- /*
- * get display scheme (if any) to apply to features
- */
- FeatureSettingsModelI featureColourScheme = new SequenceFetcher()
- .getFeatureColourScheme(source);
+ System.err
+ .println("Conflict: showProducts for alignment originally "
+ + "thought to be "
+ + (_odna ? "DNA" : "Protein")
+ + " now searching for "
+ + (dna ? "DNA" : "Protein") + " Context.");
+ }
+ AlignmentI xrefs = new CrossRef(sel, dataset)
+ .findXrefSequences(source, dna);
+ if (xrefs == null)
+ {
+ return;
+ }
+ /*
+ * get display scheme (if any) to apply to features
+ */
+ FeatureSettingsModelI featureColourScheme = new SequenceFetcher()
+ .getFeatureColourScheme(source);
+
+ AlignmentI xrefsAlignment = makeCrossReferencesAlignment(dataset,
+ xrefs);
+ final SequenceI[] sequenceSelection = AlignFrame.this.viewport
+ .getSequenceSelection();
+ if (!dna)
+ {
+ xrefsAlignment = AlignmentUtils.makeCdsAlignment(
+ xrefsAlignment.getSequencesArray(), dataset,
+ sequenceSelection);
+ xrefsAlignment.alignAs(alignment);
+ }