@galaxyproject/igv 0.0.16 → 0.0.17

package/package.json

@@ -1,6 +1,6 @@
 {
     "name": "@galaxyproject/igv",
-    "version": "0.0.16",
+    "version": "0.0.17",
     "type": "module",
     "license": "MIT",
     "files": [

package/static/index.js

@@ -2449,4 +2449,4 @@ ${l.map(p=>`    ${p}`).join(`
 `)}`);const d=a.filter(p=>p.file===void 0);let u=1;for(let p of d)p.order===void 0&&(p.order=u++);const f=d.filter(p=>p.hidden===!0);for(const p of f)await ji(p,this.genome).getFeatures({chr:"1",start:0,end:Number.MAX_SAFE_INTEGER});await this.loadTrackList(d)}cleanHouseForSession(){for(let t of this.trackViews)t.removeDOMFromColumnContainer();this.columnContainer.querySelectorAll(".igv-axis-column, .igv-column-shim, .igv-column, .igv-sample-info-column, .igv-sample-name-column, .igv-scrollbar-column, .igv-track-drag-column, .igv-gear-menu-column").forEach(t=>t.remove()),this.trackViews=[],this.circularView&&this.circularView.clearChords()}async loadReference(e,t){this.removeAllTracks(),this.roiManager.clearROIs(),this.navbar.setEnableTrackSelection(!1);let r;e.gbkURL?r=await z_(e.gbkURL):r=await Xm.createGenome(e,this);const n=this.genome===void 0||this.genome.id!==r.id;this.genome=r,this.navbar.updateGenome(r);let o=t||r.initialLocus;return Array.isArray(o)&&(o=o.join(" ")),await this.search(o,!0)||(console.error(`Cannot set initial locus ${o}`),o!==r.initialLocus&&await this.search(r.initialLocus)),n&&(this.fireEvent("genomechange",[{genome:r}]),this.circularView&&this.circularView.setAssembly({name:this.genome.id,id:this.genome.id,chromosomes:wF(this.genome)})),r}async loadGenome(e){e.genarkAccession&&(e.url=$_(e.genarkAccession)),e.url&&(Yt(e.url)&&e.url.endsWith("/hub.txt")?(e.hubURL=e.url,delete e.url):JZ(e.url)==="gbk"&&(e.gbkURL=e.url,delete e.url));let t;e.hubURL||e.url&&Yt(e.url)&&e.url.endsWith("/hub.txt")?t=(await mu(e.hubURL||e.url)).getGenomeConfig():Yt(e)||!(e.url||e.fastaURL||e.twoBitURL||e.gbkURL)?t=await ci.expandReference(this.alert,e):t=e,await this.loadReference(t);let n;return t.gbkURL||t.format==="gbk"?n=[{name:"Annotations",format:"gbk",url:t.gbkURL}]:n=t.tracks||[],n.filter(s=>s.type==="sequence").length===0&&n.push({type:"sequence",order:gu}),await this.loadTrackList(n),this.genome}updateUIWithReferenceFrameList(){const e=this.referenceFrameList;this.isMultiLocusWholeGenomeView()||ci.isWholeGenomeView(e[0].chr),this.navbar.navbarDidResize(),Ag(this.trackViews,this.doShowTrackLabels),this.doShowCenterLine&&ci.isWholeGenomeView(e[0].chr)&&this.navbar.centerLineButton.boundMouseClickHandler(),this.doShowCursorGuide&&ci.isWholeGenomeView(e[0].chr)&&this.navbar.cursorGuideButton.boundMouseClickHandler(),this.setCenterLineAndCenterLineButtonVisibility(ci.isWholeGenomeView(e[0].chr))}setCenterLineAndCenterLineButtonVisibility(e){e?this.navbar.centerLineButton.setVisibility(!1):this.navbar.centerLineButton.setVisibility(this.config.showCenterGuideButton);for(let t of this.centerLineList)e?this.setCenterLineVisibility(!e):this.setCenterLineVisibility(this.doShowCenterLine)}setTrackLabelVisibility(e){Ag(this.trackViews,e)}setROITableVisibility(e){e===!0?this.roiManager.presentTable():this.roiManager.dismissTable()}setCursorGuideVisibility(e){e?this.cursorGuide.show():this.cursorGuide.hide()}setCustomCursorGuideMouseHandler(e){this.cursorGuide.customMouseHandler=e}setCenterLineVisibility(e){for(let t of this.centerLineList)e===!0?(t.show(),t.repaint()):t.hide()}async loadTrackList(e){let t=this.trackViews.length+1;for(let o of e)o.order===void 0&&(o.order=t++);const r=[];for(const o of e)r.push(at(this,Bu,OA).call(this,o));const n=await Promise.all(r);return this.trackViews.some(({track:o})=>o.selected)&&this.navbar.setEnableTrackSelection(!0),this.reorderTracks(),await hd.call(this),this.fireEvent("trackorderchanged",[this.getTrackOrder()]),n}async loadTrack(e){const t=await this.loadTrackList([e]);return e.autoscaleGroup&&this.updateViews(),t[0]}async addTrack(e){e.order===void 0&&(e.order=this.trackViews.length);const t=new Kp(this,this.columnContainer,e);if(this.trackViews.push(t),Ag(this.trackViews,this.doShowTrackLabels),typeof e.postInit=="function")try{t.startSpinner(),await e.postInit()}finally{t.stopSpinner()}return typeof e.hasSamples=="function"&&e.hasSamples()&&(this.sampleInfo.hasAttributes()&&this.sampleInfoControl.setButtonVisibility(!0),this.config.showSampleNameButton!==!1&&this.sampleNameControl.show()),e.trackView.enableTrackSelection(this.navbar.getEnableTrackSelection()),e}async loadROI(e){return this.roiManager.loadROI(e,this.genome)}clearROIs(){this.roiManager.clearROIs()}async getUserDefinedROIs(){if(this.roiManager){const e=this.roiManager.getUserDefinedROISet();if(e===void 0)return[];const t=await e.getAllFeatures(),r=[];for(let n of Object.values(t))r.push(...n);return r}else return[]}getRulerTrackView(){const e=this.trackViews.filter(({track:t})=>t.id==="ruler");return e.length>0?e[0]:void 0}async createTrack(e){let t=await Sz(e.url||e.fastaURL);if(Yt(t)&&(t=t.trim()),t)if(e.format)e.format=e.format.toLowerCase();else if(e.fastaURL)e.format="fasta";else if(e.sourceType)e.sourceType==="htsget"&&await f2.inferFormat(e);else{const o=await ux(e);o&&(e.format=o)}e.type&&ox(e);let r=e.type?e.type.toLowerCase():void 0;if(!r){if(e.format){if(e.format==="hic"){const o=new DA(e);if(await o.readHeaderAndFooter(),o.chromosomeIndexMap.celltype)r="shoebox",e._hicFile=o;else throw Error("'.hic' files not supported")}else if(r=nx(e.format),r==="bedtype"){const o=ji(e,this.genome);e._featureSource=o;const s=await o.trackType();s&&IX().has(s)?r=s:r="annotation"}}else throw Error(`Unrecognized track:  ${JSON.stringify(e)}`);e.type=r}if(this.trackDefaults&&r){const o=this.trackDefaults[r];if(o)for(let s in o)o.hasOwnProperty(s)&&e[s]===void 0&&(e[s]=o[s])}const n=EX(r,e,this);if(n===void 0)this.alert.present(new Error(`Error creating track.  