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Created with Raphaël 2.2.03Oct230Sep29282726232221201615141312987652131Aug302625242322191817161512111098542129Jul28272625222120141312118654130Jun282724232221201716141310986532126May252423191817161312111098654328Apr262019181514131187131Mar30292824232221181615141110987432128Feb2524232221No functional changes.Mostly reformatting.Updated schema version to 65Moved the warning about the cache not being on back into the constructor & simplified the construction method for the cache. If someone doesn't inherit from this correctly they'll loose the warning but that is all.Ensembl core is now at v65. Patches to work with flat file handles in core like databases and supporting checksum derived xrefsStable_id table merged with main object tablestable_id table merged with main object tableStable_id table merged with main object tablefixed bug where class is not found and now uses the default oneReplaced RefSeq_dna_predicted with Refseq_mRNA_predicted and RefSeq_ncRNA_predicted as the RefSeq_dna_predicted have been split for release 64.Populating %attrib_codes hash from the biotype table in the production databaseSet default for do_similarity_scoring to '1'.don't have to set log_basepathcvs/release/ens…cvs/release/ensembl/62 release/62 upstream/release/62don't need to set log_basepathcvs/release/ens…cvs/release/ensembl/63 release/63 upstream/release/63don't need to set log_basepathupdated schemaAdjustment of summary attributesmerge stable_id tables with object tablesupdated definition of stable_id columnupdated definition of version columnmerge stable_id tables with their object tables, create views for old stable_id tablesschema version changeDon't delete the analysis and analysis description entries, update analysis creation dateDon't delete the analysis and analysis description entries, update analysis creation date.added -s species to optionsNew options now implemented.Implement new config option "do_similarity_scoring" (turns exonerate on or off).Documentation typoMerging of UniParc mapping code into the Xref system. This relies on being able to contact the EBI based UniParc readonly database.now encodes entities in synonymsConfiguration option "do_project_to_common_cs" implemented.Wrong package used I thinkUpdated docs.Reformat and update. General clean-up.Brought in new_fast() as a speed increase. Should probably consider moving new_fast() up to Storable.pm to give it to as many modules as possible & reduce code duplicationPull coordinate system out locally to avoid the hit for going back for the adaptorUpdated documentation for gene_archive and peptide_archive.verbose option should be de-referencedNew options (still to be implemented):Faster version of rearrange which ditches uc() and order modifying in favor of editing the input parameters directly with a tr///d. This is 35% faster than our original implementation. Test case suite has been run before this commit.