pal.distance
Class AlignmentDistanceMatrix

java.lang.Object
  pal.distance.DistanceMatrix
      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