- Member Bio::EnsEMBL::AssemblyMapper::fast_to_assembly ()
- , use map() instead.
- Member Bio::EnsEMBL::AssemblyMapper::in_assembly ()
- , use map() or list_ids() instead.
- Member Bio::EnsEMBL::AssemblyMapper::list_contig_ids ()
- , use list_ids() instead.
- Member Bio::EnsEMBL::AssemblyMapper::map_coordinates_to_assembly ()
- , use map() instead.
- Member Bio::EnsEMBL::AssemblyMapper::map_coordinates_to_rawcontig ()
- , use map() instead.
- Member Bio::EnsEMBL::ChainedAssemblyMapper::fast_to_assembly ()
- use map() instead
- Member Bio::EnsEMBL::ChainedAssemblyMapper::in_assembly ()
- . Use map() or list_ids() instead
- Member Bio::EnsEMBL::ChainedAssemblyMapper::list_contig_ids ()
- Use list_ids instead
- Member Bio::EnsEMBL::ChainedAssemblyMapper::map_coordinates_to_assembly ()
- use map() instead
- Member Bio::EnsEMBL::ChainedAssemblyMapper::map_coordinates_to_rawcontig ()
- use map() instead
- Member Bio::EnsEMBL::CircularSlice::assembly_type ()
- use version instead
- Member Bio::EnsEMBL::CircularSlice::chr_end ()
- use end() instead Returntype : int Exceptions : none Caller : SliceAdaptor, general
- Member Bio::EnsEMBL::CircularSlice::chr_name ()
- use seq_region_name() instead
- Member Bio::EnsEMBL::CircularSlice::chr_start ()
- use start() instead
- Member Bio::EnsEMBL::CircularSlice::dbID ()
- use SliceAdaptor::get_seq_region_id instead
- Member Bio::EnsEMBL::CircularSlice::get_all_genotyped_SNPs ()
- . Use get_all_genotyped_VariationFeatures insted
- Member Bio::EnsEMBL::CircularSlice::get_all_MapFrags ()
- use get_all_MiscFeatures instead
- Member Bio::EnsEMBL::CircularSlice::get_all_SNPs ()
- . Use get_all_VariationFeatures insted
- Member Bio::EnsEMBL::CircularSlice::get_all_supercontig_Slices ()
- use get_tiling_path("NTcontig") instead
- Member Bio::EnsEMBL::CircularSlice::get_Chromosome ()
- use this instead: $slice_adp->fetch_by_region('chromosome', $slice->seq_region_name)
- Member Bio::EnsEMBL::CircularSlice::get_tiling_path ()
- use project instead
- Member Bio::EnsEMBL::CircularSlice::has_MapSet ()
- use get_all_MiscFeatures instead
- Member Bio::EnsEMBL::DBEntry::get_synonyms ()
- use get_all_synonyms instead
- Member Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor::fetch_by_type ()
- use fetch_by_CoordSystems instead
- Member Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor::register_contig ()
- use register_component instead
- Member Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor::register_region ()
- use register_assembled instead
- Member Bio::EnsEMBL::DBSQL::BaseAlignFeatureAdaptor::fetch_all_by_RawContig_and_pid ()
- use fetch_all_by_Slice_and_pid instead
- Member Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::fetch_all_by_RawContig ()
- use fetch_all_by_Slice instead
- Member Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::fetch_all_by_RawContig_and_score ()
- use fetch_all_by_Slice_and_score instead
- Member Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::fetch_all_by_RawContig_constraint ()
- use fetch_all_by_RawContig_constraint instead
- Member Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::remove_by_RawContig ()
- use remove_by_Slice instead
- Member Bio::EnsEMBL::DBSQL::DBAdaptor::add_db_adaptor ()
- , please use add_db from the registry instead
- Member Bio::EnsEMBL::DBSQL::DBAdaptor::assembly_type ()
- - Use CoordSystemAdaptor to obtain default coordinate system instead.
- Member Bio::EnsEMBL::DBSQL::DBAdaptor::db ()
- Member Bio::EnsEMBL::DBSQL::DBAdaptor::get_all_db_adaptors ()
- soon : please use Bio::EnsEMBL::Registry->get_all_db_adaptors
- Member Bio::EnsEMBL::DBSQL::DBAdaptor::get_db_adaptor ()
- soon : please use Bio::EnsEMBL::Registry->get_db_adaptors
- Member Bio::EnsEMBL::DBSQL::DBAdaptor::list_supported_assemblies ()
- - Use CoordSystemAdaptor to obtain list of top-level coordinate systems instead
- Member Bio::EnsEMBL::DBSQL::DBAdaptor::remove_db_adaptor ()
- , use remove_db instead from the Registry
- Member Bio::EnsEMBL::DBSQL::DBEntryAdaptor::geneids_by_extids ()
- use list_gene_ids_by_extids instead
- Member Bio::EnsEMBL::DBSQL::DBEntryAdaptor::transcriptids_by_extids ()
- use transcriptids_by_extids instead
- Member Bio::EnsEMBL::DBSQL::DBEntryAdaptor::translationids_by_extids ()
- use list_translation_ids_by_extids instead
- Member Bio::EnsEMBL::DBSQL::ExonAdaptor::fetch_all_by_gene_id ()
- . This method should not be needed - Exons can be fetched by Transcript.
