NAME

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

SYNOPSIS

Proof of principle. Not for production use.

DESCRIPTION

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.

AUTHOR

Lincoln Stein <lstein@cshl.org>.

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.

new

            

              
              
Title   : new
Usage   : $db = Bio::DB::GFF->new(-adaptor=>'biofetch_oracle', -preferred_tags => \%preferred, @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']
-create        initialize the database
            
          

-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.