+
+ /**
+ * add a reference to a frame of aligned codons for this alignment
+ * @param codons
+ */
+ public void addCodonFrame(AlignedCodonFrame codons);
+ /**
+ * remove a particular codon frame reference from this alignment
+ * @param codons
+ * @return true if codon frame was removed.
+ */
+ public boolean removeCodonFrame(AlignedCodonFrame codons);
+ /**
+ * get all codon frames associated with this alignment
+ * @return
+ */
+ public AlignedCodonFrame[] getCodonFrames();
+ /**
+ * get a particular codon frame
+ * @param index
+ * @return
+ */
+ public AlignedCodonFrame getCodonFrame(int index);
+ /**
+ * get codon frames involving sequenceI
+ */
+ public AlignedCodonFrame[] getCodonFrame(SequenceI seq);
+ /**
+ * find sequence with given name in alignment
+ * @param token name to find
+ * @param b true implies that case insensitive matching will <em>also</em> be tried
+ * @return matched sequence or null
+ */
+ public SequenceI findName(String token, boolean b);
+