- Member Bio::EnsEMBL::DBSQL::ExonAdaptor::get_stable_entry_info ()
- . This method is no longer necessary. Exons are always fetched with their stable identifiers (if they exist) and no lazy loading is necessary.
- Member Bio::EnsEMBL::DBSQL::GeneAdaptor::fetch_all_by_DBEntry ()
- - Use fetch_all_by_external_name instead
- Member Bio::EnsEMBL::DBSQL::GeneAdaptor::fetch_by_maximum_DBLink ()
- - use fetch_all_by_external_name instead
- Member Bio::EnsEMBL::DBSQL::GeneAdaptor::fetch_by_Peptide_id ()
- , use fetch_by_translation_stable_id()
- Member Bio::EnsEMBL::DBSQL::GeneAdaptor::get_description ()
- , use gene->get_description
- Member Bio::EnsEMBL::DBSQL::GeneAdaptor::get_display_xref ()
- use $gene->display_xref
- Member Bio::EnsEMBL::DBSQL::GeneAdaptor::get_stable_entry_info ()
- use $gene->stable_id instead
- Member Bio::EnsEMBL::DBSQL::MetaContainer::get_default_assembly ()
- . Use the version of the coordinate system you are interested in instead.
- Member Bio::EnsEMBL::DBSQL::MetaContainer::get_Species ()
; please use other subroutines in this package Returntype : Bio::Species Exceptions : none Caller : ? Status :
- Member Bio::EnsEMBL::DBSQL::SequenceAdaptor::fetch_by_assembly_location ()
- use fetch_by_Slice_start_end_strand() instead.
- Member Bio::EnsEMBL::DBSQL::SequenceAdaptor::fetch_by_RawContig_start_end_strand ()
- use fetch_by_Slice_start_end_strand instead
- Member Bio::EnsEMBL::DBSQL::SliceAdaptor::fetch_by_chr_name ()
- . Use fetch by region instead
- Member Bio::EnsEMBL::DBSQL::SliceAdaptor::fetch_by_chr_start_end ()
- use fetch_by_region instead
- Member Bio::EnsEMBL::DBSQL::SliceAdaptor::fetch_by_clone_accession ()
- . Use fetch_by_region, Slice::project, Slice::expand instead.
- Member Bio::EnsEMBL::DBSQL::SliceAdaptor::fetch_by_contig_name ()
- . Use fetch_by_region(), Slice::project(), Slice::expand() instead
- Member Bio::EnsEMBL::DBSQL::SliceAdaptor::fetch_by_mapfrag ()
- use fetch_by_misc_feature_attribute('synonym',$mapfrag)
- Member Bio::EnsEMBL::DBSQL::SliceAdaptor::fetch_by_supercontig_name ()
- . Use fetch_by_region(), Slice::project() and Slice::expand() instead
- Member Bio::EnsEMBL::DBSQL::SliceAdaptor::list_overlapping_supercontigs ()
- use Slice::project instead
- Member Bio::EnsEMBL::DBSQL::TranscriptAdaptor::fetch_all_by_DBEntry ()
- . Use fetch_all_by_external_name() instead.
- Member Bio::EnsEMBL::DBSQL::TranscriptAdaptor::get_display_xref ()
- . Use $transcript->display_xref() instead.
- Member Bio::EnsEMBL::DBSQL::TranscriptAdaptor::get_stable_entry_info ()
- . Use $transcript->stable_id() instead.
- Member Bio::EnsEMBL::DBSQL::TranscriptAdaptor::store ()
- (optional) Int $analysis_id The analysis_id to use when storing this gene. This is for backward compatibility only and used to fall back to the gene analysis_id if no analysis object is attached to the transcript (which you should do for new code). Example : $transID = $tr_adaptor->store($transcript, $gene->dbID); Description: Stores a transcript in the database and returns the new internal identifier for the stored transcript. Returntype : Int Exceptions : none Caller : general Status : Stable
- Member Bio::EnsEMBL::DBSQL::TranslationAdaptor::fetch_all_by_DBEntry ()
- , this has been renames fetch_all_by_external_name
- Member Bio::EnsEMBL::DBSQL::TranslationAdaptor::fetch_all_by_external_name ()
- to instead use : TranscriptAdaptor::fetch_all_by_external_name
- Member Bio::EnsEMBL::DBSQL::TranslationAdaptor::get_stable_entry_info ()
- - This method should no longer be needed. Stable id info is fetched when the transcript is.
