Uses of Class
org.biomage.QuantitationType.QuantitationType

Packages that use QuantitationType
gov.nih.nci.caarray.services.fileparse   
gov.nih.nci.caarray.services.fileparse2   
gov.nih.nci.caarray.services.util.netcdf   
org.biomage.BioAssayData   
org.biomage.Interface   
org.biomage.QuantitationType   
 

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

Methods in gov.nih.nci.caarray.services.fileparse that return QuantitationType
static QuantitationType[] CaArrayToMageConversion.getMageTypesForParsingTypes(ParsingQuantitationType[] inArray)
           
 

Methods in gov.nih.nci.caarray.services.fileparse with parameters of type QuantitationType
 void FileParseManagerDB.createBioAssayData(java.lang.Long bioAssayId, java.lang.Long experimentId, DesignElement[] designElements, QuantitationType[] mageTypes, java.lang.Long arrayDesignId)
           
 

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

Methods in gov.nih.nci.caarray.services.fileparse2 with parameters of type QuantitationType
 void HybridizationManagerDB.createBioAssayData(long bioAssayId, long experimentId, long arrayDesignId, DesignElement[] designElements, QuantitationType[] quantitationTypes)
           
 

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

Methods in gov.nih.nci.caarray.services.util.netcdf that return QuantitationType
 QuantitationType[] NETCDFFileReader.getQuantitations(BioAssay assay)
          Gets an entire quantitation type for an assay
 

Methods in gov.nih.nci.caarray.services.util.netcdf with parameters of type QuantitationType
 java.lang.Object NETCDFFileReader.getBioAssayDatum(BioAssay assay, QuantitationType quantitationType, DesignElement designElement)
           
 java.lang.Object[] NETCDFFileReader.getQuantitationArray(BioAssay assay, QuantitationType quantitationType)
           
static java.lang.Object[] NonNumericQuantitationTypesService.translateQuantitationTypes(java.lang.Object[] inputObjects, QuantitationType type)
           
static java.lang.Object NonNumericQuantitationTypesService.translateQuantitationTypes(java.lang.Object inputObject, QuantitationType type)
           
 

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

Uses of QuantitationType in org.biomage.BioAssayData
 

Fields in org.biomage.BioAssayData declared as QuantitationType
protected  QuantitationType QuantitationTypeTuple.quantitationType
          The QuantitationType associated with the value of the BioAssayDatum.
protected  QuantitationType QuantitationTypeMap.targetQuantitationType
          The QuantitationType whose value will be produced from the values of the source QuantitationType according to the Protocol.
 

Methods in org.biomage.BioAssayData that return QuantitationType
 QuantitationType QuantitationTypeDimension.getFromQuantitationTypes(int position)
          Method to get QuantitationType from QuantitationTypes_list
 QuantitationType QuantitationTypeMap.getFromSourcesQuantitationType(int position)
          Method to get QuantitationType from SourcesQuantitationType_list
 QuantitationType QuantitationTypeTuple.getQuantitationType()
          Get method for quantitationType
 QuantitationType QuantitationTypeMap.getTargetQuantitationType()
          Get method for targetQuantitationType
 

Methods in org.biomage.BioAssayData with parameters of type QuantitationType
 void QuantitationTypeDimension.addToQuantitationTypes(int position, QuantitationType quantitationType)
          Method to add QuantitationType at position to QuantitationTypes_list
 void QuantitationTypeDimension.addToQuantitationTypes(QuantitationType quantitationType)
          Method to add QuantitationType to QuantitationTypes_list
 void QuantitationTypeMap.addToSourcesQuantitationType(int position, QuantitationType quantitationType)
          Method to add QuantitationType at position to SourcesQuantitationType_list
 void QuantitationTypeMap.addToSourcesQuantitationType(QuantitationType quantitationType)
          Method to add QuantitationType to SourcesQuantitationType_list
 void QuantitationTypeDimension.removeFromQuantitationTypes(QuantitationType quantitationType)
          Method to remove first QuantitationType from QuantitationTypes_list
 void QuantitationTypeMap.removeFromSourcesQuantitationType(QuantitationType quantitationType)
          Method to remove first QuantitationType from SourcesQuantitationType_list
 void QuantitationTypeTuple.setQuantitationType(QuantitationType quantitationType)
          Set method for quantitationType
 void QuantitationTypeMap.setTargetQuantitationType(QuantitationType targetQuantitationType)
          Set method for targetQuantitationType
 

