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org.biomage.BioAssayData
Class BioAssayData_package  view BioAssayData_package download BioAssayData_package.java

java.lang.Object
  extended byorg.biomage.BioAssayData.BioAssayData_package
All Implemented Interfaces:
java.io.Serializable

public class BioAssayData_package
extends java.lang.Object
implements java.io.Serializable

The classes defined here provide data and the information and annotation on the derivation of that data. Some of the scenarios that might occur are the following. FeatureExtraction of a single PhysicalBioAssay produces MeasuredBioAssayData that has a single BioAssay on the BioAssayDimension, typically the Features described in the ArrayDesign on the DesignElementDimension, and the Quantitations associated with the application of a FeatureExtraction protocol on the QuantitationDimension. An error model transformation might be applied that doesn't change the BioAssayDimension or the DesignElementDimension but likely changes the QuantitationDimension. A transformation on replicate Reporters or CompositeSequences might be applied on the single BioAssay that would change the DesignElementDimension and the QuantitationDimension both. Replicate and Control BioAssays might be added to the BioAssayDimension and a transformation could change the BioAssayDimension and the QuantitationDimension but not change the DesignElementDimension to produce a new DerivedBioAssayData. Or some combination of the above transformations could be performed at once to change all three dimensions. Because the classes derive from Describable, the Experimenter can provide as much detail at each level of the class hierarchy as desired.


Nested Class Summary
 class BioAssayData_package.BioAssayData_list
          Inner list class for holding multiple entries for attribute bioAssayData_list.
 class BioAssayData_package.BioAssayDimension_list
          Inner list class for holding multiple entries for attribute bioAssayDimension_list.
 class BioAssayData_package.BioAssayMap_list
          Inner list class for holding multiple entries for attribute bioAssayMap_list.
 class BioAssayData_package.CompositeSequenceDimension_list
          Inner list class for holding multiple entries for attribute compositeSequenceDimension_list.
 class BioAssayData_package.DerivedBioAssayData_list
          Inner list class for holding multiple entries for attribute derivedBioAssayData_list.
 class BioAssayData_package.DesignElementDimension_list
          Inner list class for holding multiple entries for attribute designElementDimension_list.
 class BioAssayData_package.DesignElementMap_list
          Inner list class for holding multiple entries for attribute designElementMap_list.
 class BioAssayData_package.FeatureDimension_list
          Inner list class for holding multiple entries for attribute featureDimension_list.
 class BioAssayData_package.MeasuredBioAssayData_list
          Inner list class for holding multiple entries for attribute measuredBioAssayData_list.
 class BioAssayData_package.QuantitationTypeDimension_list
          Inner list class for holding multiple entries for attribute quantitationTypeDimension_list.
 class BioAssayData_package.QuantitationTypeMap_list
          Inner list class for holding multiple entries for attribute quantitationTypeMap_list.
 class BioAssayData_package.ReporterDimension_list
          Inner list class for holding multiple entries for attribute reporterDimension_list.
 
Field Summary
 BioAssayData_package.BioAssayData_list bioAssayData_list
          Represents the dataset created when the BioAssays are created.
 BioAssayData_package.BioAssayDimension_list bioAssayDimension_list
          An ordered list of bioAssays.
 BioAssayData_package.BioAssayMap_list bioAssayMap_list
          The BioAssayMap is the description of how source MeasuredBioAssays and/or DerivedBioAssays are manipulated (mathematically) to produce DerivedBioAssays.
 BioAssayData_package.CompositeSequenceDimension_list compositeSequenceDimension_list
          Specialized DesignElementDimension to hold CompositeSequences.
 BioAssayData_package.DerivedBioAssayData_list derivedBioAssayData_list
          The output of a transformation event.
 BioAssayData_package.DesignElementDimension_list designElementDimension_list
          An ordered list of designElements.
 BioAssayData_package.DesignElementMap_list designElementMap_list
          A DesignElementMap is the description of how source DesignElements are transformed into a target DesignElement.
 BioAssayData_package.FeatureDimension_list featureDimension_list
          Specialized DesignElementDimension to hold Features.
 BioAssayData_package.MeasuredBioAssayData_list measuredBioAssayData_list
          The data associated with the MeasuredBioAssay produced by FeatureExtraction.
 BioAssayData_package.QuantitationTypeDimension_list quantitationTypeDimension_list
          An ordered list of quantitationTypes.
 BioAssayData_package.QuantitationTypeMap_list quantitationTypeMap_list
          A QuantitationTypeMap is the description of how source QuantitationTypes are mathematically transformed into a target QuantitationType.
 BioAssayData_package.ReporterDimension_list reporterDimension_list
          Specialized DesignElementDimension to hold Reporters.
 
