X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=c6c2deb8d048a47259290e3829c3b44b4b06e28b;hb=46406ae21c62b964714ce136c9d692985c17211d;hp=0878cbb1cbeaaa328887a9a8e5beb96d79bce69e;hpb=496ecb05d48de1ca8471658fd32824f808bb8823;p=jalview.git

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 0878cbb..c6c2deb 100644
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -62,6 +62,7 @@ import java.awt.event.MouseWheelListener;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
+import java.util.ListIterator;
 
 import javax.swing.JPanel;
 import javax.swing.SwingUtilities;
@@ -393,8 +394,7 @@ public class SeqPanel extends JPanel implements MouseListener,
     }
     else
     {
-      av.getRanges().scrollToVisible(seqCanvas.cursorX, seqCanvas.cursorY,
-              av);
+      av.getRanges().scrollToVisible(seqCanvas.cursorX, seqCanvas.cursorY);
     }
     setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY),
             seqCanvas.cursorX, seqCanvas.cursorY);
@@ -732,8 +732,9 @@ public class SeqPanel extends JPanel implements MouseListener,
     /*
      * set status bar message, returning residue position in sequence
      */
+    boolean isGapped = Comparison.isGap(sequence.getCharAt(column));
     final int pos = setStatusMessage(sequence, column, seq);
-    if (ssm != null && pos > -1)
+    if (ssm != null && !isGapped)
     {
       mouseOverSequence(sequence, column, pos);
     }
@@ -762,10 +763,19 @@ public class SeqPanel extends JPanel implements MouseListener,
       }
     }
 
-    if (av.isShowSequenceFeatures() && pos != -1)
+    /*
+     * add any features at the position to the tooltip; if over a gap, only
+     * add features that straddle the gap (pos may be the residue before or
+     * after the gap)
+     */
+    if (av.isShowSequenceFeatures())
     {
       List<SequenceFeature> features = ap.getFeatureRenderer()
               .findFeaturesAtRes(sequence.getDatasetSequence(), pos);
+      if (isGapped)
+      {
+        removeAdjacentFeatures(features, column + 1, sequence);
+      }
       seqARep.appendFeatures(tooltipText, pos, features,
               this.ap.getSeqPanel().seqCanvas.fr.getMinMax());
     }
@@ -790,6 +800,35 @@ public class SeqPanel extends JPanel implements MouseListener,
 
   }
 
+  /**
+   * Removes from the list of features any that start after, or end before, the
+   * given column position. This allows us to retain only those features
+   * adjacent to a gapped position that straddle the position. Contact features
+   * that 'straddle' the position are also removed, since they are not 'at' the
+   * position.
+   * 
+   * @param features
+   * @param column
+   *          alignment column (1..)
+   * @param sequence
+   */
+  protected void removeAdjacentFeatures(List<SequenceFeature> features,
+          final int column, SequenceI sequence)
+  {
+    // TODO should this be an AlignViewController method (and reused by applet)?
+    ListIterator<SequenceFeature> it = features.listIterator();
+    while (it.hasNext())
+    {
+      SequenceFeature sf = it.next();
+      if (sf.isContactFeature()
+              || sequence.findIndex(sf.getBegin()) > column
+              || sequence.findIndex(sf.getEnd()) < column)
+      {
+        it.remove();
+      }
+    }
+  }
+
   private Point lastp = null;
 
   /*
@@ -834,9 +873,10 @@ 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,
-   * or -1 for a gapped column position.
+   * (index) and id, and residue and residue position if not at a gap, for the
+   * given sequence and column position. Returns the residue position returned
+   * by Sequence.findPosition. Note this may be for the nearest adjacent residue
+   * if at a gapped position.
    * 
    * @param sequence
    *          aligned sequence object
@@ -844,7 +884,8 @@ public class SeqPanel extends JPanel implements MouseListener,
    *          alignment column
    * @param seq
    *          index of sequence in alignment
-   * @return position of column in sequence or -1 if at a gap
+   * @return sequence position of residue at column, or adjacent residue if at a
+   *         gap
    */
   int setStatusMessage(SequenceI sequence, final int column, int seq)
   {
@@ -858,36 +899,34 @@ public class SeqPanel extends JPanel implements MouseListener,
             .append(sequence.getName());
 
     String residue = null;
+
     /*
      * Try to translate the display character to residue name (null for gap).
      */
     final String displayChar = String.valueOf(sequence.getCharAt(column));
-    if (av.getAlignment().isNucleotide())
+    boolean isGapped = Comparison.isGap(sequence.getCharAt(column));
+    int pos = sequence.findPosition(column);
+
+    if (!isGapped)
     {
-      residue = ResidueProperties.nucleotideName.get(displayChar);
-      if (residue != null)
+      boolean nucleotide = av.getAlignment().isNucleotide();
+      if (nucleotide)
       {
-        text.append(" Nucleotide: ").append(residue);
+        residue = ResidueProperties.nucleotideName.get(displayChar);
       }
-    }
-    else
-    {
-      residue = "X".equalsIgnoreCase(displayChar) ? "X" : ("*"
-              .equals(displayChar) ? "STOP" : ResidueProperties.aa2Triplet
-              .get(displayChar));
-      if (residue != null)
+      else
       {
-        text.append(" Residue: ").append(residue);
+        residue = "X".equalsIgnoreCase(displayChar) ? "X" : ("*"
+                .equals(displayChar) ? "STOP"
+                : ResidueProperties.aa2Triplet.get(displayChar));
       }
-    }
+      text.append(" ").append(nucleotide ? "Nucleotide" : "Residue")
+              .append(": ").append(residue == null ? displayChar : residue);
 
-    int pos = -1;
-    if (residue != null)
-    {
-      pos = sequence.findPosition(column);
       text.append(" (").append(Integer.toString(pos)).append(")");
     }
     ap.alignFrame.statusBar.setText(text.toString());
+
     return pos;
   }
 
@@ -1527,9 +1566,20 @@ public class SeqPanel extends JPanel implements MouseListener,
         av.setSelectionGroup(null);
       }
 
+      int column = findColumn(evt);
+      boolean isGapped = Comparison.isGap(sequence.getCharAt(column));
+
+      /*
+       * find features at the position (if not gapped), or straddling
+       * the position (if at a gap)
+       */
       List<SequenceFeature> features = seqCanvas.getFeatureRenderer()
               .findFeaturesAtRes(sequence.getDatasetSequence(),
-                      sequence.findPosition(findColumn(evt)));
+                      sequence.findPosition(column));
+      if (isGapped)
+      {
+        removeAdjacentFeatures(features, column, sequence);
+      }
 
       if (!features.isEmpty())
       {