JAL-727

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

diff --git a/src/jalview/io/PileUpfile.java b/src/jalview/io/PileUpfile.java
index dd28176..e4fb76a 100755 (executable)
--- a/src/jalview/io/PileUpfile.java
+++ b/src/jalview/io/PileUpfile.java
@@ -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();