npm - @galaxyproject/igv - Versions diffs - 0.0.20 → 0.0.21 - Mend

@galaxyproject/igv 0.0.20 → 0.0.21

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (3) hide show

package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
     "name": "@galaxyproject/igv",
-    "version": "0.0.20",
+    "version": "0.0.21",
     "type": "module",
     "license": "MIT",
     "files": [

package/static/index.css CHANGED Viewed

	@@ -1 +1 @@
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1	+ .igv-overlay[data-v-4af1c099]{position:absolute;top:0;right:0;bottom:0;left:0;z-index:4096;display:flex;align-items:center;justify-content:center;background-color:rgb(224 242 254 / var(--tw-bg-opacity));--tw-bg-opacity: .3;font-size:1.25rem;line-height:1.75rem;font-weight:600;--tw-text-opacity: 1;color:rgb(14 165 233 / var(--tw-text-opacity))}.igv-overlay-title[data-v-4af1c099]{pointer-events:none;border-radius:.25rem;background-color:rgb(255 255 255 / var(--tw-bg-opacity));--tw-bg-opacity: .9;padding:.25rem .75rem},:before,:after{box-sizing:border-box;border-width:0;border-style:solid;border-color:#e5e7eb}:before,:after{--tw-content: ""}html,:host{line-height:1.5;-webkit-text-size-adjust:100%;-moz-tab-size:4;-o-tab-size:4;tab-size:4;font-family:ui-sans-serif,system-ui,sans-serif,"Apple Color Emoji","Segoe UI Emoji",Segoe UI Symbol,"Noto Color 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package/static/index.js CHANGED Viewed

