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.IX Title "Bio::DB::GFF::Adaptor::biofetch_oracle 3pm"
.TH Bio::DB::GFF::Adaptor::biofetch_oracle 3pm "2020-01-13" "perl v5.30.0" "User Contributed Perl Documentation"
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.SH "NAME"
Bio::DB::GFF::Adaptor::biofetch_oracle \-\- Cache BioFetch objects in a Bio::DB::GFF database
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
Proof of principle.  Not for production use.
.SH "DESCRIPTION"
.IX Header "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
\&\s-1EMBL\s0 database) as needed.  This allows the Generic Genome Browser to
be used as a Genbank/EMBL browser.
.SH "AUTHOR"
.IX Header "AUTHOR"
Lincoln Stein <lstein@cshl.org>.
.PP
Copyright 2002 Cold Spring Harbor Laboratory.
.PP
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.
.SS "new"
.IX Subsection "new"
.Vb 10
\& Title   : new
\& Usage   : $db = Bio::DB::GFF\->new(\-adaptor=>\*(Aqbiofetch_oracle\*(Aq, \-preferred_tags => \e%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 \*(Aqgene\*(Aq and a \*(Aqlocus\*(Aq tag).
\&                               Common defaults are provided that work well for eukaryotic
\&                               features (but not well for viral/prokaryotic)
\&              see below for additional arguments.                             
\& Status  : Public
.Ve
.PP
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:
.PP
.Vb 2
\&  Argument       Description
\&  \-\-\-\-\-\-\-\-       \-\-\-\-\-\-\-\-\-\-\-
\&
\&  \-dsn           the DBI data source, e.g. \*(Aqdbi:mysql:ens0040\*(Aq
\&
\&  \-user          username for authentication
\&
\&  \-pass          the password for authentication
\&
\&  \-proxy         [[\*(Aqhttp\*(Aq,\*(Aqftp\*(Aq],\*(Aqhttp://proxy:8080\*(Aq]
\&
\&  \-create        initialize the database
.Ve
.PP
\&\-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 \fBproxy()\fR method of Bio::DB::WebDBSeqI, except that the
argument must be passed as an array reference.