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 <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.