Constructor Summary
BioAssayData_package()
          Default constructor.
BioAssayData_package(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToBioAssayData_list(BioAssayData bioAssayData)
          Method to add BioAssayData to BioAssayData_list
 void addToBioAssayData_list(int position, BioAssayData bioAssayData)
          Method to add BioAssayData at position to BioAssayData_list
 void addToBioAssayDimension_list(BioAssayDimension bioAssayDimension)
          Method to add BioAssayDimension to BioAssayDimension_list
 void addToBioAssayDimension_list(int position, BioAssayDimension bioAssayDimension)
          Method to add BioAssayDimension at position to BioAssayDimension_list
 void addToBioAssayMap_list(BioAssayMap bioAssayMap)
          Method to add BioAssayMap to BioAssayMap_list
 void addToBioAssayMap_list(int position, BioAssayMap bioAssayMap)
          Method to add BioAssayMap at position to BioAssayMap_list
 void addToCompositeSequenceDimension_list(CompositeSequenceDimension compositeSequenceDimension)
          Method to add CompositeSequenceDimension to CompositeSequenceDimension_list
 void addToCompositeSequenceDimension_list(int position, CompositeSequenceDimension compositeSequenceDimension)
          Method to add CompositeSequenceDimension at position to CompositeSequenceDimension_list
 void addToDerivedBioAssayData_list(DerivedBioAssayData derivedBioAssayData)
          Method to add DerivedBioAssayData to DerivedBioAssayData_list
 void addToDerivedBioAssayData_list(int position, DerivedBioAssayData derivedBioAssayData)
          Method to add DerivedBioAssayData at position to DerivedBioAssayData_list
 void addToDesignElementDimension_list(DesignElementDimension designElementDimension)
          Method to add DesignElementDimension to DesignElementDimension_list
 void addToDesignElementDimension_list(int position, DesignElementDimension designElementDimension)
          Method to add DesignElementDimension at position to DesignElementDimension_list
 void addToDesignElementMap_list(DesignElementMap designElementMap)
          Method to add DesignElementMap to DesignElementMap_list
 void addToDesignElementMap_list(int position, DesignElementMap designElementMap)
          Method to add DesignElementMap at position to DesignElementMap_list
 void addToFeatureDimension_list(FeatureDimension featureDimension)
          Method to add FeatureDimension to FeatureDimension_list
 void addToFeatureDimension_list(int position, FeatureDimension featureDimension)
          Method to add FeatureDimension at position to FeatureDimension_list
 void addToMeasuredBioAssayData_list(int position, MeasuredBioAssayData measuredBioAssayData)
          Method to add MeasuredBioAssayData at position to MeasuredBioAssayData_list
 void addToMeasuredBioAssayData_list(MeasuredBioAssayData measuredBioAssayData)
          Method to add MeasuredBioAssayData to MeasuredBioAssayData_list
 void addToQuantitationTypeDimension_list(int position, QuantitationTypeDimension quantitationTypeDimension)
          Method to add QuantitationTypeDimension at position to QuantitationTypeDimension_list
 void addToQuantitationTypeDimension_list(QuantitationTypeDimension quantitationTypeDimension)
          Method to add QuantitationTypeDimension to QuantitationTypeDimension_list
 void addToQuantitationTypeMap_list(int position, QuantitationTypeMap quantitationTypeMap)
          Method to add QuantitationTypeMap at position to QuantitationTypeMap_list
 void addToQuantitationTypeMap_list(QuantitationTypeMap quantitationTypeMap)
          Method to add QuantitationTypeMap to QuantitationTypeMap_list
 void addToReporterDimension_list(int position, ReporterDimension reporterDimension)
          Method to add ReporterDimension at position to ReporterDimension_list
 void addToReporterDimension_list(ReporterDimension reporterDimension)
          Method to add ReporterDimension to ReporterDimension_list
 BioAssayData_package.BioAssayData_list getBioAssayData_list()
          Get method for bioAssayData_list
 BioAssayData_package.BioAssayDimension_list getBioAssayDimension_list()
          Get method for bioAssayDimension_list
 BioAssayData_package.BioAssayMap_list getBioAssayMap_list()
