MediaWiki:JBrowse.js

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var baseUrl = "/JBrowse/";

// 最初にdojo.jsを属性付きで読み込む
var dojoScript  = document.createElement('script');
dojoScript.type = 'text/javascript';
dojoScript.src  = baseUrl+'/src/dojo/dojo.js'
dojoScript.setAttribute("data-dojo-config", "async: 1, baseUrl: baseUrl+'src'");
var css = document.getElementsByTagName( 'link' )[0];
css.parentNode.appendChild(dojoScript, css);

// dojo.jsの読み込み完了後、init.jsを読み込む
dojoScript.onload = function(){
	var initScript  = document.createElement('script');
	initScript.type = 'text/javascript';
	initScript.src  = baseUrl+'/src/JBrowse/init.js';
	dojoScript.parentNode.appendChild(initScript, dojoScript);


	// init.jsの読み込み完了後、初期化を行う
	initScript.onload = function(){
		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",
					sourceUrl:        baseUrl,
					browserRoot:      baseUrl, 
					dataRoot:         baseUrl + "data/{{{1}}}",
					queryParams:      queryParams,
					location:         queryParams.loc,
					forceTracks:      "DNA,BAM SNPs/Coverage,BAM",
					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 );
		});
	}
}