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java.lang.Objectorg.biomage.Common.Extendable
org.biomage.Common.Describable
org.biomage.HigherLevelAnalysis.Node
public class Node
An individual component of a clustering. May contain other nodes.
Nested Class Summary |
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Nested classes/interfaces inherited from interface org.biomage.Interface.HasNodes |
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HasNodes.Nodes_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasNodeContents |
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HasNodeContents.NodeContents_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasNodeValue |
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HasNodeValue.NodeValue_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasAuditTrail |
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HasAuditTrail.AuditTrail_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasDescriptions |
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HasDescriptions.Descriptions_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasPropertySets |
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HasPropertySets.PropertySets_list |
Field Summary | |
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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 |
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security |
Fields inherited from class org.biomage.Common.Extendable |
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editable, id, securedElementId |
Constructor Summary | |
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Node()
Default constructor. |
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Node(org.xml.sax.Attributes atts)
Attribute constructor. |
Method Summary | |
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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()
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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()
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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 |
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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 |
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addToPropertySets, addToPropertySets, equals, getFromPropertySets, getId, getIsEditable, getPropertySets, getSecuredElementId, isEditable, removeElementAtFromPropertySets, removeFromPropertySets, setId, setIsEditable, setPropertySets, setSecuredElementId, toString |
Methods inherited from class java.lang.Object |
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clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
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protected java.util.List nodes
protected java.util.List nodeContents
protected java.util.List nodeValue
Constructor Detail |
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public Node()
public Node(org.xml.sax.Attributes atts)
atts:
- the attribute list.Method Detail |
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public void writeMAGEML(java.io.Writer out) throws java.io.IOException
writeMAGEML
in class Describable
java.io.IOException
public boolean emptyMAGEobject()
public void writeAttributes(java.io.Writer out) throws java.io.IOException
writeAttributes
in class Describable
java.io.IOException
public void writeAssociations(java.io.Writer out) throws java.io.IOException
writeAssociations
in class Describable
java.io.IOException
public java.lang.String getModelClassName()
getModelClassName
in class Describable
public void setNodes(HasNodes.Nodes_list nodes)
setNodes
in interface HasNodes
value
- to setpublic HasNodes.Nodes_list getNodes()
getNodes
in interface HasNodes
public void addToNodes(Node node)
addToNodes
in interface HasNodes
public void addToNodes(int position, Node node)
addToNodes
in interface HasNodes
public Node getFromNodes(int position)
getFromNodes
in interface HasNodes
public void removeElementAtFromNodes(int position)
removeElementAtFromNodes
in interface HasNodes
public void removeFromNodes(Node node)
removeFromNodes
in interface HasNodes
public void setNodeContents(HasNodeContents.NodeContents_list nodeContents)
setNodeContents
in interface HasNodeContents
value
- to setpublic HasNodeContents.NodeContents_list getNodeContents()
getNodeContents
in interface HasNodeContents
public void addToNodeContents(NodeContents nodeContents)
addToNodeContents
in interface HasNodeContents
public void addToNodeContents(int position, NodeContents nodeContents)
addToNodeContents
in interface HasNodeContents
public NodeContents getFromNodeContents(int position)
getFromNodeContents
in interface HasNodeContents
public void removeElementAtFromNodeContents(int position)
removeElementAtFromNodeContents
in interface HasNodeContents
public void removeFromNodeContents(NodeContents nodeContents)
removeFromNodeContents
in interface HasNodeContents
public void setNodeValue(HasNodeValue.NodeValue_list nodeValue)
setNodeValue
in interface HasNodeValue
value
- to setpublic HasNodeValue.NodeValue_list getNodeValue()
getNodeValue
in interface HasNodeValue
public void addToNodeValue(NodeValue nodeValue)
addToNodeValue
in interface HasNodeValue
public void addToNodeValue(int position, NodeValue nodeValue)
addToNodeValue
in interface HasNodeValue
public NodeValue getFromNodeValue(int position)
getFromNodeValue
in interface HasNodeValue
public void removeElementAtFromNodeValue(int position)
removeElementAtFromNodeValue
in interface HasNodeValue
public void removeFromNodeValue(NodeValue nodeValue)
removeFromNodeValue
in interface HasNodeValue
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