Formatting

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

diff --git a/src/jalview/io/PileUpfile.java b/src/jalview/io/PileUpfile.java
index be16169..4715d9c 100755 (executable)
--- a/src/jalview/io/PileUpfile.java
+++ b/src/jalview/io/PileUpfile.java
@@ -1,6 +1,6 @@
 /*\r
  * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
  *\r
  * This program is free software; you can redistribute it and/or\r
  * modify it under the terms of the GNU General Public License\r
@@ -34,41 +34,42 @@ import java.io.*;
 import jalview.datamodel.*;\r
 import jalview.util.*;\r
 \r
-public class PileUpfile  extends MSFfile\r
+public class PileUpfile\r
+    extends MSFfile\r
 {\r
 \r
-    /**\r
-     * Creates a new MSFfile object.\r
-     */\r
-    public PileUpfile()\r
-    {\r
-    }\r
+  /**\r
+   * Creates a new MSFfile object.\r
+   */\r
+  public PileUpfile()\r
+  {\r
+  }\r
 \r
+  /**\r
+   * Creates a new MSFfile object.\r
+   *\r
+   * @param inFile DOCUMENT ME!\r
+   * @param type DOCUMENT ME!\r
+   *\r
+   * @throws IOException DOCUMENT ME!\r
+   */\r
+  public PileUpfile(String inFile, String type)\r
+      throws IOException\r
+  {\r
+    super(inFile, type);\r
+  }\r
 \r
-    /**\r
-     * Creates a new MSFfile object.\r
-     *\r
-     * @param inFile DOCUMENT ME!\r
-     * @param type DOCUMENT ME!\r
-     *\r
-     * @throws IOException DOCUMENT ME!\r
-     */\r
-    public PileUpfile(String inFile, String type) throws IOException\r
-    {\r
-        super(inFile, type);\r
-    }\r
-   /**\r
+  /**\r
    * DOCUMENT ME!\r
    *\r
    * @return DOCUMENT ME!\r
    */\r
   public String print()\r
   {\r
-      return print(getSeqsAsArray());\r
+    return print(getSeqsAsArray());\r
   }\r
 \r
-\r
-  public  String print(SequenceI[] s)\r
+  public String print(SequenceI[] s)\r
   {\r
     StringBuffer out = new StringBuffer("PileUp\n\n");\r
 \r
@@ -86,9 +87,9 @@ public class PileUpfile  extends MSFfile
     }\r
 \r
     out.append("   MSF: " + s[0].getSequence().length +\r
-               "   Type: P    Check:  " + bigChecksum%10000 + "   ..\n\n\n");\r
+               "   Type: P    Check:  " + bigChecksum % 10000 + "   ..\n\n\n");\r
 \r
-    i=0;\r
+    i = 0;\r
     while ( (i < s.length) && (s[i] != null))\r
     {\r
       String seq = s[i].getSequenceAsString();\r
@@ -135,7 +136,7 @@ public class PileUpfile  extends MSFfile
       {\r
         String name = printId(s[j]);\r
 \r
-         out.append(new Format("%-" + maxid + "s").form(name + " "));\r
+        out.append(new Format("%-" + maxid + "s").form(name + " "));\r
 \r
         for (int k = 0; k < 5; k++)\r
         {\r