Index (openbis_standard_technologies SNAPSHOT-r1677241701 API)

A C D E F G H I J L M O P R S T U V W
All Classes All Packages

A

AbstractFormatSelectionCriterion - Class in ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto: Abstract super class of IImageRepresentationFormatSelectionCriterion which accepting matching ImageRepresentationFormat instance individually.
AbstractFormatSelectionCriterion() - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.AbstractFormatSelectionCriterion
accept(ImageRepresentationFormat) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.AbstractFormatSelectionCriterion: Returns true if the specified ImageRepresentationFormat instance is accepted by this criterion.
accept(ImageRepresentationFormat) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ColorDepthCriterion
accept(ImageRepresentationFormat) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FileTypeCriterion
accept(ImageRepresentationFormat) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.OriginalCriterion
AnalysisProcedureTest - Class in ch.systemsx.cisd.openbis.plugin.screening.client.api.v1: A test class for the methods that take an analysis procedure.

C

ch.systemsx.cisd.openbis.plugin.screening.client.api.v1 - package ch.systemsx.cisd.openbis.plugin.screening.client.api.v1: See ScreeningClientApiTest.java source code for the examples how the facade can be used.
ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1 - package ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1
ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto - package ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto: Data Transfer Objects
ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.json - package ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.json
clearWellImageCache() - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: Removes all images loaded by IScreeningOpenbisServiceFacade.loadImageWellCaching(PlateImageReference, ImageSize) and IScreeningOpenbisServiceFacade.loadThumbnailImageWellCaching(PlateImageReference) from the image cache, thus freeing the memory.
clearWellImageCache() - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade
ColorDepthCriterion - Class in ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto: Criterion based on the color depth.
ColorDepthCriterion(Integer...) - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ColorDepthCriterion: Creates an instance which allows all image representation formats with specified color depths.
compareTo(DatasetImageRepresentationFormats) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.DatasetImageRepresentationFormats
compareTo(FeatureInformation) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureInformation
compareTo(ImageChannel) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageChannel
compareTo(WellPosition) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellPosition
COMPOUND - Static variable in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.MaterialTypeIdentifier: Material identifier for a compound.
convertToFeatureVectorDatasetWellIdentifier(List<PlateWellReferenceWithDatasets>) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: Converts the given list of PlateWellReferenceWithDatasets into a list of FeatureVectorDatasetWellReference.
convertToFeatureVectorDatasetWellIdentifier(List<PlateWellReferenceWithDatasets>) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade
convertToWellPositions(List<WellIdentifier>) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: Converts the given WellIdentifiers to WellPositions
convertToWellPositions(List<WellIdentifier>) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade
COVERING_BOUNDING_BOX - ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.SizeCriterion.Type: Picks all formats where the image size covers a bounding box specified by width and height.
createFromAugmentedCode(String) - Static method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ExperimentIdentifier: Creates an ExperimentIdentifier from the given augmentedCode.
createFromAugmentedCode(String) - Static method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateIdentifier: Creates a PlateIdentifier from the given augmentedCode.
createFromCartesianDimensions(int[]) - Static method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Geometry: Creates a new instance from the given cartesian dimensions.
createFromCartesianDimensions(int, int) - Static method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Geometry: Creates a new instance from the given cartesian dimensions.
createFromPermId(String) - Static method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ExperimentIdentifier: Creates an ExperimentIdentifier from the given permId.
createFromPermId(String) - Static method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateIdentifier: Creates a PlateIdentifier from the given permId.
createFromPlateGeometryString(String) - Static method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Geometry: Creates a new instance from the given number of rows and columns.
createFromRowColDimensions(int, int) - Static method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Geometry: Creates a new instance from the given number of rows and columns.
createPlateImageReferences(IImageDatasetIdentifier, ImageDatasetMetadata, List<String>, List<WellPosition>) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: Returns the list of all plate image references for the given imageDatasetId (all tiles), and the given channelCodesOrNull and wellsToUse.
createPlateImageReferences(IImageDatasetIdentifier, ImageDatasetMetadata, List<String>, List<WellPosition>) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade
createPlateImageReferences(IImageDatasetIdentifier, List<String>, List<WellPosition>) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: Returns the list of all plate image references for the given imageDatasetId (all tiles), and the given channelCodesOrNull and wellsToUse.
createPlateImageReferences(IImageDatasetIdentifier, List<String>, List<WellPosition>) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade
createPlateImageReferences(ImageDatasetReference) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: Returns the list of all plate image references for the given imageDatasetRef.
createPlateImageReferences(ImageDatasetReference) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade
createPlateImageReferences(ImageDatasetReference, ImageDatasetMetadata, List<String>, List<WellPosition>) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: Returns the list of all plate image references for the given imageDatasetRef (all tiles), the given channelCodesOrNull and wellsOrNull.
createPlateImageReferences(ImageDatasetReference, ImageDatasetMetadata, List<String>, List<WellPosition>) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade
createPlateImageReferences(ImageDatasetReference, List<String>, List<WellPosition>) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: Returns the list of all plate image references for the given imageDatasetRef (all tiles), the given channelCodesOrNull and wellsOrNull.
createPlateImageReferences(ImageDatasetReference, List<String>, List<WellPosition>) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade
createTransformer() - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ExampleImageTransformerFactory

D

DataSetCodeAndWellPositions - Class in ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto: Helper class for parsing strings containing data set code and well positions.
DataSetCodeAndWellPositions(String) - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.DataSetCodeAndWellPositions: Creates an instane from the specified description.
DatasetIdentifier - Class in ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto: Contains data which uniquely define a dataset.
DatasetIdentifier(String, String) - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.DatasetIdentifier
DatasetImageRepresentationFormats - Class in ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto: A bean that lists all image representation formats available for a data set.
DatasetImageRepresentationFormats(IDatasetIdentifier, List<ImageRepresentationFormat>) - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.DatasetImageRepresentationFormats: Constructor.
DatasetImagesReference - Class in ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto
DatasetImagesReference() - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.DatasetImagesReference
DatasetOverlayImagesReference - Class in ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto
DatasetOverlayImagesReference() - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.DatasetOverlayImagesReference
DatasetReference - Class in ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto: Description of one plate-based screening dataset.
DatasetReference(String, String, PlateIdentifier) - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.DatasetReference: Deprecated.
DatasetReference(String, String, PlateIdentifier, ExperimentIdentifier, Geometry, Date, Map<String, String>) - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.DatasetReference: Deprecated.
DatasetReference(String, String, PlateIdentifier, Geometry, Date) - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.DatasetReference: Deprecated.
DatasetReference(String, String, String, PlateIdentifier, ExperimentIdentifier, Geometry, Date, Map<String, String>) - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.DatasetReference

E

equals(Object) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ExampleImageTransformerFactory
equals(Object) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.DatasetIdentifier
equals(Object) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.DatasetImageRepresentationFormats
equals(Object) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureInformation
equals(Object) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDataset
equals(Object) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDatasetWellReference
equals(Object) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorWithDescription
equals(Object) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Geometry
equals(Object) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageChannel
equals(Object) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageRepresentationFormat
equals(Object) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageRepresentationFormat.ImageRepresentationTransformation
equals(Object) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageSize
equals(Object) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageTransformationInfo
equals(Object) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.MaterialIdentifier
equals(Object) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.MaterialTypeIdentifier
equals(Object) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.MicroscopyImageReference
equals(Object) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PermanentIdentifier
equals(Object) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateIdentifier
equals(Object) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateImageReference
equals(Object) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateWellReferenceWithDatasets
equals(Object) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellIdentifier
equals(Object) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellMetadata
equals(Object) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellPosition
EXACTLY - ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.SizeCriterion.Type: Picks all formats where the image size is exactly as specified by width and height.
ExampleImageTransformerFactory - Class in ch.systemsx.cisd.openbis.plugin.screening.client.api.v1
ExampleImageTransformerFactory(int) - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ExampleImageTransformerFactory
ExampleImageTransformerFactory(String) - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ExampleImageTransformerFactory
ExampleImageTransformerFactory(String, int) - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ExampleImageTransformerFactory
ExperimentIdentifier - Class in ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto: Unique identifier for an experiment in openBIS.
ExperimentIdentifier(String, String, String, String) - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ExperimentIdentifier: An spaceCode == null is interpreted as the home space.
ExperimentImageMetadata - Class in ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto: Contains summary meta data for images within an experiment.
ExperimentImageMetadata(ExperimentIdentifier, Geometry, Geometry, List<ImageChannel>, ImageSize, List<ImageSize>) - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ExperimentImageMetadata

