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java.lang.Objectpal.eval.GeneralLikelihoodCalculator
public class GeneralLikelihoodCalculator
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.
Nested Class Summary |
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Nested classes/interfaces inherited from interface pal.misc.PalObjectListener |
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PalObjectListener.EventGenerator |
Constructor Summary | |
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GeneralLikelihoodCalculator(Alignment baseAlignment,
Tree tree,
RateMatrix model)
Constructor taking site pattern, tree and a rate matrix. |
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GeneralLikelihoodCalculator(Alignment baseAlignment,
Tree tree,
RateMatrix model,
RateDistribution distribution)
Constructor taking site pattern, tree rate matrix, and a rate distribution |
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GeneralLikelihoodCalculator(Alignment baseAlignment,
Tree tree,
SubstitutionModel model)
Constructor taking site pattern, tree and a general substitution model. |
Method Summary | |
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double |
calculateLogLikelihood()
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LikelihoodSummary |
calculateLogLikelihoodSummary()
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protected static void |
directProduct4(double[] v1,
double[] v2,
double[] store)
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protected static double |
dotProduct4(double[] v1,
double[] v2)
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protected static double |
dotProduct4(double[] v1,
double[] v2,
double[] v3)
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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 |
setup(Tree t,
SubstitutionModel model)
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void |
structureChanged(PalObjectEvent pe)
Signifies that the structure of the object has changed (for example in trees to topology has changed) |
protected static double |
sum4(double[] v)
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Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public GeneralLikelihoodCalculator(Alignment baseAlignment, Tree tree, RateMatrix model)
public GeneralLikelihoodCalculator(Alignment baseAlignment, Tree tree, RateMatrix model, RateDistribution distribution)
public GeneralLikelihoodCalculator(Alignment baseAlignment, Tree tree, SubstitutionModel model)
Method Detail |
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public void parametersChanged(PalObjectEvent pe)
PalObjectListener
parametersChanged
in interface PalObjectListener
public void structureChanged(PalObjectEvent pe)
PalObjectListener
structureChanged
in interface PalObjectListener
public final void setup(Tree t, SubstitutionModel model)
public void release()
LikelihoodCalculator
release
in interface LikelihoodCalculator
public double calculateLogLikelihood()
calculateLogLikelihood
in interface LikelihoodCalculator
public LikelihoodSummary calculateLogLikelihoodSummary()
protected static final double dotProduct4(double[] v1, double[] v2)
protected static final double dotProduct4(double[] v1, double[] v2, double[] v3)
protected static final void directProduct4(double[] v1, double[] v2, double[] store)
protected static final double sum4(double[] v)
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