[Biojava-dev] Plans for next biojava release - modularization

[Andreas Prlic]

Hi biojava-devs,

It is time to start working on the next biojava release.  I  would
like to modularize the current code base and apply some of the ideas
that have emerged around Richard's "biojava 3" code. In principle the
idea is that all changes should be backwards compatible with the
interfaces provided by the current biojava 1.7 release.  Backwards
compatibility shall only be broken if the functionality is being
replaced with something that works better, and gets documented
accordingly. For the build functionality I would suggest to stick with
what Richard's biojava 3 code base already is providing. Since we will
try to be backwards compatible all code development should be part of
the biojava-trunk and the first step will be to move the ant-build
scripts to a maven build process. Following this procedure will allow
to use e.g. the code refactoring tools provided by Eclipse, which
should come in handy.

The modules I would like to see should provide self-contained
functionality and cross dependencies should be restricted to a
minimum. I would suggest to have the following modules:

biojava-core: Contains everything that can not easily be modularized
or nobody volunteers to become a module maintainer.
biojava-phylogeny: Scooter expressed some interested to provide such a
module and become package maintainer for it.
biojava-structure: Everything protein structure related. I would be
package maintainer.
biojava-blast: Blast parsing is a frequently requested functionality
and it would be good to have this code self-contained. A package
maintainer for this still will need to be nominated at a later stage.
Any suggestions for other modules?

Let me know what you think about this.

Andreas