Skip to content

DEPRECATED.md

Latest commit

 

History

History
84 lines (62 loc) · 2.34 KB

DEPRECATED.md

File metadata and controls

84 lines (62 loc) · 2.34 KB

This file contains the list of methods deprecated in the Ensembl Compara API. A method is deprecated when it is not functional any more (schema/data change) or has been replaced by a better one. Backwards compatibility is provided whenever possible. When a method is deprecated, a deprecation warning is thrown whenever the method is used. The warning also contains instructions on replacing the deprecated method and when it will be removed.

Deprecated methods not yet scheduled for deletion

  • AlignedMember::get_cigar_array()
  • AlignedMember::get_cigar_breakout()
  • GenomicAlignTree::genomic_align_array()
  • GenomicAlignTree::get_all_GenomicAligns()
  • Homology::dn()
  • Homology::dnds_ratio()
  • Homology::ds()
  • Homology::lnl()
  • Homology::n()
  • Homology::s()
  • Homology::threshold_on_ds()
  • HomologyAdaptor::update_genetic_distance()

Removed methods by Ensembl release

Ensembl 116

  • Bio::EnsEMBL::Compara::Utils::MasterDatabase::find_overlapping_genome_db_ids

Ensembl 110

  • DBSQL::'*MemberAdaptor::fetch_by_stable_id()

Ensembl 100

  • DBSQL::'*MemberAdaptor::get_source_taxon_count()

Ensembl 98

  • DBSQL::DnaFragAdaptor::fetch_all_by_GenomeDB_region()

Ensembl 96

  • AlignSlice::Slice::get_all_VariationFeatures_by_VariationSet
  • AlignSlice::Slice::get_all_genotyped_VariationFeatures
  • Taggable::get_value_for_XXX()
  • Taggable::get_all_values_for_XXX()
  • Taggable::get_XXX_value()

Ensembl 93

  • DnaFrag::isMT()
  • DnaFrag::dna_type()
  • MethodLinkSpeciesSet::species_set_obj()

Ensembl 92

  • Member::print_member()
  • SyntenyRegion::regions()

Ensembl 91

  • Homology::print_homology()
  • MethodLinkSpeciesSet::get_common_classification()
  • NCBITaxon::binomial()
  • NCBITaxon::ensembl_alias_name()
  • NCBITaxon::common_name()
  • DnaFragAdaptor::is_already_stored()
  • GeneMemberAdaptor::fetch_all_by_source_Iterator()
  • GeneMemberAdaptor::fetch_all_Iterator()
  • GeneMemberAdaptor::load_all_from_seq_members()
  • GenomeDBAdaptor::fetch_all_by_low_coverage()
  • GenomeDBAdaptor::fetch_all_by_taxon_id_assembly()
  • GenomeDBAdaptor::fetch_by_taxon_id()
  • SeqMemberAdaptor::fetch_all_by_source_Iterator()
  • SeqMemberAdaptor::fetch_all_Iterator()
  • SeqMemberAdaptor::update_sequence()
  • SequenceAdaptor::fetch_by_dbIDs()

Ensembl 89

  • SpeciesTree::species_tree()