Commit bc190300 authored by Magali Ruffier's avatar Magali Ruffier
Browse files

methods as lists

parent 68318e04
......@@ -10,70 +10,70 @@ A year after deprecation (4 Ensembl releases), the method is removed from the AP
### Removed in Ensembl Release 87 ###
Bio::EnsEMBL::**AssemblyMapper**::*in_assembly()*
Bio::EnsEMBL::**AssemblyMapper**::*map_coordinates_to_assembly()*
Bio::EnsEMBL::**AssemblyMapper**::*fast_to_assembly()*
Bio::EnsEMBL::**AssemblyMapper**::*map_coordinates_to_rawcontig()*
Bio::EnsEMBL::**AssemblyMapper**::*list_contig_ids()*
Bio::EnsEMBL::**ChainedAssemblyMapper**::*in_assembly()*
Bio::EnsEMBL::**ChainedAssemblyMapper**::*map_coordinates_to_assembly()*
Bio::EnsEMBL::**ChainedAssemblyMapper**::*fast_to_assembly()*
Bio::EnsEMBL::**ChainedAssemblyMapper**::*map_coordinates_to_rawcontig()*
Bio::EnsEMBL::**ChainedAssemblyMapper**::*list_contig_ids()*
Bio::EnsEMBL::**DBEntry**::*get_synonyms()*
Bio::EnsEMBL::DBSQL::**AssemblyMapperAdaptor**::*register_region()*
Bio::EnsEMBL::DBSQL::**AssemblyMapperAdaptor**::*register_contig()*
Bio::EnsEMBL::DBSQL::**AssemblyMapperAdaptor**::*fetch_by_type()*
Bio::EnsEMBL::DBSQL::**KaryotypeBandAdaptor**::*fetch_by_chr_band()*
Bio::EnsEMBL::DBSQL::**TranslationAdaptor**::*fetch_all_by_**DBEntry**()*
Bio::EnsEMBL::DBSQL::**TranslationAdaptor**::*get_stable_entry_info()*
Bio::EnsEMBL::DBSQL::**AltAlleleGroupAdaptor**::*fetch_all_Groups()*
Bio::EnsEMBL::DBSQL::**AltAlleleGroupAdaptor**::*fetch_all_Groups_by_type()*
Bio::EnsEMBL::DBSQL::**AltAlleleGroupAdaptor**::*fetch_Group_by_id()*
Bio::EnsEMBL::DBSQL::**AltAlleleGroupAdaptor**::*fetch_Group_by_Gene_dbID()*
Bio::EnsEMBL::DBSQL::**AnalysisAdaptor**::*feature_classes()*
Bio::EnsEMBL::DBSQL::**BaseAlignFeatureAdaptor**::*fetch_all_by_RawContig_and_pid()*
Bio::EnsEMBL::DBSQL::**BaseFeatureAdaptor**::*fetch_all_by_RawContig_constraint()*
Bio::EnsEMBL::DBSQL::**BaseFeatureAdaptor**::*fetch_all_by_RawContig()*
Bio::EnsEMBL::DBSQL::**BaseFeatureAdaptor**::*fetch_all_by_RawContig_and_score()*
Bio::EnsEMBL::DBSQL::**BaseFeatureAdaptor**::*remove_by_RawContig()*
Bio::EnsEMBL::DBSQL::**DBAdaptor**::*db_handle()*
Bio::EnsEMBL::DBSQL::**DBAdaptor**::*port()*
Bio::EnsEMBL::DBSQL::**DBAdaptor**::*driver()*
Bio::EnsEMBL::DBSQL::**DBAdaptor**::*password()*
Bio::EnsEMBL::DBSQL::**DBAdaptor**::*username()*
Bio::EnsEMBL::DBSQL::**DBAdaptor**::*host()*
Bio::EnsEMBL::DBSQL::**DBAdaptor**::*reconnect_when_lost()*
Bio::EnsEMBL::DBSQL::**DBAdaptor**::*disconnect_when_inactive()*
Bio::EnsEMBL::DBSQL::**DBAdaptor**::*dbname()*
Bio::EnsEMBL::DBSQL::**DBAdaptor**::*prepare()*
Bio::EnsEMBL::DBSQL::**DBAdaptor**::*list_supported_assemblies()*
Bio::EnsEMBL::DBSQL::**DBAdaptor**::*assembly_type()*
Bio::EnsEMBL::DBSQL::**DBAdaptor**::*db()*
Bio::EnsEMBL::DBSQL::**DBAdaptor**::*source()*
Bio::EnsEMBL::DBSQL::**DBConnection**::*group()*
Bio::EnsEMBL::DBSQL::**DBConnection**::*species()*
