circular reference fix

modules/Bio/EnsEMBL/AlignStrainSlice.pm

@@ -296,7 +296,7 @@ sub get_all_Slices {
 					  -START   => $self->Slice->{'start'},
 					  -END     => $self->Slice->{'end'},
 					  -STRAND  => $self->Slice->{'strand'},
-					  -ADAPTOR => $self->Slice->{'adaptor'},
+					  -ADAPTOR => $self->Slice->adaptor(),
 					  -SEQ    => $self->Slice->{'seq'},
 					  -SEQ_REGION_NAME => $self->Slice->{'seq_region_name'},
 					  -SEQ_REGION_LENGTH => $self->Slice->{'seq_region_length'},

modules/Bio/EnsEMBL/ArchiveStableId.pm

@@ -84,7 +84,7 @@ use Bio::EnsEMBL::Root;
 our @ISA = qw(Bio::EnsEMBL::Root);
 
 use Bio::EnsEMBL::Utils::Argument qw(rearrange);
-
+use Scalar::Util qw(weaken isweak);
 
 =head2 new
 
@@ -124,7 +124,7 @@ sub new {
   $self->{'release'} = $release;
   $self->{'assembly'} = $assembly;
   $self->{'type'} = $type;
-  $self->{'adaptor'} = $adaptor;
+  $self->adaptor($adaptor);
 
   return $self;
 }
@@ -166,6 +166,8 @@ sub new_fast {
       'current_version' => $_[7],
   }, $class;
 
+  weaken($self->{adaptor})  if ( ! isweak($self->{adaptor}) );
+
   return $self;
 }
 
@@ -395,9 +397,9 @@ sub current_version {
   if (@_) {
     $self->{'current_version'} = shift;
   } elsif (! defined $self->{'current_version'}) {
-    if (defined $self->{'adaptor'}) {
+    if (defined $self->adaptor()) {
       # lazy load
-      $self->{'adaptor'}->lookup_current($self);
+      $self->adaptor()->lookup_current($self);
     }       
   }
 
@@ -522,7 +524,7 @@ sub type {
 
 sub adaptor {
   my $self = shift;
-  $self->{'adaptor'} = shift if (@_);
+  weaken($self->{'adaptor'} = shift) if (@_);
   return $self->{'adaptor'};
 }
 

modules/Bio/EnsEMBL/AssemblyExceptionFeature.pm

@@ -52,6 +52,7 @@ use vars qw(@ISA);
 
 use Bio::EnsEMBL::Feature;
 use Bio::EnsEMBL::Utils::Argument qw(rearrange);
+use Scalar::Util qw(weaken isweak);
 
 @ISA = qw(Bio::EnsEMBL::Feature);
 
@@ -105,7 +106,9 @@ sub new {
 sub new_fast {
   my $class = shift;
   my $hashref = shift;
-  return bless $hashref, $class;
+  my $self = bless $hashref, $class;
+  weaken($self->{adaptor})  if ( ! isweak($self->{adaptor}) );
+  return $self;
 }
 
 

modules/Bio/EnsEMBL/AssemblyMapper.pm

@@ -75,6 +75,7 @@ use warnings;
 
 use Bio::EnsEMBL::Mapper;
 use Bio::EnsEMBL::Utils::Exception qw(throw deprecate);
+use Scalar::Util qw(weaken);
 
 my $ASSEMBLED = 'assembled';
 my $COMPONENT = 'component';
@@ -340,7 +341,7 @@ sub fastmap {
   my $mapper  = $self->{'mapper'};
   my $asm_cs  = $self->{'asm_cs'};
   my $cmp_cs  = $self->{'cmp_cs'};
-  my $adaptor = $self->{'adaptor'};
+  my $adaptor = $self->adaptor();
   my $frm;
 
   my @tmp;
@@ -777,7 +778,7 @@ sub adaptor {
   my ( $self, $value ) = @_;
 
   if ( defined($value) ) {
-    $self->{'adaptor'} = $value;
+    weaken($self->{'adaptor'} = $value);
   }
 
   return $self->{'adaptor'};

modules/Bio/EnsEMBL/Attribute.pm

@@ -55,6 +55,7 @@ use strict;
 use warnings;
 
 use Bio::EnsEMBL::Utils::Argument qw(rearrange);
+use Scalar::Util qw(weaken isweak);
 
