X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=6532a2dbeb0d57724bc457dfbce176377a416fec;hb=b028e684c807365decd0c6e6111aa4bf368a6fa8;hp=73ccdc53966e03e5303dabfa0072ed0cea2350e9;hpb=eb3e681d6e82ccdd5d312d1981dfb306e7f479f0;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 73ccdc5..6532a2d 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -1830,7 +1830,13 @@ public class Alignment implements AlignmentI, AutoCloseable
     {
       return AlignmentUtils.alignCdsAsProtein(this, al);
     }
-    return AlignmentUtils.alignAs(this, al);
+    else if (thatIsProtein && !thisIsNucleotide)
+    {
+    	// honour sense we were called - align this according to al 
+    	return AlignmentUtils.alignAs(this, al);
+    }
+    // otherwise doing a DNA to DNA alignment - so use legacy obverse sense
+    return AlignmentUtils.alignAs(al, this);    
   }
 
   /**