F

FeatureInformation - Class in ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto: A bean that provides information about a feature.
FeatureInformation(String, String, String) - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureInformation
FeatureVector - Class in ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto: Feature vector for one well.
FeatureVector(WellPosition, double[]) - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVector: Creates an instance for the specified well assuming all features are numbers.
FeatureVector(WellPosition, double[], boolean[], String[]) - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVector: Creates an instance for the specified well.
FeatureVectorDataset - Class in ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto: Feature vectors of one dataset.
FeatureVectorDataset(FeatureVectorDatasetReference, List<String>, List<String>, List<FeatureVector>) - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDataset
FeatureVectorDatasetReference - Class in ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto: Description of one feature vector dataset.
FeatureVectorDatasetReference(String, String, PlateIdentifier, ExperimentIdentifier, Geometry, Date, IImageDatasetIdentifier, Map<String, String>) - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDatasetReference: Deprecated.
FeatureVectorDatasetReference(String, String, PlateIdentifier, Geometry, Date, IImageDatasetIdentifier) - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDatasetReference: Deprecated.
FeatureVectorDatasetReference(String, String, String, PlateIdentifier, ExperimentIdentifier, Geometry, Date, IImageDatasetIdentifier, Map<String, String>) - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDatasetReference
FeatureVectorDatasetWellReference - Class in ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto: Reference to one well in a feature vector dataset.
FeatureVectorDatasetWellReference(FeatureVectorDatasetReference, WellPosition) - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDatasetWellReference
FeatureVectorDatasetWellReference(String, String, PlateIdentifier, ExperimentIdentifier, Geometry, Date, IImageDatasetIdentifier, Map<String, String>, WellPosition) - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDatasetWellReference: Deprecated.
FeatureVectorDatasetWellReference(String, String, PlateIdentifier, Geometry, Date, IImageDatasetIdentifier, WellPosition) - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDatasetWellReference: Deprecated.
FeatureVectorDatasetWellReference(String, String, String, PlateIdentifier, ExperimentIdentifier, Geometry, Date, IImageDatasetIdentifier, Map<String, String>, WellPosition) - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDatasetWellReference
FeatureVectorWithDescription - Class in ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto: Feature vectors of one well in one feature vector dataset.
FeatureVectorWithDescription(FeatureVectorDatasetWellReference, List<String>, double[]) - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorWithDescription
FeatureVectorWithDescription(FeatureVectorDatasetWellReference, List<String>, double[], boolean[], String[]) - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorWithDescription
FileTypeCriterion - Class in ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto: Criterion based on the file type.
FileTypeCriterion(String...) - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FileTypeCriterion: Creates an instance which accepts all image representation formats of specified file types.

