@sjcrh/proteinpaint-client 2.76.2 → 2.77.0

package/dist/{Disco-b7c9bf72.js → Disco-3c427131.js}

@@ -1 +1 @@
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t==="function"?t:P(+t),c):n};c.targetRadius=function(t){return arguments.length?(i=typeof t==="function"?t:P(+t),c):i};c.startAngle=function(t){return arguments.length?(a=typeof t==="function"?t:P(+t),c):a};c.endAngle=function(t){return arguments.length?(o=typeof t==="function"?t:P(+t),c):o};c.padAngle=function(t){return arguments.length?(r=typeof t==="function"?t:P(+t),c):r};c.source=function(t){return arguments.length?(e=t,c):e};c.target=function(t){return arguments.length?(s=t,c):s};c.context=function(t){return arguments.length?(l=t==null?null:t,c):l};return c}function G(){return B()}function $(t,e){return e<t?-1:e>t?1:e>=t?0:NaN}function k(t){return t}function W(){var t=k,e=$,s=null,n=f(0),i=f(M),a=f(0);function o(o){var r,l=(o=A(o)).length,c,h,d=0,p=new Array(l),u=new 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F{constructor(t,e,s){this.radius=t;this.width=e;this.color=s}render(t){const e=g();const s={startAngle:0,endAngle:Math.PI*2,innerRadius:this.radius,outerRadius:this.radius+this.width,color:this.color,text:"No label"};const n=[];n.push(s);const i=t.append("g");i.selectAll("path").data(n).enter().append("path").attr("d",(t=>e(t))).attr("fill",(t=>t.color))}}class j{static create(){const t=new e({padding:5});t.d.style("border","1px solid #FFF").style("position","absolute").style("z-index",1001);return t}}var _;(function(t){t["Intrachromosomal"]="#1B9E77";t["Interchromosomal"]="#6A3D9A"})(_||(_={}));class H{static getColor(t,e){if(t!=e){return _.Interchromosomal.valueOf()}else{return _.Intrachromosomal.valueOf()}}}class U{render(t,e){let n=0;if(e.length>0){n=e[0].target.radius;const s=new F(n,2,"#6464641A");s.render(t)}const i=G().radius(n);const a=t.selectAll(".chord").data(e);const o=j.create();a.enter().append("path").attr("class","chord").attr("d",i).attr("fill",(t=>H.getColor(t.source.positionInChromosome.chromosome,t.target.positionInChromosome.chromosome))).on("mouseover",((t,e)=>{const n=s({holder:o.d});this.createTooltip(n,e);o.show(t.x,t.y)})).on("mouseout",(()=>{o.clear();o.hide()}))}createTooltip(t,e){{const[e,s]=t.addRow();e.text("Data type");s.append("span").style("margin-left","5px").text("Fusion transcript")}{const s=e.source.positionInChromosome;const n=e.target.positionInChromosome;const[i,a]=t.addRow();i.text("Position");a.append("span").style("margin-left","5px").text(` ${e.source.gene?e.source.gene:""} ${s.chromosome}:${s.position} ${e.source.strand=="+"?"forward":"reverse"} > `+` ${e.target.gene?e.target.gene:""} ${n.chromosome}:${n.position} ${e.target.strand=="+"?"forward":"reverse"} `)}}}class q{constructor(t,e){this.renders=t;this.legendRenderer=e;this.fusionRenderer=new U}render(t,e){const s=t.append("div").style("display","inline-block").style("font-family","Arial");const n=s.append("svg").attr("id","sjpp_disco_plot").attr("data-testid","sjpp_disco_plot").attr("width",e.width).attr("height",e.height+e.legendHeight);const i=n.append("g").attr("class","mainG").attr("transform",`translate(${e.settings.rings.labelLinesInnerRadius+e.settings.rings.labelsToLinesDistance+100},${e.height/2})`);for(const[t,s]of this.renders){const n=e.getElements(t);const a=e.getCollisions(t);s.render(i,n,a)}this.fusionRenderer.render(i,e.fusions);this.legendRenderer.render(i,e.legend,-1*(e.settings.rings.labelLinesInnerRadius+e.settings.rings.labelsToLinesDistance+50),e.width,e.height/2)}}class X{constructor(e){this.discoApp=e;this.downloadClickListener=t=>{const e=this.discoApp.state.settings.downloadImgName||"disco.plot";const s=document.createElement("a");document.body.appendChild(s);s.addEventListener("click",(()=>{const n=new XMLSerializer;const i=new Blob([n.serializeToString(t)],{type:"image/svg+xml"});s.download=e+".svg";s.href=URL.createObjectURL(i);document.body.removeChild(s)}),false);s.click()};this.geneClickListener=(e,s)=>t(this,void 0,void 0,(function*(){const{filter:t,filter0:n}=this.discoApp.app.getState().termfilter;const i={holder:this.discoApp.app.opts.holder,genome:this.discoApp.app.opts.state.args.genome,nobox:true,query:e,tklst:[{type:"mds3",dslabel:this.discoApp.app.opts.state.dslabel,hlaachange:s.join(","),filter0:n,filterObj:t}]};const a=yield import("./app-6fb77603.js").then((function(t){return t.c3}));yield a.default(i)}))}}class K{constructor(t,e,s){this.chromosomes=[];this.chromosomesOrder=[];this.keysArray=[];this.totalSizeArray=[];this.chrSizesArray=[];const n=s||e;this.settings=t;this.chromosomesOrder=[];let i=0;this.totalPadAngle=Object.keys(n).length*this.settings.padAngle;this.totalChromosomesAngle=2*Math.PI-this.totalPadAngle;for(const t in n){const e=t.slice(0,3)==="chr"?t.slice(3):t;this.chromosomesOrder.push(t);this.keysArray.push(e);this.totalSizeArray.push(i);this.chrSizesArray.push(n[t]);i+=n[t]}this.totalSize=i;let a=0;for(let t=0;t<this.keysArray.length;t++){const e=this.totalChromosomesAngle*(this.chrSizesArray[t]/i);const s=t==0?this.settings.padAngle/2:a+this.settings.padAngle;const n=t==0?this.settings.padAngle/2+e:a+this.settings.padAngle+e;const o={start:this.totalSizeArray[t],size:this.chrSizesArray[t],factor:1,startAngle:s,endAngle:n,angle:(s+n)/2,innerRadius:this.settings.chromosomeInnerRadius,outerRadius:this.settings.chromosomeInnerRadius+this.settings.chromosomeWidth,color:"#AAA",text:this.keysArray[t]};this.chromosomes.push(o);if(o.endAngle!