          Get method for bioAssayMap_list
 BioAssayData_package.CompositeSequenceDimension_list getCompositeSequenceDimension_list()
          Get method for compositeSequenceDimension_list
 BioAssayData_package.DerivedBioAssayData_list getDerivedBioAssayData_list()
          Get method for derivedBioAssayData_list
 BioAssayData_package.DesignElementDimension_list getDesignElementDimension_list()
          Get method for designElementDimension_list
 BioAssayData_package.DesignElementMap_list getDesignElementMap_list()
          Get method for designElementMap_list
 BioAssayData_package.FeatureDimension_list getFeatureDimension_list()
          Get method for featureDimension_list
 BioAssayData getFromBioAssayData_list(int position)
          Method to get BioAssayData from BioAssayData_list
 BioAssayDimension getFromBioAssayDimension_list(int position)
          Method to get BioAssayDimension from BioAssayDimension_list
 BioAssayMap getFromBioAssayMap_list(int position)
          Method to get BioAssayMap from BioAssayMap_list
 CompositeSequenceDimension getFromCompositeSequenceDimension_list(int position)
          Method to get CompositeSequenceDimension from CompositeSequenceDimension_list
 DerivedBioAssayData getFromDerivedBioAssayData_list(int position)
          Method to get DerivedBioAssayData from DerivedBioAssayData_list
 DesignElementDimension getFromDesignElementDimension_list(int position)
          Method to get DesignElementDimension from DesignElementDimension_list
 DesignElementMap getFromDesignElementMap_list(int position)
          Method to get DesignElementMap from DesignElementMap_list
 FeatureDimension getFromFeatureDimension_list(int position)
          Method to get FeatureDimension from FeatureDimension_list
 MeasuredBioAssayData getFromMeasuredBioAssayData_list(int position)
          Method to get MeasuredBioAssayData from MeasuredBioAssayData_list
 QuantitationTypeDimension getFromQuantitationTypeDimension_list(int position)
          Method to get QuantitationTypeDimension from QuantitationTypeDimension_list
 QuantitationTypeMap getFromQuantitationTypeMap_list(int position)
          Method to get QuantitationTypeMap from QuantitationTypeMap_list
 ReporterDimension getFromReporterDimension_list(int position)
          Method to get ReporterDimension from ReporterDimension_list
 BioAssayData_package.MeasuredBioAssayData_list getMeasuredBioAssayData_list()
          Get method for measuredBioAssayData_list
 BioAssayData_package.QuantitationTypeDimension_list getQuantitationTypeDimension_list()
          Get method for quantitationTypeDimension_list
 BioAssayData_package.QuantitationTypeMap_list getQuantitationTypeMap_list()
          Get method for quantitationTypeMap_list
 BioAssayData_package.ReporterDimension_list getReporterDimension_list()
          Get method for reporterDimension_list
 void removeElementAtFromBioAssayData_list(int position)
          Method to remove by position from BioAssayData_list
 void removeElementAtFromBioAssayDimension_list(int position)
          Method to remove by position from BioAssayDimension_list
 void removeElementAtFromBioAssayMap_list(int position)
          Method to remove by position from BioAssayMap_list
 void removeElementAtFromCompositeSequenceDimension_list(int position)
          Method to remove by position from CompositeSequenceDimension_list
 void removeElementAtFromDerivedBioAssayData_list(int position)
          Method to remove by position from DerivedBioAssayData_list
 void removeElementAtFromDesignElementDimension_list(int position)
          Method to remove by position from DesignElementDimension_list
 void removeElementAtFromDesignElementMap_list(int position)
          Method to remove by position from DesignElementMap_list
 void removeElementAtFromFeatureDimension_list(int position)
          Method to remove by position from FeatureDimension_list
 void removeElementAtFromMeasuredBioAssayData_list(int position)
          Method to remove by position from MeasuredBioAssayData_list
 void removeElementAtFromQuantitationTypeDimension_list(int position)
          Method to remove by position from QuantitationTypeDimension_list
 void removeElementAtFromQuantitationTypeMap_list(int position)
