pal.substmodel
Interface RateMatrixGroup

All Superinterfaces:

java.io.Serializable

All Known Implementing Classes:

NeutralSelectionRateMatrixGroup, PositiveSelectionRateMatrixGroup, SimpleRateMatrixGroup

public interface RateMatrixGroup

extends java.io.Serializable

Method Summary

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.

Method Detail

getDataType

public DataType getDataType()

getEquilibriumFrequencies

public double[] getEquilibriumFrequencies()

updateParameters

public 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

getNumberOfTransitionCategories

public int getNumberOfTransitionCategories()

getTransitionProbabilities

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

getTransitionProbabilitiesTranspose

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

getTransitionProbabilities

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

getTransitionProbabilitiesTranspose

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

getSummary

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