fix for JAL-917 - ensure all sequence strings are made uppercase before alignment

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 9994634..a27c51b 100755 (executable)
--- 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);
   }
 
   /**