window.onerror=function(msg){
    if( document.body )
        document.body.setAttribute("JSError",msg);
}

        // puts the main Browser object in this for convenience.  feel
        // free to move it into function scope if you want to keep it
        // out of the global namespace
var JBrowse;
require(['JBrowse/Browser', 'dojo/io-query', 'dojo/json' ],
        function (Browser,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: '/jbrowse/Medicago/data',
                browserRoot: '/jbrowse/Medicago',
                queryParams: queryParams,
                location: queryParams.loc,
                forceTracks: queryParams.tracks,
                initialHighlight: queryParams.highlight,
                show_nav: queryParams.nav,
                show_tracklist: queryParams.tracklist,
                show_overview: queryParams.overview,
                stores: { url: { type: "JBrowse/Store/SeqFeature/FromConfig", features: [] } },
                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 });
                },
                updateBrowserURL: true
            };

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

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