/*
* adding the parameters only if its not a submodel.
*/
protected void addParam(Variable<Double> param) {
if (isNested) {
nestedParams.add(param);
} else {
super.addVariable(param);
}
}
/*
* The One Phase Models are special cases of the birth-death chain,
* and therefore we can use this to calculate the stationay distribution
* given a infinitesimal rate matrix.
*/
public void computeStationaryDistribution() {
if (useStationaryFreqs) {
computeOnePhaseStationaryDistribution();
}
super.computeStationaryDistribution();
}
