Raw content of Bio::EnsEMBL::DBSQL::ProxySNPAdaptor
<![CDATA[=head1 LICENSE
Copyright (c) 1999-2009 The European Bioinformatics Institute and
Genome Research Limited. All rights reserved.
This software is distributed under a modified Apache license.
For license details, please see
/info/about/code_licence.html
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <ensembl-dev@ebi.ac.uk>.
Questions may also be sent to the Ensembl help desk at
<helpdesk@ensembl.org>.
=cut
=head1 NAME
Bio::EnsEMBL::DBSQL::ProxySNPAdaptor
=head1 SYNOPSIS
Designed as an abstraction over the database specific SNPAdaptors. This
is written right now to serve as a replacement for a core SNPadaptor
which doesn''t even exist yet and probably never will since SNPs are
taken from external databases. In the future some sort of DBRegistry may
remove the need for this class.
=head1 METHODS
=cut
package Bio::EnsEMBL::DBSQL::ProxySNPAdaptor;
use strict;
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
use Bio::EnsEMBL::Utils::Exception qw(throw);
use vars ('@ISA', '$AUTOLOAD');
@ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);
=head2 fetch_attributes_only
Arg [1] : int refsnp_id
Arg [2] : (optional) string source
Example : none
Description: Retrieves a snp objcet from the SNP database but does not
populate the location information. This is necessary given
the current state of the snp database because location
information has to be retrieved differently for different
species!
Returntype : Bio::EnsEMBL::SNP
Exceptions : none
Caller : snpview
=cut
sub fetch_attributes_only{
my ( $self, @args ) = @_;
my $lite_db = Bio::EnsEMBL::Registry->get_db($self->db(),'lite');
my $snp_db = Bio::EnsEMBL::Registry->get_db($self->db(),'SNP');
if( defined $snp_db ) {
my $snp_adaptor = $snp_db->get_SNPAdaptor();
return $snp_adaptor->fetch_attributes_only( @args );
}
if( defined $lite_db ) {
my $snp_adaptor = $lite_db->get_SNPAdaptor();
return $snp_adaptor->fetch_attributes_only( @args );
}
}
=head2 AUTOLOAD
Arg [1] : list of arbitrary values @args
a list of arguments to pass to the request method
Example : -
Description: AUTOLOAD method should not be called directly. It is called
implicitly when a method requested from this class cannot be
found. This method first tries to execute the requested method
in the primary adaptor. If the method cannot be found then
it searches the other attached databases for equivalent adaptors
and tries then one at a time.
Returntype : arbitrary
Exceptions : thrown if the requested method cannot be found on the primary
adaptor or on any of the attached databases.
Caller : called implicitly by perl
=cut
sub AUTOLOAD {
my ($self, @args) = @_;
#determine the method which was called
my $method = $AUTOLOAD;
#strip out fully qualified method name
$method =~ s/.*:://;
my $lite_db = Bio::EnsEMBL::Registry->get_db($self->db(),'lite');
my $snp_db = Bio::EnsEMBL::Registry->get_db($self->db(),'SNP');
if( defined $lite_db ) {
my $snp_adaptor = $lite_db->get_SNPAdaptor();
if($snp_adaptor->can($method)) {
return $snp_adaptor->$method(@args);
}
}
if( defined $snp_db ) {
my $snp_adaptor = $snp_db->get_SNPAdaptor();
if($snp_adaptor->can($method)) {
return $snp_adaptor->$method(@args);
}
}
throw("The requested method $method could not be found in lite or snp" );
}
sub DESTROY {
}
1;
__END__
]]>