dont convert to uppercase

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