including BEAGLE citation

src/dr/app/beast/BeagleVersion.java

@@ -0,0 +1,89 @@
+/*
+ * BeastVersion.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.app.beast;
+
+import beagle.BeagleInfo;
+import dr.util.Author;
+import dr.util.Citable;
+import dr.util.Citation;
+
+import java.util.Arrays;
+import java.util.List;
+
+/**
+ * This class provides a mechanism for returning the version number and
+ * citation of the BEAGLE high-performance computational library.
+ *
+ * @author Guy Baele
+ *
+ * $Id$
+ */
+
+public class BeagleVersion implements Citable {
+
+    public static final BeagleVersion INSTANCE = new BeagleVersion();
+
+    public String getVersion() {
+        return BeagleInfo.getVersion();
+    }
+
+    @Override
+    public Citation.Category getCategory() {
+        return Citation.Category.COMPUTATIONAL_LIBRARY;
+    }
+
+    @Override
+    public String getDescription() {
+        return "BEAGLE citation";
+    }
+
+    @Override
+    public List<Citation> getCitations() {
+        return Arrays.asList(CITATIONS);
+    }
+
+    public static Citation[] CITATIONS = new Citation[] {
+            new Citation(
+                    new Author[]{
+                            new Author("DL", "Ayres"),
+                            new Author("MP", "Cummings"),
+                            new Author("G", "Baele"),
+                            new Author("AE", "Darling"),
+                            new Author("PO", "Lewis"),
+                            new Author("DL", "Swofford"),
+                            new Author("JP", "Huelsenbeck"),
+                            new Author("P", "Lemey"),
+                            new Author("A", "Rambaut"),
+                            new Author("MA", "Suchard")
+                    },
+                    "BEAGLE 3: Improved performance, scaling, and usability for a high-performance computing library for statistical phylogenetics",
+                    2019,
+                    "Systematic Biology",
+                    68, 1052, 1061,
+                    "10.1093/sysbio/syz020")
+    };
+
+}

src/dr/app/beast/BeastMain.java

@@ -415,6 +415,7 @@ public static void main(String[] args) throws java.io.IOException {
                         new Arguments.Option("force_resume", "Force resuming from a saved state"),
 
                         new Arguments.StringOption("citations_file", "FILENAME", "Specify a filename to write a citation list to"),
+                        //new Arguments.Option("citations_off", "Turn off writing citations to file"),
                         new Arguments.StringOption("plugins_dir", "FILENAME", "Specify a directory to load plugins from, multiple can be separated with ':' "),
 
                         new Arguments.Option("version", "Print the version and credits and stop"),

src/dr/app/beast/BeastParser.java

@@ -25,6 +25,7 @@
 
 package dr.app.beast;
 
+import beagle.BeagleInfo;
 import dr.util.Citation;
 import dr.util.Pair;
 import dr.util.Version;
@@ -57,7 +58,10 @@ public class BeastParser extends XMLParser {
     public BeastParser(String[] args, List<String> additionalParsers, boolean verbose, boolean parserWarnings, boolean strictXML, Version version) {
         super(verbose, parserWarnings, strictXML, version);
 
+        //add BEAST citation
         addCitable(BeastVersion.INSTANCE);
+        //add BEAGLE citation
+        addCitable(BeagleVersion.INSTANCE);
 
         setup(args);
 

src/dr/util/Citation.java

@@ -243,6 +243,7 @@ public String getText() {
 
     public enum Category {
         FRAMEWORK("Framework"),
+        COMPUTATIONAL_LIBRARY("Computational library"),
         SUBSTITUTION_MODELS("Substitution Models"),
         PRIOR_MODELS("Prior Models"),
         TRAIT_MODELS("Trait Models"),