Raw content of Bio::EnsEMBL::ExternalData::Mole::DBSQL::GeneNameAdaptor 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;