Package pal.distance

Class 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
    • 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