better masking parsing

src/dr/app/beast/development_parsers.properties

@@ -339,6 +339,7 @@ dr.evomodel.treedatalikelihood.continuous.IntegratedFactorAnalysisLikelihoodPars
 # Shrinkage
 dr.inference.model.MaskFromTree
 dr.inferencexml.distribution.shrinkage.JointBayesianBridgeStatisticsParser
+dr.inferencexml.model.MaskingParser
 
 # HMC
 dr.inferencexml.hmc.CompoundPriorPreconditionerParser

src/dr/inferencexml/model/MaskedParameterParser.java

@@ -82,8 +82,7 @@ public Object parseXMLObject(XMLObject xo) throws XMLParseException {
                 }
             }
             Logger.getLogger("dr.inferencexml.model").info("Found in total " + total + " missing values\n");
-        }
-        else {
+        } else {
             int from = xo.getAttribute(FROM, 1) - 1;
             int to = xo.getAttribute(TO, parameter.getDimension()) - 1;
             int every = xo.getAttribute(EVERY, 1);

src/dr/inferencexml/model/MaskingParser.java

@@ -0,0 +1,103 @@
+/*
+ * MaskingParser.java
+ *
+ * Copyright (c) 2002-2023 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.model;
+
+import dr.inference.model.Parameter;
+import dr.xml.*;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+/**
+ * @author Marc A. Suchard
+ */
+public class MaskingParser extends AbstractXMLObjectParser {
+
+    private static final String MASKING = "masking";
+    private static final String DIMENSION = "dimension";
+    private static final String NAME = "name";
+    private static final String COMPLEMENT = "complement";
+
+    public Object parseXMLObject(XMLObject xo) throws XMLParseException {
+
+        Parameter parameter = (Parameter) xo.getChild(Parameter.class);
+
+        List<String> names = new ArrayList<>();
+        for (XMLObject cxo : xo.getAllChildren(DIMENSION)) {
+            names.add(cxo.getStringAttribute(NAME));
+        }
+
+        Map<String,Integer> dimMap = new HashMap<>();
+        for (int i = 0; i < parameter.getDimension(); ++i) {
+            String n = parameter.getDimensionName(i);
+            dimMap.put(n, i);
+        }
+
+        for (String name : names) {
+            if (dimMap.containsKey(name)) {
+                int index = dimMap.get(name);
+                parameter.setParameterValue(index, 1);
+            } else {
+                throw new XMLParseException("Dimension '" + name + "' not found");
+
+            }
+        }
+
+        if (xo.getAttribute(COMPLEMENT, false)) {
+            for (int i = 0; i < parameter.getDimension(); ++i) {
+                parameter.setParameterValue(i,1 - parameter.getParameterValue(i));
+            }
+        }
+
+        return parameter;
+    }
+
+    public XMLSyntaxRule[] getSyntaxRules() {
+        return rules;
+    }
+
+    private final XMLSyntaxRule[] rules = {
+            new ElementRule(Parameter.class),
+            AttributeRule.newBooleanRule(COMPLEMENT, true),
+            new ElementRule(DIMENSION, new XMLSyntaxRule[]{
+                    AttributeRule.newStringRule(NAME),
+            }, 1, Integer.MAX_VALUE),
+    };
+
+    public String getParserDescription() {
+        return "A binary masking as a parameter.";
+    }
+
+    public Class getReturnType() {
+        return Parameter.class;
+    }
+
+    public String getParserName() {
+        return MASKING;
+    }
+}