org.biomage.HigherLevelAnalysis
Class BioAssayDataCluster

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.HigherLevelAnalysis.BioAssayDataCluster
All Implemented Interfaces:
SecuredElementItf, java.io.Serializable, HasAuditTrail, HasClusterBioAssayData, HasDescriptions, HasNodes, HasPropertySets, HasSecurity

public class BioAssayDataCluster
extends Identifiable
implements java.io.Serializable, HasNodes, HasClusterBioAssayData

A mathematical method of higher level analysis whereby BioAssayData are grouped together into nodes.

See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasNodes
HasNodes.Nodes_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  BioAssayData clusterBioAssayData
          The BioAssayData whose values were used by the cluster algorithm.
protected  java.util.List nodes
          The nodes of the cluster.
 
Fields inherited from class org.biomage.Common.Describable
security
 
Fields inherited from class org.biomage.Common.Extendable
editable, id, securedElementId
 
Constructor Summary
BioAssayDataCluster()
          Default constructor.
BioAssayDataCluster(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToNodes(int position, Node node)
          Method to add Node at position to Nodes_list
 void addToNodes(Node node)
          Method to add Node to Nodes_list
 boolean emptyMAGEobject()
           
 BioAssayData getClusterBioAssayData()
          Get method for clusterBioAssayData
 Node getFromNodes(int position)
          Method to get Node from Nodes_list
 java.lang.String getModelClassName()
           
 HasNodes.Nodes_list getNodes()
          Get method for nodes
 void removeElementAtFromNodes(int position)
          Method to remove by position from Nodes_list
 void removeFromNodes(Node node)
          Method to remove first Node from Nodes_list
 void setAttributes(org.xml.sax.Attributes atts)
           
 void setClusterBioAssayData(BioAssayData clusterBioAssayData)
          Set method for clusterBioAssayData
 void setNodes(HasNodes.Nodes_list nodes)
          Set method for nodes
 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.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

clusterBioAssayData

protected BioAssayData clusterBioAssayData
The BioAssayData whose values were used by the cluster algorithm.


nodes

protected java.util.List nodes
The nodes of the cluster.

Constructor Detail

BioAssayDataCluster

public BioAssayDataCluster()
Default constructor.


BioAssayDataCluster

public BioAssayDataCluster(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 Identifiable

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 Identifiable
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 Identifiable
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 Identifiable
Throws:
java.io.IOException

getModelClassName

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

setClusterBioAssayData

public void setClusterBioAssayData(BioAssayData clusterBioAssayData)
Set method for clusterBioAssayData

Specified by:
setClusterBioAssayData in interface HasClusterBioAssayData
Parameters:
value - to set

getClusterBioAssayData

public BioAssayData getClusterBioAssayData()
Get method for clusterBioAssayData

Specified by:
getClusterBioAssayData in interface HasClusterBioAssayData
Returns:
value of the attribute

setNodes

public void setNodes(HasNodes.Nodes_list nodes)
Set method for nodes

Specified by:
setNodes in interface HasNodes
Parameters:
value - to set

getNodes

public HasNodes.Nodes_list getNodes()
Get method for nodes

Specified by:
getNodes in interface HasNodes
Returns:
value of the attribute

addToNodes

public void addToNodes(Node node)
Method to add Node to Nodes_list

Specified by:
addToNodes in interface HasNodes

addToNodes

public void addToNodes(int position,
                       Node node)
Method to add Node at position to Nodes_list

Specified by:
addToNodes in interface HasNodes

getFromNodes

public Node getFromNodes(int position)
Method to get Node from Nodes_list

Specified by:
getFromNodes in interface HasNodes

removeElementAtFromNodes

public void removeElementAtFromNodes(int position)
Method to remove by position from Nodes_list

Specified by:
removeElementAtFromNodes in interface HasNodes

removeFromNodes

public void removeFromNodes(Node node)
Method to remove first Node from Nodes_list

Specified by:
removeFromNodes in interface HasNodes