@gmod/jbrowse/dist/0.bundle.js

JBrowse - client-side genome browser

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t},url=__webpack_require__(718);__WEBPACK_AMD_DEFINE_ARRAY__=[__webpack_require__(546),__webpack_require__(547),__webpack_require__(550),__webpack_require__(736),__webpack_require__(561),__webpack_require__(552),__webpack_require__(563),__webpack_require__(560),__webpack_require__(872),__webpack_require__(608),__webpack_require__(565),__webpack_require__(609),__webpack_require__(343),__webpack_require__(339),__webpack_require__(548),__webpack_require__(647),__webpack_require__(878),__webpack_require__(599),__webpack_require__(831),__webpack_require__(747),__webpack_require__(566),__webpack_require__(671),__webpack_require__(722),__webpack_require__(835),__webpack_require__(693),__webpack_require__(723),__webpack_require__(622),__webpack_require__(694),__webpack_require__(1036),__webpack_require__(915),__webpack_require__(330),__webpack_require__(374),__webpack_require__(375),__webpack_require__(916),__webpack_require__(353),__webpack_require__(376),__webpack_require__(385),__webpack_require__(386),__webpack_require__(350),__webpack_require__(359),__webpack_require__(401),__webpack_require__(341),__webpack_require__(405),__webpack_require__(406),__webpack_require__(407),__webpack_require__(408),__webpack_require__(365),__webpack_require__(409),__webpack_require__(410),__webpack_require__(411),__webpack_require__(367),__webpack_require__(368),__webpack_require__(571),__webpack_require__(1028),__webpack_require__(1029),__webpack_require__(1030),__webpack_require__(1031)],__WEBPACK_AMD_DEFINE_RESULT__=function(declare,lang,on,html,query,domConstruct,keys,Deferred,DeferredList,topic,aspect,request,ioQuery,has,array,dijitContentPane,dijitBorderContainer,dijitDialog,dijitComboBox,dojoMemoryStore,dijitButton,dijitSelectBox,dijitToggleButton,dijitDropDownButton,dijitDropDownMenu,dijitCheckedMenuItem,dijitMenuItem,dijitMenuSeparator,dojoxTriStateCheckBox,dojoxHtmlEntities,Util,LazyTrie,NamesLazyTrieDojoDataStore,DojoDataStore,FeatureFiltererMixin,GenomeView,Touch,ConfigManager,InfoDialog,FileDialog,FastaFileDialog,Location,LocationChoiceDialog,SetHighlightDialog,PreferencesDialog,OpenDirectoryDialog,SetTrackHeightDialog,HelpDialog,StandaloneDatasetList,UnindexedFasta,IndexedFasta,TwoBit,dijitFocus,LazyLoad,packagejson){var dojof=Util.dojof;return require.on("error",function(t){var e=t.info&&t.info[0]&&t.info[0].mid?t.info.map(function(t){return t.mid}).join(", "):t;window.JBrowse.fatalError("Failed to load resource: "+e)}),declare(FeatureFiltererMixin,{constructor:function(t){if(this.globalKeyboardShortcuts={},this.config=t||{},!this.config.unitTestMode){"function"==typeof this.config.initExtra&&this.config.initExtra(this,t),this.startTime=new Date;var e=this;dojo.addOnLoad(function(){if(Util.isElectron()&&!e.config.dataRoot)return dojo.addClass(document.body,"jbrowse"),dojo.addClass(document.body,e.config.theme||"tundra"),void e.welcomeScreen(document.body);e.loadConfig().then(function(){e.container=dojo.byId(e.config.containerID),e.container.onselectstart=function(){return!1},e.config.initialHighlight&&"/"!=e.config.initialHighlight&&e.setHighlight(new Location(e.config.initialHighlight)),e.initPlugins().then(function(){e.loadNames(),e.loadUserCSS().then(function(){e.initTrackMetadata(),e.loadRefSeqs().then(function(){var t=e._initialLocation(),n=Util.parseLocString(t);n&&n.ref&&e.allRefs[n.ref]&&(e.refSeq=e.allRefs[n.ref]),e.ensureNonzeroContainerDimensions(),e.initView().then(function(){Touch.loadTouch(),t&&e.navigateTo(t);var n=[];e.config.alwaysOnTracks&&(n=n.concat(e.config.alwaysOnTracks.split(","))),e.config.forceTracks?n=n.concat(e.config.forceTracks.split(",")):e.cookie("tracks")?n=n.concat(e.cookie("tracks").split(",")):e.config.defaultTracks&&(e.config.defaultTracks