[Biojava-dev] [Bug 2330] New: DP/ Profile HMM bug

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2330

           Summary: DP/ Profile HMM bug
           Product: BioJava
           Version: 1.5
          Platform: All
        OS/Version: All
            Status: NEW
          Severity: normal
          Priority: P2
         Component: dist/dp
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: mark.schreiber at novartis.com


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)

This is certain to be an issue with Gaps and Alphabet manager. Make sure a
ProfileHMM can be serialized and deserialized multiple times after fixing.


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