/* * GaussianProcessSkytrackBlockUpdateOperatorParser.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.evomodelxml.coalescent.operators; import dr.evomodel.coalescent.GaussianProcessSkytrackLikelihood; import dr.evomodel.coalescent.operators.GaussianProcessSkytrackBlockUpdateOperator; import dr.inference.operators.CoercableMCMCOperator; import dr.inference.operators.CoercionMode; import dr.inference.operators.MCMCOperator; import dr.math.MathUtils; import dr.xml.*; import java.io.IOException; import java.util.logging.*; /** * */ public class GaussianProcessSkytrackBlockUpdateOperatorParser extends AbstractXMLObjectParser { public static final String BLOCK_UPDATE_OPERATOR = "gpBlockUpdateOperator"; public static final String SCALE_FACTOR = "scaleFactor"; public static final String MAX_ITERATIONS = "maxIterations"; public static final String STOP_VALUE = "stopValue"; public static final String KEEP_LOG_RECORD = "keepLogRecord"; public static final String OLD_SKYRIDE = "oldSkyride"; public String getParserName() { return BLOCK_UPDATE_OPERATOR; } public Object parseXMLObject(XMLObject xo) throws XMLParseException { boolean logRecord = xo.getAttribute(KEEP_LOG_RECORD, false); Handler gmrfHandler; Logger gmrfLogger = Logger.getLogger("dr.evomodel.coalescent.operators.GaussianProcessSkytrackBlockUpdateOperator"); gmrfLogger.setUseParentHandlers(false); if (logRecord) { gmrfLogger.setLevel(Level.FINE); try { gmrfHandler = new FileHandler("GPBlockUpdate.log." + MathUtils.getSeed()); } catch (IOException e) { throw new RuntimeException(e.getMessage()); } gmrfHandler.setLevel(Level.FINE); gmrfHandler.setFormatter(new XMLFormatter() { public String format(LogRecord record) { return "<record>\n \t<message>\n\t" + record.getMessage() + "\n\t</message>\n<record>\n"; } }); gmrfLogger.addHandler(gmrfHandler); } CoercionMode mode = CoercionMode.parseMode(xo); if (mode == CoercionMode.DEFAULT) mode = CoercionMode.COERCION_ON; double weight = xo.getDoubleAttribute(MCMCOperator.WEIGHT); double scaleFactor = xo.getDoubleAttribute(SCALE_FACTOR); // if (scaleFactor <= 0.0) { // throw new XMLParseException("scaleFactor must be greater than 0.0"); if (scaleFactor < 1.0) { throw new XMLParseException("scaleFactor must be greater than or equal to 1.0"); } int maxIterations = xo.getAttribute(MAX_ITERATIONS, 200); double stopValue = xo.getAttribute(STOP_VALUE, 0.01); if (xo.getAttribute(OLD_SKYRIDE, true)) { GaussianProcessSkytrackLikelihood gpLikelihood = (GaussianProcessSkytrackLikelihood) xo.getChild(GaussianProcessSkytrackLikelihood.class); return new GaussianProcessSkytrackBlockUpdateOperator(gpLikelihood, weight, mode, scaleFactor, maxIterations, stopValue); }else{ GaussianProcessSkytrackLikelihood gpLikelihood = (GaussianProcessSkytrackLikelihood) xo.getChild(GaussianProcessSkytrackLikelihood.class); return new GaussianProcessSkytrackBlockUpdateOperator(gpLikelihood, weight, mode, scaleFactor, maxIterations, stopValue); } } //************************************************************************ // AbstractXMLObjectParser implementation //************************************************************************ public String getParserDescription() { return "This element returns a GP block-update operator for the joint distribution of the population sizes and precision parameter."; } public Class getReturnType() { return GaussianProcessSkytrackBlockUpdateOperator.class; // return MCMCOperator.class; } public XMLSyntaxRule[] getSyntaxRules() { return rules; } private XMLSyntaxRule[] rules = new XMLSyntaxRule[]{ AttributeRule.newDoubleRule(SCALE_FACTOR), AttributeRule.newDoubleRule(MCMCOperator.WEIGHT), AttributeRule.newBooleanRule(CoercableMCMCOperator.AUTO_OPTIMIZE, true), AttributeRule.newDoubleRule(STOP_VALUE, true), AttributeRule.newIntegerRule(MAX_ITERATIONS, true), AttributeRule.newBooleanRule(OLD_SKYRIDE, true), new ElementRule(GaussianProcessSkytrackLikelihood.class) }; }