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A
- addToBioAssayDataSources(BioAssayData) - Method in class org.biomage.BioAssayData.Transformation
- Method to add BioAssayData to BioAssayDataSources_list
- addToBioAssayDataSources(int, BioAssayData) - Method in class org.biomage.BioAssayData.Transformation
- Method to add BioAssayData at position to BioAssayDataSources_list
- addToBioAssayData_list(BioAssayData) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Method to add BioAssayData to BioAssayData_list
- addToBioAssayData_list(int, BioAssayData) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Method to add BioAssayData at position to BioAssayData_list
- addToBioAssayDimension_list(BioAssayDimension) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Method to add BioAssayDimension to BioAssayDimension_list
- addToBioAssayDimension_list(int, BioAssayDimension) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Method to add BioAssayDimension at position to BioAssayDimension_list
- addToBioAssayMap_list(BioAssayMap) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Method to add BioAssayMap to BioAssayMap_list
- addToBioAssayMap_list(int, BioAssayMap) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Method to add BioAssayMap at position to BioAssayMap_list
- addToBioAssayMaps(BioAssayMap) - Method in class org.biomage.BioAssayData.BioAssayMapping
- Method to add BioAssayMap to BioAssayMaps_list
- addToBioAssayMaps(int, BioAssayMap) - Method in class org.biomage.BioAssayData.BioAssayMapping
- Method to add BioAssayMap at position to BioAssayMaps_list
- addToBioAssayTupleData(BioAssayDatum) - Method in class org.biomage.BioAssayData.BioDataTuples
- Method to add BioAssayDatum to BioAssayTupleData_list
- addToBioAssayTupleData(int, BioAssayDatum) - Method in class org.biomage.BioAssayData.BioDataTuples
- Method to add BioAssayDatum at position to BioAssayTupleData_list
- addToBioAssays(BioAssay) - Method in class org.biomage.BioAssayData.BioAssayDimension
- Method to add BioAssay to BioAssays_list
- addToBioAssays(int, BioAssay) - Method in class org.biomage.BioAssayData.BioAssayDimension
- Method to add BioAssay at position to BioAssays_list
- addToCompositeSequenceDimension_list(CompositeSequenceDimension) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Method to add CompositeSequenceDimension to CompositeSequenceDimension_list
- addToCompositeSequenceDimension_list(int, CompositeSequenceDimension) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Method to add CompositeSequenceDimension at position to CompositeSequenceDimension_list
- addToCompositeSequences(CompositeSequence) - Method in class org.biomage.BioAssayData.CompositeSequenceDimension
- Method to add CompositeSequence to CompositeSequences_list
- addToCompositeSequences(int, CompositeSequence) - Method in class org.biomage.BioAssayData.CompositeSequenceDimension
- Method to add CompositeSequence at position to CompositeSequences_list
- addToContainedFeatures(Feature) - Method in class org.biomage.BioAssayData.FeatureDimension
- Method to add Feature to ContainedFeatures_list
- addToContainedFeatures(int, Feature) - Method in class org.biomage.BioAssayData.FeatureDimension
- Method to add Feature at position to ContainedFeatures_list
- addToDerivedBioAssayData_list(DerivedBioAssayData) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Method to add DerivedBioAssayData to DerivedBioAssayData_list
- addToDerivedBioAssayData_list(int, DerivedBioAssayData) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Method to add DerivedBioAssayData at position to DerivedBioAssayData_list
- addToDesignElementDimension_list(DesignElementDimension) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Method to add DesignElementDimension to DesignElementDimension_list
- addToDesignElementDimension_list(int, DesignElementDimension) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Method to add DesignElementDimension at position to DesignElementDimension_list
- addToDesignElementMap_list(DesignElementMap) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Method to add DesignElementMap to DesignElementMap_list
- addToDesignElementMap_list(int, DesignElementMap) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Method to add DesignElementMap at position to DesignElementMap_list
- addToDesignElementMaps(DesignElementMap) - Method in class org.biomage.BioAssayData.DesignElementMapping
- Method to add DesignElementMap to DesignElementMaps_list
- addToDesignElementMaps(int, DesignElementMap) - Method in class org.biomage.BioAssayData.DesignElementMapping
- Method to add DesignElementMap at position to DesignElementMaps_list
- addToFeatureDimension_list(FeatureDimension) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Method to add FeatureDimension to FeatureDimension_list
- addToFeatureDimension_list(int, FeatureDimension) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Method to add FeatureDimension at position to FeatureDimension_list
- addToMeasuredBioAssayData_list(MeasuredBioAssayData) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Method to add MeasuredBioAssayData to MeasuredBioAssayData_list
- addToMeasuredBioAssayData_list(int, MeasuredBioAssayData) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Method to add MeasuredBioAssayData at position to MeasuredBioAssayData_list
- addToQuantitationTypeDimension_list(QuantitationTypeDimension) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Method to add QuantitationTypeDimension to QuantitationTypeDimension_list
- addToQuantitationTypeDimension_list(int, QuantitationTypeDimension) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Method to add QuantitationTypeDimension at position to QuantitationTypeDimension_list
- addToQuantitationTypeMap_list(QuantitationTypeMap) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Method to add QuantitationTypeMap to QuantitationTypeMap_list
- addToQuantitationTypeMap_list(int, QuantitationTypeMap) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Method to add QuantitationTypeMap at position to QuantitationTypeMap_list
- addToQuantitationTypeMaps(QuantitationTypeMap) - Method in class org.biomage.BioAssayData.QuantitationTypeMapping
- Method to add QuantitationTypeMap to QuantitationTypeMaps_list
- addToQuantitationTypeMaps(int, QuantitationTypeMap) - Method in class org.biomage.BioAssayData.QuantitationTypeMapping
- Method to add QuantitationTypeMap at position to QuantitationTypeMaps_list
- addToQuantitationTypes(QuantitationType) - Method in class org.biomage.BioAssayData.QuantitationTypeDimension
- Method to add QuantitationType to QuantitationTypes_list
- addToQuantitationTypes(int, QuantitationType) - Method in class org.biomage.BioAssayData.QuantitationTypeDimension
- Method to add QuantitationType at position to QuantitationTypes_list
- addToReporterDimension_list(ReporterDimension) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Method to add ReporterDimension to ReporterDimension_list
- addToReporterDimension_list(int, ReporterDimension) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Method to add ReporterDimension at position to ReporterDimension_list
- addToReporters(Reporter) - Method in class org.biomage.BioAssayData.ReporterDimension
- Method to add Reporter to Reporters_list
- addToReporters(int, Reporter) - Method in class org.biomage.BioAssayData.ReporterDimension
- Method to add Reporter at position to Reporters_list
- addToSourceBioAssays(BioAssay) - Method in class org.biomage.BioAssayData.BioAssayMap
- Method to add BioAssay to SourceBioAssays_list
- addToSourceBioAssays(int, BioAssay) - Method in class org.biomage.BioAssayData.BioAssayMap
- Method to add BioAssay at position to SourceBioAssays_list
- addToSourcesQuantitationType(QuantitationType) - Method in class org.biomage.BioAssayData.QuantitationTypeMap
- Method to add QuantitationType to SourcesQuantitationType_list
- addToSourcesQuantitationType(int, QuantitationType) - Method in class org.biomage.BioAssayData.QuantitationTypeMap
- Method to add QuantitationType at position to SourcesQuantitationType_list
- addToSummaryStatistics(NameValueType) - Method in class org.biomage.BioAssayData.BioAssayData
- Method to add NameValueType to SummaryStatistics_list
- addToSummaryStatistics(int, NameValueType) - Method in class org.biomage.BioAssayData.BioAssayData
- Method to add NameValueType at position to SummaryStatistics_list
B
- BioAssayData - class org.biomage.BioAssayData.BioAssayData.
