[Biojava-dev] Fwd: Bug in BioFetchSequenceDB

[David Huen]

This email is forwarded on behalf of Rudi Chiarito:-

----------  Forwarded Message  ----------

This code in getSequence() seems to be incomplete or wrong:

        else if (dbName.equals("swiss"))
            format = "swissprot";

By default, i.e. without custom configuration files, SystemRegistry will
end up using http://www.open-bio.org/registry/seqdatabase.ini as the
database registry. The problem with that is that the current file
contains, for swissprot, dbname=swall. Thus the class won't attempt to
parse the results in Swissprot format as it should.

Which is the right fix? Comparing dbName to "swall" rather than "swiss"?
Comparing dbName to both? Having the default seqdatabase.ini changed to
use dbname=swiss? Thanks for any help.

P.S.
The bug tracker pages are not working; they return an Error 404.