org.biomage.HigherLevelAnalysis
Class BioAssayDataCluster

java.lang.Object
  |
  +--org.biomage.Common.Extendable
        |
        +--org.biomage.Common.Describable
              |
              +--org.biomage.Common.Identifiable
                    |
                    +--org.biomage.HigherLevelAnalysis.BioAssayDataCluster

All Implemented Interfaces:

HasAuditTrail, HasClusterBioAssayData, HasDescriptions, HasNodes, HasPropertySets, HasSecurity, java.io.Serializable

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 inherited from class org.biomage.Interface.HasNodes

HasNodes.Nodes_list

Nested classes inherited from class org.biomage.Interface.HasAuditTrail

HasAuditTrail.AuditTrail_list

Nested classes inherited from class org.biomage.Interface.HasDescriptions

HasDescriptions.Descriptions_list

Nested classes inherited from class org.biomage.Interface.HasPropertySets

HasPropertySets.PropertySets_list

Field Summary

protected BioAssayData	clusterBioAssayData The BioAssayData whose values were used by the cluster algorithm.
protected HasNodes.Nodes_list	nodes The nodes of the cluster.

Fields inherited from class org.biomage.Common.Describable

auditTrail, descriptions, security

Fields inherited from class org.biomage.Common.Extendable

propertySets

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
BioAssayData	getClusterBioAssayData() Get method for clusterBioAssayData
Node	getFromNodes(int position) Method to get Node from Nodes_list
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	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

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

clusterBioAssayData

protected BioAssayData clusterBioAssayData

The BioAssayData whose values were used by the cluster algorithm.

nodes

protected HasNodes.Nodes_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

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 Identifiable

java.io.IOException

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

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

java.io.IOException

setClusterBioAssayData

public void setClusterBioAssayData(BioAssayData clusterBioAssayData)

Set method for clusterBioAssayData

Specified by:

setClusterBioAssayData in interface HasClusterBioAssayData

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

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