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i,n,r;for(;;){if(t.lookahead=3&&(t.ins_h=mr(t,t.ins_h,t.window[t.strstart+3-1]),i=t.prev[t.strstart&t.w_mask]=t.head[t.ins_h],t.head[t.ins_h]=t.strstart),t.prev_length=t.match_length,t.prev_match=t.match_start,t.match_length=2,0!==i&&t.prev_length4096)&&(t.match_length=2)),t.prev_length>=3&&t.match_length<=t.prev_length){r=t.strstart+t.lookahead-3,n=Vn(t,t.strstart-1-t.prev_match,t.prev_length-3),t.lookahead-=t.prev_length-1,t.prev_length-=2;do{++t.strstart<=r&&(t.ins_h=mr(t,t.ins_h,t.window[t.strstart+3-1]),i=t.prev[t.strstart&t.w_mask]=t.head[t.ins_h],t.head[t.ins_h]=t.strstart)}while(0!=--t.prev_length);if(t.match_available=0,t.match_length=2,t.strstart++,n&&(yr(t,!1),0===t.strm.avail_out))return 1}else if(t.match_available){if(n=Vn(t,0,t.window[t.strstart-1]),n&&yr(t,!1),t.strstart++,t.lookahead--,0===t.strm.avail_out)return 1}else t.match_available=1,t.strstart++,t.lookahead--}return t.match_available&&(n=Vn(t,0,t.window[t.strstart-1]),t.match_available=0),t.insert=t.strstart<2?t.strstart:2,e===Wn?(yr(t,!0),0===t.strm.avail_out?3:4):t.sym_next&&(yr(t,!1),0===t.strm.avail_out)?1:2};function Tr(t,e,i,n,r){this.good_length=t,this.max_lazy=e,this.nice_length=i,this.max_chain=n,this.func=r}const Ir=[new Tr(0,0,0,0,Sr),new Tr(4,4,8,4,Cr),new Tr(4,5,16,8,Cr),new Tr(4,6,32,32,Cr),new Tr(4,4,16,16,Ar),new Tr(8,16,32,32,Ar),new Tr(8,16,128,128,Ar),new Tr(8,32,128,256,Ar),new Tr(32,128,258,1024,Ar),new Tr(32,258,258,4096,Ar)];function Er(){this.strm=null,this.status=0,this.pending_buf=null,this.pending_buf_size=0,this.pending_out=0,this.pending=0,this.wrap=0,this.gzhead=null,this.gzindex=0,this.method=or,this.last_flush=-1,this.w_size=0,this.w_bits=0,this.w_mask=0,this.window=null,this.window_size=0,this.prev=null,this.head=null,this.ins_h=0,this.hash_size=0,this.hash_bits=0,this.hash_mask=0,this.hash_shift=0,this.block_start=0,this.match_length=0,this.prev_match=0,this.match_available=0,this.strstart=0,this.match_start=0,this.lookahead=0,this.prev_length=0,this.max_chain_length=0,this.max_lazy_match=0,this.level=0,this.strategy=0,this.good_match=0,this.nice_match=0,this.dyn_ltree=new Uint16Array(1146),this.dyn_dtree=new Uint16Array(122),this.bl_tree=new Uint16Array(78),pr(this.dyn_ltree),pr(this.dyn_dtree),pr(this.bl_tree),this.l_desc=null,this.d_desc=null,this.bl_desc=null,this.bl_count=new Uint16Array(16),this.heap=new Uint16Array(573),pr(this.heap),this.heap_len=0,this.heap_max=0,this.depth=new 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e===Zn&&((i=t.state).window_size=2*i.w_size,pr(i.head),i.max_lazy_match=Ir[i.level].max_lazy,i.good_match=Ir[i.level].good_length,i.nice_match=Ir[i.level].nice_length,i.max_chain_length=Ir[i.level].max_chain,i.strstart=0,i.block_start=0,i.lookahead=0,i.insert=0,i.match_length=i.prev_length=2,i.match_available=0,i.ins_h=0),e},Br=(t,e,i,n,r,s)=>{if(!t)return Qn;let o=1;if(e===Jn&&(e=6),n<0?(o=0,n=-n):n>15&&(o=2,n-=16),r<1||r>9||i!==or||n<8||n>15||e<0||e>9||s<0||s>nr||8===n&&1!==o)return dr(t,Qn);8===n&&(n=9);const a=new Er;return t.state=a,a.strm=t,a.status=hr,a.wrap=o,a.gzhead=null,a.w_bits=n,a.w_size=1<Br(t,e,or,15,8,rr),deflateInit2:Br,deflateReset:Lr,deflateResetKeep:Rr,deflateSetHeader:(t,e)=>Mr(t)||2!==t.state.wrap?Qn:(t.state.gzhead=e,Zn),deflate:(t,e)=>{if(Mr(t)||e>Gn||e<0)return t?dr(t,Qn):Qn;const i=t.state;if(!t.output||0!==t.avail_in&&!t.input||i.status===ur&&e!