[Biojava-l] pairwise dp

[Matthew Pocock]

Dear speedfreaks,

I have just checked in a new copy of the pairwise dp engine. It now runs
my test example in 8 secs instead of 110 secs on a dec alpha with the
fast vm, and runs in 32 sec vs 280 sec on my pc (233 mhz pII) with the
sun hotspot server vm. This is aprox a 10X speedup for a 3 emission
state model which has to be good.

Check out the pairwise dp demo, and see if it makes sence to you. I
haven't ensured that it is producing the 'correct' answer (next on my
list of jobs), but this wouldn't affect the performance at all (the same
number of dp cells need to be calculated whatever).

Matthew
--
Joon: You're out of your tree
Sam:  It wasn't my tree
                                                 (Benny & Joon)