X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FPileUpfile.java;h=4715d9cd0f49df7bcbb97d6c296b4397c4602c1d;hb=cbd8cafe5f1d302cf490d34a96f8231659afd402;hp=be161694fd7c5cff3f3a631264c73e2c43b87a57;hpb=4d2e0d36506302cc00677527725bcccbdf27d766;p=jalview.git

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