/*
* PearsonCorrelationParser.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.evoxml;
import dr.xml.*;
import dr.inference.model.Parameter;
import dr.inference.model.PearsonCorrelation;
/**
* @author Simon Greenhill
*/
public class PearsonCorrelationParser extends AbstractXMLObjectParser {
public static final String PEARSON_CORRELATION = "pearsonCorrelation";
public static final String LOG = "log";
public String getParserName() { return PEARSON_CORRELATION; }
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
boolean log = xo.getAttribute(LOG, false);
Parameter X = (Parameter)xo.getChild(0);
Parameter Y = (Parameter)xo.getChild(1);
// System.out.println("Correlating " + X + " with " + Y + " using log = " + log);
PearsonCorrelation pearsonCorrelation = new PearsonCorrelation(X, Y, log);
return pearsonCorrelation;
}
//************************************************************************
// AbstractXMLObjectParser implementation
//************************************************************************
public String getParserDescription() {
return "A Pearson Correlation between two Parameters";
}
public String getExample() {
return "<pearsonCorrelation id=\"r\" log=\"true\">\n"+
" <parameter idref=\"param1\"/>\n"+
" <parameter idref=\"param2\"/>\n"+
"</pearsonCorrelation>\n";
}
public Class getReturnType() { return PearsonCorrelation.class; }
public XMLSyntaxRule[] getSyntaxRules() { return rules; }
private final XMLSyntaxRule[] rules = {
// There should be two and only two Parameters (X & Y)
new ElementRule(Parameter.class, 2, 2),
// the optional log attribute has to be a Boolean
AttributeRule.newBooleanRule(LOG, true),
};
}