Package jebl.evolution.treesimulation
Class TreeSimulator
java.lang.Object
jebl.evolution.treesimulation.TreeSimulator
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
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Constructor Summary
ConstructorsConstructorDescriptionTreeSimulator
(String taxonPrefix, double[] samplingTimes) TreeSimulator
(String taxonPrefix, int taxonCount) A constructor for a given number of taxa, all sampled at the same timeTreeSimulator
(String taxonPrefix, int[] samplingCounts, double[] samplingTimes) TreeSimulator
(Collection<Taxon> taxa, String heightAttributeName) A constructor for a given collection of taxa. -
Method Summary
Modifier and TypeMethodDescriptionstatic void
A main() to test the tree simulation classes.simulate
(IntervalGenerator intervalGenerator) simulate
(IntervalGenerator intervalGenerator, boolean medianHeights)
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Constructor Details
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TreeSimulator
A constructor for a given number of taxa, all sampled at the same time- Parameters:
taxonCount
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TreeSimulator
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TreeSimulator
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TreeSimulator
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
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Method Details
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simulate
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simulate
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main
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
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