diff --git a/modules/Bio/EnsEMBL/Slice.pm b/modules/Bio/EnsEMBL/Slice.pm index d4c94eb2107f0113895fd2786bda1e2c28e9bb8a..d786e6b79b80312ba4d7fe2514e97581aeda1383 100644 --- a/modules/Bio/EnsEMBL/Slice.pm +++ b/modules/Bio/EnsEMBL/Slice.pm @@ -1850,7 +1850,6 @@ sub get_all_VariationFeatures{ } =head2 get_all_somatic_VariationFeatures - Deprecated. Please use Bio::EnsEMBL::Variation::DBSQL::VariationFeatureAdaptor::fetch_all_somatic_by_Slice_SO_terms instead. Args [1] : (optional) ArrayRef $so_terms SequenceOntology terms to limit the fetch to Args [2] : (optional) boolean $without_children @@ -1877,7 +1876,6 @@ sub get_all_VariationFeatures{ sub get_all_somatic_VariationFeatures { my ($self, $so_terms, $without_children, $included_so, $dbtype) = @_; - deprecate('get_all_somatic_VariationFeatures is deprecated and will be removed in e95. Please use Bio::EnsEMBL::Variation::DBSQL::VariationFeatureAdaptor::fetch_all_somatic_by_Slice_SO_terms instead.'); if (my $vf_adaptor = $self->_get_VariationFeatureAdaptor($dbtype)) { return $vf_adaptor->fetch_all_somatic_by_Slice_SO_terms($self, $so_terms, $without_children, $included_so); } @@ -1885,7 +1883,6 @@ sub get_all_somatic_VariationFeatures { } =head2 get_all_somatic_VariationFeatures_by_source - Deprecated. Please use Bio::EnsEMBL::Variation::DBSQL::VariationFeatureAdaptor::fetch_all_somatic_by_Slice_Source instead. Arg [1] : string $source [optional] The name of the source to query for Arg [2] : string $dbtype [optional] @@ -1903,7 +1900,6 @@ sub get_all_somatic_VariationFeatures { sub get_all_somatic_VariationFeatures_by_source { my ($self, $source, $dbtype) = @_; - deprecate('get_all_somatic_VariationFeatures_by_source is deprecated and will be removed in e95. Please use Bio::EnsEMBL::Variation::DBSQL::VariationFeatureAdaptor::fetch_all_somatic_by_Slice_Source instead.'); my $constraint = (defined($source)) ? " s.name='$source' " : undef; if (my $vf_adaptor = $self->_get_VariationFeatureAdaptor($dbtype)) { return $vf_adaptor->fetch_all_somatic_by_Slice_constraint($self, $constraint); @@ -1912,7 +1908,6 @@ sub get_all_somatic_VariationFeatures_by_source { } =head2 get_all_somatic_VariationFeatures_with_phenotype - Deprecated. Please use Bio::EnsEMBL::Variation::DBSQL::VariationFeatureAdaptor::fetch_all_somatic_with_phenotype_by_Slice instead. Arg [1] : $variation_feature_source [optional] Arg [2] : $phenotype_source [optional] Arg [3] : $phenotype_name [optional] @@ -1930,7 +1925,6 @@ sub get_all_somatic_VariationFeatures_by_source { sub get_all_somatic_VariationFeatures_with_phenotype { my ($self, $source, $p_source, $phenotype, $dbtype) = @_; - deprecate('get_all_somatic_VariationFeatures_with_phenotype is deprecated and will be removed in e95. Please use Bio::EnsEMBL::Variation::DBSQL::VariationFeatureAdaptor::fetch_all_somatic_with_phenotype_by_Slice instead.'); if (my $vf_adaptor = $self->_get_VariationFeatureAdaptor($dbtype)) { return $vf_adaptor->fetch_all_somatic_with_phenotype_by_Slice($self, $source, $p_source, $phenotype); } @@ -1939,7 +1933,6 @@ sub get_all_somatic_VariationFeatures_with_phenotype { =head2 get_all_VariationFeatures_by_Population - Deprecated. Please use Bio::EnsEMBL::Variation::DBSQL::VariationFeatureAdaptor::fetch_all_by_Slice_Population instead. Arg [1] : Bio::EnsEMBL::Variation::Population Arg [2] : $minimum_frequency [optional] Arg [3] : string $dbtype [optional] @@ -1961,7 +1954,6 @@ sub get_all_somatic_VariationFeatures_with_phenotype { sub get_all_VariationFeatures_by_Population { my ($self, $minimum_frequency, $dbtype) = @_; - deprecate('get_all_VariationFeatures_by_Population is deprecated and will be removed in e95. Please use Bio::EnsEMBL::Variation::DBSQL::VariationFeatureAdaptor::fetch_all_by_Slice_Population instead.'); if (my $vf_adaptor = $self->_get_VariationFeatureAdaptor($dbtype)) { return $vf_adaptor->fetch_all_by_Slice_Population($self, $minimum_frequency); }