Merge branch 'bug/JAL-2547tooltipOnGap' into develop

diff --combined src/jalview/appletgui/SeqPanel.java
index f58f420,b89c435..2d2e3fd
--- 1/src/jalview/appletgui/SeqPanel.java
--- 2/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@@ -39,6 -39,7 +39,7 @@@ import jalview.structure.SelectionSourc
  import jalview.structure.SequenceListener;
  import jalview.structure.StructureSelectionManager;
  import jalview.structure.VamsasSource;
+ import jalview.util.Comparison;
  import jalview.util.MappingUtils;
  import jalview.util.MessageManager;
  import jalview.viewmodel.AlignmentViewport;
@@@ -412,13 -413,13 +413,13 @@@ public class SeqPanel extends Panel imp
     * 
     * @param sequence
     *          aligned sequence object
 -   * @param res
 +   * @param column
     *          alignment column
     * @param seq
     *          index of sequence in alignment
 -   * @return position of res in sequence
 +   * @return position of column in sequence or -1 if at gap
     */
 -  void setStatusMessage(SequenceI sequence, int res, int seq)
 +  void setStatusMessage(SequenceI sequence, int column, int seq)
    {
      // TODO remove duplication of identical gui method
      StringBuilder text = new StringBuilder(32);
@@@ -429,7 -430,7 +430,7 @@@
      /*
       * Try to translate the display character to residue name (null for gap).
       */
 -    final String displayChar = String.valueOf(sequence.getCharAt(res));
 +    final String displayChar = String.valueOf(sequence.getCharAt(column));
      if (av.getAlignment().isNucleotide())
      {
        residue = ResidueProperties.nucleotideName.get(displayChar);
@@@ -452,7 -453,7 +453,7 @@@
      int pos = -1;
      if (residue != null)
      {
 -      pos = sequence.findPosition(res);
 +      pos = sequence.findPosition(column);
        text.append(" (").append(Integer.toString(pos)).append(")");
      }
  
@@@ -772,10 -773,10 +773,10 @@@
    @Override
    public void mouseMoved(MouseEvent evt)
    {
-     int res = findRes(evt);
+     final int column = findRes(evt);
      int seq = findSeq(evt);
  
-     if (seq >= av.getAlignment().getHeight() || seq < 0 || res < 0)
+     if (seq >= av.getAlignment().getHeight() || seq < 0 || column < 0)
      {
        if (tooltip != null)
        {
@@@ -785,7 -786,7 +786,7 @@@
      }
  
      SequenceI sequence = av.getAlignment().getSequenceAt(seq);
-     if (res > sequence.getLength())
+     if (column > sequence.getLength())
      {
        if (tooltip != null)
        {
@@@ -794,10 -795,12 +795,12 @@@
        return;
      }
  
-     int respos = sequence.findPosition(res);
-     if (ssm != null)
+     final char ch = sequence.getCharAt(column);
+     int respos = Comparison.isGap(ch) ? -1 : sequence.findPosition(column);
+ 
+     if (ssm != null && respos != -1)
      {
-       mouseOverSequence(sequence, res, respos);
+       mouseOverSequence(sequence, column, respos);
      }
  
      StringBuilder text = new StringBuilder();
@@@ -805,30 -808,31 +808,31 @@@
              .append(" ID: ").append(sequence.getName());
  
      String obj = null;
-     final String ch = String.valueOf(sequence.getCharAt(res));
-     if (av.getAlignment().isNucleotide())
+     if (respos != -1)
      {
-       obj = ResidueProperties.nucleotideName.get(ch);
-       if (obj != null)
+       if (av.getAlignment().isNucleotide())
        {
-         text.append(" Nucleotide: ").append(obj);
+         obj = ResidueProperties.nucleotideName.get(ch);
+         if (obj != null)
+         {
+           text.append(" Nucleotide: ").append(obj);
+         }
+       }
+       else
+       {
+         obj = (ch == 'x' || ch == 'X') ? "X" : ResidueProperties.aa2Triplet
+                 .get(String.valueOf(ch));
+         if (obj != null)
+         {
+           text.append(" Residue: ").append(obj);
+         }
        }
-     }
-     else
-     {
-       obj = "X".equalsIgnoreCase(ch) ? "X" : ResidueProperties.aa2Triplet
-               .get(ch);
        if (obj != null)
        {
-         text.append(" Residue: ").append(obj);
+         text.append(" (").append(Integer.toString(respos)).append(")");
        }
      }
  