instanceof Array||(n=n.concat(e.config.defaultTracks.split(",")))),0==n.length&&n.push("DNA"),n=Util.uniq(n),e.showTracks(n),e.passMilestone("completely initialized",{success:!0})}),e.reportUsageStats()})})})})})}},_initialLocation:function(){var t=dojo.fromJson(this.cookie("location"))||{};return this.config.location?this.config.location:t[this.refSeq.name]?t[this.refSeq.name].l||t[this.refSeq.name]:this.config.defaultLocation?this.config.defaultLocation:Util.assembleLocString({ref:this.refSeq.name,start:.4*(this.refSeq.start+this.refSeq.end),end:.6*(this.refSeq.start+this.refSeq.end)})},version:function(){return JSON.parse(packagejson).version}.call(),getPlugin:function(t,e){this.afterMilestone("initPlugins",dojo.hitch(this,function(){e(this.plugins[t])}))},_corePlugins:function(){return["RegexSequenceSearch"]},initPlugins:function(){return this._milestoneFunction("initPlugins",function(t){var e=this;this.plugins={};var n=this.config.plugins||this.config.Plugins||{};if(lang.isArray(n)||n.name||(n=function(){var t=[];for(var e in n)!lang.isObject(n[e])||"name"in n[e]||(n[e].name=e),t.push(n[e]);return t}.call(this)),lang.isArray(n)||(n=[n]),n.unshift.apply(n,this._corePlugins()),(n=array.map(n,function(t){return"object"==(void 0===t?"undefined":_typeof(t))?t:{name:t}})).length){n.forEach(function(t){var n=dojoConfig.packages.find(function(e){return e.name===t.name});n?(t.css=!!n.css&&n.pluginDir+"/"+n.css,t.js=n.location):e.fatalError("plugin "+t.name+" not found, please ensure the plugin was included in this JBrowse build")});var i=array.map(n,function(t){return new Deferred});new DeferredList(i).then(function(){t.resolve({success:!0})}),dojo.global.require(array.map(n,function(t){return t.name+"/main"}),dojo.hitch(this,function(){array.forEach(arguments,function(t,e){var r=n[e],o=i[e];if("string"==typeof t)console.error("could not load plugin "+r.name+": "+t);else{var s,a=dojo.mixin(dojo.clone(n[e]),{config:this.config[r.name]||{}});a.browser=this,a=dojo.mixin(a,{browser:this}),r.css?s=this._loadCSS({url:this.resolveUrl(r.css+"/main.css")}):(s=new Deferred).resolve(),s.then(function(){o.resolve({success:!0})}),a.cssLoaded=s,this.plugins[r.name]=new t(a)}},this)}))}else t.resolve({success:!0})})},resolveUrl:function(t){var e=this.config.browserRoot||this.config.baseUrl||"";return Util.resolveUrl(e,t)},welcomeScreen:function(t,e){var n=this;__webpack_require__.e(3).then(function(){var i=[__webpack_require__(1169)];(function(i){t.innerHTML=i;dojo.create("div",{style:{overflow:"hidden"}},n.container);dojo.byId("welcome").innerHTML="Welcome! To get started with <i>JBrowse-"+n.version+"</i>, select a sequence file or an existing data directory",on(dojo.byId("newOpen"),"click",dojo.hitch(n,"openFastaElectron")),on(dojo.byId("newOpenDirectory"),"click",function(){new OpenDirectoryDialog({browser:n,setCallback:dojo.hitch(n,"openDirectoryElectron")}).show()});try{n.loadSessions()}catch(t){console.error(t)}if(e){console.log(e);var r=dojo.byId("fatal_error_list");dojo.create("div",{className:"error",innerHTML:e},r)}request(n.resolveUrl("sample_data/json/volvox/successfully_run")).then(function(){try{document.getElementById("volvox_data_placeholder").innerHTML='The example dataset is also available. View <a href="?data=sample_data/json/volvox">Volvox test data here</a>.'}catch(t){}})}).apply(null,i)}).catch(__webpack_require__.oe)},ensureNonzeroContainerDimensions:function(){var t=this.container.offsetWidth,e=this.container.offsetHeight;t||(console.warn("JBrowse container element #"+this.config.containerID+" has no width, please set one with CSS. Setting fallback width of 640 pixels"),this.container.style.width="640px"),e||(console.warn("JBrowse container element #"+this.config.containerID+" has no height, please set one with CSS. Setting fallback height of 480 pixels"),this.container.style.height="480px")},fatalError:function(t){function e(t){return t&&(console.error(t.stack||""+t),/\.