JAL-1364 use gapMap to map RNAalifold annotation onto correct columns

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

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index f982ccc..63c6033 100755 (executable)
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -1,13 +1,13 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
@@ -572,7 +572,8 @@ public class SeqCanvas extends JComponent
           annotations = new AnnotationPanel(av);
         }
 
-        annotations.renderer.drawComponent(annotations, av, (Graphics2D) g, -1, startRes, endx + 1);
+        annotations.renderer.drawComponent(annotations, av, (Graphics2D) g,
+                -1, startRes, endx + 1);
         g.translate(0, -cHeight - ypos - 3);
       }
       g.setClip(clip);
@@ -759,7 +760,7 @@ public class SeqCanvas extends JComponent
 
     if ((group == null) && (av.getAlignment().getGroups().size() > 0))
     {
-      group = (SequenceGroup) av.getAlignment().getGroups().elementAt(0);
+      group = (SequenceGroup) av.getAlignment().getGroups().get(0);
       groupIndex = 0;
     }
 
@@ -920,8 +921,8 @@ public class SeqCanvas extends JComponent
           break;
         }
 
-        group = (SequenceGroup) av.getAlignment().getGroups().elementAt(
-                groupIndex);
+        group = (SequenceGroup) av.getAlignment().getGroups()
+                .get(groupIndex);
 
       } while (groupIndex < av.getAlignment().getGroups().size());