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 <[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 >> > -- Aulia Rahma Amin ARC05/IF03 Y! ID : aulia_ra Skype ID : aulia_ra MSN ID : [EMAIL PROTECTED] AIM ID : auliara ICQ ID : aulia_ra Homepage : http://www.aulia-ra.org _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
