/*
* SpeciesTreeBMPriorParser.java
*
* Copyright (c) 2002-2015 Alexei Drummond, Andrew Rambaut and Marc Suchard
*
* This file is part of BEAST.
* See the NOTICE file distributed with this work for additional
* information regarding copyright ownership and licensing.
*
* BEAST is free software; you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as
* published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
*
* BEAST is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public
* License along with BEAST; if not, write to the
* Free Software Foundation, Inc., 51 Franklin St, Fifth Floor,
* Boston, MA 02110-1301 USA
*/
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) })
};
}
}