Could not determine track type for file: ${e.url||e}`),void 0);else return e.roi&&e.roi.length>0&&(n.roiSets=e.roi.map(o=>new vZ(o,this.genome))),n}reorderTracks(){this.trackViews.sort(function(t,r){const n=a=>a.track.id==="ideogram"?1:a.track.id==="ruler"?2:3,o=n(t),s=n(r);if(o===s){const a=t.track.order||0,c=r.track.order||0;return a-c}else return o-s});for(let{axis:t,viewports:r,sampleInfoViewport:n,sampleNameViewport:o,outerScroll:s,dragHandle:a,gearContainer:c}of this.trackViews){t.remove();for(let{viewportElement:l}of r)l.parentNode.removeChild(l);n.viewport.remove(),o.viewport.remove(),s.remove(),a.remove(),c.remove()}const e=this.columnContainer.querySelectorAll(".igv-column");for(let{axis:t,viewports:r,sampleInfoViewport:n,sampleNameViewport:o,outerScroll:s,dragHandle:a,gearContainer:c}of this.trackViews){this.columnContainer.querySelector(".igv-axis-column").appendChild(t);for(let l=0;l<e.length;l++){const{viewportElement:h}=r[l];e[l].appendChild(h)}this.columnContainer.querySelector(".igv-sample-info-column").appendChild(n.viewport),this.columnContainer.querySelector(".igv-sample-name-column").appendChild(o.viewport),this.columnContainer.querySelector(".igv-scrollbar-column").appendChild(s),this.columnContainer.querySelector(".igv-track-drag-column").appendChild(a),this.columnContainer.querySelector(".igv-gear-menu-column").appendChild(c)}}getTrackOrder(){return this.trackViews.filter(e=>e.track&&e.track.name).map(e=>e.track.name)}getSelectedTrackViews(){return this.trackViews.filter(e=>e.track.selected===!0)}removeTrackByName(e){const t=this.trackViews.slice();for(let r of t)e===r.track.name&&this.removeTrack(r.track)}removeTrack(e){for(let t of this.trackViews)if(e===t.track){this._removeTrack(t.track);break}}_removeTrack(e){e.disposed||(this.trackViews.splice(this.trackViews.indexOf(e.trackView),1),this.fireEvent("trackremoved",[e]),this.fireEvent("trackorderchanged",[this.getTrackOrder()]),e.trackView&&e.trackView.dispose())}removeAllTracks(){const e=this.trackViews;this.trackViews=[];for(let t of e)t.track.id!=="ruler"&&t.track.id!=="ideogram"?(this.fireEvent("trackremoved",[t.track]),t.dispose()):this.trackViews.push(t)}get ideogramTrackView(){return this.trackViews[0]}get rulerTrackView(){return this.trackViews[1]}findTracks(e,t){let r=typeof e=="function"?n=>e(n.track):n=>t===n.track[e];return this.trackViews.filter(r).map(n=>n.track)}get tracks(){return this.trackViews.map(e=>e.track).filter(e=>e!==void 0)}setTrackHeight(e){this.trackHeight=e,this.trackViews.forEach(function(t){t.setTrackHeight(e)})}async visibilityChange(){this.layoutChange()}async layoutChange(){if(this.referenceFrameList.find(t=>t.bpPerPixel<0)){const t=this.calculateViewportWidth(this.referenceFrameList.length);for(let r of this.referenceFrameList)r.bpPerPixel=(r.end-r.start)/t}this.referenceFrameList&&this.navbar.navbarDidResize(),hd.call(this),this.roiManager.updateROIRegionPositions(),await this.updateViews()}async updateViews(){const e=this.trackViews;this.updateLocusSearchWidget();for(const{bpPerPixel:t,chr:r,start:n}of this.referenceFrameList)t<=b2&&await this.genome.getSequence(r,n,n+1);for(const t of this.centerLineList)t.repaint();if(this.dragObject)for(const t of e)await t.updateViews();else{const t={},r=[];for(const n of e)if(n.track.autoscaleGroup){const o=n.track.autoscaleGroup;t[o]||(t[o]=[]),t[o].push(n)}else r.push(n);if(Object.entries(t).length>0)for(const[n,o]of Object.entries(t)){const s=await Promise.all(o.map(c=>c.getInViewFeatures())),a=Sc(s.flat());for(const c of o)c.track.dataRange=Object.assign({},a),c.track.autoscale=!1;await Promise.all(o.map(c=>c.updateViews()))}await Promise.all(r.map(n=>n.updateViews()))}}repaintViews(){for(let e of this.trackViews)e.repaintViews()}updateLocusSearchWidget(){if(!this.referenceFrameList)return;const e=this.referenceFrameList,t=this.calculateViewportWidth(this.referenceFrameList.length);for(let o of e)o.end=o.start+o.bpPerPixel*t;const r=this.referenceFrameList.map(o=>o.getLocusString()).join(" "),n=e.length===1?this.genome.getChromosomeDisplayName(this.referenceFrameList[0].chr):"";this.navbar.updateLocus(r,n),this.fireEvent("locuschange",[this.referenceFrameList])}calculateViewportWidth(e){let{width:t}=this.columnContainer.getBoundingClientRect();return t-=yj+this.getSampleInfoViewportWidth()+this.getSampleNameViewportWidth()+KZ+YZ+XZ,t-=ZZ*(e-1),Math.floor(t/e)}updateReferenceFrames(e){for(const t of this.referenceFrameList)t.updateForViewportWidth(e)}updateViewportElements(e){for(let t=0;t<this.referenceFrameList.length;t++){for(const{viewports:r}of this.trackViews)r[t].setWidth(e);for(const{sampleInfoViewport:r}of this.trackViews)r.setWidth(this.getSampleInfoColumnWidth()),r.repaint()}}async syncUIState(){this.updateUIWithReferenceFrameList(),await this.updateViews(!0)}minimumBases(){return this.config.minimumBases}zoomIn(){this.zoomWithScaleFactor(.5)}zoomOut(){this.zoomWithScaleFactor(2)}async zoomWithScaleFactor(e,t,r){if(!this.referenceFrameList)return;const n=this.calculateViewportWidth(this.referenceFrameList.length);let o=r?