BUGS:

CLEANUP:
- put all things which emit a message into closures
- automate the seqtype maps (no need to make this tricky)
- consider taking this feature map extracting out of the main Annotation code...it's sort of monolithic.
- make a battery of checks (that are not hardcoded into finalize) with an array of transcript checks that perform transition checks

BUGISH:
- need a failure mode for using phylo modes with no alignments
- need to be more specific with 0 samples warning on which model failed
- make it possible to create any new XML object without sourcing it from a file or hacking the element in.

FEATURES:
- make an 'alias' model, one that simply mirrors the parameters of another one
 * for example, if you want to use acceptors and donors of all utr and 
   coding exons for both models, you should be able to alias UtrAcceptorCons
   to AcceptorCons.
- Add a "framed_state", which automatically generates 0,1,2 states, and 
  optionally generates 1T,2TA,2TG states

DONE:
- move all transcript sanity checking over to finalize, not in addFeature or anywhere else. (done?)
- allow user to control messages, warnings, and debug output
- conservation/EST foci and positions are not right
- feature output does not work with alignments
- some of the frames may be wrong 
  (exon 0,1,2 zoe frame found to map to 0,2,1 iPE frame)
- make a globals module -- singleton



future versions:
estimate isochores?
estimate MDDs?
estimate partial hmms.
