/* * LikelihoodBenchmarkerParser.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.Likelihood; import dr.inference.model.LikelihoodBenchmarker; import dr.xml.*; import java.util.ArrayList; import java.util.List; /** */ public class LikelihoodBenchmarkerParser extends AbstractXMLObjectParser { public static final String BENCHMARKER = "benchmarker"; public String getParserName() { return BENCHMARKER; } public Object parseXMLObject(XMLObject xo) throws XMLParseException { int iterationCount = 1000; if (xo.hasAttribute("iterationCount")) { iterationCount = xo.getIntegerAttribute("iterationCount"); } List<Likelihood> likelihoods = new ArrayList<Likelihood>(); for (int i = 0; i < xo.getChildCount(); i++) { Object xco = xo.getChild(i); if (xco instanceof Likelihood) { likelihoods.add((Likelihood) xco); } } if (likelihoods.size() == 0) { throw new XMLParseException("No likelihoods for benchmarking"); } return new LikelihoodBenchmarker(likelihoods, iterationCount); } //************************************************************************ // AbstractXMLObjectParser implementation //************************************************************************ public String getParserDescription() { return "This element runs a benchmark on a series of likelihood calculators."; } public Class getReturnType() { return Likelihood.class; } public XMLSyntaxRule[] getSyntaxRules() { return rules; } private final XMLSyntaxRule[] rules = { AttributeRule.newIntegerRule("iterationCount"), new ElementRule(Likelihood.class, 1, Integer.MAX_VALUE) }; }