[Biojava-l] How to read in an aligment and then start viterbi

Richard HOLLAND hollandr at gis.a-star.edu.sg
Wed May 18 21:52:51 EDT 2005

>From the exception trace it looks as though Viterbi thinks you are using
a DnaAlphabet when in fact you have a custom one. However without seeing
your code it's hard to tell if this is a bug in BioJava, or a problem in
the way Viterbi has been called.

Could you provide a sample method which shows (a) how you construct the
alphabet, (b) creating the Hmm with it, (c) reading the alignment file,
and (d) passing it to Viterbi. It doesn't have to be very complicated or
intricate as long as it shows what you are doing and produces similar


Richard Holland
Bioinformatics Specialist
GIS extension 8199
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> -----Original Message-----
> From: biojava-l-bounces at portal.open-bio.org 
> [mailto:biojava-l-bounces at portal.open-bio.org] On Behalf Of 
> Fabian Schreiber
> Sent: Thursday, May 19, 2005 12:17 AM
> To: biojava-l at biojava.org
> Subject: [Biojava-l] How to read in an aligment and then start viterbi
> Hello!
> I created a Hmm with an Alphabet, that
> contains 9 different Proteins such as ALA, ARG, etc.
> After i created this model, i want to read in an
> aligment from a file and start Viterbi with the aligment as input.
> When i do so, i always get the following error:
> [code]
> org.biojava.bio.symbol.IllegalSymbolException: Symbol ARG not 
> found in 
> alphabet DnaAlphabet
> 	at 
> org.biojava.bio.symbol.AbstractAlphabet.validate(AbstractAlpha
> bet.java:278)
> 	at 
> org.biojava.bio.symbol.LinearAlphabetIndex.indexForSymbol(Line
> arAlphabetIndex.java:117)
> 	at 
> org.biojava.bio.dist.SimpleDistribution.getWeightImpl(SimpleDi
> stribution.java:131)
> 	at 
> org.biojava.bio.dist.AbstractDistribution.getWeight(AbstractDi
> stribution.java:197)
> 	at 
> org.biojava.bio.dp.ScoreType$Probability.calculateScore(ScoreT
> ype.java:54)
> 	at 
> org.biojava.bio.dp.onehead.SingleDP.getEmission(SingleDP.java:100)
> 	at 
> org.biojava.bio.dp.onehead.SingleDP.viterbi(SingleDP.java:553)
> 	at 
> org.biojava.bio.dp.onehead.SingleDP.viterbi(SingleDP.java:488)
> [/code]
> It looks as if the alphabets (one from the hmm and the other from the 
> alignment) differ, but i debugged it carefully and also checked
> the indices of both alphabets, which are equal, but could not find
> a problem.
> Is it a bug?
> Did anyone of you experienced a similiar problem?
> Can someone help me please?
> Its really important.
> Thanks a lot
> Greetings
> Fabian
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