Raw content of Bio::EnsEMBL::ExternalData::Mole::DBSQL::GeneNameAdaptor
<![CDATA[package Bio::EnsEMBL::ExternalData::Mole::DBSQL::GeneNameAdaptor;
use strict;
use Bio::EnsEMBL::ExternalData::Mole::GeneName;
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 (['genename' , 'g']);
}
sub _columns {
my $self = shift;
return ( 'g.genename_id', 'g.entry_id',
'g.name', 'g.name_type');
}
sub fetch_by_dbID {
my $self = shift;
my $id = shift;
my $constraint = "g.genename_id = '$id'";
my ($genename_obj) = @{ $self->generic_fetch($constraint) };
return $genename_obj;
}
sub fetch_by_Entry {
my $self = shift;
my $entry = shift;
my $sth = $self->prepare(
"SELECT g.genename_id ".
"FROM genename g ".
"WHERE g.entry_id = ?");
$sth->bind_param(1, $entry->dbID, SQL_INTEGER);
$sth->execute();
my $gname_id = $sth->fetchrow();
$sth->finish();
my $genename_object = $self->fetch_by_dbID($gname_id);
return $genename_object;
}
sub fetch_by_entry_id {
my ($self, $entry_id) = @_;
my $constraint = "g.entry_id = '$entry_id'";
my ($genename_obj) = @{ $self->generic_fetch($constraint) };
return $genename_obj;
}
sub fetch_by_name {
my $self = shift;
my $name = shift;
#get all entry_ids with this name
$sth = $self->prepare(
"SELECT entry_id ".
"FROM genename ".
"WHERE name = '$name' ");
$sth->execute();
my @array = @{$sth->fetchall_arrayref()};
my @entry_ids = map {$_->[0]} @array;
my $entries = $self->fetch_all_by_dbID_list(\@entry_ids);
return $entries;
}
sub fetch_by_name_type {
my $self = shift;
my $name_type = shift;
#get all entry_ids with this name_type
$sth = $self->prepare(
"SELECT entry_id ".
"FROM genename_type ".
"WHERE name_type = '$name_type' ");
$sth->execute();
my @array = @{$sth->fetchall_arrayref()};
my @entry_ids = map {$_->[0]} @array;
my $entries = $self->fetch_all_by_dbID_list(\@entry_ids);
return $entries;
}
sub fetch_all_by_dbID_list {
my ($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 ( $genename_id, $entry_id, $name, $name_type );
$sth->bind_columns( \$genename_id, \$entry_id, \$name, \$name_type );
while($sth->fetch()) {
push @out, Bio::EnsEMBL::ExternalData::Mole::GeneName->new(
-dbID => $genename_id,
-entry_id => $entry_id,
-adaptor => $self,
-name => $name,
-name_type => $name_type,
);
}
return \@out;
}
1;
]]>