/* * LogRandomWalkOperatorParser.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.model.Parameter; import dr.inference.operators.CoercableMCMCOperator; import dr.inference.operators.CoercionMode; import dr.inference.operators.LogRandomWalkOperator; import dr.inference.operators.MCMCOperator; import dr.xml.*; /** */ public class LogRandomWalkOperatorParser extends AbstractXMLObjectParser { public static final String LOGRANDOMWALK_OPERATOR = "logRandomWalkOperator"; // Use same attributes as scale operator to help users public static final String SCALE_ALL = ScaleOperatorParser.SCALE_ALL; public static final String SCALE_ALL_IND = ScaleOperatorParser.SCALE_ALL_IND; public static final String WINDOW_SIZE = "window"; public String getParserName() { return LOGRANDOMWALK_OPERATOR; } public Object parseXMLObject(XMLObject xo) throws XMLParseException { CoercionMode mode = CoercionMode.parseMode(xo); final double weight = xo.getDoubleAttribute(MCMCOperator.WEIGHT); final double size = xo.getDoubleAttribute(WINDOW_SIZE); final boolean scaleAll = xo.getAttribute(SCALE_ALL, false); final boolean scaleAllInd = xo.getAttribute(SCALE_ALL_IND, false); if( size <= 0.0 ) { throw new XMLParseException("size must be positive"); } final Parameter parameter = (Parameter) xo.getChild(Parameter.class); return new LogRandomWalkOperator(parameter, size, mode, weight, scaleAll, scaleAllInd); } //************************************************************************ // AbstractXMLObjectParser implementation //************************************************************************ public String getParserDescription() { return "This element returns a scale operator on a given parameter."; } public Class getReturnType() { return LogRandomWalkOperator.class; } public XMLSyntaxRule[] getSyntaxRules() { return rules; } private final XMLSyntaxRule[] rules = { AttributeRule.newDoubleRule(WINDOW_SIZE), AttributeRule.newDoubleRule(MCMCOperator.WEIGHT), AttributeRule.newBooleanRule(CoercableMCMCOperator.AUTO_OPTIMIZE, true), AttributeRule.newBooleanRule(SCALE_ALL, true), AttributeRule.newBooleanRule(SCALE_ALL_IND, true), new ElementRule(Parameter.class), }; }