/*
* TwoEpochDemographicModelParser.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.coalescent;
import dr.evolution.util.Units;
import dr.evomodel.coalescent.DemographicModel;
import dr.evomodel.coalescent.TwoEpochDemographicModel;
import dr.evoxml.util.XMLUnits;
import dr.inference.model.Parameter;
import dr.xml.*;
/**
* Parses an element from an DOM document into a ExponentialGrowth.
*/
public class TwoEpochDemographicModelParser extends AbstractXMLObjectParser {
public static final String EPOCH_1 = "modernEpoch";
public static final String EPOCH_2 = "ancientEpoch";
public static final String TRANSITION_TIME = "transitionTime";
public static final String TWO_EPOCH_MODEL = "twoEpoch";
public String getParserName() {
return TWO_EPOCH_MODEL;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
Units.Type units = XMLUnits.Utils.getUnitsAttr(xo);
XMLObject cxo = xo.getChild(EPOCH_1);
DemographicModel demo1 = (DemographicModel) cxo.getChild(DemographicModel.class);
cxo = xo.getChild(EPOCH_2);
DemographicModel demo2 = (DemographicModel) cxo.getChild(DemographicModel.class);
cxo = xo.getChild(TRANSITION_TIME);
Parameter timeParameter = (Parameter) cxo.getChild(Parameter.class);
return new TwoEpochDemographicModel(demo1, demo2, timeParameter, units);
}
//************************************************************************
// AbstractXMLObjectParser implementation
//************************************************************************
public String getParserDescription() {
return "A demographic model of two epochs.";
}
public Class getReturnType() {
return TwoEpochDemographicModel.class;
}
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private XMLSyntaxRule[] rules = new XMLSyntaxRule[]{
new ElementRule(EPOCH_1,
new XMLSyntaxRule[]{new ElementRule(DemographicModel.class)},
"The demographic model for the recent epoch."),
new ElementRule(EPOCH_2,
new XMLSyntaxRule[]{new ElementRule(DemographicModel.class)},
"The demographic model for the ancient epoch."),
new ElementRule(TRANSITION_TIME,
new XMLSyntaxRule[]{new ElementRule(Parameter.class)},
"The time that splits the two epochs."),
XMLUnits.SYNTAX_RULES[0]
};
}