BioinfoFieldExtractor
Class UPGMA

java.lang.Object
  BioinfoFieldExtractor.UPGMA

public class UPGMA
extends java.lang.Object

This class is the standard implementation of Unweighted Pair Group Method with Arithmetic mean, also known as average linkage method. It is used to combine similar messages into clusters for for glocal alignment.

Author:

Serge Gorbunov

Constructor Summary

UPGMA(float[][] disM, java.util.ArrayList<java.lang.String> seq)
The constructor

Method Summary

PhylogenTree	buildTree() This method performs UPGMA algorithm to build a tree with clusters characterizing the closest related elements of the sequence.
void	clusterTrees(PhylogenTree root) Cluster "closely-related" trees into clusters
java.util.ArrayList<java.lang.Integer>	convertToDec(java.lang.String msg) Converts string to an array of dec representations of the chars
float	findDistance(PhylogenTree tree1, PhylogenTree tree2) Returns the distance between two clusters
java.util.ArrayList<PhylogenTree>	getClusters() Returns the clusters

Methods inherited from class java.lang.Object

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

Constructor Detail

UPGMA

public UPGMA(float[][] disM,
             java.util.ArrayList<java.lang.String> seq)

The constructor

Parameters:

disM - Distance matrix

seq - The sequences of messages

Method Detail

buildTree

public PhylogenTree buildTree()

This method performs UPGMA algorithm to build a tree with clusters characterizing the closest related elements of the sequence.

Returns:

A single clustered phylogenetic tree.

findDistance

public float findDistance(PhylogenTree tree1,
                          PhylogenTree tree2)

Returns the distance between two clusters

Parameters:

tree1 - Phylogenetic tree # 1

tree2 - Phylogenetic tree # 2

clusterTrees

public void clusterTrees(PhylogenTree root)

Cluster "closely-related" trees into clusters

Parameters:

root - of the tree to be clustered

getClusters

public java.util.ArrayList<PhylogenTree> getClusters()

Returns the clusters

convertToDec

public java.util.ArrayList<java.lang.Integer> convertToDec(java.lang.String msg)

Converts string to an array of dec representations of the chars