Insyght, a conserved synteny - homolog browser

04/06/2016

03:07 PM Revision 14: Apr 6th 2016, pre-release 374

02:59 PM Revision 13: Apr 6th 2016, pre-release 374 - delete all files

02:45 PM Bug #6147 (Closed): 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

Thomas Lacroix

02:45 PM Bug #6146 (Closed): Uncaught exception: java.lang.IndexOutOfBoundsException when viewing resultq from core/ disp gene set directly in ortholog table

fixed scrollPanel ensureVisible to take into account featured genomes Thomas Lacroix

02:44 PM Bug #6145: FATAL: remaining connection slots are reserved for non-replication superuser connections

changed context.xml config to not exceed postgresql max number database connection Thomas Lacroix

02:44 PM Bug #6145 (Closed): FATAL: remaining connection slots are reserved for non-replication superuser connections

Thomas Lacroix

02:44 PM Bug #6144 (Closed): the functionality "browse core / dispensable" genome" in the search tab is not longuer functioning correctly

Thomas Lacroix

02:43 PM Bug #6143 (Closed): 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

typo split[, ] instead of split[,] Thomas Lacroix

02:43 PM Feature #6142 (Closed): 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

Thomas Lacroix

02:43 PM Feature #6141 (Closed): 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

Thomas Lacroix

02:42 PM Bug #6140 (Closed): 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

Thomas Lacroix

02:42 PM Bug #6139 (Closed): In the search tab, the pre-made examples were not working properly

The examples did rely on gene's name, they now relies on proper filters Thomas Lacroix

02:41 PM Bug #6138 (Closed): 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)

Thomas Lacroix

02:41 PM Bug #6137 (Closed): some genes have multiple qualifier protein_id, display them all in the info panel with correct link to external db

Thomas Lacroix

02:41 PM Feature #6136 (Closed): direct link to GO, UniParc, PDB in the gene info panel (if available as annotation)

Thomas Lacroix

02:40 PM Bug #6135 (Closed): 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)

Thomas Lacroix

02:40 PM Feature #6134 (Closed): different shade of grey to represent the alignment based on its %identity (>85% identity = black, between 50 to 85% = dark grey, etc.)

Thomas Lacroix

02:39 PM Feature #6133 (Closed): Added support for url parameters: referenceSpecies, referenceStrain, referenceSubstrain, referenceAccnum, referenceGeneSetNames, referenceGeneSetLocusTag

Thomas Lacroix

02:30 PM Feature #6132 (Closed): report 5 last history tocken in bug reporting tool

Thomas Lacroix

03/08/2016

03:06 PM Insyght_inthecloud_vm_user_guide_1-7-1.pdf

Thomas Lacroix