All the configuration settings are in config.js and tolls.js file.
The host and version of CellBase are configured in the section below
var cellbase = { hosts: ["bioinfodev.hpc.cam.ac.uk/cellbase-4.5.0-beta"], version: "v4" }; |
The below section in config.js allows to do the following:
var opencga = { host: "bioinfodev.hpc.cam.ac.uk/opencga-1.0.0-rc3", version: "v1", projects: [ { name: "Project A", alias: "proj_a", studies : [ { name: "Study 1", alias: "std_1" } ] } ], cookies: { userName: "iva_userId", sessionId: "iva_sid" } }; |
Consequence Type, Population frequency and Protein Substitution Scores which can be found in config.js are enabled to have colors in web application. They can be modified to your needs.
var consequenceTypes = { // This is the impact color. It allows to customise both the impact categories and desired colors color: { high: "red", moderate: "orange", low: "blue", modifier: "green" }, /* 'Title' is optional. if there is no title provided then 'name' is going to be used. There are two more optional properties - 'checked' and 'color'. They can be set to display them default in web application. Similarly 'description' is optional as well. */ categories: [ { id: "", name: "", title: "Intergenic", description: "", terms: [ { id: "SO:0001631", name: "upstream_gene_variant", title: "upstream gene variant", description: "A sequence variant located 5' of a gene", impact: "modifier" }, . . . ] }, . . ] }; |
var populationFrequencies = { color: { veryRare: "red", rare: "yellow", average: "orange", common: "blue" }, studies: [ { id: "1kG_phase3", title: "1000 Genomes", populations: [ { id: "ALL", title: "All populations [ALL]", active: true }, { id: "EUR", title: "European [EUR]" }, . . . ] }, . . ] }; |
var proteinSubstitutionScores = { // This is to show the predictions in respective colors sift: { deleterious: "red", tolerated: "green" }, polyphen: { probablyDamaging: "red", possiblyDamaging: "orange", benign: "green", unknown: "black" } }; |
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