G

GENE - Static variable in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.MaterialTypeIdentifier: Material identifier for a gene.
Geometry - Class in ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto: Immutable class defining the width and height of something.
GEOMETRY_1536_32X48 - Static variable in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Geometry
GEOMETRY_384_16X24 - Static variable in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Geometry
GEOMETRY_96_8X12 - Static variable in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Geometry
getAnalysisProcedureOrNull() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.DatasetOverlayImagesReference
getAugmentedCode() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ExperimentIdentifier: Returns the augmented (full) code of this experiment.
getAugmentedCode() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.MaterialIdentifier
getAugmentedCode() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateIdentifier: Returns the augmented (full) code of this plate.
getAvailableImageTransformations() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.InternalImageChannel
getCartesianDimensions() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Geometry: Returns the cartesian coordinates as an int[].
getChannel() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.MicroscopyImageReference: channel code
getChannel() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateImageReference: channel code
getChannelCode() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageRepresentationFormat.ImageRepresentationTransformation
getChannelCodes() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetMetadata: Returns channel codes.
getChannelLabels() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetMetadata: Deprecated.
use ImageDatasetMetadata.getChannels() instead.
getChannelNames() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetMetadata: Deprecated.
use ImageDatasetMetadata.getChannels() instead.
getChannels() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ExperimentImageMetadata: Return all channels of images contained in the experiment.
getChannels() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetMetadata: Returns the list of channels for this dataset.
getChannels() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetParameters
getChannelStacks() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.LogicalImageInfo
getClasses(String) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.json.ScreeningJsonClassValueToClassObjectsMapping
getCode() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureInformation: Returns the code of the feature.
getCode() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageChannel: Returns the channel code.
getCode() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageTransformationInfo: The code of the image transformation.
getCode() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.InternalImageChannel
getCode() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.InternalImageTransformationInfo
getCode() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellMetadata
getColorDepth() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageRepresentationFormat
getColsNumOrNull() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetParameters
getColumn() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellLocation
getContainerDataSetCode(String) - Static method in class OpenBISScreeningML
getDataset() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.DatasetImageRepresentationFormats: The data set the formats relate to.
getDataset() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDataset: identifier of the dataset containing feature vectors
getDataSet(String) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade
getDataSet(String) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade
getDatasetCode() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.DatasetIdentifier: The code of this dataset.
getDatasetCode() - Method in interface ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IDatasetIdentifier: a code of the dataset
getDatasetCode() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetParameters
getDataSetCode() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.DataSetCodeAndWellPositions: Returns the data set code.
getDataSetCode() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageRepresentationFormat: Returns the data set code to which this image representation format belongs.
getDatasetIdentifiers(String, List<String>) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.IScreeningApiServer: Converts a given list of dataset codes to dataset identifiers.
getDatasetIdentifiers(List<String>) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: Converts a given list of dataset codes to dataset identifiers which can be used in other API calls.
getDatasetIdentifiers(List<String>) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade: Converts a given list of dataset codes to dataset identifiers which can be used in other API calls.
getDataSetMetaData(String[]) - Static method in class OpenBISScreeningML: Lists meta data of specified data sets.
getDataSetMetaData(List<String>) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: Returns meta data for all specified data set codes.
getDataSetMetaData(List<String>) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade
getDataSets(ExperimentIdentifier, IDataSetFilter) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: Gets proxies to the data sets owned by specified experiment and passing specified filter.
getDataSets(ExperimentIdentifier, IDataSetFilter) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade
getDataSets(PlateIdentifier, IDataSetFilter) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: Gets proxies to the data sets owned by specified plate and passing specified filter.
getDataSets(PlateIdentifier, IDataSetFilter) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade
getDataSets(PlateIdentifier, String) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: Deprecated.
use IScreeningOpenbisServiceFacade.getDataSets(PlateIdentifier, IDataSetFilter) with TypeBasedDataSetFilter.
getDataSets(PlateIdentifier, String) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade: Get proxies to the data sets owned by specified plate.
getDataSets(WellIdentifier, IDataSetFilter) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: Gets proxies to the data sets owned by specified well and passing specified filter..
getDataSets(WellIdentifier, IDataSetFilter) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade
getDataSets(WellIdentifier, String) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: Deprecated.
use IScreeningOpenbisServiceFacade.getDataSets(WellIdentifier, IDataSetFilter) with TypeBasedDataSetFilter.
getDataSets(WellIdentifier, String) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade: Get proxies to the data sets owned by specified well.
getDataSetType() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.DatasetReference: Returns data set type.
getDatasetWellReference() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorWithDescription: Identifier of the dataset and well of this feature vector.
getDatastoreServerUrl() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.DatasetIdentifier
getDatastoreServerUrl() - Method in interface ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IDatasetIdentifier: a code which points to the datastore server on which the dataset is accessible
getDepthOrNull() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageChannelStack
getDescription() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureInformation: Returns the text description of the feature.
getDescription() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.InternalImageChannel
getDescription() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.InternalImageTransformationInfo
getDesiredImageSize() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.LoadImageConfiguration: The desired size of the image.
getDimX() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Geometry: Returns the dimension on the x-axis.
getDimY() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Geometry: Returns the dimension on the y-axis.
getExperimentCode() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ExperimentIdentifier
getExperimentCode() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Plate: The code of the experiment to which the plate belongs.
getExperimentIdentifier() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.DatasetReference: Returns the identifier of the experiment that this dataset belongs to.
getExperimentIdentifier() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Plate: Get the identifier of the experiment that this plate is assigned to.
getExperimentImageMetadata(ExperimentIdentifier) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: Returns aggregated metadata for all images/plates within one experiment.
getExperimentImageMetadata(ExperimentIdentifier) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade
getExperimentImageMetadata(String, ExperimentIdentifier) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.IScreeningApiServer: Returns aggregated metadata for all images/plates within one experiment.
getExperimentPlateIdentifier() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateWellReferenceWithDatasets: Returns the experiment / plate identifier of this reference.
getFeatureCodes() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDataset: Returns the feature codes.
getFeatureCodes() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorWithDescription
getFeatureCodes() - Method in interface ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IFeatureCodesProvider: Returns the feature codes.
getFeatureLabels() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDataset: Returns the feature labels.
getFeatureList(IFeatureVectorDatasetIdentifier, String) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: Return the feature codes from the specified feature list of a specified feature data set
getFeatureList(IFeatureVectorDatasetIdentifier, String) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade
getFeatureMatrix(String, String, String[]) - Static method in class OpenBISScreeningML: Returns the feature matrix of the specified features for all locations (a location is one well position in one feature vector data set) in experiment connected to gene in [0], location annotations in [1] and feature annotation in [2].
getFeatureMatrix(String, String, String, String[]) - Static method in class OpenBISScreeningML: Returns the feature matrix of the specified features for all locations in experiment (a location is one well position in one feature vector data set) in experiment connected to gene in [0], location annotations in [1] and feature annotation in [2].
getFeatureMatrixForPlate(String, String, String[]) - Static method in class OpenBISScreeningML: Returns the feature matrix of the specified features for all locations (a location is one well position in one feature vector data set) of all feature vector data sets created by specified analysis procedure of the given plate in [0], location annotations in [1] and feature annotation in [2].
getFeatureNames() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDataset: Deprecated.
getFeatureNames() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorWithDescription: Names (and implicitly order) of the features present in each feature vector.
getFeatureVectorDatasetReferences() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateWellReferenceWithDatasets: Returns the feature vector data sets of the plate of this reference.
getFeatureVectors() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDataset: all feature vectors for a dataset
getFileType() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageRepresentationFormat
getFullDataSets(ExperimentIdentifier, IDataSetFilter) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: A list of data sets owned by specified experiment and passing specified filter.
getFullDataSets(ExperimentIdentifier, IDataSetFilter) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade
getFullDataSets(PlateIdentifier, IDataSetFilter) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: A list of data sets owned by specified plate and passing specified filter.
getFullDataSets(PlateIdentifier, IDataSetFilter) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade
getGeneMappingForPlates(String[]) - Static method in class OpenBISScreeningML: Returns the gene mapping for the given plateCodes in [0] and location annotations in [1].
getHeight() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Geometry: Returns the height.
getHeight() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetMetadata: Height of the images in this dataset.
getHeight() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageRepresentationFormat
getHeight() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageResolution
getHeight() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageSize
getId() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageChannelStack
getId() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageRepresentationFormat: Return the ID of this image representation format.
getIdentifier() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ExperimentImageMetadata: Return the experiment identifier.
getImageDataset() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetEnrichedReference
getImageDataset() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetMetadata: Identifier of this image dataset.
getImageDataset() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.LogicalImageInfo
getImageDatasetReferences() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateWellReferenceWithDatasets: Returns the image data set of the plate of this reference.
getImageInfo(String, List<String>) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.IScreeningApiServer: Returns information about logical image in the given image datasets.
getImageParameters() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.DatasetImagesReference
getImageRepresentationFormats() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.DatasetImageRepresentationFormats
getImageResolutions(String, List<String>) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.IScreeningApiServer: Returns information about available image resolutions for the given image datasets.
getImagesMetadata(String) - Static method in class OpenBISScreeningML: Fetches metadata of the image datasets for the specified plate.
getImageTransformerFactoryOrNull(List<IDatasetIdentifier>, String) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: Returns the transformer factory for the specified channel and the experiment to which the specified data sets belong.
getImageTransformerFactoryOrNull(List<IDatasetIdentifier>, String) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade
getInstance() - Static method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.json.ScreeningJsonClassValueToClassObjectsMapping
getLabel() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureInformation: Returns the label of the feature (pretty-print, but not guaranteed to be unique).
getLabel() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageChannel: Returns the channel label.
getLabel() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageTransformationInfo: The (pretty-printed) label of the image transformation.
getLabel() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.InternalImageChannel
getLabel() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.InternalImageTransformationInfo
getLinkOrCopyOfContents(String, DataSet, File) - Static method in class OpenBISScreeningML
getMatching(List<ImageRepresentationFormat>) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.AbstractFormatSelectionCriterion
getMatching(List<ImageRepresentationFormat>) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IImageRepresentationFormatSelectionCriterion: Returns all ImageRepresentationFormat objects from the specified list which fulfill this criterion.
getMatching(List<ImageRepresentationFormat>) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.SizeCriterion
getMaterialCode() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.MaterialIdentifier
getMaterialProperties() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Material
getMaterialProperties() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellMetadata
getMaterialsForWell(int, int) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateWellMaterialMapping: Returns the list of materials present in well (row,col).
getMaterialTypeCode() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.MaterialTypeIdentifier: Returns the code of this material type.
getMaterialTypeIdentifier() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.MaterialIdentifier
getMergedChannelTransformerFactorySignatureOrNull() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetParameters
getNumberOfChannels() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetMetadata: Number of channels (wavelengths) in which images have been acquired for this dataset.
getNumberOfColumns() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Geometry: Returns the number of columns.
getNumberOfRows() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Geometry: Returns the number of rows.
getNumberOfTiles() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetMetadata: Number of image tiles (or "fields") available for each well.
getOriginalImageSize() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ExperimentImageMetadata: Returns the image size if all images in the experiment have the same size.
getOutputStream(PlateImageReference) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade.IImageOutputStreamProvider
getOverlayDatasets() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetEnrichedReference
getParentImageDataset() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDatasetReference: Parent image dataset which has been analyzed to obtain the feature vectors, or null, if the data set has no parent image dataset.
getParentImageDatasetReference() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetReference: Returns the image parent dataset of this data set, or null, if this data set doesn't have a parent image dataset or the server version is too old (< 1.6) to fill it.
getPermId() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.DatasetIdentifier
getPermId() - Method in interface ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IPermanentIdentifier: Returns the permanent identifier.
getPermId() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PermanentIdentifier
getPlate() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.DatasetReference: Returns the identifier of the plate that this dataset belongs to.
getPlateCode() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateIdentifier: A code of the plate.
getPlateGeometry() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.DatasetReference: Returns the plate geometry.
getPlateGeometry() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ExperimentImageMetadata: Returns the plate geometry if all plates in the experiment have the same geometry.
getPlateGeometry() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateMetadata
getPlateGeometry() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateWellMaterialMapping: Returns the plate geometry of the plate that this mapping is for.
getPlateIdentifier() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateWellMaterialMapping: Returns the plate identifier that this plate is for.
getPlateIdentifier() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellIdentifier
getPlateMetadataList(String[]) - Static method in class OpenBISScreeningML: Experimental method that returns an array of PlateMetadata Java objects for a given list of plate codes.
getPlateMetadataList(String, List<? extends PlateIdentifier>) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.IScreeningApiServer: Fetches the contents of a given list of plates.
getPlateMetadataList(List<? extends PlateIdentifier>) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: Return full metadata for each specified plate, including wells and their properties.
getPlateMetadataList(List<? extends PlateIdentifier>) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade
getPlateProperties(PlateIdentifier) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: Returns all properties of specified plate as a map.
getPlateProperties(PlateIdentifier) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade
getPlateProperties(String) - Static method in class OpenBISScreeningML: Returns the properties of specified plate.
getPlateSample(String, PlateIdentifier) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.IScreeningApiServer: For a given plateIdentifier, return the corresponding Sample.
getProjectCode() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ExperimentIdentifier: The code of the project of this experiment.
getProjectCode() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Plate: The code of the project to which the plate belongs.
getProperties() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.DatasetReference: Returns the data set properties.
getProperties() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Material
getProperties() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateMetadata
getProperties() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellMetadata
getRegistrationDate() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.DatasetReference: Returns the registration date.
getRow() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellLocation
getRowsNumOrNull() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetParameters
getSeriesNumberOrNull() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageChannelStack
getSessionToken() - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: Return the session token for this authenticated user.
getSessionToken() - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade: Return the session token for this authenticated user.
getSingleChannelImageTransformationCode() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.LoadImageConfiguration: Code of the transformation, which should be applied to the image.
getSpaceCode() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ExperimentIdentifier: The code of the space of this experiment.
getThumbnailHeight() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetMetadata: The height of the thumbnail images, or 0 if no thumbnails are available for this data set.
getThumbnailImageSizes() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ExperimentImageMetadata: Returns a sorted list of image sizes where for all experiment's images thumbnail images of these sizes exist.
getThumbnailWidth() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetMetadata: The width of the thumbnail images, or 0 if no thumbnails are available for this data set.
getTile() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.MicroscopyImageReference: a sequential number of an image tile, starts from 0
getTile() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateImageReference: a sequential number of an image tile, starts from 0
getTileCol() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageChannelStack
getTileColsNum() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetParameters
getTileGeometry() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ExperimentImageMetadata: Returns the tiles geometry if all tiles in the experiment have the same geometry.
getTileRow() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageChannelStack
getTileRowsNum() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetParameters
getTilesCols() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetMetadata: Number of columns of image tiles (or "fields") available for each well.
getTilesRows() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetMetadata: Number of rows of image tiles (or "fields") available for each well.
getTimePointOrNull() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageChannelStack
getTransformationCode() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageRepresentationFormat.ImageRepresentationTransformation
getTransformationId() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageRepresentationFormat.ImageRepresentationTransformation
getTransformations() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageChannel: Returns the transformations defined for this channel.
getTransformations() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageRepresentationFormat
getTransformationSignature() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.InternalImageTransformationInfo
getType() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellMetadata
getValueObjects() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVector: Returns the feature vector as a list of objects.
getValues() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVector: Returns the array of numerical features.
getVocabularyFeatureFlags() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVector: Return the array of flags specifying the type of feature where true means vocabulary-based feature and false numerical feature.
getVocabularyTerms() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVector: Returns the array of vocabulary-based features.
getWavelength() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.InternalImageChannel
getWell(int, int) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateMetadata
getWellColumn() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellPosition: well column, starts from 1
getWellPosition() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVector: Returns the well position on a plate.
getWellPosition() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDatasetWellReference: Returns the well position of this reference.
getWellPosition() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateImageReference: Well position on the plate
getWellPosition() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateWellReferenceWithDatasets: Returns the well position of this reference.
getWellPosition() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellIdentifier
getWellPositions() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.DataSetCodeAndWellPositions: Returns the well positions.
getWellProperties(WellIdentifier) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: Returns all properties of specified well as a map.
getWellProperties(WellIdentifier) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade
getWellProperties(String, int, int) - Static method in class OpenBISScreeningML: Returns the properties of specified well for specified plate.
getWellRow() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellPosition: well row, starts from 1
getWells() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateMetadata
getWellSample(String, WellIdentifier) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.IScreeningApiServer: For a given wellIdentifier, return the corresponding Sample including properties.
getWidth() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Geometry: Returns the width.
getWidth() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetMetadata: Width of the images in this dataset.
getWidth() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageRepresentationFormat
getWidth() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageResolution
getWidth() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageSize

