pal.substmodel
public interface RateMatrixGroup extends java.io.Serializable
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.
|
DataType getDataType()
double[] getEquilibriumFrequencies()
void updateParameters(double[] categoryProbabilities)
categoryProbabilities
- the probabilities (summing to one) of each category (class) of substitutionint getNumberOfTransitionCategories()
void getTransitionProbabilities(double branchLength, double[][][] tableStore)
void getTransitionProbabilitiesTranspose(double branchLength, double[][][] tableStore)
void getTransitionProbabilities(double branchLength, int category, double[][] tableStore)
void getTransitionProbabilitiesTranspose(double branchLength, int category, double[][] tableStore)
java.lang.String getSummary(double[] categoryProbabilities)