Package pal.distance

Class SequencePairLikelihood

java.lang.Object
pal.distance.SequencePairLikelihood
All Implemented Interfaces:
Serializable, UnivariateFunction
public class SequencePairLikelihood extends Object implements UnivariateFunction, 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:

  • Constructor Details

    • SequencePairLikelihood

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

  • Method Details

    • 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

    • evaluate

      public final double evaluate(double arc)
      Description copied from interface: UnivariateFunction
      compute function value
      Specified by:
      evaluate in interface UnivariateFunction
      Returns:
      function value

    • getLowerBound

      public double getLowerBound()
      Description copied from interface: UnivariateFunction
      get lower bound of argument
      Specified by:
      getLowerBound in interface UnivariateFunction
      Returns:
      lower bound

    • getUpperBound

      public double getUpperBound()
      Description copied from interface: UnivariateFunction
      get upper bound of argument
      Specified by:
      getUpperBound in interface UnivariateFunction
      Returns:
      upper bound