[Biojava-l] [RELEASE PLANS] Sanger Centre core BioJava classes

[Thomas Down]

Well, things have certainly started moving in the last
day or so :)

Following Ewan's kind offer of a CVS repository, and in
the intrests of getting as much code out in public as
soon as possible, I'd like to open the core Sanger
Centre biojava classes for discussion.

There's currectly JavaDoc online at:

  http://www.sanger.ac.uk/Users/td2/biojava_core_20000121/

I'm afraid a lot of doc comments are missing at the
moment, but hopefully that'll get filled in over the
next few days.  I'm also looking at tidying up the
code itself for release (but that might be a little
difficult since one of the key developers is away at
the moment).

What's covered by the documented packages:

  - bio.seq (and subpackages) contains the core
    ideas about Sequences, and other important
    concepts.

  - bio.acedb is a package for talking to ACeDB
    databases, modelled loosely on JDBC.

Coming soon:

  - bio.alignment (Hidden Markov models, primarily).

  - stats.svm (Kernel methods for classification and
    regression).


For discussion:

  - How do the documented packages (especially
    bio.seq) fit in with your ideas of how the
    relevant concepts should be implemented in
    Java)?

  - How should a `finished' biojava release be
    structures?  I'm inclined to favour package
    naming like "org.biojava.seq", "org.biojava.acedb",
    "org.biojava.stats.svm".

Let me (and the list) know what you think!

   Thomas.
-- 
``Science is magic that works''  -- Kurt Vonnegut.