[Biojava-l] Relations between trainers

[Kalle Näslund]

Oscar Lopes wrote:

> Hi!
>
> I'm a graduate student and I'm using biojava to implement Viterbi 
> training algorithm.
> I spent some time digging in the code, but I still can't make the 
> relation between
> TrainigAlgorithm, DistributionTrainer, etc...
>
> What are the key classes that I can use? How does it work? I tried to 
> look at
> BaumWelchTrainer, but it didn't make sense how I would implement 
> Viterbi Trainig.
> Besides, I kept getting confused with DistributionTrainer and 
> DistributionTrainerContext...
>
> Can anybody help me?? It would be nice if someone explain to me how 
> the whole thing works.

Hi !

Have you found the tutorial about one of the dynamic programming 
examples included in biojava ?
The tutorial is about an HMM setup, and shows how to set it all up and 
use it. It can be found at

http://www.biojava.org/tutorials/dp-doc.html

Hopefully this will atleast get you started.

mvh Kalle