org.biomage.HigherLevelAnalysis
Class Node

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

All Implemented Interfaces:

HasAuditTrail, HasDescriptions, HasNodeContents, HasNodes, HasNodeValue, HasPropertySets, HasSecurity, java.io.Serializable

public class Node

extends Describable

implements java.io.Serializable, HasNodes, HasNodeContents, HasNodeValue

An individual component of a clustering. May contain other 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.HasNodeContents

HasNodeContents.NodeContents_list

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

HasNodeValue.NodeValue_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 HasNodeContents.NodeContents_list	nodeContents The contents of the node, expressed as either a one, two or three dimensional object.
protected HasNodes.Nodes_list	nodes Nested nodes of the BioAssayDataCluster.
protected HasNodeValue.NodeValue_list	nodeValue Values or measurements for this node that may be produced by the clustering algorithm.

Fields inherited from class org.biomage.Common.Describable

auditTrail, descriptions, security

Fields inherited from class org.biomage.Common.Extendable

propertySets

Constructor Summary

Node()
Default constructor.

Node(org.xml.sax.Attributes atts)
Attribute constructor.

Method Summary

void	addToNodeContents(int position, NodeContents nodeContents) Method to add NodeContents at position to NodeContents_list
void	addToNodeContents(NodeContents nodeContents) Method to add NodeContents to NodeContents_list
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
void	addToNodeValue(int position, NodeValue nodeValue) Method to add NodeValue at position to NodeValue_list
void	addToNodeValue(NodeValue nodeValue) Method to add NodeValue to NodeValue_list
NodeContents	getFromNodeContents(int position) Method to get NodeContents from NodeContents_list
Node	getFromNodes(int position) Method to get Node from Nodes_list
NodeValue	getFromNodeValue(int position) Method to get NodeValue from NodeValue_list
HasNodeContents.NodeContents_list	getNodeContents() Get method for nodeContents
HasNodes.Nodes_list	getNodes() Get method for nodes
HasNodeValue.NodeValue_list	getNodeValue() Get method for nodeValue
void	removeElementAtFromNodeContents(int position) Method to remove by position from NodeContents_list
void	removeElementAtFromNodes(int position) Method to remove by position from Nodes_list
void	removeElementAtFromNodeValue(int position) Method to remove by position from NodeValue_list
void	removeFromNodeContents(NodeContents nodeContents) Method to remove first NodeContents from NodeContents_list
void	removeFromNodes(Node node) Method to remove first Node from Nodes_list
void	removeFromNodeValue(NodeValue nodeValue) Method to remove first NodeValue from NodeValue_list
void	setNodeContents(HasNodeContents.NodeContents_list nodeContents) Set method for nodeContents
void	setNodes(HasNodes.Nodes_list nodes) Set method for nodes
void	setNodeValue(HasNodeValue.NodeValue_list nodeValue) Set method for nodeValue
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.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

nodes

protected HasNodes.Nodes_list nodes

Nested nodes of the BioAssayDataCluster.

nodeContents

protected HasNodeContents.NodeContents_list nodeContents

The contents of the node, expressed as either a one, two or three dimensional object.

nodeValue

protected HasNodeValue.NodeValue_list nodeValue

Values or measurements for this node that may be produced by the clustering algorithm. Typical are distance values for the nodes.

Constructor Detail

Node

public Node()

Default constructor.

Node

public Node(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 Describable

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 Describable

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 Describable

java.io.IOException

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

setNodeContents

public void setNodeContents(HasNodeContents.NodeContents_list nodeContents)

Set method for nodeContents

Specified by:

setNodeContents in interface HasNodeContents

getNodeContents

public HasNodeContents.NodeContents_list getNodeContents()

Get method for nodeContents

Specified by:

getNodeContents in interface HasNodeContents

Returns:

value of the attribute

addToNodeContents

public void addToNodeContents(NodeContents nodeContents)

Method to add NodeContents to NodeContents_list

Specified by:

addToNodeContents in interface HasNodeContents

addToNodeContents

public void addToNodeContents(int position,
                              NodeContents nodeContents)

Method to add NodeContents at position to NodeContents_list

Specified by:

addToNodeContents in interface HasNodeContents

getFromNodeContents

public NodeContents getFromNodeContents(int position)

Method to get NodeContents from NodeContents_list

Specified by:

getFromNodeContents in interface HasNodeContents

removeElementAtFromNodeContents

public void removeElementAtFromNodeContents(int position)

Method to remove by position from NodeContents_list

Specified by:

removeElementAtFromNodeContents in interface HasNodeContents

removeFromNodeContents

public void removeFromNodeContents(NodeContents nodeContents)

Method to remove first NodeContents from NodeContents_list

Specified by:

removeFromNodeContents in interface HasNodeContents

setNodeValue

public void setNodeValue(HasNodeValue.NodeValue_list nodeValue)

Set method for nodeValue

Specified by:

setNodeValue in interface HasNodeValue

getNodeValue

public HasNodeValue.NodeValue_list getNodeValue()

Get method for nodeValue

Specified by:

getNodeValue in interface HasNodeValue

Returns:

value of the attribute

addToNodeValue

public void addToNodeValue(NodeValue nodeValue)

Method to add NodeValue to NodeValue_list

Specified by:

addToNodeValue in interface HasNodeValue

addToNodeValue

public void addToNodeValue(int position,
                           NodeValue nodeValue)

Method to add NodeValue at position to NodeValue_list

Specified by:

addToNodeValue in interface HasNodeValue

getFromNodeValue

public NodeValue getFromNodeValue(int position)

Method to get NodeValue from NodeValue_list

Specified by:

getFromNodeValue in interface HasNodeValue

removeElementAtFromNodeValue

public void removeElementAtFromNodeValue(int position)

Method to remove by position from NodeValue_list

Specified by:

removeElementAtFromNodeValue in interface HasNodeValue

removeFromNodeValue

public void removeFromNodeValue(NodeValue nodeValue)

Method to remove first NodeValue from NodeValue_list

Specified by:

removeFromNodeValue in interface HasNodeValue