[beast-mcmc] r6750 committed - Added parser for SwapParameterOperator

[beast...@googlecode.com]

Revision: 6750
Author: msuchard
Date: Thu Apr 23 23:25:57 2015 UTC
Log: Added parser for SwapParameterOperator
https://code.google.com/p/beast-mcmc/source/detail?r=6750

Added:
/trunk/src/dr/inferencexml/operators/SwapParameterOperatorParser.java
Modified:
/trunk/src/dr/app/beast/development_parsers.properties

=======================================
--- /dev/null
+++ /trunk/src/dr/inferencexml/operators/SwapParameterOperatorParser.java
Thu Apr 23 23:25:57 2015 UTC
@@ -0,0 +1,79 @@
+/*
+ * SwapParameterOperatorParser.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.SwapParameterOperator;
+import dr.xml.*;
+
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ */
+public class SwapParameterOperatorParser extends AbstractXMLObjectParser {
+
+ public final static String SWAP_OPERATOR = "swapParameterOperator";
+
+ public String getParserName() {
+ return SWAP_OPERATOR;
+ }
+
+ public Object parseXMLObject(XMLObject xo) throws XMLParseException {
+
+ List<Parameter> parameterList = new ArrayList<Parameter>();
+
+ for (int i = 0; i < xo.getChildCount(); ++i) {
+ parameterList.add((Parameter) xo.getChild(i));
+ }
+
+ double weight = xo.getDoubleAttribute("weight");
+
+ return new SwapParameterOperator(parameterList, weight);
+ }
+
+
//************************************************************************
+ // AbstractXMLObjectParser implementation
+
//************************************************************************
+
+ public String getParserDescription() {
+ return "This element represents an operator that swaps values in a
multi-dimensional parameter.";
+ }
+
+ public Class getReturnType() {
+ return SwapParameterOperator.class;
+ }
+
+ public XMLSyntaxRule[] getSyntaxRules() {
+ return rules;
+ }
+
+ private XMLSyntaxRule[] rules = new XMLSyntaxRule[]{
+ AttributeRule.newDoubleRule("weight"),
+ new ElementRule(Parameter.class, 2, Integer.MAX_VALUE)
+ };
+
+}
=======================================
--- /trunk/src/dr/app/beast/development_parsers.properties Tue Apr 7
10:03:54 2015 UTC
+++ /trunk/src/dr/app/beast/development_parsers.properties Thu Apr 23
23:25:57 2015 UTC
@@ -117,6 +117,7 @@
# SIMULATION STUDIES
dr.evoxml.RandomSubsetTaxaParser
dr.evomodel.continuous.TreeTraitSimulator
+dr.inferencexml.operators.SwapParameterOperatorParser

#OPERATORS
dr.inferencexml.operators.MsatFullAncestryImportanceSamplingOperatorParser