PrimarySeq.pm/new: Changed $is_circular test to use "define",
since it fails to add is_circular attribute if the argument is 0
PrimarySeqI.pm: use Bio::Root::clone to make sure that copied objects
get all attributes from the original. Implemented in revcom(), trunc(),
translate(), transcribe() and rev_transcribe()
PrimarySeq.t: TODO tests are now fixed. All the other tests also pass