X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignSeq.java;h=0af85f145b8236d4c2a8d2d5590721d277ed6f8c;hb=38c2f5336bb602570ab698985810b870fa7390de;hp=3c1f5be415798a68fac10bb3c087d20f1c591cca;hpb=621a628afc1f6ee7a2778b9d0ae2729b88fe5bfd;p=jalview.git

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 3c1f5be..0af85f1 100755
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -1,6 +1,6 @@
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+* Copyright (C) 2006 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
@@ -751,17 +751,24 @@ public class AlignSeq
 
         for (int i = 0; i < s.length(); i++)
         {
-            String ss = s.substring(i, i + 1).toUpperCase();
+           // String ss = s.substring(i, i + 1).toUpperCase();
+            char c = s.charAt(i);
+            if ('a' <= c && c <= 'z')
+            {
+              // TO UPPERCASE !!!
+              c -= ('a' - 'A');
+            }
+
 
             try
             {
                 if (type.equals("pep"))
                 {
-                    seq1[i] = ((Integer) ResidueProperties.aaHash.get(ss)).intValue();
+                    seq1[i] = ResidueProperties.aaIndex[c];
                 }
                 else if (type.equals("dna"))
                 {
-                    seq1[i] = ((Integer) dnaHash.get(ss)).intValue();
+                    seq1[i] = ResidueProperties.nucleotideIndex[c];
                 }
 
                 if (seq1[i] > 23)