Package pal.eval
Class FastLikelihoodCalculator
- java.lang.Object
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- pal.eval.FastLikelihoodCalculator
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- 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
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Nested Class Summary
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Nested classes/interfaces inherited from interface pal.misc.PalObjectListener
PalObjectListener.EventGenerator
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Constructor Summary
Constructors Constructor Description FastLikelihoodCalculator(SitePattern pattern)
Constructor taking only site pattern.FastLikelihoodCalculator(SitePattern pattern, Tree tree, RateMatrix model)
Constructor taking site pattern, tree and model.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description double
calculateLogLikelihood()
void
parametersChanged(PalObjectEvent pe)
Signifies that parametric valued governing the state of this Object have changed.void
release()
This method should be called when the user is through using this calculator to inform it to release any resources it has allocated.void
setRateMatrix(RateMatrix rateMatrix)
void
setTree(Tree t)
void
structureChanged(PalObjectEvent pe)
Signifies that the structure of the object has changed (for example in trees to topology has changed)void
updateSitePattern(SitePattern pattern)
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Constructor Detail
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FastLikelihoodCalculator
public FastLikelihoodCalculator(SitePattern pattern)
Constructor taking only site pattern.
NOTE: setTree and setRateMatrix must both be called (in that order) before computeLikelihood.
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FastLikelihoodCalculator
public FastLikelihoodCalculator(SitePattern pattern, Tree tree, RateMatrix model)
Constructor taking site pattern, tree and model.
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Method Detail
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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 interfacePalObjectListener
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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 interfacePalObjectListener
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setRateMatrix
public final void setRateMatrix(RateMatrix rateMatrix)
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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 interfaceLikelihoodCalculator
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setTree
public final void setTree(Tree t)
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updateSitePattern
public final void updateSitePattern(SitePattern pattern)
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calculateLogLikelihood
public double calculateLogLikelihood()
- Specified by:
calculateLogLikelihood
in interfaceLikelihoodCalculator
- Returns:
- the likelihood of this tree under the given model and data.
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