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Created with Raphaël 2.2.022Aug191817161512111098542129Jul28272625222120141312118654130Jun282724232221201716141310986532126May252423191817161312111098654328Apr262019181514131187131Mar30292824232221181615141110987432128Feb252423222118171615141098743131Jan28272620181413121110765423Dec211716151413109876543Moved new operon tables to the fundamental tables section.release 63 -> 644 seperate loops doing basically the same thing so merged into one and also added rnaseqChanged column definition for linkage_type in go_xref table to CHAR(3)Adding a more generic URI parser to replace the numerous places where people parse URIs in API code (mostly to get DB params)bringing in /codon_start to represent offsets in the CDS based upon phase. The translation from phase to codon_start is non-obvious & has been documented.Made equals() methods null safeMade both equals() methods null safeDump after field extention in species table.In the species table: Extend the db_name, web_name, and common_name fromNow don't use the projection code (it seems to work better without it).Fix syntax bug introduced in last check-in.In canonical_transcript(): Remove problematic verification code that mayDue to a bug in MySQL we need to drop the unique index, change the field to varchar then reaply the index otherwise latin1 encodings can cause a constraint error to occur. This only affects the conversion of enum to varcharIn fetch_all_by_Gene(): Go through the list of fetched transcriptsadded new biotypeswhen fetch all top level, fetch unpaired as well to include densities for the whole of chromosome Yremoved as we use now in EnsemblGenomes a generic eukaryota module, which is easier to maintainInser a small nob for turning the projection code on or offAdds the missing statement for the 'get_all_CopyNumberVariantProbes' deprecated methodNew methods 'get_all_StructuralVariationFeatures' and 'get_all_CopyNumberVariantProbeFeatures' to replace 'get_all_StructuralVariations' and 'get_all_CopyNumberVariantProbes' (deprecated)Force the loading of external synonyms before getting the code to store them. Otherwise we incorrectly retrieve external synonyms from the source database with a newly assigned IDfixes when identifying other stops - 1) ribosomal frameshift ignored, 2) stop codon being automatically annotated as a seleno and 3) non numerical values in commentsfixes when identifying other stops - 1) ribosomal frameshift ignored, 2) stop codon being automatically annotated as a seleno and 3) non numerical values in commentsadded docs for operon-related tablesCorrected syntax for loading dbs from the registry.Loosen penalty for mappings to new biotype from 0.25 to 0.75.In merge(): Formatting.Penalise the exonerate scoring by multiplying by 0.75 if the target andmerging changes from branch-ensembl-63Change to field linkage_type in ontology_xrefChanged field linkage_type to varchar(3) instead of enum.Deleted enum linkage_annotation types from go_xref.In _list_dbIDs():Changing from the || test to a ternary statement due to an error raised by EG & the EST pipeline when migrating from v1.136 to v1.37 of this file. If this does not solve it then it must be the throw above which has caused it.Added more sources to retrieveSpecific display_name and description assignment to pombePomBase gene and transcript names and descriptions parsertables with same names exist in other schemas and may create collisionIn Perl, => is very different from >=.