/**
* Simulates a coalescent tree from a set of subtrees.
*
* @param subtrees an array of tree to be used as subtrees
* @param model the demographic model to use
* @param rootHeight an optional root height with which to scale the whole tree
* @param preserveSubtrees true of subtrees should be preserved
* @return a simulated coalescent tree
*/
public SimpleTree simulateTree(
Tree[] subtrees, DemographicModel model, double rootHeight, boolean preserveSubtrees) {
SimpleNode[] roots = new SimpleNode[subtrees.length];
SimpleTree tree;
for (int i = 0; i < roots.length; i++) {
roots[i] = new SimpleNode(subtrees[i], subtrees[i].getRoot());
}
// if just one taxonList then finished
if (roots.length == 1) {
tree = new SimpleTree(roots[0]);
} else {
tree = new SimpleTree(simulator.simulateCoalescent(roots, model.getDemographicFunction()));
}
if (!Double.isNaN(rootHeight) && rootHeight > 0.0) {
if (preserveSubtrees) {
limitNodes(tree, rootHeight - 1e-12);
tree.setRootHeight(rootHeight);
} else {
attemptToScaleTree(tree, rootHeight);
}
}
return tree;
}
/**
* Simulates a coalescent tree, given a taxon list.
*
* @param taxa the set of taxa to simulate a coalescent tree between
* @param model the demographic model to use
* @return a simulated coalescent tree
*/
public SimpleTree simulateTree(TaxonList taxa, DemographicModel model) {
return simulator.simulateTree(taxa, model.getDemographicFunction());
}