Commit b762e22e authored by Ian Longden's avatar Ian Longden
Browse files

removed regulatory method calls (now moved to own database)

parent 077ec5b4
......@@ -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
......
......@@ -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
......
......@@ -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
......
......@@ -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;
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment