[Biojava-l] features pre 1.0

[Matthew Pocock]

Dear all,

This is the last call for 1.0 features. What would you like to see in
BioJava?

I have changed:

o AlphabetManager now has only static methods & the instance() method is
depricated
o propper support for ambiguous symbols (like n, x)

So far we have the possibility of:

o sensible ways of retrieving databases by name
o blast parsing
o blast object model

I would like to add:

o prety printing of alignments / dp results
o alignment io framework - possibly with no implementations
  - should eventualy handle things like msa as well as simple-stupid
formats
o a ParseException that stoores:
  - uri (file name, url etc.)
  - line number
  - char offset
  - string of current line
  - message (inherited from Exception)

Wishlist (I don't have time, but mabey you do):

o structure databases support - pdb, dssp, msa etc.
o well known alphabet of secondary structure elements
o proper URI support & naming-and-directory service support
o HMMs could expose transition scores as probabilities, not log
probabilities
o world peace

Thomas is overhauling the GFF parsing code as we speak, so that may work
better.

If you don't say that you want it, we can't put it in...

Matthew

--
Joon: You're out of your tree
Sam:  It wasn't my tree
                                                 (Benny & Joon)