com.hfg.bio.phylogeny

Class PhyloNode

java.lang.Object

com.hfg.bio.phylogeny.PhyloNode

public class PhyloNode
extends java.lang.Object

Object representation of a node in a Newick format phylogenetic tree. Does not work with negative distance values.

Constructor Summary

Constructors

Constructor and Description
PhyloNode()

Method Summary

Modifier and Type	Method and Description
protected void	addEdge(Edge<PhyloNode> inEdge)
void	addEdge(PhyloNode in2ndNode, java.lang.Float inDistance)
java.lang.Float	distanceTo(PhyloNode inNode2) Calculates the distance between two nodes in the tree.
java.lang.Double	getAngle()
java.util.List<PhyloNode>	getChildNodes()
java.awt.Color	getColor()
java.lang.Float	getDistanceFromRoot()
java.util.List<Edge<PhyloNode>>	getEdges()
java.lang.String	getId()
java.lang.String	getLabel()
java.util.List<Edge<PhyloNode>>	getLeafFacingEdges() Returns the leaf-facing edges.
protected java.lang.Integer	getLineIndex()
java.lang.Float	getMaxDistanceToLeaf()
Edge<PhyloNode>	getParentEdge() Returns the root-facing edge.
PhyloNode	getParentNode()
int	getSubnodeCount()
protected java.lang.Integer	getVericalLineEndIndex()
protected java.lang.Integer	getVericalLineStartIndex()
boolean	isLeaf()
void	makeRoot()
void	orderEdgesByLeafCount()
protected boolean	removeEdge(Edge<PhyloNode> inEdge)
protected boolean	removeEdgeFrom(PhyloNode inNode)
PhyloNode	setAngle(java.lang.Double inAngleInRadians)
PhyloNode	setColor(java.awt.Color inValue)
PhyloNode	setId(int inValue)
PhyloNode	setId(java.lang.String inValue)
PhyloNode	setLabel(java.lang.String inValue)
protected void	setLineIndex(int inValue)
protected void	setRootDirection(Edge<PhyloNode> inEdge)
protected void	setVerticalLineEndIndex(int inValue)
protected void	setVerticalLineStartIndex(int inValue)
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

PhyloNode

public PhyloNode()

Method Detail

setId

public PhyloNode setId(int inValue)

setId

public PhyloNode setId(java.lang.String inValue)

getId

public java.lang.String getId()

setLabel

public PhyloNode setLabel(java.lang.String inValue)

getLabel

public java.lang.String getLabel()

setColor

public PhyloNode setColor(java.awt.Color inValue)

getColor

public java.awt.Color getColor()

getEdges

public java.util.List<Edge<PhyloNode>> getEdges()

addEdge

public void addEdge(PhyloNode in2ndNode,
                    java.lang.Float inDistance)

setAngle

public PhyloNode setAngle(java.lang.Double inAngleInRadians)

getAngle

public java.lang.Double getAngle()

addEdge

protected void addEdge(Edge<PhyloNode> inEdge)

removeEdge

protected boolean removeEdge(Edge<PhyloNode> inEdge)

removeEdgeFrom

protected boolean removeEdgeFrom(PhyloNode inNode)

isLeaf

public boolean isLeaf()

makeRoot

public void makeRoot()

setRootDirection

protected void setRootDirection(Edge<PhyloNode> inEdge)

getParentNode

public PhyloNode getParentNode()

getChildNodes

public java.util.List<PhyloNode> getChildNodes()

getParentEdge

public Edge<PhyloNode> getParentEdge()

Returns the root-facing edge.

Returns:

the root-facing Edge for the node

getLeafFacingEdges

public java.util.List<Edge<PhyloNode>> getLeafFacingEdges()

Returns the leaf-facing edges.

Returns:

the leaf-facing Edge for the node

orderEdgesByLeafCount

public void orderEdgesByLeafCount()

getDistanceFromRoot

public java.lang.Float getDistanceFromRoot()

getMaxDistanceToLeaf

public java.lang.Float getMaxDistanceToLeaf()

getSubnodeCount

public int getSubnodeCount()

distanceTo

public java.lang.Float distanceTo(PhyloNode inNode2)

Calculates the distance between two nodes in the tree.

Parameters:

inNode2 - the node to calculate the distance to

Returns:

the distance between this node and the specified node

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

setLineIndex

protected void setLineIndex(int inValue)

getLineIndex

protected java.lang.Integer getLineIndex()

setVerticalLineStartIndex

protected void setVerticalLineStartIndex(int inValue)

getVericalLineStartIndex

protected java.lang.Integer getVericalLineStartIndex()

setVerticalLineEndIndex

protected void setVerticalLineEndIndex(int inValue)

getVericalLineEndIndex

protected java.lang.Integer getVericalLineEndIndex()