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Created with Raphaël 2.2.020Feb17161514131098762131Jan3025242319181716131211109654323Dec22212019141312987652130Nov292524232221181715121110987432131Oct28272625242120191817141312111076543230Sep29282726232221201615141312987652131Aug30Adding a no_append mode and adding better documentation as it had no relation to the argsGiving it more MySQL style options and allowing more options be configured from the config file such as username and passwordFixed capitalisation of adaptor nameAdding host as an optionFaster slurp. Cannot apply to gzip because the the handle isn't open right away and you can't ask for the size via -s if its not openThis commit was manufactured by cvs2svn to create branch 'branch-it helps if you spell return correctlyBringing in a new scheme for searching by. Committed in HEAD and branchSupporting a new scheme for fetching by logic_nameMinor tweak to custom header use.New test for veracity of FASTA Serializer class. Tests custom headers and compares results for SeqDumper and FASTA Serializer.new parser for Orphanet xrefs dependent on HGNC identifiersadded new source: OrphanetThis commit was manufactured by cvs2svn to create branch 'branch-Temporary fix to solve incorrect orientation of the HG1211_PATCH until either the file contains this information or we decide to do it another wayBug fix in response to Michael Schuester's report of %SMAD binding% finding nothing.Removed stable ID foreign keys and added data file onesRemoval of out of date documentation. Website provides better documentation nowthrows rather than warns now for absent file, shoudl be caught in calleradd dnadb to vega_update database typesupport for vega_update database typeFixing an error with common namesMaking sure we're not leaking readonly variablesAdded Broad source BROAD_Magnaporthe_DB]Added Broad_MagnaportheDB to the listModule associated with the Broad Magnaporthe Comparative DB; inherits fro mthe generic broad parser, Broad_GenericParser.pmBroad generic parser; needs to be superseded by another module in order to get the right source_idShortcut method call for the current species name from the backing DBAdaptorMaking sure delegating calls work as expectedProxy resolver not quite rightAdding the padded slice code & test casesAdded a method to fetch the StructuralVariationFeature from a Slice, using the VariationSetOptional gzip supportDownload release version from public FTP. Also do checks for the other Ensembl modules which isn't a total failure but can trip people upBug found by kb3 about always throwing an error from the load from URL methodchanged deprecated fetch_by_MethodLinkSpeciesSet_DnaFrag to fetch_all_by_MethodLinkSpeciesSet_DnaFragAdded a section which does checks to make sure we have the executables available & if not then use locate to find alternatives.New version to use locations for flagging identical exonsOnly allow a biotype if it had coding in there & not non_ which would negate the codingfirst pass at helper object to be used to construct and parse common sets of command line options for misc_scripts (e.g. -dbname etc.)