public class GeneralLikelihoodCalculator extends java.lang.Object implements PalObjectListener, LikelihoodCalculator
PalObjectListener.EventGenerator
Constructor and Description |
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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.
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Modifier and Type | Method and Description |
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double |
calculateLogLikelihood() |
LikelihoodSummary |
calculateLogLikelihoodSummary() |
protected static void |
directProduct4(double[] v1,
double[] v2,
double[] store) |
protected static double |
dotProduct4(double[] v1,
double[] v2) |
protected static double |
dotProduct4(double[] v1,
double[] v2,
double[] v3) |
void |
parametersChanged(PalObjectEvent pe)
Signifies that parametric valued governing the state of this Object have changed.
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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.
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void |
setup(Tree t,
SubstitutionModel model) |
void |
structureChanged(PalObjectEvent pe)
Signifies that the structure of the object has changed (for example in trees to topology
has changed)
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protected static double |
sum4(double[] v) |
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)
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)