Constructor Detail

• SequenceSimulator

  public SequenceSimulator(SubstitutionModel model,
                           int sequenceLength,
                           boolean stochasticDistribution)

  A constructor (with no provided random number generator - a fresh one is created)

  Parameters:

  model - The substitution model used for simulation

  sequenceLength - The length of all sequences generated by this simulator

• SequenceSimulator

  public SequenceSimulator(SubstitutionModel model,
                           int sequenceLength,
                           MersenneTwisterFast random,
                           boolean stochasticDistribution)

  A constructor (with no provided random number generator - a fresh one is created)

  Parameters:

  model - The substitution model used for simulation

  sequenceLength - The length of all sequences generated by this simulator

  random - A random number generator

Method Detail

• resetSiteCategoryDistribution

  public void resetSiteCategoryDistribution(boolean stochasticDistribution)

  Reassigns model classes to each site (a site belongs to a particular class/category of the model)

• resetSiteCategoryDistribution

  public void resetSiteCategoryDistribution(double[] categoryDistribution,
                                            boolean stochasticDistribution)

• resetSiteCategoryDistribution

  public void resetSiteCategoryDistribution(double[][] posteriorCategoryDistribution)

• getSiteCategoryDistribution

  public int[] getSiteCategoryDistribution()

• resetSiteCategoryDistribution

  public void resetSiteCategoryDistribution(double[][] posteriorCategoryDistribution,
                                            SequenceSimulator base)

• resetSiteCategoryDistribution

  public void resetSiteCategoryDistribution(double[][] posteriorCategoryDistribution,
                                            int[] baseSiteCategories)

• simulate

  public void simulate(int[] startingSequence,
                       double distance,
                       int[] endingSequenceStore)

• getSimulated

  public int[] getSimulated(int[] startingSequence,
                            double distance)

• generateRoot

  public int[] generateRoot()