Package pt.ist.phylolib.command.algorithm.gcp

Class UPGMA

java.lang.Object

pt.ist.phylolib.command.algorithm.Algorithm

pt.ist.phylolib.command.algorithm.gcp.GloballyClosestPairs

pt.ist.phylolib.command.algorithm.gcp.UPGMA

All Implemented Interfaces:

ICommand<Matrix,Tree>

public final class UPGMA
extends GloballyClosestPairs

Responsible for calculating a phylogenetic tree from a distance matrix using the Unweighted Pair Group Method with Arithmetic-mean algorithm.

Nested Class Summary

Nested classes/interfaces inherited from interface pt.ist.phylolib.command.ICommand

ICommand.IGetter<T>

Field Summary

Fields inherited from interface pt.ist.phylolib.command.ICommand

COMMAND, FINISHED, STARTED, TIMING, UNUSED

Constructor Summary

Constructors

Constructor	Description
UPGMA()

Method Summary

Modifier and Type	Method	Description
protected double	dissimilarity(double ij, double ik, double jk, int ci, int cj)	Calculates the dissimilarity between a given previously existing node and a given node created by joining two existing nodes.

Methods inherited from class pt.ist.phylolib.command.algorithm.gcp.GloballyClosestPairs

processImpl

Methods inherited from class pt.ist.phylolib.command.algorithm.Algorithm

configureRequiredDistanceScope, process, requiredDistanceScope

Methods inherited from class java.lang.Object

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

Methods inherited from interface pt.ist.phylolib.command.ICommand

init

Constructor Details

UPGMA

public UPGMA()

Method Details

dissimilarity

protected double dissimilarity(double ij,
 double ik,
 double jk,
 int ci,
 int cj)

Description copied from class: GloballyClosestPairs

Calculates the dissimilarity between a given previously existing node and a given node created by joining two existing nodes.

Specified by:

dissimilarity in class GloballyClosestPairs

Parameters:

ij - the distance between the two existing nodes that were joined

ik - the distance between one of the nodes that was joined and the previously existing node

jk - the distance between another of the nodes that was joined and the previously existing node

ci - the number of elements in the cluster of one of the nodes that were joined

cj - the number of elements in the cluster of another of the nodes that were joined

Returns:

the dissimilarity between the previously existing node and the created node