X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFastaFile.java;h=0c0d186d4db118aacbd7240e9d9aad383dc2031c;hb=35229a3e24b054cc6f3a0a0903a61fc6f6462b6e;hp=b3fb3a140fce8013edfd24676a3593ced1000223;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git

diff --git a/src/jalview/io/FastaFile.java b/src/jalview/io/FastaFile.java
index b3fb3a1..0c0d186 100755
--- a/src/jalview/io/FastaFile.java
+++ b/src/jalview/io/FastaFile.java
@@ -1,20 +1,19 @@
 /*
- * 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)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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.
+ *  
+ * 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/>.
  */
 package jalview.io;
 
@@ -48,12 +47,12 @@ public class FastaFile extends AlignFile
    * Creates a new FastaFile object.
    * 
    * @param inFile
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param type
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @throws IOException
-   *                 DOCUMENT ME!
+   *           DOCUMENT ME!
    */
   public FastaFile(String inFile, String type) throws IOException
   {
@@ -69,7 +68,7 @@ public class FastaFile extends AlignFile
    * DOCUMENT ME!
    * 
    * @throws IOException
-   *                 DOCUMENT ME!
+   *           DOCUMENT ME!
    */
   public void parse() throws IOException
   {
@@ -181,13 +180,13 @@ public class FastaFile extends AlignFile
    * DOCUMENT ME!
    * 
    * @param s
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param len
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param gaps
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param displayId
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
@@ -204,7 +203,7 @@ public class FastaFile extends AlignFile
         out.append(" " + s[i].getDescription());
       }
 
-      out.append("\n");
+      out.append(newline);
 
       int nochunks = (s[i].getLength() / len) + 1;
 
@@ -215,12 +214,12 @@ public class FastaFile extends AlignFile
 
         if (end < s[i].getLength())
         {
-          out.append(s[i].getSequenceAsString(start, end) + "\n");
+          out.append(s[i].getSequenceAsString(start, end) + newline);
         }
         else if (start < s[i].getLength())
         {
           out.append(s[i].getSequenceAsString(start, s[i].getLength())
-                  + "\n");
+                  + newline);
         }
       }