X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FPileUpfile.java;h=728d1c6f2ba67d772db86abf71c83f652760d1d2;hb=2ffe2deedb1527c067060646055bddd18d41d367;hp=1cb5b4365bfdb649af201faead76a75213e53527;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git

diff --git a/src/jalview/io/PileUpfile.java b/src/jalview/io/PileUpfile.java
index 1cb5b43..728d1c6 100755
--- a/src/jalview/io/PileUpfile.java
+++ b/src/jalview/io/PileUpfile.java
@@ -131,7 +131,7 @@ public class PileUpfile
         String seq = seqhash.get(head).toString();
 
         int start = 1;
-        int end = seq.length();
+        int end = -1;
 
         if (maxLength < head.length())
         {
@@ -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);
           }