 =head2 new
 
@@ -106,7 +107,9 @@ sub new {
 sub new_fast {
   my $class = shift;
   my $hashref = shift;
-  return bless $hashref, $class;
+  my $self = bless $hashref, $class;
+  weaken($self->{adaptor})  if ( ! isweak($self->{adaptor}) );
+  return $self;
 }
 
 

modules/Bio/EnsEMBL/BaseAlignFeature.pm

@@ -102,6 +102,7 @@ package Bio::EnsEMBL::BaseAlignFeature;
 use Bio::EnsEMBL::FeaturePair;
 use Bio::EnsEMBL::Utils::Argument qw(rearrange);
 use Bio::EnsEMBL::Utils::Exception qw(throw warning);
+use Scalar::Util qw(weaken isweak);
 
 use vars qw(@ISA);
 use strict;
@@ -174,8 +175,9 @@ sub new {
 
 sub new_fast {
   my ($class, $hashref) = @_;
-
-  return bless $hashref, $class;
+  my $self = bless $hashref, $class;
+  weaken($self->{adaptor})  if ( ! isweak($self->{adaptor}) );
+  return $self;
 }
 
 

modules/Bio/EnsEMBL/ChainedAssemblyMapper.pm

@@ -84,6 +84,7 @@ use integer; #use proper arithmetic bitshifts
 use Bio::EnsEMBL::Mapper;
 use Bio::EnsEMBL::Mapper::RangeRegistry;
 use Bio::EnsEMBL::Utils::Exception qw(throw deprecate);
+use Scalar::Util qw(weaken);
 
 #2^20 = approx 10^6
 my $CHUNKFACTOR = 20;
@@ -719,7 +720,7 @@ sub component_CoordSystem {
 
 sub adaptor {
   my $self = shift;
-  $self->{'adaptor'} = shift if(@_);
+  weaken($self->{'adaptor'} = shift) if(@_);
   return $self->{'adaptor'};
 }
 

modules/Bio/EnsEMBL/DBEntry.pm

@@ -45,6 +45,7 @@ use Bio::Annotation::DBLink;
 
 use Bio::EnsEMBL::Utils::Argument qw(rearrange);
 use Bio::EnsEMBL::Utils::Exception qw(deprecate);
+use Scalar::Util qw(weaken isweak);
 
 our @ISA = qw(Bio::EnsEMBL::Storable Bio::Annotation::DBLink);
 
@@ -65,10 +66,9 @@ our @ISA = qw(Bio::EnsEMBL::Storable Bio::Annotation::DBLink);
 sub new_fast {
   my $class = shift;
   my $hashref = shift;
-
-  bless $hashref, $class;
-
-  return $hashref;
+  my $self = bless $hashref, $class;
+  weaken($self->{adaptor})  if ( ! isweak($self->{adaptor}) );
+  return $self;
 }
 
 
@@ -120,7 +120,7 @@ sub new {
 		 'DB_DISPLAY_NAME', 'INFO_TYPE', 'INFO_TEXT', 'TYPE',
                  'SECONDARY_DB_NAME', 'SECONDARY_DB_TABLE', 'LINKAGE_ANNOTATION', 'ANALYSIS'], @args );
 
-  $self->{'adaptor'} = $adaptor;
+  $self->adaptor($adaptor);
   $self->{'dbID'}    = $dbID;
 
   if( defined $primary_id ) { $self->primary_id( $primary_id ) }
@@ -569,8 +569,8 @@ sub get_all_synonyms {
   my $self = shift;
 
   # lazy-load synonyms if required
-  if (!$self->{synonyms} && $self->{adaptor}) {
-    $self->{synonyms} = $self->{adaptor}->fetch_all_synonyms($self->dbID());
+  if (!$self->{synonyms} && $self->adaptor()) {
+    $self->{synonyms} = $self->adaptor()->fetch_all_synonyms($self->dbID());
   }
 
   return $self->{synonyms};
@@ -595,7 +595,7 @@ sub get_all_dependents {
   my $self = shift;
   my $ensembl_object = shift;
 