==Wn)return dr(t,0===t.avail_out?Kn:Qn);const 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o=t.window;for(;;){if(t.lookahead<=ar){if(kr(t),t.lookahead<=ar&&e===jn)return 1;if(0===t.lookahead)break}if(t.match_length=0,t.lookahead>=3&&t.strstart>0&&(r=t.strstart-1,n=o[r],n===o[++r]&&n===o[++r]&&n===o[++r])){s=t.strstart+ar;do{}while(n===o[++r]&&n===o[++r]&&n===o[++r]&&n===o[++r]&&n===o[++r]&&n===o[++r]&&n===o[++r]&&n===o[++r]&&rt.lookahead&&(t.match_length=t.lookahead)}if(t.match_length>=3?(i=Vn(t,1,t.match_length-3),t.lookahead-=t.match_length,t.strstart+=t.match_length,t.match_length=0):(i=Vn(t,0,t.window[t.strstart]),t.lookahead--,t.strstart++),i&&(yr(t,!1),0===t.strm.avail_out))return 1}return t.insert=0,e===Wn?(yr(t,!0),0===t.strm.avail_out?3:4):t.sym_next&&(yr(t,!1),0===t.strm.avail_out)?1:2})(i,e):Ir[i.level].func(i,e);if(3!==n&&4!==n||(i.status=ur),1===n||3===n)return 0===t.avail_out&&(i.last_flush=-1),Zn;if(2===n&&(e===$n?Hn(i):e!==Gn&&(zn(i,0,0,!1),e===qn&&(pr(i.head),0===i.lookahead&&(i.strstart=0,i.block_start=0,i.insert=0))),br(t),0===t.avail_out))return 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this.offset+this.sequence.length}}const Da=function(t,e,i,n){this.chr=t,this.start=e,this.end=i,this.features=n};Da.prototype.contains=function(t,e,i){return this.chr===t&&this.start<=e&&this.end>=i},Da.prototype.containsRange=function(t){return this.chr===t.chr&&this.start<=t.start&&this.end>=t.end};const Pa=qi,za=new Set(["fastaURL","indexURL","compressedIndexURL","cytobandURL","indexed"]);class Ua{constructor(t){this.file=t.fastaURL,this.indexFile=t.indexURL||t.indexFile||this.file+".fai",this.compressedIndexFile=t.compressedIndexURL||!1,this.withCredentials=t.withCredentials,this.chromosomeNames=[],this.chromosomes={},this.sequences={},this.offsets={};const e={};for(let i in t)t.hasOwnProperty(i)&&!za.has(i)&&(e[i]=t[i]);this.config=e}async init(){return this.getIndex()}async getSequence(t,e,i){if(!this.interval||!this.interval.contains(t,e,i)){let n=e,r=i;if(i-e<5e4){const t=i-e,s=Math.round(e+t/2);n=Math.max(0,s-25e3),r=s+25e3}const s=await 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this.trackView.viewports)t.setContentHeight(25);this.trackView.setTrackHeight(25)}this.trackView.repaintViews()}}]}contextMenuItemList(t){const e=t.viewport;if(e.referenceFrame.bpPerPixel<=1){const t=e.getWidth()*e.referenceFrame.bpPerPixel,i=e.referenceFrame.chr,n=Math.floor(e.referenceFrame.start),r=Math.ceil(n+t),s=[{label:this.reversed?"View visible sequence (reversed)...":"View visible sequence...",click:async()=>{let t=await this.browser.genome.sequence.getSequence(i,n,r);t?this.reversed&&(t=Ra(t)):t="Unknown sequence",this.browser.alert.present(t)}}];return ba()&&s.push({label:"Copy visible sequence",click:async()=>{let t=await this.browser.genome.sequence.getSequence(i,n,r);t?this.reversed&&(t=Ra(t)):t="Unknown sequence";try{await navigator.clipboard.writeText(t)}catch(t){console.error(t),this.browser.alert.present(`error copying sequence to clipboard ${t}`)}}}),s.push("
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n.setAttribute("id",r),n.setAttribute("width",t.width),n.setAttribute("height",t.height),"CANVAS"===t.nodeName||"IMG"===t.nodeName?(i=this.__createElement("image"),i.setAttribute("width",t.width),i.setAttribute("height",t.height),i.setAttributeNS("http://www.w3.org/1999/xlink","xlink:href","CANVAS"===t.nodeName?t.toDataURL():t.getAttribute("src")),n.appendChild(i),this.__defs.appendChild(n)):t instanceof ll&&(n.appendChild(t.__root.childNodes[1]),this.