Raw content of Bio::EnsEMBL::ExternalData::Mole::DBSQL::DBXrefAdaptor
<![CDATA[package Bio::EnsEMBL::ExternalData::Mole::DBSQL::DBXrefAdaptor;
use strict;
use Bio::EnsEMBL::ExternalData::Mole::DBXref;
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
use Bio::EnsEMBL::ExternalData::Mole::DBSQL::DBAdaptor;
use Bio::EnsEMBL::Utils::Exception qw( deprecate throw warning stack_trace_dump );
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use vars '@ISA';
@ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);
sub _tables {
my $self = shift;
return (['dbxref' , 'dbxrf']);
}
sub _columns {
my $self = shift;
return ( 'dbxrf.dbxref_id', 'dbxrf.entry_id',
'dbxrf.database_id', 'dbxrf.primary_id',
'dbxrf.secondary_id', 'dbxrf.tertiary_id',
'dbxrf.quaternary_id');
}
sub fetch_by_dbID {
my ($self, $id) = @_;
my $constraint = "dbxrf.dbxref_id = '$id'";
my ($dbxref_obj) = @{ $self->generic_fetch($constraint) };
return $dbxref_obj;
}
sub fetch_all_by_Entry {
my $self = shift;
my $entry = shift;
my $sth = $self->prepare(
"SELECT dbxrf.dbxref_id ".
"FROM dbxref dbxrf ".
"WHERE dbxrf.entry_id = ?");
$sth->bind_param(1, $entry->dbID, SQL_INTEGER);
$sth->execute();
my @dbxrefids;
while (my $id = $sth->fetchrow) {
push @dbxrefids, $id;
}
$sth->finish();
#my @obj_ids = map {$_->[0]} @dbxrefids;
my @obj_ids = @dbxrefids;
my @dbxrefs;
foreach my $id (@obj_ids) {
my $dbxref_object = $self->fetch_by_dbID($id);
push @dbxrefs, $dbxref_object;
}
return \@dbxrefs;
}
sub fetch_all_by_entry_id {
my ($self, $id) = @_;
my $sth = $self->prepare(
"SELECT dbxrf.dbxref_id ".
"FROM dbxref dbxrf ".
"WHERE dbxrf.entry_id = ?");
$sth->bind_param(1, $id, SQL_INTEGER);
$sth->execute();
my @array = @{$sth->fetchall_arrayref()};
my @ids = map {$_->[0]} @array;
my $dbxref_objs = $self->fetch_all_by_dbID_list(\@ids);
return $dbxref_objs;
}
sub fetch_by_entry_id {
my $self = shift;
my $entry_id = shift;
my $constraint = "dbxrf.entry_id = '$entry_id'";
my ($dbxref_obj) = @{ $self->generic_fetch($constraint) };
return $dbxref_obj;
}
sub fetch_by_database_id {
my $self = shift;
my $database_id = shift;
my $constraint = "dbxrf.database_id = '$database_id'";
my ($dbxref_obj) = @{ $self->generic_fetch($constraint) };
return $dbxref_obj;
}
sub fetch_by_primary_id {
my $self = shift;
my $primary_id = shift;
my $constraint = "dbxrf.primary_id = '$primary_id'";
my ($dbxref_obj) = @{ $self->generic_fetch($constraint) };
return $dbxref_obj;
}
sub fetch_by_secondary_id {
my $self = shift;
my $secondary_id = shift;
my $constraint = "dbxrf.secondary_id = '$secondary_id'";
my ($dbxref_obj) = @{ $self->generic_fetch($constraint) };
return $dbxref_obj;
}
sub fetch_by_tertiary_id {
my $self = shift;
my $tertiary_id = shift;
my $constraint = "dbxrf.tertiary_id = '$tertiary_id'";
my ($dbxref_obj) = @{ $self->generic_fetch($constraint) };
return $dbxref_obj;
}
sub fetch_by_quaternary_id {
my $self = shift;
my $quaternary_id = shift;
my $constraint = "dbxrf.quaternary_id = '$quaternary_id'";
my ($dbxref_obj) = @{ $self->generic_fetch($constraint) };
return $dbxref_obj;
}
sub fetch_all_by_dbID_list {
my ($self,$id_list_ref) = @_;
if(!defined($id_list_ref) || ref($id_list_ref) ne 'ARRAY') {
croak("kill object id list reference argument is required");
}
return [] if(!@$id_list_ref);
my @out;
#construct a constraint like 't1.table1_id = 123'
my @tabs = $self->_tables;
my ($name, $syn) = @{$tabs[0]};
# mysql is faster and we ensure that we do not exceed the max query size by
# splitting large queries into smaller queries of 200 ids
my $max_size = 200;
my @id_list = @$id_list_ref;
while(@id_list) {
my @ids;
if(@id_list > $max_size) {
@ids = splice(@id_list, 0, $max_size);
} else {
@ids = splice(@id_list, 0);
}
my $id_str;
if(@ids > 1) {
$id_str = " IN (" . join(',', @ids). ")";
} else {
$id_str = " = " . $ids[0];
}
my $constraint = "${syn}.${name}_id $id_str";
push @out, @{$self->generic_fetch($constraint)};
}
return \@out;
}
sub _objs_from_sth {
my ($self, $sth) = @_;
my @out;
my ( $dbxref_id, $entry_id, $database_id,
$primary_id, $secondary_id,
$tertiary_id, $quaternary_id );
$sth->bind_columns( \$dbxref_id, \$entry_id, \$database_id,
\$primary_id, \$secondary_id,
\$tertiary_id, \$quaternary_id );
while($sth->fetch()) {
#print STDERR "$dbxref_id, $entry_id, $database_id, $primary_id, $secondary_id, $tertiary_id, $quaternary_id\n";
push @out, Bio::EnsEMBL::ExternalData::Mole::DBXref->new(
-adaptor => $self,
-dbID => $dbxref_id,
-entry_id => $entry_id,
-database_id => $database_id,
-primary_id => $primary_id,
-secondary_id => $secondary_id || undef,
-tertiary_id => $tertiary_id || undef,
-quaternary_id => $quaternary_id || undef
);
}
return \@out;
}
1;
]]>