org.biomage.HigherLevelAnalysis
Class Node

java.lang.Object
  extended by org.biomage.Common.Extendable
      extended by org.biomage.Common.Describable
          extended by org.biomage.HigherLevelAnalysis.Node
All Implemented Interfaces:
SecuredElementItf, java.io.Serializable, HasAuditTrail, HasDescriptions, HasNodeContents, HasNodes, HasNodeValue, HasPropertySets, HasSecurity

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/interfaces inherited from interface org.biomage.Interface.HasNodes
HasNodes.Nodes_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasNodeContents
HasNodeContents.NodeContents_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasNodeValue
HasNodeValue.NodeValue_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  java.util.List nodeContents
          The contents of the node, expressed as either a one, two or three dimensional object.
protected  java.util.List nodes
          Nested nodes of the BioAssayDataCluster.
protected  java.util.List nodeValue
          Values or measurements for this node that may be produced by the clustering algorithm.
 
Fields inherited from class org.biomage.Common.Describable
security
 
Fields inherited from class org.biomage.Common.Extendable
editable, id, securedElementId
 
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
 boolean emptyMAGEobject()
           
 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
 java.lang.String getModelClassName()
           
 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, setAttributes, 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, toString
 
Methods inherited from class java.lang.Object
clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

nodes

protected java.util.List nodes
Nested nodes of the BioAssayDataCluster.


nodeContents

protected java.util.List nodeContents
The contents of the node, expressed as either a one, two or three dimensional object.


nodeValue

protected java.util.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

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.

Overrides:
writeMAGEML in class Describable
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 Describable
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 Describable
Throws:
java.io.IOException

getModelClassName

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

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

setNodeContents

public void setNodeContents(HasNodeContents.NodeContents_list nodeContents)
Set method for nodeContents

Specified by:
setNodeContents in interface HasNodeContents
Parameters:
value - to set

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
Parameters:
value - to set

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