removed potential memory leak problems with external feature adaptors

modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm

@@ -776,6 +776,36 @@ sub dnadb {
 }
 
 
+
+=head2 deleteObj
+
+  Arg [1]    : none
+  Example    : none
+  Description: Cleans up circular reference loops so proper garbage collection
+               can occur.
+  Returntype : none
+  Exceptions : none
+  Caller     : DBAdaptorContainer::DESTROY
+
+=cut
+
+sub deleteObj {
+  my $self = shift;
+
+  #print "called deleteObj on DBAdaptor\n";
+
+  #clean up external feature adaptor references
+  if(exists $self->{'_xf_adaptors'}) {
+    foreach my $key (keys %{$self->{'_xf_adaptors'}}) {
+      $self->{'_xf_adaptors'}->{$key} = undef;
+    }
+  }
+
+  #call the superclass deleteObj method
+  $self->SUPER::deleteObj;
+}
+
+
 ###########################################################
 #
 # Support for DAS
@@ -881,9 +911,9 @@ sub add_ExternalFeatureAdaptor {
   }
 
   #if the track name exists add numbers to the end until a free name is found
-  if(exists $self->{'_xf_adaptor'}->{"$track_name"}) {
+  if(exists $self->{'_xf_adaptors'}->{"$track_name"}) {
     my $num = 2;
-    $num++ while(exists $self->{'_xf_adaptor'}->{"$track_name$num"});
+    $num++ while(exists $self->{'_xf_adaptors'}->{"$track_name$num"});
     $self->{'_xf_adaptors'}->{"$track_name$num"} = $adaptor;
   } else {
     $self->{'_xf_adaptors'}->{"$track_name"} = $adaptor;
@@ -1541,7 +1571,6 @@ sub get_all_Transcript_id{
 }
 
 
-
 =head2 delete_Exon
 
   Arg [1]    : none

modules/Bio/EnsEMBL/DBSQL/DBConnection.pm

@@ -479,7 +479,7 @@ sub deleteObj {
   foreach my $adaptor_name (keys %{$self->{'_adaptors'}}) {
     #print STDERR "\tcleaning [$adaptor_name]\n";
 
-    my $adaptor = $self->{'_adaptors'}{$adaptor_name};
+    my $adaptor = $self->{'_adaptors'}->{$adaptor_name};
 
     #call each of the adaptor deleteObj methods
     if($adaptor && $adaptor->can('deleteObj')) {
@@ -488,7 +488,7 @@ sub deleteObj {
     }
 
     #break dbadaptor -> object adaptor references
-    $self->{'_adaptors'}{$adaptor_name} = undef;
+    $self->{'_adaptors'}->{$adaptor_name} = undef;
   }
 
   #print STDERR "Cleaning up attached databases\n";

modules/Bio/EnsEMBL/External/ExternalFeatureAdaptor.pm

@@ -18,7 +18,7 @@ Bio::EnsEMBL::External::ExternalFeatureAdaptor - Allows features created externa
 
   $xf_adaptor = new ExternalFeatureAdaptorSubClass;
 
-  #explicitly add db, (can be done automatically by add_ExternalFeatureAdaptor)
+  #Connect the EnsEMBL core database:
   $xf_adaptor->db($database_adaptor);
 
   #get some features in RawContig coords
@@ -40,15 +40,14 @@ Bio::EnsEMBL::External::ExternalFeatureAdaptor - Allows features created externa
   $clone = $clone_adaptor->fetch_by_accession('AC000087');
   @feats = ${$xf_adaptor->fetch_all_by_Clone($clone);
 
+  #Add the adaptor to the ensembl core dbadaptor (implicitly sets db attribute)
+  $database_adaptor->add_ExternalFeatureAdaptor($xf_adaptor);
+
   #get some features in Slice coords
   $slice_adaptor = $database_adaptor->get_SliceAdaptor;
   $slice = $slice_adaptor->fetch_by_chr_start_end(1,100000,200000);
   @feats = @{$xf_adaptor->fetch_all_by_Slice($slice)};
 
-  #Add the external adaptor to the EnsEMBL system
-  #this also implicitly adds the dbadaptor so you don't have to call 'db'
-  $database_adaptor->add_ExternalFeatureAdaptor($xf_adaptor);
-
   #now features can be retrieved directly from slice or RawContig
   @feats = @{$slice->get_all_ExternalFeatures};
   @feats = @{$contig->get_all_ExternalFeatures};
@@ -93,10 +92,10 @@ ExternalFeature adaptor will be altered by the functions called.
 Before the non-overridden ExternalFeatureAdaptor fetch methods may be called
 an EnsEMBL core database adaptor must be attached to the ExternalFeatureAdaptor
 .  This database adaptor is required to perform the remappings between various
-coordinate system.  This may be done explicitly through a call to the db 
-accessor method, or implicitly by adding the ExternalFeatureAdaptor to the 
-database adaptor through a call to the DBAdaptor add_ExternalFeatureAdaptor 
-method. 
+coordinate system.  This may be done implicitly by adding the 
+ExternalFeatureAdaptor to the database adaptor through a call to the 
+DBAdaptor add_ExternalFeatureAdaptor method or explicitly by calling the 
+ExternalFeatureAdaptor db method.
 
 
 =head1 CONTACT
@@ -164,7 +163,10 @@ sub db {
   my ($self, $value) = @_;
 
   if($value) {
-    $self->{'db'} = $value;
+    #avoid potentially nasty memory leaks
+    if(ref $value && $value->isa("Bio::EnsEMBL::Container")) {
+      $self->{'db'} = $value->_obj;
+    }
   }     
 
   return $self->{'db'};

modules/Bio/EnsEMBL/Slice.pm

@@ -913,7 +913,8 @@ sub get_landmark_MarkerFeatures {
 
   my $lma = $self->adaptor()->db()->get_LandmarkMarkerAdaptor();
   if( ! defined $lma ) {
-    return [];
+   $self->warn("Lite database must be available to retrieve landmark markers");
+   return [];
   } else {
     return $lma->fetch_all_by_Slice( $self );
   }