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Created with Raphaël 2.2.013Sep987231Aug262322191716151211985432129Jul282725222018141387654130Jun29272422212017161514131098732131May2726252420191817161210954329Apr282726252221201918171514121187654131Mar302924232221181715141312111098742128Feb2524211817161514111098743231Jan28272625201918171413121110765423Dec21201716151413109876More informative error if missing analysisa bug fix to column allele_string in transcript_variation table. The error is caused by a deletion, such as TTG/- in CTTGTT so the allele_string should be LV/L rather than LV/-regulatory_feature_transcript->regulatory_feature_codingFixed SQLAdded entry for ZFIN expression patterns.Made regulatory_factor and regulatory_feature part of enum in object_xref so that they can have xrefs assigned to them.Created; currently just has regulatory factor schema changes (nothing else declared)This commit was manufactured by cvs2svn to create branch 'branch-cvs/release/ens…cvs/release/ensembl/33 release/33 upstream/release/33Changed spaces to tab so that db_display_label for AFFY_HC_G110 is picked upchanges from branch-vega-31-devchanges from branch-vega-31-devused new rearrangeuse GENES file now insteadbug in affy feature retrieval from database, too many featuresAdded cowRemoved $self from call to Bio::EnsEMBL::Utils::Exception::throw inreplaced do with eval require for better error messages. Added optional argument to load_all to write to stderr what configuration file is being used. This was always reported before but defualt is now not toadd synonym data fro mouse MGI datamouse synonyms added for MGI datacheck and fix if one external database source is associated with more than one ensembl object typeuse CORE::length not just lengthParser for cisRed database dumpsParser for miRanda micro-RNA regualtory featuresCommon functionality shared between parsers for different types of regulatory featuresNew version, with modular parsersonly get seq if seq object is not null. If null return an empty stringReturn undef if seq no sequence after stop codon removedChange display name for HUGO to "HGNC Symbol"module classified as stable, removed Bio:EnsEMBL::Root referencesSWISSPROT->Uniprot/SWISSPROT similar for trembldbEntry.txt fixSPTREMBL now Uniprot/SPTREMBLexternal_db_id values changedremoved delete if exist bit which was casung problemsMapper methods basically all set to be stable.status reports added plus some tiding up of docs. Two small sections still to be donestatus reports added plus some tiding up of docsALL methods now deprecated. This Module will be removed sooncheck for arguments as all of Root.pm methods now deprecate to one of these methodBug fix to gene display_xref setting.