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.
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
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Nested Class Summary
Nested classes/interfaces inherited from interface pal.misc.PalObjectListener
PalObjectListener.EventGenerator
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Constructor Summary
ConstructorsConstructorDescriptionGeneralLikelihoodCalculator
(Alignment baseAlignment, Tree tree, RateMatrix model) Constructor taking site pattern, tree and a rate matrix.GeneralLikelihoodCalculator
(Alignment baseAlignment, Tree tree, RateMatrix model, RateDistribution distribution) Constructor taking site pattern, tree rate matrix, and a rate distributionGeneralLikelihoodCalculator
(Alignment baseAlignment, Tree tree, SubstitutionModel model) Constructor taking site pattern, tree and a general substitution model. -
Method Summary
Modifier and TypeMethodDescriptiondouble
protected static final void
directProduct4
(double[] v1, double[] v2, double[] store) protected static final double
dotProduct4
(double[] v1, double[] v2) protected static final double
dotProduct4
(double[] v1, double[] v2, double[] v3) void
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.final void
setup
(Tree t, SubstitutionModel model) void
Signifies that the structure of the object has changed (for example in trees to topology has changed)protected static final double
sum4
(double[] v)
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Constructor Details
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GeneralLikelihoodCalculator
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
Constructor taking site pattern, tree and a general substitution model.
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Method Details
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parametersChanged
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
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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setup
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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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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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calculateLogLikelihoodSummary
- Returns:
- the LikelihoodSummary of this tree under the given model and data.
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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)
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