[Biojava-l] Re: Proposed addition to the SequenceDB interface

[Marc Colosimo]

Thomas Down <td2@sanger.ac.uk> wrote:

> 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")
>   );

Would this return the feature as some sort of generic gene.id feature? My
growing concern is that for each file/db/SQL format we are adding features with
their original names rather than some defined BioJava enforced named feature. I
noticed a dtd for features. Unfortunately, I don't know much about XML besides
the simple things. Could we make something like gene_id, accession_no, etc...
? By using these set names, you don't have to know what a gene_id tag is for
EMBL, genbank, SQL,.......

Or have I missed this ability in BioJava somehow?

Marc