X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FSeqCanvas.java;h=0e2773ded2a3cb6fddd31b049681864a3f8c1e2f;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=2296ab12e9a7da44373933f5190022bc7966ffb1;hpb=d053a3c980cf4318b9a19a255f9fc870e74de989;p=jalview.git

diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index 2296ab1..0e2773d 100755
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -1,19 +1,22 @@
 /*
- * 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 2.8.2b1)
+ * 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.
- * 
+ * 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/>.
+ * 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;
 
@@ -348,7 +351,7 @@ public class SeqCanvas extends Panel
     String mask = "0";
     int maxWidth = 0;
     int tmp;
-    AlignmentI alignment=av.getAlignment();
+    AlignmentI alignment = av.getAlignment();
     for (int i = 0; i < alignment.getHeight(); i++)
     {
       tmp = alignment.getSequenceAt(i).getEnd();
@@ -643,7 +646,7 @@ public class SeqCanvas extends Panel
 
     if ((group == null) && (av.getAlignment().getGroups().size() > 0))
     {
-      group = (SequenceGroup) av.getAlignment().getGroups().elementAt(0);
+      group = (SequenceGroup) av.getAlignment().getGroups().get(0);
       groupIndex = 0;
     }
 
@@ -675,7 +678,8 @@ public class SeqCanvas extends Panel
           {
             if ((bottom == -1)
                     && (i >= alHeight || !group.getSequences(null)
-                            .contains(av.getAlignment().getSequenceAt(i + 1))))
+                            .contains(
+                                    av.getAlignment().getSequenceAt(i + 1))))
             {
               bottom = sy + av.charHeight;
             }
@@ -799,8 +803,8 @@ public class SeqCanvas extends Panel
           break;
         }
 
-        group = (SequenceGroup) av.getAlignment().getGroups().elementAt(
-                groupIndex);
+        group = (SequenceGroup) av.getAlignment().getGroups()
+                .get(groupIndex);
       } while (groupIndex < av.getAlignment().getGroups().size());
 
     }