__defs.appendChild(n)),new al(n,this)}setLineDash(t){t&&t.length>0?this.lineDash=t.join(","):this.lineDash=null}drawFocusRing(){}createImageData(){}getImageData(){}putImageData(){}globalCompositeOperation(){}setTransform(){}}const hl=function(t,e,i,n){this.start=t,this.end=e,this.name=i,this.stain=0,"acen"===n?this.type="c":(this.type=n.charAt(1),"p"===this.type&&(this.stain=parseInt(n.substring(4))))};const cl=qi,ul={loadGenome:async function(t){const e=t.cytobandURL,i=t.aliasURL,n=await ja(t);let r;i&&(r=await function(t,e){return zo.loadString(t,la(e)).then((function(t){var e=cl(t),i=[];return e.forEach((function(t){!t.startsWith("#")&&t.length>0&&i.push(t.split("\t"))})),i}))}(i,n.config));const s=new dl(t,n,r);return e&&(s.cytobands=await async function(t,e,i){let n;if(fa(t)){const e=bo(t);n="";const i=e.length;for(let t=0;t1?function(t,e){let i;if(e.chromosomeOrder)Array.isArray(e.chromosomeOrder)?t.wgChromosomeNames=e.chromosomeOrder:t.wgChromosomeNames=e.chromosomeOrder.split(",").map((t=>t.trim())),i=t.wgChromosomeNames.map((e=>t.chromosomes[e])).filter((t=>void 0!==t));else{const e=Object.keys(t.chromosomes).map((e=>t.chromosomes[e].bpLength)).reduce(((t,e)=>Math.max(t,e)))/50;i=Object.values(t.chromosomes).filter((t=>t.bpLength>e));const n=i.filter((t=>r(t.name.replace("chr","")))),s=i.filter((t=>!r(t.name.replace("chr",""))));n.sort(((t,e)=>Number.parseInt(t.name.replace("chr",""))-Number.parseInt(e.name.replace("chr",""))));const o=n.map((t=>t.name));for(let t of s)o.push(t.name);t.wgChromosomeNames=o}const n=i.reduce(((t,e)=>t+e.bpLength),0);function r(t){return/^\d+$/.test(t)}t.chromosomes.all={name:"all",bpLength:n}}(this,t):this.wgChromosomeNames=e.chromosomeNames;var n={},r=this;n.all="all",this.chromosomeNames.forEach((function(t){var e=t.startsWith("chr")?t.substring(3):"chr"+t;n[e.toLowerCase()]=t,"chrM"===t&&(n.mt="chrM"),"MT"===t&&(n.chrm="MT"),n[t.toLowerCase()]=t})),i&&i.forEach((function(t){var e,i;for(i=0;it.bpLength)&&(t=i)}return t}}getChromosomes(){return this.chromosomes}getGenomeCoordinate(t,e){var i=this.getCumulativeOffset(t);if(void 0!==i)return i+e}getChromosomeCoordinate(t){let e;void 0===this.cumulativeOffsets&&(this.cumulativeOffsets=computeCumulativeOffsets.call(this));let i=0;for(let n of this.wgChromosomeNames){const r=this.cumulativeOffsets[n];if(r>t)return{chr:e,position:t-i};e=n,i=r}return{chr:this.wgChromosomeNames[this.wgChromosomeNames.length-1],position:0}}getCumulativeOffset(t){void 0===this.cumulativeOffsets&&(this.cumulativeOffsets=function(){let t=this,e={},i=0;for(let n of t.wgChromosomeNames)e[n]=Math.floor(i),i+=t.getChromosome(n).bpLength;return e}.call(this));const e=this.getChromosomeName(t);return this.cumulativeOffsets[e]}getGenomeLength(){let t=this;if(!this.bpLength){let e=0;t.wgChromosomeNames.forEach((function(i){let n=t.chromosomes[i];e+=n.bpLength})),this.bpLength=e}return this.bpLength}async getSequence(t,e,i){return t=this.getChromosomeName(t),this.sequence.getSequence(t,e,i)}addFeaturesToDB(t,e){const i=(t,e)=>{const i=this.featureDB.get(t);i&&(e=e.end-e.start>i.end-i.start?e:i),this.featureDB.set(t,e)};for(let n of t)if(n.name&&i(n.name.toUpperCase(),n),n.gene&&n.gene.name&&i(n.gene.name.toUpperCase(),n),e.searchableFields)for(let t of e.searchableFields){const e=n.getAttributeValue(t);e&&(e.indexOf(" ")>0?i(e.replaceAll(" ","+").toUpperCase(),n):i(e.toUpperCase(),n))}}}let fl,pl=0,gl=0;class ml extends Ja{constructor(t,e,i,n){super(t,e,i,n)}initializationHelper(){this.$spinner=fe("",{class:"igv-loading-spinner-container"}),this.$viewport.append(this.$spinner),this.$spinner.append(fe("
"));const t=this.trackView.track;"sequence"!==t.type&&(this.$zoomInNotice=this.createZoomInNotice(this.$viewport)),t.name&&"sequence"!==t.id&&(this.$trackLabel=fe('
