Package pal.substmodel
Interface RateMatrixGroup
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- All Superinterfaces:
java.io.Serializable
- All Known Implementing Classes:
NeutralSelectionRateMatrixGroup
,PositiveSelectionRateMatrixGroup
,SimpleRateMatrixGroup
public interface RateMatrixGroup extends java.io.Serializable
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description DataType
getDataType()
double[]
getEquilibriumFrequencies()
int
getNumberOfTransitionCategories()
java.lang.String
getSummary(double[] categoryProbabilities)
void
getTransitionProbabilities(double branchLength, double[][][] tableStore)
void
getTransitionProbabilities(double branchLength, int category, double[][] tableStore)
void
getTransitionProbabilitiesTranspose(double branchLength, double[][][] tableStore)
void
getTransitionProbabilitiesTranspose(double branchLength, int category, double[][] tableStore)
void
updateParameters(double[] categoryProbabilities)
Update internal representation based on any parameters (that are specified externally) and the given category probablitilies.
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Method Detail
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getDataType
DataType getDataType()
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getEquilibriumFrequencies
double[] getEquilibriumFrequencies()
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updateParameters
void updateParameters(double[] categoryProbabilities)
Update internal representation based on any parameters (that are specified externally) and the given category probablitilies. The controller (user of this class) should be calling this method after the parameters of an external parameterization object have been set.- Parameters:
categoryProbabilities
- the probabilities (summing to one) of each category (class) of substitution
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getNumberOfTransitionCategories
int getNumberOfTransitionCategories()
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getTransitionProbabilities
void getTransitionProbabilities(double branchLength, double[][][] tableStore)
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getTransitionProbabilitiesTranspose
void getTransitionProbabilitiesTranspose(double branchLength, double[][][] tableStore)
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getTransitionProbabilities
void getTransitionProbabilities(double branchLength, int category, double[][] tableStore)
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getTransitionProbabilitiesTranspose
void getTransitionProbabilitiesTranspose(double branchLength, int category, double[][] tableStore)
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getSummary
java.lang.String getSummary(double[] categoryProbabilities)
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