Raw content of Bio::EnsEMBL::ExternalData::Family::DBSQL::DBAdaptor
<![CDATA[
=head1 NAME - Bio::EnsEMBL::ExternalData::Family::DBSQL::DBAdaptor
=head1 SYNOPSIS
$db = Bio::EnsEMBL::ExternalData::Family::DBSQL::DBAdaptor->new(
-user => 'myusername',
-dbname => 'familydb',
-host => 'myhost',
);
$family_adaptor = $db->get_FamilyAdaptor;
$familymember_adaptor = $db->get_FamilyMemberAdaptor;
$taxon_adaptor = $db->get_TaxonAdaptor;
=head1 DESCRIPTION
This object represents a database that is implemented somehow (you shouldnt
care much as long as you can get the object). You can pull
out other objects such as Family, FamilyMember, Taxon through their respective adaptors.
=head1 CONTACT
Post questions to the EnsEMBL development list <ensembl-dev@ebi.ac.uk>
=cut
package Bio::EnsEMBL::ExternalData::Family::DBSQL::DBAdaptor;
use vars qw(@ISA);
use strict;
use Bio::EnsEMBL::DBSQL::DBConnection;
@ISA = qw( Bio::EnsEMBL::DBSQL::DBConnection );
=head2 new
Arg [..] : list of named arguments. See Bio::EnsEMBL::DBConnection.
[-CONF_FILE] optional name of a file containing configuration
information for family genome databases. If databases are
not added in this way, then they should be added via the
method add_DBAdaptor.
Example : $db = new Bio::EnsEMBL::ExternalDataba::Family::DBSQL::DBAdaptor
( -user => 'root',
-dbname => 'pog',
-host => 'caldy',
-driver => 'mysql',
-conf_file => 'conf.pl');
Description: Creates a new instance of a DBAdaptor for the family database.
Returntype : Bio::EnsEMBL::ExternalData::Family::DBAdaptor
Exceptions : none
Caller : general
=cut
sub new {
my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
my ($conf_file) = $self->_rearrange(['CONF_FILE'], @args);
$self->{'genomes'} = {};
if($conf_file) {
#read configuration file from disk
my @conf = @{do $conf_file};
foreach my $genome (@conf) {
my ($species, $assembly, $db_hash) = @$genome;
my $db;
my $module = $db_hash->{'module'};
my $mod = $module;
eval {
# require needs /'s rather than colons
if ( $mod =~ /::/ ) {
$mod =~ s/::/\//g;
}
require "${mod}.pm";
$db = $module->new(-dbname => $db_hash->{'dbname'},
-host => $db_hash->{'host'},
-user => $db_hash->{'user'},
-pass => $db_hash->{'pass'},
-port => $db_hash->{'port'},
-driver => $db_hash->{'driver'});
};
if($@) {
$self->throw("could not load module specified in configuration " .
"file:$@");
}
unless($db && ref $db && $db->isa('Bio::EnsEMBL::DBSQL::DBConnection')) {
$self->throw("[$db] specified in conf file is not a " .
"Bio::EnsEMBL::DBSQL::DBConnection");
}
$self->{'genomes'}->{"$species:$assembly"} = $db;
}
}
return $self;
}
=head2 add_db_adaptor
Arg [1] : Bio::EnsEMBL::DBSQL::DBConnection
Example : $family_db->add_db_adaptor($homo_sapiens_db);
Description: Adds a genome-containing database to compara. This database
can be used by some family methods to obtain sequence for
peptides that analysis has been performed on.
The database adaptor argument must define the get_MetaContainer
argument
so that species name and assembly type information can be
extracted from the database.
Returntype : none
Exceptions : Thrown if the argument is not a Bio::EnsEMBL::DBConnection
or if the argument does not implement a get_MetaContainer
method.
Caller : general
=cut
sub add_db_adaptor {
my ($self, $dba) = @_;
unless($dba && ref $dba && $dba->isa('Bio::EnsEMBL::DBSQL::DBConnection')) {
$self->throw("dba argument must be a Bio::EnsEMBL::DBSQL::DBConnection\n" .