$/.exec(t+="")||(t+="."),t=dojoxHtmlEntities.encode(t)),t}if(this.renderedFatalErrors){var n=dojo.byId("fatal_error_list")||document.body;dojo.create("div",{className:"error",innerHTML:e(t)+""},n)}else if(/^Could not load reference sequence/.test(t)&&this.config.datasets&&!this.config.datasets._DEFAULT_EXAMPLES)dojo.empty(this.container),new StandaloneDatasetList({datasets:this.config.datasets}).placeAt(this.container);else{var i=this.container||document.body,r=this;dojo.addClass(document.body,this.config.theme||"tundra"),Util.isElectron()?this.welcomeScreen(i,e(t)):__webpack_require__.e(2).then(function(){var n=[__webpack_require__(1170)];(function(n){if(i.innerHTML=n,t){var o=dojo.byId("fatal_error_list");dojo.create("div",{className:"error",innerHTML:e(t)+""},o)}request(r.resolveUrl("sample_data/json/volvox/successfully_run")).then(function(){try{dojo.byId("volvox_data_placeholder").innerHTML='However, it appears you have successfully run <code>./setup.sh</code>, so you can see the <a href="?data=sample_data/json/volvox">Volvox test data here</a>.'}catch(t){}})}).apply(null,n)}).catch(__webpack_require__.oe),this.renderedFatalErrors=!0}},loadSessions:function(){var t=electronRequire("fs"),e=(electronRequire("electron").remote.app,this.config.electronData+"/sessions.json"),n=JSON.parse(t.readFileSync(e,"utf8")),i=dojo.create("table",{id:"previousSessionsTable",style:{overflow:"hidden",width:"90%"}},dojo.byId("previousSessions")),r=this;if(!n.length){var o=dojo.create("tr",{},i);dojo.create("div",{innerHTML:"<ul><li>No sessions yet!</li></ul>"},o)}array.forEach(n,function(o){var s=dojo.create("tr",{},i),a=window.location.href.split("?")[0]+"?data="+Util.replacePath(o.session);dojo.create("div",{class:"dijitIconDelete",onclick:function(s){if(confirm("This will simply delete your session from the list, it won't remove any data files. Are you sure you want to continue?")){dojo.empty(i);var a=n.indexOf(o);-1!=a&&n.splice(a,1),t.writeFileSync(e,JSON.stringify(n,null,2),"utf8"),r.loadSessions()}}},s),dojo.create("td",{innerHTML:'<a href="'+a+'">'+o.session+"</a>"},s)})},loadRefSeqs:function(){var t=this;return this._milestoneFunction("loadRefSeqs",function(e){"string"==typeof this.config.refSeqs&&(this.config.refSeqs={url:this.config.refSeqs}),this.config.refSeqs.url&&this.config.refSeqs.url.match(/.fai$/)?new IndexedFasta({browser:this,faiUrlTemplate:this.config.refSeqs.url}).getRefSeqs(function(n){t.addRefseqs(n),e.resolve({success:!0})},function(t){e.reject(t)}):this.config.refSeqs.url&&this.config.refSeqs.url.match(/.2bit$/)?new TwoBit({browser:this,urlTemplate:this.config.refSeqs.url}).getRefSeqs(function(n){t.addRefseqs(n),e.resolve({success:!0})}):this.config.refSeqs.url&&this.config.refSeqs.url.match(/.fa$/)?new UnindexedFasta({browser:this,urlTemplate:this.config.refSeqs.url}).getRefSeqs(function(n){t.addRefseqs(n),e.resolve({success:!0})}):"data"in this.config.refSeqs?(this.addRefseqs(this.config.refSeqs.data),e.resolve({success:!0})):request(this.resolveUrl(this.config.refSeqs.url),{handleAs:"text",headers:{"X-Requested-With":null}}).then(function(n){t.addRefseqs(dojo.fromJson(n)),e.resolve({success:!0})},function(t){e.reject("Could not load reference sequence definitions. "+t)})})},loadUserCSS:function(){return this._milestoneFunction("loadUserCSS",function(t){this.config.css&&!lang.isArray(this.config.css)&&(this.config.css=[this.config.css]);var e=this.config.css||[];if(e.length){var n=this,i=array.map(e,function(t){return n._loadCSS(t)});new DeferredList(i).then(function(){t.resolve({success:!0})})}else t.resolve({success:!0})})},_loadCSS:function(t){var e=new Deferred;return"string"==typeof t&&(t.indexOf("{")>-1?