Merge branch 'develop' into Release_2_9_0b1_Branch

[jalview.git] / src / jalview / gui / SeqPanel.java

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 44b537b..3d43d35 100644 (file)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/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.
  * 
@@ -192,8 +192,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       }
 
       int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
-              + hgap
-              + seqCanvas.getAnnotationHeight();
+              + hgap + seqCanvas.getAnnotationHeight();
 
       int y = evt.getY();
       y -= hgap;
@@ -250,8 +249,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       }
 
       int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
-              + hgap
-              + seqCanvas.getAnnotationHeight();
+              + hgap + seqCanvas.getAnnotationHeight();
 
       y -= hgap;
 
@@ -668,11 +666,12 @@ public class SeqPanel extends JPanel implements MouseListener,
   @Override
   public void highlightSequence(SearchResults results)
   {
-    if (results == null || results.equals(lastSearchResults)) {
+    if (results == null || results.equals(lastSearchResults))
+    {
       return;
     }
     lastSearchResults = results;
-    
+
     if (av.isFollowHighlight())
     {
       /*
@@ -696,6 +695,7 @@ public class SeqPanel extends JPanel implements MouseListener,
   {
     return this.ap == null ? null : this.ap.av;
   }
+
   @Override
   public void updateColours(SequenceI seq, int index)
   {
@@ -767,9 +767,9 @@ public class SeqPanel extends JPanel implements MouseListener,
     if (av.isShowSequenceFeatures())
     {
       int rpos;
-      List<SequenceFeature> features = ap.getFeatureRenderer().findFeaturesAtRes(
-              sequence.getDatasetSequence(),
-              rpos = sequence.findPosition(res));
+      List<SequenceFeature> features = ap.getFeatureRenderer()
+              .findFeaturesAtRes(sequence.getDatasetSequence(),
+                      rpos = sequence.findPosition(res));
       seqARep.appendFeatures(tooltipText, rpos, features,
               this.ap.getSeqPanel().seqCanvas.fr.getMinMax());
     }
@@ -856,8 +856,9 @@ public class SeqPanel extends JPanel implements MouseListener,
     }
     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);
@@ -903,7 +904,7 @@ public class SeqPanel extends JPanel implements MouseListener,
          * Convert position in sequence (base 1) to sequence character array
          * index (base 0)
          */
-        int start = m.getStart() - 1;
+        int start = m.getStart() - m.getSequence().getStart();
         setStatusMessage(seq, start, sequenceIndex);
         return;
       }
@@ -1033,7 +1034,8 @@ public class SeqPanel extends JPanel implements MouseListener,
       message.append("Edit group:");
       if (editCommand == null)
       {
-        editCommand = new EditCommand(MessageManager.getString("action.edit_group"));
+        editCommand = new EditCommand(
+                MessageManager.getString("action.edit_group"));
       }
     }
     else
@@ -1046,7 +1048,8 @@ public class SeqPanel extends JPanel implements MouseListener,
       }
       if (editCommand == null)
       {
-        editCommand = new EditCommand(MessageManager.formatMessage("label.edit_params", new String[]{label}));
+        editCommand = new EditCommand(MessageManager.formatMessage(
+                "label.edit_params", new String[] { label }));
       }
     }
 
@@ -1284,14 +1287,13 @@ public class SeqPanel extends JPanel implements MouseListener,
         {
           for (int j = lastres; j < startres; j++)
           {
-            insertChar(j, new SequenceI[]
-            { seq }, fixedRight);
+            insertChar(j, new SequenceI[] { seq }, fixedRight);
           }
         }
         else
         {
-          appendEdit(Action.INSERT_GAP, new SequenceI[]
-          { seq }, lastres, startres - lastres);
+          appendEdit(Action.INSERT_GAP, new SequenceI[] { seq }, lastres,
+                  startres - lastres);
         }
       }
       else
@@ -1308,8 +1310,7 @@ public class SeqPanel extends JPanel implements MouseListener,
                 endEditing();
                 break;
               }
-              deleteChar(startres, new SequenceI[]
-              { seq }, fixedRight);
+              deleteChar(startres, new SequenceI[] { seq }, fixedRight);
             }
           }
           else
@@ -1327,8 +1328,8 @@ public class SeqPanel extends JPanel implements MouseListener,
 
