[Biojava-l] Problem with SearchProfile demo

[Aulia Rahma Amin]

Yes, it happens, always end with org.biojava.bio.BioError: Assertion
Failure. But I have no problems when running the example using BioJava
1.4.

-aulia-

> 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
>> >>
>> >>
>> >> _______________________________________________
>> >> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> >> http://lists.open-bio.org/mailman/listinfo/biojava-l
>> >>
>> >
>>
>>
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>>
>


-- 
Aulia Rahma Amin
ARC05/IF03
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