'),this.$viewport.append(this.$trackLabel),this.setTrackLabel(t.name),!1===this.browser.trackLabelsVisible&&this.$trackLabel.hide()),this.stopSpinner(),this.addMouseHandlers()}setContentHeight(t){super.setContentHeight(t),this.featureCache&&(this.featureCache.redraw=!0)}setTrackLabel(t){this.$trackLabel.empty(),this.$trackLabel.html(t);const e=this.$trackLabel.text();this.$trackLabel.attr("title",e)}startSpinner(){this.$spinner.show()}stopSpinner(){this.$spinner&&this.$spinner.hide()}checkZoomIn(){if(this.trackView.track&&"sequence"===this.trackView.track.type&&this.referenceFrame.bpPerPixel>10)return fe(this.canvas).remove(),this.canvas=void 0,!1;if(!this.viewIsReady())return!1;if((()=>{if("all"!==this.referenceFrame.chr.toLowerCase()||this.trackView.track.supportsWholeGenome){const t=this.trackView.track.visibilityWindow;return void 0!==t&&t>0&&this.referenceFrame.bpPerPixel*this.$viewport.width()>t}return!0})()){if(this.canvas&&(fe(this.canvas).remove(),this.canvas=void 0),this.trackView.track.autoHeight){const t=this.trackView.minHeight||0;this.setContentHeight(t)}return this.$zoomInNotice&&this.$zoomInNotice.show(),!1}return this.$zoomInNotice&&this.$zoomInNotice.hide(),!0}shift(){const t=this.referenceFrame;if(this.canvas&&this.canvas._data&&this.canvas._data.referenceFrame.chr===this.referenceFrame.chr&&this.canvas._data.bpPerPixel===t.bpPerPixel){const e=Math.round((this.canvas._data.bpStart-t.start)/t.bpPerPixel);this.canvas.style.left=e+"px"}}setTop(t){if(super.setTop(t),this.canvas){const e=this.$viewport.height(),i=t+this.canvas._data.pixelTop,n=i+this.canvas._data.pixelHeight;(i>0||n
0)for(let n of i.roiSets){const i=await n.getFeatures(e,r,s,t.bpPerPixel);o.push({track:n,features:i})}const a=i&&("wig"===i.type||"merged"===i.type);return this.featureCache=new bl(e,r,s,t.bpPerPixel,n,o,a),this.loading=!1,this.hideMessage(),this.stopSpinner(),this.featureCache}}catch(t){this.trackView&&!0!==this.trackView.disposed&&(this.showMessage("Error loading track data"),this.browser.alert.present(t),console.error(t))}finally{this.loading=!1,this.stopSpinner()}}}repaintDimensions(){const t=ul.isWholeGenomeView(this.referenceFrame.chr),e=t?this.$viewport.width():3*this.$viewport.width(),i=this.referenceFrame.bpPerPixel;return{bpStart:this.referenceFrame.start-(t?0:e/3*i),bpEnd:this.referenceFrame.end+(t?0:e/3*i),pixelWidth:e}}repaint(){if(void 0===this.featureCache)return;const{features:t,roiFeatures:e}=this.featureCache,{bpStart:i,bpEnd:n,pixelWidth:r}=this.repaintDimensions(),s=this.$viewport.height(),o=this.getContentHeight(),a=e?Math.max(o,s):o,l=Math.min(a,3*s);if(0===r||0===l)return void(this.canvas&&fe(this.canvas).remove());const h=Math.max(0,-this.contentTop-Math.floor(l/3)),c=this.referenceFrame.bpPerPixel,u=Math.round((i-this.referenceFrame.start)/c),d=(this.contentTop||0)+h,f=document.createElement("canvas");f.style.position="relative",f.style.display="block",f.style.width=r+"px",f.style.height=l+"px",f.style.left=u+"px",f.style.top=d+"px";const p="FILL"===this.trackView.track.displayMode||!1!==this.trackView.track.supportHiDPI?window.devicePixelRatio:1;f.width=p*r,f.height=p*l;const g=f.getContext("2d");g.scale(p,p),g.translate(0,-h);const m={context:g,pixelXOffset:u,pixelWidth:r,pixelHeight:l,pixelTop:h,bpStart:i,bpEnd:n,bpPerPixel:c,referenceFrame:this.referenceFrame,selection:this.selection,viewport:this,viewportWidth:this.$viewport.width()};this.draw(m,t,e),this.canvas&&fe(this.canvas).remove(),f._data=m,this.canvas=f,this.