H

handlePlateImage(PlateImageReference, byte[]) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IPlateImageHandler: Handles specified image file bytes for specified plate image reference.
hashCode() - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ExampleImageTransformerFactory
hashCode() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.DatasetIdentifier
hashCode() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.DatasetImageRepresentationFormats
hashCode() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureInformation
hashCode() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDataset
hashCode() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDatasetWellReference
hashCode() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorWithDescription
hashCode() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Geometry
hashCode() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageChannel
hashCode() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageRepresentationFormat
hashCode() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageSize
hashCode() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageTransformationInfo
hashCode() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.MaterialIdentifier
hashCode() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.MaterialTypeIdentifier
hashCode() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.MicroscopyImageReference
hashCode() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PermanentIdentifier
hashCode() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateIdentifier
hashCode() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateImageReference
hashCode() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateWellReferenceWithDatasets
hashCode() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellIdentifier
hashCode() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellMetadata
hashCode() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellPosition
hasThumbnails() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetMetadata: true, if this data set has thumbnails, false otherwise.

I

IDatasetIdentifier - Interface in ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto: Contains data which uniquely define a dataset
IFeatureCodesProvider - Interface in ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto: Common interface of classes providing feature codes.
IFeatureVectorDatasetIdentifier - Interface in ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto: Uniquely Identifies a feature vector dataset.
IImageDatasetIdentifier - Interface in ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto: Contains data which uniquely define an image dataset.
IImageRepresentationFormatSelectionCriterion - Interface in ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto: Interface of an image selection criterion based on ImageRepresentationFormat.
ImageChannel - Class in ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto: A class that represents an image channel.
ImageChannel(String, String) - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageChannel
ImageChannel(String, String, String, Integer, List<ImageTransformationInfo>) - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageChannel
ImageChannelStack - Class in ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto
ImageChannelStack() - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageChannelStack
ImageDatasetEnrichedReference - Class in ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto
ImageDatasetEnrichedReference() - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetEnrichedReference
ImageDatasetMetadata - Class in ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto: Metadata information about images in a specified dataset.
ImageDatasetMetadata(IImageDatasetIdentifier, List<ImageChannel>, int, int, int, int, int, int) - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetMetadata
ImageDatasetParameters - Class in ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto
ImageDatasetParameters() - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetParameters
ImageDatasetReference - Class in ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto: Description of one image dataset.
ImageDatasetReference(String, String, PlateIdentifier) - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetReference: Deprecated.
ImageDatasetReference(String, String, PlateIdentifier, ExperimentIdentifier, Geometry, Date, Map<String, String>) - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetReference: Deprecated.
ImageDatasetReference(String, String, PlateIdentifier, ExperimentIdentifier, Geometry, Date, Map<String, String>, ImageDatasetReference) - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetReference: Deprecated.
ImageDatasetReference(String, String, PlateIdentifier, Geometry, Date) - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetReference: Deprecated.
ImageDatasetReference(String, String, String, PlateIdentifier, ExperimentIdentifier, Geometry, Date, Map<String, String>, ImageDatasetReference) - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetReference
ImageRepresentationFormat - Class in ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto: An image representation format is made up of its dimensions, bit depth, and file format.
ImageRepresentationFormat(String, long, boolean, Integer, Integer, Integer, String, List<ImageRepresentationFormat.ImageRepresentationTransformation>) - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageRepresentationFormat: Constructor.
ImageRepresentationFormat.ImageRepresentationTransformation - Class in ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto
ImageRepresentationTransformation(long, String, String) - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageRepresentationFormat.ImageRepresentationTransformation
ImageResolution - Class in ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto
ImageResolution() - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageResolution
ImageSize - Class in ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto: Width and height of an image.
ImageSize(int, int) - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageSize: Creates an instance for specified width and height.
ImageTransformationInfo - Class in ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto: A class that represents an image transformation.
ImageTransformationInfo(String, String, String, boolean) - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageTransformationInfo
ImageViewer - Class in ch.systemsx.cisd.openbis.plugin.screening.client.api.v1
ImageViewer() - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ImageViewer
INSIDE_BOUNDING_BOX - ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.SizeCriterion.Type: Picks all formats where the image size is inside a bounding box specified by width and height.
INSTANCE - Static variable in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacadeFactory
InternalImageChannel - Class in ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto
InternalImageChannel() - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.InternalImageChannel
InternalImageTransformationInfo - Class in ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto
InternalImageTransformationInfo() - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.InternalImageTransformationInfo
IPermanentIdentifier - Interface in ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto: A role that represents a permanent identifier in openBIS.
IPlateImageHandler - Interface in ch.systemsx.cisd.openbis.plugin.screening.client.api.v1: Interface of classes handling plate images as byte arrays.
IScreeningApiServer - Interface in ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1: This interface is a part of the official public screening API.
IScreeningOpenbisServiceFacade - Interface in ch.systemsx.cisd.openbis.plugin.screening.client.api.v1: The service facade for the openBIS public remote API for screening and imaging.
IScreeningOpenbisServiceFacadeFactory - Interface in ch.systemsx.cisd.openbis.plugin.screening.client.api.v1: Interface for factories of IScreeningOpenbisServiceFacade instances.
isDefault() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.InternalImageTransformationInfo
isDefaultTransformation() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageTransformationInfo: Returns true, if this transformation is the default transformation for this channel.
isDesiredImageFormatPng() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.LoadImageConfiguration: Should the image be converted from its original format to PNG?
isMultidimensional() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetParameters
isOpenBisImageTransformationApplied() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.LoadImageConfiguration: Should the image transformation stored in openBIS for a channel or merged channel be applied to the image?
isOriginal() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageRepresentationFormat
isSharedPlate() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateIdentifier

J

JSON_SERVICE_URL - Static variable in interface ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.IScreeningApiServer

