[Biojava-l] Possible Submission
Mon, 15 Oct 2001 09:58:27 -0700
This is a multi-part message in MIME format.
Content-Type: text/plain; charset=us-ascii
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?
> 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.
Content-Type: text/x-vcard; charset=us-ascii;
Content-Description: Card for Robert Hubley
org:Institute for Systems Biology;Computational Biology
adr;quoted-printable:;;Institute for Systems Biology=0D=0A4225 Roosevelt Way NE=0D=0ASTE 200;Seattle;WA;98105-6099;USA