[Biojava-l] Problem with SearchProfile demo

[Mark Schreiber]

Does the problem occur with the ProfileHMM example in the cookbook?
(http://biojava.org/wiki/BioJava:CookBook:DP:HMM)

- Mark

On 7/10/07, Aulia Rahma Amin <aulia at students.itb.ac.id> wrote:
> I'm using BioJava 1.5. I didn't find this problem when using BioJava 1.4.
>
> -aulia-
>
> > Hi -
> >
> > What version of BioJava do yo have?
> >
> > - Mark
> >
> > On 7/10/07, Aulia Rahma Amin <aulia at students.itb.ac.id> wrote:
> >> I have a problem when running demos/dp/SearchProfile.java. The program
> >> return an error message :
> >>
> >> classes\demos>java dp.SearchProfile fake.fasta
> >> Loading sequences
> >> Creating profile HMM
> >> Estimating alignment as having length 999
> >> org.biojava.bio.BioError: Assertion Failure: Symbol i-791 was not an
> >> indexed member of the alphabet Transitions from i-791 despite being in
> >> the
> >> alphabet.
> >>         at
> >> org.biojava.bio.symbol.LinearAlphabetIndex.indexForSymbol(LinearAlphabetIndex.java:118)
> >>         at
> >> org.biojava.bio.dist.IndexedCount.increaseCount(IndexedCount.java:98)
> >>         at
> >> org.biojava.bio.dist.SimpleDistribution$Trainer.addCount(SimpleDistribution.java:273)
> >>         at
> >> org.biojava.bio.dist.SimpleDistributionTrainerContext.addCount(SimpleDistributionTrainerContext.java:85)
> >>         at dp.SearchProfile.randomize(SearchProfile.java:155)
> >>         at dp.SearchProfile.createProfile(SearchProfile.java:104)
> >>         at dp.SearchProfile.main(SearchProfile.java:31)
> >>
> >> I suspect this problem occur when the the program run train method in
> >> SimpleDistribution class. Is this a bug or what?
> >>
> >> Any help will be deeply appreciated...
> >>
> >> =====
> >> Aulia Rahma Amin
> >> Undergraduate Student
> >> School of Electrical Engineering and Informatics
> >> Bandung Institute of Technology
> >> Indonesia
> >>
> >>
> >> _______________________________________________
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> >> http://lists.open-bio.org/mailman/listinfo/biojava-l
> >>
> >
>
>
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