Merge branch 'master' of https://github.com/beast-dev/beast-mcmc into…

… nonparametrics

src/dr/app/beast/release_parsers.properties

@@ -35,7 +35,7 @@ dr.evoxml.PatternSubSetParser
 dr.evoxml.AscertainedSitePatternsParser
 dr.evoxml.ConvertAlignmentParser
 dr.evoxml.MergePatternsParser
-dr.evoxml.MaskedPatternsParser
+dr.evoxml.MaskedAlignmentParser
 dr.evoxml.AttributePatternsParser
 dr.evoxml.RandomTaxaSampleParser
 dr.evoxml.ConstantPatternsParser

src/dr/evolution/alignment/MaskedAlignment.java

@@ -0,0 +1,47 @@
+/*
+ * MaskedAlignment.java
+ *
+ * Copyright © 2002-2024 the BEAST Development Team
+ * http://beast.community/about
+ *
+ * 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.evolution.alignment;
+
+public class MaskedAlignment extends WrappedAlignment {
+    public MaskedAlignment(Alignment alignment, boolean[] mask) {
+        super(alignment);
+
+        this.mask = mask;
+    }
+
+    @Override
+    public int getState(int taxonIndex, int siteIndex) {
+        if (mask[siteIndex]) {
+            return alignment.getState(taxonIndex, siteIndex);
+        } else {
+            return alignment.getDataType().getUnknownState();
+        }
+    }
+
+    private final boolean[] mask;
+}

src/dr/evomodel/treedatalikelihood/BeagleDataLikelihoodInterface.java

@@ -39,6 +39,7 @@
  * @author Andrew Rambaut
  * @author Marc Suchard
  */
+@Deprecated // seems not to be used
 public interface BeagleDataLikelihoodInterface extends DataLikelihoodDelegate {
 
 }

src/dr/evoxml/MaskedPatternsParser.java → src/dr/evoxml/MaskedAlignmentParser.java

@@ -27,45 +27,47 @@
 
 package dr.evoxml;
 
+import dr.evolution.alignment.Alignment;
+import dr.evolution.alignment.MaskedAlignment;
 import dr.evolution.alignment.PatternList;
-import dr.evolution.alignment.Patterns;
 import dr.evolution.alignment.SiteList;
-import dr.evolution.alignment.SitePatterns;
 import dr.xml.*;
 
-import java.util.logging.Logger;
-
 /**
  * @author Andrew Rambaut
  *
  */
-public class MaskedPatternsParser extends AbstractXMLObjectParser {
+public class MaskedAlignmentParser extends AbstractXMLObjectParser {
 
-    public static final String MASKED_PATTERNS = "maskedPatterns";
+    public static final String MASKED_ALIGNMENT = "maskedAlignment";
     public static final String MASK = "mask";
     public static final String NEGATIVE = "negative";
     public static final String INVERSE = "inverse";
 
-    public String getParserName() { return MASKED_PATTERNS; }
+    public String getParserName() { return MASKED_ALIGNMENT; }
 
     /**
-     * Parses a patterns element and returns a patterns object.
+     * Parses an alignment element and returns a masked alignment object.
      */
     public Object parseXMLObject(XMLObject xo) throws XMLParseException {
 
-        SiteList siteList = (SiteList)xo.getChild(SiteList.class);
+        Alignment alignment = (Alignment)xo.getChild(Alignment.class);
 
         boolean inverseMask = xo.getBooleanAttribute(INVERSE, false) || xo.getBooleanAttribute(NEGATIVE, false);
         String maskString = (String)xo.getElementFirstChild(MASK);
 
