/*
* EmergingEpidemicModelParser.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.tree.Tree;
import dr.evolution.util.Units;
import dr.evomodel.coalescent.EmergingEpidemicModel;
import dr.evomodel.coalescent.ExponentialGrowthModel;
import dr.evomodel.tree.TreeModel;
import dr.evoxml.util.XMLUnits;
import dr.inference.model.Parameter;
import dr.xml.*;
/**
* Parser for the EmergingEpidemic exponential model.
*/
public class EmergingEpidemicModelParser extends AbstractXMLObjectParser {
public static String EMERGING_EPIDEMIC_MODEL = "emergingEpidemic";
// the parameters
public static String GROWTH_RATE = "growthRate";
public static String GENERATION_TIME = "generationTime";
public static String GENERATION_DISTRIBUTION_SHAPE = "generationShape";
public static String OFFSPRING_DISPERSION = "offspringDispersion";
public static String TREE = "epidemicTree";
public String getParserName() {
return EMERGING_EPIDEMIC_MODEL;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
Units.Type units = XMLUnits.Utils.getUnitsAttr(xo);
Parameter growthRateParameter = (Parameter)xo.getElementFirstChild(GROWTH_RATE);
Parameter generationTimeParameter = (Parameter)xo.getElementFirstChild(GENERATION_TIME);
Parameter generationShapeParameter = (Parameter)xo.getElementFirstChild(GENERATION_DISTRIBUTION_SHAPE);
Parameter offspringDispersionParameter = (Parameter)xo.getElementFirstChild(OFFSPRING_DISPERSION);
TreeModel tree = (TreeModel)xo.getElementFirstChild(TREE);
return new EmergingEpidemicModel(growthRateParameter, generationTimeParameter, generationShapeParameter, offspringDispersionParameter, tree, units);
}
//************************************************************************
// AbstractXMLObjectParser implementation
//************************************************************************
public String getParserDescription() {
return "A self-consistent model of emerging epidemics.";
}
public Class getReturnType() {
return EmergingEpidemicModel.class;
}
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private XMLSyntaxRule[] rules = new XMLSyntaxRule[]{
new ElementRule(GROWTH_RATE, Parameter.class),
new ElementRule(GENERATION_TIME, Parameter.class),
new ElementRule(GENERATION_DISTRIBUTION_SHAPE, Parameter.class),
new ElementRule(OFFSPRING_DISPERSION, Parameter.class),
new ElementRule(TREE, Tree.class),
XMLUnits.SYNTAX_RULES[0]
};
}