Method Detail

• getLeafBaseHeight

  double getLeafBaseHeight​(java.lang.String leafLabel)

• getBaseHeight

  double getBaseHeight​(double originalExpectSubstitutionHeight)

• getExpectedSubstitutionHeight

  double getExpectedSubstitutionHeight​(double baseHeight)

• getBaseHeightUnits

  int getBaseHeightUnits()

• initialiseParameters

  void initialiseParameters​(java.lang.String[] leafNames,
                            double[] leafHeights)

• getAllGroupRelatedParameterAccess

  NeoParameterized getAllGroupRelatedParameterAccess()

• getPrimaryGroupRelatedParameterAccess

  NeoParameterized getPrimaryGroupRelatedParameterAccess()

• getSecondaryGroupRelatedParameterAccess

  NeoParameterized getSecondaryGroupRelatedParameterAccess()

• createNewClockLeaf

  MolecularClockLikelihoodModel.Leaf createNewClockLeaf​(PatternInfo pattern,
                                                        int[] patternStateMatchup)

• createNewClockExternal

  MolecularClockLikelihoodModel.External createNewClockExternal()

• createNewClockInternal

  MolecularClockLikelihoodModel.Internal createNewClockInternal()