Raw content of Bio::EnsEMBL::ExternalData::Family::DBSQL::FamilyMemberAdaptor
<![CDATA[# $Id: FamilyMemberAdaptor.pm,v 1.11 2003/04/07 12:05:00 abel Exp $
#
# Bio::EnsEMBL::ExternalData::Family::DBSQL::FamilyMemberAdaptor
#
# Cared by Abel Ureta-Vidal <abel@ebi.ac.uk>
#
# Copyright EnsEMBL
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
FamilyAdaptor - DESCRIPTION of Object
This object represents a database of protein families.
=head1 SYNOPSIS
=head1 DESCRIPTION
=head1 CONTACT
=head1 APPENDIX
=cut
package Bio::EnsEMBL::ExternalData::Family::DBSQL::FamilyMemberAdaptor;
use vars qw(@ISA);
use strict;
use Bio::EnsEMBL::ExternalData::Family::FamilyMember;
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
@ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);
=head2 fetch_by_dbID
Title : fetch_by_dbID
Usage : $memberadaptor->fetch_by_dbID($id);
Function: fetches a FamilyMember given its internal database identifier
Example : $memberadaptor->fetch_by_dbID(1)
Returns : a Bio::EnsEMBL::ExternalData::Family::FamilyMember object if found,
undef otherwise
Args : an integer
=cut
sub fetch_by_dbID {
my ($self, $dbID) = @_;
$self->throw("dbID arg is required\n") unless ($dbID);
my $constraint = "fm.family_member_id = $dbID";
my $members = $self->_fetch_family_members($constraint);
return undef if(!@$members);
return $members->[0];
}
=head2 fetch_by_stable_id
Title : fetch_by_stable_id
Usage : $memberadaptor->fetch_by_stable_id($stable_id);
Function: fetches a FamilyMember given its stable identifier
(external_member_id)
Example : $db->fetch_by_stable_id('ENSG00000000009');
Returns : a array ref of Bio::EnsEMBL::ExternalData::Family::FamilyMembers
IMPORTANT: this method returns an array reference because the
stable_id could not be unique
i.e. the same member maybe part of more than one family
Args : an EnsEMBL Gene/Peptide stable id (e.g. ENSG00000000009) or
an Accession Number (e.g.O35622)
=cut
sub fetch_by_stable_id {
my ($self, $stable_id) = @_;
$self->throw("stable_id arg is required") unless ($stable_id);
my $constraint = "fm.external_member_id = '$stable_id'";
return $self->_fetch_family_members($constraint);
}
sub fetch_by_family_id {
my ($self, $family_id) = @_;
$self->throw("family_id arg is required\n") unless ($family_id);
my $constraint = "fm.family_id = $family_id";
return $self->_fetch_family_members($constraint);
}
sub fetch_by_dbname {
my ($self,$dbname) = @_;
$self->throw("dbname arg is required\n") unless ($dbname);
my $constraint = "ex.name = '$dbname'";
return $self->_fetch_family_members($constraint);
}
sub fetch_by_dbname_taxon {
my ($self,$dbname,$taxon_id) = @_;
$self->throw("dbname and taxon_id args are required")
unless($dbname && $taxon_id);
my $constraint = "ex.name = '$dbname' and fm.taxon_id = $taxon_id";
return $self->_fetch_family_members($constraint);
}
sub fetch_by_family_dbname {
my ($self,$family_id,$dbname) = @_;
$self->throw("family_id and dbname args are required")
unless($family_id && $dbname);
my $constraint = "fm.family_id = $family_id and ex.name = '$dbname'";
return $self->_fetch_family_members($constraint);
}
sub fetch_by_family_dbname_taxon {
my ($self,$family_id,$dbname,$taxon_id) = @_;
$self->throw("family_id, dbname and taxon_id args are required")
unless ($family_id && $dbname && $taxon_id);
my $constraint = "fm.family_id = $family_id
AND ex.name = '$dbname'
AND fm.taxon_id = $taxon_id";
return $self->_fetch_family_members($constraint);
}
sub _fetch_family_members {
my ($self, $constraint) = @_;
my $q = "SELECT fm.family_member_id, fm.family_id, fm.external_db_id,
fm.external_member_id, fm.taxon_id, fm.alignment, ex.name
FROM family_members fm, external_db ex
WHERE ex.external_db_id = fm.external_db_id";
if($constraint) {
$q .= " AND $constraint";
