/*
* CompoundSymmetricMatrixParser.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.CompoundSymmetricMatrix;
import dr.inference.model.Parameter;
import dr.xml.*;
/**
*
*/
public class CompoundSymmetricMatrixParser extends AbstractXMLObjectParser {
public final static String MATRIX_PARAMETER = "compoundSymmetricMatrix";
public static final String DIAGONAL = "diagonal";
public static final String OFF_DIAGONAL = "offDiagonal";
public static final String AS_CORRELATION = "asCorrelation";
public String getParserName() {
return MATRIX_PARAMETER;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
XMLObject cxo = xo.getChild(DIAGONAL);
Parameter diagonalParameter = (Parameter) cxo.getChild(Parameter.class);
cxo = xo.getChild(OFF_DIAGONAL);
Parameter offDiagonalParameter = (Parameter) cxo.getChild(Parameter.class);
boolean asCorrelation = xo.getAttribute(AS_CORRELATION, false);
return new CompoundSymmetricMatrix(diagonalParameter, offDiagonalParameter, asCorrelation);
}
//************************************************************************
// AbstractXMLObjectParser implementation
//************************************************************************
public String getParserDescription() {
return "A diagonal matrix parameter constructed from its diagonals.";
}
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private XMLSyntaxRule[] rules = new XMLSyntaxRule[]{
new ElementRule(DIAGONAL,
new XMLSyntaxRule[]{new ElementRule(Parameter.class)}),
new ElementRule(OFF_DIAGONAL,
new XMLSyntaxRule[]{new ElementRule(Parameter.class)}),
AttributeRule.newBooleanRule(AS_CORRELATION, true)
};
public Class getReturnType() {
return CompoundSymmetricMatrix.class;
}
}