Commit 2a541cb4 authored by Graham McVicker's avatar Graham McVicker
Browse files

removed deleteObj methods which were formerly called by the Container

parent f70f2c45
......@@ -163,15 +163,6 @@ sub fetch_by_dbID {
}
sub deleteObj {
my( $self ) = @_;
$self->{_cache} = undef;
$self->{_logic_name_cache} = undef;
$self->SUPER::deleteObj;
}
=head2 fetch_by_logic_name
Arg [1] : string $logic_name the logic name of the analysis to retrieve
......
......@@ -117,22 +117,6 @@ sub fetch_all {
return \@features;
}
#
# cleans up internal caches during garbage collection
#
sub deleteObj {
my $self = shift;
$self->SUPER::deleteObj(@_);
delete $self->{'aexc_cache'};
delete $self->{'aexc_slice_cache'};
delete $self->{'aexc_dbID_cache'};
return;
}
=head2 fetch_by_dbID
......
......@@ -1194,26 +1194,6 @@ sub _build_combined_mapper {
}
=head2 deleteObj
Arg [1] : none
Example : none
Description: Cleans up this objects references to other objects so that
proper garbage collection can occur
Returntype : none
Exceptions : none
Caller : Bio::EnsEMBL::DBConnection
=cut
sub deleteObj {
my $self = shift;
$self->SUPER::deleteObj();
}
=head2 seq_regions_to_ids
Arg [1] : Bio::EnsEMBL::CoordSystem $coord_system
......
......@@ -600,19 +600,4 @@ sub _obj_from_sth {
}
#
# Called during db destruction to clean up internal cache structures
# that result in circular references
#
sub deleteObj {
my $self = shift;
#break circular db <-> adaptor references
$self->SUPER::deleteObj();
#break circular object <-> adaptor references
}
1;
......@@ -24,9 +24,6 @@ Bio::EnsEMBL::DBSQL::BaseAdaptor - Base Adaptor for DBSQL adaptors
# get of root DBAdaptor object
$adaptor->db();
# delete memory cycles, called automatically
$adaptor->deleteObj();
# constructor, ok for inheritence
$adaptor = Bio::EnsEMBL::DBSQL::SubClassOfBaseAdaptor->new($dbobj)
......@@ -186,28 +183,6 @@ sub dbc{
}
=head2 deleteObj
Arg [1] : none
Example : none
Description: Cleans up this objects references to other objects so that
proper garbage collection can occur
Returntype : none
Exceptions : none
Caller : Bio::EnsEMBL::DBConnection
=cut
sub deleteObj {
my $self = shift;
#print STDERR "\t\tBaseAdaptor::deleteObj\n";
#remove reference to the database adaptor
$self->{'db'} = undef;
}
# list primary keys for a particular table
# args are table name and primary key field
# if primary key field is not supplied, tablename_id is assumed
......
......@@ -1021,24 +1021,6 @@ sub _objs_from_sth {
. " subclass of BaseFeatureAdaptor");
}
# deleteObj
#
# Arg [1] : none
# Example : none
# Description: Cleans up internal caches and references to other objects so
# that correct garbage collection may occur.
# Returntype : none
# Exceptions : none
# Caller : Bio::EnsEMBL::DBConnection::deleteObj
sub deleteObj {
my $self = shift;
#flush feature cache
%{$self->{'_slice_feature_cache'}} = ();
}
=head1 DEPRECATED METHODS
......
......@@ -699,24 +699,6 @@ sub _fetch_all_by_attrib {
}
#
# Called during db destruction to clean up internal cache structures etc.
#
sub deleteObj {
my $self = shift;
#break circular adaptor <-> db references
$self->SUPER::deleteObj();
#breack circular object <-> adaptor references
delete $self->{'_feature_cache'};
delete $self->{'_name_cache'};
delete $self->{'_dbID_cache'};
delete $self->{'_mapping_paths'};
delete $self->{'_top_level'};
}
=head2 store
Arg [1] : Bio::EnsEMBL::CoordSystem
......
......@@ -570,22 +570,5 @@ sub fetch_Featureset_by_Slice {
return $self->{'_density_feature_cache'}->{$key};
}
# deleteObj
#
# Arg [1] : none
# Example : none
# Description: Cleans up internal caches and references to other objects so
# that correct garbage collection may occur.
# Returntype : none
# Exceptions : none
# Caller : Bio::EnsEMBL::DBConnection::deleteObj
sub deleteObj {
my $self = shift;
#flush feature cache
%{$self->{'_density_feature_cache'}} = ();
}
1;
......@@ -201,18 +201,6 @@ sub fetch_all_by_logic_name {
}
#
# garbage collection method, automatically called when DBAdaptor is cleaned up
#
sub deleteObj {
my $self = shift;
delete $self->{'dbID_cache'};
$self->SUPER::deleteObj;
}
=head2 store
Arg [1] : list of Bio::EnsEMBL::DensityType @dt
......
......@@ -986,29 +986,6 @@ sub get_Interpro_by_geneid {
# deleteObj
# Arg [1] : none
# Example : none
# Description: Responsible for cleaning up this objects references to other
# objects so that proper garbage collection can occur.
# Returntype : none
# Exceptions : none
# Caller : DBConnection::DeleteObj
sub deleteObj {
my $self = shift;
#print STDERR "\t\tGeneAdaptor::deleteObj\n";
#call superclass destructor
$self->SUPER::deleteObj();
}
=head2 update
Arg [1] : Bio::EnsEMBL::Gene
......
......@@ -257,20 +257,5 @@ sub store {
}
#
# Called during db destruction to clean up internal cache structures
# that result in circular references
#
sub deleteObj {
my $self = shift;
#break circular db <-> adaptor references
$self->SUPER::deleteObj();
#break circular object <-> adaptor references
delete $self->{'_id_cache'};
delete $self->{'_code_cache'};
}
1;
......@@ -143,27 +143,6 @@ sub AUTOLOAD {
}
=head2 deleteObj
Args : none
Example : none
Description: breaks circular references and is recursivley called during
memory cleanup (hopefully)
Returntype : none
Exceptions : none
Caller : DBConnection->deleteObj()
=cut
sub deleteObj {
my $self = shift;
delete $self->{'_primary_adaptor'};
$self->SUPER::deleteObj();
}
=head2 DESTROY
Arg [1] : none
......
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