Bio::DB::GFF::Adaptor::biofetch man page on Fedora

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Bio::DB::GFF::Adaptor:UserfContributed Perl Bio::DB::GFF::Adaptor::biofetch(3)

NAME
       Bio::DB::GFF::Adaptor::biofetch -- 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',@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.

perl v5.14.1			  2011-07-22Bio::DB::GFF::Adaptor::biofetch(3)
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