Raw content of Bio::EnsEMBL::Funcgen::DBSQL::MetaCoordContainer use strict; use warnings; package Bio::EnsEMBL::Funcgen::DBSQL::MetaCoordContainer; use vars qw(@ISA); use strict; use Bio::EnsEMBL::DBSQL::BaseAdaptor; use Bio::EnsEMBL::Utils::Exception; @ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor); #Can remove this whole class from the API and use the core class if we can resolve problems below #remove new and inherit from Bio::EnsEMBL::DBSQL::MetaCoordContainer? sub new { my $class = shift; my $self = $class->SUPER::new(@_); # # Retrieve the list of the coordinate systems that features are stored in # and cache them # my $sql = 'SELECT mc.table_name, mc.coord_system_id, mc.max_length FROM meta_coord mc'; my @args; if($self->is_multispecies()) { $sql .= ' join coord_system cs using (coord_system_id) where cs.species_id =?'; push(@args, $self->species_id()); } my $sth = $self->prepare($sql); $sth->execute(@args); while(my ($table_name, $cs_id, $max_length) = $sth->fetchrow_array()) { $self->{'_feature_cache'}->{lc($table_name)} ||= []; push @{$self->{'_feature_cache'}->{lc($table_name)}}, $cs_id; $self->{'_max_len_cache'}->{$cs_id}->{lc($table_name)} = $max_length; } $sth->finish(); return $self; } =head2 fetch_all_CoordSystems_by_feature_type Arg [1] : string $table - the name of the table to retrieve coord systems for. E.g. 'gene', 'exon', 'dna_align_feature' Example : @css = @{$mcc->fetch_all_CoordSystems_by_feature_type('gene')}; Description: This retrieves the list of coordinate systems that features in a particular table are stored. It is used internally by the API to perform queries to these tables and to ensure that features are only stored in appropriate coordinate systems. Returntype : listref of Bio::EnsEMBL::Funcgen::CoordSystem objects Exceptions : throw if name argument not provided Caller : BaseFeatureAdaptor Status : At risk =cut # can remove this if we can get get_CoordSystemAdaptor to return Funcgen rather than core sub fetch_all_CoordSystems_by_feature_type { my $self = shift; my $table = lc(shift); #case insensitive matching throw('Name argument is required') unless $table; if(!$self->{'_feature_cache'}->{$table}) { return []; } my @cs_ids = @{$self->{'_feature_cache'}->{$table}}; my @coord_systems; my $csa = $self->db->get_FGCoordSystemAdaptor(); foreach my $cs_id (@cs_ids) { my $cs = $csa->fetch_by_dbID($cs_id); if(!$cs) { throw("meta_coord table refers to non-existant coord_system $cs_id"); } push @coord_systems, $cs; } return \@coord_systems; } =head2 fetch_max_length_by_CoordSystem_feature_type Arg [1] : Bio::EnsEMBL::Funcgen::CoordSystem $cs Arg [2] : string $table Example : $max_len = $mcc->fetch_max_length_by_CoordSystem_feature_type($cs,'gene'); Description: Returns the maximum length of features of a given type in a given coordinate system. Returntype : int or undef Exceptions : throw on incorrect argument Caller : BaseFeatureAdaptor Status : At risk =cut #can remove this if we can get Funcgen::Coordsystem to inherit from core CoordSystem sub fetch_max_length_by_CoordSystem_feature_type { my $self = shift; my $cs = shift; my $table = shift; if(!ref($cs) || !$cs->isa('Bio::EnsEMBL::Funcgen::CoordSystem')) { throw('Bio::EnsEMBL::Funcgen::CoordSystem argument expected'); } throw("Table name argument is required") unless $table; return $self->{'_max_len_cache'}->{$cs->dbID()}->{lc($table)}; } =head2 add_feature_type Arg [1] : Bio::EnsEMBL::Funcgen::CoordSystem $cs The coordinate system to associate with a feature table Arg [2] : string $table - the name of the table in which features of a given coordinate system will be stored in Arg [3] : int $length This length is used to update the max_length in the database and the internal cache. Example : $csa->add_feature_table($chr_coord_system, 'gene'); Description: This function tells the coordinate system adaptor that features from a specified table will be stored in a certain coordinate system. If this information is not already stored in the database it will be added. Returntype : none Exceptions : none Caller : BaseFeatureAdaptor Status : At risk =cut #Can also be removed if inheritance/get_CoordSystemAdaptor issues resolved sub add_feature_type { my $self = shift; my $cs = shift; my $table = lc(shift); my $length = shift; if(!ref($cs) || !$cs->isa('Bio::EnsEMBL::Funcgen::CoordSystem')) { throw('CoordSystem argument is required.'); } if(!$table) { throw('Table argument is required.'); } my $cs_ids = $self->{'_feature_cache'}->{$table} || []; my ($exists) = grep {$cs->dbID() == $_} @$cs_ids; if( $exists ) { if( !$self->{'_max_len_cache'}->{$cs->dbID()}->{$table} || $self->{'_max_len_cache'}->{$cs->dbID()}->{$table} < $length ) { my $sth = $self->prepare('UPDATE meta_coord ' . "SET max_length = $length " . 'WHERE coord_system_id = ? ' . 'AND table_name = ? '. "AND (max_length<$length ". "OR max_length is null)"); $sth->execute( $cs->dbID(), $table ); $self->{'_max_len_cache'}->{$cs->dbID()}->{$table} = $length; } return; } #store the new tablename -> coord system relationship in the db #ignore failures b/c during the pipeline multiple processes may try #to update this table and only the first will be successful my $sth = $self->prepare('INSERT IGNORE INTO meta_coord ' . 'SET coord_system_id = ?, ' . 'table_name = ?, ' . 'max_length = ? ' ); $sth->execute($cs->dbID, $table, $length ); #update the internal cache $self->{'_feature_cache'}->{$table} ||= []; push @{$self->{'_feature_cache'}->{$table}}, $cs->dbID(); $self->{'_max_len_cache'}->{$cs->dbID()}->{$table} = $length; return; } 1;