L

LARGEST_IN_BOUNDING_BOX - ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.SizeCriterion.Type: Picks that format where the image size is the largest one which just fits into a bounding box specified by width and height.
listAnalysisProcedures(ExperimentIdentifier) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: Returns an alphabetically sorted list of analysis procedure codes of all data sets of the specified experiment.
listAnalysisProcedures(ExperimentIdentifier) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade
listAnalysisProcedures(String) - Static method in class OpenBISScreeningML: Returns an alphabetically sorted list of analysis procedure codes of all data sets of a specified experiment.
listAvailableFeatureCodes(String, List<? extends IFeatureVectorDatasetIdentifier>) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.IScreeningApiServer: Groups the specified objects by a data store code and calls IDssServiceRpcScreening.listAvailableFeatureCodes(String, List) method for each group of objects on appropriate data store server.
listAvailableFeatureCodes(List<? extends IFeatureVectorDatasetIdentifier>) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: For a given set of feature vector data sets provides the list of all available features.
listAvailableFeatureCodes(List<? extends IFeatureVectorDatasetIdentifier>) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade: For a given set of feature vector data sets provides the list of all available features.
listAvailableFeatureLists(IFeatureVectorDatasetIdentifier) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: For a given feature vector data set return a list of available feature lists.
listAvailableFeatureLists(IFeatureVectorDatasetIdentifier) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade
listAvailableFeatureNames(List<? extends IFeatureVectorDatasetIdentifier>) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: Deprecated.
Use IScreeningOpenbisServiceFacade.listAvailableFeatureCodes(List) instead. Since version 1.2 of the API features are no longer identified by a name but by a code. Previous client code still works but the name will be normalized internally. "Normalized" means that the original name argument is converted to upper case and any symbol which isn't from A-Z or 0-9 is replaced by an underscore character. The FeatureVectorDataset will provide feature codes and feature labels.
listAvailableFeatureNames(List<? extends IFeatureVectorDatasetIdentifier>) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade
listAvailableFeatures(String, List<? extends IFeatureVectorDatasetIdentifier>) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.IScreeningApiServer: Groups the specified objects by a data store code and calls IDssServiceRpcScreening.listAvailableFeatures(String, List) method for each group of objects on appropriate data store server.
listAvailableFeatures(List<? extends IFeatureVectorDatasetIdentifier>) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: For a given set of feature vector data sets provide the list of all available features.
listAvailableFeatures(List<? extends IFeatureVectorDatasetIdentifier>) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade: For a given set of feature vector data sets provide the list of all available features.
listAvailableImageRepresentationFormats(String, List<? extends IDatasetIdentifier>) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.IScreeningApiServer: Groups the specified objects by a data store code and calls IDssServiceRpcScreening.listAvailableImageRepresentationFormats(String, List) method for each group of objects on appropriate data store server.
listAvailableImageRepresentationFormats(List<? extends IDatasetIdentifier>) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade
listAvailableImageRepresentationFormats(List<? extends IDatasetIdentifier>) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade
listChannels(String) - Static method in class OpenBISScreeningML: Lists all channels measured in experiment.
listDataSetFilesForExperiment(String, String) - Static method in class OpenBISScreeningML: Lists all files of all data sets for specified experiment and data set type code matching specified regular expression pattern.
listDataSetsFiles(String, String) - Static method in class OpenBISScreeningML: Lists all files of all data sets for specifies plate and data set type code matching specified regular expression pattern.
listExperiments() - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: Return the list of all visible experiments, along with their hierarchical context (space, project).
listExperiments() - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade
listExperiments() - Static method in class OpenBISScreeningML: Lists all experiment.
listExperiments(String) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: Return the list of all experiments visible to user userId, along with their hierarchical context (space, project).
listExperiments(String) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade
listExperiments(String) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.IScreeningApiServer: Return the list of all visible experiments, along with their hierarchical context (space, project).
listExperiments(String, String) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.IScreeningApiServer: Return the list of all experiments visible to user userId, along with their hierarchical context (space, project).
listFeatures(String, String) - Static method in class OpenBISScreeningML: Lists all features computed for experiment using specified analysis procedure.
listFeatureVectorDatasets(String, List<? extends PlateIdentifier>) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.IScreeningApiServer: For a given set of plates (given by space / plate bar code), provide the list of all data sets containing feature vectors for each of these plates.
listFeatureVectorDatasets(List<? extends PlateIdentifier>) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: For a given set of plates provides the list of all connected data sets containing feature vectors.
listFeatureVectorDatasets(List<? extends PlateIdentifier>) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade: For a given set of plates provides the list of all connected data sets containing feature vectors.
listFeatureVectorDatasets(List<? extends PlateIdentifier>, String) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: For a given set of plates provides the list of all connected data sets containing feature vectors and having specified analysis procedure property.
listFeatureVectorDatasets(List<? extends PlateIdentifier>, String) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade
listImageDatasets(String, List<? extends PlateIdentifier>) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.IScreeningApiServer: For a given set of plates provide the list of all data sets containing images for each of these plates.
listImageDatasets(List<? extends PlateIdentifier>) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: Deprecated.
Use IScreeningOpenbisServiceFacade.listRawImageDatasets(List) instead.
listImageDatasets(List<? extends PlateIdentifier>) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade: Deprecated.
Use ScreeningOpenbisServiceFacade.listRawImageDatasets(List) instead.
listImageMetadata(IImageDatasetIdentifier) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: For a given image data set, provide meta like like which image channels have been acquired, what is the tile geometry, the available (natural) image size(s) and the like.
listImageMetadata(IImageDatasetIdentifier) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade
listImageMetadata(String, List<? extends IImageDatasetIdentifier>) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.IScreeningApiServer: Groups the specified objects by a data store code and calls IDssServiceRpcScreening.listImageMetadata(String, List) method for each group of objects on appropriate data store server.
listImageMetadata(List<? extends IImageDatasetIdentifier>) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: For a given set of image data sets, provide meta like like which image channels have been acquired, what is the tile geometry, the available (natural) image size(s) and the like.
listImageMetadata(List<? extends IImageDatasetIdentifier>) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade
listMaterials(String) - Static method in class OpenBISScreeningML: List all material of a given type.
listPlateMaterialMapping(String, List<? extends PlateIdentifier>, MaterialTypeIdentifier) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.IScreeningApiServer: For a given list of plates, return the mapping of plate wells to materials contained in each well.
listPlateMaterialMapping(List<? extends PlateIdentifier>, MaterialTypeIdentifier) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: For a given list of plates, return the mapping of plate wells to materials contained in each well.
listPlateMaterialMapping(List<? extends PlateIdentifier>, MaterialTypeIdentifier) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade
listPlates() - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: Return the list of all visible plates assigned to any experiment, along with their hierarchical context (space, project, experiment).
listPlates() - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade: Return the list of all visible plates assigned to any experiment, along with their hierarchical context (space, project, experiment).
listPlates() - Static method in class OpenBISScreeningML: Lists all plates.
listPlates(ExperimentIdentifier) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: Return the list of all plates for the given experiment.
listPlates(ExperimentIdentifier) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade: Return the list of all plates for the given experiment.
listPlates(ExperimentIdentifier, String) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: Return the list of all plates for the given experiment and analysis procedure.
listPlates(ExperimentIdentifier, String) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade
listPlates(String) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.IScreeningApiServer: Return the list of all visible plates assigned to any experiment, along with their hierarchical context (space, project, experiment).
listPlates(String) - Static method in class OpenBISScreeningML: Lists the plates of experiment.
listPlates(String, ExperimentIdentifier) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.IScreeningApiServer: Return the list of all plates assigned to the given experiment.
listPlates(String, String) - Static method in class OpenBISScreeningML: Lists the plates of experiment and analysis procedure.
listPlateWells(ExperimentIdentifier, MaterialIdentifier, boolean) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: For the given experimentIdentifier find all plate locations that are connected to the specified materialIdentifier.
listPlateWells(ExperimentIdentifier, MaterialIdentifier, boolean) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade: For the given experimentIdentifier find all plate locations that are connected to the specified materialIdentifier.
listPlateWells(MaterialIdentifier, boolean) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: For the given materialIdentifier find all plate locations that are connected to it.
listPlateWells(MaterialIdentifier, boolean) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade: For the given materialIdentifier find all plate locations that are connected to it.
listPlateWells(PlateIdentifier) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: For the given plateIdentifier find all wells that are connected to it.
listPlateWells(PlateIdentifier) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade: For the given plateIdentifier find all wells that are connected to it.
listPlateWells(String, ExperimentIdentifier, MaterialIdentifier, boolean) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.IScreeningApiServer: For the given experimentIdentifier, find all plate locations that are connected to the specified materialIdentifier.
listPlateWells(String, MaterialIdentifier, boolean) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.IScreeningApiServer: For the given materialIdentifier, find all plate locations that are connected to it.
listPlateWells(String, PlateIdentifier) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.IScreeningApiServer: For the given plateIdentifier find all wells that are connected to it.
listRawImageDatasets(String, List<? extends PlateIdentifier>) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.IScreeningApiServer: For a given set of plates provide the list of all data sets containing raw images for each of these plates.
listRawImageDatasets(List<? extends PlateIdentifier>) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: For a given set of plates provides the list of all connected data sets containing raw images.
listRawImageDatasets(List<? extends PlateIdentifier>) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade: For a given set of plates provides the list of all connected data sets containing raw images.
listSegmentationImageDatasets(String, List<? extends PlateIdentifier>) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.IScreeningApiServer: For a given set of plates provide the list of all data sets containing segmentation images for each of these plates.
listSegmentationImageDatasets(List<? extends PlateIdentifier>) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: For a given set of plates provides the list of all connected data sets containing segmentation images (overlays).
listSegmentationImageDatasets(List<? extends PlateIdentifier>) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade: For a given set of plates provides the list of all connected data sets containing images.
listSegmentationImageDatasets(List<? extends PlateIdentifier>, String) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: For a given set of plates provides the list of all connected data sets containing segmentation images (overlays) and calculated by specified analysis procedure.
listSegmentationImageDatasets(List<? extends PlateIdentifier>, String) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade
listSegmentationObjects(String, String) - Static method in class OpenBISScreeningML: Lists all segmentation objects for the plate.
loadDataSetFile(String, String, String) - Static method in class OpenBISScreeningML: Loads file/folder of specified data set and specified file/folder path inside the data set.
loadDataSets(String, String, Object[][], String) - Static method in class OpenBISScreeningML: Loads data sets for specified plate code.
loadDataSets(String, String, String) - Static method in class OpenBISScreeningML: Loads data sets for specified plate code.
loadDataSetsForExperiment(String, String, Object[][], String) - Static method in class OpenBISScreeningML: Loads data sets for specified experiment code.
LoadEmptyImagesTest - Class in ch.systemsx.cisd.openbis.plugin.screening.client.api.v1: A test class which tests the performance of loading thumbnails.
loadFeatures(String, List<FeatureVectorDatasetReference>, List<String>) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.IScreeningApiServer: Groups the specified objects by a data store code and calls IDssServiceRpcScreening.loadFeatures(String, List, List) method for each group of objects on appropriate data store server.
loadFeatures(List<FeatureVectorDatasetReference>, List<String>) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: For a given set of data sets and a set of features (given by their code), provide all the feature vectors.
loadFeatures(List<FeatureVectorDatasetReference>, List<String>) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade: For a given set of data sets and a set of features (given by their code), provide all the feature vectors.
