psf String

src/dr/app/beast/BeagleVersion.java

@@ -29,8 +29,10 @@
 import dr.util.Author;
 import dr.util.Citable;
 import dr.util.Citation;
+import dr.util.CommonCitations;
 
 import java.util.Arrays;
+import java.util.Collections;
 import java.util.List;
 
 /**
@@ -62,28 +64,7 @@ public String getDescription() {
 
     @Override
     public List<Citation> getCitations() {
-        return Arrays.asList(CITATIONS);
+        return Collections.singletonList(CommonCitations.AYRES_2019_BEAGLE);
     }
 
-    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

@@ -61,7 +61,7 @@ public class BeastMain {
     public static final double DEFAULT_DELTA = 1.0;
     public static final int DEFAULT_SWAP_CHAIN_EVERY = 100;
 
-    private static final String CITATION_FILE_SUFFIX = "_citations.txt";
+    private static final String CITATION_FILE_SUFFIX = ".citations.txt";
 
     static class BeastConsoleApp extends jam.console.ConsoleApplication {
         XMLParser parser = null;

src/dr/evomodel/branchratemodel/BranchSpecificFixedEffects.java

@@ -28,7 +28,7 @@ public interface BranchSpecificFixedEffects {
 
     int getDimension();
 
-    abstract class Base extends AbstractModel implements BranchSpecificFixedEffects {
+    abstract class Base extends AbstractModel implements BranchSpecificFixedEffects, Citable {
 
         public Base(String name) {
             super(name);
@@ -42,6 +42,40 @@ public double[] getDifferential(double rate, final Tree tree, final NodeRef node
             }
             return result;
         }
+
+        @Override
+        public Citation.Category getCategory() {
+            return Citation.Category.MOLECULAR_CLOCK;
+        }
+
+        @Override
+        public String getDescription() {
+            return "Mixed effects clock model";
+        }
+
+        @Override
+        public List<Citation> getCitations() {
+            Citation citation = new Citation(
+                    new Author[]{
+                            new Author("M", "Bletsa"),
+                            new Author("MA", "Suchard"),
+                            new Author("X", "Ji"),
+                            new Author("S", "Gryseels"),
+                            new Author("B", "Vrancken"),
+                            new Author("G", "Baele"),
+                            new Author("M", "Worobey"),
+                            new Author("P", "Lemey")
+                    },
+                    "Divergence dating using mixed effects clock modelling: an application to HIV-1",
+                    2019,
+                    "Virus Evolution",
+                    5,
+                    "vez036",
+                    "10.1093/ve/vez036"
+            );
+            return Collections.singletonList(citation);
+        }
+
     }
 
     class None extends Base implements BranchSpecificFixedEffects {
@@ -98,6 +132,7 @@ public Parameter getFixedEffectsParameter() {
         public int getDimension() {
             return 1;
         }
+
     }
 
     class Transformed extends Base implements BranchSpecificFixedEffects {

src/dr/evomodel/coalescent/basta/BeagleMatrixExponentiationDelegate.java

@@ -56,7 +56,7 @@
 import static dr.evomodel.treedatalikelihood.BeagleFunctionality.*;
 
 @Deprecated
-public class BeagleMatrixExponentiationDelegate extends AbstractModel implements Citable {
+public class BeagleMatrixExponentiationDelegate extends AbstractModel {
 
     // 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
@@ -339,25 +339,6 @@ public void restoreState() {
     protected void acceptState() {
     }
 
-    // **************************************************************
-    // INSTANCE CITABLE
-    // **************************************************************
-
-    @Override
-    public Citation.Category getCategory() {
-        return Citation.Category.FRAMEWORK;
-    }
-
-    @Override
-    public String getDescription() {
-        return "Using BEAGLE likelihood calculation library";
-    }
-
-    @Override
-    public List<Citation> getCitations() {
-        return Collections.singletonList(CommonCitations.AYRES_2019_BEAGLE);
-    }
-
     // **************************************************************
     // INSTANCE VARIABLES
     // **************************************************************

src/dr/evomodel/treedatalikelihood/BeagleDataLikelihoodDelegate.java

@@ -57,7 +57,7 @@
  * @version $Id$
  */
 
-public class BeagleDataLikelihoodDelegate extends AbstractModel implements DataLikelihoodDelegate, Citable {
+public class BeagleDataLikelihoodDelegate extends AbstractModel implements DataLikelihoodDelegate {
 
     private static final boolean COUNT_CALCULATIONS = true; // keep a cumulative total of number of computations
 
