X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=3f572e89fbccad7c5558773a7c6b811dfb553b0a;hb=4bd4726a6cd30825c18525c2a0851e207d687423;hp=c5fb11f32b3ae2776df5064c96479eed26fb94bc;hpb=b10330c2e330e409d2fd3812f1001f9542dc1b36;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index c5fb11f..3f572e8 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -4734,6 +4734,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
           AlignmentI xrefsAlignment = makeCrossReferencesAlignment(dataset,
                   xrefs);
+          final SequenceI[] sequenceSelection = AlignFrame.this.viewport
+                  .getSequenceSelection();
+          if (!dna)
+          {
+            xrefsAlignment = AlignmentUtils.makeCdsAlignment(
+                    xrefsAlignment.getSequencesArray(), dataset,
+                    sequenceSelection);
+            xrefsAlignment.alignAs(alignment);
+          }
 
           AlignFrame newFrame = new AlignFrame(xrefsAlignment, DEFAULT_WIDTH,
                   DEFAULT_HEIGHT);
@@ -4761,14 +4770,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
            * sequences). If we are DNA, drop introns and update mappings
            */
           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.getSequencesArray());
             if (copyAlignment.getHeight() == 0)
             {
               System.err.println("Failed to make CDS alignment");
@@ -4789,7 +4796,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           else
           {
             copyAlignment = AlignmentUtils.makeCopyAlignment(
-                    sequenceSelection, xrefs.getSequencesArray());
+                    sequenceSelection, xrefs.getSequencesArray(), dataset);
           }
           copyAlignment.setGapCharacter(AlignFrame.this.viewport
                   .getGapCharacter());
@@ -4822,7 +4829,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
              * align cdna to protein - currently only if 
              * fetching and aligning Ensembl transcripts!
              */
-            if (DBRefSource.ENSEMBL.equalsIgnoreCase(source))
+            if (dna && DBRefSource.ENSEMBL.equalsIgnoreCase(source))
             {
               copyAlignment.alignAs(xrefsAlignment);
             }
@@ -4881,6 +4888,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
        * Makes an alignment containing the given sequences, and adds them to the
        * given dataset, which is also set as the dataset for the new alignment
        * 
+       * TODO: refactor to DatasetI method
+       * 
        * @param dataset
        * @param seqs
        * @return
@@ -5950,8 +5959,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void setAnnotationsVisibility(boolean visible,
           boolean forSequences, boolean forAlignment)
   {
-    for (AlignmentAnnotation aa : alignPanel.getAlignment()
-            .getAlignmentAnnotation())
+    AlignmentAnnotation[] anns = alignPanel.getAlignment()
+            .getAlignmentAnnotation();
+    if (anns == null)
+    {
+      return;
+    }
+    for (AlignmentAnnotation aa : anns)
     {
       /*
        * don't display non-positional annotations on an alignment