pal.distance
Class JukesCantorDistanceMatrix

java.lang.Object
  extended by pal.distance.DistanceMatrix
      extended by 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