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Browser.js
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Browser.js
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var _gaq = _gaq || []; // global task queue for Google Analytics
define( [
'dojo/_base/lang',
'dojo/topic',
'dijit/layout/ContentPane',
'dijit/layout/BorderContainer',
'dijit/Dialog',
'dijit/form/ComboBox',
'dijit/form/Button',
'JBrowse/Util',
'JBrowse/Store/LazyTrie',
'JBrowse/Store/Autocomplete',
'JBrowse/GenomeView',
'JBrowse/TouchScreenSupport',
'JBrowse/ConfigManager'
],
function(
lang,
topic,
dijitContentPane,
dijitBorderContainer,
dijitDialog,
dijitComboBox,
dijitButton,
Util,
LazyTrie,
AutocompleteStore,
GenomeView,
Touch,
ConfigManager
) {
var dojof = Util.dojof;
/**
* Construct a new Browser object.
* @class This class is the main interface between JBrowse and embedders
* @constructor
* @param params an object with the following properties:<br>
* <ul>
* <li><code>config</code> - list of objects with "url" property that points to a config JSON file</li>
* <li><code>containerID</code> - ID of the HTML element that contains the browser</li>
* <li><code>refSeqs</code> - object with "url" property that is the URL to list of reference sequence information items</li>
* <li><code>browserRoot</code> - (optional) URL prefix for the browser code</li>
* <li><code>tracks</code> - (optional) comma-delimited string containing initial list of tracks to view</li>
* <li><code>location</code> - (optional) string describing the initial location</li>
* <li><code>defaultTracks</code> - (optional) comma-delimited string containing initial list of tracks to view if there are no cookies and no "tracks" parameter</li>
* <li><code>defaultLocation</code> - (optional) string describing the initial location if there are no cookies and no "location" parameter</li>
* <li><code>show_nav</code> - (optional) string describing the on/off state of navigation box</li>
* <li><code>show_tracklist</code> - (optional) string describing the on/off state of track bar</li>
* <li><code>show_overview</code> - (optional) string describing the on/off state of overview</li>
* </ul>
*/
var Browser = function(params) {
this.deferredFunctions = [];
this.globalKeyboardShortcuts = {};
this.isInitialized = false;
this.config = params;
if( ! this.config.baseUrl )
this.config.baseUrl = Util.resolveUrl( window.location.href, '.' ) + '/data/';
this.startTime = Date.now();
this.container = dojo.byId(this.config.containerID);
this.container.onselectstart = function() { return false; };
this.container.genomeBrowser = this;
// init our touch device support
this.addDeferred( Touch.loadTouch );
// schedule the config load, the first step in the initialization
// process, to happen when the page is done loading
dojo.addOnLoad( dojo.hitch( this,'loadConfig' ) );
dojo.connect( this, 'onConfigLoaded', Util.debugHandler( this, 'loadUserCSS' ));
dojo.connect( this, 'onConfigLoaded', Util.debugHandler( this, 'loadRefSeqs' ));
dojo.connect( this, 'onConfigLoaded', Util.debugHandler( this, 'loadNames' ));
dojo.connect( this, 'onRefSeqsLoaded', Util.debugHandler( this, 'initView' ));
dojo.connect( this, 'onRefSeqsLoaded', Util.debugHandler( this, 'reportUsageStats' ));
};
Browser.prototype.version = function() {
var BUILD_SYSTEM_JBROWSE_VERSION;
return BUILD_SYSTEM_JBROWSE_VERSION || 'development';
}.call();
/**
* Displays links to configuration help in the main window. Called
* when the main browser cannot run at all, due to configuration
* errors or whatever.
