diff --git a/modules/Bio/EnsEMBL/CircularSlice.pm b/modules/Bio/EnsEMBL/CircularSlice.pm
index f458560c7f43f15fa00b417c66d08cfa794f112b..4596ea7296a8159f4a5105f140d9b0db612ea16f 100644
--- a/modules/Bio/EnsEMBL/CircularSlice.pm
+++ b/modules/Bio/EnsEMBL/CircularSlice.pm
@@ -880,267 +880,6 @@ sub get_all_genotyped_VariationFeatures {
}
-=head2 get_all_QtlFeatures
-
- Args : none
- Description: returns overlapping QtlFeatures
- Returntype : listref Bio::EnsEMBL::Map::QtlFeature
- Exceptions : none
- Caller : general
- Status : Stable
-
-=cut
-
-sub get_all_QtlFeatures {
- my $self = shift;
-
- if ( !$self->adaptor() ) {
- warning('Cannot get QtlFeatures without attached adaptor');
- return [];
- }
-
- my $qfAdaptor;
- if ( $self->adaptor() ) {
- $qfAdaptor = $self->adaptor()->db()->get_QtlFeatureAdaptor();
- } else {
- return [];
- }
-
- ## circular BOF
- my ($sl1, $sl2) = $self->_split;
- my ( @arr, @arr1, @arr2 );
- @arr1 = @{ $qfAdaptor->fetch_all_by_Slice_constraint($sl1) };
- @arr2 = @{ $qfAdaptor->fetch_all_by_Slice_constraint($sl2) };
- push @arr, @arr1, @arr2;
- return \@arr;
- ## circular EOF
-
-} ## end sub get_all_QtlFeatures
-
-=head2 get_all_KaryotypeBands
-
- Arg [1] : none
- Example : @kary_bands = @{$slice->get_all_KaryotypeBands};
- Description: Retrieves the karyotype bands which this slice overlaps.
- Returntype : listref oif Bio::EnsEMBL::KaryotypeBands
- Exceptions : none
- Caller : general, contigview
- Status : Stable
-
-=cut
-
-sub get_all_KaryotypeBands {
- my ($self) = @_;
-
- if ( !$self->adaptor() ) {
- warning('Cannot get KaryotypeBands without attached adaptor');
- return [];
- }
-
- my $kadp = $self->adaptor->db->get_KaryotypeBandAdaptor();
-
- ## circular BOF
- my ($sl1, $sl2) = $self->_split;
- my ( @arr, @arr1, @arr2 );
- @arr1 = @{ $kadp->fetch_all_by_Slice($sl1) };
- @arr2 = @{ $kadp->fetch_all_by_Slice($sl2) };
- push @arr, @arr1, @arr2;
- return \@arr;
- ## circular EOF
-
-} ## end sub get_all_KaryotypeBands
-
-
-=head2 get_all_compara_DnaAlignFeatures
-
- Arg [1] : string $qy_species
- The name of the species to retrieve similarity features from
- Arg [2] : string $qy_assembly
- The name of the assembly to retrieve similarity features from
- Arg [3] : string $type
- The type of the alignment to retrieve similarity features from
- Arg [4] : <optional> compara dbadptor to use.
- Example : $fs = $slc->get_all_compara_DnaAlignFeatures('Mus musculus',
- 'MGSC3',
- 'WGA');
- Description: Retrieves a list of DNA-DNA Alignments to the species specified
- by the $qy_species argument.
- The compara database must be attached to the core database
- for this call to work correctly. As well the compara database
- must have the core dbadaptors for both this species, and the
- query species added to function correctly.
- Returntype : reference to a list of Bio::EnsEMBL::DnaDnaAlignFeatures
- Exceptions : warning if compara database is not available
- Caller : contigview
- Status : Stable
-
-=cut
-
-sub get_all_compara_DnaAlignFeatures {
- my ( $self, $qy_species, $qy_assembly, $alignment_type, $compara_db )
- = @_;
-
- if ( !$self->adaptor() ) {
- warning(
- "Cannot retrieve DnaAlignFeatures without attached adaptor");
- return [];
- }
-
- unless ( $qy_species && $alignment_type # && $qy_assembly
- )
- {
- throw(
-"Query species and assembly and alignmemt type arguments are required"
- );
- }
-
- if ( !defined($compara_db) ) {
- $compara_db =
- Bio::EnsEMBL::Registry->get_DBAdaptor( "compara", "compara" );
- }
- unless ($compara_db) {
- warning(
- "Compara database must be attached to core database or passed "
- . "as an argument to "
- . "retrieve compara information" );
- return [];
- }
-
- my $dafa = $compara_db->get_DnaAlignFeatureAdaptor;
-
- ## circular BOF
- my ($sl1, $sl2) = $self->_split;
- my ( @arr, @arr1, @arr2 );
- @arr1 = @{
- $dafa->fetch_all_by_Slice( $sl1, $qy_species, $qy_assembly,
- $alignment_type ) };
- @arr2 = @{
- $dafa->fetch_all_by_Slice( $sl2, $qy_species, $qy_assembly,
- $alignment_type ) };
- push @arr, @arr1, @arr2;
- return \@arr;
- ## circular EOF
-
-} ## end sub get_all_compara_DnaAlignFeatures
-
-=head2 get_all_compara_Syntenies
-
- Arg [1] : string $query_species e.g. "Mus_musculus" or "Mus musculus"
- Arg [2] : string $method_link_type, default is "SYNTENY"
- Arg [3] : <optional> compara dbadaptor to use.
