/* * SimpleOperatorScheduleParser.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.operators; import dr.inference.operators.MCMCOperator; import dr.inference.operators.OperatorSchedule; import dr.inference.operators.SimpleOperatorSchedule; import dr.xml.*; import java.util.logging.Logger; /** * */ public class SimpleOperatorScheduleParser extends AbstractXMLObjectParser { public static final String OPERATOR_SCHEDULE = "operators"; public static final String SEQUENTIAL = "sequential"; public static final String OPTIMIZATION_SCHEDULE = "optimizationSchedule"; public static final String ACCEPTANCE_THRESHOLD = "minAcceptance"; public static final String USE_THRESHOLD = "minUsage"; public String getParserName() { return OPERATOR_SCHEDULE; } public Object parseXMLObject(XMLObject xo) throws XMLParseException { int useThreshold = xo.getAttribute(USE_THRESHOLD, 1000); double acceptanceThreshold = xo.getAttribute(ACCEPTANCE_THRESHOLD, 0.0); SimpleOperatorSchedule schedule = new SimpleOperatorSchedule(useThreshold, acceptanceThreshold); if (xo.hasAttribute(SEQUENTIAL)) { schedule.setSequential(xo.getBooleanAttribute(SEQUENTIAL)); } if (xo.hasAttribute(OPTIMIZATION_SCHEDULE)) { String type = xo.getStringAttribute(OPTIMIZATION_SCHEDULE); Logger.getLogger("dr.inference").info("Optimization Schedule: " + type); try { schedule.setOptimizationSchedule(OperatorSchedule.OptimizationTransform.valueOf(type.toUpperCase())); } catch (IllegalArgumentException iae) { throw new RuntimeException("Unsupported optimization schedule"); } } for (int i = 0; i < xo.getChildCount(); i++) { Object child = xo.getChild(i); if (child instanceof MCMCOperator) { schedule.addOperator((MCMCOperator) child); } } return schedule; } //************************************************************************ // AbstractXMLObjectParser implementation //************************************************************************ public XMLSyntaxRule[] getSyntaxRules() { return rules; } private final XMLSyntaxRule[] rules = { AttributeRule.newBooleanRule(SEQUENTIAL, true), new ElementRule(MCMCOperator.class, 1, Integer.MAX_VALUE), AttributeRule.newStringRule(OPTIMIZATION_SCHEDULE, true), AttributeRule.newDoubleRule(ACCEPTANCE_THRESHOLD, true, "Acceptance rate below which an operator will be switched off"), AttributeRule.newIntegerRule(USE_THRESHOLD, true, "Minimum number of usage before testing acceptance threshold") }; public String getParserDescription() { return "A simple operator scheduler"; } public Class getReturnType() { return SimpleOperatorSchedule.class; } }