X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FPileUpfile.java;h=f54ad9cefb4c6e3b73d2ec028e2d7fda7b39ee4f;hb=refs%2Fheads%2Fmerge%2Fdevelop_JAL-1780_JAL-653_JAL-1892;hp=e4fb76ace04b6ac8ae79a97d626911d5fa1d9e3d;hpb=e601d78bc7762386f570e346a803684c43a66ff1;p=jalview.git
diff --git a/src/jalview/io/PileUpfile.java b/src/jalview/io/PileUpfile.java
index e4fb76a..f54ad9c 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 2.6)
- * 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
@@ -83,7 +86,7 @@ public class PileUpfile extends MSFfile
StringBuffer out = new StringBuffer("PileUp");
out.append(newline);
out.append(newline);
-
+
int max = 0;
int maxid = 0;
@@ -98,8 +101,7 @@ public class PileUpfile extends MSFfile
}
out.append(" MSF: " + s[0].getSequence().length
- + " Type: P Check: " + bigChecksum % 10000
- + " ..");
+ + " Type: P Check: " + bigChecksum % 10000 + " ..");
out.append(newline);
out.append(newline);
out.append(newline);
@@ -131,8 +133,11 @@ public class PileUpfile extends MSFfile
}
maxid++;
- out.append(newline);out.append(newline);out.append("//");
- out.append(newline);out.append(newline);
+ out.append(newline);
+ out.append(newline);
+ out.append("//");
+ out.append(newline);
+ out.append(newline);
int len = 50;