Examples with NodeHeightGradientForDiscreteTrait dr.evomodel.treedatalikelihood.discrete.NodeHeightGradientForDiscreteTrait used on opensource projects

Example 1 with NodeHeightGradientForDiscreteTrait

use of dr.evomodel.treedatalikelihood.discrete.NodeHeightGradientForDiscreteTrait in project beast-mcmc by beast-dev.

the class NodeHeightGradientParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    String traitName = xo.getAttribute(TRAIT_NAME, DEFAULT_TRAIT_NAME);
    final TreeDataLikelihood treeDataLikelihood = (TreeDataLikelihood) xo.getChild(TreeDataLikelihood.class);
    BranchRateModel branchRateModel = treeDataLikelihood.getBranchRateModel();
    if (branchRateModel instanceof DefaultBranchRateModel || branchRateModel instanceof ArbitraryBranchRates) {
        Parameter branchRates = null;
        if (branchRateModel instanceof ArbitraryBranchRates) {
            branchRates = ((ArbitraryBranchRates) branchRateModel).getRateParameter();
        }
        DataLikelihoodDelegate delegate = treeDataLikelihood.getDataLikelihoodDelegate();
        if (delegate instanceof ContinuousDataLikelihoodDelegate) {
            throw new XMLParseException("Not yet implemented! ");
        } else if (delegate instanceof BeagleDataLikelihoodDelegate) {
            BeagleDataLikelihoodDelegate beagleData = (BeagleDataLikelihoodDelegate) delegate;
            return new NodeHeightGradientForDiscreteTrait(traitName, treeDataLikelihood, beagleData, branchRates);
        } else {
            throw new XMLParseException("Unknown likelihood delegate type");
        }
    } else {
        throw new XMLParseException("Only implemented for an arbitrary rates model");
    }
}