start work on cfg
fix some index bugs, implement super slow cyk
add cfg tests
work on trace back
Fix bugs in dp table init, where aux states mucking up array assignment
Fix bugs in dp table init, where aux states mucking up array assignment
fix nest tes
fix init problem for nested sates
overhaul cfg to relax CNF requirement which was getting annoying.  can now support a pair emission model, which is what needs to be done next
add little stub for pair emission model
reactivate tests
hack in support for optional alignment track.  get stored separately from normal track data.  to be used by cfg
incorporate pair emisison model.
fix cfg init such that nest states can only emit pairs
fix some bugs with alignment match detection and broken emisison model in tests.  also some idnexing issues for nested states
fix bug in traceback for paired emissions.  still bug in base case though
fix up traceback to work with pair base case
Add one last check to test
fix last commit
first try at cfg supervised learn