pal.substmodel
Class PositiveSelectionRateMatrixGroup
java.lang.Object
pal.substmodel.PositiveSelectionRateMatrixGroup
- All Implemented Interfaces:
- java.io.Serializable, RateMatrixGroup
public class PositiveSelectionRateMatrixGroup
- extends java.lang.Object
- implements RateMatrixGroup
- See Also:
- Serialized Form
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
PositiveSelectionRateMatrixGroup
public PositiveSelectionRateMatrixGroup(MutableDouble kappaStore,
MutableDouble omegaStore,
double[] freqs,
CodonTable table)
getNumberOfTransitionCategories
public int getNumberOfTransitionCategories()
- Specified by:
getNumberOfTransitionCategories
in interface RateMatrixGroup
updateParameters
public void updateParameters(double[] categoryProbabilities)
- Description copied from interface:
RateMatrixGroup
- 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.
- Specified by:
updateParameters
in interface RateMatrixGroup
- Parameters:
categoryProbabilities
- the probabilities (summing to one) of each category (class) of substitution
getEquilibriumFrequencies
public double[] getEquilibriumFrequencies()
- Specified by:
getEquilibriumFrequencies
in interface RateMatrixGroup
getDataType
public DataType getDataType()
- Specified by:
getDataType
in interface RateMatrixGroup
getTransitionProbabilities
public void getTransitionProbabilities(double branchLength,
double[][][] tableStore)
- Specified by:
getTransitionProbabilities
in interface RateMatrixGroup
getTransitionProbabilitiesTranspose
public void getTransitionProbabilitiesTranspose(double branchLength,
double[][][] tableStore)
- Specified by:
getTransitionProbabilitiesTranspose
in interface RateMatrixGroup
getTransitionProbabilities
public void getTransitionProbabilities(double branchLength,
int category,
double[][] tableStore)
- Specified by:
getTransitionProbabilities
in interface RateMatrixGroup
getTransitionProbabilitiesTranspose
public void getTransitionProbabilitiesTranspose(double branchLength,
int category,
double[][] tableStore)
- Specified by:
getTransitionProbabilitiesTranspose
in interface RateMatrixGroup
getSummary
public java.lang.String getSummary(double[] categoryProbabilities)
- Specified by:
getSummary
in interface RateMatrixGroup