- Represents the dataset created when the BioAssays are created.
- BioAssayData() - Constructor for class org.biomage.BioAssayData.BioAssayData
- Default constructor.
- BioAssayData(Attributes) - Constructor for class org.biomage.BioAssayData.BioAssayData
- Attribute constructor.
- BioAssayData_package - class org.biomage.BioAssayData.BioAssayData_package.
- The classes defined here provide data and the information and annotation on the derivation of that data.
- BioAssayData_package() - Constructor for class org.biomage.BioAssayData.BioAssayData_package
- Default constructor.
- BioAssayData_package(Attributes) - Constructor for class org.biomage.BioAssayData.BioAssayData_package
- Attribute constructor.
- BioAssayData_package.BioAssayData_list - class org.biomage.BioAssayData.BioAssayData_package.BioAssayData_list.
- Inner list class for holding multiple entries for attribute bioAssayData_list.
- BioAssayData_package.BioAssayData_list() - Constructor for class org.biomage.BioAssayData.BioAssayData_package.BioAssayData_list
- BioAssayData_package.BioAssayDimension_list - class org.biomage.BioAssayData.BioAssayData_package.BioAssayDimension_list.
- Inner list class for holding multiple entries for attribute bioAssayDimension_list.
- BioAssayData_package.BioAssayDimension_list() - Constructor for class org.biomage.BioAssayData.BioAssayData_package.BioAssayDimension_list
- BioAssayData_package.BioAssayMap_list - class org.biomage.BioAssayData.BioAssayData_package.BioAssayMap_list.
- Inner list class for holding multiple entries for attribute bioAssayMap_list.
- BioAssayData_package.BioAssayMap_list() - Constructor for class org.biomage.BioAssayData.BioAssayData_package.BioAssayMap_list
- BioAssayData_package.CompositeSequenceDimension_list - class org.biomage.BioAssayData.BioAssayData_package.CompositeSequenceDimension_list.
- Inner list class for holding multiple entries for attribute compositeSequenceDimension_list.
- BioAssayData_package.CompositeSequenceDimension_list() - Constructor for class org.biomage.BioAssayData.BioAssayData_package.CompositeSequenceDimension_list
- BioAssayData_package.DerivedBioAssayData_list - class org.biomage.BioAssayData.BioAssayData_package.DerivedBioAssayData_list.
- Inner list class for holding multiple entries for attribute derivedBioAssayData_list.
- BioAssayData_package.DerivedBioAssayData_list() - Constructor for class org.biomage.BioAssayData.BioAssayData_package.DerivedBioAssayData_list
- BioAssayData_package.DesignElementDimension_list - class org.biomage.BioAssayData.BioAssayData_package.DesignElementDimension_list.
- Inner list class for holding multiple entries for attribute designElementDimension_list.
- BioAssayData_package.DesignElementDimension_list() - Constructor for class org.biomage.BioAssayData.BioAssayData_package.DesignElementDimension_list
- BioAssayData_package.DesignElementMap_list - class org.biomage.BioAssayData.BioAssayData_package.DesignElementMap_list.
- Inner list class for holding multiple entries for attribute designElementMap_list.
- BioAssayData_package.DesignElementMap_list() - Constructor for class org.biomage.BioAssayData.BioAssayData_package.DesignElementMap_list
- BioAssayData_package.FeatureDimension_list - class org.biomage.BioAssayData.BioAssayData_package.FeatureDimension_list.
- Inner list class for holding multiple entries for attribute featureDimension_list.
- BioAssayData_package.FeatureDimension_list() - Constructor for class org.biomage.BioAssayData.BioAssayData_package.FeatureDimension_list
- BioAssayData_package.MeasuredBioAssayData_list - class org.biomage.BioAssayData.BioAssayData_package.MeasuredBioAssayData_list.
- Inner list class for holding multiple entries for attribute measuredBioAssayData_list.
- BioAssayData_package.MeasuredBioAssayData_list() - Constructor for class org.biomage.BioAssayData.BioAssayData_package.MeasuredBioAssayData_list
- BioAssayData_package.QuantitationTypeDimension_list - class org.biomage.BioAssayData.BioAssayData_package.QuantitationTypeDimension_list.
- Inner list class for holding multiple entries for attribute quantitationTypeDimension_list.
- BioAssayData_package.QuantitationTypeDimension_list() - Constructor for class org.biomage.BioAssayData.BioAssayData_package.QuantitationTypeDimension_list
- BioAssayData_package.QuantitationTypeMap_list - class org.biomage.BioAssayData.BioAssayData_package.QuantitationTypeMap_list.
- Inner list class for holding multiple entries for attribute quantitationTypeMap_list.
- BioAssayData_package.QuantitationTypeMap_list() - Constructor for class org.biomage.BioAssayData.BioAssayData_package.QuantitationTypeMap_list
- BioAssayData_package.ReporterDimension_list - class org.biomage.BioAssayData.BioAssayData_package.ReporterDimension_list.
- Inner list class for holding multiple entries for attribute reporterDimension_list.
- BioAssayData_package.ReporterDimension_list() - Constructor for class org.biomage.BioAssayData.BioAssayData_package.ReporterDimension_list
- BioAssayDatum - class org.biomage.BioAssayData.BioAssayDatum.
