[Biojava-l] GappedSymbolList

[Matthew Pocock]

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
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l@biojava.org
> > http://biojava.org/mailman/listinfo/biojava-l
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l