merge

diff --combined src/jalview/gui/AlignFrame.java
index 895f2f6,d548695..818c150
--- 1/src/jalview/gui/AlignFrame.java
--- 2/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@@ -1313,7 -1313,6 +1313,7 @@@ public class AlignFrame extends GAlignF
  
      if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
      {
 +      viewport.setExportHiddenSeqs(settings.isExportHiddenSequences());
        omitHidden = viewport.getViewAsString(false);
      }
  
@@@ -4680,6 -4679,17 +4680,17 @@@
      return showp;
    }
  
+   /**
+    * Finds and displays cross-references for the selected sequences (protein
+    * products for nucleotide sequences, dna coding sequences for peptides).
+    * 
+    * @param sel
+    *          the sequences to show cross-references for
+    * @param dna
+    *          true if from a nucleotide alignment (so showing proteins)
+    * @param source
+    *          the database to show cross-references for
+    */
    protected void showProductsFor(final SequenceI[] sel, final boolean dna,
            final String source)
    {
@@@ -4750,7 -4760,8 +4761,8 @@@
                  System.err.println("Failed to make CDS alignment");
                }
                al.getCodonFrames().clear();
-               al.getCodonFrames().addAll(copyAlignment.getCodonFrames());
+               al.addCodonFrames(copyAlignment.getCodonFrames());
+               al.addCodonFrames(cf);
  
                /*
                 * pending getting Embl transcripts to 'align', 
@@@ -4768,7 -4779,9 +4780,9 @@@
              {
                copyAlignment = AlignmentUtils.makeCopyAlignment(
                        sequenceSelection, xrefs.getSequencesArray());
-               copyAlignment.getCodonFrames().addAll(cf);
+               copyAlignment.addCodonFrames(cf);
+               al.addCodonFrames(copyAlignment.getCodonFrames());
+               al.addCodonFrames(cf);
              }
              copyAlignment.setGapCharacter(AlignFrame.this.viewport
                      .getGapCharacter());