Commit d0c7a178 authored by Alessandro Vullo's avatar Alessandro Vullo
Browse files

Removed deprecated methods, these are now borrowed from parent

parent 2134f037
......@@ -951,126 +951,6 @@ sub get_all_KaryotypeBands {
} ## end sub get_all_KaryotypeBands
=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 $features;
## circular BOF
my ($sl1, $sl2) = $self->_split;
my ( @arr, @arr1, @arr2 );
if (@arraynames) {
@arr1 = @{ $fa->fetch_all_by_Slice_arrayname( $sl1, @arraynames ) };
@arr2 = @{ $fa->fetch_all_by_Slice_arrayname( $sl2, @arraynames ) };
} else {
@arr1 = @{ $fa->fetch_all_by_Slice($sl1) };
@arr2 = @{ $fa->fetch_all_by_Slice($sl2) };
}
push @arr, @arr1, @arr2;
return \@arr;
## circular EOF
} ## end sub get_all_AffyFeatures
=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 $features;
## circular BOF
my ($sl1, $sl2) = $self->_split;
my ( @arr, @arr1, @arr2 );
if (@arraynames) {
@arr1 = @{ $fa->fetch_all_by_Slice_arrayname( $sl1, @arraynames ) };
@arr2 = @{ $fa->fetch_all_by_Slice_arrayname( $sl2, @arraynames ) };
} else {
@arr1 = @{ $fa->fetch_all_by_Slice($sl1) };
@arr2 = @{ $fa->fetch_all_by_Slice($sl2) };
}
push @arr, @arr1, @arr2;
return \@arr;
## circular EOF
} ## end sub get_all_OligoFeatures
=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 = $sa->db()->get_OligoFeatureAdaptor();
## circular BOF
my ($sl1, $sl2) = $self->_split;
my ( @arr, @arr1, @arr2 );
@arr1 = @{ $fa->fetch_all_by_Slice_type( $sl1, $type, $logic_name ) };
@arr2 = @{ $fa->fetch_all_by_Slice_type( $sl2, $type, $logic_name ) };
push @arr, @arr1, @arr2;
return \@arr;
## circular EOF
} ## end sub get_all_OligoFeatures_by_type
=head2 get_all_compara_DnaAlignFeatures
Arg [1] : string $qy_species
......
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