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Created with Raphaël 2.2.023Sep191817131211109653230Aug29272322201916151298765231Jul302926252423221918171615111043228Jun27262421201918171312111065331May302928232221171514131098732130Apr2927262423221918171615121110953227Mar26252221201918151211654128Feb27262522212019181514131211754130Jan29252422211716151410987421Dec201917141312111076543ENSCORESW-677: added method get_all_versionsCCDS db (human, mouse) updated to 74Ontology db updated to 74ENSCORESW-677: added test for get_default_version methodENSCORESW-677: added method get_default_versionaccording to rules of coding, all these methods are stableupdated seq_region statsENSPROD-55: added GenomeContainer to list of available DBAdaptorsSchema patches and version update to metaSchema version update patch (73 -> 74)replaced snp with more generic short_variation callENSPROD-55: adding test module for genome containerENSPROD-55: removing AssemblyAdaptor, wrong object and should not have been thereMust take the SO terms into a new array as current impl assumed we used shift @_[ENSCORESW-664]. Adding support for multiple variation databases from the Slice object.fixing for the new output format lineWrong file name in header[ENSCORESW-675]. Adding methods for working with AltAlleleGroup members and attribs.Documentation changes worked out with Andyget the licence rightRemoved other unnecessary dependencies.Use SequenceOntologyMapper instead of BiotypeMapper to map features to SO terms.Added SO terms to be able to perform SequenceOntologyMapper tests.Updates to reflect changes in SequenceOntologyMapper interface.Modified the interface to match the SO part in BiotypeMapper.[ENSCORESW-672]. Creating a transcript_id idx on transcript_intron_supporting_evidence.Better test. Better is. Just betterMaking a note to never ever retire this bit of codeChanged check on method translate arguments, bits of documentation andUpdate to test condition to reflect changes in table Term of ontology test database.Tests for the public method translate.Added SO terms to be able to perform SequenceOntologyMapper tests.Constructor update to avoid warningreplaced 'NULL' string with \N where necessaryTest suite for Bio::EnsEMBL::Utils::SequenceOntologyMapper.Update POD descriptionBasic mapper from Ensembl feature object to sequence ontology term.Comment on file mode restrictions using dump_(embl|genbank)Debugged problem with writing EMBL/Genbank files when opened multiplemethod takes in more than one argument, replaced shift with @_