org.geworkbench.bison.model.clusters
Class DefaultHierCluster

java.lang.Object
  org.geworkbench.bison.model.clusters.AbstractCluster
      org.geworkbench.bison.model.clusters.DefaultHierCluster

All Implemented Interfaces:

java.io.Serializable, java.lang.Comparable, java.util.Iterator, DSIdentifiable, Cluster, HierCluster

Direct Known Subclasses:

MarkerHierCluster, MicroarrayHierCluster, SimpleHierCluster

public class DefaultHierCluster
extends AbstractCluster
implements HierCluster, java.io.Serializable

Generalization of the Cluster contract that encapsulates functionality to handle Clusters generated from the Hierarchical Clustering analysis method

Author:

First Genetic Trust

See Also:

Serialized Form

Field Summary

Fields inherited from class org.geworkbench.bison.model.clusters.AbstractCluster

children, clusterID, iterator, parent

Constructor Summary

DefaultHierCluster()

Method Summary

void	addNode(HierCluster hc, int index) Adds Cluster as a child of this node
int	compareTo(java.lang.Object o) Comparable method that compares this Cluster to another Hierarchical CLuster node.
int	getDepth() Gets the Combinatorial Depth of this Cluster
double	getHeight() Gets the Algorithmic Height of this Cluster
double	getMaxHeight() Returns the Maximum Algorithmic Height of any Cluster in the Hierarchical Cluster Tree that this Cluster is a part of
HierCluster	getNode(int index) Gets a particular child from a known index
void	setDepth(int d) Sets the Combinatorial Depth of this Cluster
void	setHeight(double d) Sets the Algorithmic Height of this Cluster
java.lang.String	toString()

Methods inherited from class org.geworkbench.bison.model.clusters.AbstractCluster

addNode, getChildrenNodes, getID, getLabel, getLeafChildren, getLeafChildrenCount, getLeafChildrenCountMap, getNodesCount, getParent, hasNext, isLeaf, next, remove, remove, removeAll, reset, setID, setLabel

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.geworkbench.bison.model.clusters.HierCluster

removeAll

Methods inherited from interface org.geworkbench.bison.model.clusters.Cluster

addNode, getChildrenNodes, getLeafChildren, getLeafChildrenCount, getLeafChildrenCountMap, getNodesCount, getParent, isLeaf

Methods inherited from interface java.util.Iterator

hasNext, next, remove

Methods inherited from interface org.geworkbench.bison.datastructure.properties.DSIdentifiable

getID, setID

Constructor Detail

DefaultHierCluster

public DefaultHierCluster()

Method Detail

setHeight

public void setHeight(double d)

Sets the Algorithmic Height of this Cluster

Specified by:

setHeight in interface HierCluster

Parameters:

d - height of this node

getHeight

public double getHeight()

Gets the Algorithmic Height of this Cluster

Specified by:

getHeight in interface HierCluster

Returns:

height of this node

getMaxHeight

public double getMaxHeight()

Returns the Maximum Algorithmic Height of any Cluster in the Hierarchical Cluster Tree that this Cluster is a part of

Specified by:

getMaxHeight in interface HierCluster

Returns:

maximum height

getDepth

public int getDepth()

Gets the Combinatorial Depth of this Cluster

Specified by:

getDepth in interface HierCluster

Returns:

depth of this node

setDepth

public void setDepth(int d)

Sets the Combinatorial Depth of this Cluster

Specified by:

setDepth in interface HierCluster

Parameters:

d - depth of this node

addNode

public void addNode(HierCluster hc,
                    int index)

Adds Cluster as a child of this node

Specified by:

addNode in interface HierCluster

Parameters:

hc - child to be added

index - index at which the child is to be added

getNode

public HierCluster getNode(int index)

Gets a particular child from a known index

Specified by:

getNode in interface HierCluster

Parameters:

index - child with the index that has be retrievd

Returns:

the child node or null if no child with the given index exists

compareTo

public int compareTo(java.lang.Object o)

Comparable method that compares this Cluster to another Hierarchical CLuster node. The basis of comparison is the number of children bothe the nodes contain

Specified by:

compareTo in interface java.lang.Comparable

Parameters:

o - HierCluster to be compared to

Returns:

1 if o contains more children

-1 if this HierCluster

contains more children

0 if both have same number of children

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object