          Method to remove by position from QuantitationTypeMap_list
 void removeElementAtFromReporterDimension_list(int position)
          Method to remove by position from ReporterDimension_list
 void removeFromBioAssayData_list(BioAssayData bioAssayData)
          Method to remove first BioAssayData from BioAssayData_list
 void removeFromBioAssayDimension_list(BioAssayDimension bioAssayDimension)
          Method to remove first BioAssayDimension from BioAssayDimension_list
 void removeFromBioAssayMap_list(BioAssayMap bioAssayMap)
          Method to remove first BioAssayMap from BioAssayMap_list
 void removeFromCompositeSequenceDimension_list(CompositeSequenceDimension compositeSequenceDimension)
          Method to remove first CompositeSequenceDimension from CompositeSequenceDimension_list
 void removeFromDerivedBioAssayData_list(DerivedBioAssayData derivedBioAssayData)
          Method to remove first DerivedBioAssayData from DerivedBioAssayData_list
 void removeFromDesignElementDimension_list(DesignElementDimension designElementDimension)
          Method to remove first DesignElementDimension from DesignElementDimension_list
 void removeFromDesignElementMap_list(DesignElementMap designElementMap)
          Method to remove first DesignElementMap from DesignElementMap_list
 void removeFromFeatureDimension_list(FeatureDimension featureDimension)
          Method to remove first FeatureDimension from FeatureDimension_list
 void removeFromMeasuredBioAssayData_list(MeasuredBioAssayData measuredBioAssayData)
          Method to remove first MeasuredBioAssayData from MeasuredBioAssayData_list
 void removeFromQuantitationTypeDimension_list(QuantitationTypeDimension quantitationTypeDimension)
          Method to remove first QuantitationTypeDimension from QuantitationTypeDimension_list
 void removeFromQuantitationTypeMap_list(QuantitationTypeMap quantitationTypeMap)
          Method to remove first QuantitationTypeMap from QuantitationTypeMap_list
 void removeFromReporterDimension_list(ReporterDimension reporterDimension)
          Method to remove first ReporterDimension from ReporterDimension_list
 void setBioAssayData_list(BioAssayData_package.BioAssayData_list bioAssayData_list)
          Set method for bioAssayData_list
 void setBioAssayDimension_list(BioAssayData_package.BioAssayDimension_list bioAssayDimension_list)
          Set method for bioAssayDimension_list
 void setBioAssayMap_list(BioAssayData_package.BioAssayMap_list bioAssayMap_list)
          Set method for bioAssayMap_list
 void setCompositeSequenceDimension_list(BioAssayData_package.CompositeSequenceDimension_list compositeSequenceDimension_list)
          Set method for compositeSequenceDimension_list
 void setDerivedBioAssayData_list(BioAssayData_package.DerivedBioAssayData_list derivedBioAssayData_list)
          Set method for derivedBioAssayData_list
 void setDesignElementDimension_list(BioAssayData_package.DesignElementDimension_list designElementDimension_list)
          Set method for designElementDimension_list
 void setDesignElementMap_list(BioAssayData_package.DesignElementMap_list designElementMap_list)
          Set method for designElementMap_list
 void setFeatureDimension_list(BioAssayData_package.FeatureDimension_list featureDimension_list)
          Set method for featureDimension_list
 void setMeasuredBioAssayData_list(BioAssayData_package.MeasuredBioAssayData_list measuredBioAssayData_list)
          Set method for measuredBioAssayData_list
 void setQuantitationTypeDimension_list(BioAssayData_package.QuantitationTypeDimension_list quantitationTypeDimension_list)
          Set method for quantitationTypeDimension_list
 void setQuantitationTypeMap_list(BioAssayData_package.QuantitationTypeMap_list quantitationTypeMap_list)
          Set method for quantitationTypeMap_list
 void setReporterDimension_list(BioAssayData_package.ReporterDimension_list reporterDimension_list)
          Set method for reporterDimension_list
 void writeAssociations(java.io.Writer out)
          writeAssociations
 void writeAttributes(java.io.Writer out)
          writeAttributes
 void writeMAGEML(java.io.Writer out)
          writeMAGEML
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

