JAL-1517 update copyright to version 2.8.2

[jalview.git] / src / jalview / appletgui / PaintRefresher.java

diff --git a/src/jalview/appletgui/PaintRefresher.java b/src/jalview/appletgui/PaintRefresher.java
index 25e529b..2213629 100755 (executable)
--- a/src/jalview/appletgui/PaintRefresher.java
+++ b/src/jalview/appletgui/PaintRefresher.java
@@ -1,23 +1,25 @@
 /*
- * 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 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * 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 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.appletgui;
 
 import java.util.*;
+import java.util.List;
 
 import java.awt.*;
 
@@ -183,7 +185,13 @@ public class PaintRefresher
       {
         if (i < comp.getHeight())
         {
-          comp.getSequences().insertElementAt(a1[i], i);
+          // TODO: the following does not trigger any recalculation of
+          // height/etc, or maintain the dataset
+          List<SequenceI> alsq;
+          synchronized (alsq = comp.getSequences())
+          {
+            alsq.add(i, a1[i]);
+          }
         }
         else
         {
@@ -235,11 +243,12 @@ public class PaintRefresher
     {
       if (comps.elementAt(i) instanceof AlignmentPanel)
       {
-        tmp.addElement(((AlignmentPanel) comps.elementAt(i)));
+        tmp.addElement(comps.elementAt(i));
       }
     }
     AlignmentPanel[] result = new AlignmentPanel[tmp.size()];
-    for (int ix=0;ix<result.length;ix++) {
+    for (int ix = 0; ix < result.length; ix++)
+    {
       result[ix] = (AlignmentPanel) tmp.elementAt(ix);
     }