Package pal.substmodel

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()