loadFeaturesForDatasetWellReferences(String, List<FeatureVectorDatasetWellReference>, List<String>) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.IScreeningApiServer: Groups the specified objects by a data store code and calls IDssServiceRpcScreening.loadFeaturesForDatasetWellReferences(String, List, List) method for each group of objects on appropriate data store server.
loadFeaturesForDatasetWellReferences(List<FeatureVectorDatasetWellReference>, List<String>) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: Conceptually, for a given list of dataset well references (i.e.
loadFeaturesForDatasetWellReferences(List<FeatureVectorDatasetWellReference>, List<String>) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade
loadFeaturesForPlates(List<? extends PlateIdentifier>, List<String>) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: For a given set of plates and a set of features (given by their code), provide all the feature vectors.
loadFeaturesForPlates(List<? extends PlateIdentifier>, List<String>) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade: For a given set of plates and a set of features (given by their code), provide all the feature vectors.
loadFeaturesForPlates(List<? extends PlateIdentifier>, List<String>, String) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: For a given set of plates and a set of features (given by their code), provide all the feature vectors created by specified analysis procedure.
loadFeaturesForPlates(List<? extends PlateIdentifier>, List<String>, String) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade
loadFeaturesForPlateWells(ExperimentIdentifier, MaterialIdentifier, String, List<String>) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: For the given experimentIdentifier find all plate locations that are connected to the specified materialIdentifier and load the feature vectors for the given feature code if not null, or all available features otherwise.
loadFeaturesForPlateWells(ExperimentIdentifier, MaterialIdentifier, String, List<String>) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade
loadFeaturesForPlateWells(ExperimentIdentifier, MaterialIdentifier, List<String>) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: Deprecated.
use IScreeningOpenbisServiceFacade.loadFeaturesForPlateWells(ExperimentIdentifier, MaterialIdentifier, String, List) with third argument set to null.
loadFeaturesForPlateWells(ExperimentIdentifier, MaterialIdentifier, List<String>) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade
loadFeaturesForPlateWells(MaterialIdentifier, String, List<String>) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: For the given materialIdentifier find all plate locations that are connected to it and load the feature vectors for the given feature code if not null, or all available features otherwise.
loadFeaturesForPlateWells(MaterialIdentifier, String, List<String>) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade
loadFeaturesForPlateWells(MaterialIdentifier, List<String>) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: Deprecated.
use IScreeningOpenbisServiceFacade.loadFeaturesForPlateWells(MaterialIdentifier, String, List) with second argument set to null.
loadFeaturesForPlateWells(MaterialIdentifier, List<String>) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade
LoadImageConfiguration - Class in ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto: A DTO for transmitting information about how the images should be loaded.
LoadImageConfiguration() - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.LoadImageConfiguration
loadImages(IDatasetIdentifier, List<WellPosition>, String, ImageSize) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: Loads original images or thumbnails for a specified data set, a list of well positions (empty list means all wells), a channel, and an optional thumb nail size.
loadImages(IDatasetIdentifier, List<WellPosition>, String, ImageSize) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade
loadImages(IDatasetIdentifier, List<WellPosition>, String, ImageSize, IPlateImageHandler) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: Loads PNG-encoded images for specified data set, list of well positions (empty list means all wells), channel, and optional thumb nail size.
loadImages(IDatasetIdentifier, List<WellPosition>, String, ImageSize, IPlateImageHandler) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade
loadImages(String, int, int) - Static method in class OpenBISScreeningML: Loads the TIFF images for the given well location, all tiles and all channels and stores them in temporary files.
loadImages(String, int, int, int) - Static method in class OpenBISScreeningML: Loads the TIFF images for the given well location, tile number, and all channels and stores them in temporary files.
loadImages(String, int, int, int, String[]) - Static method in class OpenBISScreeningML: Loads the TIFF images for the given well location, tile number, and list of channels and stores them in temporary files.
loadImages(String, int, int, String[]) - Static method in class OpenBISScreeningML: Loads the TIFF images for the given well location, list of channels, and all tiles and stores them in temporary files.
loadImages(List<PlateImageReference>, boolean, IPlateImageHandler) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: Loads images for a given list of image references (given by data set code, well position, channel and tile) and hands it over to the plateImageHandler.
If convertToPng==true, the images will be converted to PNG format before being shipped, otherwise they will be shipped in the format that they are stored on the server.
loadImages(List<PlateImageReference>, boolean, IPlateImageHandler) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade
loadImages(List<PlateImageReference>, IPlateImageHandler, IImageRepresentationFormatSelectionCriterion...) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: Provides images for the specified list of image references (specified by data set code, well position, channel and tile) and image selection criteria.
loadImages(List<PlateImageReference>, IPlateImageHandler, IImageRepresentationFormatSelectionCriterion...) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade
loadImages(List<PlateImageReference>, IPlateImageHandler, ImageRepresentationFormat) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: Provides images for the specified list of image references (specified by data set code, well position, channel and tile) and specified image representation format.
loadImages(List<PlateImageReference>, IPlateImageHandler, ImageRepresentationFormat) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade
loadImages(List<PlateImageReference>, ScreeningOpenbisServiceFacade.IImageOutputStreamProvider) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: Saves images for a given list of image references (given by data set code, well position, channel and tile) in the provided output streams.
loadImages(List<PlateImageReference>, ScreeningOpenbisServiceFacade.IImageOutputStreamProvider) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade: Saves images for a given list of image references (given by data set code, well position, channel and tile) in the provided output streams.
loadImages(List<PlateImageReference>, ScreeningOpenbisServiceFacade.IImageOutputStreamProvider, boolean) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: Saves images for a given list of image references (given by data set code, well position, channel and tile) in the provided output streams.
loadImages(List<PlateImageReference>, ScreeningOpenbisServiceFacade.IImageOutputStreamProvider, boolean) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade: Saves images for a given list of image references (given by data set code, well position, channel and tile) in the provided output streams.
loadImages(List<PlateImageReference>, ImageSize, IPlateImageHandler) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: Loads PNG-encoded images for specified image references and, optionally, image size.
loadImages(List<PlateImageReference>, ImageSize, IPlateImageHandler) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade
loadImages(List<PlateImageReference>, LoadImageConfiguration, IPlateImageHandler) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: Loads images where the desired properties of the images are specified by a LoadImageConfiguration.
loadImages(List<PlateImageReference>, LoadImageConfiguration, IPlateImageHandler) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade
loadImagesBase64(String, List<PlateImageReference>) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.IScreeningApiServer: Groups the specified objects by a data store code and calls IDssServiceRpcScreening.loadImagesBase64(String, List) method for each group of objects on appropriate data store server.
loadImagesBase64(String, List<PlateImageReference>, boolean) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.IScreeningApiServer: Groups the specified objects by a data store code and calls IDssServiceRpcScreening.loadImagesBase64(String, List, boolean) method for each group of objects on appropriate data store server.
loadImagesBase64(String, List<PlateImageReference>, IImageRepresentationFormatSelectionCriterion...) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.IScreeningApiServer: Groups the specified objects by a data store code and calls IDssServiceRpcScreening.loadImagesBase64(String, List, IImageRepresentationFormatSelectionCriterion...) method for each group of objects on appropriate data store server.
loadImagesBase64(String, List<PlateImageReference>, ImageRepresentationFormat) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.IScreeningApiServer: Groups the specified objects by a data store code and calls IDssServiceRpcScreening.loadImagesBase64(String, List, ImageRepresentationFormat) method for each group of objects on appropriate data store server.
loadImagesBase64(String, List<PlateImageReference>, ImageSize) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.IScreeningApiServer: Groups the specified objects by a data store code and calls IDssServiceRpcScreening.loadImagesBase64(String, List, ImageSize) method for each group of objects on appropriate data store server.
loadImagesBase64(String, List<PlateImageReference>, LoadImageConfiguration) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.IScreeningApiServer: Groups the specified objects by a data store code and calls IDssServiceRpcScreening.loadImagesBase64(String, List, LoadImageConfiguration) method for each group of objects on appropriate data store server.
LoadImagesScreeningClientApiTest - Class in ch.systemsx.cisd.openbis.plugin.screening.client.api.v1: A test class which shows how to use API to load images.
LoadImagesScreeningClientApiTest() - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.LoadImagesScreeningClientApiTest
LoadImagesWithTransformationTest - Class in ch.systemsx.cisd.openbis.plugin.screening.client.api.v1: A test class which downloads image for one well in a data set with and without the transformation.
loadImageWellCaching(PlateImageReference, ImageSize) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: Loads an PNG-encoded image for the specified image reference and, optionally, image size.
loadImageWellCaching(PlateImageReference, ImageSize) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade
loadPhysicalThumbnails(List<PlateImageReference>, ImageRepresentationFormat, IPlateImageHandler) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: Retrieves images for the specified image references and invokes the plateImageHandler passing in image data.
loadPhysicalThumbnails(List<PlateImageReference>, ImageRepresentationFormat, IPlateImageHandler) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade
loadPhysicalThumbnails(List<PlateImageReference>, ImageRepresentationFormat, ScreeningOpenbisServiceFacade.IImageOutputStreamProvider) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: Retrieves images for the specified image references and invokes the IImageOutputStreamProvider passing in image data.
loadPhysicalThumbnails(List<PlateImageReference>, ImageRepresentationFormat, ScreeningOpenbisServiceFacade.IImageOutputStreamProvider) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade
loadPhysicalThumbnailsBase64(String, List<PlateImageReference>, ImageRepresentationFormat) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.IScreeningApiServer: Groups the specified objects by a data store code and calls IDssServiceRpcScreening.loadPhysicalThumbnailsBase64(String, List, ImageRepresentationFormat) method for each group of objects on appropriate data store server.
loadSegmentationImages(String, int, int, int, String[], String) - Static method in class OpenBISScreeningML: Has the same effect as OpenBISScreeningML.loadImages(String, int, int, int, String[]), but instead of loading raw images loads their segmentation results if available.
loadSegmentationImages(String, int, int, String[], String) - Static method in class OpenBISScreeningML: Has the same effect as OpenBISScreeningML.loadImages(String, int, int, String[]), but instead of loading raw images loads their segmentation results if available.
loadThumbnailImages(List<PlateImageReference>, IPlateImageHandler) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: Loads thumbnail images for specified data set, for a given list of image references (given by data set code, well position, channel and tile) in the provided output streams.
loadThumbnailImages(List<PlateImageReference>, IPlateImageHandler) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade
loadThumbnailImages(List<PlateImageReference>, ScreeningOpenbisServiceFacade.IImageOutputStreamProvider) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: Loads thumbnail images for specified data set, for a given list of image references (given by data set code, well position, channel and tile) in the provided output streams.
loadThumbnailImages(List<PlateImageReference>, ScreeningOpenbisServiceFacade.IImageOutputStreamProvider) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade
loadThumbnailImagesBase64(String, List<PlateImageReference>) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.IScreeningApiServer: Groups the specified objects by a data store code and calls IDssServiceRpcScreening.loadThumbnailImagesBase64(String, List) method for each group of objects on appropriate data store server.
loadThumbnailImageWellCaching(PlateImageReference) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: Loads the PNG-encoded image for the specified imageReference.
loadThumbnailImageWellCaching(PlateImageReference) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade
LoadThumbnailsPerformanceTest - Class in ch.systemsx.cisd.openbis.plugin.screening.client.api.v1: A test class which tests the performance of loading thumbnails.
LogicalImageInfo - Class in ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto
LogicalImageInfo() - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.LogicalImageInfo
login(String, String, String) - Static method in class OpenBISScreeningML: Login to the openBIS server given as url.
logout() - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.AnalysisProcedureTest
logout() - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: Closes connection with the server.
logout() - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.LoadEmptyImagesTest
logout() - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.LoadImagesWithTransformationTest
logout() - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.LoadThumbnailsPerformanceTest
logout() - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade: Closes connection with the server.
logout() - Static method in class OpenBISScreeningML: Logs out and closes the session on the server.
logoutScreening(String) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.IScreeningApiServer: Logout the session with the specified session token.