=null){a=o.endAngle}}}}class J{constructor(t,e){this.sampleName=t;this.prioritizedGenes=e}map(t){return{dt:t.dt,mname:t.mname,mClass:t.class,gene:t.gene,chr:t.chr,ref:t.ref,alt:t.alt,position:t.pos?t.pos:t.position,poschr:t.poschr,posbins:t.posbins,poslabel:t.poslabel,sampleName:this.sampleName,ssm_id:t.ssm_id,start:t.start,stop:t.stop,value:t.value,segmean:t.segmean,isPrioritized:this.prioritizedGenes.some((e=>e==t.gene)),chrA:t.chrA,chrB:t.chrB,geneA:t.geneA,geneB:t.geneB,posA:t.posA,posB:t.posB,strandA:t.strandA,strandB:t.strandB}}}class Q{map(t,e){return this.calculatePercentileForPositivesAndNegatives(t,e)}calculatePercentileForPositivesAndNegatives(t,e){const s=t.filter((t=>t>0));const n=t.filter((t=>t<0)).map((t=>-1*t));let i=NaN;let a=NaN;if(s.length>0){i=this.calculatePercentile(s,e)}if(n.length>0){a=-1*this.calculatePercentile(n,e)}return{positive:i,negative:a}}calculatePercentile(t,e){if(t.length===0){throw new Error("Array must contain at least one element.")}const s=t.sort(((t,e)=>t-e));const n=e/100*(s.length-1);const i=Math.floor(n);const a=Math.ceil(n);const o=n-i;if(i===a){return s[i]}return s[i]+o*(s[a]-s[i])}}class Y{constructor(t,e,s,l=[]){this.labelData=[];this.nonExonicSnvData=[];this.nonExonicInnerRadius=0;this.snvRingDataMap=new Map;this.snvInnerRadius=0;this.snvData=[];this.bpx=0;this.onePxArcAngle=0;this.filteredSnvData=[];this.lohData=[];this.lohInnerRadius=0;this.cnvData=[];this.cnvInnerRadius=0;this.fusionData=[];this.fusionRadius=0;this.hasPrioritizedGenes=false;this.cnvLossMaxValue=0;this.cnvGainMaxValue=0;this.percentilePositive=0;this.percentileNegative=0;this.cnvMaxPercentileAbs=0;this.lohMaxValue=undefined;this.lohMinValue=undefined;this.snvFilter=t=>t.dt==n;this.fusionFilter=t=>t.dt==i||t.dt==a;this.cnvFilter=t=>t.dt==o;this.lohFilter=t=>t.dt==r;this.compareData=(t,e)=>{const s=this.reference.chromosomesOrder.indexOf(t.chr)-this.reference.chromosomesOrder.indexOf(e.chr);if(s!=0){return s}const n=t.pos?t.pos:t.start;const i=e.pos?e.pos:e.start;return n-i};this.settings=t;this.reference=e;this.sample=s;this.lastInnerRadious=this.settings.rings.chromosomeInnerRadius;this.gainCapped=this.settings.Disco.cnvCapping;this.lossCapped=-1*this.settings.Disco.cnvCapping;this.nonExonicFilter=e=>{if(l.length>0&&this.settings.Disco.prioritizeGeneLabelsByGeneSets){return l.includes(e.gene)&&t.rings.nonExonicFilterValues.includes(yt.snvClassLayer[e.mClass])}else{return t.rings.nonExonicFilterValues.includes(yt.snvClassLayer[e.mClass])}};this.snvRingFilter=e=>{if(l.length>0&&this.settings.Disco.prioritizeGeneLabelsByGeneSets){return l.includes(e.gene)&&t.rings.snvRingFilters.includes(yt.snvClassLayer[e.mClass])}else{return t.rings.snvRingFilters.includes(yt.snvClassLayer[e.mClass])}};this.dataObjectMapper=new J(s,l)}map(t){const e=[];t.forEach((t=>{const s=this.reference.chromosomesOrder.indexOf(t.chr);const l=this.reference.chromosomesOrder.indexOf(t.chrA);const c=this.reference.chromosomesOrder.indexOf(t.chrB);if(t.dt==n){if(s!=-1&&this.snvData.length<this.settings.snv.maxMutationCount){this.addData(t,e)}}else if(t.dt==i||t.dt==a){if(l!=-1&&c!=-1){this.addData(t,e)}}else if([o,r].includes(Number(t.dt))){this.addData(t,e)}else{throw Error("Unknown mutation type!")}}));const s=e.sort(this.compareData);if(this.settings.rings.nonExonicRingEnabled){s.forEach((t=>{this.filterNonExonicSnvData(t)}))}if(this.nonExonicSnvData.length>0){this.nonExonicInnerRadius=this.lastInnerRadious-this.settings.rings.nonExonicRingWidth;this.lastInnerRadious=this.nonExonicInnerRadius}s.forEach((t=>{this.filterSnvs(t)}));s.forEach((t=>{this.filterLohs(t)}));if(this.lohData.length>0){this.lohInnerRadius=this.lastInnerRadious-this.settings.rings.lohRingWidth;this.lastInnerRadious=this.lohInnerRadius}s.forEach((t=>{this.filterCnvs(t)}));if(this.cnvData.length>0){this.cnvInnerRadius=this.lastInnerRadious-this.settings.rings.cnvRingWidth;this.lastInnerRadious=this.cnvInnerRadius;this.cappedCnvMaxAbsValue=Math.min(this.settings.Disco.cnvCapping,Math.max(Math.abs(Y.capMaxValue(this.cnvLossMaxValue,this.gainCapped,this.lossCapped)),Math.abs(Y.capMaxValue(this.cnvGainMaxValue,this.gainCapped,this.lossCapped))));const t=(new Q).map(this.cnvData.map((t=>t.value)),this.settings.Disco.cnvPercentile);this.percentilePositive=Y.capMaxValue(t.positive,this.gainCapped,this.lossCapped);this.percentileNegative=Y.capMaxValue(t.negative,this.gainCapped,this.lossCapped);this.cnvMaxPercentileAbs=Math.min(this.settings.Disco.cnvCapping,Math.max(this.percentilePositive,Math.abs(this.percentileNegative)))}s.forEach((t=>{this.filterFusion(t)}));if(this.fusionData.length>0){this.fusionRadius=this.lastInnerRadious}const l={labelData:this.labelData,nonExonicSnvData:this.nonExonicSnvData,nonExonicInnerRadius:this.nonExonicInnerRadius,snvRingDataMap:this.snvRingDataMap,snvInnerRadius:this.snvInnerRadius,snvData:this.snvData,bpx:this.bpx,onePxArcAngle:this.onePxArcAngle,filteredSnvData:this.filteredSnvData,lohData:this.lohData,lohInnerRadius:this.lohInnerRadius,cnvData:this.cnvData,cnvInnerRadius:this.cnvInnerRadius,fusionData:this.fusionData,fusionRadius:this.fusionRadius,hasPrioritizedGenes:this.hasPrioritizedGenes,cnvGainMaxValue:this.cnvGainMaxValue,cnvLossMaxValue:this.cnvLossMaxValue,cappedCnvMaxAbsValue:this.cappedCnvMaxAbsValue,percentilePositive:this.percentilePositive,percentileNegative:this.percentileNegative,cnvMaxPercentileAbs:this.cnvMaxPercentileAbs,lohMaxValue:this.lohMaxValue,lohMinValue:this.lohMinValue};return l}addData(t,e){const s=this.dataObjectMapper.map(t);if(s.isPrioritized){this.hasPrioritizedGenes=true}e.push(s)}filterNonExonicSnvData(t){if(this.snvFilter(t)){if(this.settings.rings.nonExonicRingEnabled&&this.nonExonicFilter(t)){this.nonExonicSnvData.push(t)}}}filterSnvs(t){if(this.snvFilter(t)){this.snvData.push(t);if(this.snvRingFilter(t)){if(this.snvInnerRadius==0){this.snvInnerRadius=this.lastInnerRadious-this.settings.rings.snvRingWidth;this.lastInnerRadious=this.snvInnerRadius;this.bpx=Math.floor(this.reference.totalSize/(this.reference.totalChromosomesAngle*this.snvInnerRadius));this.onePxArcAngle=1/this.snvInnerRadius}this.filteredSnvData.push(t);this.labelData.push(t);const