/* * GeneralF81ModelParser.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.oldevomodelxml.substmodel; import dr.oldevomodel.substmodel.FrequencyModel; import dr.oldevomodel.substmodel.GeneralF81Model; import dr.xml.*; import java.util.logging.Logger; /** * Parses a GeneralF81Model */ public class GeneralF81ModelParser extends AbstractXMLObjectParser { public static final String GENERAL_F81_MODEL = "generalF81Model"; public static final String FREQUENCIES = "frequencies"; public String getParserName() { return GENERAL_F81_MODEL; } public Object parseXMLObject(XMLObject xo) throws XMLParseException { FrequencyModel freqModel = null; if (xo.hasChildNamed(FREQUENCIES)) { XMLObject cxo = xo.getChild(FREQUENCIES); freqModel = (FrequencyModel) cxo.getChild(FrequencyModel.class); } Logger.getLogger("dr.evomodel").info(" General F81 Model from frequencyModel '"+ freqModel.getId() + "' (stateCount=" + freqModel.getFrequencyCount() + ")"); return new GeneralF81Model(freqModel); } //************************************************************************ // AbstractXMLObjectParser implementation //************************************************************************ public String getParserDescription() { return "A general F81 model for an arbitrary number of states."; } public Class getReturnType() { return GeneralF81ModelParser.class; } public XMLSyntaxRule[] getSyntaxRules() { return rules; } private final XMLSyntaxRule[] rules = { new ElementRule(FREQUENCIES, FrequencyModel.class) }; }