M

main(String[]) - Static method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.AnalysisProcedureTest
main(String[]) - Static method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ImageViewer
main(String[]) - Static method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.LoadEmptyImagesTest
main(String[]) - Static method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.LoadImagesScreeningClientApiTest
main(String[]) - Static method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.LoadImagesWithTransformationTest
main(String[]) - Static method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.LoadThumbnailsPerformanceTest
main(String[]) - Static method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningClientApiTest
main(String[]) - Static method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningClientApiTester
MAJOR_VERSION - Static variable in interface ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.IScreeningApiServer: The major version of this service.
Material - Class in ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto: Material with properties.
Material(MaterialTypeIdentifier, String, Map<String, String>, Map<String, Material>) - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Material
MaterialIdentifier - Class in ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto: A unique identifier for a material like e.g.
MaterialIdentifier(MaterialTypeIdentifier, String) - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.MaterialIdentifier
MaterialTypeIdentifier - Class in ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto: A unique identifier for a material type.
MaterialTypeIdentifier(String) - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.MaterialTypeIdentifier
MicroscopyImageReference - Class in ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto: Identifies one image acquired in a microscopy context.
MicroscopyImageReference(int, String, IDatasetIdentifier) - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.MicroscopyImageReference: Reference to image dataset which has no wells (like e.g.

O

OLIGO - Static variable in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.MaterialTypeIdentifier: Material identifier for an siRNA-nucleotide
OpenBISScreeningML - Class in <Unnamed>: Simple Matlab interface for openBIS for Screening.
OriginalCriterion - Class in ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto: Criterion which filters image representation formats concerning whether they are original or not.
OriginalCriterion(boolean) - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.OriginalCriterion: Creates an instance based on the specified flag.

P

parseWellPosition(String) - Static method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellPosition: Parses a well position description of the form <row number>.<column number>.
parseWellPositions(String) - Static method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellPosition: Parses a white-space separated list of well position descriptions.
PermanentIdentifier - Class in ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto: A class representing a permanent identifier in openBIS.
PermanentIdentifier(String) - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PermanentIdentifier
Plate - Class in ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto: Unique identifier for a plate which is assigned to an experiment.
Plate(String, String, String, ExperimentIdentifier) - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Plate
Plate(String, String, String, String) - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Plate: Deprecated.
Plate(String, String, String, String, ExperimentIdentifier) - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Plate
PlateIdentifier - Class in ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto: Contains data which uniquely define a plate.
PlateIdentifier(String, String) - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateIdentifier: An empty spaceCode is interpreted as the home space, a null spaceCode is interpreted as 'no space', i.e.
PlateIdentifier(String, String, String) - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateIdentifier
PlateIdentifier(String, String, String, String) - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateIdentifier
PlateImageReference - Class in ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto: Identifies one image acquired in a screening context.
PlateImageReference(int, int, int, String, IDatasetIdentifier) - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateImageReference
PlateImageReference(int, String, WellPosition, IDatasetIdentifier) - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateImageReference
PlateMetadata - Class in ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto: Holds the complete metadata of a plate and its wells.
PlateMetadata(PlateIdentifier, Geometry, Map<String, String>, List<WellMetadata>) - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateMetadata
PlateWellMaterialMapping - Class in ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto
PlateWellMaterialMapping(PlateIdentifier, Geometry, int) - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateWellMaterialMapping
PlateWellMaterialMapping(PlateIdentifier, Geometry, List<MaterialIdentifier>[]) - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateWellMaterialMapping
PlateWellReferenceWithDatasets - Class in ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto: Provides a reference to a well on a screening plate, together with available data sets for the screening plate.
PlateWellReferenceWithDatasets(Plate, WellPosition) - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateWellReferenceWithDatasets
PlateWellReferenceWithDatasets(Plate, WellPosition, List<ImageDatasetReference>, List<FeatureVectorDatasetReference>) - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateWellReferenceWithDatasets
putDataSet(ExperimentIdentifier, File, NewDataSetMetadataDTO) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: Upload a new data set to the DSS for a plate.
putDataSet(ExperimentIdentifier, File, NewDataSetMetadataDTO) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade
putDataSet(PlateIdentifier, File, NewDataSetMetadataDTO) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: Upload a new data set to the DSS for a plate.
putDataSet(PlateIdentifier, File, NewDataSetMetadataDTO) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade
putDataSet(WellIdentifier, File, NewDataSetMetadataDTO) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: Upload a new data set to the DSS for a well.
putDataSet(WellIdentifier, File, NewDataSetMetadataDTO) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade: Upload a new data set to the DSS for a well.

