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 <[EMAIL PROTECTED]> 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 - [email protected] >> http://lists.open-bio.org/mailman/listinfo/biojava-l >> > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
