org.biomage.BioAssayData
Class DerivedBioAssayData

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

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

The output of a transformation event.

See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasSummaryStatistics
HasSummaryStatistics.SummaryStatistics_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasAuditTrail
HasAuditTrail.AuditTrail_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasDescriptions
HasDescriptions.Descriptions_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasPropertySets
HasPropertySets.PropertySets_list
 
Field Summary
protected  Transformation producerTransformation
          The association between the DerivedBioAssayData and the Transformation event that produced it.
 
Fields inherited from class org.biomage.BioAssayData.BioAssayData
bioAssayDimension, bioDataValues, designElementDimension, quantitationTypeDimension, summaryStatistics
 
Fields inherited from class org.biomage.Common.Describable
security
 
Fields inherited from class org.biomage.Common.Extendable
editable, id, securedElementId
 
Constructor Summary
DerivedBioAssayData()
          Default constructor.
DerivedBioAssayData(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 boolean emptyMAGEobject()
           
 java.lang.String getModelClassName()
           
 Transformation getProducerTransformation()
          Get method for producerTransformation
 void setAttributes(org.xml.sax.Attributes atts)
           
 void setProducerTransformation(Transformation producerTransformation)
          Set method for producerTransformation
 void writeAssociations(java.io.Writer out)
          writeAssociations This method is responsible for assembling the association data into XML.
 void writeAttributes(java.io.Writer out)
          writeAttributes This method is responsible for assembling the attribute data into XML.
 void writeMAGEML(java.io.Writer out)
          writeMAGEML This method is responsible for assembling the attribute and association data into XML.
 
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, toString
 
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, equals, getFromPropertySets, getId, getIsEditable, getPropertySets, getSecuredElementId, isEditable, removeElementAtFromPropertySets, removeFromPropertySets, setId, setIsEditable, setPropertySets, setSecuredElementId
 
Methods inherited from class java.lang.Object
clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

producerTransformation

protected 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

Parameters:
atts: - the attribute list.
Method Detail

setAttributes

public void setAttributes(org.xml.sax.Attributes atts)
Overrides:
setAttributes in class BioAssayData

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
Throws:
java.io.IOException

emptyMAGEobject

public boolean emptyMAGEobject()

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
Throws:
java.io.IOException

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
Throws:
java.io.IOException

getModelClassName

public java.lang.String getModelClassName()
Overrides:
getModelClassName in class BioAssayData

setProducerTransformation

public void setProducerTransformation(Transformation producerTransformation)
Set method for producerTransformation

Specified by:
setProducerTransformation in interface HasProducerTransformation
Parameters:
value - to set

getProducerTransformation

public Transformation getProducerTransformation()
Get method for producerTransformation

Specified by:
getProducerTransformation in interface HasProducerTransformation
Returns:
value of the attribute