[Biojava-l] sequence dbs

[Cox, Greg]

Another option is to throw org.omg.CORBA.NO_IMPLEMENT in your implementation
of these methods.  Since you could set up a remote database that you could
add and remove sequences from, it might be good to keep these around.

Greg 

> -----Original Message-----
> From: Jason Stajich [mailto:jason@chg.mc.duke.edu]
> Sent: Tuesday, May 15, 2001 5:19 PM
> To: BioJava List
> Subject: [Biojava-l] sequence dbs
> 
> 
> 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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