[Biojava-l] Problem with ProfileHMM source

[Matthew Pocock]

Hello Tisanai,

Feel free to modify this code to represent the profile
HMM you want. It was code that I knocked up while
trying to debug the DP toolkit, and I never re-visited
it to make sure it worked, or even that it was a sane
architecture.

I'm only in intermitant net contact until BOSC/ISMB
(1st Aug), but after that I'd be more than happy to
get this code working with you.

Yours,

Matthew

 --- Tisanai <T.Krisanathamakul@dcs.shef.ac.uk> wrote:
> Hi,
>  
>    I have a problem with ProfileHMM source. In the
> code line 223 that is
> 
>         if(i > 1) {
>           createTransition(dO, dN);
>           createTransition(dO, mN);
>           createTransition(dN, iN);
>         }     
> 
>   If it is like this there will be no transition
> from d-1 to i-1 right?
> 
>   Why should it be like this
> 
>         if(i > 1) {
>           createTransition(dO, dN);
>           createTransition(dO, mN);
>           createTransition(dN, iN);
>         }     
>        else
>           createTransition(dN, iN);
> 
> 
> Thank you
> 
> Tisanai
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l 

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