Merge branch 'develop' into features/JAL-2446NCList

Conflicts:
	src/jalview/appletgui/SeqPanel.java

diff --cc src/jalview/appletgui/AlignFrame.java
Simple merge

diff --cc src/jalview/appletgui/IdPanel.java
Simple merge

diff --cc src/jalview/appletgui/SeqPanel.java
index c10038f,14ea222..1ca4256
--- 1/src/jalview/appletgui/SeqPanel.java
--- 2/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@@ -853,33 -863,38 +863,32 @@@ public class SeqPanel extends Panel imp
        }
      }
  
-     // use aa to see if the mouse pointer is on a
-     List<SequenceFeature> allFeatures = findFeaturesAtRes(sequence,
-             sequence.findPosition(res));
- 
-     int index = 0;
-     while (index < allFeatures.size())
+     /*
+      * add feature details to tooltip if over one or more features
+      */
+     if (respos != -1)
      {
-       SequenceFeature sf = allFeatures.get(index);
- 
-       tooltipText.append(sf.getType() + " " + sf.begin + ":" + sf.end);
- 
-       if (sf.getDescription() != null)
 -      SequenceFeature[] allFeatures = findFeaturesAtRes(sequence,
 -              sequence.findPosition(column));
 -
 -      int index = 0;
 -      while (index < allFeatures.length)
++      List<SequenceFeature> allFeatures = findFeaturesAtRes(sequence,
++              respos);
++      for (SequenceFeature sf : allFeatures)
        {
-         tooltipText.append(" " + sf.getDescription());
-       }
 -        SequenceFeature sf = allFeatures[index];
 -
+         tooltipText.append(sf.getType() + " " + sf.begin + ":" + sf.end);
  
-       if (sf.getValue("status") != null)
-       {
-         String status = sf.getValue("status").toString();
-         if (status.length() > 0)
+         if (sf.getDescription() != null)
          {
-           tooltipText.append(" (" + sf.getValue("status") + ")");
+           tooltipText.append(" " + sf.getDescription());
          }
-       }
-       tooltipText.append("\n");
  
-       index++;
+         if (sf.getValue("status") != null)
+         {
+           String status = sf.getValue("status").toString();
+           if (status.length() > 0)
+           {
+             tooltipText.append(" (" + sf.getValue("status") + ")");
+           }
+         }
+         tooltipText.append("\n");
 -
 -        index++;
+       }
      }
  
      if (tooltip == null)

diff --cc src/jalview/datamodel/SequenceI.java
Simple merge

diff --cc src/jalview/gui/AlignmentPanel.java
index 2f6e3e4,ce9e989..f3e2733
--- 1/src/jalview/gui/AlignmentPanel.java
--- 2/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@@ -34,9 -34,9 +34,10 @@@ import jalview.jbgui.GAlignmentPanel
  import jalview.math.AlignmentDimension;
  import jalview.schemes.ResidueProperties;
  import jalview.structure.StructureSelectionManager;
 +import jalview.util.Comparison;
  import jalview.util.MessageManager;
  import jalview.util.Platform;
+ import jalview.viewmodel.ViewportListenerI;
  import jalview.viewmodel.ViewportRanges;
  
  import java.awt.BorderLayout;

diff --cc src/jalview/gui/IdPanel.java
Simple merge

diff --cc src/jalview/gui/Jalview2XML.java
Simple merge

diff --cc src/jalview/gui/Jalview2XML_V1.java
Simple merge

diff --cc src/jalview/gui/SeqPanel.java
Simple merge