-        boolean[] mask = new boolean[siteList.getSiteCount()];
+        boolean[] mask = new boolean[alignment.getSiteCount()];
         int k = 0;
+        int onCount = 0;
         for (char c : maskString.toCharArray()) {
             if (Character.isDigit(c)) {
                 if (k >= mask.length) {
                     break;
                 }
                 mask[k] = (c == '0' ? inverseMask : !inverseMask);
+                if (mask[k]) {
+                    onCount += 1;
+                }
                 k++;
             }
         }
@@ -74,23 +76,11 @@ public Object parseXMLObject(XMLObject xo) throws XMLParseException {
             throw new XMLParseException("The mask needs to be the same length as the alignment (spaces are ignored)");
         }
 
-        throw new UnsupportedOperationException("This has not been implemented");
-
-        // @todo - work out how to do this. Create a MaskedSitePatterns which can then be put into a SitePatterns
-        // for compression etc. Or MaskedAlignment may make more sense here.
-//        SitePatterns patterns = new MaskedSitePatterns(siteList, mask);
-//
-//        if (patterns == null) {
-//            throw new XMLParseException("The mask needs include at least one pattern");
-//        }
-//
-//        if (xo.hasAttribute(XMLParser.ID)) {
-//            final Logger logger = Logger.getLogger("dr.evoxml");
-//            logger.info("Site patterns '" + xo.getId() + "' created by masking alignment with id '" + siteList.getId() + "'");
-//            logger.info("  pattern count = " + patterns.getPatternCount());
-//        }
-//
-//        return patterns;
+        if (onCount == 0) {
+            throw new XMLParseException("The mask needs to have at least one site unmasked");
+        }
+
+        return new MaskedAlignment(alignment, mask);
     }
 
     public XMLSyntaxRule[] getSyntaxRules() { return rules; }
@@ -103,9 +93,9 @@ public Object parseXMLObject(XMLObject xo) throws XMLParseException {
     };
 
     public String getParserDescription() {
-        return "A weighted list of the unique site patterns (unique columns) in an alignment.";
+        return "Applies a mask to an alignment so that masked sites are ambiguous.";
     }
 
-    public Class getReturnType() { return PatternList.class; }
+    public Class getReturnType() { return MaskedAlignment.class; }
 
 }

src/dr/inferencexml/operators/shrinkage/BayesianBridgeShrinkageOperatorParser.java

@@ -27,20 +27,18 @@
 
 package dr.inferencexml.operators.shrinkage;
 
-import dr.evomodel.branchratemodel.AutoCorrelatedBranchRatesDistribution;
 import dr.inference.distribution.DistributionLikelihood;
 import dr.inference.distribution.shrinkage.BayesianBridgeStatisticsProvider;
 import dr.inference.model.Parameter;
 import dr.inference.operators.shrinkage.BayesianBridgeShrinkageOperator;
 import dr.math.distributions.GammaDistribution;
 import dr.xml.*;
 
-import static dr.evoxml.MaskedPatternsParser.MASK;
-import static dr.inference.operators.MCMCOperator.WEIGHT;
-
 public class BayesianBridgeShrinkageOperatorParser extends AbstractXMLObjectParser {
 
     public final static String BAYESIAN_BRIDGE_PARSER = "bayesianBridgeGibbsOperator";
+    public final static String MASK = "mask";
+    public final static String WEIGHT = "weight";
 
     @Override
     public Object parseXMLObject(XMLObject xo) throws XMLParseException {

src/dr/inferencexml/operators/shrinkage/DimensionMismatchedBayesianBridgeShrinkageOperatorParser.java

@@ -35,12 +35,11 @@
 import dr.math.distributions.GammaDistribution;
 import dr.xml.*;
 
-import static dr.evoxml.MaskedPatternsParser.MASK;
-import static dr.inference.operators.MCMCOperator.WEIGHT;
-
 public class DimensionMismatchedBayesianBridgeShrinkageOperatorParser extends AbstractXMLObjectParser {
 
     public final static String BAYESIAN_BRIDGE_PARSER = "dimensionMismatchedBayesianBridgeGibbsOperator";
+    public final static String MASK = "mask";
+    public final static String WEIGHT = "weight";
 
     @Override
     public Object parseXMLObject(XMLObject xo) throws XMLParseException {