*/
Browser.prototype.fatalError = function( error ) {
if( error ) {
error = error+'';
if( ! /\.$/.exec(error) )
error = error + '.';
}
if( ! this.hasFatalErrors ) {
var container =
dojo.byId(this.config.containerID || 'GenomeBrowser')
|| document.body;
container.innerHTML = ''
+ '<div class="fatal_error">'
+ ' <h1>Congratulations, JBrowse is on the web!</h1>'
+ " <p>However, JBrowse could not start, either because it has not yet been configured"
+ " and loaded with data, or because of an error.</p>"
+ " <p style=\"font-size: 110%; font-weight: bold\"><a title=\"View the tutorial\" href=\"docs/tutorial/\">If this is your first time running JBrowse, click here to follow the Quick-start Tutorial to get up and running.</a></p>"
+ " <p>Otherwise, please refer to the following resources for help in getting JBrowse up and running.</p>"
+ ' <ul><li><a target="_blank" href="docs/tutorial/">Quick-start tutorial</a></li>'
+ ' <li><a target="_blank" href="http://gmod.org/wiki/JBrowse">JBrowse wiki</a></li>'
+ ' <li><a target="_blank" href="docs/config.html">Configuration reference</a></li>'
+ ' <li><a target="_blank" href="docs/featureglyphs.html">Feature glyph reference</a></li>'
+ ' </ul>'
+ ' <div id="fatal_error_list" class="errors"> <h2>Error message(s):</h2>'
+ ( error ? '<div class="error"> '+error+'</div>' : '' )
+ ' </div>'
+ '</div>'
;
this.hasFatalErrors = true;
} else {
var errors_div = dojo.byId('fatal_error_list') || document.body;
dojo.create('div', { className: 'error', innerHTML: error+'' }, errors_div );
}
};
Browser.prototype.loadRefSeqs = function() {
// load our ref seqs
if( typeof this.config.refSeqs == 'string' )
this.config.refSeqs = { url: this.config.refSeqs };
dojo.xhrGet(
{
url: this.config.refSeqs.url,
handleAs: 'json',
load: dojo.hitch( this, function(o) {
this.addRefseqs(o);
this.onRefSeqsLoaded();
}),
error: dojo.hitch( this, function(e) {
this.fatalError('Failed to load reference sequence info: '+e);
})
});
};
/**
* Event that fires when the reference sequences have been loaded.
*/
Browser.prototype.onRefSeqsLoaded = function() {};
Browser.prototype.loadUserCSS = function() {
if( this.config.css && ! dojo.isArray( this.config.css ) )
this.config.css = [ this.config.css ];
dojo.forEach( this.config.css || [], function(css) {
if( typeof css == 'string' ) {
dojo.create('style', { type: 'text/css', innerHTML: css }, this.container );
} else if( typeof css == 'object' ) {
dojo.create('link', { rel: 'stylesheet', href: css.url, type: 'text/css'}, document.head );
}
},this);
};
/**
* Load our name index.
*/
Browser.prototype.loadNames = function() {
// load our name index
if (this.config.nameUrl)
this.names = new LazyTrie(this.config.nameUrl, "lazy-{Chunk}.json");
};
Browser.prototype.initView = function() {
//set up top nav/overview pane and main GenomeView pane
dojo.addClass(document.body, "tundra");
var topPane = dojo.create( 'div',{ style: {overflow: 'hidden'}}, this.container );
var overview = dojo.create( 'div', { className: 'overview', id: 'overview' }, topPane );
// overview=0 hides the overview, but we still need it to exist
if( this.config.show_overview == 0 )
overview.style.cssText = "display: none";
if( this.config.show_nav != 0 )
this.navbox = this.createNavBox( topPane, 25 );
// make our little top-links box with links to help, etc.
