java.io.Serializable
, RateMatrixGroup
public class PositiveSelectionRateMatrixGroup extends java.lang.Object implements RateMatrixGroup
Constructor | Description |
---|---|
PositiveSelectionRateMatrixGroup(MutableDouble kappaStore,
MutableDouble omegaStore,
double[] freqs,
CodonTable table) |
Modifier and Type | Method | 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.
|
public PositiveSelectionRateMatrixGroup(MutableDouble kappaStore, MutableDouble omegaStore, double[] freqs, CodonTable table)
public int getNumberOfTransitionCategories()
getNumberOfTransitionCategories
in interface RateMatrixGroup
public void updateParameters(double[] categoryProbabilities)
RateMatrixGroup
updateParameters
in interface RateMatrixGroup
categoryProbabilities
- the probabilities (summing to one) of each category (class) of substitutionpublic double[] getEquilibriumFrequencies()
getEquilibriumFrequencies
in interface RateMatrixGroup
public DataType getDataType()
getDataType
in interface RateMatrixGroup
public void getTransitionProbabilities(double branchLength, double[][][] tableStore)
getTransitionProbabilities
in interface RateMatrixGroup
public void getTransitionProbabilitiesTranspose(double branchLength, double[][][] tableStore)
getTransitionProbabilitiesTranspose
in interface RateMatrixGroup
public void getTransitionProbabilities(double branchLength, int category, double[][] tableStore)
getTransitionProbabilities
in interface RateMatrixGroup
public void getTransitionProbabilitiesTranspose(double branchLength, int category, double[][] tableStore)
getTransitionProbabilitiesTranspose
in interface RateMatrixGroup
public java.lang.String getSummary(double[] categoryProbabilities)
getSummary
in interface RateMatrixGroup