/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* @return
*/
Set<String> getSequenceNames();
+
+ /**
+ * Returns a (possibly empty) alignment whose sequences are aligned to match
+ * the current alignment, as mapped by the given codon mappings.
+ *
+ * @param codonFrames
+ * @return
+ */
+ AlignmentI getAlignedComplement(Set<AlignedCodonFrame> codonFrames);
}