/*
* RPNcalculatorStatisticParser.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.model;
import dr.inference.model.RPNcalculatorStatistic;
import dr.inference.model.Statistic;
import dr.xml.*;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
/**
*/
public class RPNcalculatorStatisticParser extends AbstractXMLObjectParser {
public static String RPN_STATISTIC = "RPNcalculator";
public static String VARIABLE = "variable";
public static String EXPRESSION = "expression";
public String getParserName() { return RPN_STATISTIC; }
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
List<String> expressions = new ArrayList<String>();
List<String> expressionNames = new ArrayList<String>();
Map<String, Statistic> variables = new HashMap<String, Statistic>();
for(int i = 0; i < xo.getChildCount(); ++i) {
final XMLObject child = (XMLObject)xo.getChild(i);
if( child.getName().equals(EXPRESSION) ) {
expressions.add(child.getStringChild(0));
String name = child.hasAttribute(Statistic.NAME) ? child.getStringAttribute(Statistic.NAME) :
("expression_" + expressionNames.size());
expressionNames.add(name);
} else if( child.getName().equals(VARIABLE) ) {
Statistic s = (Statistic)child.getChild(Statistic.class);
if( s.getDimension() != 1 ) {
throw new XMLParseException("Sorry, no support for multi-dimentional yet");
}
//assert s.getDimension() == 1; // for now
String name = child.hasAttribute(Statistic.NAME) ? child.getStringAttribute(Statistic.NAME) :
s.getDimensionName(0);
variables.put(name, s);
} else {
throw new XMLParseException("Unknown element found in " + getParserName() + " element:" + child);
}
}
final String name = xo.hasAttribute(Statistic.NAME) ? xo.getStringAttribute(Statistic.NAME) : RPN_STATISTIC;
final String[] e = expressions.toArray(new String[expressions.size()]);
final String[] enames = expressionNames.toArray(new String[expressionNames.size()]);
try {
return new RPNcalculatorStatistic(name, e, enames, variables);
} catch ( RuntimeException err) {
throw new XMLParseException(err.getMessage());
}
}
public String getParserDescription() {
return "This element returns a statistic evaluated from arbitrary expression.";
}
public Class getReturnType() { return RPNcalculatorStatistic.class; }
public XMLSyntaxRule[] getSyntaxRules() { return rules; }
private final XMLSyntaxRule[] rules = {
new ElementRule(EXPRESSION,
new XMLSyntaxRule[] { new ElementRule(String.class) }, 1, Integer.MAX_VALUE),
new ElementRule(VARIABLE,
new XMLSyntaxRule[] { new ElementRule(Statistic.class) } , 1, Integer.MAX_VALUE)
};
}