[Biojava-l] problems with the profilehmm demo

[Mark Schreiber]

Hi -

This is a bug that has been submitted to bugzilla. Strangely it was
not an issue in the pre-releases of biojava.  I was kind of hoping
someone else would fix it but I guess I will have to find time to take
a look.

- Mark

On 8/28/07, Daniel Rohrbach <daniel.rohrbach at web.de> wrote:
> 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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