SpeciesTreeBMPriorParser.java

package dr.evomodelxml.speciation;

import dr.evomodel.speciation.SpeciesTreeBMPrior;
import dr.evomodel.speciation.SpeciesTreeModel;
import dr.inference.distribution.ParametricDistributionModel;
import dr.inference.model.Parameter;
import dr.xml.*;

/**
 */
public class SpeciesTreeBMPriorParser extends AbstractXMLObjectParser {
    public static final String TIPS = "tipsDistribution";

    public static final String STPRIOR = "STPopulationPrior";

    public static final String LOG_ROOT = "log_root";
    public static final String STSIGMA = "STsigma";
    public static final String SIGMA = "sigma";

       public String getParserDescription() {
            return "";
        }

        public Class getReturnType() {
            return SpeciesTreeBMPrior.class;
        }

        public String getParserName() {
            return STPRIOR;
        }

        public Object parseXMLObject(XMLObject xo) throws XMLParseException {
            final SpeciesTreeModel st = (SpeciesTreeModel) xo.getChild(SpeciesTreeModel.class);

            //ParametricDistributionModel pr = (ParametricDistributionModel) xo.getChild(ParametricDistributionModel.class);
            final Object child = xo.getChild(SIGMA);
            Parameter popSigma = child != null ? (Parameter)((XMLObject) child).getChild(Parameter.class) : null;
            Parameter stSigma = (Parameter)((XMLObject)xo.getChild(STSIGMA)).getChild(Parameter.class);

            final XMLObject cxo = (XMLObject) xo.getChild(TIPS);
            final ParametricDistributionModel tipsPrior =
                    (ParametricDistributionModel) cxo.getChild(ParametricDistributionModel.class);
            final boolean logRoot = xo.getAttribute(LOG_ROOT, false);
            return new SpeciesTreeBMPrior(st, popSigma, stSigma, tipsPrior, logRoot);
        }

        public XMLSyntaxRule[] getSyntaxRules() {
            return new XMLSyntaxRule[]{
                    AttributeRule.newBooleanRule(LOG_ROOT, true),
                    new ElementRule(SpeciesTreeModel.class),
                    new ElementRule(TIPS,
                            new XMLSyntaxRule[] { new ElementRule(ParametricDistributionModel.class) }),
                    //new ElementRule(ParametricDistributionModel.class),
                    new ElementRule(SIGMA, new XMLSyntaxRule[] { new ElementRule(Parameter.class) }, true),
                    new ElementRule(STSIGMA, new XMLSyntaxRule[] { new ElementRule(Parameter.class) })
            };
        }
}