var linkContainer = dojo.create('div', { className: 'topLink' });
dojo.create('a', {
className: 'powered_by',
innerHTML: 'JBrowse',
href: 'http://jbrowse.org',
title: 'powered by JBrowse'
}, linkContainer );
var embedded = this.config.show_nav == 0 || this.config.show_tracklist == 0 || this.config.show_overview == 0;
if( embedded )
linkContainer.appendChild( this.makeFullViewLink() );
else
linkContainer.appendChild( this.makeShareLink() );
if( this.config.show_nav != 0 )
linkContainer.appendChild( this.makeHelpDialog() );
( this.config.show_nav == 0 ? this.container : this.navbox ).appendChild( linkContainer );
this.viewElem = document.createElement("div");
this.viewElem.className = "dragWindow";
this.container.appendChild( this.viewElem);
this.containerWidget = new dijitBorderContainer({
liveSplitters: false,
design: "sidebar",
gutters: false
}, this.container);
var contentWidget =
new dijitContentPane({region: "top"}, topPane);
//create location trapezoid
if( this.config.show_nav != 0 ) {
this.locationTrap = dojo.create('div', {className: 'locationTrap'}, topPane );
this.locationTrap.className = "locationTrap";
}
// hook up GenomeView
this.view = this.viewElem.view =
new GenomeView(this, this.viewElem, 250, this.refSeq, 1/200,
this.config.browserRoot);
dojo.connect( this.view, "onFineMove", this, "onFineMove" );
dojo.connect( this.view, "onCoarseMove", this, "onCoarseMove" );
this.browserWidget =
new dijitContentPane({region: "center"}, this.viewElem);
dojo.connect( this.browserWidget, "resize", this, 'onResize' );
dojo.connect( this.browserWidget, "resize", this.view, 'onResize' );
//set up track list
// this.createTrackList( dojo.hitch(this, function(){this.containerWidget.startup();}));
this.createTrackList( dojo.hitch( this, function(){
this.containerWidget.startup();
this.onResize();
this.view.onResize();
//set initial location
var oldLocMap = dojo.fromJson( this.cookie('location') ) || {};
if (this.config.location) {
this.navigateTo(this.config.location);
} else if (oldLocMap[this.refSeq.name]) {
this.navigateTo( oldLocMap[this.refSeq.name].l || oldLocMap[this.refSeq.name] );
} else if (this.config.defaultLocation){
this.navigateTo(this.config.defaultLocation);
} else {
this.navigateTo( Util.assembleLocString({
ref: this.refSeq.name,
start: 0.4 * ( this.refSeq.start + this.refSeq.end ),
end: 0.6 * ( this.refSeq.start + this.refSeq.end )
})
);
}
// make our global keyboard shortcut handler
dojo.connect( document.body, 'onkeypress', this, 'globalKeyHandler' );
// configure our event routing
this._initEventRouting();
this.isInitialized = true;
//if someone calls methods on this browser object
//before it's fully initialized, then we defer
//those functions until now
dojo.forEach( this.deferredFunctions, function(f) {
f.call(this);
},this );
this.deferredFunctions = [];
}));
};
/**
* Initialize our event routing, which is mostly echoing logical
* commands from the user interacting with the views.
* @private
*/
Browser.prototype._initEventRouting = function() {
this.subscribe('/jbrowse/v1/v/tracks/hide', dojo.hitch( this, function( trackConfigs ) {
this.publish( '/jbrowse/v1/c/tracks/hide', trackConfigs );
}));
this.subscribe('/jbrowse/v1/v/tracks/show', dojo.hitch( this, function( trackConfigs ) {
this.addRecentlyUsedTracks( dojo.map(trackConfigs, function(c){ return c.label;}) );
this.publish( '/jbrowse/v1/c/tracks/show', trackConfigs );
}));
};
/**
* Reports some anonymous usage statistics about this browsing
* instance. Currently reports the number of tracks in the instance
* and their type (feature, wiggle, etc), and the number of reference
* sequences and their average length.
*/
Browser.prototype.reportUsageStats = function() {
if( this.config.suppressUsageStatistics )
return;
var stats = this._calculateClientStats();
this._reportGoogleUsageStats( stats );
this._reportCustomUsageStats( stats );
};
// phones home to google analytics
Browser.prototype._reportGoogleUsageStats = function( stats ) {
_gaq.push.apply( _gaq, [
['_setAccount', 'UA-7115575-2'],
['_setDomainName', 'none'],
['_setAllowLinker', true],
['_setCustomVar', 1, 'tracks-count', stats['tracks-count'], 3 ],
['_setCustomVar', 2, 'refSeqs-count', stats['refSeqs-count'], 3 ],
['_setCustomVar', 3, 'refSeqs-avgLen', stats['refSeqs-avgLen'], 3 ],
['_setCustomVar', 4, 'jbrowse-version', stats['ver'], 3 ],
['_setCustomVar', 5, 'loadTime', stats['loadTime'], 3 ],
['_trackPageview']
]);
var ga = document.createElement('script');
ga.type = 'text/javascript';
ga.async = true;
ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www')
+ '.google-analytics.com/ga.js';
var s = document.getElementsByTagName('script')[0];
s.parentNode.insertBefore(ga, s);
};
// phones home to custom analytics at jbrowse.org
Browser.prototype._reportCustomUsageStats = function(stats) {
// phone home with a GET request made by a script tag
dojo.create(
'img',
{ style: {
display: 'none'
},
src: 'http://jbrowse.org/analytics/clientReport?'
