X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fio%2FPIRFile.java;h=07dc6b544357331d8f0d9558af973e48280e159c;hb=57c960648b550f10c7db40e39c7bb6a761d732b1;hp=ef06b0cb6c1269db2f40eda805e01d1db8fc9e9e;hpb=8a6fa9ea9900d0f106529c3f6283e7f9d76dd2cb;p=jalview.git

diff --git a/src/jalview/io/PIRFile.java b/src/jalview/io/PIRFile.java
index ef06b0c..07dc6b5 100755
--- a/src/jalview/io/PIRFile.java
+++ b/src/jalview/io/PIRFile.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, 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 file is part of Jalview.
  * 
@@ -127,16 +127,19 @@ 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
@@ -144,21 +147,26 @@ 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");
+                    + (s[i].getEnd() - s[i].getStart() + 1) + " residues");
+            out.append(newline);
           }
         }
       }
@@ -171,11 +179,13 @@ 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);
         }
       }