Package pal.eval

Class FastLikelihoodCalculator

java.lang.Object
pal.eval.FastLikelihoodCalculator
All Implemented Interfaces:
LikelihoodCalculator, PalObjectListener
public class FastLikelihoodCalculator extends Object implements PalObjectListener, LikelihoodCalculator
Title: Fast Likelihood Calculator
Description: A fast likelihood calculator
Original code by Matthew Goode. This calculates the likelihood of similar trees (or a single changing tree) on the same site pattern fast by remembering partial likelihoods of invariant subtrees. This class should be avoided if the underlying tree doesn't change (use GeneralLikelihoodCalculator). A new framework will be added one day to accomodate optimising tree topologies.
Version:
$Id: FastLikelihoodCalculator.java,v 1.11 2002/09/08 03:46:12 matt Exp $
Author:
Matthew Goode, Alexei Drummond

  • Constructor Details

    • FastLikelihoodCalculator

      public FastLikelihoodCalculator(SitePattern pattern)
      Constructor taking only site pattern.
      NOTE: setTree and setRateMatrix must both be called (in that order) before computeLikelihood.

    • FastLikelihoodCalculator

      public FastLikelihoodCalculator(SitePattern pattern, Tree tree, RateMatrix model)
      Constructor taking site pattern, tree and 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

    • setRateMatrix

      public final void setRateMatrix(RateMatrix rateMatrix)

    • 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

    • setTree

      public final void setTree(Tree t)

    • updateSitePattern

      public final void updateSitePattern(SitePattern pattern)

    • calculateLogLikelihood

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