[Biojava-l] [Biojava-dev] BioJava 3 Begins - Volunteers please!

Mark Schreiber markjschreiber at gmail.com
Tue Oct 21 09:26:41 UTC 2008

>> Blast: the Blast parsing modules are among the most frequently used
>> ones in biojava 1.6. To make people use biojava v3 it will be crucial
>> to have a port of them to the new version. Does anybody want to take
>> care of that?
> I'll second that. Blast is vital. We'd really appreciate a volunteer,
> please!

BlastXML output would certainly be the easiest place to start. I also
think with the new Thing/ ThingBuilder framework it will be possible
to develop all manner of parsers for the vagaries of Blast text output
that come with each new release of Blast. Possible but maybe not a
good idea. I don't think that output was ever supposed to be machine
readable.  The table formatted output (-m8 I think) would be a better

Given the DTD it should be possible to do a quick JAXB binding. How
would that work in the Thing/ ThingBuilder paradigm?

- Mark

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