Examples with BranchSpecificSubstitutionParameterBranchModel dr.evomodel.branchmodel.BranchSpecificSubstitutionParameterBranchModel used on opensource projects

Example 1 with BranchSpecificSubstitutionParameterBranchModel

use of dr.evomodel.branchmodel.BranchSpecificSubstitutionParameterBranchModel in project beast-mcmc by beast-dev.

the class BranchSubstitutionParameterGradientParser method parseXMLObject.

@Override
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    String traitName = xo.getAttribute(TRAIT_NAME, DEFAULT_TRAIT_NAME);
    boolean useHessian = xo.getAttribute(USE_HESSIAN, false);
    final TreeDataLikelihood treeDataLikelihood = (TreeDataLikelihood) xo.getChild(TreeDataLikelihood.class);
    BranchSpecificSubstitutionParameterBranchModel branchModel = (BranchSpecificSubstitutionParameterBranchModel) xo.getChild(BranchModel.class);
    BeagleDataLikelihoodDelegate beagleData = (BeagleDataLikelihoodDelegate) treeDataLikelihood.getDataLikelihoodDelegate();
    BranchRateModel branchRateModel = (BranchRateModel) xo.getChild(BranchRateModel.class);
    CompoundParameter branchParameter = branchModel.getBranchSpecificParameters(branchRateModel);
    return new BranchSubstitutionParameterGradient(traitName, treeDataLikelihood, beagleData, branchParameter, branchRateModel, useHessian);
}

Example 2 with BranchSpecificSubstitutionParameterBranchModel

use of dr.evomodel.branchmodel.BranchSpecificSubstitutionParameterBranchModel in project beast-mcmc by beast-dev.

the class BranchSpecificSubstitutionParameterBranchModelParser method parseXMLObject.

@Override
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    List<Parameter> parameters = new ArrayList<>();
    for (XMLObject xoc : xo.getAllChildren(OLD_PARAMETER)) {
        Parameter parameter = (Parameter) xoc.getChild(Parameter.class);
        parameters.add(parameter);
    }
    List<BranchRateModel> branchRateModels = new ArrayList<>();
    for (XMLObject xoc : xo.getAllChildren(NEW_PARAMETER)) {
        BranchRateModel branchRateModel = (BranchRateModel) xoc.getChild(BranchRateModel.class);
        branchRateModels.add(branchRateModel);
    }
    ParameterReplaceableSubstitutionModel substitutionModel = (ParameterReplaceableSubstitutionModel) xo.getChild(ParameterReplaceableSubstitutionModel.class);
    TreeModel tree = (TreeModel) xo.getChild(TreeModel.class);
    return new BranchSpecificSubstitutionParameterBranchModel(BRANCH_SPECIFIC_SUBSTITUTION_PARAMETER_BRANCH_MODEL, parameters, branchRateModels, substitutionModel, tree);
}