+ dojo.objectToQuery( stats )
},
document.body
);
};
Browser.prototype._calculateClientStats = function() {
var scn = screen || window.screen;
// make a flat (i.e. non-nested) object for the stats, so that it
// encodes compactly in the query string
var date = new Date();
var stats = {
ver: this.version || 'dev',
'refSeqs-count': this.refSeqOrder.length,
'refSeqs-avgLen':
! this.refSeqOrder.length
? null
: dojof.reduce(
dojo.map( this.refSeqOrder,
function(name) {
var ref = this.allRefs[name];
if( !ref )
return 0;
return ref.end - ref.start;
},
this
),
'+'
),
'tracks-count': this.config.tracks.length,
// screen geometry
'scn-h': scn ? scn.height : null,
'scn-w': scn ? scn.width : null,
// window geometry
'win-h':document.body.offsetHeight,
'win-w': document.body.offsetWidth,
// container geometry
'el-h': this.container.offsetHeight,
'el-w': this.container.offsetWidth,
// time param to prevent caching
t: date.getTime()/1000,
// also get local time zone offset
tzoffset: date.getTimezoneOffset(),
loadTime: (date.getTime() - this.startTime)/1000
};
// count the number and types of tracks
dojo.forEach( this.config.tracks, function(trackConfig) {
var typeKey = 'track-types-'+ trackConfig.type || 'null';
stats[ typeKey ] =
( stats[ typeKey ] || 0 ) + 1;
});
return stats;
};
Browser.prototype.publish = function() {
return topic.publish.apply( topic, arguments );
};
Browser.prototype.subscribe = function() {
return topic.subscribe.apply( topic, arguments );
};
Browser.prototype.onResize = function() {
if( this.navbox )
this.view.locationTrapHeight = dojo.marginBox( this.navbox ).h;
};
/**
* Get the list of the most recently used tracks, stored for this user
* in a cookie.
* @returns {Array[Object]} as <code>[{ time: (integer), label: (track label)}]</code>
*/
Browser.prototype.getRecentlyUsedTracks = function() {
return dojo.fromJson( this.cookie( 'recentTracks' ) || '[]' );
};
/**
* Add the given list of tracks as being recently used.
* @param trackLabels {Array[String]} array of track labels to add
*/
Browser.prototype.addRecentlyUsedTracks = function( trackLabels ) {
var seen = {};
var newRecent =
Util.uniq(
dojo.map( trackLabels, function(label) {
return {
label: label,
time: Math.round( new Date() / 1000 ) // secs since epoch
};
},this)
.concat( dojo.fromJson( this.cookie('recentTracks')) || [] ),
function(entry) {
return entry.label;
}
)
// limit by default to 20 recent tracks
.slice( 0, this.config.maxRecentTracks || 10 );
// set the recentTracks cookie, good for one year
this.cookie( 'recentTracks', newRecent, { expires: 365 } );
return newRecent;
};
/**
* Load our configuration file(s) based on the parameters thex
* constructor was passed. Does not return until all files are
* loaded and merged in.
* @returns nothing meaningful
*/
Browser.prototype.loadConfig = function () {
var c = new ConfigManager({ config: this.config, browser: this });
c.getFinalConfig( dojo.hitch(this, function( finishedConfig ) {
this.config = finishedConfig;
// index the track configurations by name
this.trackConfigsByName = {};
dojo.forEach( this.config.tracks || [], function(conf){
this.trackConfigsByName[conf.label] = conf;
},this);
this.onConfigLoaded();
}));
};
/**
* Hook run after the configuration is all loaded.
*/
Browser.prototype.onConfigLoaded = function() {
// coerce some config keys to boolean
dojo.forEach( ['show_tracklist','show_nav','show_overview'], function(v) {
this.config[v] = this._coerceBoolean( this.config[v] );
},this);
};
/**
* Coerce a value of unknown type to a boolean, treating string 'true'
* and 'false' as the values they indicate, and string numbers as
* numbers.
