[Biojava-l] Another problem with TaxonFactories

[Richard HOLLAND]

biojavax should circumvent this. have a look in the org.biojavax.bio packages in biojava-live for a sneak preview. Basically we have adopted the BioSQL conventions, and created a new NCBITaxon class to represent the table from the database. The code is written to work with Hibernate for database access, so that you can search the taxa any way you wish - no need for a TaxonFactory in this new version.

Docs and HowTos will be provided when this biojavax thing is finished. Mark won't set a date but personally I'd like to see it out by the end of the year.

cheers,
Richard


-----Original Message-----
From:	biojava-l-bounces at portal.open-bio.org on behalf of "Andreas Dräger"
Sent:	Fri 10/7/2005 11:14 PM
To:	biojava-l at biojava.org
Cc:	
Subject:	[Biojava-l] Another problem with TaxonFactories
Hello,

every monday NCBI releases a new version of taxon names, merged nodes etc. A
scientific name of a taxon might be changed someday. If a TaxonFactory only
allowes to search for a taxon by scientific name which is the case at the
moment at least for SimpleTaxonFactory, we might lose information, if we
want to perform a database update for example. I would like to suggest to
extend this for the NCBI-Taxon ID so that we can consider changed names
properties. By the way, one does not easily understand that the parameter
called 'String id' is the 'scientific name' in reality. I would like to
suggest to change that.

Andreas

-- 
Highspeed-Freiheit. Bei GMX supergünstig, z.B. GMX DSL_Cityflat,
DSL-Flatrate für nur 4,99 Euro/Monat*  http://www.gmx.net/de/go/dsl
_______________________________________________
Biojava-l mailing list  -  Biojava-l at biojava.org
http://biojava.org/mailman/listinfo/biojava-l