(dojo.create("style",{"data-from":"JBrowse Config",type:"text/css",innerHTML:t},document.head),e.resolve(!0)):t={url:t}),"object"==(void 0===t?"undefined":_typeof(t))&&LazyLoad.css(t.url,function(){e.resolve(!0)}),e},loadNames:function(){return this._milestoneFunction("loadNames",function(t){var e,n=dojo.mixin(dojo.clone(this.config.names||{}),this.config.autocomplete||{});if(n.url||(n.url=this.config.nameUrl||"data/names/"),n.baseUrl&&(n.url=Util.resolveUrl(n.baseUrl,n.url)),e=n.type){var i=this;-1==e.indexOf("/")&&(e="JBrowse/Store/Names/"+e),dojo.global.require([e],function(e){i.nameStore=new e(dojo.mixin({browser:i},n)),t.resolve({success:!0})})}else this.nameStore=new DojoDataStore({store:new NamesLazyTrieDojoDataStore({browser:this,namesTrie:new LazyTrie(n.url,"lazy-{Chunk}.json"),stopPrefixes:n.stopPrefixes,resultLimit:n.resultLimit||15,tooManyMatchesMessage:n.tooManyMatchesMessage})}),t.resolve({success:!0})})},compareReferenceNames:function(t,e){return this.regularizeReferenceName(t).localeCompare(this.regularizeReferenceName(e))},regularizeLocation:function(t){var e=this.findReferenceSequence(t.ref||t.objectName);return e&&(t.ref=e.name),t},regularizeReferenceName:function(t){return this.config.exactReferenceSequenceNames?t:t=t.toLowerCase().replace(/^chro?m?(osome)?/,"chr").replace(/^co?n?ti?g/,"ctg").replace(/^scaff?o?l?d?/,"scaffold").replace(/^([a-z]*)0+/,"$1").replace(/^(\d+)$/,"chr$1")},initView:function(){var t=this;return this._milestoneFunction("initView",function(e){var n=this;dojo.addClass(this.container,"jbrowse"),dojo.addClass(document.body,this.config.theme||"tundra");var i=dojo.create("div",{style:{overflow:"hidden"}},this.container),r=this.browserMeta(),o=new InfoDialog({title:"About "+r.title,content:r.description,className:"about-dialog"}),s=dojo.create("div",{className:this.config.show_nav?"menuBar":"topLink"});t.menuBar=s,this.config.show_menu&&(this.config.show_nav?i:this.container).appendChild(s);var a=dojo.create("div",{className:"overview",id:"overview"},i);function l(){new HelpDialog(lang.mixin(t.config.quickHelp||{},{browser:t})).show()}if(this.overviewDiv=a,this.config.show_overview||(a.style.cssText="display: none"),Util.isElectron()&&!this.config.hideGenomeOptions?(this.addGlobalMenuItem(this.config.classicMenu?"file":"dataset",new dijitMenuItem({id:"menubar_dataset_file",label:"Open sequence file",iconClass:"dijitIconFolderOpen",onClick:dojo.hitch(this,"openFastaElectron")})),this.addGlobalMenuItem(this.config.classicMenu?"file":"dataset",new dijitMenuItem({id:"menubar_dataset_directory",label:"Open data directory",iconClass:"dijitIconFolderOpen",onClick:function(){new OpenDirectoryDialog({browser:t,setCallback:dojo.hitch(t,"openDirectoryElectron")}).show()}})),this.addGlobalMenuItem(this.config.classicMenu?"file":"dataset",new dijitMenuItem({id:"menubar_dataset_save",label:"Save session",iconClass:"dijitIconSave",onClick:dojo.hitch(this,"saveData")})),this.addGlobalMenuItem(this.config.classicMenu?"file":"dataset",new dijitMenuItem({id:"menubar_dataset_home",label:"Return to main menu",iconClass:"dijitIconTask",onClick:dojo.hitch(this,function(){var e=t.container||document.body;t.welcomeScreen(e)})}))):this.config.hideGenomeOptions||this.addGlobalMenuItem(this.config.classicMenu?"file":"dataset",new dijitMenuItem({id:"menubar_dataset_open",label:"Open sequence file",iconClass:"dijitIconFolderOpen",onClick:dojo.hitch(this,"openFasta")})),this.config.show_nav&&(this.navbox=this.createNavBox(i),this.config.classicMenu?(this.config.datasets&&!this.config.dataset_id&&console.warn("In JBrowse configuration, datasets specified, but dataset_id not set.  