bioAssayData_list

public BioAssayData_package.BioAssayData_list bioAssayData_list
Represents the dataset created when the BioAssays are created. BioAssayData is the entry point to the values. Because the actual values are represented by a different object, BioDataValues, which can be memory intensive, the annotation of the transformation can be gotten separate from the data.


quantitationTypeDimension_list

public BioAssayData_package.QuantitationTypeDimension_list quantitationTypeDimension_list
An ordered list of quantitationTypes.


designElementDimension_list

public BioAssayData_package.DesignElementDimension_list designElementDimension_list
An ordered list of designElements. It will be realized as one of its three subclasses.


derivedBioAssayData_list

public BioAssayData_package.DerivedBioAssayData_list derivedBioAssayData_list
The output of a transformation event.


measuredBioAssayData_list

public BioAssayData_package.MeasuredBioAssayData_list measuredBioAssayData_list
The data associated with the MeasuredBioAssay produced by FeatureExtraction.


bioAssayDimension_list

public BioAssayData_package.BioAssayDimension_list bioAssayDimension_list
An ordered list of bioAssays.


quantitationTypeMap_list

public BioAssayData_package.QuantitationTypeMap_list quantitationTypeMap_list
A QuantitationTypeMap is the description of how source QuantitationTypes are mathematically transformed into a target QuantitationType.


designElementMap_list

public BioAssayData_package.DesignElementMap_list designElementMap_list
A DesignElementMap is the description of how source DesignElements are transformed into a target DesignElement.


bioAssayMap_list

public BioAssayData_package.BioAssayMap_list bioAssayMap_list
The BioAssayMap is the description of how source MeasuredBioAssays and/or DerivedBioAssays are manipulated (mathematically) to produce DerivedBioAssays.


compositeSequenceDimension_list

public BioAssayData_package.CompositeSequenceDimension_list compositeSequenceDimension_list
Specialized DesignElementDimension to hold CompositeSequences.


reporterDimension_list

public BioAssayData_package.ReporterDimension_list reporterDimension_list
Specialized DesignElementDimension to hold Reporters.


featureDimension_list

public BioAssayData_package.FeatureDimension_list featureDimension_list
Specialized DesignElementDimension to hold Features.

Constructor Detail

BioAssayData_package

public BioAssayData_package()
Default constructor.


BioAssayData_package

public BioAssayData_package(org.xml.sax.Attributes atts)
Attribute constructor. Looks up the attributes in the parameter and casts them from strings appropriately

Method Detail

writeMAGEML

public void writeMAGEML(java.io.Writer out)
                 throws java.io.IOException
writeMAGEML

This method is responsible for assembling the attribute and association data into XML. It creates the object tag and then calls the writeAttributes and writeAssociation methods.


writeAttributes

public void writeAttributes(java.io.Writer out)
                     throws java.io.IOException
writeAttributes

This method is responsible for assembling the attribute data into XML. It calls the super method to write out all attributes of this class and it's ancestors.


writeAssociations

public void writeAssociations(java.io.Writer out)
                       throws java.io.IOException
writeAssociations

This method is responsible for assembling the association data into XML. It calls the super method to write out all associations of this class's ancestors.


setBioAssayData_list

public void setBioAssayData_list(BioAssayData_package.BioAssayData_list bioAssayData_list)
Set method for bioAssayData_list


getBioAssayData_list

public BioAssayData_package.BioAssayData_list getBioAssayData_list()
Get method for bioAssayData_list


addToBioAssayData_list

public void addToBioAssayData_list(BioAssayData bioAssayData)
Method to add BioAssayData to BioAssayData_list


addToBioAssayData_list

public void addToBioAssayData_list(int position,
                                   BioAssayData bioAssayData)
Method to add BioAssayData at position to BioAssayData_list


getFromBioAssayData_list

public BioAssayData getFromBioAssayData_list(int position)
Method to get BioAssayData from BioAssayData_list


removeElementAtFromBioAssayData_list

public void removeElementAtFromBioAssayData_list(int position)
Method to remove by position from BioAssayData_list


removeFromBioAssayData_list

public void removeFromBioAssayData_list(BioAssayData bioAssayData)
Method to remove first BioAssayData from BioAssayData_list


setQuantitationTypeDimension_list

public void setQuantitationTypeDimension_list(BioAssayData_package.QuantitationTypeDimension_list quantitationTypeDimension_list)
Set method for quantitationTypeDimension_list


getQuantitationTypeDimension_list

public BioAssayData_package.QuantitationTypeDimension_list getQuantitationTypeDimension_list()
Get method for quantitationTypeDimension_list


addToQuantitationTypeDimension_list

public void addToQuantitationTypeDimension_list(QuantitationTypeDimension quantitationTypeDimension)
Method to add QuantitationTypeDimension to QuantitationTypeDimension_list


addToQuantitationTypeDimension_list

public void addToQuantitationTypeDimension_list(int position,
                                                QuantitationTypeDimension quantitationTypeDimension)
Method to add QuantitationTypeDimension at position to QuantitationTypeDimension_list


