Class SequenceSimulator

java.lang.Object
pal.substmodel.SequenceSimulator

public class SequenceSimulator extends Object
  • Constructor Details

    • 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 Details

    • 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()