- A single cell of the quantitation, bioAssay, designElement matrix.
- BioAssayDatum() - Constructor for class org.biomage.BioAssayData.BioAssayDatum
- Default constructor.
- BioAssayDatum(Attributes) - Constructor for class org.biomage.BioAssayData.BioAssayDatum
- Attribute constructor.
- BioAssayDimension - class org.biomage.BioAssayData.BioAssayDimension.
- An ordered list of bioAssays.
- BioAssayDimension() - Constructor for class org.biomage.BioAssayData.BioAssayDimension
- Default constructor.
- BioAssayDimension(Attributes) - Constructor for class org.biomage.BioAssayData.BioAssayDimension
- Attribute constructor.
- BioAssayMap - class org.biomage.BioAssayData.BioAssayMap.
- The BioAssayMap is the description of how source MeasuredBioAssays and/or DerivedBioAssays are manipulated (mathematically) to produce DerivedBioAssays.
- BioAssayMap() - Constructor for class org.biomage.BioAssayData.BioAssayMap
- Default constructor.
- BioAssayMap(Attributes) - Constructor for class org.biomage.BioAssayData.BioAssayMap
- Attribute constructor.
- BioAssayMapping - class org.biomage.BioAssayData.BioAssayMapping.
- Container of the mappings of the input BioAssay dimensions to the output BioAssay dimension.
- BioAssayMapping() - Constructor for class org.biomage.BioAssayData.BioAssayMapping
- Default constructor.
- BioAssayMapping(Attributes) - Constructor for class org.biomage.BioAssayData.BioAssayMapping
- Attribute constructor.
- BioDataCube - class org.biomage.BioAssayData.BioDataCube.
- A three-dimensional cube representation of the data.
- BioDataCube() - Constructor for class org.biomage.BioAssayData.BioDataCube
- Default constructor.
- BioDataCube(Attributes) - Constructor for class org.biomage.BioAssayData.BioDataCube
- Attribute constructor.
- BioDataTuples - class org.biomage.BioAssayData.BioDataTuples.
- A relational, tuple representation of the data.
- BioDataTuples() - Constructor for class org.biomage.BioAssayData.BioDataTuples
- Default constructor.
- BioDataTuples(Attributes) - Constructor for class org.biomage.BioAssayData.BioDataTuples
- Attribute constructor.
- BioDataValues - class org.biomage.BioAssayData.BioDataValues.
- The actual values for the BioAssayCube.
- BioDataValues() - Constructor for class org.biomage.BioAssayData.BioDataValues
- Default constructor.
- BioDataValues(Attributes) - Constructor for class org.biomage.BioAssayData.BioDataValues
- Attribute constructor.
- bioAssay - Variable in class org.biomage.BioAssayData.BioAssayDatum
- The BioAssay associated with the value of the BioAssayDatum.
- bioAssayDataSources - Variable in class org.biomage.BioAssayData.Transformation
- The BioAssayData sources that the Transformation event uses to produce the target DerivedBioAssayData.
- bioAssayData_list - Variable in class org.biomage.BioAssayData.BioAssayData_package
- Represents the dataset created when the BioAssays are created.
- bioAssayDimension - Variable in class org.biomage.BioAssayData.BioAssayData
- The BioAssays of the BioAssayData.
- bioAssayDimension_list - Variable in class org.biomage.BioAssayData.BioAssayData_package
- An ordered list of bioAssays.
- bioAssayMapTarget - Variable in class org.biomage.BioAssayData.BioAssayMap
- The DerivedBioAssay that is produced by the sources of the BioAssayMap.
- bioAssayMap_list - Variable in class org.biomage.BioAssayData.BioAssayData_package
- The BioAssayMap is the description of how source MeasuredBioAssays and/or DerivedBioAssays are manipulated (mathematically) to produce DerivedBioAssays.
- bioAssayMapping - Variable in class org.biomage.BioAssayData.Transformation
- The collection of mappings for the BioAssays.
- bioAssayMaps - Variable in class org.biomage.BioAssayData.BioAssayMapping
- The maps for the BioAssays.
- bioAssayTupleData - Variable in class org.biomage.BioAssayData.BioDataTuples
- The collection of BioAssayData tuples.
- bioAssays - Variable in class org.biomage.BioAssayData.BioAssayDimension
- The BioAssays for this Dimension
- bioDataValues - Variable in class org.biomage.BioAssayData.BioAssayData
- The data values of the BioAssayData.
C
- CompositeSequenceDimension - class org.biomage.BioAssayData.CompositeSequenceDimension.
- Specialized DesignElementDimension to hold CompositeSequences.
- CompositeSequenceDimension() - Constructor for class org.biomage.BioAssayData.CompositeSequenceDimension
- Default constructor.
- CompositeSequenceDimension(Attributes) - Constructor for class org.biomage.BioAssayData.CompositeSequenceDimension
- Attribute constructor.
- compositeSequenceDimension_list - Variable in class org.biomage.BioAssayData.BioAssayData_package
- Specialized DesignElementDimension to hold CompositeSequences.
- compositeSequences - Variable in class org.biomage.BioAssayData.CompositeSequenceDimension
- The CompositeSequences for this Dimension.
- containedFeatures - Variable in class org.biomage.BioAssayData.FeatureDimension
- The features for this dimension.
- cube - Variable in class org.biomage.BioAssayData.BioDataCube
- Three dimension array, indexed by the three dimensions to provide the data for the BioAssayData.
D
- DerivedBioAssayData - class org.biomage.BioAssayData.DerivedBioAssayData.
- The output of a transformation event.
- DerivedBioAssayData() - Constructor for class org.biomage.BioAssayData.DerivedBioAssayData
- Default constructor.
- DerivedBioAssayData(Attributes) - Constructor for class org.biomage.BioAssayData.DerivedBioAssayData
- Attribute constructor.
- DesignElementDimension - class org.biomage.BioAssayData.DesignElementDimension.
- An ordered list of designElements.
- DesignElementDimension() - Constructor for class org.biomage.BioAssayData.DesignElementDimension
- Default constructor.
- DesignElementDimension(Attributes) - Constructor for class org.biomage.BioAssayData.DesignElementDimension
- Attribute constructor.
- DesignElementMap - class org.biomage.BioAssayData.DesignElementMap.
- A DesignElementMap is the description of how source DesignElements are transformed into a target DesignElement.
- DesignElementMap() - Constructor for class org.biomage.BioAssayData.DesignElementMap
- Default constructor.
