[Biojava-l] extra seqDB things to add

[Matthew Pocock]

How about this:

Keep biojava.jar dependance-free
o define all the interfaces here
o define usefull but (possibly) minimalistc implementations if
appropreate
  (e.g. simple file indexing using an ascii table, or Java
serialization)
o as-and-when people become inspired, create implementations for widely
  used sequence index formats (blast, srs etc.)

Add a CVS module biojava-extras that can have arbitrary dependancies
o within that have java packages rooted at org.biojava.extra
o org.biojava.extra.seq.db.BioperlIndexedSequenceDB uses berkley DB so
that it can
  read/write index files in the same format as bioperl
o add other bindings that requre 3rd party libraries

I think it should be possible to write code that reads blast indexes.
Ensembl has some C code to do it, and it is vaguely readable. So we
could have org.biojava.bio.seq.db.BlastIndexedSequenceDB if you want it.

Matthew

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