* @private
*/
Browser.prototype._coerceBoolean = function(val) {
if( typeof val == 'string' ) {
val = val.toLowerCase();
if( val == 'true' ) {
return true;
}
else if( val == 'false' )
return false;
else
return parseInt(val);
}
else if( typeof val == 'boolean' ) {
return val;
}
else {
return true;
}
};
/**
* Add a function to be executed once JBrowse is initialized
* @param f function to be executed
*/
Browser.prototype.addDeferred = function(f) {
if (this.isInitialized)
f();
else
this.deferredFunctions.push(f);
};
/**
* @param refSeqs {Array} array of refseq records to add to the browser
*/
Browser.prototype.addRefseqs = function( refSeqs ) {
this.allRefs = this.allRefs || {};
this.refSeqOrder = this.refSeqOrder || [];
var refCookie = this.cookie('refseq');
dojo.forEach( refSeqs, function(r) {
if( ! this.allRefs[r.name] )
this.refSeqOrder.push(r.name);
this.allRefs[r.name] = r;
if( refCookie && r.name.toLowerCase() == refCookie.toLowerCase() ) {
this.refSeq = r;
}
},this);
this.refSeqOrder = this.refSeqOrder.sort();
this.refSeq = this.refSeq || refSeqs[0];
};
/**
* @private
*/
Browser.prototype.onFineMove = function(startbp, endbp) {
if( this.locationTrap ) {
var length = this.view.ref.end - this.view.ref.start;
var trapLeft = Math.round((((startbp - this.view.ref.start) / length)
* this.view.overviewBox.w) + this.view.overviewBox.l);
var trapRight = Math.round((((endbp - this.view.ref.start) / length)
* this.view.overviewBox.w) + this.view.overviewBox.l);
var locationTrapStyle = dojo.isIE
? "top: " + this.view.overviewBox.t + "px;"
+ "height: " + this.view.overviewBox.h + "px;"
+ "left: " + trapLeft + "px;"
+ "width: " + (trapRight - trapLeft) + "px;"
+ "border-width: 0px"
: "top: " + this.view.overviewBox.t + "px;"
+ "height: " + this.view.overviewBox.h + "px;"
+ "left: " + this.view.overviewBox.l + "px;"
+ "width: " + (trapRight - trapLeft) + "px;"
+ "border-width: " + "0px "
+ (this.view.overviewBox.w - trapRight) + "px "
+ this.view.locationTrapHeight + "px " + trapLeft + "px;";
this.locationTrap.style.cssText = locationTrapStyle;
}
};
/**
* Asynchronously create the track list.
* @private
*/
Browser.prototype.createTrackList = function( callback ) {
if( ! this.config.tracks )
this.config.tracks = [];
// set a default baseUrl in each of the track confs if needed
if( this.config.sourceUrl ) {
dojo.forEach( this.config.tracks, function(t) {
if( ! t.baseUrl )
t.baseUrl = this.config.baseUrl;
},this);
}
// find the tracklist class to use
var tl_class = this.config.show_tracklist == 0 ? 'Null' :
(this.config.trackSelector||{}).type ? this.config.trackSelector.type :
'Simple';
var metaDataSourceClasses = dojo.map(
(this.config.trackMetadata||{}).sources || [],
function( sourceDef ) {
var url = sourceDef.url || 'trackMeta.csv';
var type = sourceDef.type || (
/\.csv$/i.test(url) ? 'csv' :
/\.js(on)?$/i.test(url) ? 'json' :
'csv'
);
var storeClass = sourceDef['class']
|| { csv: 'dojox/data/CsvStore', json: 'dojox/data/JsonRestStore' }[type];
if( !storeClass ) {
console.error( "No store class found for type '"
+type+"', cannot load track metadata from URL "+url);
return null;
}
return { class_: storeClass, url: url };
});
// load all the classes we need
require( Array.prototype.concat.apply( ['JBrowse/View/TrackList/'+tl_class, 'JBrowse/Store/TrackMetaData'],
dojo.map( metaDataSourceClasses, function(c) { return c.class_; } )
),
dojo.hitch( this, function( trackListClass, MetaDataStore ) { // more args after the first 2
var mdStores = [];
for( var i = 2; i<arguments.length; i++ ) {
mdStores.push( new (arguments[i])({url: metaDataSourceClasses[i-2].url}) );
}
var trackMeta = new MetaDataStore(
dojo.mixin( this.config.trackMetadata || {}, {
trackConfigs: this.config.tracks,
browser: this,
metadataStores: mdStores
})
);
// instantiate the tracklist and the track metadata object
this.trackListView = new trackListClass(
dojo.mixin(
dojo.clone( this.config.trackSelector ) || {},
{
trackConfigs: this.config.tracks,
browser: this,
trackMetaData: trackMeta
}
)
);
// bind the 't' key as a global keyboard shortcut
this.setGlobalKeyboardShortcut( 't', this.trackListView, 'toggle' );
// listen for track-visibility-changing messages from
// views and update our tracks cookie
this.subscribe( '/jbrowse/v1/v/tracks/changed', dojo.hitch( this, function() {
this.cookie( "tracks",
this.view.visibleTrackNames().join(','),
{expires: 60});
}));
// figure out what initial track list we will use:
// from a param passed to our instance, or from a cookie, or
// the passed defaults, or the last-resort default of "DNA"?
