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