getFromQuantitationTypeDimension_list

public QuantitationTypeDimension getFromQuantitationTypeDimension_list(int position)
Method to get QuantitationTypeDimension from QuantitationTypeDimension_list


removeElementAtFromQuantitationTypeDimension_list

public void removeElementAtFromQuantitationTypeDimension_list(int position)
Method to remove by position from QuantitationTypeDimension_list


removeFromQuantitationTypeDimension_list

public void removeFromQuantitationTypeDimension_list(QuantitationTypeDimension quantitationTypeDimension)
Method to remove first QuantitationTypeDimension from QuantitationTypeDimension_list


setDesignElementDimension_list

public void setDesignElementDimension_list(BioAssayData_package.DesignElementDimension_list designElementDimension_list)
Set method for designElementDimension_list


getDesignElementDimension_list

public BioAssayData_package.DesignElementDimension_list getDesignElementDimension_list()
Get method for designElementDimension_list


addToDesignElementDimension_list

public void addToDesignElementDimension_list(DesignElementDimension designElementDimension)
Method to add DesignElementDimension to DesignElementDimension_list


addToDesignElementDimension_list

public void addToDesignElementDimension_list(int position,
                                             DesignElementDimension designElementDimension)
Method to add DesignElementDimension at position to DesignElementDimension_list


getFromDesignElementDimension_list

public DesignElementDimension getFromDesignElementDimension_list(int position)
Method to get DesignElementDimension from DesignElementDimension_list


removeElementAtFromDesignElementDimension_list

public void removeElementAtFromDesignElementDimension_list(int position)
Method to remove by position from DesignElementDimension_list


removeFromDesignElementDimension_list

public void removeFromDesignElementDimension_list(DesignElementDimension designElementDimension)
Method to remove first DesignElementDimension from DesignElementDimension_list


setDerivedBioAssayData_list

public void setDerivedBioAssayData_list(BioAssayData_package.DerivedBioAssayData_list derivedBioAssayData_list)
Set method for derivedBioAssayData_list


getDerivedBioAssayData_list

public BioAssayData_package.DerivedBioAssayData_list getDerivedBioAssayData_list()
Get method for derivedBioAssayData_list


addToDerivedBioAssayData_list

public void addToDerivedBioAssayData_list(DerivedBioAssayData derivedBioAssayData)
Method to add DerivedBioAssayData to DerivedBioAssayData_list


addToDerivedBioAssayData_list

public void addToDerivedBioAssayData_list(int position,
                                          DerivedBioAssayData derivedBioAssayData)
Method to add DerivedBioAssayData at position to DerivedBioAssayData_list


getFromDerivedBioAssayData_list

public DerivedBioAssayData getFromDerivedBioAssayData_list(int position)
Method to get DerivedBioAssayData from DerivedBioAssayData_list


removeElementAtFromDerivedBioAssayData_list

public void removeElementAtFromDerivedBioAssayData_list(int position)
Method to remove by position from DerivedBioAssayData_list


removeFromDerivedBioAssayData_list

public void removeFromDerivedBioAssayData_list(DerivedBioAssayData derivedBioAssayData)
Method to remove first DerivedBioAssayData from DerivedBioAssayData_list


setMeasuredBioAssayData_list

public void setMeasuredBioAssayData_list(BioAssayData_package.MeasuredBioAssayData_list measuredBioAssayData_list)
Set method for measuredBioAssayData_list


getMeasuredBioAssayData_list

public BioAssayData_package.MeasuredBioAssayData_list getMeasuredBioAssayData_list()
Get method for measuredBioAssayData_list


addToMeasuredBioAssayData_list

public void addToMeasuredBioAssayData_list(MeasuredBioAssayData measuredBioAssayData)
Method to add MeasuredBioAssayData to MeasuredBioAssayData_list


addToMeasuredBioAssayData_list

public void addToMeasuredBioAssayData_list(int position,
                                           MeasuredBioAssayData measuredBioAssayData)
Method to add MeasuredBioAssayData at position to MeasuredBioAssayData_list


getFromMeasuredBioAssayData_list

public MeasuredBioAssayData getFromMeasuredBioAssayData_list(int position)
Method to get MeasuredBioAssayData from MeasuredBioAssayData_list


