/* * RandomWalkIntegerNodeHeightWeightedOperatorParser.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.operators; import dr.xml.*; import dr.inference.operators.MCMCOperator; import dr.evomodel.operators.RandomWalkIntegerNodeHeightWeightedOperator; import dr.inference.model.Parameter; /** * @author Chieh-Hsi Wu * * The parser for random walk integer node height weighted operator. */ public class RandomWalkIntegerNodeHeightWeightedOperatorParser extends AbstractXMLObjectParser { public static final String RANDOM_WALK_INT_NODE_HEIGHT_WGT_OP = "randomWalkIntegerNodeHeightWeightedOperator"; public static final String WINDOW_SIZE = "windowSize"; public static final String INTERNAL_NODE_HEIGHTS = "internalNodeHeights"; public String getParserName() { return RANDOM_WALK_INT_NODE_HEIGHT_WGT_OP; } public Object parseXMLObject(XMLObject xo) throws XMLParseException { double weight = xo.getDoubleAttribute(MCMCOperator.WEIGHT); double d = xo.getDoubleAttribute(WINDOW_SIZE); if (d != Math.floor(d)) { throw new XMLParseException("The window size of a " + RANDOM_WALK_INT_NODE_HEIGHT_WGT_OP + " should be an integer"); } int windowSize = (int)d; Parameter parameter = (Parameter) xo.getChild(Parameter.class); Parameter internalNodeHeights = (Parameter)xo.getElementFirstChild(INTERNAL_NODE_HEIGHTS); return new RandomWalkIntegerNodeHeightWeightedOperator(parameter, windowSize, weight, internalNodeHeights); } public String getParserDescription() { return "This element returns a random walk node height weighted operator on a given parameter."; } public Class getReturnType() { return RandomWalkIntegerNodeHeightWeightedOperator.class; } public XMLSyntaxRule[] getSyntaxRules() { return rules; } private XMLSyntaxRule[] rules = new XMLSyntaxRule[]{ AttributeRule.newDoubleRule(WINDOW_SIZE), AttributeRule.newDoubleRule(MCMCOperator.WEIGHT), new ElementRule(Parameter.class), new ElementRule(INTERNAL_NODE_HEIGHTS, new XMLSyntaxRule[]{new ElementRule(Parameter.class)}) }; }