Examples with SmoothSkygridLikelihood dr.evomodel.coalescent.smooth.SmoothSkygridLikelihood used on opensource projects

Example 1 with SmoothSkygridLikelihood

use of dr.evomodel.coalescent.smooth.SmoothSkygridLikelihood in project beast-mcmc by beast-dev.

the class SmoothSkygridLikelihoodParser method parseXMLObject.

@Override
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    List<IntervalList> intervalList = new ArrayList<>();
    List<TreeIntervals> debugIntervalList = new ArrayList<>();
    if (xo.hasChildNamed(INTERVALS)) {
        XMLObject cxo = xo.getChild(INTERVALS);
        for (int i = 0; i < cxo.getChildCount(); ++i) {
            intervalList.add((IntervalList) cxo.getChild(i));
        }
    } else {
        XMLObject cxo = xo.getChild(POPULATION_TREE);
        for (int i = 0; i < cxo.getChildCount(); ++i) {
            TreeModel tree = (TreeModel) cxo.getChild(i);
            intervalList.add(new BigFastTreeIntervals(tree));
            debugIntervalList.add(new TreeIntervals(tree));
        }
    }
    Parameter logPopSizes = (Parameter) xo.getElementFirstChild(POPULATION_PARAMETER);
    Parameter gridPoints = (Parameter) xo.getElementFirstChild(GRID_POINTS);
    if (!SmoothSkygridLikelihood.checkValidParameters(logPopSizes, gridPoints)) {
        throw new XMLParseException("Invalid initial parameters");
    }
    SmoothSkygridLikelihood likelihood = new SmoothSkygridLikelihood(xo.getId(), intervalList, logPopSizes, gridPoints);
    likelihood.setDebugIntervalList(debugIntervalList);
    return likelihood;
}