- DesignElementMap(Attributes) - Constructor for class org.biomage.BioAssayData.DesignElementMap
- Attribute constructor.
- DesignElementMapping - class org.biomage.BioAssayData.DesignElementMapping.
- Container of the mappings of the input DesignElement dimensions to the output DesignElement dimension.
- DesignElementMapping() - Constructor for class org.biomage.BioAssayData.DesignElementMapping
- Default constructor.
- DesignElementMapping(Attributes) - Constructor for class org.biomage.BioAssayData.DesignElementMapping
- Attribute constructor.
- derivedBioAssayDataTarget - Variable in class org.biomage.BioAssayData.Transformation
- The association between the DerivedBioAssayData and the Transformation event that produced it.
- derivedBioAssayData_list - Variable in class org.biomage.BioAssayData.BioAssayData_package
- The output of a transformation event.
- designElement - Variable in class org.biomage.BioAssayData.BioAssayDatum
- The DesignElement associated with the value of the BioAssayDatum.
- designElementDimension - Variable in class org.biomage.BioAssayData.BioAssayData
- The DesignElements of the BioAssayData.
- designElementDimension_list - Variable in class org.biomage.BioAssayData.BioAssayData_package
- An ordered list of designElements.
- designElementMap_list - Variable in class org.biomage.BioAssayData.BioAssayData_package
- A DesignElementMap is the description of how source DesignElements are transformed into a target DesignElement.
- designElementMapping - Variable in class org.biomage.BioAssayData.Transformation
- The collection of mappings for the DesignElements.
- designElementMaps - Variable in class org.biomage.BioAssayData.DesignElementMapping
- The maps for the DesignElements.
F
- FeatureDimension - class org.biomage.BioAssayData.FeatureDimension.
- Specialized DesignElementDimension to hold Features.
- FeatureDimension() - Constructor for class org.biomage.BioAssayData.FeatureDimension
- Default constructor.
- FeatureDimension(Attributes) - Constructor for class org.biomage.BioAssayData.FeatureDimension
- Attribute constructor.
- featureDimension_list - Variable in class org.biomage.BioAssayData.BioAssayData_package
- Specialized DesignElementDimension to hold Features.
G
- getBioAssay() - Method in class org.biomage.BioAssayData.BioAssayDatum
- Get method for bioAssay
- getBioAssayDataSources() - Method in class org.biomage.BioAssayData.Transformation
- Get method for bioAssayDataSources
- getBioAssayData_list() - Method in class org.biomage.BioAssayData.BioAssayData_package
- Get method for bioAssayData_list
- getBioAssayDimension() - Method in class org.biomage.BioAssayData.BioAssayData
- Get method for bioAssayDimension
- getBioAssayDimension_list() - Method in class org.biomage.BioAssayData.BioAssayData_package
- Get method for bioAssayDimension_list
- getBioAssayMapTarget() - Method in class org.biomage.BioAssayData.BioAssayMap
- Get method for bioAssayMapTarget
- getBioAssayMap_list() - Method in class org.biomage.BioAssayData.BioAssayData_package
- Get method for bioAssayMap_list
- getBioAssayMapping() - Method in class org.biomage.BioAssayData.Transformation
- Get method for bioAssayMapping
- getBioAssayMaps() - Method in class org.biomage.BioAssayData.BioAssayMapping
- Get method for bioAssayMaps
- getBioAssayTupleData() - Method in class org.biomage.BioAssayData.BioDataTuples
- Get method for bioAssayTupleData
- getBioAssays() - Method in class org.biomage.BioAssayData.BioAssayDimension
- Get method for bioAssays
- getBioDataValues() - Method in class org.biomage.BioAssayData.BioAssayData
- Get method for bioDataValues
- getCompositeSequenceDimension_list() - Method in class org.biomage.BioAssayData.BioAssayData_package
- Get method for compositeSequenceDimension_list
- getCompositeSequences() - Method in class org.biomage.BioAssayData.CompositeSequenceDimension
- Get method for compositeSequences
- getContainedFeatures() - Method in class org.biomage.BioAssayData.FeatureDimension
- Get method for containedFeatures
- getCube() - Method in class org.biomage.BioAssayData.BioDataCube
- Get method for cube
- getDerivedBioAssayDataTarget() - Method in class org.biomage.BioAssayData.Transformation
- Get method for derivedBioAssayDataTarget
- getDerivedBioAssayData_list() - Method in class org.biomage.BioAssayData.BioAssayData_package
- Get method for derivedBioAssayData_list
- getDesignElement() - Method in class org.biomage.BioAssayData.BioAssayDatum
- Get method for designElement
- getDesignElementDimension() - Method in class org.biomage.BioAssayData.BioAssayData
- Get method for designElementDimension
- getDesignElementDimension_list() - Method in class org.biomage.BioAssayData.BioAssayData_package
- Get method for designElementDimension_list
- getDesignElementMap_list() - Method in class org.biomage.BioAssayData.BioAssayData_package
- Get method for designElementMap_list
- getDesignElementMapping() - Method in class org.biomage.BioAssayData.Transformation
- Get method for designElementMapping
- getDesignElementMaps() - Method in class org.biomage.BioAssayData.DesignElementMapping
- Get method for designElementMaps
- getFeatureDimension_list() - Method in class org.biomage.BioAssayData.BioAssayData_package
- Get method for featureDimension_list
- getFromBioAssayDataSources(int) - Method in class org.biomage.BioAssayData.Transformation
- Method to get BioAssayData from BioAssayDataSources_list
- getFromBioAssayData_list(int) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Method to get BioAssayData from BioAssayData_list
- getFromBioAssayDimension_list(int) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Method to get BioAssayDimension from BioAssayDimension_list
- getFromBioAssayMap_list(int) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Method to get BioAssayMap from BioAssayMap_list
- getFromBioAssayMaps(int) - Method in class org.biomage.BioAssayData.BioAssayMapping
- Method to get BioAssayMap from BioAssayMaps_list
- getFromBioAssayTupleData(int) - Method in class org.biomage.BioAssayData.BioDataTuples
- Method to get BioAssayDatum from BioAssayTupleData_list
- getFromBioAssays(int) - Method in class org.biomage.BioAssayData.BioAssayDimension
- Method to get BioAssay from BioAssays_list
- getFromCompositeSequenceDimension_list(int) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Method to get CompositeSequenceDimension from CompositeSequenceDimension_list
- getFromCompositeSequences(int) - Method in class org.biomage.BioAssayData.CompositeSequenceDimension
- Method to get CompositeSequence from CompositeSequences_list
