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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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