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

[Michael Heuer]

On Fri, 11 Jul 2003, Matthew Pocock wrote:

> > Also, I'm not really sure how to go about using the StAX stuff.
>
> Are the biojava and source-forge StAX APIs synchronized now? Anybody
> know? Perhaps we should write a simple StAX tutorial. I'll see if I get
> any time in the next week.

The biojava and sourceforge StAX APIs are not in sync, due to all of the
dependent code in biojava.  There are examples of how to use each of the
handlers, with lazy id mapping, in the javadoc of the sourceforge
version.

Maybe a good plan would be to

1) move the sf version to a new package name
2) create another PRE_I'm_about_to_screw_things_up tag/branch on HEAD
3) refactor biojava classes to use the sf version (involves updating
package, swapping StAXDelegationContext for DelegationManager, and
introducing lazy id mapping where helpful)

A last TODO would be to update SAX2StAXAdaptor to work with the newer XML
APIs.

I'm willing to help where necessary.

   michael