/*
* HierarchicalGraphLikelihoodParser.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.distribution;
import dr.inference.distribution.HierarchicalGraphLikelihood;
import dr.inference.model.Likelihood;
import dr.inference.model.MatrixParameter;
import dr.inference.model.Parameter;
import dr.xml.*;
/**
* @author Gabriela Cybis
*/
public class HierarchicalGraphLikelihoodParser extends AbstractXMLObjectParser {
public static final String HIERARCHICAL_INDICATOR = "hierarchicalIndicator";
public static final String STRATA_INDICATOR = "strataIndicator";
public static final String PROB = "prob";
public String getParserName() {
return HierarchicalGraphLikelihood.HIERARCHICAL_GRAPH_LIKELIHOOD;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
XMLObject cxo = xo.getChild(HIERARCHICAL_INDICATOR);
Parameter hierarchicalIndicator = (Parameter) cxo.getChild(Parameter.class);
cxo = xo.getChild(STRATA_INDICATOR);
MatrixParameter strataIndicatorMatrix = new MatrixParameter("matrix");
int dim = 0;
for (int i = 0; i < cxo.getChildCount(); i++) {
Parameter parameter = (Parameter) cxo.getChild(i);
strataIndicatorMatrix.addParameter(parameter);
if (i == 0)
dim = parameter.getDimension();
else if (dim != parameter.getDimension())
throw new XMLParseException("All parameters must have the same dimension to construct a rectangular matrix");
}
if (hierarchicalIndicator.getDimension()!= strataIndicatorMatrix.getRowDimension())
throw new XMLParseException("Hierarchical and starta parameters don't have the same dimentions");
cxo = xo.getChild(PROB);
Parameter prob = (Parameter) cxo.getChild(Parameter.class);
return new HierarchicalGraphLikelihood(hierarchicalIndicator, strataIndicatorMatrix, prob);
}
//************************************************************************
// AbstractXMLObjectParser implementation
//************************************************************************
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private final XMLSyntaxRule[] rules = {
new ElementRule(HIERARCHICAL_INDICATOR,
new XMLSyntaxRule[]{new ElementRule(Parameter.class)}),
new ElementRule(STRATA_INDICATOR,
new XMLSyntaxRule[]{new ElementRule(Parameter.class, 1, Integer.MAX_VALUE)}),
new ElementRule(PROB,
new XMLSyntaxRule[]{new ElementRule(Parameter.class)}),
};
public String getParserDescription() {
return "Calculates the likelihood of strata graph given hierarchical graph and p.";
}
public Class getReturnType() {
return Likelihood.class;
}
}