[Biojava-l] New stuff on main trunk

[Matthew Pocock]

Dear all,

We seem to be getting quite a few downloads of 1.0, which is great. The
1.0 branch will remain feature-stable with no additional
classes/interfaces, and only maintainance bug fixes. However, now that
there is a 'stable' biojava out there, we can start to add cool stuff to
the main trunk.

So far, I have moved a few classes to the utils package
(AlphabetManager.ListWrapper being the most important), and started a
re-write of the dp code. Also, I have fleshed out the database package
org.biojava.bio.seq.db with AbstractSequenceDB, SequenceDBWrapper (a
view onto an underlying database) and SubSequenceDB (lets you pass
arround part of a dabase as if it were a complete database).

If anybody out there has things they want to see in BioJava, then mail
the list. Just to get the ball rolling, here is my wish-list:

Species naming classes - a tree going from kingdom down to sub-species
(like the organism classification in EMBL).
References - standard objects for stooring literature references
Expression data interfaces
Pathway graphs
Protein structure - pdb, dssp etc.

If a group of you are keen about any of these, or some other project,
then please tell us, and let's see if we can get a few of them
implemented.

Thanks.

Matthew