Method Detail

• 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

  java.lang.String getSummary​(double[] categoryProbabilities)