[r]:this.referenceFrameList;for(let s of o)s.zoomWithScaleFactor(this,e,n,t)}async addMultiLocusPanel(e,t,r,n){if(!this.referenceFrameList)return;const o=this.calculateViewportWidth(1+this.referenceFrameList.length),s=this.calculateViewportWidth(this.referenceFrameList.length)/this.calculateViewportWidth(1+this.referenceFrameList.length);for(let f of this.referenceFrameList)f.bpPerPixel*=s;const a=(r-t)/o,c=new SA(this.genome,e,t,r,a),l=n?this.referenceFrameList.indexOf(n):this.referenceFrameList.length-1,h=1+l,{viewportElement:d}=this.trackViews[0].viewports[l],u=Fg.insertAfter(d.parentElement);if(this.fireEvent("didchangecolumnlayout"),h===this.referenceFrameList.length){this.referenceFrameList.push(c);for(let f of this.trackViews){const p=Dm(f,u,c);f.viewports.push(p)}}else{this.referenceFrameList.splice(h,0,c);for(let f of this.trackViews){const p=Dm(f,u,c);f.viewports.splice(h,0,p)}}this.centerLineList=this.createCenterLineList(this.columnContainer),hd.call(this),await this.updateViews(!0)}createCenterLineList(e){const t=e.querySelectorAll(".igv-center-line");for(let o=0;o<t.length;o++)t[o].remove();const r=[],n=e.querySelectorAll(".igv-column");for(let o=0;o<n.length;o++)r.push(new fZ(this,this.referenceFrameList[o],n[o]));return r}async removeMultiLocusPanel(e){const t=this.referenceFrameList.indexOf(e),{viewportElement:r}=this.trackViews[0].viewports[t];Fg.removeColumnAtIndex(t,r.parentElement),this.fireEvent("didchangecolumnlayout");for(let{viewports:o}of this.trackViews)o[t].dispose(),o.splice(t,1);if(this.referenceFrameList.splice(t,1),this.referenceFrameList.length===1&&this.getRulerTrackView())for(let o of this.getRulerTrackView().viewports)o.dismissLocusLabel();const n=this.calculateViewportWidth(1+this.referenceFrameList.length)/this.calculateViewportWidth(this.referenceFrameList.length);await this.rescaleForMultiLocus(n)}async gotoMultilocusPanel(e){const t=this.referenceFrameList.indexOf(e);this.columnContainer.querySelectorAll(".igv-column").forEach((n,o)=>{o===t||n.remove()}),this.columnContainer.querySelectorAll(".igv-column-shim").forEach(n=>n.remove());for(let n of this.trackViews){const o=n.viewports[t];n.viewports.filter((s,a)=>a!==t).forEach(s=>s.dispose()),n.viewports=[o]}const r=this.calculateViewportWidth(1);e.bpPerPixel=(e.end-e.start)/r,this.referenceFrameList=[e],this.trackViews.forEach(({viewports:n})=>n.forEach(o=>o.setWidth(r))),this.centerLineList=this.createCenterLineList(this.columnContainer),this.updateUIWithReferenceFrameList(),await this.updateViews(!0)}async rescaleForMultiLocus(e){const t=this.calculateViewportWidth(this.referenceFrameList.length);for(let r of this.referenceFrameList)r.bpPerPixel*=e;for(let{viewports:r}of this.trackViews)for(let n of r)n.setWidth(t);this.centerLineList=this.createCenterLineList(this.columnContainer),this.updateUIWithReferenceFrameList(),await this.updateViews()}async goto(e,t,r){await this.search(e+":"+t+"-"+r)}async search(e,t){const r=await dX(this,e);return this.updateLoci(r,t)}async updateLoci(e,t){if(e&&e.length>0){this.referenceFrameList=RX(e,this.genome,this.flanking,this.minimumBases(),this.calculateViewportWidth(e.length),this.isSoftclipped());for(let r of this.trackViews)r.removeViewportsFromColumnContainer();this.columnContainer.querySelectorAll(".igv-column-shim, .igv-column").forEach(r=>r.remove()),Fg.insertBefore(this.columnContainer.querySelector(".igv-sample-info-column"),this.referenceFrameList.length),this.fireEvent("didchangecolumnlayout");for(let r of this.trackViews)r.createViewports(this,this.columnContainer,this.referenceFrameList);return this.centerLineList=this.createCenterLineList(this.columnContainer),this.updateUIWithReferenceFrameList(),t||await this.updateViews(),!0}else return!1}async loadSampleInfo(e){await this.sampleInfo.loadSampleInfo(e),this.config.sampleinfo?this.config.sampleinfo.push(e):this.config.sampleinfo=[e];for(const{sampleInfoViewport:r}of this.trackViews)r.setWidth(this.getSampleInfoColumnWidth());this.findTracks(r=>typeof r.getSamples=="function").length>0&&(this.sampleInfoControl.performClickWithState(this,!0),this.sampleInfoControl.setButtonVisibility(!0));for(const{sampleInfoViewport:r}of this.trackViews)r.repaint()}async discardSampleInfo(){this.sampleInfo.discard();for(const{sampleInfoViewport:t}of this.trackViews)t.setWidth(this.getSampleInfoColumnWidth());this.findTracks(t=>typeof t.getSamples=="function").length>0&&(this.sampleInfoControl.performClickWithState(this,!1),this.sampleInfoControl.setButtonVisibility(!1));for(const{sampleInfoViewport:t}of this.trackViews)t.repaint();await this.layoutChange()}getSampleInfoColumnWidth(){if(this.sampleInfo.attributeCount){const t=this.findTracks(s=>typeof s.getSamples=="function").length>0,r=this.sampleInfo.hasAttributes(),n=this.sampleInfoControl.showSampleInfo;return t&&r&&n?this.sampleInfo.attributeCount*ea+zm:0}else return 0}on(e,t){this.eventHandlers[e]||(this.eventHandlers[e]=[]),this.eventHandlers[e].push(t)}un(e,t){this.off(e,t)}off(e,t){if(!e)this.eventHandlers={};else if(!t)this.eventHandlers[e]=[];else{const r=this.eventHandlers[e];if(!r||r.length===0)console.warn("No handlers to remove for event: "+e);else{const n=r.indexOf(t);n!