/*
* RandomWalkIntegerSetSizeWeightedOperatorParser.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.xml.*;
import dr.inference.operators.MCMCOperator;
import dr.evomodel.operators.RandomWalkIntegerSetSizeWeightedOperator;
import dr.inference.model.Parameter;
import dr.evomodel.tree.MicrosatelliteSamplerTreeModel;
/**
* @author Chieh-Hsi Wu
*
* This is the parser for the random walk integer set size weighted operator.
*/
public class RandomWalkIntegerSetSizeWeightedOperatorParser extends AbstractXMLObjectParser {
public static final String RANDOM_WALK_INT_SET_SIZE_WGT_OP = "randomWalkIntegerSetSizeWeightedOperator";
public static final String WINDOW_SIZE = "windowSize";
public static final String BASE_SET_SIZE = "baseSetSize";
public String getParserName() {
return RANDOM_WALK_INT_SET_SIZE_WGT_OP;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
double weight = xo.getDoubleAttribute(MCMCOperator.WEIGHT);
double d = xo.getDoubleAttribute(WINDOW_SIZE);
if (d != Math.floor(d)) {
throw new XMLParseException("The window size of a " + RANDOM_WALK_INT_SET_SIZE_WGT_OP + " should be an integer");
}
double baseSetSize = xo.getDoubleAttribute(BASE_SET_SIZE);
int windowSize = (int)d;
Parameter parameter = (Parameter) xo.getChild(Parameter.class);
MicrosatelliteSamplerTreeModel msatSampleTreeModel = (MicrosatelliteSamplerTreeModel)xo.getChild(MicrosatelliteSamplerTreeModel.class);
return new RandomWalkIntegerSetSizeWeightedOperator(parameter, windowSize, weight, msatSampleTreeModel, baseSetSize);
}
public String getParserDescription() {
return "This element returns a random walk set size weighted operator on a given parameter.";
}
public Class getReturnType() {
return RandomWalkIntegerSetSizeWeightedOperator.class;
}
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private XMLSyntaxRule[] rules = new XMLSyntaxRule[]{
AttributeRule.newDoubleRule(WINDOW_SIZE),
AttributeRule.newDoubleRule(MCMCOperator.WEIGHT),
AttributeRule.newDoubleRule(BASE_SET_SIZE),
new ElementRule(Parameter.class),
new ElementRule(MicrosatelliteSamplerTreeModel.class)
};
}