[Biojava-l] Help me, please!!

mark.schreiber at novartis.com mark.schreiber at novartis.com
Wed May 25 09:40:47 EDT 2005

Hello Daniela -

I'm not sure I can immediately help but can you tell us your biojava 
version and send an example program that shows the problem. We need to 
develop some more test cases for the DP package. I suspect there are some 
bugs that we need to find.

- Mark

Daniela Saccol <daniela.saccol at gmail.com>
Sent by: biojava-l-bounces at portal.open-bio.org
05/24/2005 02:39 AM
Please respond to Daniela Saccol

        To:     biojava-l at biojava.org
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-l] Help me, please!!


I am starting to work with the Biojava and I am finding problems for
which not meeting the answers. If somebody could help me, I would be
immensely been thankful. I have a HMM that have 81 main states, a
beginning state, an end state, 82 delete states and 82 insert states.
The states delete do not emit symbols, as well as beginning and end.
The states main and insert emit.  The problem occurs when I give the
following command:
DP dp = DPFactory.DEFAULT.createDP(seqPromoter); 
>From this point, the program does not execute more, but also it does
not emit errors. I read in some place that this could happen in one of
the versions of the Biojava, because this not accepted more than one
DotState (I have 82). This is truthful? In case that yes, the
following versions of the Biojava correct this problem? Which? In case
that not, somebody has idea of how can correct it?

Thank you very much,

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