I have submitted this as a bug report. It seems to be a bug in all HMM code. Some initial testing suggests it is a problem with Flyweight symbols (States) not behaiving properly.
My tests of ProfileHMMs still worked about 7-8 months ago. According to CVS the only thing that happened after that time to classes that might be relevant was a semi-automated removal of crud from the code (unused parameters etc). It is very hard to tell which change did the damage. I suspect I will have to write some unit tests for the DP classes. Somehow I think this should have happened about 6 years ago (MRP, are you listening!!) but better late than never : ) - Mark On 7/10/07, Aulia Rahma Amin <[EMAIL PROTECTED]> wrote: > 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 > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