$viewport.append(fe(f))}refresh(){if(!this.canvas||!this.featureCache)return;const t=this.canvas._data;t.context.clearRect(0,0,this.canvas.width,this.canvas.height);const{features:e,roiFeatures:i}=this.featureCache;this.draw(t,e,i)}draw(t,e,i){if(e&&(t.features=e,this.trackView.track.draw(t)),i&&i.length>0)for(let e of i)t.features=e.features,e.track.draw(t)}containsPosition(t,e){return this.referenceFrame.chr===t&&e>=this.referenceFrame.start&&e<=this.referenceFrame.calculateEnd(this.getWidth())}isLoading(){return this.loading}savePNG(){if(!this.canvas)return;const t=this.canvas._data,e=t?t.pixelTop:0,i=window.devicePixelRatio,n=this.$viewport.width()*i,r=this.$viewport.height()*i,s=-fe(this.canvas).position().left*i,o=(-this.contentTop-e)*i,a=this.canvas.getContext("2d").getImageData(s,o,n,r),l=document.createElement("canvas"),h=l.getContext("2d");l.width=a.width,l.height=a.height,h.putImageData(a,0,0),Qi((this.$trackLabel.text()?this.$trackLabel.text():"image")+".png",l.toDataURL("image/png"))}saveSVG(){let{width:t,height:e}=this.browser.columnContainer.getBoundingClientRect();const i=new ll({width:t,height:8e3,backdropColor:"white",multiLocusGap:0,viewbox:{x:0,y:0,width:t,height:8e3}});this.renderViewportToSVG(i,{deltaX:32,deltaY:32}),i.setHeight(e);const n=(this.trackView.track.name||this.trackView.track.id).replace(/\W/g,""),r=this.browser.referenceFrameList.indexOf(this.referenceFrame),s=i.getSerializedSvg(!0),o=URL.createObjectURL(new Blob([s],{type:"application/octet-stream"}));Qi(`${n}_referenceFrame_${r}_guid_${_e.guid()}.svg`,o)}renderViewportToSVG(t,{deltaX:e,deltaY:i}){if(this.$zoomInNotice&&this.$zoomInNotice.is(":visible"))return;const{width:n,height:r}=this.$viewport.get(0).getBoundingClientRect(),s=`${(this.trackView.track.name||this.trackView.track.id).replace(/\W/g,"")}_referenceFrame_${this.browser.referenceFrameList.indexOf(this.referenceFrame)}_guid_${_e.guid()}`;this.drawSVGWithContext(t,n,r,s,e,i+this.contentTop,-this.contentTop)}renderSVGContext(t,{deltaX:e,deltaY:i}){if(this.renderViewportToSVG(t,{deltaX:e,deltaY:i}),(!this.$zoomInNotice||!this.$zoomInNotice.is(":visible"))&&this.$trackLabel&&!0===this.browser.trackLabelsVisible){const{x:n,y:r,width:s,height:o}=_e.relativeDOMBBox(this.$viewport.get(0),this.$trackLabel.get(0));this.renderTrackLabelSVG(t,e+n,i+r,s,o)}}renderTrackLabelSVG(t,e,i,n,r){const s=`${(this.trackView.track.name||this.trackView.track.id).replace(/\W/g,"")}_track_label_guid_${_e.guid()}`;t.saveWithTranslationAndClipRect(s,e,i,n,r,0),t.fillStyle="white",t.fillRect(0,0,n,r),t.font="12px Arial",t.fillStyle="rgb(68, 68, 68)";const{width:o}=t.measureText(this.$trackLabel.text()),a=.25*(n-o),l=.7*(r-12);t.fillText(this.$trackLabel.text(),a,r-l),t.strokeStyle="rgb(68, 68, 68)",t.strokeRect(0,0,n,r),t.restore()}drawSVGWithContext(t,e,i,n,r,s,o){t.saveWithTranslationAndClipRect(n,r,s,e,i,o);let{start:a,bpPerPixel:l}=this.referenceFrame;const h={context:t,viewport:this,referenceFrame:this.referenceFrame,top:o,pixelTop:o,pixelWidth:e,pixelHeight:i,bpStart:a,bpEnd:a+e*l,bpPerPixel:l,viewportWidth:e,selection:this.selection},c=this.featureCache?this.featureCache.features:void 0,u=this.featureCache?this.featureCache.roiFeatures:void 0;this.draw(h,c,u),t.restore()}get cachedFeatures(){return this.featureCache?this.featureCache.features:[]}clearCache(){this.featureCache=void 0,this.canvas&&(this.canvas._data=void 0)}async getFeatures(t,e,i,n,r){if(this.featureCache&&this.featureCache.containsRange(e,i,n,r))return this.featureCache.features;if("function"==typeof t.getFeatures){const s=await t.getFeatures(e,i,n,r,this);return this.checkContentHeight(s),s}}needsRepaint(){if(!this.canvas)return!0;const t=this.canvas._data;return!t||this.referenceFrame.startt.bpEnd||this.referenceFrame.chr!==t.referenceFrame.chr||this.referenceFrame.bpPerPixel!=t.bpPerPixel}needsReload(){if(!this.featureCache)return!0;const{chr:t,bpPerPixel:e}=this.referenceFrame,{bpStart:i,bpEnd:n}=this.repaintDimensions();return!this.featureCache.containsRange(t,i,n,e)}createZoomInNotice(t){const e=fe("",{class:"igv-zoom-in-notice-container"});t.append(e);const i=fe("
