pal.substmodel
Interface RateMatrixGroup
- All Superinterfaces:
- java.io.Serializable
- All Known Implementing Classes:
- NeutralSelectionRateMatrixGroup, PositiveSelectionRateMatrixGroup, SimpleRateMatrixGroup
public interface RateMatrixGroup
- extends java.io.Serializable
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)