var origTracklist =
this.config.forceTracks
|| this.cookie( "tracks" )
|| this.config.defaultTracks
|| "DNA";
this.showTracks( origTracklist );
callback();
}));
};
/**
* @private
*/
Browser.prototype.onVisibleTracksChanged = function() {
};
/**
* navigate to a given location
* @example
* gb=dojo.byId("GenomeBrowser").genomeBrowser
* gb.navigateTo("ctgA:100..200")
* gb.navigateTo("f14")
* @param loc can be either:<br>
* <chromosome>:<start> .. <end><br>
* <start> .. <end><br>
* <center base><br>
* <feature name/ID>
*/
Browser.prototype.navigateTo = function(loc) {
if (!this.isInitialized) {
this.deferredFunctions.push(function() { this.navigateTo(loc); });
return;
}
// if it's a foo:123..456 location, go there
var location = Util.parseLocString( loc );
if( location ) {
this.navigateToLocation( location );
}
// otherwise, if it's just a word, try to figure out what it is
else {
// is it just the name of one of our ref seqs?
var ref = Util.matchRefSeqName( loc, this.allRefs );
if( ref ) {
// see if we have a stored location for this ref seq in a
// cookie, and go there if we do
var oldLoc;
try {
oldLoc = Util.parseLocString(
dojo.fromJson(
this.cookie("location")
)[ref.name].l
);
oldLoc.ref = ref.name; // force the refseq name; older cookies don't have it
} catch (x) {}
if( oldLoc ) {
this.navigateToLocation( oldLoc );
} else {
// if we don't just go to the middle 80% of that refseq
this.navigateToLocation({ref: ref.name, start: ref.end*0.1, end: ref.end*0.9 });
}
}
// lastly, try to search our feature names for it
this.searchNames( loc );
}
};
// given an object like { ref: 'foo', start: 2, end: 100 }, set the
// browser's view to that location. any of ref, start, or end may be
// missing, in which case the function will try set the view to
// something that seems intelligent
Browser.prototype.navigateToLocation = function( location ) {
// validate the ref seq we were passed
var ref = location.ref ? Util.matchRefSeqName( location.ref, this.allRefs )
: this.refSeq;
if( !ref )
return;
location.ref = ref.name;
// clamp the start and end to the size of the ref seq
location.start = Math.max( 0, location.start || 0 );
location.end = Math.max( location.start,
Math.min( ref.end, location.end || ref.end )
);
// if it's the same sequence, just go there
if( location.ref == this.refSeq.name) {
this.view.setLocation( this.refSeq,
location.start,
location.end
);
}
// if different, we need to poke some other things before going there
else {
// record names of open tracks and re-open on new refseq
var curTracks = this.view.visibleTrackNames();
this.refSeq = this.allRefs[location.ref];
this.view.setLocation( this.refSeq,
location.start,
location.end );
this.showTracks( curTracks );
}
return;
};
/**
* Given a string name, search for matching feature names and set the
* view location to any that match.