}
my $sth = $self->prepare($q);
$sth->execute();
my ($family_member_id, $family_id, $external_db_id, $external_member_id,
$taxon_id, $alignment_string, $external_db_name);
$sth->bind_columns(\$family_member_id, \$family_id, \$external_db_id,
\$external_member_id, \$taxon_id, \$alignment_string,
\$external_db_name);
my @members;
while($sth->fetch) {
my $member = new Bio::EnsEMBL::ExternalData::Family::FamilyMember();
$member->adaptor($self);
$member->dbID($family_member_id);
$member->family_id($family_id);
$member->external_db_id($external_db_id);
$member->database($external_db_name);
$member->stable_id($external_member_id);
$member->taxon_id($taxon_id);
$member->alignment_string($alignment_string);
push @members, $member;
}
return \@members;
}
sub get_external_db_id_by_dbname {
my ($self, $dbname) = @_;
$self->throw("Should give a defined databasename as argument\n")
unless (defined $dbname);
my $q = "SELECT external_db_id FROM external_db WHERE name = ?";
$q = $self->prepare($q);
$q->execute($dbname);
my $rowhash = $q->fetchrow_hashref;
return $rowhash->{external_db_id};
}
sub get_dbname_by_external_db_id {
my ($self, $external_db_id) = @_;
$self->throw("Should give a defined external_db_id as argument\n")
unless (defined $external_db_id);
my $q = "SELECT name FROM external_db WHERE external_db_id = ?";
$q = $self->prepare($q);
$q->execute($external_db_id);
my $rowhash = $q->fetchrow_hashref;
return $rowhash->{name};
}
=head2 store
Arg [1] : int family_id
Arg [2] : Bio::EnsEMBL::ExternalData::Family::FamilyMember $member
Example : $member_id = $family_member_adaptor->store($family_id, $member);
Description: Stores a family member object in the database. On success the
family member id is returned
Returntype : int
Exceptions : thrown if incorrect argument supplied
Caller : general
=cut
sub store {
my ($self,$family_id,$member) = @_;
unless($member->isa('Bio::EnsEMBL::ExternalData::Family::FamilyMember')) {
$self->throw(
"member arg must be a [Bio::EnsEMBL::ExternalData::Family::FamilyMember]"
. "not a $member");
}
my $sth =
$self->prepare("INSERT INTO family_members (family_id, external_db_id,
taxon_id, external_member_id,
alignment)
VALUES (?,?,?,?,?)");
$sth->execute($family_id,
$member->external_db_id,
$member->taxon_id,
$member->primary_id,
$member->alignment_string);
$member->dbID( $sth->{'mysql_insertid'} );
$member->adaptor($self);
if (defined $member->taxon) {
$self->db->get_TaxonAdaptor->store_if_needed($member->taxon);
}
return $member->dbID;
}
=head2 update
Arg [1] : Bio::EnsEMBL::ExternalData::Family::FamilyMember
Example :
Description: Updates the attributes of a family member that has already been
stored in the database. This is useful to update attributes
such as a the alignment string which may have been calculated
after the families were alreated created. On success this
method returns the dbID of the updated member
Returntype : int
Exceptions : thrown if incorrect argument is provided
thrown if the member to be updated does not have a dbID
Caller : general
=cut
sub update {
my ($self, $member) = @_;
unless($member->isa('Bio::EnsEMBL::ExternalData::Family::FamilyMember')) {
$self->throw(
"member arg must be a [Bio::EnsEMBL::ExternalData::Family::FamilyMember".
"not a [$member]");
}
unless($member->dbID) {
$self->throw("Family member does not have a dbID and cannot be updated");
}
my $sth =
$self->prepare("UPDATE family_members
SET family_id = ?,
external_db_id = ?,
external_member_id = ?,
taxon_id = ?,
alignment = ?
WHERE family_member_id = ?");
$sth->execute($member->family_id, $member->external_db_id,
$member->primary_id, $member->taxon_id,
$member->alignment_string, $member->dbID);
return $member->dbID;
}
1;
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