X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqPanel.java;h=db6add722dfd4578ae8973ffcae2e8708c2a52ea;hb=9876fdccf311378e690c1f9e18db52675d427b89;hp=700f82d4ebdb4a1d0f14794fd9f97475413b721d;hpb=c97f556291e878a0c8e82ebf521a07f67c90234a;p=jalview.git

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index 700f82d..db6add7 100644
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -432,8 +432,9 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     }
     else
     {
-      residue = "X".equalsIgnoreCase(displayChar) ? "X"
-              : ResidueProperties.aa2Triplet.get(displayChar);
+      residue = "X".equalsIgnoreCase(displayChar) ? "X" : ("*"
+              .equals(displayChar) ? "STOP" : ResidueProperties.aa2Triplet
+              .get(displayChar));
       if (residue != null)
       {
         text.append(" Residue: ").append(residue);
@@ -446,36 +447,8 @@ 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());
-
   }
 
   /**
@@ -497,6 +470,10 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     for (Match m : results.getResults())
     {
       SequenceI seq = m.getSequence();
+      if (seq.getDatasetSequence() != null)
+      {
+        seq = seq.getDatasetSequence();
+      }
 
       if (seq == ds)
       {
@@ -587,8 +564,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       }
       if (features != null && features.length > 0)
       {
-        seqCanvas.getFeatureRenderer().amendFeatures(new SequenceI[]
-        { sequence }, features, false, ap);
+        seqCanvas.getFeatureRenderer().amendFeatures(
+                new SequenceI[] { sequence }, features, false, ap);
 
         seqCanvas.highlightSearchResults(null);
       }
@@ -630,8 +607,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       }
 
       int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
-              + hgap
-              + seqCanvas.getAnnotationHeight();
+              + hgap + seqCanvas.getAnnotationHeight();
 
       int y = evt.getY();
       y -= hgap;
@@ -688,8 +664,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       }
 
       int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
-              + hgap
-              + seqCanvas.getAnnotationHeight();
+              + hgap + seqCanvas.getAnnotationHeight();
 
       y -= hgap;
 
@@ -823,8 +798,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     }
     else
     {
-      obj = "X".equalsIgnoreCase(ch) ? "X"
-              : ResidueProperties.aa2Triplet.get(ch);
+      obj = "X".equalsIgnoreCase(ch) ? "X" : ResidueProperties.aa2Triplet
+              .get(ch);
       if (obj != null)
       {
         text.append(" Residue: ").append(obj);
@@ -908,13 +883,15 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       for (int i = 0; i < features.length; i++)
       {
         if (av.getFeaturesDisplayed() == null
-                || !av.getFeaturesDisplayed().isVisible(features[i].getType()))
+                || !av.getFeaturesDisplayed().isVisible(
+                        features[i].getType()))
         {
           continue;
         }
 
         if (features[i].featureGroup != null
-                && !seqCanvas.fr.checkGroupVisibility(features[i].featureGroup,false))
+                && !seqCanvas.fr.checkGroupVisibility(
+                        features[i].featureGroup, false))
         {
           continue;
         }
@@ -1070,8 +1047,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       if (editCommand == null)
       {
         editCommand = new EditCommand(MessageManager.formatMessage(
-                "label.edit_params", new String[]
-                { label }));
+                "label.edit_params", new String[] { label }));
       }
     }
 
@@ -1305,14 +1281,14 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         {
           for (int j = lastres; j < startres; j++)
           {
-            insertChar(j, new SequenceI[]
-            { seq }, fixedRight);
+            insertChar(j, new SequenceI[] { seq }, fixedRight);
           }
         }
         else
         {
-          editCommand.appendEdit(Action.INSERT_GAP, new SequenceI[]
-          { seq }, lastres, startres - lastres, av.getAlignment(), true);
+          editCommand.appendEdit(Action.INSERT_GAP,
+                  new SequenceI[] { seq }, lastres, startres - lastres,
+                  av.getAlignment(), true);
         }
       }
       else
@@ -1327,8 +1303,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
               endEditing();
               break;
             }
-            deleteChar(startres, new SequenceI[]
-            { seq }, fixedRight);
+            deleteChar(startres, new SequenceI[] { seq }, fixedRight);
           }
         }
         else
@@ -1346,8 +1321,9 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
           if (max > 0)
           {
-            editCommand.appendEdit(Action.DELETE_GAP, new SequenceI[]
-            { seq }, startres, max, av.getAlignment(), true);
+            editCommand.appendEdit(Action.DELETE_GAP,
+                    new SequenceI[] { seq }, startres, max,
+                    av.getAlignment(), true);
           }
         }
       }
@@ -1952,22 +1928,24 @@ public class SeqPanel extends Panel implements MouseMotionListener,
   protected boolean selectionFromTranslation(SequenceGroup seqsel,
           ColumnSelection colsel, SelectionSource source)
   {
-    if (!(source instanceof AlignViewportI)) {
+    if (!(source instanceof AlignViewportI))
+    {
       return false;
     }
     final AlignViewportI sourceAv = (AlignViewportI) source;
-    if (sourceAv.getCodingComplement() != av && av.getCodingComplement() != sourceAv)
+    if (sourceAv.getCodingComplement() != av
+            && av.getCodingComplement() != sourceAv)
     {
       return false;
     }
-  
+
     /*
      * Map sequence selection
      */
     SequenceGroup sg = MappingUtils.mapSequenceGroup(seqsel, sourceAv, av);
     av.setSelectionGroup(sg);
     av.isSelectionGroupChanged(true);
-  
+
     /*
      * Map column selection
      */
@@ -1975,10 +1953,10 @@ public class SeqPanel extends Panel implements MouseMotionListener,
             av);
     av.setColumnSelection(cs);
     av.isColSelChanged(true);
-  
+
     ap.scalePanelHolder.repaint();
     ap.repaint();
-  
+
     return true;
   }