@@ -1097,25 +1097,6 @@ public long getTotalCalculationCount() {
         return totalPartialsUpdateCount;
     }
 
-    // **************************************************************
-    // INSTANCE CITABLE
-    // **************************************************************
-
-    @Override
-    public Citation.Category getCategory() {
-        return Citation.Category.FRAMEWORK;
-    }
-
-    @Override
-    public String getDescription() {
-        return "BEAGLE likelihood calculation library";
-    }
-
-    @Override
-    public List<Citation> getCitations() {
-        return Collections.singletonList(CommonCitations.AYRES_2019_BEAGLE);
-    }
-
     private void releaseBeagle() throws Throwable {
         if (beagle != null && releaseSingleton) {
             beagle.finalize();

src/dr/evomodel/treedatalikelihood/MultiPartitionDataLikelihoodDelegate.java

@@ -60,7 +60,7 @@
  * @version $Id$
  */
 
-public class MultiPartitionDataLikelihoodDelegate extends AbstractModel implements DataLikelihoodDelegate, Citable {
+public class MultiPartitionDataLikelihoodDelegate extends AbstractModel implements DataLikelihoodDelegate {
 
     private static final boolean COUNT_CALCULATIONS = true; // keep a cumulative total of number of computations
 
@@ -1321,25 +1321,6 @@ public long getTotalCalculationCount() {
         return totalPartialsUpdateCount;
     }
 
-    // **************************************************************
-    // INSTANCE CITABLE
-    // **************************************************************
-
-    @Override
-    public Citation.Category getCategory() {
-        return Citation.Category.FRAMEWORK;
-    }
-
-    @Override
-    public String getDescription() {
-        return "BEAGLE likelihood calculation library";
-    }
-
-    @Override
-    public List<Citation> getCitations() {
-        return Collections.singletonList(CommonCitations.AYRES_2019_BEAGLE);
-    }
-
     // **************************************************************
     // INSTANCE VARIABLES
     // **************************************************************

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";

src/dr/inference/operators/AdaptableVarianceMultivariateNormalOperator.java

@@ -886,7 +886,7 @@ public XMLSyntaxRule[] getSyntaxRules() {
 
     @Override
     public Citation.Category getCategory() {
-        return Citation.Category.FRAMEWORK;
+        return Citation.Category.ADVANCED_ESTIMATION_METHODS;
     }
 
     @Override

src/dr/util/Citation.java

@@ -96,14 +96,14 @@ public Citation(Author[] authors, String title, int year, String journal, String
         this(authors, title, year, journal, -1, location, null);
     }
 
-    public Citation(Author[] authors, String title, int year, String journal, int volumn, String location,
+    public Citation(Author[] authors, String title, int year, String journal, int volume, String location,
                     String DOI) {
         this.authors = authors;
         this.title = title;
         this.year = year;
         this.journal = journal;
         this.location = location;
-        this.volume = volumn;
+        this.volume = volume;
         this.startpage = -1;
         this.endpage = -1;
         this.DOI = DOI;
@@ -244,6 +244,7 @@ public String getText() {
     public enum Category {
         FRAMEWORK("Framework"),
         COMPUTATIONAL_LIBRARY("High-Performance Computing"),
+        ADVANCED_ESTIMATION_METHODS("Advanced Estimation Methods"),
         SUBSTITUTION_MODELS("Substitution Models"),
         PRIOR_MODELS("Prior Models"),
         TRAIT_MODELS("Trait Models"),