From 77990c6dd3cd98fdc4dcceadab599529533d68fb Mon Sep 17 00:00:00 2001
From: Glenn Proctor <gp1@sanger.ac.uk>
Date: Thu, 24 Mar 2005 15:16:11 +0000
Subject: [PATCH] Added fetch_all_regulatory_features()
---
modules/Bio/EnsEMBL/Gene.pm | 25 +++++++++++++++++++++++++
modules/Bio/EnsEMBL/Transcript.pm | 20 ++++++++++++++++++++
modules/Bio/EnsEMBL/Translation.pm | 22 ++++++++++++++++++++++
3 files changed, 67 insertions(+)
diff --git a/modules/Bio/EnsEMBL/Gene.pm b/modules/Bio/EnsEMBL/Gene.pm
index 99c907091a..4e10fa7465 100755
--- a/modules/Bio/EnsEMBL/Gene.pm
+++ b/modules/Bio/EnsEMBL/Gene.pm
@@ -880,4 +880,29 @@ sub get_all_DAS_Features{
return \%das_features;
}
+
+=head2 fetch_all_regulatory_features
+
+ Arg [1] : If set, regulatory features on transcripts belonging to this gene
+ are returned as well.
+ Example : @features = $gene->fetch_all_regulatory_features(1);
+ Description: Gets all the regulatory features associated with a
+ particular gene, and (optionally) its transcripts.
+ Each feature only appears once.
+ Returntype : Listref of Bio::EnsEMBL::RegulatoryFeature
+ Exceptions : If arg is not of correct type.
+ Caller : ?
+
+=cut
+
+sub fetch_all_regulatory_features {
+
+ my ($self, $recursive) = @_;
+
+ my $rfa = $self->adaptor->db->get_RegulatoryFeatureAdaptor();
+
+ return $rfa->fetch_all_by_gene($self, $recursive);
+
+}
+
1;
diff --git a/modules/Bio/EnsEMBL/Transcript.pm b/modules/Bio/EnsEMBL/Transcript.pm
index 44b7ca349a..4c3bb36d1b 100755
--- a/modules/Bio/EnsEMBL/Transcript.pm
+++ b/modules/Bio/EnsEMBL/Transcript.pm
@@ -1959,6 +1959,26 @@ sub get_all_DAS_Features{
return \%das_features;
}
+=head2 fetch_all_regulatory_features
+ Arg [1] : none
+ Example : @features = $transcript->fetch_all_regulatory_features();
+ Description: Gets all the regulatory features associated with this transcript.
+ Each feature only appears once.
+ Returntype : Listref of Bio::EnsEMBL::RegulatoryFeature
+ Exceptions : If arg is not of correct type.
+ Caller : ?
+
+=cut
+
+sub fetch_all_regulatory_features {
+
+ my ($self) = @_;
+
+ my $rfa = $self->adaptor->db->get_RegulatoryFeatureAdaptor();
+
+ return $rfa->fetch_all_by_transcript($self);
+
+}
1;
diff --git a/modules/Bio/EnsEMBL/Translation.pm b/modules/Bio/EnsEMBL/Translation.pm
index c97f560b9f..99e4471560 100755
--- a/modules/Bio/EnsEMBL/Translation.pm
+++ b/modules/Bio/EnsEMBL/Translation.pm
@@ -798,4 +798,26 @@ sub get_all_DAS_Features{
return \%das_features;
}
+=head2 fetch_all_regulatory_features
+
+ Arg [1] : none
+ Example : @features = $translation->fetch_all_regulatory_features();
+ Description: Gets all the regulatory features associated with this translation.
+ Each feature only appears once.
+ Returntype : Listref of Bio::EnsEMBL::RegulatoryFeature
+ Exceptions : If arg is not of correct type.
+ Caller : ?
+
+=cut
+
+sub fetch_all_regulatory_features {
+
+ my ($self) = @_;
+
+ my $rfa = $self->adaptor->db->get_RegulatoryFeatureAdaptor();
+
+ return $rfa->fetch_all_by_translation($self);
+
+}
+
1;
--
GitLab