@gmod/jbrowse/src/JBrowse/main.js

JBrowse - client-side genome browser

import 'babel-polyfill'

require([
    'JBrowse/Browser',
    'JBrowse/Util',
    'JBrowse/QueryParamConfigMapper',
    'dojo/io-query',
    'dojo/json',
    'css!../../css/genome.scss',

    // instruct build/glob-loader.js to insert includes for every bit of JBrowse and plugin code
    //!! glob-loader, please include every JBrowse and plugin module here

],
function (
    Browser,
    Util,
    QueryParamConfigMapper,
    ioQuery,
    JSON,
) {
    // the initial configuration of this JBrowse
    // instance

    // NOTE: this initial config is the same as any
    // other JBrowse config in any other file.  this
    // one just sets defaults from URL query params.
    // If you are embedding JBrowse in some other app,
    // you might as well just set this initial config
    // to something like { include: '../my/dynamic/conf.json' },
    // or you could put the entire
    // dynamically-generated JBrowse config here.

    // parse the query vars in the page URL
    var queryParams = ioQuery.queryToObject( window.location.search.slice(1) );

    var config = {
        containerID: "GenomeBrowser",

        dataRoot: queryParams.data,
        queryParams: queryParams,
        location: queryParams.loc,
        forceTracks: queryParams.tracks,
        initialHighlight: queryParams.highlight,
        show_nav: queryParams.nav,
        show_tracklist: queryParams.tracklist,
        show_overview: queryParams.overview,
        show_menu: queryParams.menu,
        show_fullviewlink: queryParams.fullviewlink,
        show_tracklabels: queryParams.tracklabels,
        update_browser_title: queryParams.browsertitle,
        highResolutionMode: queryParams.highres,
        stores: { url: { type: "JBrowse/Store/SeqFeature/FromConfig", features: [] } },
        bookmarks: { },
        makeFullViewURL: function( browser ) {

            // the URL for the 'Full view' link
            // in embedded mode should be the current
            // view URL, except with 'nav', 'tracklist',
            // and 'overview' parameters forced to 1.

            return browser.makeCurrentViewURL({ nav: 1, tracklist: 1, overview: 1 });
        },
        electronData: queryParams.electronData || (Util.isElectron() && electronRequire('electron').remote.app.getPath('userData'))
    };
    dojo.addOnLoad(() => {
        // see if we can load some configuration from the data-config attribute of our container
        try {
            let elementConfig = document.getElementById(config.containerID).getAttribute('data-config')
            if (elementConfig) {
                if (!/^\s*{/.test(elementConfig)) elementConfig = `{${elementConfig}}`
                elementConfig = JSON.parse(elementConfig)
                config = Object.assign({},config,elementConfig)
            }
        } catch(e) {
            console.error(e)
        }

        //if there is ?addFeatures in the query params,
        //define a store for data from the URL
        if( queryParams.addFeatures ) {
            config.stores.url.features = JSON.parse( queryParams.addFeatures );
        }

        // if there is ?addTracks in the query params, add
        // those track configurations to our initial
        // configuration
        if( queryParams.addTracks ) {
            config.tracks = JSON.parse( queryParams.addTracks );
        }

        // if there is ?addBookmarks, add those to configuration
        if( queryParams.addBookmarks ) {
            config.bookmarks.features = JSON.parse( queryParams.addBookmarks );
        }

        // if there is ?addStores in the query params, add
        // those store configurations to our initial
        // configuration
        if( queryParams.addStores ) {
            config.stores = JSON.parse( queryParams.addStores );
        }

        // this handles dot notation versions of addTracks, addBookmarks, and addStores
        // see config doc for details
        QueryParamConfigMapper().handleQueryParams(config,queryParams);

        // create a JBrowse global variable holding the JBrowse instance
        window.JBrowse = new Browser( config );

        window.JBrowse.afterMilestone('loadRefSeqs', function() { dojo.destroy(dojo.byId('LoadingScreen')); });
    })
});