==-1&&this.eventHandlers[e].splice(n,1)}}}fireEvent(e,t,r){const n=this.eventHandlers[e];if(n===void 0||n.length===0)return;const o=r||window;return n.map(function(a){return a.apply(o,t)})[0]}dispose(){this.removeEventHandlers();for(let e of this.trackViews)e.dispose();this.roiManager&&this.roiManager.dispose()}toJSON(){const e={version:IA()};if(this.showSampleNames!==void 0&&(e.showSampleNames=this.showSampleNames),this.sampleNameViewportWidth&&(e.sampleNameViewportWidth=this.sampleNameViewportWidth),e.reference=this.genome.toJSON(),e.reference.fastaURL instanceof File)throw new Error(`Error. Sessions cannot include local file references ${e.reference.fastaURL.name}.`);if(e.reference.indexURL instanceof File)throw new Error(`Error. Sessions cannot include local file references ${e.reference.indexURL.name}.`);const t=[];let r=this.trackViews[0];for(let{referenceFrame:l}of r.viewports){const h=l.getLocusString();t.push(h)}e.locus=t.length===1?t[0]:t;const n=this.roiManager.toJSON();n&&(e.roi=n,this.roiManager.showOverlays||(e.showROIOverlays=!1)),this.qtlSelections.isEmpty()||(e.qtlSelections=this.qtlSelections.toJSON());const o=[],s=[];for(const{track:l}of this.trackViews)try{let h;typeof l.getState=="function"?h=Qt.localFileInspection(l.getState()):l.config&&(h=Qt.localFileInspection(l.config)),h&&(h.browser&&delete h.browser,h.order=l.order,o.push(h))}catch(h){const d=`Track: ${l.name}: ${h}`;console.error(d),s.push(d)}if(s.length>0){let l=1,h="Errors encountered saving session: </br>";for(let d of s)h+=` (${l++}) ${d.toString()} <br/>`;throw Error(h)}e.tracks=o;const a=[];for(const l of o)for(const h of Object.keys(l))(h==="file"||h==="indexFile")&&a.push(l[h]);const c=[];if(this.config.sampleinfo){e.sampleinfo=this.config.sampleinfo;for(const l of this.sampleInfo.sampleInfoFiles){const h=Qt.localFileInspection({url:l});h.file&&c.push(h.file)}c.length>0&&a.push(...c)}return a.length>0&&alert(`This session includes reference(s) to local file(s):
 ${a.map(l=>`    ${l}`).join(`
 `)}
-Local files cannot be loaded automatically when a saved session is restored.`),e}compressedSession(){const e=JSON.stringify(this.toJSON());return dO(e)}sessionURL(){const e=window.location.href.slice(),t=e.indexOf("?");return(t>0?e.substring(0,t):e)+"?sessionURL=blob:"+this.compressedSession()}mouseDownOnViewport(e,t){var r;r=gc(e),this.vpMouseDown={viewport:t,lastMouseX:r.x,mouseDownX:r.x,lastMouseY:r.y,mouseDownY:r.y,referenceFrame:t.referenceFrame}}cancelTrackPan(){const e=this.dragObject;this.dragObject=void 0,this.isScrolling=!1,this.vpMouseDown=void 0,e&&e.viewport.referenceFrame.start!==e.start&&(this.updateViews(),this.fireEvent("trackdragend",[e.viewport]))}isTrackPanning(){return this.dragObject}isSoftclipped(){return this.trackViews.find(t=>t.track.showSoftClips===!0)!==void 0}startTrackDrag(e){this.dragTrack=e}updateTrackDrag(e){if(e&&this.dragTrack){const t=this.dragTrack,r=this.trackViews.indexOf(e),n=this.trackViews.indexOf(t),o=this.trackViews;o[r]=t,o[n]=e;const s=this.trackViews[r].track.order;this.trackViews[n].track.order=s;const a=o.length;let c=s;if(r<n)for(let l=r+1;l<a;l++){const h=o[l].track;if(h.order<=c)h.order=Math.min(Number.MAX_SAFE_INTEGER,c+1),c=h.order;else break}else for(let l=r-1;l>0;l--){const h=o[l].track;if(h.order>=c)h.order=Math.max(-Number.MAX_SAFE_INTEGER,c-1),c=h.order;else break}this.reorderTracks()}}endTrackDrag(){this.dragTrack?(this.dragTrack=void 0,this.fireEvent("trackorderchanged",[this.getTrackOrder()])):this.dragTrack=void 0}addEventHandlers(){this.addWindowResizeHandler(),this.addRootMouseUpHandler(),this.addRootMouseLeaveHandler(),this.addColumnContainerEventHandlers(),this.addKeyboardHandler()}removeEventHandlers(){this.removeWindowResizeHandler(),this.removeRootMouseUpHandler(),this.removeRootMouseLeaveHandler(),this.removeColumnContainerEventHandlers(),this.removeKeyboardHandler()}addWindowResizeHandler(){this.boundWindowResizeHandler=hd.bind(this),window.addEventListener("resize",this.boundWindowResizeHandler)}removeWindowResizeHandler(){window.removeEventListener("resize",this.boundWindowResizeHandler)}addRootMouseUpHandler(){this.boundRootMouseUpHandler=xl.bind(this),this.root.addEventListener("mouseup",this.boundRootMouseUpHandler)}removeRootMouseUpHandler(){this.root.removeEventListener("mouseup",this.boundRootMouseUpHandler)}addRootMouseLeaveHandler(){this.boundRootMouseLeaveHandler=xl.bind(this),this.root.addEventListener("mouseleave",this.boundRootMouseLeaveHandler)}removeRootMouseLeaveHandler(){this.root.removeEventListener("mouseleave",this.boundRootMouseLeaveHandler)}addColumnContainerEventHandlers(){this.boundColumnContainerMouseMoveHandler=qy.bind(this),this.boundColumnContainerTouchMoveHandler=qy.bind(this),this.boundColumnContainerMouseLeaveHandler=xl.bind(this),this.boundColumnContainerMouseUpHandler=xl.bind(this),this.boundColumnContainerTouchEndHandler=xl.bind(this),this.columnContainer.addEventListener("mousemove",this.boundColumnContainerMouseMoveHandler),this.columnContainer.addEventListener("touchmove",this.boundColumnContainerTouchMoveHandler),this.columnContainer.addEventListener("mouseleave",this.boundColumnContainerMouseLeaveHandler),this.columnContainer.addEventListener("mouseup",this.boundColumnContainerMouseUpHandler),this.columnContainer.addEventListener("touchend",this.boundColumnContainerTouchEndHandler)}removeColumnContainerEventHandlers(){this.columnContainer.removeEventListener("mousemove",this.boundColumnContainerMouseMoveHandler),this.columnContainer.removeEventListener("touchmove",this.boundColumnContainerTouchMoveHandler),this.columnContainer.removeEventListener("mouseleave",this.boundColumnContainerMouseLeaveHandler),this.columnContainer.removeEventListener("mouseup",this.boundColumnContainerMouseUpHandler),this.columnContainer.removeEventListener("touchend",this.boundColumnContainerTouchEndHandler)}addKeyboardHandler(){this.keyUpHandler=eJ.bind(this),document.addEventListener("keyup",this.keyUpHandler)}removeKeyboardHandler(){console.log("Remove