");return e.append(i),i.text("Zoom in to see features"),e.hide(),e}viewIsReady(){return this.browser&&this.browser.referenceFrameList&&this.referenceFrame}addMouseHandlers(){const t=this.$viewport.get(0);this.addViewportContextMenuHandler(t);const e=t=>{this.enableClick=!0,this.browser.mouseDownOnViewport(t,this),_e.pageCoordinates(t)};t.addEventListener("mousedown",e),t.addEventListener("touchstart",e);const i=t=>{this.browser.dragObject||this.browser.isScrolling?(this.browser.cancelTrackPan(),this.enableClick=!1):(this.browser.cancelTrackPan(),this.browser.endTrackDrag())};t.addEventListener("mouseup",i),t.addEventListener("touchend",i),"function"==typeof this.trackView.track.hoverText&&t.addEventListener("mousemove",(t=>{if(0===t.buttons&&Date.now()-gl>100){gl=Date.now();const e=this.createClickState(t);if(e){const t=this.trackView.track.hoverText(e);t?this.$viewport[0].setAttribute("title",t):this.$viewport[0].removeAttribute("title")}}})),this.addViewportClickHandler(this.$viewport.get(0)),this.trackView.track.name&&"sequence"!==this.trackView.track.config.type&&this.addTrackLabelClickHandler(this.$trackLabel.get(0))}addViewportContextMenuHandler(t){t.addEventListener("contextmenu",(t=>{if(this.browser.dragObject)return!1;const e=this.createClickState(t);if(void 0===e)return!1;t.preventDefault();let i=[];if("function"==typeof this.trackView.track.contextMenuItemList){const t=this.trackView.track.contextMenuItemList(e);t&&(i=t)}i.length>0&&i.push({label:fe("
")}),i.push({label:"Save Image (PNG)",click:()=>this.savePNG()}),i.push({label:"Save Image (SVG)",click:()=>this.saveSVG()}),this.browser.menuPopup.presentTrackContextMenu(t,i)}))}addViewportClickHandler(t){t.addEventListener("click",(t=>{if(this.enableClick&&this.canvas){if(3===t.which||t.ctrlKey)return;if(fe(".igv-popover").hide(),this.browser.dragObject||this.browser.isScrolling)return;t.preventDefault();const e=_e.translateMouseCoordinates(t,this.$viewport.get(0)).x,i=_e.translateMouseCoordinates(t,this.canvas).x,n=this.referenceFrame,r=Math.floor(n.start+n.toBP(i)),s=Date.now();if(s-pl
t));t[this.browser.referenceFrameList.indexOf(this.referenceFrame)]=e,i=t.join(" ")}this.browser.search(i)}else this.browser.zoomWithScaleFactor(.5,t,this.referenceFrame)}else t.shiftKey&&"function"==typeof this.trackView.track.shiftClick?this.trackView.track.shiftClick(r,t):"function"==typeof this.trackView.track.popupData&&(fl=setTimeout((()=>{const e=this.getPopupContent(t);e&&(this.popover&&this.popover.dispose(),this.popover=new Oi(this.browser.columnContainer),this.popover.presentContentWithEvent(t,e)),window.clearTimeout(fl),fl=void 0}),this.browser.constants.doubleClickDelay));pl=s}}))}addTrackLabelClickHandler(t){t.addEventListener("click",(t=>{t.stopPropagation();const{track:e}=this.trackView;let i;"function"==typeof e.description?i=e.description():e.description&&(i=`${e.description}
`),i&&(this.popover&&this.popover.dispose(),this.popover=new Oi(this.browser.columnContainer,e.name||""),this.popover.presentContentWithEvent(t,i))}))}createClickState(t){if(!this.canvas)return;const e=this.referenceFrame,i=_e.translateMouseCoordinates(t,this.$viewport.get(0)),n=_e.translateMouseCoordinates(t,this.canvas),r=e.start+e.toBP(i.x);return{event:t,viewport:this,referenceFrame:e,genomicLocation:r,y:i.y-this.contentTop,canvasX:n.x,canvasY:n.y}}getPopupContent(t){const e=this.createClickState(t);if(void 0===e)return;let i=this.trackView.track;const n=i.popupData(e),r=this.browser.fireEvent("trackclick",[i,n]);let s;return void 0===r||!0===r?n&&n.length>0&&(s=n.map((t=>{if(t.name){const e=`${t.name} ${t.value}`;return`${e}
