X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FPileUpfile.java;h=efe80e561a6e3fcb636d42a2a3d54dbf37986d9d;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=00190750d5889a68ef72f3c0dbfa46946098f2fe;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git

diff --git a/src/jalview/io/PileUpfile.java b/src/jalview/io/PileUpfile.java
index 0019075..efe80e5 100755
--- a/src/jalview/io/PileUpfile.java
+++ b/src/jalview/io/PileUpfile.java
@@ -1,19 +1,20 @@
 /*
- * 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 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.io;
 
@@ -57,6 +58,7 @@ public class PileUpfile extends MSFfile
    * 
    * @throws IOException
    *           DOCUMENT ME!
+
    */
   public PileUpfile(String inFile, String type) throws IOException
   {
@@ -80,7 +82,9 @@ 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;
@@ -96,15 +100,18 @@ public class PileUpfile extends MSFfile
     }
 
     out.append("   MSF: " + s[0].getSequence().length
-            + "   Type: P    Check:  " + bigChecksum % 10000
-            + "   ..\n\n\n");
+            + "   Type: P    Check:  " + bigChecksum % 10000 + "   ..");
+    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 +132,11 @@ 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 +173,7 @@ public class PileUpfile extends MSFfile
             }
             else
             {
-              out.append("\n");
+              out.append(newline);
             }
           }
           else
@@ -170,13 +181,13 @@ 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 +196,7 @@ public class PileUpfile extends MSFfile
         j++;
       }
 
-      out.append("\n");
+      out.append(newline);
     }
 
     return out.toString();