[Dynamite] (no subject)

[Ewan Birney]

> ...this is not total fluff---the point is that loop states change the
> actual functionality of the model, whereas singlet states that aren't loop
> states (like INSERT_QUERY_* above) don't change the functionality (the
> scores returned by algorithms will be the same; it will just shave a bit
> off the running time of the algorithm because you don't store a whole
> bunch of empty cells in the matrix).


No. Because there are singlet->singlet potential transitions and the
viterbi or posterior score when we jump into the polymer matrix is data
dependent and path (through singlet) dependent.



 > 
> in other words, singlets are just a compiler pragma unless they're in loop
> cliques. does that make any sense?
> 
> this is why i favoured "loop" as a name (because loops are the only point
> of having special states really; they are the only kinds of special state
> which aren't just optimisation tricks).
> 


I like singlet.


> ian
>