e=this.calculateArcAngle(t);let s=this.snvRingDataMap.get(e);if(!s){s=new Array}s.push(t);this.snvRingDataMap.set(e,s)}}}filterFusion(t){if(this.fusionFilter(t)){t.isPrioritized=true;this.fusionData.push(t);this.labelData.push(t)}}filterLohs(t){if(this.lohFilter(t)){if(this.lohMaxValue==undefined||this.lohMaxValue<t.value){this.lohMaxValue=t.segmean}if(this.lohMinValue==undefined||this.lohMinValue>t.value){this.lohMinValue=t.segmean}this.lohData.push(t)}}filterCnvs(t){if(this.cnvFilter(t)){if(this.cnvGainMaxValue==undefined||this.cnvGainMaxValue<t.value){this.cnvGainMaxValue=t.value}if(this.cnvLossMaxValue==undefined||this.cnvLossMaxValue>t.value){this.cnvLossMaxValue=t.value}this.cnvData.push(t)}}calculateArcAngle(t){const e=this.reference.chromosomes[this.reference.chromosomesOrder.findIndex((e=>t.chr==e))];const s=Math.floor(t.position/this.bpx);return e.startAngle+s*this.onePxArcAngle}static capMaxValue(t,e,s){if(t&&Math.sign(t)==1){return t>e?e:t}if(Math.sign(t)==-1){return t<s?s:t}return 0}static capMinValue(t,e=1){if(Math.sign(t)==1){return t>e?t:e}if(Math.sign(t)==-1){return t<-1*e?t:-1*e}return 1}}class Z{constructor(t,e,s,n,i,a,o,r,l){this.snvTitle=t;this.cnvTitle=e;this.lohTitle=s;this.fusionTitle=n;this.snvClassMap=i;this.cnvClassMap=a;this.cnvRenderingType=o;this.lohLegend=l;this.fusionLegend=r}legendCount(){return(this.snvClassMap.size>0?1:0)+(this.cnvClassMap.size>0?1:0)+(this.lohLegend?1:0)+(this.fusionLegend?1:0)}}class tt{constructor(t,e,s,n,i){this.source=t;this.target=e;this.genes=s;this.count=n;this.endpts=i}}class et{constructor(t,e,s,n,i,a,o,r){this.startAngle=t;this.endAngle=e;this.radius=s;this.gene=n;this.value=i;this.genes=a;this.positionInChromosome=o;this.strand=r}}class st{constructor(t,e,s){this.radius=t;this.sampleName=e;this.reference=s}map(t){const e=[];t.forEach((t=>{const s=new Set;s.add(t.geneA);s.add(t.geneB);const n=new et(this.calculateStartAngle(t.chrA,t.posA),this.calculateEndAngle(t.chrA,t.posA),this.radius,t.geneA,t.value,s,{chromosome:t.chrA,position:t.posA},t.strandA);const i=new et(this.calculateStartAngle(t.chrB,t.posB),this.calculateEndAngle(t.chrB,t.posB),this.radius,t.geneB,t.value,s,{chromosome:t.chrB,position:t.posB},t.strandB);const a=new tt(n,i,"genes",-1,"Endpoints");e.push(a)}));return e}calculateStartAngle(t,e){const s=this.reference.chromosomesOrder.indexOf(t);const n=this.reference.chromosomes[s];return n.startAngle+(n.endAngle-n.startAngle)*(Number(e)/n.size)-.01}calculateEndAngle(t,e){const s=this.reference.chromosomesOrder.indexOf(t);const n=this.reference.chromosomes[s];return.01+n.startAngle+(n.endAngle-n.startAngle)*(Number(e)/n.size)}}class nt{static provide(t){const e=Math.min(Math.max(t,0),1);const s=Math.round(e*255);return`rgb(${s}, ${s}, ${s})`}}class it{constructor(t,e){this.minValue=t;this.maxValue=e;this.colorStartValue=nt.provide(t);this.colorEndValue=nt.provide(e)}}var at;(function(t){t[t["CHROMOSOME"]=0]="CHROMOSOME";t[t["LABEL"]=1]="LABEL";t[t["NONEXONICSNV"]=2]="NONEXONICSNV";t[t["SNV"]=3]="SNV";t[t["CNV"]=4]="CNV";t[t["LOH"]=5]="LOH";t[t["FUSION"]=6]="FUSION"})(at||(at={}));class ot{constructor(t,e,s,n,i,a,o){this.settings=t;this.rings=e;this.legend=s;this.fusions=n;this.genesetName=a;this.width=1.2*(this.settings.horizontalPadding+this.settings.rings.labelLinesInnerRadius+this.settings.rings.labelsToLinesDistance);this.height=2*(this.settings.rings.labelLinesInnerRadius+this.settings.rings.labelsToLinesDistance+this.settings.verticalPadding);this.legendHeight=this.calculateLegendHeight(s);this.snvDataLength=i.snvData.length;this.filteredSnvDataLength=i.filteredSnvData.length;this.snvDataLengthAll=o;this.cnvMaxValue=i.cnvGainMaxValue;this.cnvMinValue=i.cnvLossMaxValue;this.cappedCnvMaxAbsValue=i.cappedCnvMaxAbsValue;this.negativePercentile80=i.percentileNegative;this.positivePercentile80=i.percentilePositive}getElements(t){switch(t){case at.CHROMOSOME:return this.rings.chromosomesRing?this.rings.chromosomesRing.elements:[];case at.LABEL:return this.rings.labelsRing.elementsToDisplay;case at.NONEXONICSNV:return this.rings.nonExonicArcRing?this.rings.nonExonicArcRing.elements:[];case at.SNV:return this.rings.snvArcRing?this.rings.snvArcRing.elements:[];case at.CNV:return this.rings.cnvArcRing?this.rings.cnvArcRing.elements:[];case at.LOH:return this.rings.lohArcRing?this.rings.lohArcRing.elements:[];default:throw new Error(`ringType ${t} not defined`)}}getCollisions(t){if(t==at.LABEL){return this.rings.labelsRing.collisions}else{return undefined}}calculateLegendHeight(t){const e=this.settings.legend.rowHeight;return e*t.legendCount()}}class rt{constructor(t,e,s){this.innerRadius=t;this.outerRadius=t+e;this.width=e;this.elements=s}}class lt{constructor(){const t={};for(const e in l){t[l[e].label]=l[e];t[e]=l[e]}this.mlabel=t}static getInstance(){if(!lt.instance){lt.instance=new lt}return lt.instance}}class ct{constructor(t,e,s){this.snvType=t;this.color=e;this.count=s}}class ht{constructor(t,e,s,n){this.snvClassMap=new Map;this.svnInnerRadius=t;this.svnWidth=e;this.sampleName=s;this.reference=n;this.bpx=Math.floor(this.reference.totalSize/(this.reference.totalChromosomesAngle*t));this.onePxArcAngle=1/t}map(t){const e=[];for(const s of t.keys()){const n=t.get(s);if(n){const t=n.length;for(let i=0;i<n.length;i++){const a=n[i];const o=this.snvClassMap.get(a.mClass);if(o){this.snvClassMap.set(a.mClass,this.createSnvLegend(a.mClass,++o.count))}else{this.snvClassMap.set(a.mClass,this.createSnvLegend(a.mClass,1))}const