Package pal.substmodel
Class PositiveSelectionRateMatrixGroup
- java.lang.Object
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- pal.substmodel.PositiveSelectionRateMatrixGroup
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- All Implemented Interfaces:
java.io.Serializable
,RateMatrixGroup
public class PositiveSelectionRateMatrixGroup extends java.lang.Object implements RateMatrixGroup
- See Also:
- Serialized Form
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Constructor Summary
Constructors Constructor Description PositiveSelectionRateMatrixGroup(MutableDouble kappaStore, MutableDouble omegaStore, double[] freqs, CodonTable table)
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Method Summary
All Methods Instance Methods Concrete 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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Constructor Detail
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PositiveSelectionRateMatrixGroup
public PositiveSelectionRateMatrixGroup(MutableDouble kappaStore, MutableDouble omegaStore, double[] freqs, CodonTable table)
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Method Detail
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getNumberOfTransitionCategories
public int getNumberOfTransitionCategories()
- Specified by:
getNumberOfTransitionCategories
in interfaceRateMatrixGroup
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updateParameters
public void updateParameters(double[] categoryProbabilities)
Description copied from interface:RateMatrixGroup
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.- Specified by:
updateParameters
in interfaceRateMatrixGroup
- Parameters:
categoryProbabilities
- the probabilities (summing to one) of each category (class) of substitution
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getEquilibriumFrequencies
public double[] getEquilibriumFrequencies()
- Specified by:
getEquilibriumFrequencies
in interfaceRateMatrixGroup
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getDataType
public DataType getDataType()
- Specified by:
getDataType
in interfaceRateMatrixGroup
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getTransitionProbabilities
public void getTransitionProbabilities(double branchLength, double[][][] tableStore)
- Specified by:
getTransitionProbabilities
in interfaceRateMatrixGroup
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getTransitionProbabilitiesTranspose
public void getTransitionProbabilitiesTranspose(double branchLength, double[][][] tableStore)
- Specified by:
getTransitionProbabilitiesTranspose
in interfaceRateMatrixGroup
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getTransitionProbabilities
public void getTransitionProbabilities(double branchLength, int category, double[][] tableStore)
- Specified by:
getTransitionProbabilities
in interfaceRateMatrixGroup
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getTransitionProbabilitiesTranspose
public void getTransitionProbabilitiesTranspose(double branchLength, int category, double[][] tableStore)
- Specified by:
getTransitionProbabilitiesTranspose
in interfaceRateMatrixGroup
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getSummary
public java.lang.String getSummary(double[] categoryProbabilities)
- Specified by:
getSummary
in interfaceRateMatrixGroup
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