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 A method is deprecated when it is not functional any more (schema/data change) or has been replaced by a better one.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

All modules under these namespaces will be deleted

  • Bio::EnsEMBL::Compara::Filter in Ensembl 101
  • Bio::EnsEMBL::Compara::Production::Projection in Ensembl 101

All files (e.g. scripts) under these directories will be deleted

  • scripts/projection in Ensembl 101

Deprecated methods scheduled for deletion

  • AlignedMember::get_cigar_breakout() in Ensembl 102
  • AlignedMember::get_cigar_array() in Ensembl 102

Deprecated methods not yet scheduled for deletion

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

Methods removed in previous versions of Ensembl

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()