Package pal.distance

Class PairwiseDistance

  • All Implemented Interfaces:
    java.io.Serializable
    public class PairwiseDistance
extends java.lang.Object
implements java.io.Serializable
    determines the (observed and ML) distance between a pair of sequences
    Version:
    $Id: PairwiseDistance.java,v 1.10 2002/09/08 03:47:01 matt Exp $
    Author:
    Korbinian Strimmer
    See Also:
    Serialized Form

    • Field Summary

      Fields 
      Modifier and Type Field Description
      double distance
      last estimated distance
      double distanceSE
      last estimate standard error of a distance

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      double getDistance​(byte[] s1, byte[] s2)
      compute distance between two sequences (not necessarly in the given alignment but with the same weights in the site pattern)
      double getDistance​(int s1, int s2)
      compute distance between two sequences in the given alignment
      void updateModel​(SubstitutionModel m)
      update model of substitution
      void updateSitePattern​(SitePattern sp)
      update site pattern

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Field Detail

      • distance

        public double distance
        last estimated distance

      • distanceSE

        public double distanceSE
        last estimate standard error of a distance

    • Constructor Detail

      • PairwiseDistance

        public PairwiseDistance​(SitePattern sp)
        Constructor 1 (estimate observed distances only)
        Parameters:
        sp - site pattern

      • PairwiseDistance

        public PairwiseDistance​(SitePattern sp,
                        SubstitutionModel m)
        Constructor 2 (uses evolutionary model)
        Parameters:
        sp - site pattern
        m - evolutionary model

    • Method Detail

      • updateModel

        public void updateModel​(SubstitutionModel m)
        update model of substitution
        Parameters:
        model - of substitution

      • updateSitePattern

        public void updateSitePattern​(SitePattern sp)
        update site pattern
        Parameters:
        site - pattern

      • getDistance

        public double getDistance​(int s1,
                          int s2)
        compute distance between two sequences in the given alignment
        Parameters:
        s1 - number of first sequence
        s2 - number of second sequence
        Returns:
        estimated distance (observed or ML, depending on constructor used)

      • getDistance

        public double getDistance​(byte[] s1,
                          byte[] s2)
        compute distance between two sequences (not necessarly in the given alignment but with the same weights in the site pattern)
        Parameters:
        s1 - site pattern of first sequence
        s2 - site pattern of second sequence
        Returns:
        estimated distance (observed or ML, depending on constructor used)