* @return hashtable of alignment properties (or null if none are defined)
*/
public Hashtable getProperties();
+
+ /**
+ * 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);
+
}