public Object parseXMLObject(XMLObject xo) throws XMLParseException {
// final int overSampling = xo.getAttribute(OVERSAMPLING, 1);
final boolean normalize = xo.getAttribute(NORMALIZE, false);
final double normalizeBranchRateTo = xo.getAttribute(NORMALIZE_BRANCH_RATE_TO, Double.NaN);
TreeModel tree = (TreeModel) xo.getChild(TreeModel.class);
ParametricDistributionModel distributionModel =
(ParametricDistributionModel) xo.getElementFirstChild(DISTRIBUTION);
// Parameter rateCategoryParameter = (Parameter) xo.getElementFirstChild(RATE_CATEGORIES);
Parameter rateCategoryQuantilesParameter =
(Parameter) xo.getElementFirstChild(RATE_CATEGORY_QUANTILES);
Logger.getLogger("dr.evomodel").info("Using continuous relaxed clock model.");
// Logger.getLogger("dr.evomodel").info(" over sampling = " + overSampling);
Logger.getLogger("dr.evomodel")
.info(" parametric model = " + distributionModel.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 (xo.hasAttribute(NORMALIZED_MEAN)) {
dbr.setNormalizedMean(xo.getDoubleAttribute(NORMALIZED_MEAN));
}*/
return new ContinuousBranchRates(
tree, /*rateCategoryParameter, */
rateCategoryQuantilesParameter,
distributionModel, /*overSampling,*/
normalize,
normalizeBranchRateTo);
}
public TaxaConstraint(TaxonList taxons, ParametricDistributionModel p, boolean isMono) {
this.taxons = taxons;
this.isMonophyletic = isMono;
if (p != null) {
final UnivariateFunction univariateFunction = p.getProbabilityDensityFunction();
lower = univariateFunction.getLowerBound();
upper = univariateFunction.getUpperBound();
} else {
lower = 0;
upper = Double.POSITIVE_INFINITY;
}
}