[Biojava-l] biojava-ensembl 1.3.9 released

[Thomas Down]

Hi...

I've just put together a new release of the biojava-ensembl
code, which works with the latest BioJava code, and current
(schemaVersion 9) Ensembl databases (earlier database versions
are still supported).

For those who haven't seen it before, biojava-ensembl offers
full read-only access to the sequence, assembly, and annotation
data stored in Ensembl core databases, using standard BioJava
interfaces.  Note that all this is separate from the ensj
codebase, which provides an Ensembl-specific API rather than
using BioJava interfaces.

For those who have used it before, there are have been
a number of recent changes which make it worth upgrading:

   - The previously separate `ensembl' module has been merged
     into biojava-ensembl

   - There have been many, many, architectural changes under
     the hood to improve performance and avoid excessive memory
     usage.

   - The SequenceDB.filter method from BioJava 1.3 is supported.
     This can be used for problems such as finding a transcript
     feature by ID, or finding where a particular clone appears
     in the assembly.

   - Sequences publish informative feature-schemas.

   - The assembly has been collapsed from three levels
     down to two -- FPC contigs are no longer exposed as
     first-class sequences.

biojava-ensembl is available from

   http://www.biojava.org/download/biojava-ensembl/

or from BioJava CVS (checkout biojava-ensembl).

Let me know if there are any problems with this release,

     Thomas.