pal.distance
Class AlignmentDistanceMatrix

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

public class AlignmentDistanceMatrix
extends DistanceMatrix
implements java.io.Serializable

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

See Also:
Serialized Form

Fields inherited from class pal.distance.DistanceMatrix
distance, idGroup, numSeqs
 
Constructor Summary
  AlignmentDistanceMatrix(SitePattern sp)
          compute observed distances
  AlignmentDistanceMatrix(SitePattern sp, boolean immediateCompute)
          compute observed distances
  AlignmentDistanceMatrix(SitePattern sp, SubstitutionModel m)
          compute maximum-likelihood distances
protected AlignmentDistanceMatrix(SitePattern sp, SubstitutionModel m, boolean immediateCompute)
          compute maximum-likelihood distances
 
Method Summary
 double getProgress()
          Returns -1 if not doing anything, or a number between 0 and 1
 void recompute(SitePattern sp)
          recompute maximum-likelihood distances under new site pattern
 void recompute(SubstitutionModel m)
          recompute maximum-likelihood distances under new model
 
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

AlignmentDistanceMatrix

public AlignmentDistanceMatrix(SitePattern sp)
compute observed distances
Parameters:
sp - site pattern

AlignmentDistanceMatrix

public AlignmentDistanceMatrix(SitePattern sp,
                               boolean immediateCompute)
compute observed distances
Parameters:
sp - site pattern
immediateCompute - - signifies whether to calculate distances from within constructor (if no should call recompute() at some point!)

AlignmentDistanceMatrix

public AlignmentDistanceMatrix(SitePattern sp,
                               SubstitutionModel m)
compute maximum-likelihood distances
Parameters:
sp - site pattern
m - evolutionary model

AlignmentDistanceMatrix

protected AlignmentDistanceMatrix(SitePattern sp,
                                  SubstitutionModel m,
                                  boolean immediateCompute)
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!)
Method Detail

recompute

public void recompute(SubstitutionModel m)
recompute maximum-likelihood distances under new model
Parameters:
m - evolutionary model

recompute

public void recompute(SitePattern sp)
recompute maximum-likelihood distances under new site pattern
Parameters:
sp - site pattern

getProgress

public final double getProgress()
Returns -1 if not doing anything, or a number between 0 and 1