Uses of QuantitationType in org.biomage.Interface
 

Methods in org.biomage.Interface that return QuantitationType
 QuantitationType HasQuantitationTypes.getFromQuantitationTypes(int position)
          Method to get QuantitationType from QuantitationTypes_list
 QuantitationType HasSourcesQuantitationType.getFromSourcesQuantitationType(int position)
          Method to get QuantitationType from SourcesQuantitationType_list
 QuantitationType HasQuantitationType.getQuantitationType()
          Get method for quantitationType
 QuantitationType HasTargetQuantitationType.getTargetQuantitationType()
          Get method for targetQuantitationType
 

Methods in org.biomage.Interface with parameters of type QuantitationType
 void HasQuantitationTypes.addToQuantitationTypes(int position, QuantitationType quantitationType)
          Method to add QuantitationType at position to QuantitationTypes_list
 void HasQuantitationTypes.addToQuantitationTypes(QuantitationType quantitationType)
          Method to add QuantitationType to QuantitationTypes_list
 void HasSourcesQuantitationType.addToSourcesQuantitationType(int position, QuantitationType quantitationType)
          Method to add QuantitationType at position to SourcesQuantitationType_list
 void HasSourcesQuantitationType.addToSourcesQuantitationType(QuantitationType quantitationType)
          Method to add QuantitationType to SourcesQuantitationType_list
 void HasQuantitationTypes.removeFromQuantitationTypes(QuantitationType quantitationType)
          Method to remove first QuantitationType from QuantitationTypes_list
 void HasSourcesQuantitationType.removeFromSourcesQuantitationType(QuantitationType quantitationType)
          Method to remove first QuantitationType from SourcesQuantitationType_list
 void HasQuantitationType.setQuantitationType(QuantitationType quantitationType)
          Set method for quantitationType
 void HasTargetQuantitationType.setTargetQuantitationType(QuantitationType targetQuantitationType)
          Set method for targetQuantitationType
 

Uses of QuantitationType in org.biomage.QuantitationType
 

Subclasses of QuantitationType in org.biomage.QuantitationType
 class ConfidenceIndicator
          Indication of some measure of confidence for a standard quantitation type.
 class DerivedSignal
          A calculated measurement of the intensity of a signal, for example, after a transformation involving normalization and/or replicate DesignElements.
 class Error
          Error measurement of a quantitation.
 class ExpectedValue
          Indication of what value is expected of the associated standard quantitation type.
 class Failed
          Values associated with this QuantitationType indicate a failure of some kind for a particular DesignElement for a BioAssay.
 class MeasuredSignal
          Best measure from feature extraction as to the presence and intensity of the signal.
 class PresentAbsent
          Indicates relative presence or absence.
 class PValue
          Measurement of the accuracy of a quantitation.
 class Ratio
          The ratio of two or more signals, typically between two channels.
 class SpecializedQuantitationType
          User defined quantitation type.
 class StandardQuantitationType
          Superclass for the named quantitation type.
 

Fields in org.biomage.QuantitationType declared as QuantitationType
protected  QuantitationType ConfidenceIndicator.targetQuantitationType
          The association between a ConfidenceIndicator and the QuantitationType its is an indicator for.
 

Methods in org.biomage.QuantitationType that return QuantitationType
 QuantitationType QuantitationType_package.getFromQuantitationType_list(int position)
          Method to get QuantitationType from QuantitationType_list
 QuantitationType ConfidenceIndicator.getTargetQuantitationType()
          Get method for targetQuantitationType
 

Methods in org.biomage.QuantitationType with parameters of type QuantitationType
 void QuantitationType_package.addToQuantitationType_list(int position, QuantitationType quantitationType)
          Method to add QuantitationType at position to QuantitationType_list
 void QuantitationType_package.addToQuantitationType_list(QuantitationType quantitationType)
          Method to add QuantitationType to QuantitationType_list
 void QuantitationType_package.removeFromQuantitationType_list(QuantitationType quantitationType)
          Method to remove first QuantitationType from QuantitationType_list
 void ConfidenceIndicator.setTargetQuantitationType(QuantitationType targetQuantitationType)
          Set method for targetQuantitationType