"not a [$dba]");
}
my $mc = $dba->get_MetaContainer;
my $species = $mc->get_Species->binomial;
my $assembly = $mc->get_default_assembly;
$self->{'genomes'}->{"$species:$assembly"} = $dba;
}
=head2 get_db_adaptor
Arg [1] : string $species
the name of the species to obtain a genome DBAdaptor for.
Arg [2] : string $assembly
the name of the assembly to obtain a genome DBAdaptor for.
Example : $hs_db = $db->get_db_adaptor('Homo sapiens','NCBI31');
Description: Obtains a DBAdaptor for the requested genome if it has been
specified in the configuration file passed into this objects
constructor, or subsequently added using the add_genome
method. If the DBAdaptor is not available (i.e. has not
been specified by one of the abbove methods) undef is returned.
Returntype : Bio::EnsEMBL::DBSQL::DBConnection
Exceptions : none
Caller : Bio::EnsEMBL::Compara::GenomeDBAdaptor
=cut
sub get_db_adaptor {
my ($self, $species, $assembly) = @_;
unless($species && $assembly) {
$self->throw("species and assembly arguments are required\n");
}
return $self->{'genomes'}->{"$species:$assembly"};
}
=head2 get_FamilyAdaptor
Args : none
Example : my $family_adaptor = $db->get_FamilyAdaptor;
Description: retrieve the FamilyAdaptor which is used for reading and writing
Bio::EnsEMBL::ExternalData::Family::Family objects from and to
the SQL database.
Returntype : Bio::EnsEMBL::ExternalData::Family::DBSQL::FamilyAdaptor
Exceptions : none
Caller : general
=cut
sub get_FamilyAdaptor {
my ($self) = @_;
return $self->_get_adaptor
( "Bio::EnsEMBL::ExternalData::Family::DBSQL::FamilyAdaptor" );
}
=head2 get_FamilyMemberAdaptor
Args : none
Example : my $familymember_adaptor = $db->get_FamilyMemberAdaptor;
Description: retrieve the FamilyMemberAdaptor which is used for reading and writing
Bio::EnsEMBL::ExternalData::Family::FamilyMember objects from and to
the SQL database.
Returntype : Bio::EnsEMBL::ExternalData::Family::DBSQL::FamilyMemberAdaptor
Exceptions : none
Caller : general
=cut
sub get_FamilyMemberAdaptor {
my ($self) = @_;
return $self->_get_adaptor
( "Bio::EnsEMBL::ExternalData::Family::DBSQL::FamilyMemberAdaptor" );
}
=head2 get_TaxonAdaptor
Args : none
Example : my $taxon__adaptor = $db->get_TaxonAdaptor;
Description: retrieve the TaxonAdaptor which is used for reading and writing
Bio::EnsEMBL::ExternalData::Family::Taxon objects from and to
the SQL database.
Returntype : Bio::EnsEMBL::ExternalData::Family::DBSQL::TaxonAdaptor
Exceptions : none
Caller : general
=cut
sub get_TaxonAdaptor {
my ($self) = @_;
return $self->_get_adaptor
( "Bio::EnsEMBL::ExternalData::Family::DBSQL::TaxonAdaptor" );
}
=head2 get_GenomeDBAdaptor
Args : none
Example : my $genome_dba = $db->get_GenomeDBAdaptor;
Description: Retrieves a genome db adaptor which can be used to retrieve
genome containing databases
Returntype : Bio::EnsEMBL::ExternalData::Family::DBSQL::GenomeDBAdaptor
Exceptions : none
Caller : general
=cut
sub get_GenomeDBAdaptor {
my ($self) = @_;
return $self->_get_adaptor
( "Bio::EnsEMBL::ExternalData::Family::DBSQL::GenomeDBAdaptor" );
}
1;
]]>