Dataset selector will not be shown."),this.config.datasets&&this.config.dataset_id?this.renderDatasetSelect(s):(this.poweredByLink=dojo.create("a",{className:"powered_by",innerHTML:this.browserMeta().title,title:"powered by JBrowse"},s),t.poweredBy_clickHandle=dojo.connect(this.poweredByLink,"onclick",dojo.hitch(o,"show")))):this.renderDatasetSelect(s),this.addGlobalMenuItem("file",new dijitMenuItem({id:"menubar_fileopen",label:"Open track file or URL",iconClass:"dijitIconFolderOpen",onClick:dojo.hitch(this,"openFileDialog")})),this.addGlobalMenuItem("file",new dijitMenuSeparator),this.fileDialog=new FileDialog({browser:this}),this.addGlobalMenuItem("file",new dijitMenuItem({id:"menubar_combotrack",label:"Add combination track",iconClass:"dijitIconSample",onClick:dojo.hitch(this,"createCombinationTrack")})),this.renderGlobalMenu("file",{text:this.config.classicMenu?"File":"Track"},s),this.addGlobalMenuItem("view",new dijitMenuItem({id:"menubar_sethighlight",label:"Set highlight",iconClass:"dijitIconFilter",onClick:function(){new SetHighlightDialog({browser:t,setCallback:dojo.hitch(t,"setHighlightAndRedraw")}).show()}})),this._highlightClearButton=new dijitMenuItem({id:"menubar_clearhighlight",label:"Clear highlight",iconClass:"dijitIconFilter",onClick:dojo.hitch(this,function(){var t=this.getHighlight();t&&(this.clearHighlight(),this.view.redrawRegion(t))})}),this._updateHighlightClearButton(),this.subscribe("/jbrowse/v1/n/globalHighlightChanged",dojo.hitch(this,"_updateHighlightClearButton")),this.addGlobalMenuItem("view",this._highlightClearButton),this.addGlobalMenuItem("view",new dijitMenuItem({label:"Resize quant. tracks",id:"menubar_settrackheight",title:"Set all visible quantitative tracks to a new height",iconClass:"jbrowseIconVerticalResize",onClick:function(){new SetTrackHeightDialog({setCallback:function(e){var n=t.view.visibleTracks();array.forEach(n,function(t){/\b(XYPlot|Density)/.test(t.config.type)&&(t.trackHeightChanged=!0,t.updateUserStyles({height:e}))})}}).show()}})),this.config.disableSearch||this.addGlobalMenuItem("view",new dijitMenuItem({label:"Search features",id:"menubar_search",title:"Search for features",onClick:function(){var t=dojo.mixin(dojo.clone(n.config.names||{}),n.config.autocomplete||{}),e=t.dialog||"JBrowse/View/Dialog/Search";dojo.global.require([e],function(e){new e(dojo.mixin({browser:n},t)).show()})}})),this.renderGlobalMenu("view",{text:"View"},s),this.renderGlobalMenu("options",{text:"Options",title:"configure JBrowse"},s)),this.config.show_nav&&(this.addGlobalMenuItem("help",new dijitMenuItem({id:"menubar_about",label:"About",onClick:dojo.hitch(o,"show")})),this.setGlobalKeyboardShortcut("?",l),this.addGlobalMenuItem("help",new dijitMenuItem({id:"menubar_generalhelp",label:"General",iconClass:"jbrowseIconHelp",onClick:l})),this.renderGlobalMenu("help",{},s),!this.config.classicMenu)){var u=lang.getObject("config.datasets."+this.config.dataset_id+".name",!1,this);this.menuBarDatasetName=dojo.create("div",{className:"dataset-name",innerHTML:u,title:"name of current dataset",style:{display:u?"inline-block":"none"}},s)}if(this.config.show_nav&&this.config.show_tracklist&&this.config.show_overview&&!Util.isElectron()){var c=this.makeShareLink();c&&s.appendChild(c)}else if(Util.isElectron()){var d=this.makeSnapLink();d&&s.appendChild(d)}else this.config.show_fullviewlink&&s.appendChild(this.makeFullViewLink());this.viewElem=document.createElement("div"),this.viewElem.className="dragWindow",this.container.appendChild(this.viewElem),this.containerWidget=new dijitBorderContainer({liveSplitters:!1,design:"sidebar",gutters:!1},this.container);new dijitContentPane({region:"top"},i);function h(){var e=t.makeCurrentViewURL();t.config.updateBrowserURL&&window.history&&window.history.replaceState&&window.history.replaceState({},"",e),t.config.update_browser_title&&(document.title=t.browserMeta().title+" "+t.view.visibleRegionLocString())}this.view=this.viewElem.view=new