R

REQUIRES_OPENBIS_AS_API - Static variable in class OpenBISScreeningML: The required version ("major.minor") of the screening API on the openBIS application server.
REQUIRES_OPENBIS_DSS_API - Static variable in class OpenBISScreeningML: The required version ("major.minor") of the screening API on the openBIS datastore server.
runTest() - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.AnalysisProcedureTest
runTest() - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.LoadEmptyImagesTest
runTest() - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.LoadImagesWithTransformationTest
runTest() - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.LoadThumbnailsPerformanceTest

S

saveImageTransformerFactory(List<IDatasetIdentifier>, String, IImageTransformerFactory) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: Saves the specified transformer factory for the specified channel and the experiment to which the specified data sets belong.
saveImageTransformerFactory(List<IDatasetIdentifier>, String, IImageTransformerFactory) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade
ScreeningClientApiTest - Class in ch.systemsx.cisd.openbis.plugin.screening.client.api.v1: A test class which shows how to use API.
ScreeningClientApiTest() - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningClientApiTest
ScreeningClientApiTester - Class in ch.systemsx.cisd.openbis.plugin.screening.client.api.v1: A test class which shows how to use API.
ScreeningClientApiTester() - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningClientApiTester
ScreeningJsonClassValueToClassObjectsMapping - Class in ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.json
ScreeningObjectMapper - Class in ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.json: Jackson library object mapper used in screening OpenBIS.
ScreeningObjectMapper() - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.json.ScreeningObjectMapper
ScreeningOpenbisServiceFacade - Class in ch.systemsx.cisd.openbis.plugin.screening.client.api.v1: A client side facade of openBIS and Datastore Server API.
ScreeningOpenbisServiceFacade.IImageOutputStreamProvider - Interface in ch.systemsx.cisd.openbis.plugin.screening.client.api.v1: An interface to provide mapping between image references and output streams where the images should be saved.
ScreeningOpenbisServiceFacadeFactory - Class in ch.systemsx.cisd.openbis.plugin.screening.client.api.v1: Default implementation of IScreeningOpenbisServiceFacadeFactory.
ScreeningOpenbisServiceFacadeFactory() - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacadeFactory
searchForMaterials(SearchCriteria) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: Exposes material search functionaliy (used for ScreeningML)
searchForMaterials(SearchCriteria) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade: Searchs for Material given a search criteria.
searchForSamples(SearchCriteria) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: Exposes material search functionaliy (used for ScreeningML)
searchForSamples(SearchCriteria) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade: Searchs for Samples given a search criteria.
SERVICE_NAME - Static variable in interface ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.IScreeningApiServer: Name of this service for which it is registered at the RPC name server.
SERVICE_URL - Static variable in interface ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.IScreeningApiServer: Service part of the URL to access this service remotely.
setAnalysisProcedureOrNull(String) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.DatasetOverlayImagesReference
setAvailableImageTransformations(List<InternalImageTransformationInfo>) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.InternalImageChannel
setChannels(List<InternalImageChannel>) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetParameters
setChannelStacks(List<ImageChannelStack>) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.LogicalImageInfo
setCode(String) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.InternalImageChannel
setCode(String) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.InternalImageTransformationInfo
setColsNumOrNull(Integer) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetParameters
setColumn(int) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellLocation
setDatasetCode(String) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetParameters
setDefault(boolean) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.InternalImageTransformationInfo
setDepthOrNull(Float) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageChannelStack
setDescription(String) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.InternalImageChannel
setDescription(String) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.InternalImageTransformationInfo
setDesiredImageFormatPng(boolean) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.LoadImageConfiguration: Set whether the image should be converted from its original format to PNG.
setDesiredImageSize(ImageSize) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.LoadImageConfiguration: Set the desired size of the image.
setHeight(int) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageResolution
setId(long) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageChannelStack
setImageDataset(DatasetImagesReference) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetEnrichedReference
setImageDataset(ImageDatasetEnrichedReference) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.LogicalImageInfo
setImageParameters(ImageDatasetParameters) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.DatasetImagesReference
setLabel(String) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.InternalImageChannel
setLabel(String) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.InternalImageTransformationInfo
setMergedChannelTransformerFactorySignatureOrNull(String) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetParameters
setMultidimensional(boolean) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetParameters
setOpenBisImageTransformationApplied(boolean) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.LoadImageConfiguration: Set whether the image transformation stored in openBIS for a channel or merged channel should be applied.
setOverlayDatasets(List<DatasetOverlayImagesReference>) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetEnrichedReference
setRow(int) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellLocation
setRowsNumOrNull(Integer) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetParameters
setSeriesNumberOrNull(Integer) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageChannelStack
setSingleChannelImageTransformationCode(String) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.LoadImageConfiguration: Sets the code of the transformation, which should be applied to the image.
setTileCol(int) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageChannelStack
setTileColsNum(int) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetParameters
setTileRow(int) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageChannelStack
setTileRowsNum(int) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetParameters
setTimePointOrNull(Float) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageChannelStack
setTransformationSignature(String) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.InternalImageTransformationInfo
setWavelength(Integer) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.InternalImageChannel
setWidth(int) - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageResolution
SizeCriterion - Class in ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto: Criterion based on the image size.
SizeCriterion(int, int, SizeCriterion.Type) - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.SizeCriterion: Creates an instance for the specified image size and criterion type.
SizeCriterion.Type - Enum in ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto
SMALLEST_COVERING_BOUNDING_BOX - ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.SizeCriterion.Type: Picks that format where the image size is the smallest one covering a bounding box specified by width and height.

T

toPlateGeometryStr() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Geometry: Renders this in the form <width>X<height>.
toString() - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ExampleImageTransformerFactory
toString() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.DatasetIdentifier
toString() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.DatasetImageRepresentationFormats
toString() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.DatasetReference
toString() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ExperimentIdentifier
toString() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureInformation
toString() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVector
toString() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDataset
toString() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDatasetReference
toString() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDatasetWellReference
toString() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorWithDescription
toString() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Geometry: Renders this in the form {<width>,<height>}.
toString() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageChannel
toString() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetMetadata
toString() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageRepresentationFormat.ImageRepresentationTransformation
toString() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageRepresentationFormat
toString() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageSize
toString() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageTransformationInfo
toString() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.LoadImageConfiguration
toString() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.MaterialIdentifier
toString() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.MaterialTypeIdentifier
toString() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.MicroscopyImageReference
toString() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PermanentIdentifier
toString() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Plate
toString() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateIdentifier
toString() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateImageReference
toString() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateWellReferenceWithDatasets
toString() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellIdentifier
toString() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellMetadata
toString() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellPosition
tryCreate(String, String) - Static method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade: Creates a service facade which communicates with the openBIS server at the specified URL for an authenticated user.
tryCreate(String, String) - Static method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacadeFactory: Creates a service facade which communicates with the openBIS server at the specified URL for an authenticated user.
tryCreate(String, String, String) - Static method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade: Creates a service facade which communicates with the openBIS server at the specified URL.
tryCreate(String, String, String) - Static method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacadeFactory: Creates a service facade which communicates with the openBIS server at the specified URL.
tryCreateForTest(String, String, IScreeningApiServer) - Static method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade: This constructor is only for use in tests.
tryCreateWithLocalDss(String, String, IDssServiceRpcScreening) - Static method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade: Creates a service facade which communicates with the openBIS server at the specified URL for an authenticated user.
tryCreateWithLocalDss(String, String, IDssServiceRpcScreening, long) - Static method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade
tryGetDescription() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageChannel: Returns the channel' description or null, if this channel has no description.
tryGetDescription() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageTransformationInfo: The description of the image transformation, or null, if the image transformation has no description.
tryGetProjectCode() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateIdentifier
tryGetSpaceCode() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateIdentifier: A code of the space to which the plate belongs or null if it is a shared plate.
tryGetWavelength() - Method in class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageChannel: Returns the channel's wavelength or null, if the wavelength is not known.
tryLoginScreening(String, String) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.IScreeningApiServer: Authenticates the user with a given password.
tryToCreate(String, String) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacadeFactory: Tries to create a facade object for specified session token and server URL.
tryToCreate(String, String) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacadeFactory
tryToCreate(String, String, String) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacadeFactory: Tries to create a facade object for specified user ID, password and server URL.
tryToCreate(String, String, String) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacadeFactory

U

updatePlateProperties(PlateIdentifier, Map<String, String>) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: Updates properties of specified plate.
updatePlateProperties(PlateIdentifier, Map<String, String>) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade
updatePlateProperties(String, Object[][]) - Static method in class OpenBISScreeningML: Updates properties of specified plate.
updateWellProperties(WellIdentifier, Map<String, String>) - Method in interface ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade: Updates properties of specified well.
updateWellProperties(WellIdentifier, Map<String, String>) - Method in class ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade
updateWellProperties(String, int, int, Object[][]) - Static method in class OpenBISScreeningML: Updates properties of specified well for specified plate.
uploadDataSet(String, String, String, Object[][]) - Static method in class OpenBISScreeningML: Uploads specified data set for specified plate.
uploadDataSetForExperimentAndParents(String, Object[], String, String, Object[][]) - Static method in class OpenBISScreeningML: Uploads a data set to the specified experiment, setting the data set parents.
uploadDataSetForPlateAndParents(String, Object[], String, String, Object[][]) - Static method in class OpenBISScreeningML: Uploads specified data set for specified plate.

V

valueOf(String) - Static method in enum ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.SizeCriterion.Type: Returns the enum constant of this type with the specified name.
values() - Static method in enum ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.SizeCriterion.Type: Returns an array containing the constants of this enum type, in the order they are declared.
VERSION - Static variable in class OpenBISScreeningML: The version of the API.

W

WellIdentifier - Class in ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto: Contains data which uniquely define a well on a plate.
WellIdentifier(PlateIdentifier, WellPosition, String) - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellIdentifier
WellLocation - Class in ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto
WellLocation() - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellLocation
WellMetadata - Class in ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto: WellMetadata holds a complete set of metadata for an openBIS well.
WellMetadata(PlateIdentifier, String, String, String, WellPosition, Map<String, String>, Map<String, Material>) - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellMetadata
WellPosition - Class in ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto: Identifier of a well on a screening plate, contains row and column number.
WellPosition(int, int) - Constructor for class ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellPosition

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