pal.substmodel

Class PositiveSelectionRateMatrixGroup

java.lang.Object

pal.substmodel.PositiveSelectionRateMatrixGroup

All Implemented Interfaces:

java.io.Serializable, RateMatrixGroup

public class PositiveSelectionRateMatrixGroup
extends java.lang.Object
implements RateMatrixGroup

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
PositiveSelectionRateMatrixGroup(MutableDouble kappaStore, MutableDouble omegaStore, double[] freqs, CodonTable table)

Method Summary

Methods

Modifier and Type	Method and 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.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

PositiveSelectionRateMatrixGroup

public PositiveSelectionRateMatrixGroup(MutableDouble kappaStore,
                                MutableDouble omegaStore,
                                double[] freqs,
                                CodonTable table)

Method Detail

getNumberOfTransitionCategories

public int getNumberOfTransitionCategories()

Specified by:

getNumberOfTransitionCategories in interface RateMatrixGroup

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 interface RateMatrixGroup

Parameters:

categoryProbabilities - the probabilities (summing to one) of each category (class) of substitution

getEquilibriumFrequencies

public double[] getEquilibriumFrequencies()

Specified by:

getEquilibriumFrequencies in interface RateMatrixGroup

getDataType

public DataType getDataType()

Specified by:

getDataType in interface RateMatrixGroup

getTransitionProbabilities

public void getTransitionProbabilities(double branchLength,
                              double[][][] tableStore)

Specified by:

getTransitionProbabilities in interface RateMatrixGroup

getTransitionProbabilitiesTranspose

public void getTransitionProbabilitiesTranspose(double branchLength,
                                       double[][][] tableStore)

Specified by:

getTransitionProbabilitiesTranspose in interface RateMatrixGroup

getTransitionProbabilities

public void getTransitionProbabilities(double branchLength,
                              int category,
                              double[][] tableStore)

Specified by:

getTransitionProbabilities in interface RateMatrixGroup

getTransitionProbabilitiesTranspose

public void getTransitionProbabilitiesTranspose(double branchLength,
                                       int category,
                                       double[][] tableStore)

Specified by:

getTransitionProbabilitiesTranspose in interface RateMatrixGroup

getSummary

public java.lang.String getSummary(double[] categoryProbabilities)

Specified by:

getSummary in interface RateMatrixGroup