[Biojava-l] changed (improved) SequenceDB and stuff

[Gerald Loeffler]

Jason Stajich wrote:
> While you're thinking about SequenceDBs - I'm working on a methodology
> from the bioperl end to manage a MutableSeqDB - I want to be able to add /
> update/ delete sequences from a 'real' database.  This is going to require
> a transactional db on the back end and/or careful code, but we a looking
> to see if we can do it with the ensembl project's db first.  This
> would ideally something that would make its way into the biocorba idl as
> well as implemented in the bio* project's code.  More details to come as I
> finalize the design proposal.

sounds very interesting!

I'm currently thinking/working on an implementation of SequenceDB whose
getSequence() method goes (via JDBC) into a relational database, fetches
data associated with the requested sequence and instantiates a Sequence
object. The object of the SequenceDB-sub-class does not know anything
about the database content, it just passes on the request for a sequence
to the relational DB. Should be similary to what you are planning except
that mine is strictly read-only while yours is read/write/update.

Seems that the MutableSeqDB you mention should be a sub-interface of
SequenceDB with replaceSequence() and addSequence() methods...

	good luck,
	gerald
> 
> > A possible way to manage change to the BioJava API could be to introduce
> > versioning and restrict incomptible changes to the (rare) increases in
> > the major version number. The symbol/seq-part of BioJava could be
> > designated 1.0 right now, and future incompatible changes (like the
> > ambiguity change or this db-naming change) may only occur in one go when
>   moving to 2.0....
> >
> >       cheers,
> >       gerald
> >
> > >
> > >      What do you think?
> > >
> > >           Hilmar
> >
> > --
> >    Gerald.Loeffler@vienna.at _________________ Software Architect
> >    http://www.imp.univie.ac.at ____ http://www.daemonstration.com
> >    OOA&D, Java, J2EE, JSP, Servlets, JavaBeans, ODBMS, RDBMS, XML
> > _______________________________________________
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> > http://biojava.org/mailman/listinfo/biojava-l
> >
> 
> Jason Stajich
> Center for Human Genetics
> Duke University Medical Center
> jason@chg.mc.duke.edu
> (919)684-1806 (office)
> (919)684-2275 (fax)
> http://wwwchg.mc.duke.edu/
> 
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-- 
   Gerald.Loeffler@vienna.at _________________ Software Architect
   http://www.imp.univie.ac.at ____ http://www.daemonstration.com
   OOA&D, Java, J2EE, JSP, Servlets, JavaBeans, ODBMS, RDBMS, XML