- getFromContainedFeatures(int) - Method in class org.biomage.BioAssayData.FeatureDimension
- Method to get Feature from ContainedFeatures_list
- getFromDerivedBioAssayData_list(int) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Method to get DerivedBioAssayData from DerivedBioAssayData_list
- getFromDesignElementDimension_list(int) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Method to get DesignElementDimension from DesignElementDimension_list
- getFromDesignElementMap_list(int) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Method to get DesignElementMap from DesignElementMap_list
- getFromDesignElementMaps(int) - Method in class org.biomage.BioAssayData.DesignElementMapping
- Method to get DesignElementMap from DesignElementMaps_list
- getFromFeatureDimension_list(int) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Method to get FeatureDimension from FeatureDimension_list
- getFromMeasuredBioAssayData_list(int) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Method to get MeasuredBioAssayData from MeasuredBioAssayData_list
- getFromQuantitationTypeDimension_list(int) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Method to get QuantitationTypeDimension from QuantitationTypeDimension_list
- getFromQuantitationTypeMap_list(int) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Method to get QuantitationTypeMap from QuantitationTypeMap_list
- getFromQuantitationTypeMaps(int) - Method in class org.biomage.BioAssayData.QuantitationTypeMapping
- Method to get QuantitationTypeMap from QuantitationTypeMaps_list
- getFromQuantitationTypes(int) - Method in class org.biomage.BioAssayData.QuantitationTypeDimension
- Method to get QuantitationType from QuantitationTypes_list
- getFromReporterDimension_list(int) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Method to get ReporterDimension from ReporterDimension_list
- getFromReporters(int) - Method in class org.biomage.BioAssayData.ReporterDimension
- Method to get Reporter from Reporters_list
- getFromSourceBioAssays(int) - Method in class org.biomage.BioAssayData.BioAssayMap
- Method to get BioAssay from SourceBioAssays_list
- getFromSourcesQuantitationType(int) - Method in class org.biomage.BioAssayData.QuantitationTypeMap
- Method to get QuantitationType from SourcesQuantitationType_list
- getFromSummaryStatistics(int) - Method in class org.biomage.BioAssayData.BioAssayData
- Method to get NameValueType from SummaryStatistics_list
- getMeasuredBioAssayData_list() - Method in class org.biomage.BioAssayData.BioAssayData_package
- Get method for measuredBioAssayData_list
- getProducerTransformation() - Method in class org.biomage.BioAssayData.DerivedBioAssayData
- Get method for producerTransformation
- getQuantitationType() - Method in class org.biomage.BioAssayData.BioAssayDatum
- Get method for quantitationType
- getQuantitationTypeDimension() - Method in class org.biomage.BioAssayData.BioAssayData
- Get method for quantitationTypeDimension
- getQuantitationTypeDimension_list() - Method in class org.biomage.BioAssayData.BioAssayData_package
- Get method for quantitationTypeDimension_list
- getQuantitationTypeMap_list() - Method in class org.biomage.BioAssayData.BioAssayData_package
- Get method for quantitationTypeMap_list
- getQuantitationTypeMapping() - Method in class org.biomage.BioAssayData.Transformation
- Get method for quantitationTypeMapping
- getQuantitationTypeMaps() - Method in class org.biomage.BioAssayData.QuantitationTypeMapping
- Get method for quantitationTypeMaps
- getQuantitationTypes() - Method in class org.biomage.BioAssayData.QuantitationTypeDimension
- Get method for quantitationTypes
- getReporterDimension_list() - Method in class org.biomage.BioAssayData.BioAssayData_package
- Get method for reporterDimension_list
- getReporters() - Method in class org.biomage.BioAssayData.ReporterDimension
- Get method for reporters
- getSourceBioAssays() - Method in class org.biomage.BioAssayData.BioAssayMap
- Get method for sourceBioAssays
- getSourcesQuantitationType() - Method in class org.biomage.BioAssayData.QuantitationTypeMap
- Get method for sourcesQuantitationType
- getSummaryStatistics() - Method in class org.biomage.BioAssayData.BioAssayData
- Get method for summaryStatistics
- getTargetQuantitationType() - Method in class org.biomage.BioAssayData.QuantitationTypeMap
- Get method for targetQuantitationType
- getValue() - Method in class org.biomage.BioAssayData.BioAssayDatum
- Get method for value
M
- MeasuredBioAssayData - class org.biomage.BioAssayData.MeasuredBioAssayData.
- The data associated with the MeasuredBioAssay produced by FeatureExtraction.
- MeasuredBioAssayData() - Constructor for class org.biomage.BioAssayData.MeasuredBioAssayData
- Default constructor.
- MeasuredBioAssayData(Attributes) - Constructor for class org.biomage.BioAssayData.MeasuredBioAssayData
- Attribute constructor.
- measuredBioAssayData_list - Variable in class org.biomage.BioAssayData.BioAssayData_package
- The data associated with the MeasuredBioAssay produced by FeatureExtraction.
O
- org.biomage.BioAssayData - package org.biomage.BioAssayData
P
- producerTransformation - Variable in class org.biomage.BioAssayData.DerivedBioAssayData
- The association between the DerivedBioAssayData and the Transformation event that produced it.
Q
- QuantitationTypeDimension - class org.biomage.BioAssayData.QuantitationTypeDimension.
- An ordered list of quantitationTypes.
- QuantitationTypeDimension() - Constructor for class org.biomage.BioAssayData.QuantitationTypeDimension
- Default constructor.
- QuantitationTypeDimension(Attributes) - Constructor for class org.biomage.BioAssayData.QuantitationTypeDimension
- Attribute constructor.
- QuantitationTypeMap - class org.biomage.BioAssayData.QuantitationTypeMap.
- A QuantitationTypeMap is the description of how source QuantitationTypes are mathematically transformed into a target QuantitationType.
- QuantitationTypeMap() - Constructor for class org.biomage.BioAssayData.QuantitationTypeMap
- Default constructor.
- QuantitationTypeMap(Attributes) - Constructor for class org.biomage.BioAssayData.QuantitationTypeMap
- Attribute constructor.
- QuantitationTypeMapping - class org.biomage.BioAssayData.QuantitationTypeMapping.
- Container of the mappings of the input QuantitationType dimensions to the output QuantitationType dimension.
- QuantitationTypeMapping() - Constructor for class org.biomage.BioAssayData.QuantitationTypeMapping
- Default constructor.
- QuantitationTypeMapping(Attributes) - Constructor for class org.biomage.BioAssayData.QuantitationTypeMapping
- Attribute constructor.
