[Biojava-l] Problem with SearchProfile demo

[Mark Schreiber]

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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