/*
* AlloppChangeNumHybridizationsParser.java
*
* Copyright (c) 2002-2017 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.evomodel.alloppnet.parsers;
import dr.evomodel.alloppnet.operators.AlloppChangeNumHybridizations;
import dr.evomodel.alloppnet.speciation.AlloppSpeciesBindings;
import dr.evomodel.alloppnet.speciation.AlloppSpeciesNetworkModel;
import dr.inference.operators.MCMCOperator;
import dr.xml.*;
/**
* Created with IntelliJ IDEA.
* User: Graham
* Date: 22/07/12
* Time: 11:24
*/
public class AlloppChangeNumHybridizationsParser extends AbstractXMLObjectParser {
public static final String CHANGE_NUM_HYBRIDIZATIONS = "changeNumHybridizations";
public String getParserName() {
return CHANGE_NUM_HYBRIDIZATIONS;
}
@Override
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
AlloppSpeciesBindings apsp = (AlloppSpeciesBindings) xo.getChild(AlloppSpeciesBindings.class);
AlloppSpeciesNetworkModel apspnet = (AlloppSpeciesNetworkModel) xo.getChild(AlloppSpeciesNetworkModel.class);
if (apspnet.getOneHybridization()) {
throw new XMLParseException("oneHybridization is set to true but there is a changeNumHybridizations operator");
}
final double weight = xo.getDoubleAttribute(MCMCOperator.WEIGHT);
return new AlloppChangeNumHybridizations(apspnet, apsp, weight);
}
@Override
public XMLSyntaxRule[] getSyntaxRules() {
return new XMLSyntaxRule[]{
AttributeRule.newDoubleRule(MCMCOperator.WEIGHT),
new ElementRule(AlloppSpeciesBindings.class),
new ElementRule(AlloppSpeciesNetworkModel.class)
};
}
@Override
public String getParserDescription() {
return "Operator which changes the number of tetraploid subtrees (hybridizations) by merging and splitting them.";
}
@Override
public Class getReturnType() {
return AlloppChangeNumHybridizations.class;
}
}