de.jstacs.sequenceScores.statisticalModels.trainable.phylo

Class PhyloTree

java.lang.Object

de.jstacs.sequenceScores.statisticalModels.trainable.phylo.PhyloTree

All Implemented Interfaces:

Storable, Cloneable

public class PhyloTree
extends Object
implements Cloneable, Storable

This class implements a simple (phylogenetic) tree. A PhyloTree contains the root node of type PhyloNode

Author:

Michael Scharfe

Constructor Summary

Constructors

Constructor and Description
PhyloTree(StringBuffer xml) The standard constructor for the interface Storable.
PhyloTree(String name, PhyloNode root) Construct an instance of the class PhyloTree

Method Summary

Modifier and Type	Method and Description
PhyloTree	clone()
ArrayList<PhyloNode>	getAllLeafs() This method returns a list of PhyloNodes that represent the leafs of the tree
String	getName() This method returns the name of the PhyloTree
int	getNumberOfNodes() This method returns the total number of nodes in the tree
PhyloNode	getRoot() This method returns the root node of the tree
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

PhyloTree

public PhyloTree(String name,
                 PhyloNode root)

Construct an instance of the class PhyloTree

Parameters:

name - the name of the PhyloTree

root - the root node

PhyloTree

public PhyloTree(StringBuffer xml)
          throws NonParsableException

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

Parameters:

xml - the XML representation as StringBuffer

Throws:

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

Method Detail

clone

public PhyloTree clone()
                throws CloneNotSupportedException

Overrides:

clone in class Object

Throws:

CloneNotSupportedException

getName

public String getName()

This method returns the name of the PhyloTree

Returns:

the name of the tree

getRoot

public PhyloNode getRoot()

This method returns the root node of the tree

Returns:

the root node

getNumberOfNodes

public int getNumberOfNodes()

This method returns the total number of nodes in the tree

Returns:

the number of nodes in the tree

getAllLeafs

public ArrayList<PhyloNode> getAllLeafs()

This method returns a list of PhyloNodes that represent the leafs of the tree

Returns:

the leafs of the tree

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