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Created with Raphaël 2.2.06Dec54328Nov26252322181514121187531Oct302925242321181715121110987432130Sep27262523191817131211109653230Aug29272322201916151298765231Jul302926252423221918171615111043228Jun27262421201918171312111065331May302928232221171514131098732130Apr2927262423221918171615121110953227Mar26252221201918151211654128Feb27added patch_74_75_d.sqlremove unused lineadded get_transcript_count and get_alt_transcript_count methodssmall typoadded test for new count_all_by_Slice methodadded method count_all_by_Sliceadded remove methods for slices and sequences- Added a fake 'HAP' type to be able to load HAPs from fake 'patch_type' files for HAPs.genome container now uses genome_statistics table in core schematable schema updated to include genome_statistics tablepatch_73_74_h.sql was never releasedtest databases updated to include patch_74_75_c.sqlnew genome_statistics tableadded patch_74_75_c.sqlTests counting transcripts by source(s)Added support for counting objects by source(s)Tests counting of transcripts by sourceTest support for counting genes by source(s)corrected typoadd test to check multiple mappings[ENSCORESW-777]. Added GeneAdaptor support for fetching genes by source(s).[ENSCORESW-777]. Tests GeneAdaptor support for fetching by source(s).[ENSCORESW-777]. Added TranscriptAdaptor support for fetching by source(s).[ENSCORESW-777]. Tests TranscriptAdaptor support for fetching by source(s).fetch_all_by_biotype as in GeneAdaptor, which implies the inclusion of method biotype_contraintuse parent does inheritence, too. (ds23).Patches applied to human empty test DBPatches applied to circular slice core DBPatches applied to human core test DBBumping the versionMerge from HEAD. Deprecating the fetch_nearest_Gene_by_Feature() method. It is unreliable and a replacement is being developedcvs/release/ens…cvs/release/ensembl/74Deprecating the fetch_nearest_Gene_by_Feature() method. It is unreliable and a replacement is being developedrevisions to CliHelper to support dbs where no production name is set, and to improve default behaviour where single_species mode not specified. Also expanded test coverage to support this, adding the nameless and test_collection test dbs for this purposetransfer method called on an Exon will return an Exon, not a GeneUpdated version to 75[ENSCORESW-752]. Updated _columns, store, update and _objs_from_sth methods to take into accountAdd column source in a specific order so the table definition comparison between a patched db and current one succeedsAdded licenceStart of Ensembl 75 core table definitions: first two patchesPatch for the addition of transcript source column