JAL-2110 ensuring mapped dbrefs between protein and cds

[jalview.git] / src / jalview / datamodel / Alignment.java

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 2b194cc..f5665db 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -30,7 +30,6 @@ import java.util.Collections;
 import java.util.Enumeration;
 import java.util.HashSet;
 import java.util.Hashtable;
-import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
@@ -1724,6 +1723,10 @@ public class Alignment implements AlignmentI
     {
       return AlignmentUtils.alignProteinAsDna(this, al);
     }
+    else if (thatIsProtein && thisIsNucleotide)
+    {
+      return AlignmentUtils.alignCdsAsProtein(this, al);
+    }
     return AlignmentUtils.alignAs(this, al);
   }