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

[Fabian Schreiber]

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(AbstractAlphabet.java:278)
	at 
org.biojava.bio.symbol.LinearAlphabetIndex.indexForSymbol(LinearAlphabetIndex.java:117)
	at 
org.biojava.bio.dist.SimpleDistribution.getWeightImpl(SimpleDistribution.java:131)
	at 
org.biojava.bio.dist.AbstractDistribution.getWeight(AbstractDistribution.java:197)
	at 
org.biojava.bio.dp.ScoreType$Probability.calculateScore(ScoreType.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