- Description: gets all the compara syntenyies for a specfic species
- Returns : arrayref of Bio::EnsEMBL::Compara::SyntenyRegion
- Status : Stable
-
-=cut
-
-sub get_all_compara_Syntenies {
- my ( $self, $qy_species, $method_link_type, $compara_db ) = @_;
-
- if ( !$self->adaptor() ) {
- warning("Cannot retrieve features without attached adaptor");
- return [];
- }
-
- unless ($qy_species) {
- throw("Query species and assembly arguments are required");
- }
-
- unless ( defined $method_link_type ) {
- $method_link_type = "SYNTENY";
- }
-
- if ( !defined($compara_db) ) {
- $compara_db =
- Bio::EnsEMBL::Registry->get_DBAdaptor( "compara", "compara" );
- }
- unless ($compara_db) {
- warning(
- "Compara database must be attached to core database or passed "
- . "as an argument to "
- . "retrieve compara information" );
- return [];
- }
- my $gdba = $compara_db->get_GenomeDBAdaptor();
- my $mlssa = $compara_db->get_MethodLinkSpeciesSetAdaptor();
- my $dfa = $compara_db->get_DnaFragAdaptor();
- my $sra = $compara_db->get_SyntenyRegionAdaptor();
-
- my $this_gdb =
- $gdba->fetch_by_core_DBAdaptor( $self->adaptor()->db() );
- my $query_gdb = $gdba->fetch_by_registry_name($qy_species);
- my $mlss =
- $mlssa->fetch_by_method_link_type_GenomeDBs( $method_link_type,
- [ $this_gdb, $query_gdb ] );
-
- my $cs = $self->coord_system()->name();
- my $sr = $self->seq_region_name();
- my ($dnafrag) =
- @{ $dfa->fetch_all_by_GenomeDB_region( $this_gdb, $cs, $sr ) };
-
- ## circular BOF
- my ($sl1, $sl2) = $self->_split;
- my ( @arr, @arr1, @arr2 );
- @arr1 = @{
- $sra->fetch_all_by_MethodLinkSpeciesSet_DnaFrag( $mlss, $dnafrag,
- $sl1->start, $sl1->end )
- };
- @arr2 = @{
- $sra->fetch_all_by_MethodLinkSpeciesSet_DnaFrag( $mlss, $dnafrag,
- $sl2->start, $sl2->end )
- };
- push @arr, @arr1, @arr2;
- return \@arr;
- ## circular EOF
-
-} ## end sub get_all_compara_Syntenies
-
-=head2 get_all_Haplotypes
-
- Arg [1] : (optional) boolean $lite_flag
- if true lightweight haplotype objects are used
- Example : @haplotypes = $slice->get_all_Haplotypes;
- Description: Retrieves all of the haplotypes on this slice. Only works
- if the haplotype adaptor has been attached to the core adaptor
- via $dba->add_db_adaptor('haplotype', $hdba);
- Returntype : listref of Bio::EnsEMBL::External::Haplotype::Haplotypes
- Exceptions : warning is Haplotype database is not available
- Caller : contigview, general
- Status : Stable
-
-=cut
-
-sub get_all_Haplotypes {
- my ( $self, $lite_flag ) = @_;
-
- if ( !$self->adaptor() ) {
- warning("Cannot retrieve features without attached adaptor");
- return [];
- }
-
- my $haplo_db = $self->adaptor->db->get_db_adaptor('haplotype');
-
- unless ($haplo_db) {
- warning( "Haplotype database must be attached to core database to "
- . "retrieve haplotype information" );
- return [];
- }
-
- my $haplo_adaptor = $haplo_db->get_HaplotypeAdaptor;
-
- ## circular BOF
- my ($sl1, $sl2) = $self->_split;
- my ( @arr, @arr1, @arr2 );
- @arr1 = @{ $haplo_adaptor->fetch_all_by_Slice( $sl1, $lite_flag ) };
- @arr2 = @{ $haplo_adaptor->fetch_all_by_Slice( $sl2, $lite_flag ) };
- push @arr, @arr1, @arr2;
- return \@arr;
- ## circular EOF
-
-} ## end sub get_all_Haplotypes
-
-
-
=head2 get_all_DASFeatures
Arg [1] : none
@@ -1173,63 +912,6 @@ sub get_all_DASFeatures {
}
-# GENERIC FEATURES (See DBAdaptor.pm)
-
-=head2 get_generic_features
-
- Arg [1] : (optional) List of names of generic feature types to return.
- If no feature names are given, all generic features are
- returned.
- Example : my %features = %{$slice->get_generic_features()};
- Description: Gets generic features via the generic feature adaptors that
- have been added via DBAdaptor->add_GenricFeatureAdaptor (if
- any)
- Returntype : Hash of named features.
- Exceptions : none
- Caller : none
- Status : Stable
-
-=cut
-
-sub get_generic_features {
-
- my ( $self, @names ) = @_;
-
- if ( !$self->adaptor() ) {
- warning('Cannot retrieve features without attached adaptor');
- return [];
- }
-
- 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
- ## circular BOF
- my ($sl1, $sl2) = $self->_split;
- my ( @arr1, @arr2 );
- my $features_ref;
- @arr1 = @{ $adaptor_obj->fetch_all_by_Slice($sl1) };
- @arr2 = @{ $adaptor_obj->fetch_all_by_Slice($sl2) };
- push @{$features_ref}, @arr1, @arr2;
- ## circular EOF
-
- # add each feature to the hash to be returned
- foreach my $feature (@$features_ref) {
- $features{$adaptor_name} = $feature;
- }
- } ## end foreach my $adaptor_name ( ...)
-
- return \%features;
-
-} ## end sub get_generic_features
-
=head2 project_to_slice
Arg [1] : Slice to project to.