Method Detail

• getTypeID

  int getTypeID​()

  get numerical code describing the data type

  Returns:

  integer code identifying a data type

• getModelID

  int getModelID​()

  get numerical code describing the model type

  Returns:

  integer code identifying a substitution model

• getUniqueName

  java.lang.String getUniqueName​()

  Returns:

  a short unique human-readable identifier for this rate matrix.

• getDimension

  int getDimension​()

  Returns:

  the dimension of this rate matrix.

• getEquilibriumFrequencies

  double[] getEquilibriumFrequencies​()

  Returns:

  stationary frequencies (sum = 1.0)

• getEquilibriumFrequency

  double getEquilibriumFrequency​(int i)

  Returns:

  stationary frequency (sum = 1.0) for ith state Preferred method for infrequent use.

• getDataType

  DataType getDataType​()

  Get the data type of this rate matrix

• getRelativeRates

  double[][] getRelativeRates​()

  Deprecated. try not to use.

  Returns:

  rate matrix (transition: from 1st index to 2nd index)

• getTransitionProbability

  double getTransitionProbability​(int fromState,
                                  int toState)

  Parameters:

  fromState - The state from which we are starting

  toState - The resulting state

  Returns:

  the probability of going from one state to another given the current distance

• getTransitionProbabilities

  void getTransitionProbabilities​(double[][] probabilityStore)

  A utility method for speed, transfers trans prob information quickly into store

• setDistance

  void setDistance​(double distance)

  Sets the distance (such as time/branch length) used when calculating the probabilities. This method may well take the most time!

• setDistanceTranspose

  void setDistanceTranspose​(double distance)

  Sets the distance (such as time/branch length) used when calculating the probabilities.

• addPalObjectListener

  void addPalObjectListener​(PalObjectListener pol)

  Add a PalObjectListener to be notified of changes to the model. Only the parametersChanged method will generally be called

• removePalObjectListener

  void removePalObjectListener​(PalObjectListener pol)

• getOrthogonalHints

  OrthogonalHints getOrthogonalHints​()

  Returns:

  an orthogonal hints object for orthogonal optimisation (may return null for no hints)

• clone

  java.lang.Object clone​()

• setParametersNoScale

  double setParametersNoScale​(double[] parameters)

• scale

  void scale​(double scaleValue)