methods as lists

bc190300 · Magali Ruffier · 68318e04 · bc190300
Commit bc190300 authored Nov 10, 2015 by Magali Ruffier
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DEPRECATED.md DEPRECATED.md +66 -66

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--- a/DEPRECATED.md
+++ b/DEPRECATED.md
@@ -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()*