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Commits on Mar 16, 2013
  1. this for sure doesn't work, but we've removed all the errors with reg…

    committed Mar 16, 2013
    …ard to affine automata system
  2. revised picture

    committed Mar 15, 2013
Commits on Mar 15, 2013
  1. added picture of 3 matrix setup

    committed Mar 15, 2013
  2. made SOME progress, but I'm realizing tht I dont know what I'm doing …

    committed Mar 15, 2013
    …(without a board on hand)
  3. still an eror in here

    committed Mar 15, 2013
Commits on Mar 14, 2013
  1. removed .swp

    committed Mar 14, 2013
  2. fuck

    committed Mar 14, 2013
  3. started modifying underlying automata for affine system (taking some …

    committed Mar 14, 2013
    …of the higher level decisions and baking them in)
Commits on Mar 12, 2013
Commits on Mar 9, 2013
  1. didn't like the last change

    committed Mar 9, 2013
  2. seeing if this looks better

    committed Mar 9, 2013
  3. playing with diagram

    committed Mar 9, 2013
  4. this is good

    committed Mar 9, 2013
  5. update to TODO.txt

    committed Mar 9, 2013
  6. we're on a roll

    committed Mar 9, 2013
  7. another mistake

    committed Mar 9, 2013
  8. stuff to remember (graphic)

    committed Mar 9, 2013
  9. modifyed the gap costs for affine gap model, started preparing to tac…

    committed Mar 8, 2013
    …kle the who ties during backtracking thing
  10. added output corresponding to last commit - mind you, the backtrackin…

    committed Mar 8, 2013
    …g process handles -ties- very poorly, so the solutions here have strong likelihood of being -wrong-
Commits on Mar 8, 2013
  1. Another important note

    committed Mar 8, 2013
  2. Important note on runtime

    committed Mar 8, 2013
  3. did BETTER tests, my guess is that garbage collection has alot to do …

    committed Mar 8, 2013
    …with performance. These new results indicate (to me) that the more gaps we have the LONGER the algorithm will take...makes sense...here our heavily gapped takes around 2900 ms on average to complete - as opposed to the somewhat similar (arguable just as divergent) that takes on average 390 ms and varies much less.
Commits on Mar 6, 2013
  1. adding output

    committed Mar 6, 2013
  2. some more additions

    committed Mar 6, 2013
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