X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FPileUpfile.java;h=79c6531ee68529bb793f00db9693f49446c15817;hb=a5be53df96dabea00429121a742ae476872640eb;hp=00190750d5889a68ef72f3c0dbfa46946098f2fe;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git

diff --git a/src/jalview/io/PileUpfile.java b/src/jalview/io/PileUpfile.java
index 0019075..79c6531 100755
--- a/src/jalview/io/PileUpfile.java
+++ b/src/jalview/io/PileUpfile.java
@@ -1,19 +1,22 @@
 /*
- * 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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.
- * 
+ * 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/>.
+ * 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;
 
@@ -32,10 +35,10 @@ package jalview.io;
  * found in Emboss (thanks David Martin!)
  * 
  */
-import java.io.*;
+import jalview.datamodel.SequenceI;
+import jalview.util.Format;
 
-import jalview.datamodel.*;
-import jalview.util.*;
+import java.io.IOException;
 
 public class PileUpfile extends MSFfile
 {
@@ -73,14 +76,18 @@ public class PileUpfile extends MSFfile
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public String print()
   {
     return print(getSeqsAsArray());
   }
 
+  @Override
   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 +103,18 @@ 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)
       {
@@ -125,16 +135,15 @@ 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;
 
-    int nochunks = (max / len) + 1;
-
-    if ((max % len) == 0)
-    {
-      nochunks--;
-    }
+    int nochunks = (max / len) + (max % len > 0 ? 1 : 0);
 
     for (i = 0; i < nochunks; i++)
     {
@@ -162,7 +171,7 @@ public class PileUpfile extends MSFfile
             }
             else
             {
-              out.append("\n");
+              out.append(newline);
             }
           }
           else
@@ -170,13 +179,13 @@ 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 +194,7 @@ public class PileUpfile extends MSFfile
         j++;
       }
 
-      out.append("\n");
+      out.append(newline);
     }
 
     return out.toString();