org.biomage.HigherLevelAnalysis
Class HigherLevelAnalysis_package

java.lang.Object
  extended by org.biomage.HigherLevelAnalysis.HigherLevelAnalysis_package
All Implemented Interfaces:
java.io.Serializable

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

Describes the results of performing analysis on the result of the BioAssayData from an Experiment.

See Also:
Serialized Form

Nested Class Summary
 class HigherLevelAnalysis_package.BioAssayDataCluster_list
          Inner list class for holding multiple entries for attribute bioAssayDataCluster.
 
Field Summary
 HigherLevelAnalysis_package.BioAssayDataCluster_list bioAssayDataCluster_list
          A mathematical method of higher level analysis whereby BioAssayData are grouped together into nodes.
 
Constructor Summary
HigherLevelAnalysis_package()
          Default constructor.
HigherLevelAnalysis_package(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToBioAssayDataCluster_list(BioAssayDataCluster bioAssayDataCluster)
          Method to add BioAssayDataCluster to BioAssayDataCluster_list
 void addToBioAssayDataCluster_list(int position, BioAssayDataCluster bioAssayDataCluster)
          Method to add BioAssayDataCluster at position to BioAssayDataCluster_list
 boolean emptyMAGEobject()
           
 HigherLevelAnalysis_package.BioAssayDataCluster_list getBioAssayDataCluster_list()
          Get method for bioAssayDataCluster_list
 BioAssayDataCluster getFromBioAssayDataCluster_list(int position)
          Method to get BioAssayDataCluster from BioAssayDataCluster_list
 java.lang.String getModelClassName()
           
 void removeElementAtFromBioAssayDataCluster_list(int position)
          Method to remove by position from BioAssayDataCluster_list
 void removeFromBioAssayDataCluster_list(BioAssayDataCluster bioAssayDataCluster)
          Method to remove first BioAssayDataCluster from BioAssayDataCluster_list
 void setBioAssayDataCluster_list(HigherLevelAnalysis_package.BioAssayDataCluster_list bioAssayDataCluster_list)
          Set method for bioAssayDataCluster_list
 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 java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

bioAssayDataCluster_list

public HigherLevelAnalysis_package.BioAssayDataCluster_list bioAssayDataCluster_list
A mathematical method of higher level analysis whereby BioAssayData are grouped together into nodes.

Constructor Detail

HigherLevelAnalysis_package

public HigherLevelAnalysis_package()
Default constructor.


HigherLevelAnalysis_package

public HigherLevelAnalysis_package(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

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.

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.

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.

Throws:
java.io.IOException

getModelClassName

public java.lang.String getModelClassName()

setBioAssayDataCluster_list

public void setBioAssayDataCluster_list(HigherLevelAnalysis_package.BioAssayDataCluster_list bioAssayDataCluster_list)
Set method for bioAssayDataCluster_list

Parameters:
value - to set

getBioAssayDataCluster_list

public HigherLevelAnalysis_package.BioAssayDataCluster_list getBioAssayDataCluster_list()
Get method for bioAssayDataCluster_list

Returns:
value of the attribute

addToBioAssayDataCluster_list

public void addToBioAssayDataCluster_list(BioAssayDataCluster bioAssayDataCluster)
Method to add BioAssayDataCluster to BioAssayDataCluster_list


addToBioAssayDataCluster_list

public void addToBioAssayDataCluster_list(int position,
                                          BioAssayDataCluster bioAssayDataCluster)
Method to add BioAssayDataCluster at position to BioAssayDataCluster_list


getFromBioAssayDataCluster_list

public BioAssayDataCluster getFromBioAssayDataCluster_list(int position)
Method to get BioAssayDataCluster from BioAssayDataCluster_list


removeElementAtFromBioAssayDataCluster_list

public void removeElementAtFromBioAssayDataCluster_list(int position)
Method to remove by position from BioAssayDataCluster_list


removeFromBioAssayDataCluster_list

public void removeFromBioAssayDataCluster_list(BioAssayDataCluster bioAssayDataCluster)
Method to remove first BioAssayDataCluster from BioAssayDataCluster_list