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Created with Raphaël 2.2.021Dec201918171413121130Nov292827232221201716151413129876532129Oct2625242322171615121110985432128Sep272524212019181714131210764331Aug30292827222120171615141096331Jul2724201817131211109543229Jun2827262521201815141312876543131May302925242322211716151411987432127Apr2625232019181716131211543230Mar29added new modules for VB array mapping/xreffingAdded an eprof_reset method that clears $globalinitialize variable with_coverageCorrect some of the examples in the SYNOPSIS, and make some POD codeMinor comment changes.Formatting, mainly.Add the ncRNA for CulexAdd POD for the private methods.Merge the binning methods into one, get_bins().Move lightweight() further down.Document most of the rest of the methods, but not the binning methods orDocumented slice(), entries(), is_populated(), populate(), and count().Add POD for Description and Contact and start to document methods:Require populate() to be called explicitly before calling count() or anyWrote Name and Synopsis POD sections.Display_xref_id, not all genes have. With a left join we sort this out.Use throw() from Bio::EnsEMBL::Utils::Exception rather than croak() fromJoin with the xref table to get the xref.display_label.Replace magic constant with symbolic constant.Formatting.Make the RepeatFeature feature collection use STRAIGHT_JOIN since theIntroduce symbolic constants for indexing the individual featureBe smarter about doing SQL queries:Fetch (almost) the same data that the get_all_RepeatFeatures() method onfixfixCorrectly spell "indices".Add getter/setter for the array of feature collection entries:Add code for handling feature collections.change port to 5306 if db version >= 48 and host =ensembldb.ensembl.orgset port to 5306 if database version >= 48 added remove_DBAdaptor method. (Nathans code - tested)This commit was manufactured by cvs2svn to create branch 'branch-Make an exception for the 'bdgpinsituexpr' source.Revert to revision 1.10.Unbreak.Do the case-sensitivity thing with the Dbxref accessions.Revert to earlier version without special collation for xref.accession.Concerning FlyBase names: Only use the first variation of a name and