pal.distance
Class JukesCantorDistanceMatrix

java.lang.Object
  pal.distance.DistanceMatrix
      pal.distance.JukesCantorDistanceMatrix

All Implemented Interfaces:

java.io.Serializable, IdGroup

public class JukesCantorDistanceMatrix
extends DistanceMatrix

compute jukes-cantor corrected distance matrix

Version:

$Id: JukesCantorDistanceMatrix.java,v 1.5 2002/12/05 04:27:28 matt Exp $

Author:

Alexei Drummond, Korbinian Strimmer

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from interface pal.misc.IdGroup

IdGroup.Utils

Constructor Summary

JukesCantorDistanceMatrix(Alignment alignment)
compute jukes-cantor corrected distances

JukesCantorDistanceMatrix(DistanceMatrix dist)
compute jukes-cantor corrected distances (assumes nucleotides as underlying data)

JukesCantorDistanceMatrix(DistanceMatrix dist, int numStates)
compute jukes-cantor corrected distances

JukesCantorDistanceMatrix(SitePattern sitePattern)
compute jukes-cantor corrected distances

Method Summary

Methods inherited from class pal.distance.DistanceMatrix

absoluteDistance, addDistance, getClonedDistances, getClosestIndex, getClosestIndex, getDistance, getDistances, getIdCount, getIdentifier, getIdGroup, getSize, isSymmetric, meanDistance, printPHYLIP, setDistance, setDistances, setIdentifier, setIdGroup, squaredDistance, toString, whichIdNumber

Methods inherited from class java.lang.Object

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

Constructor Detail

JukesCantorDistanceMatrix

public JukesCantorDistanceMatrix(DistanceMatrix dist)

compute jukes-cantor corrected distances (assumes nucleotides as underlying data)

Parameters:

dist - distance matrix

JukesCantorDistanceMatrix

public JukesCantorDistanceMatrix(DistanceMatrix dist,
                                 int numStates)

compute jukes-cantor corrected distances

Parameters:

dist - distance matrix

numStates - number of states of underlying data

JukesCantorDistanceMatrix

public JukesCantorDistanceMatrix(Alignment alignment)

compute jukes-cantor corrected distances

Parameters:

alignment - Alignment

JukesCantorDistanceMatrix

public JukesCantorDistanceMatrix(SitePattern sitePattern)

compute jukes-cantor corrected distances

Parameters:

sitePattern - SitePattern