/*
* LogRandomWalkOperatorParser.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.inferencexml.operators;
import dr.inference.model.Parameter;
import dr.inference.operators.CoercableMCMCOperator;
import dr.inference.operators.CoercionMode;
import dr.inference.operators.LogRandomWalkOperator;
import dr.inference.operators.MCMCOperator;
import dr.xml.*;
/**
*/
public class LogRandomWalkOperatorParser extends AbstractXMLObjectParser {
public static final String LOGRANDOMWALK_OPERATOR = "logRandomWalkOperator";
// Use same attributes as scale operator to help users
public static final String SCALE_ALL = ScaleOperatorParser.SCALE_ALL;
public static final String SCALE_ALL_IND = ScaleOperatorParser.SCALE_ALL_IND;
public static final String WINDOW_SIZE = "window";
public String getParserName() {
return LOGRANDOMWALK_OPERATOR;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
CoercionMode mode = CoercionMode.parseMode(xo);
final double weight = xo.getDoubleAttribute(MCMCOperator.WEIGHT);
final double size = xo.getDoubleAttribute(WINDOW_SIZE);
final boolean scaleAll = xo.getAttribute(SCALE_ALL, false);
final boolean scaleAllInd = xo.getAttribute(SCALE_ALL_IND, false);
if( size <= 0.0 ) {
throw new XMLParseException("size must be positive");
}
final Parameter parameter = (Parameter) xo.getChild(Parameter.class);
return new LogRandomWalkOperator(parameter, size, mode, weight, scaleAll, scaleAllInd);
}
//************************************************************************
// AbstractXMLObjectParser implementation
//************************************************************************
public String getParserDescription() {
return "This element returns a scale operator on a given parameter.";
}
public Class getReturnType() {
return LogRandomWalkOperator.class;
}
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private final XMLSyntaxRule[] rules = {
AttributeRule.newDoubleRule(WINDOW_SIZE),
AttributeRule.newDoubleRule(MCMCOperator.WEIGHT),
AttributeRule.newBooleanRule(CoercableMCMCOperator.AUTO_OPTIMIZE, true),
AttributeRule.newBooleanRule(SCALE_ALL, true),
AttributeRule.newBooleanRule(SCALE_ALL_IND, true),
new ElementRule(Parameter.class),
};
}