X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FPileUpfile.java;h=571c469038a24f4fa408c0c5b4202c5b5619e30d;hb=86838d2566aadd780bd460bdc1276eec77875e26;hp=00190750d5889a68ef72f3c0dbfa46946098f2fe;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git

diff --git a/src/jalview/io/PileUpfile.java b/src/jalview/io/PileUpfile.java
index 0019075..571c469 100755
--- a/src/jalview/io/PileUpfile.java
+++ b/src/jalview/io/PileUpfile.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * 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.
  * 
@@ -80,8 +80,10 @@ public class PileUpfile extends MSFfile
 
   public String print(SequenceI[] s)
   {
-    StringBuffer out = new StringBuffer("PileUp\n\n");
-
+    StringBuffer out = new StringBuffer("PileUp");
+    out.append(newline);
+    out.append(newline);
+    
     int max = 0;
     int maxid = 0;
 
@@ -97,14 +99,18 @@ public class PileUpfile extends MSFfile
 
     out.append("   MSF: " + s[0].getSequence().length
             + "   Type: P    Check:  " + bigChecksum % 10000
-            + "   ..\n\n\n");
+            + "   ..");
+    out.append(newline);
+    out.append(newline);
+    out.append(newline);
 
     i = 0;
     while ((i < s.length) && (s[i] != null))
     {
       String seq = s[i].getSequenceAsString();
       out.append(" Name: " + printId(s[i]) + " oo  Len:  " + seq.length()
-              + "  Check:  " + checksums[i] + "  Weight:  1.00\n");
+              + "  Check:  " + checksums[i] + "  Weight:  1.00");
+      out.append(newline);
 
       if (seq.length() > max)
       {
@@ -125,7 +131,8 @@ public class PileUpfile extends MSFfile
     }
 
     maxid++;
-    out.append("\n\n//\n\n");
+    out.append(newline);out.append(newline);out.append("//");
+    out.append(newline);out.append(newline);
 
     int len = 50;
 
@@ -162,7 +169,7 @@ public class PileUpfile extends MSFfile
             }
             else
             {
-              out.append("\n");
+              out.append(newline);
             }
           }
           else
@@ -170,13 +177,13 @@ public class PileUpfile extends MSFfile
             if (start < s[j].getSequence().length)
             {
               out.append(s[j].getSequenceAsString().substring(start));
-              out.append("\n");
+              out.append(newline);
             }
             else
             {
               if (k == 0)
               {
-                out.append("\n");
+                out.append(newline);
               }
             }
           }
@@ -185,7 +192,7 @@ public class PileUpfile extends MSFfile
         j++;
       }
 
-      out.append("\n");
+      out.append(newline);
     }
 
     return out.toString();