handler"),document.addEventListener("keyup",this.keyUpHandler)}static uncompressSession(e){let t;if(e.indexOf("/gzip;base64")>0){t=Ho(e);let r="";for(let n of t)r+=String.fromCharCode(n);return r}else{let r=e.substring(5);return uO(r)}}createCircularView(e,t){return t=t===!0,this.circularView=kG(e,this),this.circularViewControl=new rh(this.navbar.toggleButtonContainer,this),this.circularView.setAssembly({name:this.genome.id,id:this.genome.id,chromosomes:wF(this.genome)}),this.circularViewVisible=t,this.circularView}get circularViewVisible(){return this.circularView!==void 0&&this.circularView.visible}set circularViewVisible(e){this.circularView&&(this.circularView.visible=e,this.circularViewControl.setState(e))}get overlayTrackButton(){return this.navbar.overlayTrackButton}get roiTableControl(){return this.navbar.roiTableControl}get sampleNameControl(){return this.navbar.sampleNameControl}get sampleInfoControl(){return this.navbar.sampleInfoControl}async blat(e){return ma({sequence:e,browser:this,name:"Blat",title:"Blat"})}};Bu=new WeakSet,OA=async function(e){Yt(e)&&(e=JSON.parse(e));let t;try{t=await this.createTrack(e)}catch(r){let n=r.message||r.error||r.toString();const o={401:"Access unauthorized",403:"Access forbidden",404:"Not found"};o.hasOwnProperty(n)&&(n=o[n]),n=`${n} : ${To(e.url)?e.url.name:e.url}`;const s=new Error(n);throw console.error(s),s}if(t)return await this.addTrack(t)};let Lc=Du;function JZ(i){let e;if(i instanceof File)e=i.name;else if(typeof i=="string")e=i;else throw new Error("Input must be a File object or a URL string");return e.split(".").pop().split("?")[0]}async function hd(i){if(this.referenceFrameList===void 0||this.referenceFrameList.length===0)return;const e=this.calculateViewportWidth(this.referenceFrameList.length);this.updateReferenceFrames(e),this.updateViewportElements(e),await this.syncUIState()}function qy(i){i.preventDefault();const{x:e,y:t}=gc(i);if(this.vpMouseDown){const{viewport:r,referenceFrame:n}=this.vpMouseDown,o=Math.abs(e-this.vpMouseDown.mouseDownX)>Math.abs(t-this.vpMouseDown.mouseDownY);if(!this.dragObject&&!this.isScrolling){if(o)this.vpMouseDown.mouseDownX&&Math.abs(e-this.vpMouseDown.mouseDownX)>this.constants.dragThreshold&&(this.dragObject={viewport:r,start:n.start});else if(this.vpMouseDown.mouseDownY&&Math.abs(t-this.vpMouseDown.mouseDownY)>this.constants.scrollThreshold){this.isScrolling=!0;const s=r.viewportElement.clientHeight,a=r.trackView.maxViewportContentHeight();this.vpMouseDown.r=s/a}}if(this.dragObject){const s=!this.isSoftclipped();let a=this.vpMouseDown.lastMouseX-e;n.shiftPixels(a,r.viewportElement.clientWidth,s)&&this.updateViews(),this.fireEvent("trackdrag")}if(this.isScrolling){const s=this.vpMouseDown.lastMouseY-t;r.trackView.scrollByPixels(s)}this.vpMouseDown.lastMouseX=e,this.vpMouseDown.lastMouseY=t}}function xl(i){this.cancelTrackPan(),this.endTrackDrag()}async function eJ(i){if(!(!this.referenceFrameList||this.referenceFrameList.length>1)&&(i.code==="KeyF"||i.code==="KeyB")){const e=this.getSelectedTrackViews();if(e.length>0){const t=e[0].track;if(typeof t.nextFeatureAfter=="function"){const r=this.referenceFrameList[0],n=r.viewport?r.viewport.getWidth():this.calculateViewportWidth(this.referenceFrameList.length),o=r.chr.toLowerCase()==="all",s=t.visibilityWindow;if(o||s&&s>0&&r.bpPerPixel*n>s)return;const a=i.code==="KeyF",c=r.chr,l=r.center,h=await t.nextFeatureAfter(c,l,a);if(h){const d=await this.genome.getChromosomeName(h.chr);if(c===d){const u=(h.start+h.end)/2;if(i.shiftKey){const f=this.config.minimumBases||40,p=Math.max(f,1.1*(h.end-h.start));r.start=Math.max(0,u-p/2),r.end=u+p/2,r.bpPerPixel=(r.end-r.start)/n}else r.shift(u-l);this.updateViews()}else{r.chr=d;const u=(h.start+h.end)/2;if(i.shiftKey){const 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rJ(){for(let i of Oa)i.dispose(),i.root.remove();Oa=[]}async function nJ(){for(let i of Oa)await i.visibilityChange()}function HA(i){return i.minimumBases===void 0&&(i.minimumBases=40),i.showIdeogram===void 0&&(i.showIdeogram=!0),i.showCytobandNames==null&&(i.showCytobandNames=!1),i.showCircularView===void 0&&(i.showCircularView=!1),i.showCircularViewButton===void 0&&(i.showCircularViewButton=!1),i.showTrackLabelButton===void 0&&(i.showTrackLabelButton=!0),i.showTrackLabels===void 0&&(i.showTrackLabels=!0),i.showCursorTrackingGuideButton===void 0&&(i.showCursorTrackingGuideButton=!0),i.showCursorGuide===void 0&&(i.showCursorGuide=i.showCursorTrackingGuide||!1),i.showCenterGuideButton===void 0&&(i.showCenterGuideButton=!0),i.showCenterGuide===void 0&&(i.showCenterGuide=!1),i.showSampleNames===void 0&&(i.showSampleNames=!1),i.showSVGButton===void 0&&(i.showSVGButton=!0),i.showControls===void 0&&(i.showControls=!0),i.showNavigation===void 0&&(i.showNavigation=!0),i.showRuler===void 0&&(i.showRuler=!0),i.flanking===void 0&&(i.flanking=1e3),i.pairsSupported===void 0&&(i.pairsSupported=!0),i.tracks||(i.tracks=[]),i}function oJ(i){var e,t,r,n,o,s,a,c,l,h;c=window.location.href,s={},e=c.indexOf("?"),t=c.lastIndexOf("#");let d,u,f;if(e>=0)for(t<0&&(t=c.length),r=e+1;r<t;)n=c.indexOf("&",r),n<0&&(n=t),o=c.substring(r,n),a=o.split("=",2),a.length===2?