Examples with GMRFSkyrideGradient dr.evomodel.coalescent.GMRFSkyrideGradient used on opensource projects

Example 1 with GMRFSkyrideGradient

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

the class GMRFSkyrideGradientParser method parseXMLObject.

@Override
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    // Parameter parameter = (Parameter) xo.getChild(Parameter.class);
    TreeModel tree = (TreeModel) xo.getChild(TreeModel.class);
    OldGMRFSkyrideLikelihood skyrideLikelihood = (OldGMRFSkyrideLikelihood) xo.getChild(OldGMRFSkyrideLikelihood.class);
    String wrtParameterCase = (String) xo.getAttribute(WRT_PARAMETER);
    GMRFGradient.WrtParameter type = GMRFGradient.WrtParameter.factory(wrtParameterCase);
    if (type != null) {
        type.getWarning((GMRFMultilocusSkyrideLikelihood) skyrideLikelihood);
        return new GMRFGradient((GMRFMultilocusSkyrideLikelihood) skyrideLikelihood, type);
    }
    // Old behaviour
    GMRFSkyrideGradient.WrtParameter wrtParameter = setupWrtParameter(wrtParameterCase);
    NodeHeightTransform nodeHeightTransform = (NodeHeightTransform) xo.getChild(NodeHeightTransform.class);
    return new GMRFSkyrideGradient(skyrideLikelihood, wrtParameter, tree, nodeHeightTransform);
}