[Biojava-l] Re: DP bug query

[Matthew Pocock]

(cc'ed to the list)

Hi Richard,

This is because it should be looking for a parser under the name "token", not "symbol". I have
changed my copy & checked it into CVS. I guess I need to check the demos more frequently. I
don't actualy remember what this demo did. It is all a bit hazey back there.

Best of luck,

Matthew

"Richard K. Belew" wrote:

> hi matthew,
>
> i'm brand new to the biojava list so please excuse newbie tendancies.
>
> but the following query was buried in my (8 nov) thread around tutorials:
>
> > > Matthew Pocock wrote:
> > >
> > > The DP objects have changed a bit since the 1.01 release - and for the
> > > better. We should put up a new snapshot of the project on the web-site
> > > as soon as I fix a show-stopper bug in the alphabet indexing code.
> >
> > ah!  i am having problems running the SearchProfile demo:
> >
> > > Loading sequences
> > > java.util.NoSuchElementException: There is no parser 'symbol' defined in
> > >               alphabet PROTEIN+X
> > >         at org.biojava.bio.symbol.AbstractAlphabet.getParser(AbstractAlphabet.java:58)
> > >         at SearchProfile.readSequenceDB(SearchProfile.java:110)
> > >         at SearchProfile.main(SearchProfile.java:21)
> >
> > maybe this is related?
>
> if this is unrelated to your new fixes i'll continue to dig in on it.
>
> and since a few other topics have come and gone thru the list i
> thought this might have slid by?
>
> thanks again,
>         rik
>
> --
> Richard K. Belew                          rik@cs.ucsd.edu
>                               http://www.cs.ucsd.edu/~rik
> Computer Science & Engr. Dept.
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