r=s;const l=s+this.onePxArcAngle;const c=lt.getInstance().mlabel?lt.getInstance().mlabel[a.mClass]:undefined;const h={startAngle:r,endAngle:l,innerRadius:this.svnInnerRadius+i*this.svnWidth/t,outerRadius:this.svnInnerRadius+(i+1)*this.svnWidth/t,color:c.color,text:a.gene,dataClass:c.label,mname:a.mname,chr:a.chr,pos:a.position,sampleName:[a.sampleName]};e.push(h)}}}return e}createSnvLegend(t,e){const s=lt.getInstance().mlabel[t];return new ct(s.label,s.color,e)}}class dt{constructor(t,e,s,n){this.text=t;this.cnvType=e;this.color=s;this.value=n}}var pt;(function(t){t[t["Loss"]=0]="Loss";t[t["Gain"]=1]="Gain";t[t["Cap"]=2]="Cap"})(pt||(pt={}));var ut;(function(t){t["heatmap"]="heatmap";t["bar"]="bar"})(ut||(ut={}));class gt{static getColor(t,e,s=0){const n=e.cnv;const i=e.Disco.cnvRenderingType==ut.heatmap?e.Disco.cnvCapping:s;const a=e.Disco.cnvRenderingType==ut.heatmap?-1*e.Disco.cnvCapping:-1*s;if(t<a){return n.cappedLossColor}else if(t>=a&&t<=0){return n.lossColor}else if(t>0&&t<=i){return n.ampColor}else{return n.cappedAmpColor}}}class mt{constructor(t,e,s,n,i,a=0,o=0,r=0,l=0,c="",h){this.cnvClassMap=new Map;this.cnvInnerRadius=t;this.cnvWidth=e;this.settings=s;this.sampleName=n;this.reference=i;this.cnvMaxValue=a;this.cnvMinValue=o;this.cnvMaxAbsValue=r;this.cnvAbsPercentile=l;this.cnvUnit=c;this.cnvRenderingType=h;this.gainCapped=Math.min(l,this.settings.Disco.cnvCapping);this.lossCapped=-1*Math.min(l,this.settings.Disco.cnvCapping);this.lossOnly=a<=0;this.gainOnly=o>=0;this.onePxArcAngle=1/this.cnvInnerRadius;const d=new dt("Max",a>0?pt.Gain:pt.Loss,this.getColor(a),a);const p=new dt("Min",o>0?pt.Gain:pt.Loss,this.getColor(o),o);const u=new dt("Capping",pt.Loss,this.getColor(o>0?o:a),this.settings.Disco.cnvCapping);this.cnvClassMap.set(pt.Gain,d);this.cnvClassMap.set(pt.Loss,p);this.cnvClassMap.set(pt.Cap,u)}map(t){const e=[];t.forEach((t=>{let s=this.calculateStartAngle(t);let n=this.calculateEndAngle(t);if(n-s<this.onePxArcAngle){const t=this.onePxArcAngle-(n-s);s=s-t/2;n=s+t/2}const i=this.calculateInnerRadius(t);const a=this.calculateOuterRadius(t);const o=this.getColor(t.value);const r={startAngle:s,endAngle:n,innerRadius:i,outerRadius:a,color:o,text:t.gene,chr:t.chr,start:t.start,stop:t.stop,value:t.value,unit:this.cnvUnit,sampleName:[this.sampleName]};e.push(r)}));return e}calculateStartAngle(t){const e=this.reference.chromosomesOrder.indexOf(t.chr);const s=this.reference.chromosomes[e];return s.startAngle+(s.endAngle-s.startAngle)*(Number(t.start)/s.size)}calculateEndAngle(t){const e=this.reference.chromosomesOrder.indexOf(t.chr);const s=this.reference.chromosomes[e];return s.startAngle+(s.endAngle-s.startAngle)*(Number(t.stop)/s.size)}getColor(t){return gt.getColor(t,this.settings,this.cnvAbsPercentile)}calculateInnerRadius(t){if(this.cnvRenderingType==ut.heatmap){return this.cnvInnerRadius}if(this.gainOnly){return this.cnvInnerRadius}if(this.lossOnly){const e=this.cnvInnerRadius+this.cnvWidth;return e+Y.capMinValue(this.cnvWidth*Y.capMaxValue(t.value,this.gainCapped,this.lossCapped)/this.cnvAbsPercentile)}const e=this.cnvInnerRadius+this.cnvWidth/2;if(Math.sign(t.value)==1){return e}if(Math.sign(t.value)==-1){return e+Y.capMinValue(Y.capMaxValue(t.value,this.gainCapped,this.lossCapped)/this.cnvAbsPercentile*(this.cnvWidth/2))}return 1}calculateOuterRadius(t){const e=this.cnvInnerRadius+this.cnvWidth;if(this.cnvRenderingType==ut.heatmap){return e}if(this.gainOnly){return this.cnvInnerRadius+Y.capMinValue(this.cnvWidth*Y.capMaxValue(t.value,this.gainCapped,this.lossCapped)/this.cnvAbsPercentile)}if(this.lossOnly){return e}const s=this.cnvInnerRadius+this.cnvWidth/2;if(Math.sign(t.value)==1){return s+Y.capMinValue(Y.capMaxValue(t.value,this.gainCapped,this.lossCapped)/this.cnvMaxAbsValue*(this.cnvWidth/2))}if(Math.sign(t.value)==-1){return s}return 1}}class ft{constructor(t,e){this.points=new Array;this.points=t;this.color=e}}class vt{static createLabel(t,e,s,n,i,a,o,r,l,c,h=false,d,p,u){const g=(t+e)/2;const m=g-Math.PI/2;const f=`rotate(${g*180/Math.PI-90}) translate(${n})${g>Math.PI?"rotate(180)":""}`;const v=g>Math.PI?"end":"";const A=s;const x=n-d;const M=[];const R={x:A*Math.cos(m),y:A*Math.sin(m)};const b={x:x*Math.cos(m),y:x*Math.sin(m)};M.push(R);M.push(b);const C=new ft(M,o);const y={startAngle:t,endAngle:e,innerRadius:s,outerRadius:n,angle:g,value:i,text:a,color:o,transform:f,textAnchor:v,ccAngle:m,line:C,isPrioritized:h,start:c,stop:c,chr:l,mutationsTooltip:p?[p]:undefined,fusionTooltip:u?[u]:undefined};return y}static createMovedLabel(t,e){const s=t.startAngle+e;const n=t.endAngle+e;const i=(s+n)/2;const a=i-Math.PI/2;const o=t.innerRadius;const r=t.outerRadius-2;const l=(r-o)/3;const c=Math.cos(t.ccAngle);const h=Math.sin(t.ccAngle);const d=Math.cos(t.ccAngle+e);const p=Math.sin(t.ccAngle+e);const u=[];const g={x:o*c,y:o*h};const m={x:(o+l)*c,y:(o+l)*h};const f={x:(o+2*l)*d,y:(o+2*l)*p};const v={x:(o+3*l)*d,y:(o+3*l)*p};u.push(g);u.push(m);u.push(f);u.push(v);const A=new ft(u,t.color);const x="rotate("+(i*180/Math.PI-90)+")"+"translate("+t.outerRadius+")"+(i>Math.PI?"rotate(180)":"");const M=i>Math.PI?"end":"";const R=t.mutationsTooltip?t.mutationsTooltip[0].color:t.fusionTooltip?t.fusionTooltip[0].color:undefined;const b={startAngle:s,endAngle:n,innerRadius:t.innerRadius,outerRadius:t.outerRadius,angle:i,value:t.value,text:t.text,transform:x,textAnchor:M,ccAngle:a,color:R,line:A,isPrioritized:t.isPrioritized,start:t.start,stop:t.stop,chr:t.chr,mutationsTooltip:t.mutationsTooltip,fusionTooltip:t.fusionTooltip};return b}}class At{constructor(t,e,s,n=0){this.labelMap=new Map;this.settings=t;this.sampleName=e;this.reference=s;this.cnvMaxPercentileAbs=n}map(t,e=[]){const s=this.settings.rings.labelLinesInnerRadius;const a=s+this.settings.rings.labelsToLinesDistance;t.forEach((t=>{if(t.dt==n){const e=this.calculateStartAngle(t.chr,t.position);const n=this.calculateEndAngle(t.chr,t.position);const i=lt.getInstance().mlabel?lt.getInstance().mlabel[t.mClass]:undefined;this.addLabelOrMutation(t,t.gene,t.mname,e,n,s,a,i.color,i.label)}if(t.dt==i){const e=H.getColor(t.chrA,t.chrB);if(t.geneA){const n=this.calculateStartAngle(t.chrA,t.posA);const i=this.calculateEndAngle(t.chrA,t.posA);this.addLabelOrFusion(t,t.geneA,t.posA,n,i,s,a,e)}if(t.geneB&&t.geneA!