MetaCoordContainer.pm

Go to the documentation of this file.

=head1 LICENSE
 
See the NOTICE file distributed with this work for additional information
regarding copyright ownership.
 
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
 
     http://www.apache.org/licenses/LICENSE-2.0
 
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
 
=cut
 
 
=head1 CONTACT
 
  Please email comments or questions to the public Ensembl
  developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.
 
  Questions may also be sent to the Ensembl help desk at
  <http://www.ensembl.org/Help/Contact>.
 
=cut
 
package Bio::EnsEMBL::DBSQL::MetaCoordContainer;
 
use strict;
use warnings;
 
use vars qw(@ISA);
use strict;
 
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
use Bio::EnsEMBL::Utils::Exception;
 
@ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);
 
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 @coord_systems =
    @{ $self->db()->dnadb()->get_CoordSystemAdaptor->fetch_all() };
 
  my @cs_ids;
  foreach my $cs (@coord_systems) { push( @cs_ids, $cs->dbID() ) }
 
  my $sth = $self->prepare(
              'SELECT mc.table_name, mc.coord_system_id, mc.max_length '
                . 'FROM meta_coord mc '
                . 'WHERE mc.coord_system_id in ('
                . join( ',', @cs_ids )
                . ')' );
 
  $sth->execute();
 
  while ( my ( $table_name, $cs_id, $max_length ) =
          $sth->fetchrow_array() )
  {
    $table_name = lc($table_name);
 
    $self->{'_feature_cache'}->{$table_name} ||= [];
 
    push( @{ $self->{'_feature_cache'}->{$table_name} }, $cs_id );
    $self->{'_max_len_cache'}->{$cs_id}->{$table_name} = $max_length;
  }
  $sth->finish();
 
  return $self;
} ## end sub new
 
 
 
 
=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::CoordSystem objects
  Exceptions : throw if name argument not provided
  Caller     : BaseFeatureAdaptor
  Status     : Stable
 
=cut
 
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_CoordSystemAdaptor();
 
  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::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     : Stable
 
=cut
 
 
sub fetch_max_length_by_CoordSystem_feature_type {
  my $self = shift;
  my $cs = shift;
  my $table = shift;
 
  if(!ref($cs) || !$cs->isa('Bio::EnsEMBL::CoordSystem')) {
    throw('Bio::EnsEMBL::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::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     : Stable
 
=cut
 
 
sub add_feature_type {
  my $self = shift;
  my $cs   = shift;
  my $table = lc(shift);
  my $length = shift;
  if(!ref($cs) || !$cs->isa('Bio::EnsEMBL::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 $insert_ignore = $self->insert_ignore_clause();
  my $sth = $self->prepare(qq{ ${insert_ignore} INTO meta_coord
                                      (coord_system_id, table_name, max_length)
                               VALUES (?, ?, ?)
                             } );
 
  $sth->execute($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;
}
 
 
=head2 remove_feature_type
 
  Arg [1]    : Bio::EnsEMBL::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 are being removed
  Example    : $csa->remove_feature_table($chr_coord_system, 'gene');
  Description: This function tells the coordinate system adaptor that
               features have been fully removed from a certain coordinate system.
               Use with caution as it will cause issues if there are still features
               left.
  Returntype : none
  Exceptions : none
  Caller     : BaseFeatureAdaptor
  Status     : Stable
 
=cut
 
sub remove_feature_type {
  my $self = shift;
  my $cs   = shift;
  my $table = lc(shift);
  my $length = shift;
  if(!ref($cs) || !$cs->isa('Bio::EnsEMBL::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 ) {
    my $sth = $self->prepare('DELETE FROM meta_coord ' .
                             'WHERE coord_system_id = ? ' .
                             'AND table_name = ? ');
    $sth->execute( $cs->dbID(), $table );
    delete $self->{'_max_len_cache'}->{$cs->dbID()}->{$table};
  }
 
  return;
}
 
 
1;