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

DataType getDataType()

getEquilibriumFrequencies

double[] getEquilibriumFrequencies()

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

getNumberOfTransitionCategories

int getNumberOfTransitionCategories()

getTransitionProbabilities

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

getTransitionProbabilitiesTranspose

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

getTransitionProbabilities

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

getTransitionProbabilitiesTranspose

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

getSummary

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