X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignSeq.java;h=a27c51bc71763c716df8a84769c682630227b6c7;hb=f7f284d2b85186bb9133e7d9d0a245661ba349c8;hp=9994634366d19c1aa4b038d654bf355db9d1dc0d;hpb=24083e614ed7907e0e3e2b631d642d6179ff7b20;p=jalview.git

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 9994634..a27c51b 100755
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -126,7 +126,7 @@ public class AlignSeq
    */
   public AlignSeq(SequenceI s1, SequenceI s2, String type)
   {
-    SeqInit(s1, s1.getSequenceAsString().toUpperCase(), s2, s2.getSequenceAsString().toUpperCase(),
+    SeqInit(s1, s1.getSequenceAsString(), s2, s2.getSequenceAsString(),
             type);
   }
 
@@ -143,7 +143,7 @@ public class AlignSeq
   public AlignSeq(SequenceI s1, String string1, SequenceI s2,
           String string2, String type)
   {
-    SeqInit(s1, string1, s2, string2, type);
+    SeqInit(s1, string1.toUpperCase(), s2, string2.toUpperCase(), type);
   }
 
   /**