(l=a[0],h=decodeURIComponent(a[1]),l==="file"?d=h.split(","):l==="index"?u=h.split(","):l==="name"?f=h.split(","):l==="genome"?(h.startsWith("https://")||h.startsWith("http://"))&&!h.endsWith(".json")?i.reference={fastaURL:h,indexURL:h+".fai"}:(i[l]=h,i.reference=void 0):(l==="reference"&&(i.genome=void 0),i[l]=h),r=n+1):r++;if(d){i.tracks||(i.tracks=[]);for(let p=0;p<d.length;p++){if(d[p].endsWith(".xml")||d[p].endsWith(".json")){i.sessionURL=d[p];break}const m={url:d[p]};u&&u.length>p&&(m.indexURL=u[p]),f&&f.length>p&&(m.name=f[p]),i.tracks.push(m)}}return s}async function sJ(i,e){return await Lc.prototype.createTrack.call(e,i)}const aJ=Ee.setApiKey;function lJ(i){return Ee.setOauthToken(i)}function cJ(i,e){return Ee.setOauthToken(i,e)}const hJ=Ee.oauth;var Gy={AlertDialog:n2,TrackUtils:Pj,IGVGraphics:ge,MenuUtils:ix,DataRangeDialog:rx,createTrack:sJ,createBrowser:tJ,removeBrowser:iJ,removeAllBrowsers:rJ,visibilityChange:nJ,setGoogleOauthToken:lJ,setOauthToken:cJ,oauth:hJ,version:IA,setApiKey:aJ,TrackBase:Qt,registerTrackClass:TX,registerTrackCreatorFunction:NX,registerFileFormats:e$,loadSessionFile:Lc.loadSessionFile,loadHub:mu};class dJ extends Error{}class uJ{constructor(e=1e3,t=!1){xe(this,"throttlePeriod");xe(this,"rejectSkipped");xe(this,"queuedPromises",{});xe(this,"pendingPromise",!1);this.throttlePeriod=e,this.rejectSkipped=t}skipPromise(e){if(!this.rejectSkipped)return;const t=this.queuedPromises[e];t==null||t.reject(new dJ)}async enqueue(e,t,r=0){return new 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text-sm"},pJ={key:1,class:"absolute inset-2 border-4 border-dashed border-sky-600 rounded flex items-center justify-center pointer-events-none bg-sky-200 bg-opacity-80 text-sky-600 text-xl font-semibold z-256"},Qy="hg38",gJ="annotation",mJ=500,bJ="https://s3.amazonaws.com/igv.org.genomes/genomes.json",wJ="http://cdn.jsdelivr.net/gh/galaxyproject/galaxy-test-data/gencode.v29.annotation.gff3",vJ=Me({__name:"Plugin",props:{datasetId:{},root:{},settings:{},specs:{},tracks:{}},emits:["update"],setup(i,{emit:e}){const t={extension:"gff3",id:"__test__",metadata_dbkey:"hg18",name:"TEST DATASET"},r=new uJ(mJ),n=i,o=e,s=ce(!1),a=ce(""),c=ce(null);let l=null,h=[];xi(()=>{d()}),Ri(()=>{u()}),ct(()=>{var T;return(T=n.settings.source)==null?void 0:T.genome},()=>r.enqueue(b,void 0,"loadGenome")),ct(()=>n.settings.locus,()=>r.enqueue(I,void 0,"locusSearch")),ct(()=>n.tracks,()=>r.enqueue(w,void 0,"loadTracks"));async function d(){if(n.settings.source.genome)await b();else if(n.datasetId){const T=await v(n.datasetId);if(T){const N=T.metadata_dbkey||Qy,M=await f(N)||await f(Qy),L=M?{source:M}:{},z=[{urlDataset:{id:T.id}}];o("update",L,z),console.debug("[igv] Updating values.",L,z)}}else a.value="Genome selection required. Open the side panel and choose options."}function u(){l&&(Gy.removeBrowser(l),l=void 0)}async function f(T){const N=["fasta_indexes","twobit"],M=m3();for(const B of N){const O=(await M.getDataTable(B)).find(H=>{var R;return Array.isArray((R=H.value)==null?void 0:R.row)&&H.value.row.includes(T)});if(O)return{genome:O.value,origin:"builtin"}}const U=(await g3().getDataJson(bJ)).find(B=>{var x;return((x=B.value)==null?void 0:x.id)===T});return U?{genome:U.value,origin:"igv"}:null}function p(){const T=n.settings.source.genome;if(T){if(n.settings.source.origin==="igv")return T;{const N=T.id,M=T.columns||[],L=T.row||[],z=T.table,U=M.indexOf("path");if(U>=0&&L.length>U){const B=L[U].split("/").pop(),x=`${n.root}api/tool_data/${z}/fields/${N}/files/`;if(z==="fasta_indexes")return{id:N,fastaURL:`${x}${B}`,indexURL:`${x}${B}.fai`};if(z==="twobit")return{id:N,twoBitURL:`${x}${B}`}}}}}function m(T){return T==="__test__"?wJ:`${n.root}api/datasets/${T}/display`}async function v(T){if(T==="__test__")return t;try{const{data:N}=await Is().GET(`/api/datasets/${T}`);return N}catch(N){return a.value=`Failed to retrieve dataset details for: ${T}`,console.error(a.value,N),null}}function g(T,N){var z;const M=N?(z=Wy[N])==null?void 0:z.index:null;return M&&T!=="__test__"?`${n.root}api/datasets/${T}/metadata_file?metadata_file=${M}`:null}async function b(){const T=p();if(T)try{l?(l.off("locuschange",F),await l.loadGenome(T)):c.value&&(l=await Gy.createBrowser(c.value,{genome:T})),await w(!0),await I(),a.value="",l.on("locuschange",F);const N=l.root.querySelector(".igv-navbar");N&&Object.assign(N.style,{flexFlow:"column",height:"unset",paddingBottom:"3px"})}catch(N){a.value="Failed to load genome.",console.error(a.value,N),u()}}async function w(T=!1){if(l){const N=await _();console.debug("[igv] Resolved Tracks",N);const{toAdd:M,toRemove:L}=S(N,h,T);for(const z of L){const U=l.trackViews.find(B=>B.track.name===z.name);U&&(console.debug(`[igv] Removing existing track 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z=parseInt(L[2].replace(/,/g,""),10),U=parseInt(L[3].replace(/,/g,""),10);return Number.isInteger(z)&&Number.isInteger(U)&&z<U}else return!1}}function A(T){var z,U,B;let N=!1;const M=[],L=(z=T.dataTransfer)==null?void 0:z.getData("text");try{const x=L?JSON.parse(L):[];if(Array.isArray(x)&&x.length>0){const O=x[0];if(O&&typeof O=="object"){const H=O.id?