Bio::EnsEMBL::DBSQL::**DBEntryAdaptor**::*geneids_by_extids()*
Bio::EnsEMBL::DBSQL::**DBEntryAdaptor**::*translationids_by_extids()*
Bio::EnsEMBL::DBSQL::**DBEntryAdaptor**::*transcriptids_by_extids()*
Bio::EnsEMBL::DBSQL::**DataFileAdaptor**::*DataFile_to_extension()*
Bio::EnsEMBL::DBSQL::**ExonAdaptor**::*get_stable_entry_info()*
Bio::EnsEMBL::DBSQL::**ExonAdaptor**::*fetch_all_by_gene_id()*
Bio::EnsEMBL::DBSQL::**GeneAdaptor**::*fetch_nearest_Gene_by_Feature()*
Bio::EnsEMBL::DBSQL::**GeneAdaptor**::*fetch_by_maximum_DBLink()*
Bio::EnsEMBL::DBSQL::**GeneAdaptor**::*get_display_xref()*
Bio::EnsEMBL::DBSQL::**GeneAdaptor**::*get_description()*
Bio::EnsEMBL::DBSQL::**GeneAdaptor**::*fetch_all_by_**DBEntry**()*
Bio::EnsEMBL::DBSQL::**GeneAdaptor**::*get_stable_entry_info()*
Bio::EnsEMBL::DBSQL::**GeneAdaptor**::*fetch_by_Peptide_id()*
Bio::EnsEMBL::DBSQL::**MetaContainer**::*get_Species()*
Bio::EnsEMBL::DBSQL::**MetaContainer**::*get_default_assembly()*
Bio::EnsEMBL::DBSQL::**ProteinFeatureAdaptor**::*fetch_by_translation_id()*
Bio::EnsEMBL::DBSQL::**ProteinFeatureAdaptor**::*fetch_all_by_feature_and_dbID()*
Bio::EnsEMBL::DBSQL::**RepeatConsensusAdaptor**::*fetch_by_class_seq()*
- Bio::EnsEMBL::**AssemblyMapper**::*in_assembly()*
- Bio::EnsEMBL::**AssemblyMapper**::*map_coordinates_to_assembly()*
- Bio::EnsEMBL::**AssemblyMapper**::*fast_to_assembly()*
- Bio::EnsEMBL::**AssemblyMapper**::*map_coordinates_to_rawcontig()*
- Bio::EnsEMBL::**AssemblyMapper**::*list_contig_ids()*
- Bio::EnsEMBL::**ChainedAssemblyMapper**::*in_assembly()*
- Bio::EnsEMBL::**ChainedAssemblyMapper**::*map_coordinates_to_assembly()*
- Bio::EnsEMBL::**ChainedAssemblyMapper**::*fast_to_assembly()*
- Bio::EnsEMBL::**ChainedAssemblyMapper**::*map_coordinates_to_rawcontig()*
- Bio::EnsEMBL::**ChainedAssemblyMapper**::*list_contig_ids()*
- Bio::EnsEMBL::**DBEntry**::*get_synonyms()*
- Bio::EnsEMBL::DBSQL::**AssemblyMapperAdaptor**::*register_region()*
- Bio::EnsEMBL::DBSQL::**AssemblyMapperAdaptor**::*register_contig()*
- Bio::EnsEMBL::DBSQL::**AssemblyMapperAdaptor**::*fetch_by_type()*
- Bio::EnsEMBL::DBSQL::**KaryotypeBandAdaptor**::*fetch_by_chr_band()*
- Bio::EnsEMBL::DBSQL::**TranslationAdaptor**::*fetch_all_by_**DBEntry**()*
- Bio::EnsEMBL::DBSQL::**TranslationAdaptor**::*get_stable_entry_info()*
- Bio::EnsEMBL::DBSQL::**AltAlleleGroupAdaptor**::*fetch_all_Groups()*
- Bio::EnsEMBL::DBSQL::**AltAlleleGroupAdaptor**::*fetch_all_Groups_by_type()*
- Bio::EnsEMBL::DBSQL::**AltAlleleGroupAdaptor**::*fetch_Group_by_id()*
- Bio::EnsEMBL::DBSQL::**AltAlleleGroupAdaptor**::*fetch_Group_by_Gene_dbID()*
- Bio::EnsEMBL::DBSQL::**AnalysisAdaptor**::*feature_classes()*
- Bio::EnsEMBL::DBSQL::**BaseAlignFeatureAdaptor**::*fetch_all_by_RawContig_and_pid()*
- Bio::EnsEMBL::DBSQL::**BaseFeatureAdaptor**::*fetch_all_by_RawContig_constraint()*
- Bio::EnsEMBL::DBSQL::**BaseFeatureAdaptor**::*fetch_all_by_RawContig()*
