[Biojava-l] Problem with SearchProfile demo

[Aulia Rahma Amin]

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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>>
>