`}return"
"===t?t:t.html?t.html:`${t}
`})).join("")):"string"==typeof r&&(s=r),s}}class bl{constructor(t,e,i,n,r,s,o){this.chr=t,this.bpStart=e,this.bpEnd=i,this.bpPerPixel=n,this.features=r,this.roiFeatures=s,this.multiresolution=o}containsRange(t,e,i,n){const r=this.multiresolution?this.bpPerPixel/n:1;return e>=this.bpStart&&i<=this.bpEnd&&t===this.chr&&r>.5&&r<2}overlapsRange(t,e,i){return this.chr===t&&i>=this.bpStart&&e<=this.bpEnd}}function yl(t,e){if(!(t.length<6))return{chr:t[0],start:t[1],end:t[2],chr1:t[8],start1:Number.parseInt(t[9]),end1:Number.parseInt(t[10]),chr2:t[13],start2:Number.parseInt(t[14]),end2:Number.parseInt(t[15]),name:t[3],score:Number(t[4]),value:Number(t[5]),color:"."===t[7]?void 0:"0"===t[7]?"rgb(0,0,0)":t[7]};console.log("Skipping line: "+t.join(" "))}const vl=new Set(["transcript","primary_transcript","processed_transcript","mRNA","mrna","lnc_RNA","miRNA","ncRNA","rRNA","scRNA","snRNA","snoRNA","tRNA"]),wl=new Set(["CDS","cds"]),_l=new Set(["start_codon","stop_codon"]),xl=new Set(["5UTR","3UTR","UTR","five_prime_UTR","three_prime_UTR","3'-UTR","5'-UTR"]),kl=new Set(["exon","coding-exon"]),Sl=new Set;for(let _y of[wl,_l,xl,kl])for(let xy of _y)Sl.add(xy);function Cl(t){return t.includes("intron")}function Al(t){return wl.has(t)||_l.has(t)}function Tl(t){return xl.has(t)}function Il(t){return vl.has(t)||t.endsWith("RNA")||t.endsWith("transcript")}function El(t){return Sl.has(t)||t.endsWith("RNA")||Cl(t)}const Ml=new Set(["id","parent","name"]);class Rl{constructor(t){Object.assign(this,t)}popupData(t){const e=this.geneObject?this.geneObject.popupData():[];if(this.geneObject&&e.push("
"),this.name&&e.push({name:"Name",value:this.name}),e.push({name:"Type",value:this.type}),e.push({name:"Source",value:this.source}),void 0!==this.score&&e.push({name:"Score",value:this.score}),this.attributeString){const t=Ol(this.attributeString,this.delim);for(let[i,n]of t)void 0!==n&&n.length>0&&!Ml.has(i.toLowerCase())&&e.push({name:i+":",value:n})}return e.push({name:"Location",value:`${this.chr}:${$i(this.start+1)}-${$i(this.end)}`}),e}getAttributeValue(t){if(this.hasOwnProperty(t))return this[t];if(this._attributeCache||(this._attributeCache=new Map),this._attributeCache.has(t))return this._attributeCache.get(t);{const e=Ol(this.attributeString,this.delim);let i;for(let[n,r]of e)if(n===t){i=r;break}return this._attributeCache.set(t,i),i}}}class Ll extends Rl{constructor(t){super(t),this.exons=[],this.parts=[]}addExon(t){this.exons.push(t),this.start=Math.min(this.start,t.start),this.end=Math.max(this.end,t.end)}addPart(t){this.parts.push(t)}assembleParts(){if(0===this.parts.length)return;this.parts.sort((function(t,e){return t.start-e.start}));let t=this.parts[0].start,e=this.parts[0].end;for(let i=1;i=e&&i.start<=t)return i}addCDS(t){let e;const i=this.exons;for(let n of i)if(n.start<=t.start&&n.end>=t.end){e=n;break}e?