pal.distance
Class JukesCantorDistanceMatrix

java.lang.Object
  |
  +--pal.distance.DistanceMatrix
        |
        +--pal.distance.JukesCantorDistanceMatrix
All Implemented Interfaces:
IdGroup, java.io.Serializable

public class JukesCantorDistanceMatrix
extends DistanceMatrix

compute jukes-cantor corrected distance matrix

See Also:
Serialized Form

Fields inherited from class pal.distance.DistanceMatrix
distance, idGroup, numSeqs
 
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
 
Methods inherited from class pal.distance.DistanceMatrix
absoluteDistance, addDistance, getDistances, getIdCount, getIdentifier, getIdGroup, getSize, isSymmetric, meanDistance, printPHYLIP, setDistance, setIdentifier, 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