- quantitationType - Variable in class org.biomage.BioAssayData.BioAssayDatum
- The QuantitationType associated with the value of the BioAssayDatum.
- quantitationTypeDimension - Variable in class org.biomage.BioAssayData.BioAssayData
- The QuantitationTypes of the BioAssayData.
- quantitationTypeDimension_list - Variable in class org.biomage.BioAssayData.BioAssayData_package
- An ordered list of quantitationTypes.
- quantitationTypeMap_list - Variable in class org.biomage.BioAssayData.BioAssayData_package
- A QuantitationTypeMap is the description of how source QuantitationTypes are mathematically transformed into a target QuantitationType.
- quantitationTypeMapping - Variable in class org.biomage.BioAssayData.Transformation
- The collection of mappings for the QuantitationTypes.
- quantitationTypeMaps - Variable in class org.biomage.BioAssayData.QuantitationTypeMapping
- The maps for the QuantitationTypes.
- quantitationTypes - Variable in class org.biomage.BioAssayData.QuantitationTypeDimension
- The QuantitationTypes for this Dimension.
R
- ReporterDimension - class org.biomage.BioAssayData.ReporterDimension.
- Specialized DesignElementDimension to hold Reporters.
- ReporterDimension() - Constructor for class org.biomage.BioAssayData.ReporterDimension
- Default constructor.
- ReporterDimension(Attributes) - Constructor for class org.biomage.BioAssayData.ReporterDimension
- Attribute constructor.
- removeElementAtFromBioAssayDataSources(int) - Method in class org.biomage.BioAssayData.Transformation
- Method to remove by position from BioAssayDataSources_list
- removeElementAtFromBioAssayData_list(int) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Method to remove by position from BioAssayData_list
- removeElementAtFromBioAssayDimension_list(int) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Method to remove by position from BioAssayDimension_list
- removeElementAtFromBioAssayMap_list(int) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Method to remove by position from BioAssayMap_list
- removeElementAtFromBioAssayMaps(int) - Method in class org.biomage.BioAssayData.BioAssayMapping
- Method to remove by position from BioAssayMaps_list
- removeElementAtFromBioAssayTupleData(int) - Method in class org.biomage.BioAssayData.BioDataTuples
- Method to remove by position from BioAssayTupleData_list
- removeElementAtFromBioAssays(int) - Method in class org.biomage.BioAssayData.BioAssayDimension
- Method to remove by position from BioAssays_list
- removeElementAtFromCompositeSequenceDimension_list(int) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Method to remove by position from CompositeSequenceDimension_list
- removeElementAtFromCompositeSequences(int) - Method in class org.biomage.BioAssayData.CompositeSequenceDimension
- Method to remove by position from CompositeSequences_list
- removeElementAtFromContainedFeatures(int) - Method in class org.biomage.BioAssayData.FeatureDimension
- Method to remove by position from ContainedFeatures_list
- removeElementAtFromDerivedBioAssayData_list(int) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Method to remove by position from DerivedBioAssayData_list
- removeElementAtFromDesignElementDimension_list(int) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Method to remove by position from DesignElementDimension_list
- removeElementAtFromDesignElementMap_list(int) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Method to remove by position from DesignElementMap_list
- removeElementAtFromDesignElementMaps(int) - Method in class org.biomage.BioAssayData.DesignElementMapping
- Method to remove by position from DesignElementMaps_list
- removeElementAtFromFeatureDimension_list(int) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Method to remove by position from FeatureDimension_list
- removeElementAtFromMeasuredBioAssayData_list(int) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Method to remove by position from MeasuredBioAssayData_list
- removeElementAtFromQuantitationTypeDimension_list(int) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Method to remove by position from QuantitationTypeDimension_list
- removeElementAtFromQuantitationTypeMap_list(int) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Method to remove by position from QuantitationTypeMap_list
- removeElementAtFromQuantitationTypeMaps(int) - Method in class org.biomage.BioAssayData.QuantitationTypeMapping
- Method to remove by position from QuantitationTypeMaps_list
- removeElementAtFromQuantitationTypes(int) - Method in class org.biomage.BioAssayData.QuantitationTypeDimension
- Method to remove by position from QuantitationTypes_list
- removeElementAtFromReporterDimension_list(int) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Method to remove by position from ReporterDimension_list
- removeElementAtFromReporters(int) - Method in class org.biomage.BioAssayData.ReporterDimension
- Method to remove by position from Reporters_list
- removeElementAtFromSourceBioAssays(int) - Method in class org.biomage.BioAssayData.BioAssayMap
- Method to remove by position from SourceBioAssays_list
- removeElementAtFromSourcesQuantitationType(int) - Method in class org.biomage.BioAssayData.QuantitationTypeMap
- Method to remove by position from SourcesQuantitationType_list
- removeElementAtFromSummaryStatistics(int) - Method in class org.biomage.BioAssayData.BioAssayData
- Method to remove by position from SummaryStatistics_list
- removeFromBioAssayDataSources(BioAssayData) - Method in class org.biomage.BioAssayData.Transformation
- Method to remove first BioAssayData from BioAssayDataSources_list
- removeFromBioAssayData_list(BioAssayData) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Method to remove first BioAssayData from BioAssayData_list
- removeFromBioAssayDimension_list(BioAssayDimension) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Method to remove first BioAssayDimension from BioAssayDimension_list
- removeFromBioAssayMap_list(BioAssayMap) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Method to remove first BioAssayMap from BioAssayMap_list
- removeFromBioAssayMaps(BioAssayMap) - Method in class org.biomage.BioAssayData.BioAssayMapping
- Method to remove first BioAssayMap from BioAssayMaps_list
- removeFromBioAssayTupleData(BioAssayDatum) - Method in class org.biomage.BioAssayData.BioDataTuples
- Method to remove first BioAssayDatum from BioAssayTupleData_list
- removeFromBioAssays(BioAssay) - Method in class org.biomage.BioAssayData.BioAssayDimension
- Method to remove first BioAssay from BioAssays_list
- removeFromCompositeSequenceDimension_list(CompositeSequenceDimension) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Method to remove first CompositeSequenceDimension from CompositeSequenceDimension_list
- removeFromCompositeSequences(CompositeSequence) - Method in class org.biomage.BioAssayData.CompositeSequenceDimension
- Method to remove first CompositeSequence from CompositeSequences_list
- removeFromContainedFeatures(Feature) - Method in class org.biomage.BioAssayData.FeatureDimension
- Method to remove first Feature from ContainedFeatures_list
- removeFromDerivedBioAssayData_list(DerivedBioAssayData) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Method to remove first DerivedBioAssayData from DerivedBioAssayData_list
- removeFromDesignElementDimension_list(DesignElementDimension) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Method to remove first DesignElementDimension from DesignElementDimension_list
- removeFromDesignElementMap_list(DesignElementMap) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Method to remove first DesignElementMap from DesignElementMap_list
