jebl.evolution.treesimulation

Class TreeSimulator

java.lang.Object

jebl.evolution.treesimulation.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 and Description
TreeSimulator(java.util.Collection<Taxon> taxa, java.lang.String heightAttributeName) A constructor for a given collection of taxa.
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)

Method Summary

Methods

Modifier and Type	Method and Description
static void	main(java.lang.String[] args) A main() to test the tree simulation classes.
RootedTree	simulate(IntervalGenerator intervalGenerator)
RootedTree	simulate(IntervalGenerator intervalGenerator, boolean medianHeights)

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

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

simulate

public RootedTree simulate(IntervalGenerator intervalGenerator)

simulate

public RootedTree simulate(IntervalGenerator intervalGenerator,
                  boolean medianHeights)

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 -