*
* @return
*/
- Set<AlignedCodonFrame> getCodonFrames();
+ List<AlignedCodonFrame> getCodonFrames();
/**
- * Set the codon frame mappings (replacing any existing set).
+ * Set the codon frame mappings (replacing any existing list).
*/
- void setCodonFrames(Set<AlignedCodonFrame> acfs);
+ void setCodonFrames(List<AlignedCodonFrame> acfs);
/**
* get codon frames involving sequenceI
* @return
*/
public boolean hasValidSequence();
+
+ /**
+ * Update any mappings to 'virtual' sequences to compatible real ones, if
+ * present in the added sequences. Returns a count of mappings updated.
+ *
+ * @param seqs
+ * @return
+ */
+ int realiseMappings(List<SequenceI> seqs);
+
+ /**
+ * Returns the first AlignedCodonFrame that has a mapping between the given
+ * dataset sequences
+ *
+ * @param mapFrom
+ * @param mapTo
+ * @return
+ */
+ AlignedCodonFrame getMapping(SequenceI mapFrom, SequenceI mapTo);
}