[Biojava-l] Proposed addition to the SequenceDB interface

[Thomas Down]

Hi...

I'm considering adding a filter(FeatureFilter); method to
SequenceDB, which allows features to be extracted from a
whole database, rather than just a single sequence.  Typical
usage would be:

  SequenceDB seqDB = ...
  FeatureHolder mygene = seqDB.filter(
      new FeatureFilter.ByAnnotation("gene.id", "BRCA2")
  );

I can't see this breaking any code.  To make life easy,
We can put a naive implementation of the filter method
on AbstractSequenceDB.  Obviously, the hope is that
specific implementations will provide nice, optimized
implementations (for database like BioSQL and biojava-ensembl
this should be quite easy).

The `dumb' sequence database interface (SequenceDBLite)
would remain unchanged.

Are there any objections to this plan?  Or any better
suggestions?  If not, I'll add it as soon as the dust
from the bootcamp has settled a bit.

    Thomas.