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Created with Raphaël 2.2.027Aug26252423201918171613121195429Jul27262322212019161413128762129Jun282524222118171615141110987432128May272421201917141211765423Apr222120191615141312876131Mar3029252322191817161512109853125Feb2423191817161211109543231Jan292826252120191815141312118754324Dec231817161514111042127Nov25232019181716131211109654230Oct29282723222120In map_indel(): Fix documentation to mention right return type. FromIn map_coordinates(): Fix documentation and argument checking errorIn add_map_coordinates(): Correct spelling in documentation and removeUpdated to deal with cases where not all of the patch scaffold is included in the toplevel.Small change to slice().Allow $transcript->translation(undef) to break connection fromAllow $translation->transcript(undef) to break connection toUnbreak new().In new(): When comparing slices, also take the coordinate system namesIn new(): Document undocumented named arguments to do with canonicalIn slice(): Transfer all supporting features to the new slice if a newIn fetch_all_by_Slice(): Sort on start position as we say we're doing.In _fetch_by_object_type(): Detect if the external DB name and/orThings noticed by Michael S.:In new(): Make sure we know what we're testing for.Fixes from Michael S.:Fix package documentation, pointed out by Michael S.Fixed misleading documentation, pointed out by Michael S.Fix faulty documentation, pointed out by Michael S.Update API version to 60.Update DBEntryAdaptor for the renaming of go_xref to ontology_xref.RENAME GoXref.pm --> OntologyXref.pmApply patch_59_60_b.sql to table.sql# patch_59_60_b.sqlApply patch_59_60_a.sql to table.sql*** empty log message ***those labelled as unnamed, use the accession insteadUse the following order of biotypes when setting canonicalIn equals(): Test for identity even before calling assert_ref() on theIn equals(): If the argument is the same as $self, return true at once.Change the way we add canonical transcripts.Add method equals():Add equals() method:Add equals() method:New method for features: equals()Fixed time format - use MySQL now() instead of perl time()Add an is_canonical() method to the Transcript object. Set is_canonicalpanda addedformat slightly changed and use new exception typesDo not assume that canonical_transcript() returns a useful value.