|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectjebl.evolution.treesimulation.TreeSimulator
public class 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.
Constructor Summary | |
---|---|
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 | |
---|---|
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 |
---|
public TreeSimulator(java.lang.String taxonPrefix, int taxonCount)
taxonCount
- public TreeSimulator(java.lang.String taxonPrefix, double[] samplingTimes)
public TreeSimulator(java.lang.String taxonPrefix, int[] samplingCounts, double[] samplingTimes)
public TreeSimulator(java.util.Collection<Taxon> taxa, java.lang.String heightAttributeName)
taxa
- Method Detail |
---|
public RootedTree simulate(IntervalGenerator intervalGenerator)
public RootedTree simulate(IntervalGenerator intervalGenerator, boolean medianHeights)
public static void main(java.lang.String[] args)
args
-
|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |