update author list in license for (JAL-826)

[jalview.git] / src / jalview / io / BLCFile.java

diff --git a/src/jalview/io/BLCFile.java b/src/jalview/io/BLCFile.java
index 46cf02a..03b2edf 100755 (executable)
--- a/src/jalview/io/BLCFile.java
+++ b/src/jalview/io/BLCFile.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 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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.io;
 
@@ -44,12 +43,12 @@ public class BLCFile extends AlignFile
    * Creates a new BLCFile object.
    * 
    * @param inFile
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param type
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @throws IOException
-   *                 DOCUMENT ME!
+   *           DOCUMENT ME!
    */
   public BLCFile(String inFile, String type) throws IOException
   {
@@ -143,7 +142,7 @@ public class BLCFile extends AlignFile
         {
           // header lines - keep them for the alignment comments.
           headerLines.append(line);
-          headerLines.append("\n");
+          headerLines.append(newline);
           numHeaderLines++;
         }
       } while (!idsFound);
@@ -197,7 +196,7 @@ public class BLCFile extends AlignFile
     if (seqs.size() > 0)
     {
       if (headerLines.length() > 1 + numHeaderLines) // could see if buffer is
-                                                      // just whitespace or not.
+        // just whitespace or not.
         setAlignmentProperty("Comments", headerLines.toString());
       setAlignmentProperty("iteration", "" + iterationCount);
     }
@@ -217,7 +216,7 @@ public class BLCFile extends AlignFile
    * DOCUMENT ME!
    * 
    * @param s
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
@@ -241,7 +240,7 @@ public class BLCFile extends AlignFile
         out.append(" " + s[i].getDescription());
       }
 
-      out.append("\n");
+      out.append(newline);
 
       if (s[i].getSequence().length > max)
       {
@@ -251,7 +250,8 @@ public class BLCFile extends AlignFile
       i++;
     }
 
-    out.append("* iteration 1\n");
+    out.append("* iteration 1");
+    out.append(newline);
 
     for (int j = 0; j < max; j++)
     {
@@ -271,10 +271,11 @@ public class BLCFile extends AlignFile
         i++;
       }
 
-      out.append("\n");
+      out.append(newline);
     }
 
-    out.append("*\n");
+    out.append("*");
+    out.append(newline);
 
     return out.toString();
   }