[Biojava-l] RNATools possible bug

[Thomas Down]

On Mon, Dec 03, 2001 at 10:32:03AM -0500, Simon Foote wrote:
> I've found a slight problem with RNATools when transcribing/translating 
> DNA to RNA to protein.
> 
> Not sure if its a bug or I did something wrong.  
> I'm justing doing a simple RNATools.transcribe on a DNA symbol list.  
> 
> It throws the following error:
> 
> Exception in thread "main" 
> org.biojava.bio.symbol.IllegalSymbolException: Token
> `phe' does not appear as a named symbol in alphabet `PROTEIN-TERM'
>         at 
> org.biojava.bio.seq.io.NameTokenization.parseToken(NameTokenization.java:85)


Okay, this crept in when I landed the SymbolTokenizations
patch a week or two back.  The new NameTokenization
(replacing NameParser et al.) was defaulting to case-sensitive
parsing of symbol names.  This was wrong...  I've changed
it now in CVS (may take an hour or so to propogate to the
anonymous CVS server).  There's also now a couple of extra
cases in the test suite, which check the whole translation-table
system.

Thanks for spotting this,

    Thomas.