=t.geneB){const n=this.calculateStartAngle(t.chrB,t.posB);const i=this.calculateEndAngle(t.chrB,t.posB);this.addLabelOrFusion(t,t.geneB,t.posB,n,i,s,a,e)}}}));const o=Array.from(this.labelMap.values());o.forEach((t=>{e.forEach((e=>{if(t.stop>=e.start&&e.stop>=t.start&&t.chr==e.chr){const s={value:e.value,color:gt.getColor(e.value,this.settings,this.cnvMaxPercentileAbs),chr:e.chr,start:e.start,stop:e.stop};if(t.cnvTooltip){t.cnvTooltip.push(s)}else{t.cnvTooltip=[];t.cnvTooltip.push(s)}}}))}));return Array.from(this.labelMap.values())}addLabelOrMutation(t,e,s,n,i,a,o,r,l){const c=this.labelMap.get(e);const h={mname:s,color:r,dataClass:l,chr:t.chr,position:t.position};if(!c){this.labelMap.set(e,vt.createLabel(n,i,a,o,t.value,e,r,l,t.chr,t.position,t.isPrioritized,this.settings.rings.labelsToLinesGap,h))}else{if(c.mutationsTooltip){c.start=Math.min(c.start,t.position);c.stop=Math.max(c.stop,t.position);c.mutationsTooltip.push(h)}else{c.mutationsTooltip=[];c.start=Math.min(c.start,t.position);c.stop=Math.max(c.stop,t.position);c.mutationsTooltip.push(h)}}}addLabelOrFusion(t,e,s,n,i,a,o,r){const l=this.labelMap.get(e);const c={color:r,chrA:t.chrA,chrB:t.chrB,posA:t.posA,posB:t.posB,geneA:t.geneA,geneB:t.geneB,strandA:t.strandA,strandB:t.strandB};if(!l){this.labelMap.set(e,vt.createLabel(n,i,a,o,t.value,e,r,"Fusion transcript",t.chr,t.position,t.isPrioritized,this.settings.rings.labelsToLinesGap,undefined,c))}else{if(l.fusionTooltip){l.start=Math.min(l.start,s);l.stop=Math.max(l.stop,s);l.fusionTooltip.push(c)}else{l.fusionTooltip=[];l.start=Math.min(l.start,s);l.stop=Math.max(l.stop,s);l.fusionTooltip.push(c)}}}calculateStartAngle(t,e){const s=this.reference.chromosomesOrder.findIndex((e=>e==t));const n=this.reference.chromosomes[s];return n.startAngle+(n.endAngle-n.startAngle)*(Number(e)/n.size)}calculateEndAngle(t,e){const s=this.reference.chromosomesOrder.findIndex((e=>e==t));const n=this.reference.chromosomes[s];return n.startAngle+(n.endAngle-n.startAngle)*(Number(e)/n.size)}}class xt extends rt{constructor(t,e,s){super(t.rings.labelLinesInnerRadius,t.rings.labelsToLinesDistance,e.sort(((t,e)=>t.startAngle<e.startAngle?-1:t.startAngle>e.startAngle?1:0)));this.elementsToDisplay=[];this.settings=t;this.hasPrioritizedGenes=s;const n=2*Math.PI*(t.rings.labelLinesInnerRadius+t.rings.labelsToLinesDistance);this.overlapAngle=this.settings.label.overlapAngleFactor*this.settings.label.fontSize/n;this.calculateCollisions()}calculateCollisions(){this.collisions=[];let t=[];t=this.elements.filter((t=>t.isPrioritized));if(this.settings.label.prioritizeGeneLabelsByGeneSets){this.elementsToDisplay=this.getLabelsWithPrioritizedGenes(t)}else if(this.hasPrioritizedGenes){const t=this.elements.filter((t=>t.isPrioritized));const e=this.getLabelsWithPrioritizedGenes(t);const s=this.elements.filter((t=>!t.isPrioritized));const n=[...s,...e].sort(((t,e)=>t.startAngle-e.startAngle));this.elementsToDisplay=this.getAllLabels(n)}else{this.elementsToDisplay=this.getLabelsWithPrioritizedGenes(this.elements)}}getLabelsWithPrioritizedGenes(t){const e=[];let s={endAngle:0};t.forEach(((t,n)=>{if(n==0){e.push(t);s=t}else{const n=s.endAngle-t.startAngle+this.overlapAngle;if(n>0&&n<this.settings.label.maxDeltaAngle){const i=vt.createMovedLabel(t,n);e===null||e===void 0?void 0:e.push(i);s=i}if(n<=0){e.push(t);s=t}}}));return e}getAllLabels(t){var e;const s=[];let n={endAngle:0};const i=t.length;let a=-1;for(let o=0;o<t.length;o++){const r=t[o];if(r.isPrioritized){s.push(r);a=o;n=r;continue}if(o==0){if(i>1){if(this.isElementOverlappingNextCancerGene(t,a,r,0)){continue}s.push(r);n=r}continue}const l=n.endAngle-r.startAngle+this.overlapAngle;if(l>0&&l<this.settings.label.maxDeltaAngle){if(o==length-1){s.push(r);continue}if(this.isElementOverlappingNextCancerGene(t,a,r,l)){continue}const i=vt.createMovedLabel(r,l);(e=this.collisions)===null||e===void 0?void 0:e.push(i);s.push(r);n=i}if(l<=0){if(this.isElementOverlappingNextCancerGene(t,a,r,0)){continue}s.push(r);n=r}}return s}isElementOverlappingNextCancerGene(t,e,s,n){const i=this.getNextLabelWithCancerGene(t,e);if(i){const t=s.endAngle+n-i.startAngle+this.overlapAngle;if(t>0){return true}}return false}getNextLabelWithCancerGene(t,e){return t.find(((t,s)=>t.isPrioritized&&s>e))}}class Mt{constructor(t,e,s,n){this.nonExonicInnerRadius=t;this.nonExonicWidht=e;this.sampleName=s;this.reference=n;this.onePxArcAngle=1/t}map(t){const e=this.nonExonicInnerRadius;const s=e+this.nonExonicWidht;const n=[];t.forEach((t=>{const i=lt.getInstance().mlabel?lt.getInstance().mlabel[t.mClass]:undefined;const a=this.calculateStartAngle(t);const o=this.calculateEndAngle(t);const r={startAngle:a,endAngle:o,innerRadius:e,outerRadius:s,color:i.color,text:t.gene,dataClass:i.label,mname:t.mname,chr:t.chr,pos:t.position,sampleName:[t.sampleName]};n.push(r)}));return n}calculateStartAngle(t){const e=this.reference.chromosomesOrder.indexOf(t.chr);const s=this.reference.chromosomes[e];return s.startAngle+(s.endAngle-s.startAngle)*(Number(t.position)/s.size)-this.onePxArcAngle}calculateEndAngle(t){const