X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FPIRFile.java;h=adbf81a02538be17f80bfd5e3fdcde9daafebec4;hb=581e7e5a0736b3b5e5ade54656c194b399b2a3ec;hp=4c10abe664671fa759a5547b0b71e44b0b447637;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git

diff --git a/src/jalview/io/PIRFile.java b/src/jalview/io/PIRFile.java
index 4c10abe..adbf81a 100755
--- a/src/jalview/io/PIRFile.java
+++ b/src/jalview/io/PIRFile.java
@@ -1,20 +1,22 @@
 /*
- * 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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.io;
 
@@ -128,16 +130,19 @@ public class PIRFile extends AlignFile
         // tRNA N3
         // other functional RNA N1
 
-        out.append(">N1;" + s[i].getName() + "\n");
+        out.append(">N1;" + s[i].getName());
+        out.append(newline);
         if (s[i].getDescription() == null)
         {
           out.append(s[i].getName() + " "
                   + (s[i].getEnd() - s[i].getStart() + 1));
-          out.append(is_NA ? " bases\n" : " residues\n");
+          out.append(is_NA ? " bases" : " residues");
+          out.append(newline);
         }
         else
         {
-          out.append(s[i].getDescription() + "\n");
+          out.append(s[i].getDescription());
+          out.append(newline);
         }
       }
       else
@@ -145,23 +150,26 @@ public class PIRFile extends AlignFile
 
         if (useModellerOutput)
         {
-          out.append(">P1;" + s[i].getName() + "\n");
+          out.append(">P1;" + s[i].getName());
+          out.append(newline);
           md = new ModellerDescription(s[i]);
-          out.append(md.getDescriptionLine() + "\n");
+          out.append(md.getDescriptionLine());
+          out.append(newline);
         }
         else
         {
-          out.append(">P1;" + printId(s[i]) + "\n");
+          out.append(">P1;" + printId(s[i]));
+          out.append(newline);
           if (s[i].getDescription() != null)
           {
-            out.append(s[i].getDescription() + "\n");
+            out.append(s[i].getDescription());
+            out.append(newline);
           }
           else
           {
-            out
-                    .append(s[i].getName() + " "
-                            + (s[i].getEnd() - s[i].getStart() + 1)
-                            + " residues\n");
+            out.append(s[i].getName() + " "
+                    + (s[i].getEnd() - s[i].getStart() + 1) + " residues");
+            out.append(newline);
           }
         }
       }
@@ -174,11 +182,13 @@ public class PIRFile extends AlignFile
 
         if (end < seq.length())
         {
-          out.append(seq.substring(start, end) + "\n");
+          out.append(seq.substring(start, end));
+          out.append(newline);
         }
         else if (start < seq.length())
         {
-          out.append(seq.substring(start) + "\n");
+          out.append(seq.substring(start));
+          out.append(newline);
         }
       }