Merge branch 'features/sequenceFeatureRefactor' into develop

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

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index d0da010..beafa8c 100644 (file)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -185,6 +185,10 @@ public class AlignmentPanel extends GAlignmentPanel implements
     {
       overviewPanel.setBoxPosition();
     }
+    if (this.alignFrame.getSplitViewContainer() != null)
+    {
+      ((SplitFrame) this.alignFrame.getSplitViewContainer()).adjustLayout();
+    }
 
     repaint();
   }
@@ -1322,30 +1326,29 @@ public class AlignmentPanel extends GAlignmentPanel implements
           sy = s * av.getCharHeight() + scaleHeight;
 
           SequenceI seq = av.getAlignment().getSequenceAt(s);
-          SequenceFeature[] features = seq.getDatasetSequence()
-                  .getSequenceFeatures();
+          SequenceFeature[] features = seq.getSequenceFeatures();
           SequenceGroup[] groups = av.getAlignment().findAllGroups(seq);
           for (res = 0; res < alwidth; res++)
           {
             text = new StringBuffer();
-            Object obj = null;
+            String triplet = null;
             if (av.getAlignment().isNucleotide())
             {
-              obj = ResidueProperties.nucleotideName.get(seq.getCharAt(res)
+              triplet = ResidueProperties.nucleotideName.get(seq
+                      .getCharAt(res)
                       + "");
             }
             else
             {
-              obj = ResidueProperties.aa2Triplet.get(seq.getCharAt(res)
+              triplet = ResidueProperties.aa2Triplet.get(seq.getCharAt(res)
                       + "");
             }
 
-            if (obj == null)
+            if (triplet == null)
             {
               continue;
             }
 
-            String triplet = obj.toString();
             int alIndex = seq.findPosition(res);
             gSize = groups.length;
             for (g = 0; g < gSize; g++)
@@ -1493,7 +1496,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
               .getStructureSelectionManager();
       ssm.removeStructureViewerListener(getSeqPanel(), null);
       ssm.removeSelectionListener(getSeqPanel());
-      ssm.removeEditListener(av);
+      ssm.removeCommandListener(av);
       ssm.removeStructureViewerListener(getSeqPanel(), null);
       ssm.removeSelectionListener(getSeqPanel());
       av.setAlignment(null);