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java.lang.Objectorg.biomage.Common.Extendable
org.biomage.Common.Describable
org.biomage.Common.Identifiable
org.biomage.HigherLevelAnalysis.BioAssayDataCluster
public class BioAssayDataCluster
A mathematical method of higher level analysis whereby BioAssayData are grouped together into 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.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 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 |
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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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BioAssayDataCluster()
Default constructor. |
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BioAssayDataCluster(org.xml.sax.Attributes atts)
Attribute constructor. |
Method Summary | |
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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()
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BioAssayData |
getClusterBioAssayData()
Get method for clusterBioAssayData |
Node |
getFromNodes(int position)
Method to get Node from Nodes_list |
java.lang.String |
getModelClassName()
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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 |
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getIdentifier, getName, setIdentifier, setName, toString |
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, 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 |
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 BioAssayData clusterBioAssayData
protected java.util.List nodes
Constructor Detail |
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public BioAssayDataCluster()
public BioAssayDataCluster(org.xml.sax.Attributes atts)
atts:
- the attribute list.Method Detail |
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public void setAttributes(org.xml.sax.Attributes atts)
setAttributes
in class Identifiable
public void writeMAGEML(java.io.Writer out) throws java.io.IOException
writeMAGEML
in class Identifiable
java.io.IOException
public boolean emptyMAGEobject()
public void writeAttributes(java.io.Writer out) throws java.io.IOException
writeAttributes
in class Identifiable
java.io.IOException
public void writeAssociations(java.io.Writer out) throws java.io.IOException
writeAssociations
in class Identifiable
java.io.IOException
public java.lang.String getModelClassName()
getModelClassName
in class Identifiable
public void setClusterBioAssayData(BioAssayData clusterBioAssayData)
setClusterBioAssayData
in interface HasClusterBioAssayData
value
- to setpublic BioAssayData getClusterBioAssayData()
getClusterBioAssayData
in interface HasClusterBioAssayData
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
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