Chown2Builder
TransferFacility - Class in omero.gateway.facility: Facility which provides data transfer functionality, i.e.
TransferFacilityHelper - Class in omero.gateway.facility: Encapsulates some functionality needed by the TransferFacility
type(Iterable<String>) - Method in class omero.gateway.util.Requests.DiskUsageBuilder
type(Class<? extends IObject>...) - Method in class omero.gateway.util.Requests.DiskUsageBuilder
type(String...) - Method in class omero.gateway.util.Requests.DiskUsageBuilder

U

UINT16_TYPE - Static variable in class omero.gateway.model.PixelsData: Identifies the type used to store pixel values.
UINT32_TYPE - Static variable in class omero.gateway.model.PixelsData: Identifies the type used to store pixel values.
UINT8_TYPE - Static variable in class omero.gateway.model.PixelsData: Identifies the type used to store pixel values.
UINT_16 - Static variable in class omero.gateway.rnd.DataSink: Identifies the type used to store pixel values.
UINT_32 - Static variable in class omero.gateway.rnd.DataSink: Identifies the type used to store pixel values.
UINT_8 - Static variable in class omero.gateway.rnd.DataSink: Identifies the type used to store pixel values.
UintConverter - Class in omero.gateway.rnd: Packs a sequence of bytes representing an unsigned big-endian integer into an integer value of appropriate integer type.
UintConverter() - Constructor for class omero.gateway.rnd.UintConverter
unfold(int[][]) - Static method in class omero.gateway.util.Mask: Transforms a 2 dimensional array into a one dimensional array; the opposite of the fold method.
UNKNOWN - Static variable in class omero.gateway.model.FileAnnotationData: Indicates that the format is not recognized.
unloadCollections(IObject) - Static method in class omero.gateway.util.ModelMapper: Unlinks the collections linked to the specified IObject.
updateObject(SecurityContext, IObject, Parameters) - Method in class omero.gateway.facility.DataManagerFacility: Updates the specified object.
updateObjects(SecurityContext, List<IObject>, Parameters) - Method in class omero.gateway.facility.DataManagerFacility: Updates the specified IObjects and returned the updated IObjects.
updateTable(SecurityContext, TableData) - Method in class omero.gateway.facility.TablesFacility: Saves the (modified) TableData back to the server.
UploadMask - Class in omero.gateway.util: Uploaded for masks.
UploadMask(long) - Constructor for class omero.gateway.util.UploadMask: Creates a new instance.
USER - Static variable in class omero.gateway.model.GroupData: Identifies the User group.
UserCredentials - Class in omero.gateway: Holds username and password of a user
UserCredentials() - Constructor for class omero.gateway.UserCredentials: Creates an empty instance
UserCredentials(String, String) - Constructor for class omero.gateway.UserCredentials: Creates a new instance
Utils - Class in omero.gateway.util: Collection of methods used to set the name of files to import and to handle enumerations.
Utils() - Constructor for class omero.gateway.util.Utils

V

valueOf(String) - Static method in enum omero.gateway.exception.ConnectionStatus: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum omero.gateway.model.SearchScope: Returns the enum constant of this type with the specified name.
values() - Static method in enum omero.gateway.exception.ConnectionStatus: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum omero.gateway.model.SearchScope: Returns an array containing the constants of this enum type, in the order they are declared.

W

WELL_COLUMN_INDEX - Static variable in class omero.gateway.model.TableResult: Identifies the index of the Well column.
WellData - Class in omero.gateway.model: The data that makes up an OME Well and the Experimenter that owns this Well.
WellData() - Constructor for class omero.gateway.model.WellData: Creates a new instance.
WellData(Well) - Constructor for class omero.gateway.model.WellData: Creates a new instance.
WELLS - Static variable in class omero.gateway.model.PlateData: Identifies the PlateI.WELLS field.
WellSampleData - Class in omero.gateway.model: The data that makes up an OME WellSample along with links to its images and the Experimenter that owns this WellSample.
WellSampleData() - Constructor for class omero.gateway.model.WellSampleData: Creates a new instance.
WellSampleData(WellSample) - Constructor for class omero.gateway.model.WellSampleData: Creates a new instance.

X

XML - Static variable in class omero.gateway.model.FileAnnotationData: Identifies the XML file formats.
XMLAnnotationData - Class in omero.gateway.model: Defines an XML Annotation.
XMLAnnotationData() - Constructor for class omero.gateway.model.XMLAnnotationData: Creates a new instance.
XMLAnnotationData(String) - Constructor for class omero.gateway.model.XMLAnnotationData: Creates a new instance.
XMLAnnotationData(XmlAnnotation) - Constructor for class omero.gateway.model.XMLAnnotationData: Creates a new instance.

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