#8705 [Bug] : Sometimes 2 references genomes are selected in the taxonomic browser (2 nodes in yellow) ; impossible to change the group for them...
#8706 [Feature] : Taxonomic browser, core / dispensable genome functionality : upon header selection, select all nodes in appropriate categories
#8707 [Bug] : Fixed examples taxon ids for release Archaea
#8708 [Bug] : Fixed functionality to send email via smtp inra to report uncaught exception
#8709 [Improvment] : Modified user interface to deal with database changes in schema: removal of elements.description (-> sequences.definition), elements.date_seq (-> sequences.date_seq), elements.version (-> sequences.version), genes.residue (-> prot_feat.proteine)
#8710 [Bug]: Error when the database was empty. Redirect user to use the guide to add data or check out http://genome.jouy.inra.fr/Insyght/ to test functionalities
#8711 [Bug]: When transfering q genes from synteny to ortholog table view, s_insertion genes were transeferd as well
#8712 [Bug]: Synteny symbol not displaying correct number of pairs, it was missing gene mismatch and insertion
#8713 [Bug]: Compared organisms not sorted correctly for scope Whole organism
#8714 [Bug]: Navigation jumps when moving with >> or << in ortholog table or genomic organisation
rev 425 (June 2016)
Major changes:
#6502 [Feature] : over-representation (P-Value Fisher's Exact test) of orthologs whithin phenotype+ organisms in comparison to phenotype-organisms
Minor changes:
#6501 [Bug] : text above taxonomic browser search tab step 2 was not displaying properly
#6503 [Feature] : gene filter on PValue score if applicable
#6504 [Feature] : show info on PValue in ortholog table too
#6505 [Feature] : utilities to convert error report into stack trace with symbolMap file
#6506 [Bug] : max connection idle : better configuration of the context.xml config file (max total 97 SQL requests in parallel)
rev 374 (Apr 2016)
Minor changes:
#6132 [Feature] report 5 last history tocken in bug reporting tool
#6133 [Feature] Added support for url parameters: referenceSpecies, referenceStrain, referenceSubstrain, referenceAccnum, referenceGeneSetNames, referenceGeneSetLocusTag
#6134 [Feature] different shade of grey to represent the alignment based on its identity (>85 identity = black, between 50 to 85% = dark grey, etc.)
#6135 [Bug] : some genes have multiple qualifier protein_id (some ref to other db such as tigr, start with REF), this did pose a problem for the blast2seq link when it was the case ; exemple gene id 5727 EF0944 of E faecalis v583 (db origami_test)
#6136 [Feature] : direct link to GO, UniParc, PDB in the gene info panel (if available as annotation)
#6137 [Bug] : some genes have multiple qualifier protein_id, display them all in the info panel with correct link to external db
#6138 [Bug] : some gene have qualifier protein_id with ref to other db (EMBL) enclosed in curly braces, this did pose a problem for the blast2seq link when it was the case ; exemple gene id 41305 metS of Listeria Monocytogenes strain 08-5578 (db origami_test)
#6139 [Bug] : In the search tab, the pre-made examples were not working properly
#6140 [Bug] : The compared genomes list in the tab orthologs table and genomic organisation did contains public organisms with no element ; those organisms are now hidden from the result list
#6141 [Feature] : switch to no color for symbols q_gene_insertion or s_gene_insertion in genomic orga view when expanding a q or s insertion region
#6142 [Feature] : Better management of info panel: When we click on synteny info, we want to keep this disclosure panel open as we click on other synteny
#6143 [Bug] : The presence / absence homology filter did not work correctly with multiple organisms in the box : java.lang.Exception: could not parse orga id as integer : presence
#6144 [Bug] : the functionality "browse core / dispensable" genome" in the search tab is not longuer functioning correctly
#6145 [Bug] : FATAL: remaining connection slots are reserved for non-replication superuser connections
#6146 [Bug] : Uncaught exception: java.lang.IndexOutOfBoundsException when viewing resultq from core/ disp gene set directly in ortholog table
#6147 [Bug] : color is not displayed correctly at first within the core / dispensable genome browser of the search page, it appears right after clicking on another node
rev 326 (Feb 2016)
Minor changes:
#5813 [Feature] WEB APP: migrate to GWT 2.7 and GSS
#5814 [Feature] WEB APP: locus tag and functional annotation links to EnsemblGenomes, GOA, Interpro, Unipro, KEGG, PFAM, NCBI, blast2seq alignment viewer
#5815 [Feature] WEB APP: export the ortholog table in .csv format ; simple output counting the number of orthologs per cell
#5816 [Feature] WEB APP: more distinguishable colors for synteny ; ortholog not in synteny colored in grey to make the synyeny stand out more.
#5817 [Feature] WEB APP: SELECT REFERENCE -> build your reference gene set among available molecules : new filter on protein lenght
#5818 [Feature] WEB APP: singleton synteny display the gene homology directly instead of a synteny of 1 to expand
#5819 [Bug] WEB APP: some special characters were not displaying correctly on some web browser, changed to more widely supported characters
rev 280 (Sept 2015)
Major changes:
#5823 [Feature] WEB APP: support of multiple organisms with identical taxo_id
#5824 [Feature] WEB APP: support of draft genomes with many contigs ; some queries regarding those genomes are still taking too much time though
Minor changes:
#5820 [Feature] WEB APP: export sequences of genes within a genomic region
#5821 [Feature] WEB APP: taxonomic browser: automatic selection of the deeper node before branching
#5822 [Feature] WEB APP: Select reference : functionality to have a direct access to the core / dispensable gene set for reference node
#5833 [Improvement] WEB APP: Automatic and anonymous bug reporting tool