/*
* ExchangeOperatorParser.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.evomodel.operators.ExchangeOperator;
import dr.evomodel.tree.TreeModel;
import dr.inference.operators.MCMCOperator;
import dr.xml.*;
/**
*/
public class ExchangeOperatorParser {
public static final String NARROW_EXCHANGE = "narrowExchange";
public static final String WIDE_EXCHANGE = "wideExchange";
public static XMLObjectParser NARROW_EXCHANGE_OPERATOR_PARSER = new AbstractXMLObjectParser() {
public String getParserName() {
return NARROW_EXCHANGE;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
final TreeModel treeModel = (TreeModel) xo.getChild(TreeModel.class);
final double weight = xo.getDoubleAttribute(MCMCOperator.WEIGHT);
return new ExchangeOperator(ExchangeOperator.NARROW, treeModel, weight);
}
// ************************************************************************
// AbstractXMLObjectParser implementation
// ************************************************************************
public String getParserDescription() {
return "This element represents a narrow exchange operator. "
+ "This operator swaps a random subtree with its uncle.";
}
public Class getReturnType() {
return ExchangeOperator.class;
}
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private final XMLSyntaxRule[] rules = {
AttributeRule.newDoubleRule(MCMCOperator.WEIGHT),
new ElementRule(TreeModel.class)
};
};
public static XMLObjectParser WIDE_EXCHANGE_OPERATOR_PARSER = new AbstractXMLObjectParser() {
public String getParserName() {
return WIDE_EXCHANGE;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
final TreeModel treeModel = (TreeModel) xo.getChild(TreeModel.class);
if (treeModel.getExternalNodeCount() <= 2) {
throw new XMLParseException("Tree with fewer than 3 taxa");
}
final double weight = xo.getDoubleAttribute(MCMCOperator.WEIGHT);
return new ExchangeOperator(ExchangeOperator.WIDE, treeModel, weight);
}
// ************************************************************************
// AbstractXMLObjectParser implementation
// ************************************************************************
public String getParserDescription() {
return "This element represents a wide exchange operator. "
+ "This operator swaps two random subtrees.";
}
public Class getReturnType() {
return ExchangeOperator.class;
}
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private final XMLSyntaxRule[] rules;{
rules = new XMLSyntaxRule[]{
AttributeRule.newDoubleRule(MCMCOperator.WEIGHT),
new ElementRule(TreeModel.class)
};
}
};
}