[Biojava-l] GappedSymbolList

[Matthew Pocock]

Hi Robin,

Problem re-created and fixed here. We have altered TokenParser and the demo -
they both do prety much what is expected now  (at least no crashes).

Tell us if this doesn't work for you.

Matthew

"Emig, Robin" wrote:

> it still doesn't fix the parsing problem for protein, check out
> TestAmbiguity I add code to test some of the protein alphabet
> -Robin
>
> -----Original Message-----
> From: biojava-l-admin@biojava.org [mailto:biojava-l-admin@biojava.org]On
> Behalf Of Matthew Pocock
> Sent: Wednesday, December 20, 2000 9:50 AM
> To: Emig, Robin; 'biojava-l@biojava.org'
> Subject: Re: [Biojava-l] GappedSymbolList
>
> I have checked in a new AlphabetManager.xml that should fix the symptom but
> not
> the cause. I think there is an 'issue' in either SimpleAlphabet or
> TokenParser.
> If this new file doesn't fix your problem, I will chase up the proper fix.
>
> Matthew
>
> Matthew Pocock wrote:
>
> > Hi Robin,
> >
> > "Emig, Robin" wrote:
> >
> > >         Ok, I'm a little confused about how to actually use a
> > > gappedsymbollist. I can add gaps just fine but what If I wanted to print
> > > out?
> > > ACGT------AHXXHFF
> >
> > You should be able to get this output by calling seqString on the gapped
> > instance. The gap symbol has a getToken method that returns '-'.
> >
> > >
> > >         I have no idea how to do that. Also, the parsers don't
> understand
> > > the GapSymbol, ie you can add it to the alphabet, but you cant parse
> '-'.
> >
> > This is odd. Could you try the symbol.TestAmbiguity demo? It works for me
> and
> > includes a parsed gap character. I am guessing that your sequence is
> protein
> > - mabey something is up with how SimpleAlphabet is implemented but is
> masked
> > for DNA (somehow...).
> >
> > Matthew
> >
> > >
> > > -Robin
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> >
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