Uses of Class
org.biomage.BioAssay.BioAssay

Packages that use BioAssay
gov.nih.nci.caarray.services.bioassaydata   
gov.nih.nci.caarray.services.experiment   
gov.nih.nci.caarray.services.fileparse   
gov.nih.nci.caarray.services.fileparse2   
gov.nih.nci.caarray.services.util.netcdf   
org.biomage.BioAssay   
org.biomage.BioAssayData   
org.biomage.Experiment   
org.biomage.Interface   
 

Uses of BioAssay in gov.nih.nci.caarray.services.bioassaydata
 

Methods in gov.nih.nci.caarray.services.bioassaydata that return BioAssay
 BioAssay BioAssayDataInfo.getBioAssay()
           
 

Constructors in gov.nih.nci.caarray.services.bioassaydata with parameters of type BioAssay
BioAssayDataInfo(BioAssayData bioAssayData, BioAssay bioAssay, java.io.File dataFile, SourceType sourceType, Array array, Experiment experiment, java.lang.String username)
          Creates a new instance.
 

Uses of BioAssay in gov.nih.nci.caarray.services.experiment
 

Methods in gov.nih.nci.caarray.services.experiment with parameters of type BioAssay
 boolean ExperimentManagerDB.deleteBioAssayFromExperiment(BioAssay bioAssay, Experiment experiment)
           
 

Uses of BioAssay in gov.nih.nci.caarray.services.fileparse
 

Methods in gov.nih.nci.caarray.services.fileparse that return BioAssay
static BioAssay[] CaArrayToMageConversion.getMageTypesForBioAssays(ParsingBioAssay[] inArray)
           
 

Uses of BioAssay in gov.nih.nci.caarray.services.fileparse2
 

Methods in gov.nih.nci.caarray.services.fileparse2 with parameters of type BioAssay
 void HybridizationManagerDB.saveBioAssay(BioAssay bioAssay)
           
 

Uses of BioAssay in gov.nih.nci.caarray.services.util.netcdf
 

Methods in gov.nih.nci.caarray.services.util.netcdf with parameters of type BioAssay
 java.lang.Object NETCDFFileReader.getBioAssayDatum(BioAssay assay, QuantitationType quantitationType, DesignElement designElement)
           
 java.lang.String NETCDFFileReader.getCubeStringBDQ(BioAssay assay)
          Get the cube in the order people like to see it
 java.lang.String NETCDFFileReader.getCubeStringBQD(BioAssay assay)
          Get the cube in the caArray natural order
 java.lang.Object[] NETCDFFileReader.getQuantitationArray(BioAssay assay, QuantitationType quantitationType)
           
 QuantitationType[] NETCDFFileReader.getQuantitations(BioAssay assay)
          Gets an entire quantitation type for an assay
 

Constructors in gov.nih.nci.caarray.services.util.netcdf with parameters of type BioAssay
NETCDFCreator(DesignElement[] designElementDimension, QuantitationType[] quantitationTypeDimension, BioAssay[] bioAssayDimension)
          Constructs the class with the neccessary items as arrays
 

Uses of BioAssay in org.biomage.BioAssay
 

Subclasses of BioAssay in org.biomage.BioAssay
 class DerivedBioAssay
          A BioAssay that is created by the Transformation BioEvent from one or more MeasuredBioAssays or DerivedBioAssays.
 class MeasuredBioAssay
          A measured bioAssay is the direct processing of information in a physical bioAssay by the featureExtraction event.
 class PhysicalBioAssay
          A bioAssay created by the bioAssayCreation event (e.g.
 

Methods in org.biomage.BioAssay that return BioAssay
 BioAssay BioAssay_package.getFromBioAssay_list(int position)
          Method to get BioAssay from BioAssay_list
 

Methods in org.biomage.BioAssay with parameters of type BioAssay
 void BioAssay_package.addToBioAssay_list(BioAssay bioAssay)
          Method to add BioAssay to BioAssay_list
 void BioAssay_package.addToBioAssay_list(int position, BioAssay bioAssay)
          Method to add BioAssay at position to BioAssay_list
 void BioAssay_package.removeFromBioAssay_list(BioAssay bioAssay)
          Method to remove first BioAssay from BioAssay_list
 

Uses of BioAssay in org.biomage.BioAssayData
 

Fields in org.biomage.BioAssayData declared as BioAssay
protected  BioAssay BioAssayTuple.bioAssay
          The BioAssay associated with the value of the BioAssayDatum.
 