-     if (obj != null)
-     {
-       text.append(" (").append(Integer.toString(respos)).append(")");
-     }
- 
      ap.alignFrame.statusBar.setText(text.toString());
  
      StringBuilder tooltipText = new StringBuilder();
@@@ -837,7 -841,7 +841,7 @@@
      {
        for (int g = 0; g < groups.length; g++)
        {
-         if (groups[g].getStartRes() <= res && groups[g].getEndRes() >= res)
+         if (groups[g].getStartRes() <= column && groups[g].getEndRes() >= column)
          {
            if (!groups[g].getName().startsWith("JTreeGroup")
                    && !groups[g].getName().startsWith("JGroup"))
@@@ -853,33 -857,38 +857,38 @@@
        }
      }
  
-     // use aa to see if the mouse pointer is on a
-     SequenceFeature[] allFeatures = findFeaturesAtRes(sequence,
-             sequence.findPosition(res));
- 
-     int index = 0;
-     while (index < allFeatures.length)
+     /*
+      * add feature details to tooltip if over one or more features
+      */
+     if (respos != -1)
      {
-       SequenceFeature sf = allFeatures[index];
+       SequenceFeature[] allFeatures = findFeaturesAtRes(sequence,
+               sequence.findPosition(column));
  
-       tooltipText.append(sf.getType() + " " + sf.begin + ":" + sf.end);
- 
-       if (sf.getDescription() != null)
+       int index = 0;
+       while (index < allFeatures.length)
        {
-         tooltipText.append(" " + sf.getDescription());
-       }
+         SequenceFeature sf = allFeatures[index];
  
-       if (sf.getValue("status") != null)
-       {
-         String status = sf.getValue("status").toString();
-         if (status.length() > 0)
+         tooltipText.append(sf.getType() + " " + sf.begin + ":" + sf.end);
+ 
+         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 --combined src/jalview/gui/SeqPanel.java
index a435fee,2884c50..20e585a
--- 1/src/jalview/gui/SeqPanel.java
--- 2/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@@ -788,7 -788,7 +788,7 @@@ public class SeqPanel extends JPanel im
        }
      }
  
-     if (av.isShowSequenceFeatures())
+     if (av.isShowSequenceFeatures() && pos != -1)
      {
        List<SequenceFeature> features = ap.getFeatureRenderer()
                .findFeaturesAtRes(sequence.getDatasetSequence(), pos);
@@@ -861,7 -861,8 +861,8 @@@
    /**
     * Sets the status message in alignment panel, showing the sequence number
     * (index) and id, residue and residue position for the given sequence and
-    * column position. Returns the calculated residue position in the sequence.
+    * column position. Returns the calculated residue position in the sequence,
+    * or -1 for a gapped column position.
     * 
     * @param sequence
     *          aligned sequence object
@@@ -869,7 -870,7 +870,7 @@@
     *          alignment column
     * @param seq
     *          index of sequence in alignment
 -   * @return position of res in sequence
 +   * @return position of column in sequence or -1 if at a gap
     */
    int setStatusMessage(SequenceI sequence, final int column, int seq)
    {
@@@ -907,9 -908,9 +908,9 @@@
      }
  
      int pos = -1;
-     pos = sequence.findPosition(column);
      if (residue != null)
      {
+       pos = sequence.findPosition(column);
        text.append(" (").append(Integer.toString(pos)).append(")");
      }
      ap.alignFrame.statusBar.setText(text.toString());