JAL-2292 verify mixed case alignment actually aligns

diff --git a/test/jalview/analysis/TestAlignSeq.java b/test/jalview/analysis/TestAlignSeq.java
index 62250eb..44bea81 100644 (file)
--- a/test/jalview/analysis/TestAlignSeq.java
+++ b/test/jalview/analysis/TestAlignSeq.java
@@ -121,7 +121,9 @@ public class TestAlignSeq
     assertEquals(as.getAStr1(), as.getAStr2().toUpperCase(Locale.ROOT));
 
     Mapping s1tos2 = as.getMappingFromS1(false);
-    checkMapping(s1tos2,s1,ns2);
+    assertEquals("ASdFA",as.getAStr2());
+    // verify mapping is consistent between original all-caps sequences
+    checkMapping(s1tos2,s1,s2);
   }
 
   @Test(groups = { "Functional" })