X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FPileUpfile.java;h=4715d9cd0f49df7bcbb97d6c296b4397c4602c1d;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=fa7780227d9e018d013840f64b64ef6087b1ab64;hpb=174230b4233d9ce80f94527768d2cd2f76da11ab;p=jalview.git

diff --git a/src/jalview/io/PileUpfile.java b/src/jalview/io/PileUpfile.java
index fa77802..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");
 
@@ -80,21 +81,21 @@ public class PileUpfile  extends MSFfile
     int[] checksums = new int[s.length];
     while (i < s.length)
     {
-      checksums[i] = checkSum(s[i].getSequence());
+      checksums[i] = checkSum(s[i].getSequenceAsString());
       bigChecksum += checksums[i];
       i++;
     }
 
-    out.append("   MSF: " + s[0].getSequence().length() +
-               "   Type: P    Check:  " + bigChecksum%10000 + "   ..\n\n\n");
+    out.append("   MSF: " + s[0].getSequence().length +
+               "   Type: P    Check:  " + bigChecksum % 10000 + "   ..\n\n\n");
 
-    i=0;
+    i = 0;
     while ( (i < s.length) && (s[i] != null))
     {
-      String seq = s[i].getSequence();
+      String seq = s[i].getSequenceAsString();
       out.append(" Name: " + printId(s[i]) +
                  " oo  Len:  " +
-                 s[i].getSequence().length() + "  Check:  " + checksums[i] +
+                 seq.length() + "  Check:  " + checksums[i] +
                  "  Weight:  1.00\n");
 
       if (seq.length() > max)
@@ -135,17 +136,17 @@ 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++)
         {
           int start = (i * 50) + (k * 10);
           int end = start + 10;
 
-          if ( (end < s[j].getSequence().length()) &&
-              (start < s[j].getSequence().length()))
+          if ( (end < s[j].getSequence().length) &&
+              (start < s[j].getSequence().length))
           {
-            out.append(s[j].getSequence().substring(start, end));
+            out.append(s[j].getSequence(start, end));
 
             if (k < 4)
             {
@@ -158,9 +159,9 @@ public class PileUpfile  extends MSFfile
           }
           else
           {
-            if (start < s[j].getSequence().length())
+            if (start < s[j].getSequence().length)
             {
-              out.append(s[j].getSequence().substring(start));
+              out.append(s[j].getSequenceAsString().substring(start));
               out.append("\n");
             }
             else