[Biojava-l] BioJava 1.3pre1

[Thomas Down]

On Mon, Jan 13, 2003 at 08:10:21PM -0500, Brian Gilman wrote:
> On 1/13/03 6:31 PM, "Thomas Down" <td2@sanger.ac.uk> wrote:
> 
> Hey Thomas,
> 
>     Do you have a doc that describes the functionality in this release??
> Something like a feature matrix would be nice to see.

Now, there's a question!  This release has largely been
many, many, incremental improvements over 1.2.  But you're
right, it's time to start putting together the improvements
list ready for the 1.30-final release.  Here's a start,
all additions and corrections welcomed:

  - Many, many, additions to the FeatureFilter language
    and its associated support code, allowing more
    sophisticated querying, and better optimization of
    these queries at the back end.

  - FeatureFilters can now be applied to SequenceDBs as well
    as Sequences, allowing feature-centric querying of entire
    databases (biojava-ensembl now takes advantage of this).

  - Sequences can publish metadata about their annotations.

  - Memory-optimized SymbolList implementations
  
  - Improvements to the handler code for building object
    models from search results (Keith?).  BlastXML support.

  - Core properties of Features may now be mutable.
 
  - BioSQL adaptors rewritten for better scalability and
    strictly correct implementation of the ChangeEvent framework.

  - Updates to sequence-file parsers, and support for GAME 1.2

  - OBDA-compliant support for indexed flatfiles.

  - BioFetch.

  - Hashtable-based fast search libraries, similar to the
    SSAHA algorithm (requires J2SE 1.4 or better).

  - Many bugs fixed!

I know I've missed some important bits here, so let's get
it updated before the release.

    Thomas.