From fd7742551319891fe0e452d474962fd958e6f281 Mon Sep 17 00:00:00 2001
From: Alessandro Vullo <avullo@ebi.ac.uk>
Date: Wed, 31 Jul 2013 10:22:17 +0000
Subject: [PATCH] Removed get_all_ExternalFeatures method, now borrowed from
parent where the corresponding adaptor handle the circular slice case
---
modules/Bio/EnsEMBL/CircularSlice.pm | 47 ----------------------------
1 file changed, 47 deletions(-)
diff --git a/modules/Bio/EnsEMBL/CircularSlice.pm b/modules/Bio/EnsEMBL/CircularSlice.pm
index 5735983f5d..f458560c7f 100644
--- a/modules/Bio/EnsEMBL/CircularSlice.pm
+++ b/modules/Bio/EnsEMBL/CircularSlice.pm
@@ -1173,53 +1173,6 @@ sub get_all_DASFeatures {
}
-=head2 get_all_ExternalFeatures
-
- Arg [1] : (optional) string $track_name
- If specified only features from ExternalFeatureAdaptors with
- the track name $track_name are retrieved.
- If not set, all features from every ExternalFeatureAdaptor are
- retrieved.
- Example : @x_features = @{$slice->get_all_ExternalFeatures}
- Description: Retrieves features on this slice from external feature adaptors
- Returntype : listref of Bio::SeqFeatureI implementing objects in slice
- coordinates
- Exceptions : none
- Caller : general
- Status : Stable
-
-=cut
-
-sub get_all_ExternalFeatures {
- my ( $self, $track_name ) = @_;
- if ( !$self->adaptor() ) {
- warning("Cannot retrieve features without attached adaptor");
- return [];
- }
- my $features = [];
- my $xfa_hash = $self->adaptor->db->get_ExternalFeatureAdaptors;
- my @xf_adaptors = ();
- if ($track_name) {
- #use a specific adaptor
- if ( exists $xfa_hash->{$track_name} ) {
- push @xf_adaptors, $xfa_hash->{$track_name};
- }
- } else {
- #use all of the adaptors
- push @xf_adaptors, values %$xfa_hash;
- }
-
- ## circular BOF
- my ($sl1, $sl2) = $self->_split;
- foreach my $xfa (@xf_adaptors) {
- push @$features, @{ $xfa->fetch_all_by_Slice($sl1) };
- push @$features, @{ $xfa->fetch_all_by_Slice($sl2) };
- }
- return $features;
- ## circular EOF
-
-} ## end sub get_all_ExternalFeatures
-
# GENERIC FEATURES (See DBAdaptor.pm)
=head2 get_generic_features
--
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