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Created with Raphaël 2.2.022Aug21201716151413109876432131Jul3027262524232019181613119543229Jun282726252322212019181514131211876131May30292824232221171615141098632127Apr26252423201918171613121110543130Mar292827242322added a get_total method for snp densityadjust the total count summinginsert ignore so it does not complain if an alias already exists in the databaseadding the right values in the right orderUse correct coordinate system version.Removed caching for memory conservation.check length before coord_systema bit of text formattingadded trinomial database name supportOverride set_methods for WormBase species to allow non-exact matching to Uniprot recordsWhen creating the backup table, use CREATE TABLE LIKE and INSERT SELECTTidying up.typomessages a little bit more informativeif there is no previous database, no mapping neededNew eval mode. Seems to work for us.cvs/attic/Root_…cvs/attic/Root_branch-ensembl-xrefconfigWe MUST allow empty attributes to be storedStricter checking semantics.for method transcript_display_xref_sources, updated the ignore setup to be consistent with refactoring of DisplayXrefs.pmadded a new species, physcomitrella_patensAllowed for absence of Stable IDs in otherfeatures databases. Added dbID to debug prints.Removing warningsNow can search DBs more than just otherfeaturesAllow users to ignore seemingly wrong coordinatesget non reference slices when using split_chromosomes_by_size in the density scriptsget non reference slices when using split_chromosomes_by_size in the density scriptsstore only if value if positiveI think the world is not ready for this change yetFixing the code for responses for the load* methodsMaking sure multiple includes of the registry does not result in major issues with error detection (earlier work suggested a possible issue with this)Need to record the construction of the object is the last time we used itif assembly has changed between two releases, skip database completely (no mapping required)We can now set a reconnection timeout outside of the normal realms of MySQL disconnect/reconnect. This means we have something closer to a pooled connection which stays active for as long as people need it & dies off at the required rateadded missing UniGene sources where requiredForgot \n in the log outputIgnore the do_uplaod command as we only write into the xref DBUp batch searches for checksums to 1000Use note() not print()Forgot to edit the mapper to do the checksum mapping. Not goodAdded the missing help function trigger