Package pal.distance

Class AlignmentDistanceMatrix

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

public class AlignmentDistanceMatrix extends DistanceMatrix implements 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:
  • Constructor Details

    • 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 Details

    • 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