@@ -2449,4 +2449,4 @@ ${c.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 Zm.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 ${o}`),o!==r.initialLocus&&await this.search(r.initialLocus)),n&&(this.fireEvent("genomechange",[{genome:r}]),this.circularView&&this.circularView.setAssembly({name:this.genome.id,id:this.genome.id,chromosomes:vF(this.genome)})),r}async loadGenome(e){e.genarkAccession&&(e.url=$_(e.genarkAccession)),e.url&&(Yt(e.url)&&e.url.endsWith("/hub.txt")?(e.hubURL=e.url,delete e.url):iJ(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(),kg(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){kg(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 Yp(this,this.columnContainer,e);if(this.trackViews.push(t),kg(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 Tz(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 p2.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&&NX().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=MX(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 CZ(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,l=r.track.order||0;return a-l}else return o-s});for(let{axis:t,viewports:r,sampleInfoViewport:n,sampleNameViewport:o,outerScroll:s,dragHandle:a,gearContainer:l}of this.trackViews){t.remove();for(let{viewportElement:c}of r)c.parentNode.removeChild(c);n.viewport.remove(),o.viewport.remove(),s.remove(),a.remove(),l.remove()}const e=this.columnContainer.querySelectorAll(".igv-column");for(let{axis:t,viewports:r,sampleInfoViewport:n,sampleNameViewport:o,outerScroll:s,dragHandle:a,gearContainer:l}of this.trackViews){this.columnContainer.querySelector(".igv-axis-column").appendChild(t);for(let c=0;c<e.length;c++){const{viewportElement:h}=r[c];e[c].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(l)}}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<=w2&&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(l=>l.getInViewFeatures())),a=kc(s.flat());for(const l of o)l.track.dataRange=Object.assign({},a),l.track.autoscale=!1;await Promise.all(o.map(l=>l.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-=xj+this.getSampleInfoViewportWidth()+this.getSampleNameViewportWidth()+ZZ+JZ+eJ,t-=tJ*(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,l=new SA(this.genome,e,t,r,a),c=n?this.referenceFrameList.indexOf(n):this.referenceFrameList.length-1,h=1+c,{viewportElement:d}=this.trackViews[0].viewports[c],u=yg.insertAfter(d.parentElement);if(this.fireEvent("didchangecolumnlayout"),h===this.referenceFrameList.length){this.referenceFrameList.push(l);for(let f of this.trackViews){const p=zm(f,u,l);f.viewports.push(p)}}else{this.referenceFrameList.splice(h,0,l);for(let f of this.trackViews){const p=zm(f,u,l);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 mZ(this,this.referenceFrameList[o],n[o]));return r}async removeMultiLocusPanel(e){const t=this.referenceFrameList.indexOf(e),{viewportElement:r}=this.trackViews[0].viewports[t];yg.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 pX(this,e);return this.updateLoci(r,t)}async updateLoci(e,t){if(e&&e.length>0){this.referenceFrameList=zX(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()),yg.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*Js+Lm: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:c}of r.viewports){const h=c.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:c}of this.trackViews)try{let h;typeof c.getState=="function"?h=Qt.localFileInspection(c.getState()):c.config&&(h=Qt.localFileInspection(c.config)),h&&(h.browser&&delete h.browser,h.order=c.order,o.push(h))}catch(h){const d=`Track: ${c.name}: ${h}`;console.error(d),s.push(d)}if(s.length>0){let c=1,h="Errors encountered saving session: </br>";for(let d of s)h+=` (${c++}) ${d.toString()} <br/>`;throw Error(h)}e.tracks=o;const a=[];for(const c of o)for(const h of Object.keys(c))(h==="file"||h==="indexFile")&&a.push(c[h]);const l=[];if(this.config.sampleinfo){e.sampleinfo=this.config.sampleinfo;for(const c of this.sampleInfo.sampleInfoFiles){const h=Qt.localFileInspection({url:c});h.file&&l.push(h.file)}l.length>0&&a.push(...l)}return a.length>0&&alert(`This session includes reference(s) to local file(s):
 ${a.map(c=>`    ${c}`).join(`
 `)}
-Local files cannot be loaded automatically when a saved session is restored.`),e}compressedSession(){const e=JSON.stringify(this.toJSON());return pO(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=pc(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 l=s;if(r<n)for(let c=r+1;c<a;c++){const h=o[c].track;if(h.order<=l)h.order=Math.min(Number.MAX_SAFE_INTEGER,l+1),l=h.order;else break}else for(let c=r-1;c>0;c--){const h=o[c].track;if(h.order>=l)h.order=Math.max(-Number.MAX_SAFE_INTEGER,l-1),l=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=_l.bind(this),this.root.addEventListener("mouseup",this.boundRootMouseUpHandler)}removeRootMouseUpHandler(){this.root.removeEventListener("mouseup",this.boundRootMouseUpHandler)}addRootMouseLeaveHandler(){this.boundRootMouseLeaveHandler=_l.bind(this),this.root.addEventListener("mouseleave",this.boundRootMouseLeaveHandler)}removeRootMouseLeaveHandler(){this.root.removeEventListener("mouseleave",this.boundRootMouseLeaveHandler)}addColumnContainerEventHandlers(){this.boundColumnContainerMouseMoveHandler=Gy.bind(this),this.boundColumnContainerTouchMoveHandler=Gy.bind(this),this.boundColumnContainerMouseLeaveHandler=_l.bind(this),this.boundColumnContainerMouseUpHandler=_l.bind(this),this.boundColumnContainerTouchEndHandler=_l.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=rJ.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=Oo(e);let r="";for(let n of t)r+=String.fromCharCode(n);return r}else{let r=e.substring(5);return gO(r)}}createCircularView(e,t){return t=t===!0,this.circularView=EG(e,this),this.circularViewControl=new rh(this.navbar.toggleButtonContainer,this),this.circularView.setAssembly({name:this.genome.id,id:this.genome.id,chromosomes:vF(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 ga({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} : ${Eo(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 zc=Du;function iJ(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 Gy(i){i.preventDefault();const{x:e,y:t}=pc(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 _l(i){this.cancelTrackPan(),this.endTrackDrag()}async function rJ(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",l=r.chr,c=r.center,h=await t.nextFeatureAfter(l,c,a);if(h){const d=await this.genome.getChromosomeName(h.chr);if(l===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-c);this.updateViews()}else{r.chr=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=r.start+p,r.bpPerPixel=(r.end-r.start)/n}else r.start=u-n*r.bpPerPixel/2,r.end=r.start+n*r.bpPerPixel;this.updateViews()}}}}}}function kg(i,e){for(let{viewports:t}of i)for(let r of t)r.trackLabelElement&&(t.indexOf(r)===0&&e===!0?r.trackLabelElement.style.display="block":r.trackLabelElement.style.display="none")}let Oa=[];async function nJ(i,e){e===void 0&&(e={}),ci.KNOWN_GENOMES||await ci.initializeGenomes(e),HA(e),e.queryParametersSupported&&lJ(e),e.apiKey&&Ee.setApiKey(e.apiKey),e.oauthToken&&Ee.setOauthToken(e.oauthToken),e.clientId&&!Ps()&&await CO({client_id:e.clientId,apiKey:e.apiKey,scope:"https://www.googleapis.com/auth/userinfo.profile"});const t=new zc(e,i);Oa.push(t);const r=e.sessionURL||e.session||e.hubURL;return r?await t.loadSession({url:r}):await t.loadSessionObject(e),t.navbar.navbarDidResize(),t}function oJ(i){i.dispose(),i.root.remove(),Oa=Oa.filter(e=>e!==i)}function 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