From b1df279000fab2124eddd800faed12e193dab7d1 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 16 Jun 2005 09:48:26 +0000
Subject: [PATCH] dont convert to uppercase

---
 src/jalview/io/FastaFile.java |    5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/src/jalview/io/FastaFile.java b/src/jalview/io/FastaFile.java
index adfa967..458465e 100755
--- a/src/jalview/io/FastaFile.java
+++ b/src/jalview/io/FastaFile.java
@@ -43,7 +43,6 @@ public class FastaFile extends AlignFile {
         String id = "";
         StringBuffer seq = new StringBuffer();
         int count = 0;
-        boolean flag = false;
 
         int sstart = 0;
         int send = 0;
@@ -60,10 +59,10 @@ public class FastaFile extends AlignFile {
                     if (count != 0) {
                         if (sstart != 0) {
                             seqs.addElement(new Sequence(id,
-                                    seq.toString().toUpperCase(), sstart, send));
+                                    seq.toString(), sstart, send));
                         } else {
                             seqs.addElement(new Sequence(id,
-                                    seq.toString().toUpperCase(), 1,
+                                    seq.toString(), 1,
                                     seq.length()));
                         }
                     }
-- 
1.7.10.2