[Bioperl-l] Event generated parsing

Jason Eric Stajich jason@cgt.mc.duke.edu
Fri, 26 Oct 2001 13:54:30 -0400 (EDT)

Okay - got my first pass at event generated parsing out there in the
Bio::SearchIO stuff - just parses ncbi blast xml into Bio::Search objects.
I'm not totally happy with my lumping of events into hashes so if someone
wants to refactor this code because you think it is a bad design - please
feel free.  I'm going to leave at is because I'm not really sure I want to
have the SearchResultEventBuilder to have to keep track of all the states.
I declare open season for anyone who wants to jump in an help here on
Search Parsing.

In doing this I built Bio::SearchIO::EventGeneratorI and
Bio::SearcIO::EventHandlerI interfaces - I these are just a subset of
basic SAX interfaces, but nice to have a bioperl twist on these as I don't
think there is really a SAX interface file in the bioperl way.  Anyways,
would like to make these the general event parsing interfaces so that
if/when we begin a refactoring SeqIO or when I start writing the another
parser that is not for Search Results.

Any complaints with creating Bio::Event::EventGeneratorI,
Bio::Event::EventHandlerI which are essentially the same as the SearchIO

Jason Stajich
Duke University