X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignedCodonFrame.java;h=207069a48784ebd69611dd1cb89802eca8683940;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=3b592497c3648180ec051c017a276c559f314665;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git

diff --git a/src/jalview/datamodel/AlignedCodonFrame.java b/src/jalview/datamodel/AlignedCodonFrame.java
index 3b59249..207069a 100644
--- a/src/jalview/datamodel/AlignedCodonFrame.java
+++ b/src/jalview/datamodel/AlignedCodonFrame.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
- * This program 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 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
  * 
- * This program 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.
+ * 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.
  * 
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * 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/>.
  */
 package jalview.datamodel;
 
@@ -37,8 +36,8 @@ public class AlignedCodonFrame
   public int[][] codons = null;
 
   /**
-   * width of protein sequence alignement implicit assertion that codons.length >=
-   * aaWidth
+   * width of protein sequence alignement implicit assertion that codons.length
+   * >= aaWidth
    */
   public int aaWidth = 0;
 
@@ -258,7 +257,7 @@ public class AlignedCodonFrame
    * test to see if codon frame involves seq in any way
    * 
    * @param seq
-   *                a nucleotide or protein sequence
+   *          a nucleotide or protein sequence
    * @return true if a mapping exists to or from this sequence to any translated
    *         sequence
    */
@@ -273,9 +272,9 @@ public class AlignedCodonFrame
    * 
    * @param seq
    * @param index
-   *                position in seq
+   *          position in seq
    * @param results
-   *                where highlighted regions go
+   *          where highlighted regions go
    */
   public void markMappedRegion(SequenceI seq, int index,
           SearchResults results)