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

[Richard Holland]

JAXB would follow the exact same Thing/ThingBuilder pattern, but with the
following subtle differences...

0. Your root data model object as generated by JAXB should be modified to
implement Thing, making it a JAXBThing.
1. JAXBReader (extends ThingReader) would open and read the file using JAXB
and directly construct JAXBThings.
2. JAXBReceiver (extends ThingReceiver) be a pass-through interface with
just one method, something like setJAXBThing() to pass in the already-parsed
JAXBThing directly.
3. Any converters would expand/deflate data from other formats to/from the
JAXBThing object directly.


Richard.

2008/10/21 Mark Schreiber <markjschreiber at gmail.com>

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



-- 
Richard Holland, BSc MBCS
Finance Director, Eagle Genomics Ltd
M: +44 7500 438846 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/