*/
Browser.prototype.searchNames = function( /**String*/ loc ) {
var brwsr = this;
this.names.exactMatch( loc, function(nameMatches) {
var goingTo,
i;
var post1_4 = typeof nameMatches[0][0] == 'string';
//first check for exact case match
for (i = 0; i < nameMatches.length; i++) {
if (nameMatches[i][ post1_4 ? 0 : 1 ] == loc)
goingTo = nameMatches[i];
}
//if no exact case match, try a case-insentitive match
if (!goingTo) {
for (i = 0; i < nameMatches.length; i++) {
if (nameMatches[i][ post1_4 ? 0 : 1].toLowerCase() == loc.toLowerCase())
goingTo = nameMatches[i];
}
}
//else just pick a match
if (!goingTo) goingTo = nameMatches[0];
var startbp = parseInt( goingTo[ post1_4 ? 4 : 3 ]);
var endbp = parseInt( goingTo[ post1_4 ? 5 : 4 ]);
var flank = Math.round((endbp - startbp) * .2);
//go to location, with some flanking region
brwsr.navigateTo( goingTo[ post1_4 ? 3 : 2]
+ ":" + (startbp - flank)
+ ".." + (endbp + flank));
brwsr.showTracks(brwsr.names.extra[nameMatches[0][ post1_4 ? 1 : 0 ]]);
});
};
/**
* load and display the given tracks
* @example
* gb=dojo.byId("GenomeBrowser").genomeBrowser
* gb.showTracks(["DNA","gene","mRNA","noncodingRNA"])
* @param trackNameList {Array|String} array or comma-separated string
* of track names, each of which should correspond to the "label"
* element of the track information
*/
Browser.prototype.showTracks = function( trackNames ) {
if( !this.isInitialized ) {
this.deferredFunctions.push( function() { this.showTracks(trackNames); } );
return;
}
if( typeof trackNames == 'string' )
trackNames = trackNames.split(',');
if( ! trackNames )
return;
var trackConfs = dojo.filter(
dojo.map( trackNames, function(n) {
return this.trackConfigsByName[n];
}, this),
function(c) {return c;} // filter out confs that are missing
);
// publish some events with the tracks to instruct the views to show them.
this.publish( '/jbrowse/v1/c/tracks/show', trackConfs );
this.publish( '/jbrowse/v1/n/tracks/visibleChanged' );
};
/**
* @returns {String} locstring representation of the current location<br>
* (suitable for passing to navigateTo)
*/
Browser.prototype.visibleRegion = function() {
return Util.assembleLocString({
ref: this.view.ref.name,
start: this.view.minVisible(),
end: this.view.maxVisible()
});
};
Browser.prototype.makeHelpDialog = function () {
// make a div containing our help text
var browserRoot = this.config.browserRoot || "";
var helpdiv = document.createElement('div');
helpdiv.style.display = 'none';
helpdiv.className = "helpDialog";
helpdiv.innerHTML = ''
+ '<div class="main" style="float: left; width: 49%;">'
+ '<dl>'
+ '<dt>Moving</dt>'
+ '<dd><ul>'
+ ' <li>Move the view by clicking and dragging in the track area, or by clicking <img height="20px" src="'+browserRoot+'img/slide-left.png"> or <img height="20px" src="'+browserRoot+'img/slide-right.png"> in the navigation bar.</li>'
+ ' <li>Center the view at a point by clicking on either the track scale bar or overview bar, or by shift-clicking in the track area.</li>'
+ '</ul></dd>'
+ '<dt>Zooming</dt>'
+ '<dd><ul>'
+ ' <li>Zoom in and out by clicking <img height="20px" src="'+browserRoot+'img/zoom-in-1.png"> or <img height="20px" src="'+browserRoot+'img/zoom-out-1.png"> in the navigation bar.</li>'
+ ' <li>Select a region and zoom to it ("rubber-band" zoom) by clicking and dragging in the overview or track scale bar, or shift-clicking and dragging in the track area.</li>'
+ ' </ul>'
+ '</dd>'
+ '<dt>Selecting Tracks</dt>'
+ '<dd><ul><li>Turn a track on by dragging its track label from the "Available Tracks" area into the genome area.</li>'
