[Biojava-l] Problem with SearchProfile demo

[Aulia Rahma Amin]

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