pal.substmodel
Class NeutralSelectionRateMatrixGroup

java.lang.Object
  extended by pal.substmodel.NeutralSelectionRateMatrixGroup
All Implemented Interfaces:
java.io.Serializable, RateMatrixGroup

public class NeutralSelectionRateMatrixGroup
extends java.lang.Object
implements RateMatrixGroup

See Also:
Serialized Form

Constructor Summary
NeutralSelectionRateMatrixGroup(MutableDouble kappaStore, double[] freqs, CodonTable table)
           
 
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.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

NeutralSelectionRateMatrixGroup

public NeutralSelectionRateMatrixGroup(MutableDouble kappaStore,
                                       double[] freqs,
                                       CodonTable table)
Method Detail

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

getNumberOfTransitionCategories

public int getNumberOfTransitionCategories()
Specified by:
getNumberOfTransitionCategories 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