             if (max > 0)
             {
-              appendEdit(Action.DELETE_GAP, new SequenceI[]
-              { seq }, startres, max);
+              appendEdit(Action.DELETE_GAP, new SequenceI[] { seq },
+                      startres, max);
             }
           }
         }
@@ -1338,14 +1339,13 @@ public class SeqPanel extends JPanel implements MouseListener,
           {
             for (int j = lastres; j < startres; j++)
             {
-              insertChar(j, new SequenceI[]
-              { seq }, fixedRight);
+              insertChar(j, new SequenceI[] { seq }, fixedRight);
             }
           }
           else
           {
-            appendEdit(Action.INSERT_NUC, new SequenceI[]
-            { seq }, lastres, startres - lastres);
+            appendEdit(Action.INSERT_NUC, new SequenceI[] { seq }, lastres,
+                    startres - lastres);
           }
         }
       }
@@ -1401,8 +1401,7 @@ public class SeqPanel extends JPanel implements MouseListener,
     final Edit edit = new EditCommand().new Edit(action, seq, pos, count,
             av.getAlignment().getGapCharacter());
 
-    editCommand.appendEdit(edit, av.getAlignment(),
-            true, null);
+    editCommand.appendEdit(edit, av.getAlignment(), true, null);
   }
 
   void deleteChar(int j, SequenceI[] seq, int fixedColumn)
@@ -1468,21 +1467,23 @@ public class SeqPanel extends JPanel implements MouseListener,
         av.setSelectionGroup(null);
       }
 
-      List<SequenceFeature> features = seqCanvas.getFeatureRenderer().findFeaturesAtRes(
-              sequence.getDatasetSequence(),
-              sequence.findPosition(findRes(evt)));
+      List<SequenceFeature> features = seqCanvas.getFeatureRenderer()
+              .findFeaturesAtRes(sequence.getDatasetSequence(),
+                      sequence.findPosition(findRes(evt)));
 
-      if (features != null && features.size()> 0)
+      if (features != null && features.size() > 0)
       {
         SearchResults highlight = new SearchResults();
-        highlight.addResult(sequence, features.get(0).getBegin(),
-                features.get(0).getEnd());
+        highlight.addResult(sequence, features.get(0).getBegin(), features
+                .get(0).getEnd());
         seqCanvas.highlightSearchResults(highlight);
       }
-      if (features != null && features.size()> 0)
+      if (features != null && features.size() > 0)
       {
-        seqCanvas.getFeatureRenderer().amendFeatures(new SequenceI[]
-        { sequence }, features.toArray(new SequenceFeature[features.size()]), false, ap);
+        seqCanvas.getFeatureRenderer().amendFeatures(
+                new SequenceI[] { sequence },
+                features.toArray(new SequenceFeature[features.size()]),
+                false, ap);
 
         seqCanvas.highlightSearchResults(null);
       }
@@ -1597,10 +1598,11 @@ public class SeqPanel extends JPanel implements MouseListener,
 
     if (javax.swing.SwingUtilities.isRightMouseButton(evt))
     {
-      List<SequenceFeature> allFeatures = ap.getFeatureRenderer().findFeaturesAtRes(
-              sequence.getDatasetSequence(), sequence.findPosition(res));
+      List<SequenceFeature> allFeatures = ap.getFeatureRenderer()
+              .findFeaturesAtRes(sequence.getDatasetSequence(),
+                      sequence.findPosition(res));
       Vector links = new Vector();
-      for (SequenceFeature sf:allFeatures)
+      for (SequenceFeature sf : allFeatures)
       {
         if (sf.links != null)
         {
@@ -1916,8 +1918,7 @@ public class SeqPanel extends JPanel implements MouseListener,
     // handles selection messages...
     // TODO: extend config options to allow user to control if selections may be
     // shared between viewports.
-    boolean iSentTheSelection = (av == source
-            || (source instanceof AlignViewport && ((AlignmentViewport) source)
+    boolean iSentTheSelection = (av == source || (source instanceof AlignViewport && ((AlignmentViewport) source)
             .getSequenceSetId().equals(av.getSequenceSetId())));
     if (iSentTheSelection || !av.followSelection)
     {
@@ -2033,11 +2034,13 @@ public class SeqPanel extends JPanel implements MouseListener,
   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;
     }