X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqPanel.java;fp=src%2Fjalview%2Fappletgui%2FSeqPanel.java;h=10db71a837aedb103d8a56c679a550c7f6b49203;hb=f06554784411ddbf871d642e66c8dcb7f147d4a8;hp=86dedfc189b079b020877873ce64d63f4d1c4ad4;hpb=cf06ee5d732af6cc874115aece1138adafca8ad7;p=jalview.git

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index 86dedfc..10db71a 100644
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -20,21 +20,10 @@
  */
 package jalview.appletgui;
 
-import java.awt.BorderLayout;
-import java.awt.Font;
-import java.awt.FontMetrics;
-import java.awt.Panel;
-import java.awt.Point;
-import java.awt.event.InputEvent;
-import java.awt.event.MouseEvent;
-import java.awt.event.MouseListener;
-import java.awt.event.MouseMotionListener;
-import java.util.List;
-import java.util.Vector;
-
 import jalview.api.AlignViewportI;
 import jalview.commands.EditCommand;
 import jalview.commands.EditCommand.Action;
+import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.SearchResults;
 import jalview.datamodel.SearchResults.Match;
@@ -52,6 +41,17 @@ import jalview.util.MappingUtils;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
 
+import java.awt.BorderLayout;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Panel;
+import java.awt.Point;
+import java.awt.event.InputEvent;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.util.Vector;
+
 public class SeqPanel extends Panel implements MouseMotionListener,
         MouseListener, SequenceListener, SelectionListener
 {
@@ -446,36 +446,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       pos = sequence.findPosition(res);
       text.append(" (").append(Integer.toString(pos)).append(")");
     }
-    // Object obj = null;
-    // if (av.getAlignment().isNucleotide())
-    // {
-    // obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res)
-    // + "");
-    // if (obj != null)
-    // {
-    // text.append(" Nucleotide: ");
-    // }
-    // }
-    // else
-    // {
-    // obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
-    // if (obj != null)
-    // {
-    // text.append("  Residue: ");
-    // }
-    // }
-    //
-    // if (obj != null)
-    // {
-    //
-    // if (obj != "")
-    // {
-    // text.append(obj + " (" + sequence.findPosition(res) + ")");
-    // }
-    // }
 
     ap.alignFrame.statusBar.setText(text.toString());
-
   }
 
   /**
@@ -483,23 +455,37 @@ public class SeqPanel extends Panel implements MouseMotionListener,
    * search results.
    * 
    * @param results
+   * @return true if results were matched, false if not
    */
-  private void setStatusMessage(SearchResults results)
+  private boolean setStatusMessage(SearchResults results)
   {
-    List<Match> matches = results.getResults();
-    if (!matches.isEmpty())
+    AlignmentI al = this.av.getAlignment();
+    int sequenceIndex = al.findIndex(results);
+    if (sequenceIndex == -1)
+    {
+      return false;
+    }
+    SequenceI ds = al.getSequenceAt(sequenceIndex).getDatasetSequence();
+    for (Match m : results.getResults())
     {
-      Match m = matches.get(0);
       SequenceI seq = m.getSequence();
-      int sequenceIndex = this.av.getAlignment().findIndex(seq);
+      if (seq.getDatasetSequence() != null)
+      {
+        seq = seq.getDatasetSequence();
+      }
 
-      /*
-       * Convert position in sequence (base 1) to sequence character array index
-       * (base 0)
-       */
-      int start = m.getStart() - 1;
-      setStatusMessage(seq, start, sequenceIndex);
+      if (seq == ds)
+      {
+        /*
+         * Convert position in sequence (base 1) to sequence character array
+         * index (base 0)
+         */
+        int start = m.getStart() - 1;
+        setStatusMessage(seq, start, sequenceIndex);
+        return true;
+      }
     }
+    return false;
   }
 
   public void mousePressed(MouseEvent evt)