X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAMSAFile.java;h=c39675bae0ea20410a7611c52df0ff560c6de49e;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=20cf7456b7c91093ff6278444cf6d961faee5827;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git

diff --git a/src/jalview/io/AMSAFile.java b/src/jalview/io/AMSAFile.java
index 20cf745..c39675b 100644
--- a/src/jalview/io/AMSAFile.java
+++ b/src/jalview/io/AMSAFile.java
@@ -1,20 +1,20 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
  * 
- * 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.
+ *  
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * 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.io;
 
@@ -61,7 +61,7 @@ public class AMSAFile extends jalview.io.FastaFile
           out.append(" " + aa.description);
         }
 
-        out.append("\n");
+        out.append(newline);
 
         int nochunks = Math.min(aa.annotations.length, al.getWidth()) / len
                 + 1;
@@ -86,11 +86,15 @@ public class AMSAFile extends jalview.io.FastaFile
             {
               ch = aa.annotations[k].displayCharacter;
             }
-
+            if (ch.length() > 1)
+            {
+              this.warningMessage = "Truncated column annotation to first letter.";
+              ch = ch.substring(0, 1);
+            }
             out.append(ch);
 
           }
-          out.append("\n");
+          out.append(newline);
         }
       }
     }