JAL-2547 don't show features in tooltip over a gap

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index d46cc34..b89c435 100644 (file)
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -39,6 +39,7 @@ import jalview.structure.SelectionSource;
 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;
@@ -772,10 +773,10 @@ public class SeqPanel extends Panel implements MouseMotionListener,
   @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 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     }
 
     SequenceI sequence = av.getAlignment().getSequenceAt(seq);
-    if (res > sequence.getLength())
+    if (column > sequence.getLength())
     {
       if (tooltip != null)
       {
@@ -794,10 +795,12 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       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 @@ public class SeqPanel extends Panel implements MouseMotionListener,
             .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 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     {
       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 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       }
     }
 
-    // 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];
-
-      tooltipText.append(sf.getType() + " " + sf.begin + ":" + sf.end);
+      SequenceFeature[] allFeatures = findFeaturesAtRes(sequence,
+              sequence.findPosition(column));
 
-      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 --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 7dfac5e..2884c50 100644 (file)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -788,7 +788,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       }
     }
 
-    if (av.isShowSequenceFeatures())
+    if (av.isShowSequenceFeatures() && pos != -1)
     {
       List<SequenceFeature> features = ap.getFeatureRenderer()
               .findFeaturesAtRes(sequence.getDatasetSequence(), pos);
@@ -861,7 +861,8 @@ public class SeqPanel extends JPanel implements MouseListener,
   /**
    * 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
@@ -907,9 +908,9 @@ public class SeqPanel extends JPanel implements MouseListener,
     }
 
     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());