- * If any cDNA/protein mappings can be made between the alignments, offer to
- * open a linked alignment with split frame option.
+ * Ensure datasets are created for the new alignment as
+ * mappings operate on dataset sequences
+ */
+ toAdd.setDataset(null);
+
+ /*
+ * Check if any added sequence could be the object of a mapping or
+ * cross-reference; if so, make the mapping explicit
+ */
+ getAlignment().realiseMappings(toAdd.getSequences());
+
+ /*
+ * If any cDNA/protein mappings exist or can be made between the alignments,
+ * offer to open a split frame with linked alignments