e=this.reference.chromosomesOrder.indexOf(t.chr);const s=this.reference.chromosomes[e];return this.onePxArcAngle+s.startAngle+(s.endAngle-s.startAngle)*(Number(t.position)/s.size)}}class Rt{constructor(t,e,s,n){this.lohInnerRadius=t;this.lohWidth=e;this.sampleName=s;this.reference=n}map(t){const e=[];t.forEach((t=>{const s=this.calculateStartAngle(t);const n=this.calculateEndAngle(t);const i=this.lohInnerRadius;const a=i+this.lohWidth;const o=nt.provide(t.segmean);const r={startAngle:s,endAngle:n,innerRadius:i,outerRadius:a,color:o,text:t.gene,chr:t.chr,start:t.start,stop:t.stop,value:t.segmean};e.push(r)}));return e}calculateStartAngle(t){const e=this.reference.chromosomesOrder.indexOf(t.chr);const s=this.reference.chromosomes[e];return s.startAngle+(s.endAngle-s.startAngle)*(Number(t.start)/s.size)}calculateEndAngle(t){const e=this.reference.chromosomesOrder.indexOf(t.chr);const s=this.reference.chromosomes[e];return s.startAngle+(s.endAngle-s.startAngle)*(Number(t.stop)/s.size)}}class bt{constructor(t,e,s,n,i,a){this.labelsRing=t;this.chromosomesRing=e;this.nonExonicArcRing=s;this.snvArcRing=n;this.cnvArcRing=i;this.lohArcRing=a}}class Ct{constructor(t,e,s,n,i){this.nonExonicArcRing=undefined;this.settings=t;this.dataMapper=e;this.reference=s;this.sampleName=n;this.genesetName=i}map(t){const e=this.dataMapper.map(t);const s=new At(this.settings,this.sampleName,this.reference,e.cnvMaxPercentileAbs);const i=s.map(e.labelData,e.cnvData);const a=new xt(this.settings,i,e.hasPrioritizedGenes);const o=new rt(this.settings.rings.chromosomeInnerRadius,this.settings.rings.chromosomeWidth,this.reference.chromosomes);const r=new Mt(e.nonExonicInnerRadius,this.settings.rings.nonExonicRingWidth,this.sampleName,this.reference);const l=r.map(e.nonExonicSnvData);if(l.length>0){this.nonExonicArcRing=new rt(e.nonExonicInnerRadius,this.settings.rings.nonExonicRingWidth,l)}this.snvArcsMapper=new ht(e.snvInnerRadius,this.settings.rings.snvRingWidth,this.sampleName,this.reference);const c=this.snvArcsMapper.map(e.snvRingDataMap);if(c.length>0){this.snvArcRing=new rt(e.snvInnerRadius,this.settings.rings.snvRingWidth,c)}const h=new Rt(e.lohInnerRadius,this.settings.rings.lohRingWidth,this.sampleName,this.reference);const d=h.map(e.lohData);if(d.length>0){this.lohArcRing=new rt(e.lohInnerRadius,this.settings.rings.lohRingWidth,d)}this.cnvArcsMapper=new mt(e.cnvInnerRadius,this.settings.rings.cnvRingWidth,this.settings,this.sampleName,this.reference,e.percentilePositive,e.percentileNegative,e.cappedCnvMaxAbsValue,e.cnvMaxPercentileAbs,this.settings.cnv.unit,this.settings.Disco.cnvRenderingType);const p=this.cnvArcsMapper.map(e.cnvData);if(p.length>0){this.cnvArcRing=new rt(e.cnvInnerRadius,this.settings.rings.cnvRingWidth,p)}const u=new st(e.fusionRadius,this.sampleName,this.reference);const g=u.map(e.fusionData);let m;if(this.settings.legend.lohLegendEnabled&&e.lohMinValue&&e.lohMaxValue){m=new it(e.lohMinValue,e.lohMaxValue)}const f=new Z(this.settings.legend.snvTitle,this.settings.legend.cnvTitle,this.settings.legend.lohTitle,this.settings.legend.fusionTitle,this.snvArcsMapper?this.snvArcsMapper.snvClassMap:new Map,this.cnvArcsMapper?this.cnvArcsMapper.cnvClassMap:new Map,this.settings.Disco.cnvRenderingType,g.length>0,m);const v=new bt(a,o,this.nonExonicArcRing,this.snvArcRing,this.cnvArcRing,this.lohArcRing);return new ot(this.settings,v,f,g,e,this.genesetName,t.filter((t=>t.dt==n)).length)}}class yt{constructor(t){this.settings=t}map(t){var e,s;const n=t.args.chromosomes;const i=t.args.genome.majorchr;const a=t.args.sampleName;const o=t.args.genome;const r=((e=o===null||o===void 0?void 0:o.geneset)===null||e===void 0?void 0:e[0])?o.geneset[0].lst:[];const l=((s=o===null||o===void 0?void 0:o.geneset)===null||s===void 0?void 0:s[0])?o.geneset[0].name:"";const c=t.args.data;const h=new K(this.settings,i,n);const d=new Y(this.settings,h,a,r);return new Ct(this.settings,d,h,a,l).map(c)}}yt.snvClassLayer={M:"exonic",E:"exonic",F:"exonic",N:"exonic",S:"exonic",D:"exonic",I:"exonic",P:"exonic",L:"exonic",Utr3:"exonic",Utr5:"exonic",ProteinAltering:"exonic",mnv:"non-exonic",ITD:"non-exonic",insertion:"non-exonic",deletion:"non-exonic",Intron:"non-exonic",X:"non-exonic",noncoding:"non-exonic"};class wt{constructor(t){this.cappedCnvMaxAbsValue=t}map(t){const e=[];let s=0;if(t.snvClassMap){this.mapSnv(t,e,s++)}if(t.cnvRenderingType==ut.heatmap){this.mapCnvHeatmap(t,e,s++)}else if(t.cnvRenderingType==ut.bar){if(t.cnvClassMap){this.mapCnvBar(t,e,s++)}}if(t.lohLegend){this.mapLoh(t,e,s++)}if(t.fusionLegend){this.mapFusion(t,e,s++)}return e}mapSnv(t,e,s){const n=[];let i=0;for(const[e,s]of t.snvClassMap){n.push({termid:t.snvTitle,key:e,text:`${s.snvType} (${s.count})`,color:s.color,order:i++,border:"1px solid #ccc"})}e.push({name:t.snvTitle,order:s,items:n})}mapCnvBar(t,e,s){if(!t.cnvClassMap)return;const n=t.cnvClassMap.get(pt.Gain);const i=t.cnvClassMap.get(pt.Loss);const a=t.cnvClassMap.get(pt.Cap);if(n&&i&&a){let o=0;const r=[];if(n.value>0){r.push({termid:t.cnvTitle,key:pt.Gain,text:`Max: ${n.value}`,color:n.color,order:o++,border:"1px solid #ccc"})}if(i.value<0){r.push({termid:t.cnvTitle,key:pt.Loss,text:`Min: ${i.value}`,color:i.color,order:o++,border:"1px solid #ccc"})}r.push({termid:t.cnvTitle,key:pt.Cap,text:`Capping: ${a.value}`,color:a.color,order:o++,border:"1px solid #ccc"});e.push({name:t.cnvTitle,order:s,items:r})}}mapCnvHeatmap(t,e,s){if(!t.cnvClassMap)return;const n=t.cnvClassMap.get(pt.Gain);const i=t.cnvClassMap.get(pt.Loss);const a=t.cnvClassMap.get(pt.Cap);if(n&&i&&a){let o=0;const r=[];if(n.value>0){r.push({termid:t.cnvTitle,key:pt.Gain,text:"Copy number