pal.distance
Class AlignmentDistanceMatrix

java.lang.Object
  extended by pal.distance.DistanceMatrix
      extended by pal.distance.AlignmentDistanceMatrix
All Implemented Interfaces:
java.io.Serializable, IdGroup

public class AlignmentDistanceMatrix
extends DistanceMatrix
implements java.io.Serializable

compute distance matrix (observed and ML) from alignment (SitePattern)

Version:
$Id: AlignmentDistanceMatrix.java,v 1.10 2003/03/23 00:13:36 matt Exp $
Author:
Korbinian Strimmer, Alexei Drummond
See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from interface pal.misc.IdGroup
IdGroup.Utils
 
Constructor Summary
AlignmentDistanceMatrix(SitePattern sp)
          compute observed distances
AlignmentDistanceMatrix(SitePattern sp, AlgorithmCallback callback)
          compute observed distances
AlignmentDistanceMatrix(SitePattern sp, SubstitutionModel m)
          compute maximum-likelihood distances
AlignmentDistanceMatrix(SitePattern sp, SubstitutionModel m, AlgorithmCallback callback)
          compute maximum-likelihood distances
 
Method Summary
 void recompute(SitePattern sp, AlgorithmCallback callback)
          recompute observed distances under new site pattern
 void recompute(SitePattern sp, SubstitutionModel model)
          recompute maximum-likelihood distances under new site pattern
 void recompute(SitePattern sp, SubstitutionModel model, AlgorithmCallback callback)
          recompute maximum-likelihood distances under new site pattern
 
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

AlignmentDistanceMatrix

public AlignmentDistanceMatrix(SitePattern sp)
compute observed distances

Parameters:
sp - site pattern

AlignmentDistanceMatrix

public AlignmentDistanceMatrix(SitePattern sp,
                               AlgorithmCallback callback)
compute observed distances

Parameters:
sp - site pattern
callback - An algorithm callback to monitor progress

AlignmentDistanceMatrix

public AlignmentDistanceMatrix(SitePattern sp,
                               SubstitutionModel m)
compute maximum-likelihood distances

Parameters:
sp - site pattern
m - evolutionary model
immediateCompute - - signifies whether to calculate distances from within constructor (if no should call recompute() at some point!)

AlignmentDistanceMatrix

public AlignmentDistanceMatrix(SitePattern sp,
                               SubstitutionModel m,
                               AlgorithmCallback callback)
compute maximum-likelihood distances

Parameters:
sp - site pattern
m - evolutionary model
callback - An algorithm callback to monitor progress
Method Detail

recompute

public void recompute(SitePattern sp,
                      AlgorithmCallback callback)
recompute observed distances under new site pattern

Parameters:
sp - site pattern

recompute

public void recompute(SitePattern sp,
                      SubstitutionModel model)
recompute maximum-likelihood distances under new site pattern

Parameters:
sp - site pattern

recompute

public void recompute(SitePattern sp,
                      SubstitutionModel model,
                      AlgorithmCallback callback)
recompute maximum-likelihood distances under new site pattern

Parameters:
sp - site pattern