removed deleteObj methods which were formerly called by the Container

modules/Bio/EnsEMBL/DBSQL/AnalysisAdaptor.pm

@@ -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

modules/Bio/EnsEMBL/DBSQL/AssemblyExceptionFeatureAdaptor.pm

@@ -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
 

modules/Bio/EnsEMBL/DBSQL/AssemblyMapperAdaptor.pm

@@ -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

modules/Bio/EnsEMBL/DBSQL/AttributeAdaptor.pm

@@ -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;

modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm

@@ -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

modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm

@@ -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
 

modules/Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm

@@ -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

modules/Bio/EnsEMBL/DBSQL/DensityFeatureAdaptor.pm

@@ -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;

modules/Bio/EnsEMBL/DBSQL/DensityTypeAdaptor.pm

@@ -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

modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm

@@ -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

modules/Bio/EnsEMBL/DBSQL/MiscSetAdaptor.pm

@@ -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;

modules/Bio/EnsEMBL/DBSQL/ProxyAdaptor.pm

@@ -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