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.
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