X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=b310ab9f448bfe79bf310a04214a883a78ff125c;hb=ce36ce68c3ec8d050f70163833e28f58e26bde89;hp=54b1cb615e5816bf38ae423a15a362238fc9fbc9;hpb=d2299844ae932a515a5007f30caf766a2c83ad97;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 54b1cb6..b310ab9 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -4763,12 +4763,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           AlignmentI copyAlignment = null;
           final SequenceI[] sequenceSelection = AlignFrame.this.viewport
                   .getSequenceSelection();
-          // List<AlignedCodonFrame> cf = xrefs.getCodonFrames();
           boolean copyAlignmentIsAligned = false;
           if (dna)
           {
             copyAlignment = AlignmentUtils.makeCdsAlignment(
-                    sequenceSelection, dataset);
+                    sequenceSelection, dataset, xrefsAlignment);
             if (copyAlignment.getHeight() == 0)
             {
               System.err.println("Failed to make CDS alignment");