/*
* MarkovModulatedHiddenClassRewardParser.java
*
* Copyright (c) 2002-2016 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.substmodel;
import dr.evomodel.substmodel.MarkovModulatedSubstitutionModel;
import dr.evolution.datatype.HiddenDataType;
import dr.inference.model.Parameter;
import dr.xml.*;
/**
* @author Marc A. Suchard
*/
public class MarkovModulatedHiddenClassRewardParser extends AbstractXMLObjectParser {
public static final String PARSER_NAME = "hiddenClassRewardParameter";
public static final String NAME = "name";
public static final String CLASS_NUMBER = "class";
@Override
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
MarkovModulatedSubstitutionModel substitutionModel = (MarkovModulatedSubstitutionModel) xo.getChild(MarkovModulatedSubstitutionModel.class);
HiddenDataType hiddenDataType = (HiddenDataType) substitutionModel.getDataType();
int classNumber = xo.getIntegerAttribute(CLASS_NUMBER);
int hiddenClassCount = hiddenDataType.getHiddenClassCount();
if (classNumber < 1 || classNumber > hiddenClassCount) {
throw new XMLParseException("Invalid class number in " + xo.getId());
}
classNumber--; // Use zero-indexed number
int stateCount = hiddenDataType.getStateCount() / hiddenClassCount;
// Construct reward parameter
Parameter parameter = new Parameter.Default(stateCount * hiddenClassCount, 0.0);
for (int i = 0; i < stateCount; ++i) {
parameter.setParameterValue(i + classNumber * stateCount, 1.0);
}
if (xo.hasAttribute(NAME)) {
parameter.setId((String) xo.getAttribute(NAME));
} else {
parameter.setId(substitutionModel.getId() + "_" + Integer.toString(classNumber + 1));
}
return parameter;
}
/**
* @return an array of syntax rules required by this element.
* Order is not important.
*/
@Override
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private XMLSyntaxRule[] rules = {
AttributeRule.newIntegerRule(CLASS_NUMBER),
AttributeRule.newStringRule(NAME, true),
new ElementRule(MarkovModulatedSubstitutionModel.class),
};
@Override
public String getParserDescription() {
return "Generates a reward parameter to log hidden classes in Markov-modulated substitutionProcess";
}
@Override
public Class getReturnType() {
return Parameter.class;
}
/**
* @return Parser name, which is identical to name of xml element parsed by it.
*/
public String getParserName() {
return PARSER_NAME;
}
}