[Biojava-l] Possible Submission

Robert Hubley rhubley@systemsbiology.org
Mon, 15 Oct 2001 09:58:27 -0700

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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,


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.

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