/*
* FunkyPriorMixerOperatorParser.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.FunkyPriorMixerOperator;
import dr.evomodel.tree.TreeModel;
import dr.inference.model.Parameter;
import dr.inference.operators.CoercableMCMCOperator;
import dr.inference.operators.CoercionMode;
import dr.inference.operators.MCMCOperator;
import dr.inference.operators.RandomWalkOperator;
import dr.xml.*;
/**
* @author Marc A. Suchard
* @author John J. Welch
*/
public class FunkyPriorMixerOperatorParser extends AbstractXMLObjectParser {
public static final String FUNKY_OPERATOR = "funkyPriorMixerOperator";
public static final String WINDOW_SIZE = "windowSize";
public static final String UPPER = "upper";
public static final String LOWER = "lower";
public static final String BOUNDARY_CONDITION = "boundaryCondition";
public String getParserName() {
return FUNKY_OPERATOR;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
CoercionMode mode = CoercionMode.parseMode(xo);
double weight = xo.getDoubleAttribute(MCMCOperator.WEIGHT);
double windowSize = xo.getDoubleAttribute(WINDOW_SIZE);
Parameter parameter = (Parameter) xo.getChild(Parameter.class);
TreeModel treeModel = (TreeModel) xo.getChild(TreeModel.class);
RandomWalkOperator.BoundaryCondition condition = RandomWalkOperator.BoundaryCondition.valueOf(
xo.getAttribute(BOUNDARY_CONDITION, RandomWalkOperator.BoundaryCondition.reflecting.name()));
return new FunkyPriorMixerOperator(treeModel, parameter, windowSize, condition, weight, mode);
}
//************************************************************************
// AbstractXMLObjectParser implementation
//************************************************************************
public String getParserDescription() {
return "This element returns a random walk operator on a given parameter.";
}
public Class getReturnType() {
return MCMCOperator.class;
}
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private final XMLSyntaxRule[] rules = {
AttributeRule.newDoubleRule(WINDOW_SIZE),
AttributeRule.newDoubleRule(MCMCOperator.WEIGHT),
AttributeRule.newBooleanRule(CoercableMCMCOperator.AUTO_OPTIMIZE, true),
new StringAttributeRule(BOUNDARY_CONDITION, null, RandomWalkOperator.BoundaryCondition.values(), true),
new ElementRule(Parameter.class),
new ElementRule(TreeModel.class)
};
}