- Bio::EnsEMBL::DBSQL::**BaseFeatureAdaptor**::*fetch_all_by_RawContig_and_score()*
- Bio::EnsEMBL::DBSQL::**BaseFeatureAdaptor**::*remove_by_RawContig()*
- Bio::EnsEMBL::DBSQL::**DBAdaptor**::*db_handle()*
- Bio::EnsEMBL::DBSQL::**DBAdaptor**::*port()*
- Bio::EnsEMBL::DBSQL::**DBAdaptor**::*driver()*
- Bio::EnsEMBL::DBSQL::**DBAdaptor**::*password()*
- Bio::EnsEMBL::DBSQL::**DBAdaptor**::*username()*
- Bio::EnsEMBL::DBSQL::**DBAdaptor**::*host()*
- Bio::EnsEMBL::DBSQL::**DBAdaptor**::*reconnect_when_lost()*
- Bio::EnsEMBL::DBSQL::**DBAdaptor**::*disconnect_when_inactive()*
- Bio::EnsEMBL::DBSQL::**DBAdaptor**::*dbname()*
- Bio::EnsEMBL::DBSQL::**DBAdaptor**::*prepare()*
- Bio::EnsEMBL::DBSQL::**DBAdaptor**::*list_supported_assemblies()*
- Bio::EnsEMBL::DBSQL::**DBAdaptor**::*assembly_type()*
- Bio::EnsEMBL::DBSQL::**DBAdaptor**::*db()*
- Bio::EnsEMBL::DBSQL::**DBAdaptor**::*source()*
- Bio::EnsEMBL::DBSQL::**DBConnection**::*group()*
- Bio::EnsEMBL::DBSQL::**DBConnection**::*species()*
- Bio::EnsEMBL::DBSQL::**DBEntryAdaptor**::*geneids_by_extids()*
- Bio::EnsEMBL::DBSQL::**DBEntryAdaptor**::*translationids_by_extids()*
- Bio::EnsEMBL::DBSQL::**DBEntryAdaptor**::*transcriptids_by_extids()*
- Bio::EnsEMBL::DBSQL::**DataFileAdaptor**::*DataFile_to_extension()*
- Bio::EnsEMBL::DBSQL::**ExonAdaptor**::*get_stable_entry_info()*
- Bio::EnsEMBL::DBSQL::**ExonAdaptor**::*fetch_all_by_gene_id()*
- Bio::EnsEMBL::DBSQL::**GeneAdaptor**::*fetch_nearest_Gene_by_Feature()*
- Bio::EnsEMBL::DBSQL::**GeneAdaptor**::*fetch_by_maximum_DBLink()*
- Bio::EnsEMBL::DBSQL::**GeneAdaptor**::*get_display_xref()*
- Bio::EnsEMBL::DBSQL::**GeneAdaptor**::*get_description()*
- Bio::EnsEMBL::DBSQL::**GeneAdaptor**::*fetch_all_by_**DBEntry**()*
- Bio::EnsEMBL::DBSQL::**GeneAdaptor**::*get_stable_entry_info()*
- Bio::EnsEMBL::DBSQL::**GeneAdaptor**::*fetch_by_Peptide_id()*
- Bio::EnsEMBL::DBSQL::**MetaContainer**::*get_Species()*
- Bio::EnsEMBL::DBSQL::**MetaContainer**::*get_default_assembly()*
- Bio::EnsEMBL::DBSQL::**ProteinFeatureAdaptor**::*fetch_by_translation_id()*
- Bio::EnsEMBL::DBSQL::**ProteinFeatureAdaptor**::*fetch_all_by_feature_and_dbID()*
- Bio::EnsEMBL::DBSQL::**RepeatConsensusAdaptor**::*fetch_by_class_seq()*
### Removed in Ensembl Release 84 ###
Bio::EnsEMBL::DBSQL::**CoordSystemAdaptor**::*_fetch_by_attrib()*
Bio::EnsEMBL::DBSQL::**CoordSystemAdaptor**::*_fetch_all_by_attrib()*
Bio::EnsEMBL::DBSQL::**MetaContainer**::*get_short_name()*
Bio::EnsEMBL::DBSQL::**MetaContainer**::*get_max_assembly_contig()*
- Bio::EnsEMBL::DBSQL::**CoordSystemAdaptor**::*_fetch_by_attrib()*
- Bio::EnsEMBL::DBSQL::**CoordSystemAdaptor**::*_fetch_all_by_attrib()*
- Bio::EnsEMBL::DBSQL::**MetaContainer**::*get_short_name()*
- Bio::EnsEMBL::DBSQL::**MetaContainer**::*get_max_assembly_contig()*
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