From 039594a00b40c65c2864485c1c6ea939a49399a9 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 15 May 2018 12:02:12 +0100
Subject: [PATCH] JAL-1264 exclude score-only from 'Add Reference Annotations'

---
 src/jalview/analysis/AlignmentUtils.java |   39 +++++++++++++-----------
 src/jalview/gui/AlignFrame.java          |   48 ++++++++++++++----------------
 2 files changed, 44 insertions(+), 43 deletions(-)

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index d1217bf..87aaf08 100644
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -1461,28 +1461,31 @@ public class AlignmentUtils
       final List<AlignmentAnnotation> result = new ArrayList<>();
       for (AlignmentAnnotation dsann : datasetAnnotations)
       {
-        /*
-         * Find matching annotations on the alignment. If none is found, then
-         * add this annotation to the list of 'addable' annotations for this
-         * sequence.
-         */
-        final Iterable<AlignmentAnnotation> matchedAlignmentAnnotations = al
-                .findAnnotations(seq, dsann.getCalcId(), dsann.label);
-        if (!matchedAlignmentAnnotations.iterator().hasNext())
+        if (dsann.annotations != null) // ignore non-positional annotation
         {
-          result.add(dsann);
-          if (labelForCalcId != null)
+          /*
+           * Find matching annotations on the alignment. If none is found, then
+           * add this annotation to the list of 'addable' annotations for this
+           * sequence.
+           */
+          final Iterable<AlignmentAnnotation> matchedAlignmentAnnotations = al
+                  .findAnnotations(seq, dsann.getCalcId(), dsann.label);
+          if (!matchedAlignmentAnnotations.iterator().hasNext())
           {
-            labelForCalcId.put(dsann.getCalcId(), dsann.label);
+            result.add(dsann);
+            if (labelForCalcId != null)
+            {
+              labelForCalcId.put(dsann.getCalcId(), dsann.label);
+            }
           }
         }
-      }
-      /*
-       * Save any addable annotations for this sequence
-       */
-      if (!result.isEmpty())
-      {
-        candidates.put(seq, result);
+        /*
+         * Save any addable annotations for this sequence
+         */
+        if (!result.isEmpty())
+        {
+          candidates.put(seq, result);
+        }
       }
     }
   }
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 89066cb..3f74327 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -139,9 +139,9 @@ import java.net.URL;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Deque;
-import java.util.Enumeration;
-import java.util.Hashtable;
+import java.util.HashSet;
 import java.util.List;
+import java.util.Set;
 import java.util.Vector;
 
 import javax.swing.JCheckBoxMenuItem;
@@ -3903,35 +3903,33 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
 
     if (viewport.getAlignment().getAlignmentAnnotation()
-            .hashCode() != _annotationScoreVectorHash)
+            .hashCode() == _annotationScoreVectorHash)
     {
-      sortByAnnotScore.removeAll();
-      // almost certainly a quicker way to do this - but we keep it simple
-      Hashtable scoreSorts = new Hashtable();
-      AlignmentAnnotation aann[];
-      for (SequenceI sqa : viewport.getAlignment().getSequences())
+      return;
+    }
+
+    sortByAnnotScore.removeAll();
+    Set<String> scoreSorts = new HashSet<>();
+    for (SequenceI sqa : viewport.getAlignment().getSequences())
+    {
+      AlignmentAnnotation[] anns = sqa.getAnnotation();
+      for (int i = 0; anns != null && i < anns.length; i++)
       {
-        aann = sqa.getAnnotation();
-        for (int i = 0; aann != null && i < aann.length; i++)
+        AlignmentAnnotation aa = anns[i];
+        if (aa != null && aa.hasScore() && aa.sequenceRef != null)
         {
-          if (aann[i].hasScore() && aann[i].sequenceRef != null)
-          {
-            scoreSorts.put(aann[i].label, aann[i].label);
-          }
+          scoreSorts.add(aa.label);
         }
       }
-      Enumeration labels = scoreSorts.keys();
-      while (labels.hasMoreElements())
-      {
-        addSortByAnnotScoreMenuItem(sortByAnnotScore,
-                (String) labels.nextElement());
-      }
-      sortByAnnotScore.setVisible(scoreSorts.size() > 0);
-      scoreSorts.clear();
-
-      _annotationScoreVectorHash = viewport.getAlignment()
-              .getAlignmentAnnotation().hashCode();
     }
+    for (String label : scoreSorts)
+    {
+      addSortByAnnotScoreMenuItem(sortByAnnotScore, label);
+    }
+    sortByAnnotScore.setVisible(!scoreSorts.isEmpty());
+
+    _annotationScoreVectorHash = viewport.getAlignment()
+            .getAlignmentAnnotation().hashCode();
   }
 
   /**
-- 
1.7.10.2