GenomeView({browser:this,elem:this.viewElem,config:this.config.view,stripeWidth:250,refSeq:this.refSeq,zoomLevel:.005}),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"),dojo.connect(this,"onCoarseMove",h),this.subscribe("/jbrowse/v1/n/tracks/visibleChanged",h),this.subscribe("/jbrowse/v1/n/globalHighlightChanged",h),this.afterMilestone("loadRefSeqs",dojo.hitch(this,function(){this.afterMilestone("initTrackMetadata",dojo.hitch(this,function(){this.createTrackList().then(dojo.hitch(this,function(){this.containerWidget.startup(),this.onResize(),on(document.body,"keypress",dojo.hitch(this,"globalKeyHandler")),this._initEventRouting(),e.resolve({success:!0})}))}))}))})},createCombinationTrack:function(){void 0===this._combinationTrackCount&&(this._combinationTrackCount=0);var t=new Deferred,e={browser:this,refSeq:this.refSeq,type:"JBrowse/Store/SeqFeature/Combination"},n=this.addStoreConfig(void 0,e);e.name=n,this.getStore(n,function(e){t.resolve(!0)});var i=this;t.promise.then(function(){var t={type:"JBrowse/View/Track/Combination",label:"combination_track"+i._combinationTrackCount++,key:"Combination Track "+i._combinationTrackCount,metadata:{Description:"Drag-and-drop interface that creates a track out of combinations of other tracks."},store:n};i.publish("/jbrowse/v1/v/tracks/new",[t]),i.publish("/jbrowse/v1/v/tracks/show",[t])})},renderDatasetSelect:function(t){var e=this;if(this.config.classicMenu){var n=this.config.datasets||{},i=[];for(var r in n)/^_/.test(r)||i.push(Object.assign({id:r},n[r]));var o=new dijitComboBox({name:"dataset",className:"dataset_select",value:this.config.datasets[this.config.dataset_id].name,store:new dojoMemoryStore({data:i}),onChange:function(t){if(!t)return!1;var n=i.find(function(e){return e.name===t}).id,r=(e.config.datasets||{})[n];return r&&(window.location=r.url),!1}});o.placeAt(t),o.focusNode.onclick=function(){this.select()},this.config.datasetSelectorWidth&&(o.domNode.style.width=this.config.datasetSelectorWidth,o.focusNode.style.width=this.config.datasetSelectorWidth)}else{if(this.config.datasets&&this.config.dataset_id)for(var r in this.addGlobalMenuItem("dataset",new dijitMenuSeparator),this.config.datasets)if(!/^_/.test(r)){var s=this.config.datasets[r];this.addGlobalMenuItem("dataset",new dijitMenuItem({id:"menubar_dataset_bookmark_"+r,label:r==this.config.dataset_id?"<b>"+s.name+"</b>":s.name,iconClass:"dijitIconBookmark",onClick:dojo.hitch(s,function(){window.location=this.url})}))}this.renderGlobalMenu("dataset",{text:"Genome"},t)}},saveSessionDir:function(t){var e=electronRequire("fs"),n=this.config.electronData+"/sessions.json",i=[];try{i=JSON.parse(e.readFileSync(n,"utf8"))}catch(t){console.error(t)}var r=Util.replacePath(t);array.every(i,function(t){return t.session!=r})&&i.push({session:r}),e.writeFileSync(n,JSON.stringify(i,null,2),"utf8")},openDirectoryElectron:function(t){this.saveSessionDir(t),window.location="?data="+Util.replacePath(t)},openConfig:function(t){if(confirm("If you have opened any new tracks, please save them before continuing. Are you sure you want to continue?")){var e=electronRequire("fs"),n=this.config.dataRoot,i=JSON.parse(e.readFileSync(n+"/trackList.json","utf8"));if(i.plugins=i.plugins||{},lang.isArray(i.plugins)){var r={};array.forEach(i.plugins,function(t){r[t]={name:t,location:n+"/"+t}}),i.plugins=r}array.forEach(t,function(t){var e=t.match(/\/(\w+)$/)[1];i.plugins[e]={location:t,name:e}});try{e.writeFileSync(n+"/trackList.json",JSON.stringify(i,null,2))}catch(t){console.error("Failed to save trackList.json",t)}window.location.reload()}},saveData:function(){if(confirm("This will overwrite tracks and config data in your data directory. Are you sure you want to continue?")){var t=electronRequire("fs"),e=this.config.dataRoot,n=array.map(this.config.tracks,function(t){var e=lang.clone(t);return this.getStore(e.store,lang.hitch(this,function(t){e.storeClass=t.config.type,e.urlTemplate||(lang.mixin(e,t.saveStore()),e.histograms&&e.histograms.store&&this.getStore(e.histograms.store,function(t){lang.mixin(e.histograms,t.saveStore())})),delete e.store})),e},this),i=(array.filter(Util.uniq(this.config.plugins),function(t){return"RegexSequenceSearch"!