Raw content of Bio::EnsEMBL::ExternalData::SangerSNP::DBAdaptor
<![CDATA[package Bio::EnsEMBL::ExternalData::SangerSNP::DBAdaptor;
=head1 NAME
Bio::EnsEMBL::ExternalData::SangerSNP::DBAdaptor -
Database adaptor for a SangerSNP database
=head1 SYNOPSIS
$db_adaptor = Bio::EnsEMBL::ExternalData::SangerSNP::DBAdaptor->new(
-user => 'root',
-pass => 'secret',
-dbname => 'pog',
-host => 'caldy',
-driver => 'Oracle'
);
$snp_adaptor = $db_adaptor->get_SangerSNPAdaptor;
=head1 DESCRIPTION
This object represents a SangerSNP database. Once created you can retrieve object
adaptors that allow you to create objects from data in the SangerSNP database.
It delegates its connection responsibilities to the DBConnection class (no
longer inherited from) and its object adaptor retrieval to the static
Bio::EnsEMBL::Registry.
=head1 LICENCE
This code is distributed under an Apache style licence:
Please see /code_licence.html for details
=head1 AUTHORS
Steve Searle <searle@sanger.ac.uk>
=head1 CONTACT
Post questions to the EnsEMBL development list ensembl-dev@ebi.ac.uk
=cut
use strict;
use Bio::EnsEMBL::DBSQL::DBAdaptor;
use Bio::EnsEMBL::ExternalData::SangerSNP::DBConnection;
use Bio::EnsEMBL::Utils::Exception qw(throw warning deprecate);
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::DBSQL::DBAdaptor);
=head2 new
Arg [-DNADB]: (optional) Bio::EnsEMBL::ExternalData::SangerSNP::DBAdaptor DNADB
All sequence, assembly, contig information etc, will be
retrieved from this database instead.
Arg [..] : Other args are passed to
Bio::EnsEMBL::ExternalData::SangerSNP::DBConnection
Exmaple : $db = new Bio::EnsEMBL::ExternalData::SangerSNP::DBAdaptor(
-species => 'Homo_sapiens',
-group => 'sangersnp'
-user => 'root',
-dbname => 'pog',
-host => 'caldy',
-driver => 'Oracle');
Description: Constructor for DBAdaptor.
Returntype : Bio::EnsEMBL::ExternalData::SangerSNP::DBAdaptor
Exceptions : none
Caller : general
=cut
sub new {
my($class, @args) = @_;
my $self ={};
bless $self,$class;
$self->dbc(new Bio::EnsEMBL::ExternalData::SangerSNP::DBConnection(@args));
my ($species, $group, $con, $dnadb) =
rearrange([qw(SPECIES GROUP DBCONN DNADB)], @args);
if(defined($con)){
$self->dbc($con);
}
else{
$self->dbc(new Bio::EnsEMBL::ExternalData::SangerSNP::DBConnection(@args));
}
if(defined($species)){
$self->species($species);
}
else{
$self->species("DEFAULT");
}
if(defined($group)){
$self->group($group);
}
$self = Bio::EnsEMBL::Utils::ConfigRegistry::gen_load($self);
if(defined $dnadb) {
$self->dnadb($dnadb);
}
return $self;
}
=head2 get_available_adaptors
Example : my %object_adaptors = %{ $dbadaptor->get_available_adaptors };
Description : returns a lookup hash of object adaptors for this DBAdaptor
Return type : Hashref
Exceptions : none
Caller : Bio::EnsEMBL::Utils::ConfigRegistry
=cut
sub get_available_adaptors{
my %pairs = (
# "SangerSNPBase" => "Bio::EnsEMBL::ExternalData::SangerSNP::SangerSNPBaseAdaptor",
"Variation" => "Bio::EnsEMBL::ExternalData::SangerSNP::VariationAdaptor",
"TranscriptVariation" => "Bio::EnsEMBL::ExternalData::SangerSNP::TranscriptVariationAdaptor",
);
return (\%pairs);
}
1;
]]>