Package pal.substmodel

Class NeutralSelectionRateMatrixGroup

java.lang.Object
pal.substmodel.NeutralSelectionRateMatrixGroup
All Implemented Interfaces:
Serializable, RateMatrixGroup
public class NeutralSelectionRateMatrixGroup extends Object implements RateMatrixGroup
See Also:

  • Constructor Details

    • NeutralSelectionRateMatrixGroup

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

  • Method Details

    • 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 String getSummary(double[] categoryProbabilities)
      Specified by:
      getSummary in interface RateMatrixGroup