Formatting

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

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