[Biojava-l] SAX Package

[Wiepert, Mathieu]

I have made some minor changes (I hope) to the sax package.  I did this to
add preliminary support for GCG blastn, and to make the BlastLikeSAXParser
XSLT processor compliant.

If I broke anything, I apologize mightily, and I am sure you will let me
know.

If anyone wants to test out the XSLT processing, I used Saxon, in the
following way:

java -classpath
"E:\Saxon\saxon.jar;E:\Biojava\biojava-live\biojava.jar;E:\biojava\biojava-l
ive\xerces.jar;." com.icl.saxon.StyleSheet -o
E:\biojava\test\output\blastn.xml -x
org.biojava.bio.program.sax.BlastLikeSAXParser
E:\biojava\biojava-live\demos\files\ncbiblast\blastn.out
e:\biojava\Biojava-live\demos\eventbasedsaxparsing\stylesheets\copyall.xsl

Change all the path's for your own setup, but note the -x option to Saxon,
telling it to use the BlastLikeSAXParser.  I have placed two xsl stylesheets
in demos\eventbasedparsing\stylesheets.  Copyall.xsl spits out all the
events to your output, and hitlist.xsl mimics the tutorial demo output
(actually puts out an HTML web page of it though, not straight text).

I added the XSLT processing to allow for more flexibility with transforming
the output, and to handle the odd characters($, <>, etc.)

My thanks to Simon and Matthew, they put up with lots of off-group emails.