Constructor Detail

• MultiRateMatrixHandler

  public MultiRateMatrixHandler​(NeoRateMatrix[] rateMatrices,
                                double[] equilibriumFrequencies,
                                double[] initialClassProportions)

Method Detail

• setSubstitutionClassProbabilities

  public void setSubstitutionClassProbabilities​(double[] classProportions)

• setSubstitutionClassProbabilities

  public void setSubstitutionClassProbabilities​(double[] classProportions,
                                                int startIndex)

• getNumberOfSubstitutionClasses

  public final int getNumberOfSubstitutionClasses()

• getCopy

  public final MultiRateMatrixHandler getCopy()

• getEquilibriumFrequencies

  public final double[] getEquilibriumFrequencies()

• getTransitionProbabilities

  public void getTransitionProbabilities​(double distance,
                                         double[][][] store)

• getTransitionProbabilities

  public void getTransitionProbabilities​(double distance,
                                         int category,
                                         double[][] store)

• getTransitionProbabilitiesTranspose

  public void getTransitionProbabilitiesTranspose​(double distance,
                                                  double[][][] store)

• getTransitionProbabilitiesTranspose

  public void getTransitionProbabilitiesTranspose​(double distance,
                                                  int category,
                                                  double[][] store)

• report

  public void report​(java.io.PrintWriter out)

  Reporting stuff

  Parameters:

  out - where to report too

• getSubstitutionClassLowerLimit

  public final double getSubstitutionClassLowerLimit()

• getSubstitutionClassUpperLimit

  public final double getSubstitutionClassUpperLimit()

• getSubstitutionClassDefaultValue

  public final double getSubstitutionClassDefaultValue()

• getLowerLimit

  public double getLowerLimit​(int n)

  Description copied from interface: NeoParameterized
  get lower parameter limit

  Specified by:

  getLowerLimit in interface NeoParameterized

  Parameters:

  n - parameter number

  Returns:

  lower bound

• getUpperLimit

  public double getUpperLimit​(int n)

  Description copied from interface: NeoParameterized
  get upper parameter limit

  Specified by:

  getUpperLimit in interface NeoParameterized

  Parameters:

  n - parameter number

  Returns:

  upper bound

• getDefaultValue

  public double getDefaultValue​(int n)

• getNumberOfParameters

  public int getNumberOfParameters()

  Description copied from interface: NeoParameterized
  get number of parameters

  Specified by:

  getNumberOfParameters in interface NeoParameterized

  Returns:

  number of parameters

• setAllParameters

  public void setAllParameters​(double[] rateParameters,
                               double[] classProportions)

• setParameters

  public void setParameters​(double[] parameters,
                            int startIndex)

  Description copied from interface: NeoParameterized
  set model parameter

  Specified by:

  setParameters in interface NeoParameterized

  Parameters:

  parameters - the array holding the parameters

  startIndex - the index into the array that the related parameters start at

• getParameters

  public void getParameters​(double[] parameterStore,
                            int startIndex)

  Description copied from interface: NeoParameterized
  get model parameter

  Specified by:

  getParameters in interface NeoParameterized

  startIndex - the index into the array that the related parameters start at

• getDefaultValues

  public void getDefaultValues​(double[] store,
                               int startIndex)

  Description copied from interface: NeoParameterized
  get default value parameter values

  Specified by:

  getDefaultValues in interface NeoParameterized