/**
* Creates an object to simulate data for a given set of models, a tree, parameters and unobserved
* states. A different model can be given for each rate class.
*
* @param m Map from site class to model
* @param t The tree
* @param p The parameters
* @param unobserved The unobserved states
* @throws Models.RateCategory.RateException Thrown if there is an issue with a rate category in
* the model (e.g. a badly formatted rate).
* @throws Models.Model.ModelException Thrown if there is a problem with the model (e.g. the rate
* categories differ in their states)
* @throws TreeException Thrown if there is a problem with the tree.
* @throws Parameters.Parameters.ParameterException Thrown if there is a problem with the
* parameters (e.g. a required parameter is not present)
*/
public Simulate(Map<String, Model> m, Tree t, Parameters p, Alignment unobserved)
throws RateException, ModelException, TreeException, ParameterException {
P = new HashMap<>();
for (Entry<String, Model> e : m.entrySet()) {
P.put(e.getKey(), new Probabilities(e.getValue(), t, p));
}
this.missing = unobserved;
this.t = new HashMap<>();
for (String s : m.keySet()) {
this.t.put(s, t);
}
random = new Random();
// If the parameters setting doesn't include branch lengths parameters then
// add them from the tree. The paramter / branch length interaction is a
// bit counter-inutative and probably needs changing but in the mean time
// this is here to make errors less likely.
for (Branch b : t) {
if (!p.hasParam(b.getChild())) {
p.addParameter(Parameter.newFixedParameter(b.getChild(), b.getLength()));
}
}
}