=t}),{});lang.isArray(this.config.plugins)?array.forEach(this.config.plugins,function(t){i[t]="object"==(void 0===t?"undefined":_typeof(t))?t:{name:t}}):i=this.config.plugins;var r={tracks:n,refSeqs:this.config.refSeqs,refSeqOrder:this.config.refSeqOrder,plugins:i};try{t.writeFileSync(Util.unReplacePath(e)+"/trackList.json",JSON.stringify(r,null,2))}catch(t){alert("Unable to save track data"),console.error(t)}}},openFastaElectron:function(){this.fastaFileDialog=this.fastaFileDialog||new FastaFileDialog({browser:this});electronRequire("electron").remote.app;var t=electronRequire("fs");electronRequire("path");this.fastaFileDialog.show({openCallback:dojo.hitch(this,function(e){var n=e.trackConfs||[];if(n.length){var i={tracks:[{label:n[0].label,key:n[0].key,type:"SequenceTrack",category:"Reference sequence",useAsRefSeqStore:!0,chunkSize:2e4}],refSeqs:o,refSeqOrder:e.refSeqOrder};if(n[0].store.fasta&&n[0].store.fai){var r=Util.replacePath(n[0].store.fasta.url),o=Util.replacePath(n[0].store.fai.url);i.tracks[0].storeClass="JBrowse/Store/SeqFeature/IndexedFasta",i.tracks[0].urlTemplate=r,i.tracks[0].faiUrlTemplate=o,i.refSeqs=o}else if("JBrowse/Store/SeqFeature/TwoBit"==n[0].store.type){var s=Util.replacePath(n[0].store.blob.url);i.tracks[0].storeClass="JBrowse/Store/SeqFeature/TwoBit",i.tracks[0].urlTemplate=s,i.refSeqs=s}else{r=Util.replacePath(n[0].store.fasta.url);try{if(t.statSync(r).size>1e8)return void alert("Unindexed file too large. You must have an index file (.fai) for sequence files larger than 100 MB.")}catch(t){console.error(t)}i.tracks[0].storeClass="JBrowse/Store/SeqFeature/UnindexedFasta",i.tracks[0].urlTemplate=r,i.refSeqs=r}var a=this.config.electronData;t.existsSync(a)||t.mkdirSync(a),a+="/"+n[0].label;try{t.existsSync(a)||t.mkdirSync(a),t.writeFileSync(a+"/trackList.json",JSON.stringify(i,null,2)),t.closeSync(t.openSync(a+"/tracks.conf","w")),this.saveSessionDir(a),window.location=window.location.href.split("?")[0]+"?data="+Util.replacePath(a)}catch(t){alert("Failed to save session"),console.error(t)}}})})},openFasta:function(){var t=this;this.fastaFileDialog=this.fastaFileDialog||new FastaFileDialog({browser:this}),this.fastaFileDialog.show({openCallback:function(e){return new Promise(function(n,i){var r=e.trackConfs||[],o=_slicedToArray(r,1)[0];if(!o)return i("no track configs");var s=o.store;if(!s)return i("no store config");dojo.global.require([s.type],function(r){if(/\/Unindexed/i.test(s.type)&&s.fasta&&s.fasta.size>1e8)return alert("Unindexed file too large. You must have an index file (.fai) for sequence files larger than 100 MB."),i("sequence file too large");new r(Object.assign({browser:t},s)).getRefSeqs(function(i){t.teardown();var r=new t.constructor({refSeqs:{data:i},refSeqOrder:e.refSeqOrder});r.afterMilestone("completely initialized",function(){s.name="refseqs",r.addStoreConfig(s.name,s),o.store="refseqs",r.publish("/jbrowse/v1/v/tracks/new",[o])}),n()},function(e){t.fatalError("Error getting refSeq: "+e),i(e)})})})}})},browserMeta:function(){var t=this.config.aboutThisBrowser||{};t.title=t.title||"JBrowse";var e=this.version;return t.description?t.description+='<div class="powered_by">Powered by <a target="_blank" href="http://jbrowse.org">JBrowse '+e+"</a>.