gain",width:100,domain:[0,1],minLabel:0,maxLabel:n.value,order:o++,isLegendItem:true,dt:4,scale:c([0,1],["white",n.color])})}if(i.value<0){r.push({termid:t.cnvTitle,key:pt.Loss,text:"Copy number loss",width:100,domain:[0,1],minLabel:0,maxLabel:i.value,order:o++,isLegendItem:true,dt:4,scale:c([0,1],["white",i.color])})}r.push({termid:t.cnvTitle,key:pt.Cap,text:`Capping: ${a.value}`,color:a.color,order:o++,border:"1px solid #ccc"});e.push({name:t.cnvTitle,order:s,items:r})}}mapLoh(t,e,s){if(!t.lohLegend)return;const n=[];n.push({termid:t.lohTitle,key:"min",text:"min",color:t.lohLegend.colorStartValue,order:0,border:"1px solid #ccc"});n.push({termid:t.lohTitle,key:"max",text:"max",color:t.lohLegend.colorEndValue,order:1,border:"1px solid #ccc"});e.push({name:t.lohTitle,order:s,items:n})}mapFusion(t,e,s){const n=[];n.push({termid:t.fusionTitle,key:_.Interchromosomal,text:"Interchromosomal",color:_.Interchromosomal.valueOf(),order:0,border:"1px solid #ccc"});n.push({termid:t.fusionTitle,key:_.Intrachromosomal,text:"Intrachromosomal",color:_.Intrachromosomal.valueOf(),order:1,border:"1px solid #ccc"});e.push({name:t.fusionTitle,order:s,items:n})}}class It{constructor(t=0,e){this.fontSize=e;this.legendJSONMapper=new wt(t)}render(t,e,s,n,i){const a=v({holder:t.append("g").attr("data-testid","sjpp_disco_plot_legend"),rectFillFxn:t=>t.color,iconStroke:"#aaa"});const o={xOffset:s};const r=this.legendJSONMapper.map(e);a(r,{settings:Object.assign({},{svgw:n,svgh:i,dimensions:o,fontsize:this.fontSize})})}}class Lt{constructor(t,e,s){this.padAngle=t;this.innerRadius=e;this.outerRadius=s}render(t,e){const s=W().padAngle(this.padAngle).value((t=>t.size)).sort(null);const n=s(e);const i=g().innerRadius(this.innerRadius).outerRadius(this.outerRadius);const a=t.append("g").attr("data-testid","sjpp_chromosomes_arc_group");a.selectAll("path").data(n).enter().append("path").attr("d",i).attr("fill","black");a.selectAll("text").data(n).enter().append("text").attr("transform",(t=>`translate(${i.centroid(t)}) rotate(${t.data.angle*180/Math.PI-90})${t.data.angle>Math.PI?"rotate(180)":""}`)).attr("dy","0.35em").attr("text-anchor","middle").text((t=>t.data.text)).style("fill","white")}}class Dt{constructor(t,e){this.animationDuration=t;this.geneClickListener=e}render(t,e,n){const i=t.append("g");const a=x().x((t=>t.x)).y((t=>t.y));const o=j.create();i.selectAll(".group").data(e).enter().append("g").attr("class","group").each(((t,e,n)=>{const i=h(n[e]);i.append("text").attr("class","chord-text").attr("dy",".35em").attr("transform",t.transform).style("text-anchor",t.textAnchor).style("font-size","12px").style("fill",t.color).style("cursor","pointer").text(t.text).on("click",(()=>{if(t.mutationsTooltip){this.geneClickListener(t.text,t.mutationsTooltip.map((t=>t.mname)))}})).on("mouseover",(e=>{const n=s({holder:o.d});this.createTooltip(n,t);o.show(e.x,e.y)})).on("mouseout",(()=>{o.clear();o.hide()}));i.append("path").attr("class","chord-tick").datum(t.line.points).style("stroke",t.color).style("fill","none").attr("d",a)}));i.selectAll(".group").each(((t,e,s)=>{const i=n?n.find((e=>e.text===t.text)):undefined;if(i){const t=h(s[e]);t.selectAll(".chord-text").datum(i).transition().duration(this.animationDuration).attr("transform",i.transform).style("text-anchor",i.textAnchor);t.selectAll(".chord-tick").datum(i.line.points).transition().duration(this.animationDuration).style("fill","none").attr("d",a)}}))}createTooltip(t,e){if(e.mutationsTooltip){const[s,n]=t.addRow();s.text("Gene");n.append("span").style("margin-left","5px").text(e.text);e.mutationsTooltip.forEach((e=>{{const[s,n]=t.addRow();s.text("Consequence");n.append("span").text(e.mname);n.append("span").style("margin-left","5px").style("color",e.color).text(e.dataClass)}{const[s,n]=t.addRow();s.text("Mutation");n.append("span").text(`${e.chr}:${e.position}`)}}))}if(e.fusionTooltip){const[s,n]=t.addRow();s.text("Data type");n.append("span").text("Fusion transcript");e.fusionTooltip.forEach((e=>{const[s,n]=t.addRow();s.text("Break points");n.append("span").text(` ${e.geneA?e.geneA:""} ${e.chrA}:${e.posA} \n\t\t\t\t\t\t${e.strandA=="+"?"forward":"reverse"} > `+`${e.geneB?e.geneB:""} ${e.chrB}:${e.posB} ${e.strandB=="+"?"forward":"reverse"} `)}))}if(e.cnvTooltip){e.cnvTooltip.forEach((e=>{const[s,n]=t.addRow();s.text("CNV");n.append("span").style("color",e.color).text(e.value).append("span").style("margin-left","5px").text(`${e.chr}:${e.start}-${e.stop}`)}))}}}function Tt(t={}){const e={downloadImgName:"disco.plot",Disco:{cnvCapping:5,isOpen:false,prioritizeGeneLabelsByGeneSets:false,showPrioritizeGeneLabelsByGeneSets:false,cnvRenderingType:ut.heatmap,cnvPercentile:80},rings:{nonExonicRingWidth:20,snvRingWidth:20,lohRingWidth:20,cnvRingWidth:30,snvRingFilters:["exonic"],chromosomeInnerRadius:190,chromosomeWidth:20,labelLinesInnerRadius:210,labelsToLinesDistance:30,labelsToLinesGap:2,nonExonicRingEnabled:true,nonExonicFilterValues:["non-exonic"]},verticalPadding:70,horizontalPadding:500,layerScaler:1,padAngle:.002,label:{fontSize:12,maxDeltaAngle:.05,animationDuration:1e3,overlapAngleFactor:5},cnv:{capping:5,ampColor:"#D6683C",lossColor:"#67a9cf",cappedAmpColor:"#8B0000",cappedLossColor:"#00008B",unit:"Unit"},snv:{maxMutationCount:1e4},legend:{snvTitle:"SNV",cnvTitle:"CNV",lohTitle:"LOH",fusionTitle:"SV",lohLegendEnabled:true,fontSize:12,rowHeight:48},menu:{padding:5}};return d(e,t)}class Pt{constructor(t){this.geneClickListener=t}render(t,e){const i=g();const a=t.append("g");const o=j.create();a.selectAll("path").data(e).enter().append("path").attr("d",(t=>i(t))).attr("fill",(t=>t.color)).on("mouseover",((t,e)=>{const i=s({holder:o.d});const