/* * CenteredScaleOperatorParser.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.CenteredScaleOperator; import dr.inference.operators.CoercableMCMCOperator; import dr.inference.operators.CoercionMode; import dr.inference.operators.MCMCOperator; import dr.xml.*; /** */ public class CenteredScaleOperatorParser extends AbstractXMLObjectParser { public static final String CENTERED_SCALE = "centeredScale"; public static final String SCALE_FACTOR = "scaleFactor"; public String getParserName() { return CENTERED_SCALE; } public Object parseXMLObject(XMLObject xo) throws XMLParseException { Parameter parameter = (Parameter) xo.getChild(Parameter.class); double scale = xo.getDoubleAttribute(SCALE_FACTOR); double weight = xo.getDoubleAttribute(MCMCOperator.WEIGHT); CenteredScaleOperator op = new CenteredScaleOperator(parameter); op.setWeight(weight); op.scaleFactor = scale; op.mode = CoercionMode.parseMode(xo); return op; } public String getParserDescription() { return "A centered-scale operator. This operator scales the the values of a multi-dimensional parameter so as to perserve the mean. It does this by expanding or conrtacting the parameter values around the mean."; } public Class getReturnType() { return CenteredScaleOperator.class; } public XMLSyntaxRule[] getSyntaxRules() { return rules; } private XMLSyntaxRule[] rules = new XMLSyntaxRule[]{ AttributeRule.newDoubleRule(MCMCOperator.WEIGHT), AttributeRule.newDoubleRule(SCALE_FACTOR), AttributeRule.newBooleanRule(CoercableMCMCOperator.AUTO_OPTIMIZE, true), new ElementRule(Parameter.class) }; }