[O]:Object.values(O);for(const R of H)((U=R.object)==null?void 0:U.model_class)==="HistoryDatasetAssociation"&&((B=R.object)!=null&&B.id)&&R.element_identifier?M.push({id:R.object.id,name:R.element_identifier}):R.history_content_type==="dataset"&&R.id?M.push({id:R.id,name:R.name}):N=!0}else N=!0}else N=!0}catch{a.value="Failed to parse dropped data."}if(N||M.length===0)a.value="Please make sure to only drop valid history datasets.",console.debug("[igv] Dropped Content",L);else{const x=[...n.tracks,...M.map(O=>({urlDataset:O}))];o("update",{},x),a.value="",console.debug("[igv] Dropped Tracks",x)}s.value=!1}function E(T){const N=Object.keys(T).sort(),M=JSON.stringify(T,N);let L=2166136261;for(let z=0;z<M.length;z++)L^=M.charCodeAt(z),L+=(L<<1)+(L<<4)+(L<<7)+(L<<8)+(L<<24);return(L>>>0).toString(36)}function y(T){const N=T==null?void 0:T.toLowerCase();if(N){const M=Wy[N];if(M!=null&&M.type)return M.type}return gJ}function S(T,N,M=!1){const L=new Map(N.map(B=>[B.name,B])),z=N.filter(B=>{const x=T.find(O=>O.name===B.name);return M||!x||E(x)!==E(B)});return{toAdd:T.filter(B=>{const x=L.get(B.name);return M||!x||E(B)!==E(x)}),toRemove:z}}async function _(){const T=[];for(const z of n.tracks){const U=z.urlDataset,B=U?await v(U.id):null,x=z.displayMode,O=z.color,H=(B==null?void 0:B.extension)||null,R=z.indexUrlDataset,D=z.name||(B==null?void 0:B.name)||"",$=z.type&&z.type!=="auto"?z.type:y(H),j=U?m(U.id):null,X=R?m(R.id):g(U==null?void 0:U.id,H),G={color:O,displayMode:x,format:H,indexURL:X,name:D,type:$,url:j};console.debug("[igv] Track:",G),T.push(G)}const N=new Set,M=new Map,L=[];return T.forEach((z,U)=>{const B=z.name||`track-${E(z)}`,x=JSON.stringify({...z,name:B}),O=typeof(z==null?void 0:z.url)=="string"&&z.url.trim().length>0,H=N.has(x);if(O&&!H){const R=M.get(B)??0;let D=B;R>0&&(D=`${B} ~ ${R}`),M.set(B,R+1),N.add(x),L.push({...z,name:D,order:U})}else console.warn(O?`[igv] Duplicate track skipped: '${B}'`:`[igv] Invalid track skipped: '${B}'`)}),L}return(T,N)=>(Pe(),ft("div",{class:"h-screen overflow-auto",onDragover:N[0]||(N[0]=Df(M=>s.value=!0,["prevent"])),onDragleave:N[1]||(N[1]=Df(M=>s.value=!1,["prevent"])),onDrop:Df(A,["prevent"])},[a.value?(Pe(),ft("div",fJ,cn(a.value),1)):nr("",!0),tt("div",{ref_key:"viewport",ref:c},null,512),s.value?(Pe(),ft("div",pJ," Drop Track Datasets! 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s=this.trackViews[r].track.order;this.trackViews[n].track.order=s;const a=o.length;let c=s;if(r<n)for(let l=r+1;l<a;l++){const h=o[l].track;if(h.order<=c)h.order=Math.min(Number.MAX_SAFE_INTEGER,c+1),c=h.order;else break}else for(let l=r-1;l>0;l--){const h=o[l].track;if(h.order>=c)h.order=Math.max(-Number.MAX_SAFE_INTEGER,c-1),c=h.order;else break}this.reorderTracks()}}endTrackDrag(){this.dragTrack?(this.dragTrack=void 0,this.fireEvent("trackorderchanged",[this.getTrackOrder()])):this.dragTrack=void 0}addEventHandlers(){this.addWindowResizeHandler(),this.addRootMouseUpHandler(),this.addRootMouseLeaveHandler(),this.addColumnContainerEventHandlers(),this.addKeyboardHandler()}removeEventHandlers(){this.removeWindowResizeHandler(),this.removeRootMouseUpHandler(),this.removeRootMouseLeaveHandler(),this.removeColumnContainerEventHandlers(),this.removeKeyboardHandler()}addWindowResizeHandler(){this.boundWindowResizeHandler=hd.bind(this),window.addEventListener("resize",this.boundWindowResizeHandler)}removeWindowResizeHandler(){window.removeEventListener("resize",this.boundWindowResizeHandler)}addRootMouseUpHandler(){this.boundRootMouseUpHandler=xl.bind(this),this.root.addEventListener("mouseup",this.boundRootMouseUpHandler)}removeRootMouseUpHandler(){this.root.removeEventListener("mouseup",this.boundRootMouseUpHandler)}addRootMouseLeaveHandler(){this.boundRootMouseLeaveHandler=xl.bind(this),this.root.addEventListener("mouseleave",this.boundRootMouseLeaveHandler)}removeRootMouseLeaveHandler(){this.root.removeEventListener("mouseleave",this.boundRootMouseLeaveHandler)}addColumnContainerEventHandlers(){this.boundColumnContainerMouseMoveHandler=qy.bind(this),this.boundColumnContainerTouchMoveHandler=qy.bind(this),this.boundColumnContainerMouseLeaveHandler=xl.bind(this),this.boundColumnContainerMouseUpHandler=xl.bind(this),this.boundColumnContainerTouchEndHandler=xl.bind(this),this.columnContainer.addEventListener("mousemove",this.boundColumnContainerMouseMoveHandler),this.columnContainer.addEventListener("touchmove",this.boundColumnContainerTouchMoveHandler),this.columnContainer.addEventListener("mouseleave",this.boundColumnContainerMouseLeaveHandler),this.columnContainer.addEventListener("mouseup",this.boundColumnContainerMouseUpHandler),this.columnContainer.addEventListener("touchend",this.boundColumnContainerTouchEndHandler)}removeColumnContainerEventHandlers(){this.columnContainer.removeEventListener("mousemove",this.boundColumnContainerMouseMoveHandler),this.columnContainer.removeEventListener("touchmove",this.boundColumnContainerTouchMoveHandler),this.columnContainer.removeEventListener("mouseleave",this.boundColumnContainerMouseLeaveHandler),this.columnContainer.removeEventListener("mouseup",this.boundColumnContainerMouseUpHandler),this.columnContainer.removeEventListener("touchend",this.boundColumnContainerTouchEndHandler)}addKeyboardHandler(){this.keyUpHandler=eJ.bind(this),document.addEventListener("keyup",this.keyUpHandler)}removeKeyboardHandler(){console.log("Remove handler"),document.addEventListener("keyup",this.keyUpHandler)}static uncompressSession(e){let t;if(e.indexOf("/gzip;base64")>0){t=Ho(e);let r="";for(let n of t)r+=String.fromCharCode(n);return r}else{let r=e.substring(5);return uO(r)}}createCircularView(e,t){return t=t===!0,this.circularView=kG(e,this),this.circularViewControl=new rh(this.navbar.toggleButtonContainer,this),this.circularView.setAssembly({name:this.genome.id,id:this.genome.id,chromosomes:wF(this.genome)}),this.circularViewVisible=t,this.circularView}get circularViewVisible(){return this.circularView!