Class TreeSimulator


  • public class TreeSimulator
    extends java.lang.Object
    This class provides the framework for (backwards-through-time) tree simulation. Basically, this takes a set of tips (optionally at different dates) and repeatedly coalesces them together until the MRCA is reached and the tree is returned. The time intervals between nodes are provided by the IntervalGenerator and an implementation of this is the CoalescentIntervalGenerator in the jebl.evolution.coalescent package.
    Version:
    $Id: TreeSimulator.java 1053 2010-05-10 13:00:31Z rambaut $
    Author:
    Andrew Rambaut
    • Constructor Summary

      Constructors 
      Constructor Description
      TreeSimulator​(java.lang.String taxonPrefix, double[] samplingTimes)  
      TreeSimulator​(java.lang.String taxonPrefix, int taxonCount)
      A constructor for a given number of taxa, all sampled at the same time
      TreeSimulator​(java.lang.String taxonPrefix, int[] samplingCounts, double[] samplingTimes)  
      TreeSimulator​(java.util.Collection<Taxon> taxa, java.lang.String heightAttributeName)
      A constructor for a given collection of taxa.
    • Constructor Detail

      • TreeSimulator

        public TreeSimulator​(java.lang.String taxonPrefix,
                             int taxonCount)
        A constructor for a given number of taxa, all sampled at the same time
        Parameters:
        taxonCount -
      • TreeSimulator

        public TreeSimulator​(java.lang.String taxonPrefix,
                             double[] samplingTimes)
      • TreeSimulator

        public TreeSimulator​(java.lang.String taxonPrefix,
                             int[] samplingCounts,
                             double[] samplingTimes)
      • TreeSimulator

        public TreeSimulator​(java.util.Collection<Taxon> taxa,
                             java.lang.String heightAttributeName)
        A constructor for a given collection of taxa. If the taxa have the attribute given by heightAttributeName then this will be used, otherwise a height of 0.0 will be assumed.
        Parameters:
        taxa -
    • Method Detail

      • main

        public static void main​(java.lang.String[] args)
        A main() to test the tree simulation classes. In this case the interval generator is a simple anonymous class that simply returns the uniform random deviate that it is passed.
        Parameters:
        args -