[Biojava-l] New package for databases

[Gerald Loeffler]

i opt for

	org.biojava.bio.seq.db

and i also would naturally take over the task of putting my
SequenceDBInstallation related work into this package.

In addition, i'd like to donate some of my utility classes (for design
by contract, equality and hashcodes) (which i do not want to miss when
coding for BioJava) to the existing package

	org.biojava.utils

Furthermore, i'd really be great if the stuff related to blast parsing
would make it into 1.0. I'm aware that there wasn't much response to my
proposed object model for sequence similarity searches, but it is still
my opinion that it pretty much models this area correctly. Furthermore,
it shields the user from the details on how the parsing is done (e.g.
directly or via simons wonderful idea of a SAX-based parser). Hence i
would like to introduce that into 1.0 as well - supposedly into a new
package named

	org.biojava.seq.search

Is this OK?

	cheers,
	gerald

Thomas Down wrote:
> 
> Hi...
> 
> It's looking as though the SequenceDB interface and it's
> associated implementations and support might be starting to
> take on a life of it's own.  In particular, we have Gerald's
> SequenceDBInstallation interface about to go in, and
> suggestions about modifiable SequenceDBs.
> 
> Before this happens, I move that we create a new package.
> This should mean only minor changes for current users, but
> will avoid the possible need to move lots of classes around
> later on.
> 
> Suggested names:
> 
>   org.biojava.bio.seq.database
>   org.biojava.bio.seq.db
> 
> Does anyone have any objections to this happening as a pre-1.0
> stabilisation change?  Which name is preferred?
> 
> Thomas.
> --
> He looked up with big brown eyes.  ``They're really only
> tiny little A-bombs, honest.''
>                                      -- David Brin.
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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