/*
* YuleModelParser.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.evolution.util.Units;
import dr.evomodel.speciation.BirthDeathGernhard08Model;
import dr.evoxml.util.XMLUnits;
import dr.inference.model.Parameter;
import dr.xml.*;
import java.util.logging.Logger;
/**
* @author Alexei Drummond
*/
public class YuleModelParser extends AbstractXMLObjectParser {
public static final String YULE_MODEL = "yuleModel";
public static final String YULE = "yule";
public static final String BIRTH_RATE = "birthRate";
public String getParserName() {
return YULE_MODEL;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
final Units.Type units = XMLUnits.Utils.getUnitsAttr(xo);
final XMLObject cxo = xo.getChild(BIRTH_RATE);
final boolean conditonalOnRoot = xo.getAttribute(BirthDeathModelParser.CONDITIONAL_ON_ROOT, false);
final Parameter brParameter = (Parameter) cxo.getChild(Parameter.class);
Logger.getLogger("dr.evomodel").info("\nUsing Yule prior on tree");
return new BirthDeathGernhard08Model(xo.getId(), brParameter, null, null,
BirthDeathGernhard08Model.TreeType.UNSCALED, units, conditonalOnRoot);
}
//************************************************************************
// AbstractXMLObjectParser implementation
//************************************************************************
public String getParserDescription() {
return "A speciation model of a simple constant rate Birth-death process.";
}
public Class getReturnType() {
return BirthDeathGernhard08Model.class;
}
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private final XMLSyntaxRule[] rules = {
AttributeRule.newBooleanRule(BirthDeathModelParser.CONDITIONAL_ON_ROOT, true),
new ElementRule(BIRTH_RATE,
new XMLSyntaxRule[]{new ElementRule(Parameter.class)}),
XMLUnits.SYNTAX_RULES[0]
};
}