removeElementAtFromMeasuredBioAssayData_list

public void removeElementAtFromMeasuredBioAssayData_list(int position)
Method to remove by position from MeasuredBioAssayData_list


removeFromMeasuredBioAssayData_list

public void removeFromMeasuredBioAssayData_list(MeasuredBioAssayData measuredBioAssayData)
Method to remove first MeasuredBioAssayData from MeasuredBioAssayData_list


setBioAssayDimension_list

public void setBioAssayDimension_list(BioAssayData_package.BioAssayDimension_list bioAssayDimension_list)
Set method for bioAssayDimension_list


getBioAssayDimension_list

public BioAssayData_package.BioAssayDimension_list getBioAssayDimension_list()
Get method for bioAssayDimension_list


addToBioAssayDimension_list

public void addToBioAssayDimension_list(BioAssayDimension bioAssayDimension)
Method to add BioAssayDimension to BioAssayDimension_list


addToBioAssayDimension_list

public void addToBioAssayDimension_list(int position,
                                        BioAssayDimension bioAssayDimension)
Method to add BioAssayDimension at position to BioAssayDimension_list


getFromBioAssayDimension_list

public BioAssayDimension getFromBioAssayDimension_list(int position)
Method to get BioAssayDimension from BioAssayDimension_list


removeElementAtFromBioAssayDimension_list

public void removeElementAtFromBioAssayDimension_list(int position)
Method to remove by position from BioAssayDimension_list


removeFromBioAssayDimension_list

public void removeFromBioAssayDimension_list(BioAssayDimension bioAssayDimension)
Method to remove first BioAssayDimension from BioAssayDimension_list


setQuantitationTypeMap_list

public void setQuantitationTypeMap_list(BioAssayData_package.QuantitationTypeMap_list quantitationTypeMap_list)
Set method for quantitationTypeMap_list


getQuantitationTypeMap_list

public BioAssayData_package.QuantitationTypeMap_list getQuantitationTypeMap_list()
Get method for quantitationTypeMap_list


addToQuantitationTypeMap_list

public void addToQuantitationTypeMap_list(QuantitationTypeMap quantitationTypeMap)
Method to add QuantitationTypeMap to QuantitationTypeMap_list


addToQuantitationTypeMap_list

public void addToQuantitationTypeMap_list(int position,
                                          QuantitationTypeMap quantitationTypeMap)
Method to add QuantitationTypeMap at position to QuantitationTypeMap_list


getFromQuantitationTypeMap_list

public QuantitationTypeMap getFromQuantitationTypeMap_list(int position)
Method to get QuantitationTypeMap from QuantitationTypeMap_list


removeElementAtFromQuantitationTypeMap_list

public void removeElementAtFromQuantitationTypeMap_list(int position)
Method to remove by position from QuantitationTypeMap_list


removeFromQuantitationTypeMap_list

public void removeFromQuantitationTypeMap_list(QuantitationTypeMap quantitationTypeMap)
Method to remove first QuantitationTypeMap from QuantitationTypeMap_list


setDesignElementMap_list

public void setDesignElementMap_list(BioAssayData_package.DesignElementMap_list designElementMap_list)
Set method for designElementMap_list


getDesignElementMap_list

public BioAssayData_package.DesignElementMap_list getDesignElementMap_list()
Get method for designElementMap_list


addToDesignElementMap_list

public void addToDesignElementMap_list(DesignElementMap designElementMap)
Method to add DesignElementMap to DesignElementMap_list


addToDesignElementMap_list

public void addToDesignElementMap_list(int position,
                                       DesignElementMap designElementMap)
Method to add DesignElementMap at position to DesignElementMap_list


getFromDesignElementMap_list

public DesignElementMap getFromDesignElementMap_list(int position)
Method to get DesignElementMap from DesignElementMap_list


removeElementAtFromDesignElementMap_list

public void removeElementAtFromDesignElementMap_list(int position)
Method to remove by position from DesignElementMap_list


removeFromDesignElementMap_list

public void removeFromDesignElementMap_list(DesignElementMap designElementMap)
Method to remove first DesignElementMap from DesignElementMap_list


setBioAssayMap_list

public void setBioAssayMap_list(BioAssayData_package.BioAssayMap_list bioAssayMap_list)
Set method for bioAssayMap_list


getBioAssayMap_list

public BioAssayData_package.BioAssayMap_list getBioAssayMap_list()
Get method for bioAssayMap_list


