Raw content of Bio::EnsEMBL::DBSQL::MergedAdaptor
<![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::MergedAdaptor
=head1 SYNOPSIS
$merged_adaptor = new Bio::EnsEMBL::DBSQL::MergedAdaptor(
-species => "human",
-type => "Population"
);
=head1 DESCRIPTION
The MergedAdaptor object is merely a list of adaptors. AUTOLOAD is used
to call a subroutine on each adaptor and merge the results.
=head1 METHODS
=cut
package Bio::EnsEMBL::DBSQL::MergedAdaptor;
use vars qw(@ISA);
use strict;
use Bio::EnsEMBL::Utils::Exception qw(throw warning deprecate);
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use Bio::EnsEMBL::Registry;
my $reg = "Bio::EnsEMBL::Registry";
=head2 new
Example : $MergedAdaptor = new
: Bio::EnsEMBL::DBSQL::MergedAdaptor(-species=> 'human', -type =>'Population', -groups => ['Sanger','Ensembl']);
Arg [SPECIES]: (optional) string
species name to get adaptors for
Arg [TYPE] : (optional) string
type to get adaptors for
Arg [GROUPS] : (optional) ref to list
Description: Creates a new MergedAdaptor
Returntype : Bio::EnsEMBL::DBSQL::MergedAdaptor
Exceptions : throws if species or type not specified
Caller : general
Status : At Risk
: Under development
=cut
sub new {
my ($class,@args) = @_;
my $self ={};
bless $self,$class;
my ($species, $type, $groups) =
rearrange([qw(SPECIES TYPE GROUPS)], @args);
if(!defined($species)|| !defined($type)){
die "Species and Type must be specified\n";
}
my @adaps;
if (!defined ($groups)){
#get all adaptors for that species and type
@adaps = @{$reg->get_all_adaptors(-species => $species, -type => $type)};
}
else{
#get only specified adaptors for the particular groups
foreach my $group (@{$groups}){
push @adaps, $reg->get_adaptor($species,$group,$type);
}
}
my @list =();
push(@list,@adaps);
$self->{'list'}= \@list;
return $self;
}
=head2 add_list
Example : $MergedAdaptor->add_list(@adaptors);
Description: adds a list of adaptors to the Merged adaptor list.
Returntype : none
Exceptions : none
Status : At Risk
: Under development
=cut
sub add_list{
my ($self, @arr) = @_;
foreach my $adap (@arr){
$self->add_adaptor($adap);
}
}
=head2 add_adaptor
Example : $MergedAdaptor->add_adaptor(@adaptors);
Description: adds an adaptor to the Merged adaptor list.
Returntype : none
Exceptions : none
Status : At Risk
: Under development
=cut
sub add_adaptor{
my ($self,$adaptor)=@_;
if(!defined ($self->{'list'})){
my @list =();
push(@list,$adaptor);
$self->{'list'}= \@list;
}
else{
push(@{$self->{'list'}},$adaptor);
}
}
sub printit{
my ($self)=@_;
foreach my $adaptor (@{$self->{'list'}}){
print "printit $adaptor\t".$adaptor->db->group()."\n";
}
}
use vars '$AUTOLOAD';
sub AUTOLOAD {
my ($self,@args) = @_;
my @array_return=();
my $ref_return = undef;
$AUTOLOAD =~ /^.*::(\w+)+$/ ;
my $sub = $1;
foreach my $adaptor (@{$self->{'list'}}) {
my $ref;
if($adaptor->can($sub)){
$ref = $adaptor->$sub(@args);
if( ref($ref) eq 'ARRAY' ) {
push @array_return, @{$ref};
} else {
push @array_return, $ref;
}
}
else{ # end of can
warn("In Merged Adaptor $adaptor cannot call sub $sub");
}
}
return \@array_return;
}
sub DESTROY{
}
1;
]]>