Commit e2a0c596 authored by Andreas Kusalananda Kähäri's avatar Andreas Kusalananda Kähäri
Browse files

Deprecated the following three methods:

  - get_all_AffyFeatures()
  - get_all_OligoFeatures()
  - get_all_OligoFeatures_by_type()

Functionality is instead provided by the Ensembl Functional Genomics
API.
parent 1a94b667
......@@ -2469,108 +2469,6 @@ sub get_all_MiscFeatures {
return $mfa->fetch_all_by_Slice($self);
}
=head2 get_all_AffyFeatures
Args : (optional) list of strings - array names
Example : $slice->get_all_AffyFeatures();
Description: Retrieves all AffyFeature objects which overlap this slice.
Returntype : listref of Bio::EnsEMBL::AffyFeature objects
Exceptions : none
Caller : general
Status : Stable
=cut
sub get_all_AffyFeatures {
my $self = shift;
my @arraynames = @_;
my $sa = $self->adaptor();
if ( ! $sa ) {
warning( "Cannot retrieve features without attached adaptor." );
}
my $fa = $sa->db()->get_AffyFeatureAdaptor();
my $features;
if ( @arraynames ) {
$features = $fa->fetch_all_by_Slice_arrayname( $self, @arraynames );
} else {
$features = $fa->fetch_all_by_Slice( $self );
}
return $features;
}
=head2 get_all_OligoFeatures
Args : (optional) list of strings - array names
Example : $slice->get_all_OligoFeatures();
Description: Retrieves all OligoFeature objects which overlap this slice.
Optionally just retrieve OligoFeature objects generated by
probes from named arrays.
Returntype : listref of Bio::EnsEMBL::OligoFeature objects
Exceptions : none
Caller : general
Status : Stable
=cut
sub get_all_OligoFeatures {
my $self = shift;
my @arraynames = @_;
my $sa = $self->adaptor();
if ( ! $sa ) {
warning( "Cannot retrieve features without attached adaptor." );
}
my $fa = $sa->db()->get_OligoFeatureAdaptor();
my $features;
if ( @arraynames ) {
$features = $fa->fetch_all_by_Slice_arrayname( $self, @arraynames );
} else {
$features = $fa->fetch_all_by_Slice( $self );
}
return $features;
}
=head2 get_all_OligoFeatures_by_type
Arg [1] : string - type of array (e.g. AFFY or OLIGO)
Arg [2] : (optional) string - logic name
Example : $slice->get_all_OligoFeatures_by_type('OLIGO');
Description: Retrieves all OligoFeature objects which overlap this slice and
were created by probes from the specified type of array.
Returntype : listref of Bio::EnsEMBL::OligoFeature objects
Exceptions : throws if no type
Caller : general
Status : Stable
=cut
sub get_all_OligoFeatures_by_type {
my ($self, $type, $logic_name) = @_;
throw('Need type as parameter') if !$type;
my $sa = $self->adaptor();
if ( ! $sa ) {
warning( "Cannot retrieve features without attached adaptor." );
}
my $fa = $sa->db()->get_OligoFeatureAdaptor();
my $features = $fa->fetch_all_by_Slice_type( $self, $type, $logic_name );
return $features;
}
=head2 get_all_MarkerFeatures
Arg [1] : (optional) string logic_name
......@@ -3186,8 +3084,101 @@ sub is_circular { return 0; }
=head1 DEPRECATED METHODS
=head2 get_all_AffyFeatures
Description: DEPRECATED, use functionality provided by the Ensembl
Functional Genomics API instead.
=cut
sub get_all_AffyFeatures {
deprecate( 'Use functionality provided by the '
. 'Ensembl Functional Genomics API instead.' );
throw('Can not delegate deprecated functionality.');
# Old code:
# my $self = shift;
# my @arraynames = @_;
#
# my $sa = $self->adaptor();
# if ( ! $sa ) {
# warning( "Cannot retrieve features without attached adaptor." );
# }
# my $fa = $sa->db()->get_AffyFeatureAdaptor();
# my $features;
#
# if ( @arraynames ) {
# $features = $fa->fetch_all_by_Slice_arrayname( $self, @arraynames );
# } else {
# $features = $fa->fetch_all_by_Slice( $self );
# }
# return $features;
}
=head2 get_all_OligoFeatures
Description: DEPRECATED, use functionality provided by the Ensembl
Functional Genomics API instead.
=cut
sub get_all_OligoFeatures {
deprecate( 'Use functionality provided by the '
. 'Ensembl Functional Genomics API instead.' );
throw('Can not delegate deprecated functionality.');
# Old code:
# my $self = shift;
# my @arraynames = @_;
#
# my $sa = $self->adaptor();
# if ( ! $sa ) {
# warning( "Cannot retrieve features without attached adaptor." );
# }
# my $fa = $sa->db()->get_OligoFeatureAdaptor();
# my $features;
#
# if ( @arraynames ) {
# $features = $fa->fetch_all_by_Slice_arrayname( $self, @arraynames );
# } else {
# $features = $fa->fetch_all_by_Slice( $self );
# }
# return $features;
}
=head2 get_all_OligoFeatures_by_type
Description: DEPRECATED, use functionality provided by the Ensembl
Functional Genomics API instead.
=cut
sub get_all_OligoFeatures_by_type {
deprecate( 'Use functionality provided by the '
. 'Ensembl Functional Genomics API instead.' );
throw('Can not delegate deprecated functionality.');
# Old code:
# my ($self, $type, $logic_name) = @_;
#
# throw('Need type as parameter') if !$type;
#
# my $sa = $self->adaptor();
# if ( ! $sa ) {
# warning( "Cannot retrieve features without attached adaptor." );
# }
# my $fa = $sa->db()->get_OligoFeatureAdaptor();
#
# my $features = $fa->fetch_all_by_Slice_type( $self, $type, $logic_name );
#
# return $features;
}
=head2 get_all_supercontig_Slices
Description: DEPRECATED use get_tiling_path("NTcontig") instead
......
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