Commit fd774255 authored by Alessandro Vullo's avatar Alessandro Vullo
Browse files

Removed get_all_ExternalFeatures method, now borrowed from parent where the...

Removed get_all_ExternalFeatures method, now borrowed from parent where the corresponding adaptor handle the circular slice case
parent a012e095
......@@ -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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