JAL-3187 derived peptide variants tweaks and tests

[jalview.git] / src / jalview / gui / SeqPanel.java

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index bc17cc2..75bf0cc 100644 (file)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -910,12 +910,12 @@ public class SeqPanel extends JPanel
                 .findComplementFeaturesAtResidue(ds, pos);
         if (mf != null)
         {
-          List<String> pv = mf.findProteinVariants();
-          for (String s : pv)
+          for (SequenceFeature sf : mf.features)
           {
-            if (!infos.contains(s))
+            String pv = mf.findProteinVariants(sf);
+            if (pv.length() > 0 && !infos.contains(pv))
             {
-              infos.addAll(pv);
+              infos.add(pv);
             }
           }
         }
@@ -1065,7 +1065,7 @@ public class SeqPanel extends JPanel
                   pos);
           if (mf != null)
           {
-            seqARep.appendFeatures(tooltipText, pos, mf.features, fr2);
+            seqARep.appendFeatures(tooltipText, pos, mf, fr2);
           }
         }
       }
@@ -2254,11 +2254,11 @@ public class SeqPanel extends JPanel
     final int column = pos.column;
     final int seq = pos.seqIndex;
     SequenceI sequence = av.getAlignment().getSequenceAt(seq);
-    List<SequenceFeature> features = ap.getFeatureRenderer()
-            .findFeaturesAtColumn(sequence, column + 1);
-
-    PopupMenu pop = new PopupMenu(ap, null, features);
-    pop.show(this, evt.getX(), evt.getY());
+    if (sequence != null)
+    {
+      PopupMenu pop = new PopupMenu(ap, sequence, column);
+      pop.show(this, evt.getX(), evt.getY());
+    }
   }
 
   /**