de.jstacs.sequenceScores.statisticalModels.trainable.phylo

Class PhyloNode

java.lang.Object

de.jstacs.sequenceScores.statisticalModels.trainable.phylo.PhyloNode

All Implemented Interfaces:

Storable, Cloneable

public class PhyloNode
extends Object
implements Cloneable, Storable

This class implements a node in a PhyloTree A PhyloNode contains some basic informations of itself and the incoming edge Furthermore it contains a list of PhyloNodes that represent the children nodes

Author:

Michael Scharfe

Constructor Summary

Constructors

Constructor and Description
PhyloNode() Basic constructor
PhyloNode(StringBuffer xml) The standard constructor for the interface Storable.

Method Summary

Modifier and Type	Method and Description
void	addChild(PhyloNode node) This method adds a children node to the current instance
PhyloNode	clone()
ArrayList<PhyloNode>	getAllLeafs() This method returns a list of PhyloNodes that are leafs in the subtree starting from this instance
ArrayList<PhyloNode>	getChildrenNodes() This method returns a list of PhyloNodes that are children of this instance
int	getId() This method returns the ID of the current PhyloNode
String	getName() This method returns the name of the current instance
int	getNumberOfAllNodesBelow() This method returns the total number of PhyloNodes in the subtree starting from this instance
double	getWeight() This method return the weight (length, rate ...) for the incoming edge
void	setId(int id) This method set the ID of the current PhyloNode The ID should be unique in the PhyloTree
void	setName(String name) This method set a name for the current instance
void	setWeight(double w) This method set the weight (length, rate ...) for the incoming edge
StringBuffer	toXML() This method returns an XML representation as StringBuffer of an instance of the implementing class.

Methods inherited from class java.lang.Object

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

Constructor Detail

PhyloNode

public PhyloNode()

Basic constructor

PhyloNode

public PhyloNode(StringBuffer xml)
          throws NonParsableException

The standard constructor for the interface Storable. Constructs a PhyloNode out of an XML representation.

Parameters:

xml - the XML representation as StringBuffer

Throws:

NonParsableException - if the PhyloNode could not be reconstructed out of the StringBuffer xml

Method Detail

clone

public PhyloNode clone()
                throws CloneNotSupportedException

Overrides:

clone in class Object

Throws:

CloneNotSupportedException

addChild

public void addChild(PhyloNode node)

This method adds a children node to the current instance

Parameters:

node - the children node

setName

public void setName(String name)

This method set a name for the current instance

Parameters:

name - the name of the PhyloNode

getName

public String getName()

This method returns the name of the current instance

Returns:

the name of the PhyloNode

setId

public void setId(int id)

This method set the ID of the current PhyloNode The ID should be unique in the PhyloTree

Parameters:

id - the ID of the node

getId

public int getId()

This method returns the ID of the current PhyloNode

Returns:

the ID of the node

setWeight

public void setWeight(double w)

This method set the weight (length, rate ...) for the incoming edge

Parameters:

w - the weight

getWeight

public double getWeight()

This method return the weight (length, rate ...) for the incoming edge

Returns:

the weight

getNumberOfAllNodesBelow

public int getNumberOfAllNodesBelow()

This method returns the total number of PhyloNodes in the subtree starting from this instance

Returns:

the total number of nodes

getChildrenNodes

public ArrayList<PhyloNode> getChildrenNodes()

This method returns a list of PhyloNodes that are children of this instance

Returns:

the children nodes

getAllLeafs

public ArrayList<PhyloNode> getAllLeafs()

This method returns a list of PhyloNodes that are leafs in the subtree starting from this instance

Returns:

the list of leafs

toXML

public StringBuffer toXML()

Description copied from interface: Storable

This method returns an XML representation as StringBuffer of an instance of the implementing class.

Specified by:

toXML in interface Storable

Returns:

the XML representation