/*
* MicrosatelliteModelSelectOperatorParser.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.operators;
import dr.inference.model.Parameter;
import dr.inference.operators.MCMCOperator;
import dr.evomodel.operators.MicrosatelliteModelSelectOperator;
import dr.xml.*;
/**
* Parser for MicrosatelliteModelSelectOperatorParser
*/
public class MicrosatelliteModelSelectOperatorParser extends AbstractXMLObjectParser {
public static final String MODEL_INDICATORS = "modelIndicators";
public static final String MODEL_CHOOSE = "modelChoose";
public String getParserName() {
return "msatModelSelectOperator";
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
double weight = xo.getDoubleAttribute(MCMCOperator.WEIGHT);
Parameter modelChoose = (Parameter)xo.getElementFirstChild(MODEL_CHOOSE);
XMLObject xoInd = xo.getChild(MODEL_INDICATORS);
int childNum = xoInd.getChildCount();
System.out.println("There are 12 potential models");
Parameter[] modelIndicators = new Parameter[childNum];
for(int i = 0; i < modelIndicators.length; i++){
modelIndicators[i] = (Parameter)xoInd.getChild(i);
}
return new MicrosatelliteModelSelectOperator(modelChoose, modelIndicators, weight);
}
//************************************************************************
// AbstractXMLObjectParser implementation
//************************************************************************
public String getParserDescription() {
return "This element returns a microsatellite averaging operator on a given parameter.";
}
public Class getReturnType() {
return MCMCOperator.class;
}
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private XMLSyntaxRule[] rules = new XMLSyntaxRule[]{
AttributeRule.newDoubleRule(MCMCOperator.WEIGHT),
new ElementRule(MODEL_CHOOSE, new XMLSyntaxRule[]{new ElementRule(Parameter.class)}),
new ElementRule(MODEL_INDICATORS, new XMLSyntaxRule[]{new ElementRule(Parameter.class,1,Integer.MAX_VALUE)}),
};
}