BEAGLE is now cited by default

src/dr/evomodel/treelikelihood/BeagleTreeLikelihood.java

@@ -84,7 +84,7 @@
 
 @SuppressWarnings("serial")
 @Deprecated // Switching to TreeDataLikelihood
-public class BeagleTreeLikelihood extends AbstractSinglePartitionTreeLikelihood implements ThreadAwareLikelihood, Citable {
+public class BeagleTreeLikelihood extends AbstractSinglePartitionTreeLikelihood implements ThreadAwareLikelihood {
 
     // This property is a comma-delimited list of resource numbers (0 == CPU) to
     // allocate each BEAGLE instance to. If less than the number of instances then
@@ -1534,18 +1534,4 @@ public double[] getSiteLogLikelihoods() {
         return siteLogLikelihoods;
     }
 
-    @Override
-    public Citation.Category getCategory() {
-        return Citation.Category.FRAMEWORK;
-    }
-
-    @Override
-    public String getDescription() {
-        return "Using BEAGLE likelihood calculation library";
-    }
-
-    public List<Citation> getCitations() {
-        return Collections.singletonList(CommonCitations.AYRES_2019_BEAGLE);
-    }
-
 }//END: class

src/dr/evomodel/treelikelihood/MarkovJumpsBeagleTreeLikelihood.java

@@ -46,6 +46,7 @@
 import dr.inference.markovjumps.MarkovJumpsType;
 import dr.inference.model.Parameter;
 import dr.inference.model.Variable;
+import dr.util.Citable;
 import dr.util.Citation;
 import dr.util.CommonCitations;
 
@@ -62,7 +63,7 @@
  *         Journal of Mathematical Biology, 56, 391-412.
  */
 public class MarkovJumpsBeagleTreeLikelihood extends AncestralStateBeagleTreeLikelihood
-        implements MarkovJumpsRegisterAcceptor, MarkovJumpsTraitProvider {
+        implements MarkovJumpsRegisterAcceptor, MarkovJumpsTraitProvider, Citable {
 
     public MarkovJumpsBeagleTreeLikelihood(PatternList patternList, MutableTreeModel treeModel,
                                            BranchModel branchModel,
@@ -672,15 +673,18 @@ private double getExpectedTreeLength() {
         }
     }
 
+    @Override
+    public Citation.Category getCategory() {
+        return Citation.Category.COUNTING_PROCESSES;
+    }
+
     @Override
     public String getDescription() {
-        return super.getDescription() + " (first citation) with MarkovJumps inference techniques (second citation)";
+        return "MarkovJumps inference techniques";
     }
 
     public List<Citation> getCitations() {
-        List<Citation> citationList = new ArrayList<Citation>(super.getCitations());
-        citationList.add(CommonCitations.MININ_2008_COUNTING);
-        return citationList;
+        return Collections.singletonList(CommonCitations.MININ_2008_COUNTING);
     }
 
     public static final String ALL_HISTORY = "history_all";