Class SequenceSimulator


  • public class SequenceSimulator
    extends java.lang.Object
    • 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()