==void 0&&this.circularView.visible}set circularViewVisible(e){this.circularView&&(this.circularView.visible=e,this.circularViewControl.setState(e))}get overlayTrackButton(){return this.navbar.overlayTrackButton}get roiTableControl(){return this.navbar.roiTableControl}get sampleNameControl(){return this.navbar.sampleNameControl}get sampleInfoControl(){return this.navbar.sampleInfoControl}async blat(e){return 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qy(i){i.preventDefault();const{x:e,y:t}=gc(i);if(this.vpMouseDown){const{viewport:r,referenceFrame:n}=this.vpMouseDown,o=Math.abs(e-this.vpMouseDown.mouseDownX)>Math.abs(t-this.vpMouseDown.mouseDownY);if(!this.dragObject&&!this.isScrolling){if(o)this.vpMouseDown.mouseDownX&&Math.abs(e-this.vpMouseDown.mouseDownX)>this.constants.dragThreshold&&(this.dragObject={viewport:r,start:n.start});else if(this.vpMouseDown.mouseDownY&&Math.abs(t-this.vpMouseDown.mouseDownY)>this.constants.scrollThreshold){this.isScrolling=!0;const s=r.viewportElement.clientHeight,a=r.trackView.maxViewportContentHeight();this.vpMouseDown.r=s/a}}if(this.dragObject){const s=!this.isSoftclipped();let a=this.vpMouseDown.lastMouseX-e;n.shiftPixels(a,r.viewportElement.clientWidth,s)&&this.updateViews(),this.fireEvent("trackdrag")}if(this.isScrolling){const s=this.vpMouseDown.lastMouseY-t;r.trackView.scrollByPixels(s)}this.vpMouseDown.lastMouseX=e,this.vpMouseDown.lastMouseY=t}}function xl(i){this.cancelTrackPan(),this.endTrackDrag()}async function eJ(i){if(!(!this.referenceFrameList||this.referenceFrameList.length>1)&&(i.code==="KeyF"||i.code==="KeyB")){const e=this.getSelectedTrackViews();if(e.length>0){const t=e[0].track;if(typeof t.nextFeatureAfter=="function"){const r=this.referenceFrameList[0],n=r.viewport?r.viewport.getWidth():this.calculateViewportWidth(this.referenceFrameList.length),o=r.chr.toLowerCase()==="all",s=t.visibilityWindow;if(o||s&&s>0&&r.bpPerPixel*n>s)return;const a=i.code==="KeyF",c=r.chr,l=r.center,h=await t.nextFeatureAfter(c,l,a);if(h){const d=await this.genome.getChromosomeName(h.chr);if(c===d){const u=(h.start+h.end)/2;if(i.shiftKey){const f=this.config.minimumBases||40,p=Math.max(f,1.1*(h.end-h.start));r.start=Math.max(0,u-p/2),r.end=u+p/2,r.bpPerPixel=(r.end-r.start)/n}else r.shift(u-l);this.updateViews()}else{r.chr=d;const u=(h.start+h.end)/2;if(i.shiftKey){const 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Lc.prototype.createTrack.call(e,i)}const aJ=Ee.setApiKey;function lJ(i){return Ee.setOauthToken(i)}function cJ(i,e){return Ee.setOauthToken(i,e)}const hJ=Ee.oauth;var Gy={AlertDialog:n2,TrackUtils:Pj,IGVGraphics:ge,MenuUtils:ix,DataRangeDialog:rx,createTrack:sJ,createBrowser:tJ,removeBrowser:iJ,removeAllBrowsers:rJ,visibilityChange:nJ,setGoogleOauthToken:lJ,setOauthToken:cJ,oauth:hJ,version:IA,setApiKey:aJ,TrackBase:Qt,registerTrackClass:TX,registerTrackCreatorFunction:NX,registerFileFormats:e$,loadSessionFile:Lc.loadSessionFile,loadHub:mu};class dJ extends Error{}class uJ{constructor(e=1e3,t=!1){xe(this,"throttlePeriod");xe(this,"rejectSkipped");xe(this,"queuedPromises",{});xe(this,"pendingPromise",!1);this.throttlePeriod=e,this.rejectSkipped=t}skipPromise(e){if(!this.rejectSkipped)return;const t=this.queuedPromises[e];t==null||t.reject(new dJ)}async enqueue(e,t,r=0){return new 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v(n.datasetId);if(T){const N=T.metadata_dbkey||Qy,M=await f(N)||await f(Qy),L=M?{source:M}:{},z=[{urlDataset:{id:T.id}}];o("update",L,z),console.debug("[igv] Updating values.",L,z)}}else a.value="Genome selection required. 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v(T){if(T==="__test__")return t;try{const{data:N}=await Is().GET(`/api/datasets/${T}`);return N}catch(N){return a.value=`Failed to retrieve dataset details for: ${T}`,console.error(a.value,N),null}}function g(T,N){var z;const M=N?(z=Wy[N])==null?void 0:z.index:null;return M&&T!=="__test__"?`${n.root}api/datasets/${T}/metadata_file?metadata_file=${M}`:null}async function b(){const T=p();if(T)try{l?(l.off("locuschange",F),await l.loadGenome(T)):c.value&&(l=await Gy.createBrowser(c.value,{genome:T})),await w(!0),await I(),a.value="",l.on("locuschange",F);const N=l.root.querySelector(".igv-navbar");N&&Object.assign(N.style,{flexFlow:"column",height:"unset",paddingBottom:"3px"})}catch(N){a.value="Failed to load genome.",console.error(a.value,N),u()}}async function w(T=!1){if(l){const N=await _();console.debug("[igv] Resolved Tracks",N);const{toAdd:M,toRemove:L}=S(N,h,T);for(const z of L){const U=l.trackViews.find(B=>B.track.name===z.name);U&&(console.debug(`[igv] Removing existing track 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