[Biojava-l] viterbi training in biojava

[Richard Holland]

I've modified BaumWelchSampler in CVS so that it accepts alternative
score types as an additional parameter to singleSequenceIterator().

cheers,
Richard.


On Tue, 2006-05-30 at 16:43 +0100, wendy wong wrote:
> thanks! i only need one head so BaumWelchSampler works fine with me.
> The default SCORETYPE is probability and when I tried it the score
> goes back and forth, like + for one time and - for the next time. I
> then changed it to LOGODDS  and recompiled biojava and now that the
> score is steadily increasing. I was wondering if the SCORETYPE could
> be passed in as an argument in the next version of biojava?
> 
> thanks,
> wendy
> 
> 
> On 30 May 2006 12:19:15 +0100, David Huen <smh1008 at cam.ac.uk> wrote:
> > On May 30 2006, wendy wong wrote:
> >
> > >Hi,
> > >
> > >I was wondering if viterbi training is implemented in biojava, or if
> > >there's any open source version implemented using biojava?
> > >
> > There is one-head viterbi training already I think. The training framework
> > doesn't work for two-head - I wrote a viterbi training API that works for
> > two head but it is not fully compatible with the existing API so I never
> > put it into CVS, plus it doesn't have Baum-Welch implemented either.
> >
> > If it is any use to you you can have it.
> >
> > Regards,
> > David
> >
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-- 
Richard Holland (BioMart Team)
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
UNITED KINGDOM
Tel: +44-(0)1223-494416