Package pal.distance

Class SequencePairLikelihood

  • All Implemented Interfaces:
    java.io.Serializable, UnivariateFunction
    public class SequencePairLikelihood
extends java.lang.Object
implements UnivariateFunction, java.io.Serializable
    computation of the (negative) log-likelihood for a pair of sequences
    Version:
    $Id: SequencePairLikelihood.java,v 1.11 2002/12/05 04:27:28 matt Exp $
    Author:
    Korbinian Strimmer
    See Also:
    Serialized Form

    • Constructor Detail

      • SequencePairLikelihood

        public SequencePairLikelihood​(SitePattern sp,
                              SubstitutionModel m)
        initialisation
        Parameters:
        sp - site pattern
        m - model of substitution

    • 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

      • setSequences

        public void setSequences​(int s1,
                         int s2)
        specification of two sequences in the given alignment
        Parameters:
        s1 - number of first sequence
        s2 - number of second sequence

      • setSequences

        public void setSequences​(byte[] s1,
                         byte[] s2)
        specification of two sequences (not necessarily 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