[Biojava-l] Massaging multi-query BLAST XML output...

[David Huen]

On Thu, 10 Jul 2003, DeAngelo Lampkin wrote:

> 
> >I would strongly recommend using the BlastXMLParserFacade class instead of
> >the BlastXMLParser class unless setting up StAX parsers appeals to you.
> >There is a demo of the use of the latter in the biojava-live repository.
> 
> I looked everywhere for BlastXMLParserFacade, but I couldn't find it.  Do you happen to recall which package it sits in? 
> 
> Also, I'm not really sure how to go about using the StAX stuff.  For the time being, I'll just create my own data structures using vanilla SAX.
> 
Ah, OK, I begin to see the problem.  I would recommend that you use the
biojava-live version straight from CVS.  While that is the development
version, it also has the latest stuff and fixes in it.

BlastXMLParserFacade was introduced last month to give a uniform method of
use between the XML and the text parsing frameworks. A demo was also
uploaded to show its use.  This was in response to some queries as to use
of this package.

You can work out how to use the CVS here:-
http://cvs.biojava.org/

The module you want is biojava-live from the biojava repository.

I think you can also use WebCVS to download it:-
http://cvs.biojava.org/cgi-bin/viewcvs/viewcvs.cgi/biojava-live/?cvsroot=biojava

I suspect that clicking "Download tarball" here will create you a tarball
of the sources. I don't know if it will include the CVS directories that
will allow you to use CVS to resync with the latest sources later.

To compile the sources, you will want the Ant package from the Apache
Jakarta team (jakarta.apache.org).  That must be installed to compile.

When you have all that working, going into the biojava-live directory and
type:-

ant

and it will compile and create th biojava.jar for you wihtin the ant-build
directory somewhere.

ant javadocs

will make the javadocs

Personally, I would rather go for the command line version and set it up
once.  Thereafter you can track the bleeding edge by typing

cvs update -d

and having it sync with the current repository.

Rgds,
DH