Package pal.eval

Class FastLikelihoodCalculator

  • All Implemented Interfaces:
    LikelihoodCalculator, PalObjectListener
    public class FastLikelihoodCalculator
extends java.lang.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 Detail

      • 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 Detail

      • 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

      • 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)