- removeFromDesignElementMaps(DesignElementMap) - Method in class org.biomage.BioAssayData.DesignElementMapping
- Method to remove first DesignElementMap from DesignElementMaps_list
- removeFromFeatureDimension_list(FeatureDimension) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Method to remove first FeatureDimension from FeatureDimension_list
- removeFromMeasuredBioAssayData_list(MeasuredBioAssayData) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Method to remove first MeasuredBioAssayData from MeasuredBioAssayData_list
- removeFromQuantitationTypeDimension_list(QuantitationTypeDimension) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Method to remove first QuantitationTypeDimension from QuantitationTypeDimension_list
- removeFromQuantitationTypeMap_list(QuantitationTypeMap) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Method to remove first QuantitationTypeMap from QuantitationTypeMap_list
- removeFromQuantitationTypeMaps(QuantitationTypeMap) - Method in class org.biomage.BioAssayData.QuantitationTypeMapping
- Method to remove first QuantitationTypeMap from QuantitationTypeMaps_list
- removeFromQuantitationTypes(QuantitationType) - Method in class org.biomage.BioAssayData.QuantitationTypeDimension
- Method to remove first QuantitationType from QuantitationTypes_list
- removeFromReporterDimension_list(ReporterDimension) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Method to remove first ReporterDimension from ReporterDimension_list
- removeFromReporters(Reporter) - Method in class org.biomage.BioAssayData.ReporterDimension
- Method to remove first Reporter from Reporters_list
- removeFromSourceBioAssays(BioAssay) - Method in class org.biomage.BioAssayData.BioAssayMap
- Method to remove first BioAssay from SourceBioAssays_list
- removeFromSourcesQuantitationType(QuantitationType) - Method in class org.biomage.BioAssayData.QuantitationTypeMap
- Method to remove first QuantitationType from SourcesQuantitationType_list
- removeFromSummaryStatistics(NameValueType) - Method in class org.biomage.BioAssayData.BioAssayData
- Method to remove first NameValueType from SummaryStatistics_list
- reporterDimension_list - Variable in class org.biomage.BioAssayData.BioAssayData_package
- Specialized DesignElementDimension to hold Reporters.
- reporters - Variable in class org.biomage.BioAssayData.ReporterDimension
- The reporters for this dimension.
S
- setBioAssay(BioAssay) - Method in class org.biomage.BioAssayData.BioAssayDatum
- Set method for bioAssay
- setBioAssayDataSources(HasBioAssayDataSources.BioAssayDataSources_list) - Method in class org.biomage.BioAssayData.Transformation
- Set method for bioAssayDataSources
- setBioAssayData_list(BioAssayData_package.BioAssayData_list) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Set method for bioAssayData_list
- setBioAssayDimension(BioAssayDimension) - Method in class org.biomage.BioAssayData.BioAssayData
- Set method for bioAssayDimension
- setBioAssayDimension_list(BioAssayData_package.BioAssayDimension_list) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Set method for bioAssayDimension_list
- setBioAssayMapTarget(DerivedBioAssay) - Method in class org.biomage.BioAssayData.BioAssayMap
- Set method for bioAssayMapTarget
- setBioAssayMap_list(BioAssayData_package.BioAssayMap_list) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Set method for bioAssayMap_list
- setBioAssayMapping(BioAssayMapping) - Method in class org.biomage.BioAssayData.Transformation
- Set method for bioAssayMapping
- setBioAssayMaps(HasBioAssayMaps.BioAssayMaps_list) - Method in class org.biomage.BioAssayData.BioAssayMapping
- Set method for bioAssayMaps
- setBioAssayTupleData(HasBioAssayTupleData.BioAssayTupleData_list) - Method in class org.biomage.BioAssayData.BioDataTuples
- Set method for bioAssayTupleData
- setBioAssays(HasBioAssays.BioAssays_list) - Method in class org.biomage.BioAssayData.BioAssayDimension
- Set method for bioAssays
- setBioDataValues(BioDataValues) - Method in class org.biomage.BioAssayData.BioAssayData
- Set method for bioDataValues
- setCompositeSequenceDimension_list(BioAssayData_package.CompositeSequenceDimension_list) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Set method for compositeSequenceDimension_list
- setCompositeSequences(HasCompositeSequences.CompositeSequences_list) - Method in class org.biomage.BioAssayData.CompositeSequenceDimension
- Set method for compositeSequences
- setContainedFeatures(HasContainedFeatures.ContainedFeatures_list) - Method in class org.biomage.BioAssayData.FeatureDimension
- Set method for containedFeatures
- setCube(Object[][][]) - Method in class org.biomage.BioAssayData.BioDataCube
- Set method for cube
- setDerivedBioAssayDataTarget(DerivedBioAssayData) - Method in class org.biomage.BioAssayData.Transformation
- Set method for derivedBioAssayDataTarget
- setDerivedBioAssayData_list(BioAssayData_package.DerivedBioAssayData_list) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Set method for derivedBioAssayData_list
- setDesignElement(DesignElement) - Method in class org.biomage.BioAssayData.BioAssayDatum
- Set method for designElement
- setDesignElementDimension(DesignElementDimension) - Method in class org.biomage.BioAssayData.BioAssayData
- Set method for designElementDimension
- setDesignElementDimension_list(BioAssayData_package.DesignElementDimension_list) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Set method for designElementDimension_list
- setDesignElementMap_list(BioAssayData_package.DesignElementMap_list) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Set method for designElementMap_list
- setDesignElementMapping(DesignElementMapping) - Method in class org.biomage.BioAssayData.Transformation
- Set method for designElementMapping
- setDesignElementMaps(HasDesignElementMaps.DesignElementMaps_list) - Method in class org.biomage.BioAssayData.DesignElementMapping
- Set method for designElementMaps
- setFeatureDimension_list(BioAssayData_package.FeatureDimension_list) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Set method for featureDimension_list
- setMeasuredBioAssayData_list(BioAssayData_package.MeasuredBioAssayData_list) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Set method for measuredBioAssayData_list
- setProducerTransformation(Transformation) - Method in class org.biomage.BioAssayData.DerivedBioAssayData
- Set method for producerTransformation
- setQuantitationType(QuantitationType) - Method in class org.biomage.BioAssayData.BioAssayDatum
- Set method for quantitationType
- setQuantitationTypeDimension(QuantitationTypeDimension) - Method in class org.biomage.BioAssayData.BioAssayData
- Set method for quantitationTypeDimension
- setQuantitationTypeDimension_list(BioAssayData_package.QuantitationTypeDimension_list) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Set method for quantitationTypeDimension_list
- setQuantitationTypeMap_list(BioAssayData_package.QuantitationTypeMap_list) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Set method for quantitationTypeMap_list
- setQuantitationTypeMapping(QuantitationTypeMapping) - Method in class org.biomage.BioAssayData.Transformation
- Set method for quantitationTypeMapping
- setQuantitationTypeMaps(HasQuantitationTypeMaps.QuantitationTypeMaps_list) - Method in class org.biomage.BioAssayData.QuantitationTypeMapping
- Set method for quantitationTypeMaps
- setQuantitationTypes(HasQuantitationTypes.QuantitationTypes_list) - Method in class org.biomage.BioAssayData.QuantitationTypeDimension
- Set method for quantitationTypes
