X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=a8577125dd39eda017270013fcaa9964c3928fdc;hb=0ca96db9937136626dcd867e122d1762b28e15bd;hp=31ffdfded164e0dd7d7b4cb495f06eb684351c6d;hpb=63c08febd1f76249b308628611857b9698baaf8d;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 31ffdfd..a857712 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -303,8 +303,13 @@ public class Sequence extends ASequence implements SequenceI
     }
     else
     {
-      System.err
+      if (datasetSequence.getSequenceFeatures() != features
+              && datasetSequence.getSequenceFeatures() != null
+              && datasetSequence.getSequenceFeatures().length > 0)
+      {
+        System.err
               .println("Warning: JAL-2046 side effect ? Possible implementation error: overwriting dataset sequence features by setting sequence features on alignment");
+      }
       datasetSequence.setSequenceFeatures(features);
     }
   }