Method Detail

• getDataType

  DataType getDataType()

• getNumberOfTransitionCategories

  int getNumberOfTransitionCategories()

• getTransitionCategoryProbability

  double getTransitionCategoryProbability​(int category)

• getTransitionCategoryProbabilities

  double[] getTransitionCategoryProbabilities()

  Returns:

  all the category probabilites for each category respectively.

• getTransitionProbabilities

  void getTransitionProbabilities​(double branchLength,
                                  double[][][] tableStore)

  Table is organized as [transition_group][from][to]

• getTransitionProbabilitiesTranspose

  void getTransitionProbabilitiesTranspose​(double branchLength,
                                           double[][][] tableStore)

  Table is organized as [transition_group][to][from]

• getTransitionProbabilities

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

  Table is organized as [transition_group][from][to]

• getTransitionProbabilitiesTranspose

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

  Table is organized as [transition_group][to][from]

• getEquilibriumFrequencies

  double[] getEquilibriumFrequencies()

  Should return a double[] array of the related equilibrium frequencies. As a rule, callers should not alter the returned array (it may be used internally)

• addPalObjectListener

  void addPalObjectListener​(PalObjectListener l)

• removePalObjectListener

  void removePalObjectListener​(PalObjectListener l)

• getOrthogonalHints

  OrthogonalHints getOrthogonalHints()

  May return null

• clone

  java.lang.Object clone()