- setReporterDimension_list(BioAssayData_package.ReporterDimension_list) - Method in class org.biomage.BioAssayData.BioAssayData_package
- Set method for reporterDimension_list
- setReporters(HasReporters.Reporters_list) - Method in class org.biomage.BioAssayData.ReporterDimension
- Set method for reporters
- setSourceBioAssays(HasSourceBioAssays.SourceBioAssays_list) - Method in class org.biomage.BioAssayData.BioAssayMap
- Set method for sourceBioAssays
- setSourcesQuantitationType(HasSourcesQuantitationType.SourcesQuantitationType_list) - Method in class org.biomage.BioAssayData.QuantitationTypeMap
- Set method for sourcesQuantitationType
- setSummaryStatistics(HasSummaryStatistics.SummaryStatistics_list) - Method in class org.biomage.BioAssayData.BioAssayData
- Set method for summaryStatistics
- setTargetQuantitationType(QuantitationType) - Method in class org.biomage.BioAssayData.QuantitationTypeMap
- Set method for targetQuantitationType
- setValue(Object) - Method in class org.biomage.BioAssayData.BioAssayDatum
- Set method for value
- sourceBioAssays - Variable in class org.biomage.BioAssayData.BioAssayMap
- The sources of the BioAssayMap that are used to produce a target DerivedBioAssay.
- sourcesQuantitationType - Variable in class org.biomage.BioAssayData.QuantitationTypeMap
- The QuantitationType sources for values for the transformation.
- summaryStatistics - Variable in class org.biomage.BioAssayData.BioAssayData
- Statistics on the Quality of the BioAssayData.
T
- Transformation - class org.biomage.BioAssayData.Transformation.
- The process by which derivedBioAssays are created from measuredBioAssays and/or derivedBioAssays.
- Transformation() - Constructor for class org.biomage.BioAssayData.Transformation
- Default constructor.
- Transformation(Attributes) - Constructor for class org.biomage.BioAssayData.Transformation
- Attribute constructor.
- targetQuantitationType - Variable in class org.biomage.BioAssayData.QuantitationTypeMap
- The QuantitationType whose value will be produced from the values of the source QuantitationType according to the Protocol.
V
- value - Variable in class org.biomage.BioAssayData.BioAssayDatum
- The datum value.
W
- writeAssociations(Writer) - Method in class org.biomage.BioAssayData.BioAssayData
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.BioAssayData.BioAssayData_package
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.BioAssayData.BioAssayDatum
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.BioAssayData.BioAssayDimension
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.BioAssayData.BioAssayMap
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.BioAssayData.BioAssayMapping
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.BioAssayData.BioDataCube
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.BioAssayData.BioDataTuples
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.BioAssayData.BioDataValues
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.BioAssayData.CompositeSequenceDimension
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.BioAssayData.DerivedBioAssayData
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.BioAssayData.DesignElementDimension
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.BioAssayData.DesignElementMap
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.BioAssayData.DesignElementMapping
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.BioAssayData.FeatureDimension
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.BioAssayData.MeasuredBioAssayData
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.BioAssayData.QuantitationTypeDimension
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.BioAssayData.QuantitationTypeMap
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.BioAssayData.QuantitationTypeMapping
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.BioAssayData.ReporterDimension
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.BioAssayData.Transformation
- writeAssociations
- writeAttributes(Writer) - Method in class org.biomage.BioAssayData.BioAssayData
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.BioAssayData.BioAssayData_package
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.BioAssayData.BioAssayDatum
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.BioAssayData.BioAssayDimension
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.BioAssayData.BioAssayMap
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.BioAssayData.BioAssayMapping
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.BioAssayData.BioDataCube
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.BioAssayData.BioDataTuples
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.BioAssayData.BioDataValues
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.BioAssayData.CompositeSequenceDimension
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.BioAssayData.DerivedBioAssayData
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.BioAssayData.DesignElementDimension
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.BioAssayData.DesignElementMap
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.BioAssayData.DesignElementMapping
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.BioAssayData.FeatureDimension
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.BioAssayData.MeasuredBioAssayData
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.BioAssayData.QuantitationTypeDimension
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.BioAssayData.QuantitationTypeMap
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.BioAssayData.QuantitationTypeMapping
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.BioAssayData.ReporterDimension
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.BioAssayData.Transformation
- writeAttributes
- writeMAGEML(Writer) - Method in class org.biomage.BioAssayData.BioAssayData
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.BioAssayData.BioAssayData_package
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.BioAssayData.BioAssayDatum
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.BioAssayData.BioAssayDimension
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.BioAssayData.BioAssayMap
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.BioAssayData.BioAssayMapping
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.BioAssayData.BioDataCube
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.BioAssayData.BioDataTuples
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.BioAssayData.BioDataValues
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.BioAssayData.CompositeSequenceDimension
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.BioAssayData.DerivedBioAssayData
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.BioAssayData.DesignElementDimension
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.BioAssayData.DesignElementMap
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.BioAssayData.DesignElementMapping
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.BioAssayData.FeatureDimension
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.BioAssayData.MeasuredBioAssayData
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.BioAssayData.QuantitationTypeDimension
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.BioAssayData.QuantitationTypeMap
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.BioAssayData.QuantitationTypeMapping
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.BioAssayData.ReporterDimension
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.BioAssayData.Transformation
- writeMAGEML
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