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for each object, methods are explicitly defined

[ENSCORESW-499]. schemaPatches.t checks that the table.sql patch set matches what is in the patched database

there should not be any, and we end up adding data which is not an ontology

miscellaneous section removed
removed hard coded html tags for schema file, this is now at the top of the file
merged two description tags for interpro table, was only using the second one

[ENSCORESW-494]. IN statement is now generically handled rather than repeating the same logic over and over again

[ENSCORESW-493]. Fixing a number of naming issues in ontology schema. Also had to introduce a patch for is_obsolete

Renamed 'old' reference to the coord_system variable. coord_system had been renamed to central_coord_system.

[ENSCORESW-490]. Point raised by Dan. Default GFF3 for source is . not ensembl. Using . and supporting basic features

[ENSCORESW-490]. Fixing the GFF serializer which would add an additional ; at times and now supports a custom source field. Gene and transcript now both emit this

before, used to log any similarity event
now, only log similarity event if we have not been able to map a stable id
if we have been able to map it, we trust that mapping and do not want to confuse the user with all the potential alternative mappings we could have used

[ENSCORESW-478] and [ENSCORESW-467]. Brought in a Perl::Critic test being run on the lowest level. Tests are only run when we have the ENV TEST_AUTHOR is set to a true value. Otherwise it does not impact on the current test cases. Also had to fix a number of issues associcated with these flags. Mostly were due to not using warnings or strict. Anything I felt was ok or not my call has been annotated with a no critic flag.

[ENSCORESW-458]. _remap() (only used by KaryotypeAdaptor AFAIK) was not working. Used seq region names for commparisons when fastmap() returns seq region ids. Fixed to using just seq_region_ids. Issues originally raised by Steve S

[ENSCORESW-479]. Making this module better at handling homologue Compara errors and also get it to die when you try to get homologues without a compara adaptor configured

[ENSCORESW-475] fixing the dbentry return to prioritise genes, transcripts and translations found on reference slices