Methods in org.biomage.BioAssayData that return BioAssay
 BioAssay BioAssayTuple.getBioAssay()
          Get method for bioAssay
 BioAssay BioAssayDimension.getFromBioAssays(int position)
          Method to get BioAssay from BioAssays_list
 BioAssay BioAssayMap.getFromSourceBioAssays(int position)
          Method to get BioAssay from SourceBioAssays_list
 

Methods in org.biomage.BioAssayData with parameters of type BioAssay
 void BioAssayDimension.addToBioAssays(BioAssay bioAssay)
          Method to add BioAssay to BioAssays_list
 void BioAssayDimension.addToBioAssays(int position, BioAssay bioAssay)
          Method to add BioAssay at position to BioAssays_list
 void BioAssayMap.addToSourceBioAssays(BioAssay bioAssay)
          Method to add BioAssay to SourceBioAssays_list
 void BioAssayMap.addToSourceBioAssays(int position, BioAssay bioAssay)
          Method to add BioAssay at position to SourceBioAssays_list
 void BioAssayDimension.removeFromBioAssays(BioAssay bioAssay)
          Method to remove first BioAssay from BioAssays_list
 void BioAssayMap.removeFromSourceBioAssays(BioAssay bioAssay)
          Method to remove first BioAssay from SourceBioAssays_list
 void BioAssayTuple.setBioAssay(BioAssay bioAssay)
          Set method for bioAssay
 

Uses of BioAssay in org.biomage.Experiment
 

Methods in org.biomage.Experiment that return BioAssay
 BioAssay Experiment.getFromBioAssays(int position)
          Method to get BioAssay from BioAssays_list
 BioAssay ExperimentDesign.getFromTopLevelBioAssays(int position)
          Method to get BioAssay from TopLevelBioAssays_list
 

Methods in org.biomage.Experiment with parameters of type BioAssay
 void Experiment.addToBioAssays(BioAssay bioAssay)
          Method to add BioAssay to BioAssays_list
 void Experiment.addToBioAssays(int position, BioAssay bioAssay)
          Method to add BioAssay at position to BioAssays_list
 void ExperimentDesign.addToTopLevelBioAssays(BioAssay bioAssay)
          Method to add BioAssay to TopLevelBioAssays_list
 void ExperimentDesign.addToTopLevelBioAssays(int position, BioAssay bioAssay)
          Method to add BioAssay at position to TopLevelBioAssays_list
 void Experiment.removeFromBioAssays(BioAssay bioAssay)
          Method to remove first BioAssay from BioAssays_list
 void ExperimentDesign.removeFromTopLevelBioAssays(BioAssay bioAssay)
          Method to remove first BioAssay from TopLevelBioAssays_list
 

Uses of BioAssay in org.biomage.Interface
 

Methods in org.biomage.Interface that return BioAssay
 BioAssay HasBioAssay.getBioAssay()
          Get method for bioAssay
 BioAssay HasBioAssays.getFromBioAssays(int position)
          Method to get BioAssay from BioAssays_list
 BioAssay HasSourceBioAssays.getFromSourceBioAssays(int position)
          Method to get BioAssay from SourceBioAssays_list
 BioAssay HasTopLevelBioAssays.getFromTopLevelBioAssays(int position)
          Method to get BioAssay from TopLevelBioAssays_list
 

Methods in org.biomage.Interface with parameters of type BioAssay
 void HasBioAssays.addToBioAssays(BioAssay bioAssay)
          Method to add BioAssay to BioAssays_list
 void HasBioAssays.addToBioAssays(int position, BioAssay bioAssay)
          Method to add BioAssay at position to BioAssays_list
 void HasSourceBioAssays.addToSourceBioAssays(BioAssay bioAssay)
          Method to add BioAssay to SourceBioAssays_list
 void HasSourceBioAssays.addToSourceBioAssays(int position, BioAssay bioAssay)
          Method to add BioAssay at position to SourceBioAssays_list
 void HasTopLevelBioAssays.addToTopLevelBioAssays(BioAssay bioAssay)
          Method to add BioAssay to TopLevelBioAssays_list
 void HasTopLevelBioAssays.addToTopLevelBioAssays(int position, BioAssay bioAssay)
          Method to add BioAssay at position to TopLevelBioAssays_list
 void HasBioAssays.removeFromBioAssays(BioAssay bioAssay)
          Method to remove first BioAssay from BioAssays_list
 void HasSourceBioAssays.removeFromSourceBioAssays(BioAssay bioAssay)
          Method to remove first BioAssay from SourceBioAssays_list
 void HasTopLevelBioAssays.removeFromTopLevelBioAssays(BioAssay bioAssay)
          Method to remove first BioAssay from TopLevelBioAssays_list
 void HasBioAssay.setBioAssay(BioAssay bioAssay)
          Set method for bioAssay