[Biojava-l] sequence dbs

[Matthew Pocock]

Hi - back from Genova - great conference. Anyhow...

If you create a SeqDBLite interface without the troublesome methods, and 
have SequenceDB inherit from this and add back the troubling ones, then 
I think we are OK. Existing code that purely uses SequenceDB to 
fetch-by-index should over time use SeqDBLite instead. Your remote 
sequence db implementations then become SeqDBLite implementors and 
everything is hunkey-dorey.

Or am I missing something?

M

ps - not sure how to handle the multiple-sequence-types-in-db problem.

Jason Stajich wrote:

> I started to work on this at biojava bootcamp, didn't get very far because
> of the following:
> seq.db.SequenceDB currently have the following methods that one cannot
> implement for 'remote' databases.  
> 
> <   Set ids();
> <   SequenceIterator sequenceIterator();
> 
> <   void addSequence(Sequence seq)
> <   throws IllegalIDException, BioException, ChangeVetoException;
> <   void removeSequence(String id)
> <   throws IllegalIDException, BioException, ChangeVetoException;
> 
> I started to split these methods into separate interfaces -
> LocalSequenceDB for the ids() and seuenceIterator and UpdateableSequenceDB
> for add/remove.  This of course breaks all classes which depend on
> SequenceDB.  The other option is to create RemoteSequenceDB which throws
> VetoExceptions for add/remove calls and some other exception for
> ids()/sequenceIterator().  
> 
> BTW: An example of a RemoteDB is web EMBL queries which we will patch
> through HTTP to extract a sequence from this database (will be talking to
> Heikki's web script).  Similarly if the GenBank parsing works we can pass
> queries to NCBI GenBank to query on an accession number.
> 
> One other major issue is: what if we do not know what type of sequence we
> are obtaining (prot or [dr]na)?  Biojava likes to have these things
> established in the parser - but I won't really be able to divine anything
> from an accession number.  ideas?
> 
> -jason
> 
> Jason Stajich
> jason@chg.mc.duke.edu
> Center for Human Genetics
> Duke University Medical Center 
> http://www.chg.duke.edu/ 
> 
> 
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