+ ' <li>Turn a track off by dragging its track label from the genome area back into the "Available Tracks" area.</li>'
+ ' </ul>'
+ '</dd>'
+ '</dl>'
+ '</div>'
+ '<div class="main" style="float: right; width: 49%;">'
+ '<dl>'
+ '<dt>Searching</dt>'
+ '<dd><ul>'
+ ' <li>Jump to a feature or reference sequence by typing its name in the search box and pressing Enter.</li>'
+ ' <li>Jump to a specific region by typing the region into the search box as: <span class="example">ref:start..end</span>.</li>'
+ ' </ul>'
+ '</dd>'
+ '<dt>Example Searches</dt>'
+ '<dd>'
+ ' <dl class="searchexample">'
+ ' <dt>uc0031k.2</dt><dd>jumps to the feature named <span class="example">uc0031k.2</span>.</dd>'
+ ' <dt>chr4</dt><dd>jumps to chromosome 4</dd>'
+ ' <dt>chr4:79,500,000..80,000,000</dt><dd>jumps the region on chromosome 4 between 79.5Mb and 80Mb.</dd>'
+ ' </dl>'
+ '</dd>'
+ '<dt>JBrowse Configuration</dt>'
+ '<dd><ul><li><a target="_blank" href="docs/tutorial/">Quick-start tutorial</a></li>'
+ ' <li><a target="_blank" href="http://gmod.org/wiki/JBrowse">JBrowse wiki</a></li>'
+ ' <li><a target="_blank" href="docs/config.html">Configuration reference</a></li>'
+ ' <li><a target="_blank" href="docs/featureglyphs.html">Feature glyph reference</a></li>'
+ ' </ul>'
+ '</dd>'
+ '</dl>'
+ '</div>'
;
this.container.appendChild( helpdiv );
var dialog = new dijitDialog({
"class": 'help_dialog',
refocus: false,
draggable: false,
title: "JBrowse Help"
}, helpdiv );
// make a Help link that will show the dialog and set a handler on it
var helplink = document.createElement('a');
helplink.className = 'topLink';
helplink.title = 'Help';
helplink.style.cursor = 'help';
helplink.appendChild( document.createTextNode('Help'));
dojo.connect(helplink, 'onclick', function() { dialog.show(); });
this.setGlobalKeyboardShortcut( '?', dialog, 'show' );
dojo.connect( document.body, 'onkeydown', function(evt) {
if( evt.keyCode != dojo.keys.SHIFT && evt.keyCode != dojo.keys.CTRL && evt.keyCode != dojo.keys.ALT )
dialog.hide();
});
return helplink;
};
/**
* Create a global keyboard shortcut.
* @param keychar the character of the key that is typed
* @param [...] additional arguments passed to dojo.hitch for making the handler
*/
Browser.prototype.setGlobalKeyboardShortcut = function( keychar ) {
// warn if redefining
if( this.globalKeyboardShortcuts[ keychar ] )
console.warn("WARNING: JBrowse global keyboard shortcut '"+keychar+"' redefined");
// make the wrapped handler func
var func = dojo.hitch.apply( dojo, Array.prototype.slice.call( arguments, 1 ) );
// remember it
this.globalKeyboardShortcuts[ keychar ] = func;
};
/**
* Key event handler that implements all global keyboard shortcuts.
*/
Browser.prototype.globalKeyHandler = function( evt ) {
var shortcut = this.globalKeyboardShortcuts[ evt.keyChar ];
if( shortcut ) {
shortcut.call( this );
evt.stopPropagation();
}
};
Browser.prototype.makeShareLink = function () {
// don't make the link if we were explicitly configured not to
if( ( 'share_link' in this.config ) && !this.config.share_link )
return null;
var browser = this;
var viewURL = '#';
// make the share link
var link = dojo.create(
'a',
{
className: 'topLink',
href: '#',
innerHTML: 'Share',
title: 'share this view',
style: {
position: 'relative'
},
onclick: function() {
console.log('click!');
URLinput.value = viewURL;
previewLink.href = viewURL;
sharePane.show();
var lp = dojo.position(link);
dojo.style( sharePane.domNode, {
top: (lp.y+lp.h) + 'px',
right: 0,
left: ''
});
URLinput.select();