- Member Bio::EnsEMBL::Exon::_get_stable_entry_info ()
- .
- Member Bio::EnsEMBL::Exon::created ()
- . Do not use.
- Member Bio::EnsEMBL::Exon::modified ()
- . Do not use.
- Member Bio::EnsEMBL::Exon::temporary_id ()
- . This should not be necessary.
- Member Bio::EnsEMBL::Exon::type ()
- . Do not use.
- Member Bio::EnsEMBL::FeaturePair::feature1 ()
- use start(), end(), strand(), slice(), etc. methods instead
- Member Bio::EnsEMBL::FeaturePair::feature2 ()
- use hstart(), hend(), hstrand() etc. methods instead
- Member Bio::EnsEMBL::FeaturePair::gffstring ()
- do not use
- Member Bio::EnsEMBL::FeaturePair::hend_phase ()
- do not use
- Member Bio::EnsEMBL::FeaturePair::hphase ()
- do not use
- Member Bio::EnsEMBL::FeaturePair::set_featurepair_fields ()
- do not use
- Member Bio::EnsEMBL::FeaturePair::validate ()
- do not use
- Member Bio::EnsEMBL::FeaturePair::validate_prot_feature ()
- do not use
- Member Bio::EnsEMBL::Gene::add_DBLink ()
- This method has been deprecated in favour of the add_DBEntry method. Objects are responible for holding only xrefs directly associated with themselves now.
- Member Bio::EnsEMBL::Gene::chr_name ()
- . Use project, tranform, or transfer to obtain this gene in another coord system. Use $gene->slice->seq_region_name to get the name of the underlying coord system. Or $gene->slice->name().
- Member Bio::EnsEMBL::Gene::confidence ()
- . Use status() instead.
- Member Bio::EnsEMBL::Gene::fetch_coded_for_regulatory_factors ()
- : Fetches any regulatory_factors that are coded for by this gene. Returntype : Listref of Bio::Ensembl::RegulatoryFactor Exceptions : Caller : ? Status : At Risk : under development
- Member Bio::EnsEMBL::Gene::temporary_id ()
- : Use dbID or stable_id or something else instead
- Member Bio::EnsEMBL::Gene::type ()
- . Use biotype() instead.
- Member Bio::EnsEMBL::IdentityXref::query_end ()
- . Use xref_end() instead. Status : At Risk
- Member Bio::EnsEMBL::IdentityXref::query_identity ()
- . Use xref_identity() instead. Status : At Risk
- Member Bio::EnsEMBL::IdentityXref::query_start ()
- . Use xref_start() instead. Status : At Risk
- Member Bio::EnsEMBL::IdentityXref::target_identity ()
- . Use ensembl_identity() instead. Status : At Risk
- Member Bio::EnsEMBL::IdentityXref::translation_end ()
- . Use ensembl_end() instead. Status : At Risk
- Member Bio::EnsEMBL::IdentityXref::translation_start ()
- . Use ensembl_start() instead. Status : At Risk
- Member Bio::EnsEMBL::KaryotypeBand::chr_name ()
- - use $kary_band->slice()->seq_region_name() instead
- Member Bio::EnsEMBL::Map::DBSQL::MarkerFeatureAdaptor::fetch_all_by_RawContig_and_priority ()
- use fetch_all_by_Slice_and_priority instead
- Member Bio::EnsEMBL::Map::DitagFeature::fetch_ditag ()
- , use ditag() instead
- Member Bio::EnsEMBL::Map::MapLocation::chromosome ()
- use chromosome_name() instead
- Member Bio::EnsEMBL::Map::Qtl::source_database ()
- . Use get_synonyms or add_synonym instead.
- Member Bio::EnsEMBL::Map::Qtl::source_primary_id ()
- . Use get_synonyms or add_synonym instead.
- Member Bio::EnsEMBL::PredictionTranscript::get_cdna ()
- - use spliced_seq() or translateable_seq instead
- Member Bio::EnsEMBL::PredictionTranscript::get_exon_count ()
- - use get_all_Exons instead
- Member Bio::EnsEMBL::PredictionTranscript::set_exon_count ()
- - this method does nothing now
- Member Bio::EnsEMBL::Registry::load_registry_with_web_adaptors ()
- : Use load_registry_from_db instead.