-  return  $self->{adaptor}->get_all_dependents($self->dbID(), $ensembl_object);
+  return  $self->adaptor()->get_all_dependents($self->dbID(), $ensembl_object);
 }
 
 =head2 get_all_masters
@@ -616,7 +616,7 @@ sub get_all_masters {
   my $self = shift;
   my $ensembl_object = shift;
 
-  return  $self->{adaptor}->get_all_masters($self->dbID(), $ensembl_object);
+  return  $self->adaptor()->get_all_masters($self->dbID(), $ensembl_object);
 }
 
 

modules/Bio/EnsEMBL/DBSQL/TranslationAdaptor.pm

@@ -827,7 +827,6 @@ sub fetch_all_by_Transcript_list {
 
       my $tl =  Bio::EnsEMBL::Translation->new
         (-dbID => $tl_id,
-         -adaptor => $self,
          -seq_start => $seq_start,
          -seq_end => $seq_end,
          -start_exon => $start_exon,
@@ -836,7 +835,8 @@ sub fetch_all_by_Transcript_list {
          -version => $version,
 	 -created_date => $created_date || undef,
 	 -modified_date => $modified_date || undef);
-
+      
+      $tl->adaptor($self);
       $tr->translation($tl);
 
       push @out, $tl;

modules/Bio/EnsEMBL/DnaPepAlignFeature.pm

@@ -35,6 +35,7 @@ package Bio::EnsEMBL::DnaPepAlignFeature;
 use strict;
 
 use Bio::EnsEMBL::BaseAlignFeature;
+use Scalar::Util qw(weaken isweak);
 
 use vars qw(@ISA);
 
@@ -62,8 +63,9 @@ use vars qw(@ISA);
 
 sub new_fast {
   my ($class, $hashref) = @_;
-
-  return bless $hashref, $class;
+  my $self = bless $hashref, $class;
+  weaken($self->{adaptor})  if ( ! isweak($self->{adaptor}) );
+  return $self;
 }
 
 

modules/Bio/EnsEMBL/Feature.pm

@@ -74,6 +74,8 @@ use Bio::EnsEMBL::Slice;
 use Bio::EnsEMBL::StrainSlice;
 use vars qw(@ISA);
 
+use Scalar::Util qw(weaken isweak);
+
 @ISA = qw(Bio::EnsEMBL::Storable);
 
 
@@ -145,14 +147,16 @@ sub new {
       }
   }
 
-  return bless({'start'    => $start,
+  my $self =  bless({'start'    => $start,
                 'end'      => $end,
                 'strand'   => $strand,
                 'slice'    => $slice,
                 'analysis' => $analysis,
-                'adaptor'  => $adaptor,
                 'seqname'  => $seqname,
                 'dbID'     => $dbID}, $class);
+
+  $self->adaptor($adaptor);
+  return $self;
 }
 
 
@@ -171,7 +175,9 @@ sub new {
 sub new_fast {
   my $class = shift;
   my $hashref = shift;
-  return bless $hashref, $class;
+  my $self = bless $hashref, $class;
+  weaken($self->{adaptor})  if ( ! isweak($self->{adaptor}) );
+  return $self;
 }
 
 =head2 start
@@ -1544,5 +1550,4 @@ sub id {
   return $self->{'dbID'};
 }
 
-
 1;

modules/Bio/EnsEMBL/IndividualSliceFactory.pm

@@ -26,6 +26,7 @@ use Bio::EnsEMBL::Utils::Sequence qw(reverse_comp);
 use Bio::EnsEMBL::Slice;
 use Bio::EnsEMBL::Mapper;
 use Bio::EnsEMBL::Utils::Exception qw(throw deprecate warning);
+use Scalar::Util qw(weaken);
 
