Raw content of Bio::EnsEMBL::DBSQL::MetaCoordContainer
<![CDATA[=head1 LICENSE
Copyright (c) 1999-2009 The European Bioinformatics Institute and
Genome Research Limited. All rights reserved.
This software is distributed under a modified Apache license.
For license details, please see
/info/about/code_licence.html
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <ensembl-dev@ebi.ac.uk>.
Questions may also be sent to the Ensembl help desk at
<helpdesk@ensembl.org>.
=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 $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;
]]>