From c43a7310a2203eaab2bf26757c66d86993e255bf Mon Sep 17 00:00:00 2001
From: Glenn Proctor <gp1@sanger.ac.uk>
Date: Fri, 20 Jun 2003 10:08:54 +0000
Subject: [PATCH] Added get_generic_features
---
modules/Bio/EnsEMBL/Slice.pm | 45 ++++++++++++++++++++++++++++++++++++
1 file changed, 45 insertions(+)
diff --git a/modules/Bio/EnsEMBL/Slice.pm b/modules/Bio/EnsEMBL/Slice.pm
index 78b7402b80..78cb5bce1c 100644
--- a/modules/Bio/EnsEMBL/Slice.pm
+++ b/modules/Bio/EnsEMBL/Slice.pm
@@ -1476,6 +1476,51 @@ sub accession_number {
=head2 sub DEPRECATED methods
=cut
+###############################################################################
+
+# GENERIC FEATURES (See DBAdaptor.pm)
+
+=head2 get_generic_features
+
+ Arg [1] : (optional) List of names of generic feature types to return. If no feature
+ names are given, all generic features are returned.
+ Example : my %features = $slice->get_generic_features()
+ Description: Gets generic features via the generic feature adaptors that have been added
+ via DBAdaptor->add_GenericFeatureAdaptor (if any)
+ Returntype : Hash of named features.
+ Exceptions : none
+ Caller : none
+
+=cut
+
+sub get_generic_features() {
+
+ my ($self, @names) = @_;
+
+ my $db = $self->adaptor()->db();
+
+ my %features = {}; # this will hold the results
+
+ # get the adaptors for each feature
+ my %adaptors = $db->get_GenericFeatureAdaptors(@names);
+
+ foreach my $adaptor_name (keys(%adaptors)) {
+
+ my $adaptor_obj = %adaptors->{$adaptor_name};
+ # get the features and add them to the hash
+ my $features_ref = $adaptor_obj->fetch_all_by_Slice($self);
+ # add each feature to the hash to be returned
+ foreach my $feature (@$features_ref) {
+ %features->{$adaptor_name} = $feature;
+ }
+ }
+
+ return %features;
+
+}
+
+
+
# sub DEPRECATED METHODS #
###############################################################################
--
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