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DEPRECATED.md

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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 A method is deprecated when it is not functional any more (schema/data change) or has been replaced by a better one.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 scheduled for deletion

  • DBSQL::DnaFragAdaptor::fetch_all_by_GenomeDB_region() in Ensembl 98
  • DBSQL::'*MemberAdaptor::get_source_taxon_count() in Ensembl 99

Deprecated methods not yet scheduled for deletion

  • GenomicAlignTree::genomic_align_array()
  • GenomicAlignTree::get_all_GenomicAligns()

Methods removed in previous versions of Ensembl

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()