 =head2 new
 =cut
@@ -38,26 +39,42 @@ sub new{
 
     my ($population_name, $coord_system, $start, $end, $strand, $seq_region_name, $seq_region_length, $adaptor) = rearrange(['POPULATION', 'COORD_SYSTEM','START','END','STRAND','SEQ_REGION_NAME','SEQ_REGION_LENGTH', 'ADAPTOR'],@_);
 
-    return bless {
+    my $self = bless {
 	population_name => $population_name,
 	coord_system => $coord_system,
 	start => $start,
 	end => $end,
 	strand => $strand,
 	seq_region_name => $seq_region_name,
-	seq_region_length => $seq_region_length,
-	adaptor => $adaptor},$class;
+	seq_region_length => $seq_region_length},$class;
+
+    $self->adaptor($adaptor);
+    return $self;
+}
+
+sub adaptor {
+  my $self = shift;
+
+  if(@_) {
+    my $ad = shift;
+    if($ad && (!ref($ad) || !$ad->isa('Bio::EnsEMBL::DBSQL::BaseAdaptor'))) {
+      throw('Adaptor argument must be a Bio::EnsEMBL::DBSQL::BaseAdaptor');
+    }
+    weaken($self->{'adaptor'} = $ad);
+  }
+
+  return $self->{'adaptor'}
 }
 
 sub get_all_IndividualSlice{
     my $self = shift;
 
     my $slice;
-    if(!$self->{'adaptor'}) {
+    if(!$self->adaptor) {
 	warning('Cannot get IndividualSlice features without attached adaptor');
 	return '';
     }
-    my $variation_db = $self->{'adaptor'}->db->get_db_adaptor('variation');
+    my $variation_db = $self->adaptor->db->get_db_adaptor('variation');
 
     unless($variation_db) {
 	warning("Variation database must be attached to core database to " .
@@ -80,7 +97,7 @@ sub get_all_IndividualSlice{
 					      -strand => $self->{'strand'},
 					      -seq_region_name => $self->{'seq_region_name'},
 					      -seq_region_length => $self->{'seq_region_length'},
-					      -adaptor => $self->{'adaptor'}
+					      -adaptor => $self->adaptor
 					      );
 	    my $population = $population_adaptor->fetch_by_name($self->{'population_name'}); 
 	    #check that there is such population in the database

modules/Bio/EnsEMBL/Map/Ditag.pm

@@ -100,10 +100,10 @@ sub new {
                      'name'        => $name,
                      'type'        => $type,
 		     'tag_count'   => $tag_count,
-		     'sequence'    => $sequence,
-                     'adaptor'     => $adaptor,
+		     'sequence'    => $sequence
                     }, $class);
 
+  $self->adaptor($adaptor);
   return $self;
 }
 

modules/Bio/EnsEMBL/Map/DitagFeature.pm

@@ -134,7 +134,6 @@ sub new {
 
   my $self = bless( {'dbID'          => $dbID,
                      'analysis'      => $analysis,
-                     'adaptor'       => $adaptor,
                      'slice'         => $slice,
                      'start'         => $start,
                      'end'           => $end,
@@ -150,6 +149,7 @@ sub new {
 		     'ditag'         => $ditag,
                     }, $class);
 
+  $self->adaptor($adaptor);
   return $self;
 }
 

modules/Bio/EnsEMBL/Map/Marker.pm

@@ -78,7 +78,6 @@ sub new {
   my $class = ref($caller) || $caller;
 
   my $self = bless( {'dbID'            => $dbID,
-                     'adaptor'         => $adaptor,
                      'left_primer'     => $left_primer,
                      'right_primer'    => $right_primer,
                      'min_primer_dist' => $min_primer_dist,
@@ -88,6 +87,8 @@ sub new {
                      'display_marker_synonym' => $display_synonym
                     }, $class);
 
+  $self->adaptor($adaptor);
+
   #only load the marker synononyms if they were supplied, otherwise they 
   # will be lazy-loaded
   if($syns && @$syns) {
@@ -275,7 +276,7 @@ sub get_all_MarkerSynonyms {
   
   #lazy-load the marker synonyms if they haven't been retrieved
   if(!exists $self->{'marker_synonyms'} && 
-     $self->{'adaptor'} && $self->{'dbID'}) {
+     $self->adaptor && $self->{'dbID'}) {
     $self->adaptor->fetch_attributes($self);
   }
   
