Package pal.substmodel
Class SimpleRateMatrixGroup
java.lang.Object
pal.substmodel.SimpleRateMatrixGroup
- All Implemented Interfaces:
Serializable
,RateMatrixGroup
- See Also:
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Constructor Summary
ConstructorsConstructorDescriptionSimpleRateMatrixGroup
(NeoRateMatrix[] baseMatrices, double[] equilibriumFrequencies, double[] initialClassProbabilities, DataType dataType) -
Method Summary
Modifier and TypeMethodDescriptiondouble
getDefaultValue
(int n) double[]
double
getLowerLimit
(int n) int
int
getSummary
(double[] parameters, 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) double
getUpperLimit
(int n) void
setParameters
(double[] parameters, double[] categoryProbabilities) Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
Methods inherited from interface pal.substmodel.RateMatrixGroup
getSummary, updateParameters
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Constructor Details
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SimpleRateMatrixGroup
public SimpleRateMatrixGroup(NeoRateMatrix[] baseMatrices, double[] equilibriumFrequencies, double[] initialClassProbabilities, DataType dataType)
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Method Details
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getNumberOfParameters
public int getNumberOfParameters() -
getLowerLimit
public double getLowerLimit(int n) -
getUpperLimit
public double getUpperLimit(int n) -
getDefaultValue
public double getDefaultValue(int n) -
setParameters
public void setParameters(double[] parameters, double[] categoryProbabilities) -
getEquilibriumFrequencies
public double[] getEquilibriumFrequencies()- Specified by:
getEquilibriumFrequencies
in interfaceRateMatrixGroup
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getDataType
- Specified by:
getDataType
in interfaceRateMatrixGroup
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getNumberOfTransitionCategories
public int getNumberOfTransitionCategories()- Specified by:
getNumberOfTransitionCategories
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
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