Package pal.eval

Class GeneralLikelihoodCalculator

java.lang.Object
pal.eval.GeneralLikelihoodCalculator
All Implemented Interfaces:
LikelihoodCalculator, PalObjectListener
public class GeneralLikelihoodCalculator extends Object implements PalObjectListener, LikelihoodCalculator
Title: General Likelihood Calculator
Description: A General likelihood calculator
This calculates the likelihood of an topologically invariant tree (on an unchanging alignment) quickly by remembering partial likelihoods of invariant subtrees, and by essentially generating site patterns for each sub tree. Works with Rate Distributions and other more complex SubstitutionModels. Will optimise (as in computational time) itself when using Nucleotide based data.
Version:
$Id: GeneralLikelihoodCalculator.java,v 1.10 2004/01/12 09:30:27 matt Exp $
Author:
Matthew Goode

  • Constructor Details

    • GeneralLikelihoodCalculator

      public GeneralLikelihoodCalculator(Alignment baseAlignment, Tree tree, RateMatrix model)
      Constructor taking site pattern, tree and a rate matrix.

    • GeneralLikelihoodCalculator

      public GeneralLikelihoodCalculator(Alignment baseAlignment, Tree tree, RateMatrix model, RateDistribution distribution)
      Constructor taking site pattern, tree rate matrix, and a rate distribution

    • GeneralLikelihoodCalculator

      public GeneralLikelihoodCalculator(Alignment baseAlignment, Tree tree, SubstitutionModel model)
      Constructor taking site pattern, tree and a general substitution model.

  • Method Details

    • parametersChanged

      public void parametersChanged(PalObjectEvent pe)
      Description copied from interface: PalObjectListener
      Signifies that parametric valued governing the state of this Object have changed. Parameters don't have to be visible ones For example, in trees the branch lengths have changed.
      Specified by:
      parametersChanged in interface PalObjectListener

    • structureChanged

      public void structureChanged(PalObjectEvent pe)
      Description copied from interface: PalObjectListener
      Signifies that the structure of the object has changed (for example in trees to topology has changed)
      Specified by:
      structureChanged in interface PalObjectListener

    • setup

      public final void setup(Tree t, SubstitutionModel model)

    • release

      public void release()
      Description copied from interface: LikelihoodCalculator
      This method should be called when the user is through using this calculator to inform it to release any resources it has allocated.
      Specified by:
      release in interface LikelihoodCalculator

    • calculateLogLikelihood

      public double calculateLogLikelihood()
      Specified by:
      calculateLogLikelihood in interface LikelihoodCalculator
      Returns:
      the likelihood of this tree under the given model and data.

    • calculateLogLikelihoodSummary

      public LikelihoodSummary calculateLogLikelihoodSummary()
      Returns:
      the LikelihoodSummary of this tree under the given model and data.

    • dotProduct4

      protected static final double dotProduct4(double[] v1, double[] v2)

    • dotProduct4

      protected static final double dotProduct4(double[] v1, double[] v2, double[] v3)

    • directProduct4

      protected static final void directProduct4(double[] v1, double[] v2, double[] store)

    • sum4

      protected static final double sum4(double[] v)