[Fwd: Re: [Biojava-l] readFastaProtein ?]

[Matthew Pocock]

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Hi Josselin,

I found this code lurking in the 1_10 branch:

     private static SymbolParser getProteinParser() {
        try {
            return DNATools.getDNA().getParser("token");
        } catch (BioException ex) {
            throw new BioError(ex, "Assertion failing: Couldn't get PROTEIN token 
parser");
        }
     }

This uses DNATools! Oops. It is fixed on the main BioJava trunk (which 
you can access via anonymous CVS using the instructions a 
cvs.biojava.org). If you have source-code for the 1_10 release, you can 
fix this problem yourself. If not, I can send you a patched 
biojava-1_10.jar. Either way, I will make sure that this is fixed in CVS 
on that branch.

Does this solve your problem, or do you need more help?

Matthew

ps sory for any hastle caused - your test code & file made finding the 
problem much easier
.

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