[Biojava-l] Problem with SearchProfile demo

[Mark Schreiber]

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 <aulia at students.itb.ac.id> 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 <aulia at students.itb.ac.id> 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 <aulia at students.itb.ac.id> 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  -  Biojava-l at lists.open-bio.org
> >> >> http://lists.open-bio.org/mailman/listinfo/biojava-l
> >> >>
> >> >
> >>
> >>
> >> _______________________________________________
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> >> http://lists.open-bio.org/mailman/listinfo/biojava-l
> >>
> >
>
>
> --
> Aulia Rahma Amin
> ARC05/IF03
> Y! ID : aulia_ra
> Skype ID : aulia_ra
> MSN ID : aulia_ra at hotmail.com
> AIM ID : auliara
> ICQ ID : aulia_ra
> Homepage : http://www.aulia-ra.org
>
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