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