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Created with Raphaël 2.2.011Apr10953227Mar2625222120191815141211654128Feb27262522212019181514131211754130Jan2925242221171615141110987421Dec20191817141312111076543230Nov2928272623222120191817161413129876532131Oct3029262524232218171615121098543128Sep2725242118171413121110654330Aug29242322212017161514Added a new -intro option in the script to include external text/html file in the Introduction sectionFixed the issue to get the list of columns from the SQL query.-Allows @link tags in the @description tagswhen assigning names to transcript via existing gene name, store under a separate external_db to avoid having the same source on different levelsPatched the method "usage"do not ignore Uniprot_genename entrieswhen projecting gene name to transcript, use display label as dbprimary_acc- Added the new tags @example and @sqlENSCORESW-308: updated schema with is_obsoleteENSCORESW-308: added tests for is_obsoleteENSCORESW-308: added support for is_obsoleteadded support for is_obsoletein the example, using the same name when creating the new object and when applying methods to itit is more important that seq() returns a String and not that it can return undefApplied Will Spooner's patch to help in diagnosing absent meta keys for stopping rendering.Altered shebang for system independence.Added a new set of Gramene specific soruces for AthalianaTAIR GO associatation file parser for A.thalianaTAIR identifiers parser for A.thalianaGramene pathway xrefs parserGramene various ontologies parserEC parser from Gramenepass a new reference to files_to_parse array to make sure of any side effects when calling the run methodAdded specific sources for gene names and descriptions assignments for A.thalianaIntroducing a proxy Feature class to allow custom limitation of the boundaries of the feature. This implementation influences the get_all_ methods while leaving the standard methods unaffected.adding a line returnIt is the yearly copyright update from 2012 to 2013Cleaning up doc tagAllowing _ as a location separatorupdate error message in set_source_id_to_external_name method to make it clear what is the problemdisabled ncRNA sources for Zmays as we have no such data for this speciesUnbreak POD.corrected the species oryza_indicareverting back to 1.54 since these are changes not ready for prime timeremoving the adding of species if they are in the force_speices list. unintented side effect of limiting it to just those force speciesdo not restrict on team when looking for declarationsfixed tax if for A. lyratachanges for PhenotypeFeature API in variationremoved all the other .sql files and had just one from the schema patcherupdating to release 71