Provided by: libbio-perl-perl_1.7.2-2_all bug


       Bio::DB::GFF::Adaptor::biofetch -- Cache BioFetch objects in a Bio::DB::GFF database


       Proof of principle.  Not for production use.


       This adaptor is a proof-of-principle.  It is used to fetch BioFetch sequences into a
       Bio::DB::GFF database (currently uses a hard-coded EMBL database) as needed.  This allows
       the Generic Genome Browser to be used as a Genbank/EMBL browser.


       Lincoln Stein <>.

       Copyright 2002 Cold Spring Harbor Laboratory.

       This library is free software; you can redistribute it and/or modify it under the same
       terms as Perl itself.

        Title   : new
        Usage   : $db = Bio::DB::GFF->new(-adaptor=>'biofetch',@args)
        Function: create a new adaptor
        Returns : a Bio::DB::GFF object
        Args    :   -adaptor : required.  Which adaptor to use; biofetch for mysql, biofetch_oracle for Oracle
                    -preferred_tags : optional.  A hash of {classname => weight,...}
                                      used to determine the class and name of the feature
                                      when a choice of possible feature classes is available
                                      (e.g. a feature has both a 'gene' and a 'locus' tag).
                                      Common defaults are provided that work well for eukaryotic
                                      features (but not well for viral/prokaryotic)
                     see below for additional arguments.
        Status  : Public

       This is the constructor for the adaptor.  It is called automatically by Bio::DB::GFF->new.
       In addition to arguments that are common among all adaptors, the following class-specific
       arguments are recgonized:

         Argument       Description
         --------       -----------

         -dsn           the DBI data source, e.g. 'dbi:mysql:ens0040'

         -user          username for authentication

         -pass          the password for authentication

         -proxy         [['http','ftp'],'http://proxy:8080']

         -source        source to use for loaded features ('EMBL')

       -dsn,-user and -pass indicate the local database to cache results in, and as are per
       Bio::DB::GFF::Adaptor::dbi.  The -proxy argument allows you to set the biofetch web proxy,
       and uses the same syntax described for the proxy() method of Bio::DB::WebDBSeqI, except
       that the argument must be passed as an array reference.