[Biojava-l] problems with the profilehmm demo

Daniel Rohrbach daniel.rohrbach at web.de
Tue Aug 28 13:36:25 UTC 2007

Hi all,

i'm trying to run the  "How do I make a ProfileHMM" example but it doesn't want to work.  I copied the code to my program and when I start it I get the following exceptions:

Exception in thread "main" java.lang.IndexOutOfBoundsException: Can't find symbol for index 0
        at org.biojava.bio.symbol.LinearAlphabetIndex.symbolForIndex(LinearAlphabetIndex.java:106)
        at org.biojava.bio.dist.SimpleDistribution$Trainer.trainImpl(SimpleDistribution.java:332)
        at org.biojava.bio.dist.SimpleDistribution$Trainer.train(SimpleDistribution.java:306)
        at org.biojava.bio.dist.SimpleDistributionTrainerContext.train(SimpleDistributionTrainerContext.java:126)
        at biojavatests.HMMTest.main(HMMTest.java:71)

The error occurs at mt.train(). It seems that there was no, wrong or empty alphabet set for the trainer that shall be used. 

here the link to the examplepage: http://biojava.org/wiki/BioJava:CookBook:DP:HMM
any help on this topic?

Thanks in advance
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