Examples with MixtureModelBranchRates dr.evomodel.branchratemodel.MixtureModelBranchRates used on opensource projects

Example 1 with MixtureModelBranchRates

use of dr.evomodel.branchratemodel.MixtureModelBranchRates in project beast-mcmc by beast-dev.

the class MixtureModelBranchRatesParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    ArrayList<ParametricDistributionModel> modelsList = new ArrayList<ParametricDistributionModel>();
    final boolean normalize = xo.getAttribute(NORMALIZE, false);
    final double normalizeBranchRateTo = xo.getAttribute(NORMALIZE_BRANCH_RATE_TO, Double.NaN);
    final boolean useQuantilesForRates = xo.getAttribute(USE_QUANTILE, true);
    TreeModel tree = (TreeModel) xo.getChild(TreeModel.class);
    for (int i = 0; i < xo.getChildCount(); i++) {
        Object child = xo.getChild(i);
        if (child instanceof XMLObject) {
            if (((XMLObject) child).getName().equals(DISTRIBUTION)) {
                XMLObject childXML = (XMLObject) child;
                modelsList.add((ParametricDistributionModel) childXML.getChild(0));
            }
        }
    }
    //Parameter rateCategoryParameter = (Parameter) xo.getElementFirstChild(RATE_CATEGORIES);
    ParametricDistributionModel[] models = modelsList.toArray(new ParametricDistributionModel[modelsList.size()]);
    Parameter rateCategoryQuantilesParameter = (Parameter) xo.getElementFirstChild(RATE_CATEGORY_QUANTILES);
    Parameter distributionIndexParameter = (Parameter) xo.getElementFirstChild(DISTRIBUTION_INDEX);
    Logger.getLogger("dr.evomodel").info("Using random discretized relaxed clock model with a mixture distribution.");
    for (int i = 0; i < models.length; i++) {
        Logger.getLogger("dr.evomodel").info("  parametric model " + (i + 1) + " = " + models[i].getModelName());
    }
    //Logger.getLogger("dr.evomodel").info("   rate categories = " + rateCategoryParameter.getDimension());
    Logger.getLogger("dr.evomodel").info("   rate categories = " + rateCategoryQuantilesParameter.getDimension());
    if (normalize) {
        Logger.getLogger("dr.evomodel").info("   mean rate is normalized to " + normalizeBranchRateTo);
    }
    if (xo.hasAttribute(SINGLE_ROOT_RATE)) {
        //singleRootRate = xo.getBooleanAttribute(SINGLE_ROOT_RATE);
        Logger.getLogger("dr.evomodel").warning("   WARNING: single root rate is not implemented!");
    }
    if (!useQuantilesForRates) {
        Logger.getLogger("dr.evomodel").info("Rates are set to not being drawn using quantiles. Thus they are not drawn from any particular distribution.");
    }
    return new MixtureModelBranchRates(tree, rateCategoryQuantilesParameter, models, distributionIndexParameter, useQuantilesForRates, normalize, normalizeBranchRateTo);
}