[Biojava-l] New package for databases

[Matthew Pocock]

Hi.

Gerald Loeffler wrote:

> i opt for
>
>         org.biojava.bio.seq.db

I seccond that

>
>
> 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

Cool. Feel free to invent a suitable sub-package of utils if you are adding
groups of related classes.

> 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

I sudgest one of:
org.biojava.bio.program.search  - my preference
org.biojava.bio.search

>
>
> Is this OK?
>

Cool.

>
>         cheers,
>         gerald
>