@@ -404,7 +405,7 @@ sub get_all_MapLocations {
 
   #lazy-load the map locations if they have not been fetched yet
   if(!exists $self->{'map_locations'} && 
-     $self->{'adaptor'} && $self->{'dbID'}) {
+     $self->adaptor && $self->{'dbID'}) {
     $self->adaptor->fetch_attributes($self);
   }
 
@@ -435,7 +436,7 @@ sub get_MapLocation {
 
   #lazy-load the map locations if they have not been fetched yet
   if(!exists $self->{'map_locations'} && 
-     $self->{'adaptor'} && $self->{'dbID'}) {
+     $self->adaptor && $self->{'dbID'}) {
     $self->adaptor->fetch_attributes($self);
   }
 

modules/Bio/EnsEMBL/Map/MarkerFeature.pm

@@ -73,9 +73,8 @@ sub new {
 
   my $class = ref($caller) || $caller;
 
-  return bless( {
+  my $self = bless( {
 		 'dbID'        => $dbID,
-		 'adaptor'     => $adaptor,
 		 'start'       => $start,
 		 'end'         => $end,
 		 'strand'      => 0,
@@ -84,6 +83,9 @@ sub new {
 		 'marker_id'   => $marker_id,
 		 'marker'      => $marker,
      'map_weight'  => $map_weight }, $class);
+
+  $self->adaptor($adaptor);
+  return $self;
 }
 
 
@@ -132,9 +134,9 @@ sub marker {
 
   if(@_) {
     $self->{'marker'} = shift;
-  } elsif(!$self->{'marker'} && $self->{'adaptor'} && $self->{'marker_id'}) {
+  } elsif(!$self->{'marker'} && $self->adaptor && $self->{'marker_id'}) {
     #lazy load the marker if it is not already loaded
-    my $ma = $self->{'adaptor'}->db->get_MarkerAdaptor;
+    my $ma = $self->adaptor->db->get_MarkerAdaptor;
     $self->{'marker'} = $ma->fetch_by_dbID($self->{'marker_id'});
   }
 

modules/Bio/EnsEMBL/Map/Qtl.pm

@@ -75,7 +75,6 @@ sub new {
   $class = ref( $class ) ||$class;
   my $self = bless( {
 		     'dbID'           => $dbID,
-		     'adaptor'        => $adaptor,
 		     'flank_marker_1' => $flank_marker_1,
 		     'flank_marker_2' => $flank_marker_2,
 		     'peak_marker'    => $peak_marker,
@@ -83,7 +82,7 @@ sub new {
 		     'lod_score'      => $lod_score,
 		     'synonyms'       => $synonyms
 		    }, $class );
-
+  $self->adaptor($adaptor);
   return $self;
 }
 

modules/Bio/EnsEMBL/Map/QtlFeature.pm

@@ -62,7 +62,6 @@ sub new {
 
   $class = ref( $class ) ||$class;
   my $self = bless( {
-		     'adaptor'  => $adaptor,
 		     'slice'    => $slice,
 		     'start'    => $start,
 		     'end'      => $end,
@@ -71,6 +70,7 @@ sub new {
          'strand'   => 0
 		    }, $class );
 
+  $self->adaptor($adaptor);
   return $self;
 }
 

modules/Bio/EnsEMBL/MappedSlice.pm

@@ -181,7 +181,7 @@ sub new {
   # need to weaken reference to prevent circular reference
   weaken($self->{'container'} = $container);
 
-  $self->{'adaptor'} = $adaptor if (defined($adaptor));
+  $self->adaptor($adaptor) if (defined($adaptor));
   $self->{'name'} = $name if (defined($name));
 
   $self->{'slice_mapper_pairs'} = [];
@@ -275,7 +275,7 @@ sub get_all_Slice_Mapper_pairs {
 
 sub adaptor {
   my $self = shift;
-  $self->{'adaptor'} = shift if (@_);
+  weaken($self->{'adaptor'} = shift) if (@_);
   return $self->{'adaptor'};
 }