From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 6 Jul 2005 12:16:42 +0000 (+0000)
Subject: Sequence to Uppercase before checksum
X-Git-Tag: Release_2_01~25
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=13b2b876b5bc46693d881b4551842279158311f5;p=jalview.git

Sequence to Uppercase before checksum
---

diff --git a/src/jalview/io/PileUpfile.java b/src/jalview/io/PileUpfile.java
index 1cb5b43..c200c5e 100755
--- a/src/jalview/io/PileUpfile.java
+++ b/src/jalview/io/PileUpfile.java
@@ -175,18 +175,20 @@ public class PileUpfile
     //String chars =  "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz.*~&@";
     int check = 0;
 
+    String sequence = seq.toUpperCase();
+
     String index = "--------------------------------------&---*---.-----------------@ABCDEFGHIJKLMNOPQRSTUVWXYZ------ABCDEFGHIJKLMNOPQRSTUVWXYZ----@";
     index += "--------------------------------------------------------------------------------------------------------------------------------";
 
-    for (int i = 0; i < seq.length(); i++)
+    for (int i = 0; i < sequence.length(); i++)
     {
       try
       {
-        if (i < seq.length())
+        if (i < sequence.length())
         {
-          int pos = index.indexOf(seq.substring(i, i + 1));
+          int pos = index.indexOf(sequence.charAt(i));
 
-          if (!index.substring(pos, pos + 1).equals("_"))
+          if (index.charAt(pos)!='_')
           {
             check += ( ( (i % 57) + 1) * pos);
           }