Interface RateMatrixGroup

All Superinterfaces:
Serializable
All Known Implementing Classes:
NeutralSelectionRateMatrixGroup, PositiveSelectionRateMatrixGroup, SimpleRateMatrixGroup

public interface RateMatrixGroup extends Serializable
  • Method Details

    • getDataType

      DataType getDataType()
    • getEquilibriumFrequencies

      double[] getEquilibriumFrequencies()
    • updateParameters

      void updateParameters(double[] categoryProbabilities)
      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.
      Parameters:
      categoryProbabilities - the probabilities (summing to one) of each category (class) of substitution
    • getNumberOfTransitionCategories

      int getNumberOfTransitionCategories()
    • getTransitionProbabilities

      void getTransitionProbabilities(double branchLength, double[][][] tableStore)
    • getTransitionProbabilitiesTranspose

      void getTransitionProbabilitiesTranspose(double branchLength, double[][][] tableStore)
    • getTransitionProbabilities

      void getTransitionProbabilities(double branchLength, int category, double[][] tableStore)
    • getTransitionProbabilitiesTranspose

      void getTransitionProbabilitiesTranspose(double branchLength, int category, double[][] tableStore)
    • getSummary

      String getSummary(double[] categoryProbabilities)