removed regulatory method calls (now moved to own database)

modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm

@@ -264,8 +264,7 @@ sub get_available_adaptors{
       Gene                     KaryotypeBand        MiscSet
       MiscFeature              OligoArray           OligoFeature
       OligoProbe               PredictionTranscript PredictionExon
-      ProteinFeature           ProteinAlignFeature  RegulatoryFeature
-      RegulatoryFactor         RegulatorySearchRegion RepeatConsensus
+      ProteinFeature           ProteinAlignFeature  RepeatConsensus
       RepeatFeature            Sequence             SimpleFeature
       Slice                    SupportingFeature    Transcript
       TranscriptSupportingFeature Translation       UnmappedObject

modules/Bio/EnsEMBL/Gene.pm

@@ -1037,32 +1037,6 @@ sub get_all_DAS_Features{
 }
 
 
-=head2 get_all_regulatory_features
-
-  Arg [1]    : Boolean $recursive
-               If set, regulatory features on transcripts belonging to this
-               gene are returned as well
-  Example    : @features = $gene->get_all_regulatory_features(1);
-  Description: Gets all the regulatory features associated with a particular
-               gene, and (optionally) its transcripts. Each feature only
-               appears once.
-  Returntype : Listref of Bio::EnsEMBL::RegulatoryFeature objects
-  Exceptions : If arg is not of correct type.
-  Caller     : general
-  Status     : At Risk
-             : regulatory features are under development
-
-=cut
-
-sub get_all_regulatory_features {
-
-   my ($self, $recursive) = @_;
-
-   my $rfa = $self->adaptor->db->get_RegulatoryFeatureAdaptor();
-
-   return $rfa->fetch_all_by_gene($self, $recursive);
-
-}
 
 
 =head2 add_unconventional_transcript_association

modules/Bio/EnsEMBL/Transcript.pm

@@ -2149,49 +2149,6 @@ sub get_all_DAS_Features {
 }
 
 
-=head2 fetch_all_regulatory_features
-
-  Arg [1]    : none
-  Example    : @features = $transcript->fetch_all_regulatory_features();
-  Description: Gets all the regulatory features associated with this transcript.
-               Each feature only appears once.
-  Returntype : Listref of Bio::EnsEMBL::RegulatoryFeature
-  Exceptions : If arg is not of correct type.
-  Caller     : ?
-  Status    : At Risk
-
-=cut
-
-sub fetch_all_regulatory_features {
-   my ($self) = @_;
-
-   my $rfa = $self->adaptor->db->get_RegulatoryFeatureAdaptor();
-
-   return $rfa->fetch_all_by_transcript($self);
-}
-
-
-=head2 fetch_coded_for_regulatory_factors
-
-  Arg [1]    : none
-  Example    : $transcript->fetch_coded_for_regualtory_factors()
-  Description: Fetches any regulatory_factors that are coded for by this transcript
-  Returntype : Listref of Bio::Ensembl::RegulatoryFactor
-  Exceptions :
-  Caller     : ?
-  Status     : At Risk
-             : under development
-
-=cut
-
-sub fetch_coded_for_regulatory_factors {
-  my ($self) = @_;
-
-  my $rfa = $self->adaptor->db->get_RegulatoryFactorAdaptor();
-
-  return $rfa->fetch_factors_coded_for_by_transcript($self);
-}
-
 
 =head2 _compare_xrefs
 

modules/Bio/EnsEMBL/Translation.pm

@@ -1008,27 +1008,5 @@ sub get_all_DAS_Features{
   return $self->SUPER::get_all_DAS_Features($slice);
 }
 
-=head2 get_all_regulatory_features
-
-  Example    : @features = $translation->get_all_regulatory_features();
-  Description: Gets all the regulatory features associated with this
-               translation.
-               Each feature only appears once.
-  Returntype : Listref of Bio::EnsEMBL::RegulatoryFeature
-  Exceptions : If arg is not of correct type.
-  Caller     : general
-  Status     : At Risk
-             : Regulatory features are currently under development and are 
-             : likely to change.
-
-=cut
-
-sub get_all_regulatory_features {
-   my ($self) = @_;
-
-   my $rfa = $self->adaptor->db->get_RegulatoryFeatureAdaptor();
-
-   return $rfa->fetch_all_by_translation($self);
-}
 
 1;