addToBioAssayMap_list

public void addToBioAssayMap_list(BioAssayMap bioAssayMap)
Method to add BioAssayMap to BioAssayMap_list


addToBioAssayMap_list

public void addToBioAssayMap_list(int position,
                                  BioAssayMap bioAssayMap)
Method to add BioAssayMap at position to BioAssayMap_list


getFromBioAssayMap_list

public BioAssayMap getFromBioAssayMap_list(int position)
Method to get BioAssayMap from BioAssayMap_list


removeElementAtFromBioAssayMap_list

public void removeElementAtFromBioAssayMap_list(int position)
Method to remove by position from BioAssayMap_list


removeFromBioAssayMap_list

public void removeFromBioAssayMap_list(BioAssayMap bioAssayMap)
Method to remove first BioAssayMap from BioAssayMap_list


setCompositeSequenceDimension_list

public void setCompositeSequenceDimension_list(BioAssayData_package.CompositeSequenceDimension_list compositeSequenceDimension_list)
Set method for compositeSequenceDimension_list


getCompositeSequenceDimension_list

public BioAssayData_package.CompositeSequenceDimension_list getCompositeSequenceDimension_list()
Get method for compositeSequenceDimension_list


addToCompositeSequenceDimension_list

public void addToCompositeSequenceDimension_list(CompositeSequenceDimension compositeSequenceDimension)
Method to add CompositeSequenceDimension to CompositeSequenceDimension_list


addToCompositeSequenceDimension_list

public void addToCompositeSequenceDimension_list(int position,
                                                 CompositeSequenceDimension compositeSequenceDimension)
Method to add CompositeSequenceDimension at position to CompositeSequenceDimension_list


getFromCompositeSequenceDimension_list

public CompositeSequenceDimension getFromCompositeSequenceDimension_list(int position)
Method to get CompositeSequenceDimension from CompositeSequenceDimension_list


removeElementAtFromCompositeSequenceDimension_list

public void removeElementAtFromCompositeSequenceDimension_list(int position)
Method to remove by position from CompositeSequenceDimension_list


removeFromCompositeSequenceDimension_list

public void removeFromCompositeSequenceDimension_list(CompositeSequenceDimension compositeSequenceDimension)
Method to remove first CompositeSequenceDimension from CompositeSequenceDimension_list


setReporterDimension_list

public void setReporterDimension_list(BioAssayData_package.ReporterDimension_list reporterDimension_list)
Set method for reporterDimension_list


getReporterDimension_list

public BioAssayData_package.ReporterDimension_list getReporterDimension_list()
Get method for reporterDimension_list


addToReporterDimension_list

public void addToReporterDimension_list(ReporterDimension reporterDimension)
Method to add ReporterDimension to ReporterDimension_list


addToReporterDimension_list

public void addToReporterDimension_list(int position,
                                        ReporterDimension reporterDimension)
Method to add ReporterDimension at position to ReporterDimension_list


getFromReporterDimension_list

public ReporterDimension getFromReporterDimension_list(int position)
Method to get ReporterDimension from ReporterDimension_list


removeElementAtFromReporterDimension_list

public void removeElementAtFromReporterDimension_list(int position)
Method to remove by position from ReporterDimension_list


removeFromReporterDimension_list

public void removeFromReporterDimension_list(ReporterDimension reporterDimension)
Method to remove first ReporterDimension from ReporterDimension_list


setFeatureDimension_list

public void setFeatureDimension_list(BioAssayData_package.FeatureDimension_list featureDimension_list)
Set method for featureDimension_list


getFeatureDimension_list

public BioAssayData_package.FeatureDimension_list getFeatureDimension_list()
Get method for featureDimension_list


addToFeatureDimension_list

public void addToFeatureDimension_list(FeatureDimension featureDimension)
Method to add FeatureDimension to FeatureDimension_list


addToFeatureDimension_list

public void addToFeatureDimension_list(int position,
                                       FeatureDimension featureDimension)
Method to add FeatureDimension at position to FeatureDimension_list


getFromFeatureDimension_list

public FeatureDimension getFromFeatureDimension_list(int position)
Method to get FeatureDimension from FeatureDimension_list


removeElementAtFromFeatureDimension_list

public void removeElementAtFromFeatureDimension_list(int position)
Method to remove by position from FeatureDimension_list


removeFromFeatureDimension_list

public void removeFromFeatureDimension_list(FeatureDimension featureDimension)
Method to remove first FeatureDimension from FeatureDimension_list