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

java.lang.Object
  extended byorg.biomage.Common.Extendable
      extended byorg.biomage.Common.Describable
          extended byorg.biomage.Common.Identifiable
              extended byorg.biomage.BioAssayData.BioAssayData
                  extended byorg.biomage.BioAssayData.DerivedBioAssayData
All Implemented Interfaces:
org.biomage.Interface.HasAuditTrail, org.biomage.Interface.HasBioAssayDimension, org.biomage.Interface.HasBioDataValues, org.biomage.Interface.HasDescriptions, org.biomage.Interface.HasDesignElementDimension, org.biomage.Interface.HasProducerTransformation, org.biomage.Interface.HasPropertySets, org.biomage.Interface.HasQuantitationTypeDimension, org.biomage.Interface.HasSecurity, org.biomage.Interface.HasSummaryStatistics, java.io.Serializable

public class DerivedBioAssayData
extends BioAssayData
implements java.io.Serializable, org.biomage.Interface.HasProducerTransformation

The output of a transformation event.


Nested Class Summary
 
Nested classes inherited from class org.biomage.Interface.HasSummaryStatistics
org.biomage.Interface.HasSummaryStatistics.SummaryStatistics_list
 
Nested classes inherited from class org.biomage.Interface.HasAuditTrail
org.biomage.Interface.HasAuditTrail.AuditTrail_list
 
Nested classes inherited from class org.biomage.Interface.HasDescriptions
org.biomage.Interface.HasDescriptions.Descriptions_list
 
Nested classes inherited from class org.biomage.Interface.HasPropertySets
org.biomage.Interface.HasPropertySets.PropertySets_list
 
Field Summary
private  Transformation producerTransformation
          The association between the DerivedBioAssayData and the Transformation event that produced it.
 
Fields inherited from class org.biomage.BioAssayData.BioAssayData
 
Fields inherited from class org.biomage.Common.Identifiable
 
Fields inherited from class org.biomage.Common.Describable
 
Fields inherited from class org.biomage.Common.Extendable
 
Constructor Summary
DerivedBioAssayData()
          Default constructor.
DerivedBioAssayData(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 Transformation getProducerTransformation()
          Get method for producerTransformation
 void setProducerTransformation(Transformation producerTransformation)
          Set method for producerTransformation
 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 org.biomage.BioAssayData.BioAssayData
addToSummaryStatistics, addToSummaryStatistics, getBioAssayDimension, getBioDataValues, getDesignElementDimension, getFromSummaryStatistics, getQuantitationTypeDimension, getSummaryStatistics, removeElementAtFromSummaryStatistics, removeFromSummaryStatistics, setBioAssayDimension, setBioDataValues, setDesignElementDimension, setQuantitationTypeDimension, setSummaryStatistics
 
Methods inherited from class org.biomage.Common.Identifiable
getIdentifier, getName, setIdentifier, setName
 
Methods inherited from class org.biomage.Common.Describable
addToAuditTrail, addToAuditTrail, addToDescriptions, addToDescriptions, getAuditTrail, getDescriptions, getFromAuditTrail, getFromDescriptions, getSecurity, removeElementAtFromAuditTrail, removeElementAtFromDescriptions, removeFromAuditTrail, removeFromDescriptions, setAuditTrail, setDescriptions, setSecurity
 
Methods inherited from class org.biomage.Common.Extendable
addToPropertySets, addToPropertySets, getFromPropertySets, getPropertySets, removeElementAtFromPropertySets, removeFromPropertySets, setPropertySets
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

producerTransformation

private Transformation producerTransformation
The association between the DerivedBioAssayData and the Transformation event that produced it.

Constructor Detail

DerivedBioAssayData

public DerivedBioAssayData()
Default constructor.


DerivedBioAssayData

public DerivedBioAssayData(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.

Overrides:
writeMAGEML in class BioAssayData

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.

Overrides:
writeAttributes in class BioAssayData

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.

Overrides:
writeAssociations in class BioAssayData

setProducerTransformation

public void setProducerTransformation(Transformation producerTransformation)
Set method for producerTransformation

Specified by:
setProducerTransformation in interface org.biomage.Interface.HasProducerTransformation

getProducerTransformation

public Transformation getProducerTransformation()
Get method for producerTransformation

Specified by:
getProducerTransformation in interface org.biomage.Interface.HasProducerTransformation