</div>":t.description='<div class="default_about">  <img class="logo" src="'+this.resolveUrl("img/JBrowseLogo_small.png")+'">  <h1>JBrowse '+e+'</h1>  <div class="tagline">A next-generation genome browser<br> built with JavaScript and HTML5.</div>  <a class="mainsite" target="_blank" href="http://jbrowse.org">JBrowse website</a>  <div class="gmod">JBrowse is a <a target="_blank" href="http://gmod.org">GMOD</a> project.</div>  <div class="copyright">'+JSON.parse(packagejson).copyright+"</div>"+(Object.keys(this.plugins).length>1&&!this.config.noPluginsForAboutBox?'  <div class="loaded-plugins">Loaded plugins<ul class="plugins-list">'+array.map(Object.keys(this.plugins),function(t){var e=this.plugins[t];return"<li>"+(e.url?'<a href="'+e.url+'">':"")+e.name+(e.url?"</a>":"")+(e.author?" ("+e.author+")":"")+"</li>"},this).join("")+"  </ul></div>":"")+"</div>",t},registerTrackType:function(t){var e=this.getTrackTypes(),n=t.type,i=t.defaultForStoreTypes||[];t.label;e.knownTrackTypes.push(n),t.label&&(e.trackTypeLabels[n]=t.label);var r={};e.knownTrackTypes=array.filter(e.knownTrackTypes,function(t){var e=r[t];return r[t]=!0,!e}),array.forEach(i,function(t){e.trackTypeDefaults[t]=n}),this._knownTrackTypes=e},getTrackTypes:function(){return this._knownTrackTypes||(this._knownTrackTypes={trackTypeDefaults:{"JBrowse/Store/SeqFeature/BAM":"JBrowse/View/Track/Alignments2","JBrowse/Store/SeqFeature/CRAM":"JBrowse/View/Track/Alignments2","JBrowse/Store/SeqFeature/NCList":"JBrowse/View/Track/CanvasFeatures","JBrowse/Store/SeqFeature/BigWig":"JBrowse/View/Track/Wiggle/XYPlot","JBrowse/Store/SeqFeature/VCFTabix":"JBrowse/View/Track/CanvasVariants","JBrowse/Store/SeqFeature/VCFTribble":"JBrowse/View/Track/CanvasVariants","JBrowse/Store/SeqFeature/GFF3":"JBrowse/View/Track/CanvasFeatures","JBrowse/Store/SeqFeature/BigBed":"JBrowse/View/Track/CanvasFeatures","JBrowse/Store/SeqFeature/GFF3Tabix":"JBrowse/View/Track/CanvasFeatures","JBrowse/Store/SeqFeature/BED":"JBrowse/View/Track/CanvasFeatures","JBrowse/Store/SeqFeature/BEDTabix":"JBrowse/View/Track/CanvasFeatures","JBrowse/Store/SeqFeature/GTF":"JBrowse/View/Track/CanvasFeatures","JBrowse/Store/SeqFeature/StaticChunked":"JBrowse/View/Track/Sequence","JBrowse/Store/SeqFeature/UnindexedFasta":"JBrowse/View/Track/Sequence","JBrowse/Store/SeqFeature/IndexedFasta":"JBrowse/View/Track/Sequence","JBrowse/Store/SeqFeature/TwoBit":"JBrowse/View/Track/Sequence"},knownTrackTypes:["JBrowse/View/Track/Alignments","JBrowse/View/Track/Alignments2","JBrowse/View/Track/FeatureCoverage","JBrowse/View/Track/SNPCoverage","JBrowse/View/Track/HTMLFeatures","JBrowse/View/Track/CanvasFeatures","JBrowse/View/Track/HTMLVariants","JBrowse/View/Track/CanvasVariants","JBrowse/View/Track/Wiggle/XYPlot","JBrowse/View/Track/Wiggle/Density","JBrowse/View/Track/Sequence"],trackTypeLabels:{}}),this._knownTrackTypes},openFileDialog:function(){this.fileDialog.show({openCallback:dojo.hitch(this,function(t){var e=t.trackConfs||[];e.length&&(array.forEach(e,function(t){var e=t.store;if(e&&"object"==(void 0===e?"undefined":_typeof(e))){delete t.store;var n=this.addStoreConfig(e.name,e);t.store=n}if((e=t.histograms&&t.histograms.store)&&"object"==(void 0===e?"undefined":_typeof(e))){delete t.histograms.store;n=this.addStoreConfig(e.name,e);t.histograms.store=n}},this),this.publish("/jbrowse/v1/v/tracks/new",e),"openImmediately"==t.trackDisposition&&this.publish("/jbrowse/v1/v/tracks/show",e))})})},addTracks:function(t){this._addTrackConfigs(t)},replaceTracks:function(t){this._replaceTrackConfigs(t)},deleteTracks:function(t){this._deleteTrackConfigs(t)},renderGlobalMenu:function(t,e,n){this.afterMilestone("initView",function(){var i=this.makeGlobalMenu(t);if(i){e=dojo.mixin({className:t,innerHTML:'<span class="icon"></span> '+(e.text||Util.ucFirst(t)),dropDown:i,id:"dropdownbutto