[Dynamite] (no subject)

[Ian Holmes]

On Tue, 25 Jul 2000, Ewan Birney wrote:

> In genewise the pre-matrix special states are
> 
>    PRE_CODON, PRE_INTRON_1, PRE_INTRON2, PRE_INTRON3 
> 
> ie, a full mini-genscan parser.
> 
> 
> This means you can't factor out these states; you do have to calculate
> them.
> 
> perhaps I am missing your point. hmmmmmmmmm.

i didn't mean that you didn't have to calculate them; only that you only
had to calculate them once per column (the definition of a special state)

my point was that i thought it was possible for the program to
automatically detect which states were special states, with the exception
of loop states. however i'm now actually less certain of that than when i
started ;-) so i think we should forget it and just do what Dynamite does.
(which, of course, i should have realised straight off)