- Member Bio::EnsEMBL::Root::_rearrange ()
- Member Bio::EnsEMBL::Root::stack_trace ()
- Member Bio::EnsEMBL::Root::stack_trace_dump ()
- Member Bio::EnsEMBL::Root::throw ()
- Member Bio::EnsEMBL::Root::verbose ()
- Member Bio::EnsEMBL::Root::warn ()
- Member Bio::EnsEMBL::Slice::assembly_type ()
- use version instead
- Member Bio::EnsEMBL::Slice::chr_end ()
- use end() instead Returntype : int Exceptions : none Caller : SliceAdaptor, general
- Member Bio::EnsEMBL::Slice::chr_name ()
- use seq_region_name() instead
- Member Bio::EnsEMBL::Slice::chr_start ()
- use start() instead
- Member Bio::EnsEMBL::Slice::dbID ()
- use SliceAdaptor::get_seq_region_id instead
- Member Bio::EnsEMBL::Slice::get_all_CopyNumberVariantProbes ()
- . Use get_all_CopyNumberVariantProbeFeatures instead
- Member Bio::EnsEMBL::Slice::get_all_genotyped_SNPs ()
- . Use get_all_genotyped_VariationFeatures insted
- Member Bio::EnsEMBL::Slice::get_all_MapFrags ()
- use get_all_MiscFeatures instead
- Member Bio::EnsEMBL::Slice::get_all_OligoFeatures ()
- , use functionality provided by the Ensembl Functional Genomics API instead.
- Member Bio::EnsEMBL::Slice::get_all_OligoFeatures_by_type ()
- , use functionality provided by the Ensembl Functional Genomics API instead.
- Member Bio::EnsEMBL::Slice::get_all_SNPs ()
- . Use get_all_VariationFeatures insted
- Member Bio::EnsEMBL::Slice::get_all_StructuralVariations ()
- . Use get_all_StructuralVariationFeatures instead
- Member Bio::EnsEMBL::Slice::get_all_supercontig_Slices ()
- use get_tiling_path("NTcontig") instead
- Member Bio::EnsEMBL::Slice::get_all_VariationFeatures ()
) Description : Returns all germline variation features on this slice. This function will only work correctly if the variation database has been attached to the core database. If (the
parameter) $filter is "genotyped" return genotyped SNPs only, otherwise return all germline variations. ReturnType : listref of Bio::EnsEMBL::Variation::VariationFeature Exceptions : none Caller : contigview, snpview Status : At Risk : Variation database is under development.
- Member Bio::EnsEMBL::Slice::get_Chromosome ()
- use this instead: $slice_adp->fetch_by_region('chromosome', $slice->seq_region_name)
- Member Bio::EnsEMBL::Slice::get_tiling_path ()
- use project instead
- Member Bio::EnsEMBL::Slice::has_MapSet ()
- use get_all_MiscFeatures instead
- Member Bio::EnsEMBL::StrainSlice::get_all_differences_Slice ()
- use get_all_AlleleFeatures instead
- Member Bio::EnsEMBL::Transcript::confidence ()
- . Use status() instead.
- Member Bio::EnsEMBL::Transcript::created ()
- - this attribute is not part of transcript anymore
- Member Bio::EnsEMBL::Transcript::modified ()
- - this attribute is not part of transcript anymore
- Member Bio::EnsEMBL::Transcript::sort ()
- . This method is no longer needed. Exons are sorted automatically when added to the transcript.
- Member Bio::EnsEMBL::Transcript::temporary_id ()
- : Use dbID or stable_id or something else instead
- Member Bio::EnsEMBL::Transcript::type ()
- . Use biotype() instead.
- Member Bio::EnsEMBL::Translation::temporary_id ()
- This method should not be needed. Use dbID, stable_id or something else.
- Member Bio::EnsEMBL::Utils::ConversionSupport::user_confirm ()
- - please use user_proceed() instead
- Member Bio::EnsEMBL::Utils::Exception::deprecate ()
Example : use Bio::EnsEMBL::Utils::Exception qw(deprecate) sub old_sub { deprecate('Please use new_sub() instead'); } Description: Prints a warning to STDERR that the method which called deprecate() is
. Also prints the line number and file from which the
method was called. Deprecated warnings only appear once for each location the method was called from. No message is displayed if the level of verbosity is lower than the level of the warning. Returntype : none Exceptions : warning every time Caller :
methods
- Member Bio::EnsEMBL::Utils::IO::Serializer::print_sequence ()
- - This feature is becoming FASTASerializer