(e.cdStart=e.cdStart?Math.min(t.start,e.cdStart):t.start,e.cdEnd=e.cdEnd?Math.max(t.end,e.cdEnd):t.end):console.error("No exon found spanning "+t.start+"-"+t.end),this.cdStart=this.cdStart?Math.min(t.start,this.cdStart):t.start,this.cdEnd=this.cdEnd?Math.max(t.end,this.cdEnd):t.end}addUTR(t){let e;const i=this.exons;for(let n=0;n=t.end){e=i[n];break}e?t.start===e.start&&t.end===e.end?e.utr=!0:(t.ende.start&&(e.cdEnd=t.start)):console.error("No exon found spanning "+cds.start+"-"+cds.end)}finish(){this.assembleParts();var t=this.cdStart,e=this.cdEnd;this.exons.sort((function(t,e){return t.start-e.start})),t&&this.exons.forEach((function(i){(i.ende)&&(i.utr=!0)}))}popupData(t){const e=super.popupData(t);for(let i of this.exons)if(!i.pseudo&&t>=i.start&&t");const n=i.popupData(t);for(let t of n)e.push(t)}for(let i of this.parts)if(t>=i.start&&t");const n=i.popupData(t);for(let t of n)e.push(t)}return e}}function Bl(t,e){const i=e.format;if(t.length<9)return;const n="gff3"===i?"=":" ";return new Rl({source:zl(t[1]),type:t[2],chr:t[0],start:parseInt(t[3])-1,end:parseInt(t[4]),score:"."===t[5]?void 0:Number(t[5]),strand:t[6],phase:"."===t[7]?0:parseInt(t[7]),attributeString:t[8],delim:n})}function Nl(t,e){const i=Bl(t,e);if(!i)return;const n=Ol(i.attributeString,i.delim);for(let[t,e]of n){const n=t.toLowerCase();"color"===n||"colour"===n?i.color=xo.createColorString(e):"ID"===t?i.id=e:"Parent"===t&&(i.parent=e)}return i}function Fl(t,e){const i=Bl(t,e);if(!i)return;const n=Ol(i.attributeString,i.delim);let r,s;switch(i.type){case"gene":r="gene_id";break;case"transcript":r="transcript_id",s="gene_id";break;default:s="transcript_id"}for(let[t,e]of n){const n=t.toLowerCase();"color"===n||"colour"===n?i.color=xo.createColorString(e):t===r?i.id=e:t===s&&(i.parent=e)}return i}function Ol(t,e,i=!1){var n=[];for(let r of t.split(";")){r=r.trim();const t=r.indexOf(e);if(t>0&&t2?parseInt(t[2]):n+1;if(isNaN(n)||isNaN(r))return new Ul("Unparsable bed record.");const s=new Jl({chr:i,start:n,end:r,score:1e3});try{if(t.length>3){if(t[3].indexOf(";")>0&&t[3].indexOf("=")>0){const i=Ol(t[3],"=",!0);s.attributes={};for(let t of i)s.attributes[t[0]]=t[1],null!=e.nameField&&t[0]===e.nameField&&(s.name=t[1])}s.name||(s.name="."===t[3]?"":t[3])}if(t.length>4&&(s.score="."===t[4]?0:Number(t[4]),isNaN(s.score)))return s;if(t.length>5&&(s.strand=t[5],"."!==s.strand&&"+"!==s.strand&&"-"!==s.strand))return s;if(t.length>6&&(s.cdStart=parseInt(t[6]),isNaN(s.cdStart)))return s;if(t.length>7&&(s.cdEnd=parseInt(t[7]),isNaN(s.cdEnd)))return s;if(t.length>8&&"."!==t[8]&&"0"!==t[8]&&(s.color=xo.createColorString(t[8])),t.length>11){const e=parseInt(t[9]);if(e>1e3)return s;const i=t[10].replace(/,$/,"").split(","),r=t[11].replace(/,$/,"").split(",");if(i.length!==r.length||e!==i.length)return s;const o=[];for(let t=0;t0&&(Zl(o,s.cdStart,s.cdEnd),s.exons=o)}if(e){let i=e.thicknessColumn,n=e.colorColumn;n&&ni?n.utr=!0:(e>=r&&e<=t&&(n.cdStart=e),i>=r&&i<=t&&(n.cdEnd=i))}}function Yl(t,e){var i,n,r,s,o,a,l;if(!(t.length<9))return i=t[0],n=parseInt(t[1]),r=parseInt(t[2]),o=t[3],a=Number(t[4]),s=t[5].trim(),l=Number(t[6]),0===a&&(a=l),{chr:i,start:n,end:r,name:o,score:a,strand:s,signal:l,pValue:Number(t[7]),qValue:Number(t[8])}}function Ql(t,e){if(t.length<=3)return;const i={chr:t[0],start:parseInt(t[1]),end:parseInt(t[2]),value:Number(t[3])};if(e){let n=e.colorColumn;n&&n0)for(var d=l.split(","),f=0;fu&&(u=m),h.spanning_frag_coords.push({left:g,right:m})}return h.start=c,h.end=u,h}}function ih(t,e){if(t.length<7)return null;const i={chr:t[0],start:parseInt(t[1])-1,end:parseInt(t[2]),"Strongest SNP-risk allele":t[3],"Disease/Phenotype":t[4],"P-value":t[5],"Odds ratio or beta":t[6]};return t.length>6&&(i.PUBMEDID=`${t[7]}`),i}function nh(t,e){const i=e.customFormat;if(t.length1&&(e=t)}else{this.setDecoder(n.format);const t=i.split(this.delimiter||"\t");try{const i=Object.assign({columnNames:e},n);if(this.decode(t,i))break;t.length>1&&(e=t)}catch(i){t.length>1&&(e=t)}}}if(e){n.columnNames=e;for(let t=0;t