[Biojava-l] Possible Submission

[David Waring]

I have been working on the Phred code (..program.phred). I have a parser for
.phd files that uses JLex/Cup. I had been concerned about using this within
Biojava since there is no support for Jlex and Cup. According to the JFlex
documentation it is compatible with Jlex, so adding JFlex support to Biojava
would help me. We have written parsers for many other formats including .ace
(phrap output). Eventually we could role these into Biojava also.

David


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|   David Waring
|   Systems Programmer
|   University of Washington Genome Center
|   dwaring@u.washington.edu
|   (206) 221-6902
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> -----Original Message-----
> From: biojava-l-admin@biojava.org [mailto:biojava-l-admin@biojava.org]On
> Behalf Of Robert Hubley
> Sent: Monday, October 15, 2001 9:58 AM
> Cc: biojava-l@biojava.org
> Subject: [Biojava-l] Possible Submission
>
>
>
> I have developed a parsing framework called LSAX that I would
> like to submit to BioJava.  It was inspired by the work of Cambridge
> Antibody Technology (Simon Brocklehurst et al.) on the BioJava
> BlastLikeSaxParser.  The idea is the same -- create a bridge
> between XML applications and Non-XML data.  The difference
> between the CAT parser and LSAX is in the design of the raw
> file parser.  I use LEX (actually JFLEX) to tokenize the raw
> data files and generate Start, Data, and End SAX events.  I have
> developed two parsers using this framework an NCBI Blast and
> a Fasta parser.  The advantage to using LEX is that you can specify
> the rules of your parser at a high level with regular expressions.  The
> actual parser is then auto-generated using JFLEX and is often times
> faster than a parser you would write by hand.
>
> Let me know if you would like to include this in BioJava,
>
> -R
>
>
>
>
>
> Thomas Down wrote:
>
> > On Fri, Oct 12, 2001 at 05:22:14PM -0700, Robert Hubley wrote:
> > > Hi all,
> > >
> > > I have some code that I thought I could contribute to the
> > > biojava project.  What is the procedure for doing so?
> >
> > Hi...
> >
> > Most of the day-to-day business of BioJava takes place on
> > this mailing list, so you've come to the right place.  Could
> > you post a brief description of the code you've written?
> >
> > If you decide you want to contribute some code, small patches
> > can be checked in by one of the existing developers.  But if it's
> > more than 2 or 3 files, it may be easier to get a read/write
> > account for accessing the project's CVS repository, then check
> > things in yourself.
> >
> > Thanks,
> >
> >      Thomas.
>