a=structuredClone(e);a.dt=n;a.class=e.dataClass;a.gene=a.text;{const[t,e]=i.addRow();t.text("Consequence");e.append("span").text(a.mname);e.append("span").style("margin-left","5px").style("color",a.color).style("font-size",".8em").text(a.dataClass)}{const[t,e]=i.addRow();t.text(a.ref&&a.alt?"Mutation":"Position");e.append("span").text(`${a.chr}:${a.pos+1} ${a.ref&&a.alt?a.ref+">"+a.alt:""}`)}if(a.gene){const[t,e]=i.addRow();t.text("Gene");e.text(a.gene)}if(a.occurrence>1){const[t,e]=i.addRow();t.text("Occurrence");e.text(a.occurrence)}o.show(t.x,t.y)})).on("mouseout",(()=>{o.clear();o.hide()})).on("click",((t,e)=>{this.geneClickListener(e.text,[e.mname])}))}}class Ot{constructor(t,e){this.svnWidth=t;this.geneClickListener=e}render(t,e){if(e.length>0){const s=e[0].innerRadius;const n=new F(s,this.svnWidth,"#6464641A");n.render(t)}const i=g();const a=t.append("g");const o=j.create();a.selectAll("path").data(e).enter().append("path").attr("d",(t=>i(t))).attr("fill",(t=>t.color)).on("mouseover",((t,e)=>{const i=s({holder:o.d});const a=structuredClone(e);a.dt=n;a.class=e.dataClass;a.gene=a.text;{const[t,e]=i.addRow();t.text("Consequence");e.append("span").text(a.mname);e.append("span").style("margin-left","5px").style("color",a.color).style("font-size",".8em").text(a.dataClass)}{const[t,e]=i.addRow();t.text(a.ref&&a.alt?"Mutation":"Position");e.append("span").text(`${a.chr}:${a.pos+1} ${a.ref&&a.alt?a.ref+">"+a.alt:""}`)}if(a.gene){const[t,e]=i.addRow();t.text("Gene");e.text(a.gene)}if(a.occurrence>1){const[t,e]=i.addRow();t.text("Occurrence");e.text(a.occurrence)}o.show(t.x,t.y)})).on("mouseout",(()=>{o.clear();o.hide()})).on("click",((t,e)=>{this.geneClickListener(e.text,[e.mname])}))}}class Nt{render(t,e){const n=g();const i=t.append("g");const a=j.create();i.selectAll("path").data(e).enter().append("path").attr("d",(t=>n(t))).attr("fill",(t=>t.color)).on("mouseover",((t,e)=>{const n=s({holder:a.d});const i=structuredClone(e);i.dt=r;i.gene=i.text;{const[t,e]=n.addRow();t.text("Data type");e.append("span").style("margin-left","5px").text("Loss of Heterozygosity")}const[o,l]=n.addRow();o.text("Position");l.append("span").text(`${e.chr}:${e.start}-${e.stop}`);a.show(t.x,t.y)})).on("mouseout",(()=>{a.clear();a.hide()}))}}class Et{render(t,e){const n=g();const i=t.append("g");const a=j.create();i.selectAll("path").data(e).enter().append("path").attr("d",(t=>n(t))).attr("fill",(t=>t.color)).on("mouseover",((t,e)=>{const n=structuredClone(e);n.dt=o;n.samples=[{sample_id:e.sampleName}];n.gene=n.text;const i=s({holder:a.d});{const[t,e]=i.addRow();t.text("Copy number change");e.html(`<span style="background:${n.color}">&nbsp;&nbsp;</span> ${n.value}`)}{const[t,e]=i.addRow();t.text("Position");e.text(n.chr+":"+n.start+"-"+n.stop)}{const[t,e]=i.addRow();t.text("Unit");e.text(n.value)}a.show(t.x,t.y)})).on("mouseout",(()=>{a.clear();a.hide()}))}}class Vt{constructor(t=0,e=0){this.positivePercentile80=t;this.negativePercentile80=e}render(t,e){const n=g();const i=t.append("g");const a=j.create();i.selectAll("path").data(e).enter().append("path").attr("d",(t=>n(t))).attr("fill",(t=>c([this.negativePercentile80,0,this.positivePercentile80],[t.color,"white",t.color]).clamp(true)(t.value))).on("mouseover",((t,e)=>{const n=s({holder:a.d});const i=structuredClone(e);i.dt=o;i.samples=[{sample_id:e.sampleName}];i.gene=i.text;{const[t,e]=n.addRow();t.text("Copy number change");e.html(`<span style="background:${i.color}">&nbsp;&nbsp;</span> ${i.value}`)}{const[t,e]=n.addRow();t.text("Position");e.text(i.chr+":"+i.start+"-"+i.stop)}{const[t,e]=n.addRow();t.text("Unit");e.text(i.value)}a.show(t.x,t.y)})).on("mouseout",(()=>{a.clear();a.hide()}))}}class St{constructor(t){this.recreateViewModel=false;this.type="Disco";this.opts=t;this.isOpen=false;this.discoInteractions=new X(this)}init(){return t(this,void 0,void 0,(function*(){const t=this.app.getState();const e=t.plots.find((t=>t.id===this.id)).settings;this.stateViewModelMapper=new yt(e);this.viewModel=this.stateViewModelMapper.map(t);const s=this.opts.holder;const n=s.append("div").style("display","inline-block").style("vertical-align","top");const i=n.append("div");const a=n.append("div");const o=this.getConfigInputsOptions(this.viewModel);this.features=yield u({topbar:R({app:this.app,id:this.id,downloadHandler:()=>this.discoInteractions.downloadClickListener(s.select('svg[id="sjpp_disco_plot"]').node()),callback:()=>this.toggleVisibility(this.isOpen),isOpen:()=>this.isOpen,holder:i}),config:b({app:this.app,id:this.id,holder:a,isOpen:()=>this.isOpen,inputs:o})})}))}getConfigInputsOptions(t){const e=[];if(t.settings.Disco.showPrioritizeGeneLabelsByGeneSets){const s=[{boxLabel:t.genesetName,label:`Filter mutations`,type:"checkbox",chartType:"Disco",settingsKey:"prioritizeGeneLabelsByGeneSets",title:`Only show mutations for ${t.genesetName} genes`}];e.push(...s)}const s=[{label:"CNV capping",type:"number",chartType:"Disco",settingsKey:"cnvCapping",title:"Cnv capping",min:0},{boxLabel:"",label:"CNV rendering type",type:"radio",chartType:"Disco",settingsKey:"cnvRenderingType",title:"CNV rendering type",options:[{label:"Heatmap",value:ut.heatmap},{label:"Bar",value:ut.bar}]},{label:"CNV percentile",type:"number",chartType:"Disco",settingsKey:"cnvPercentile",title:"Cnv percentile",min:1,max:100}];e.push(...s);return e}main(){return t(this,void 0,void 0,(function*(){const t=this.state.settings;this.isOpen=t.Disco.isOpen;if(this.recreateViewModel){this.stateViewModelMapper=new yt(t);this.viewModel=this.stateViewModelMapper.map(this.app.getState())}this.recreateViewModel=true;if(this.viewModel){const e=this.opts.holder;e.select('div[id="sjpp_disco_plot_holder_div"]').remove();const s=e.append("div").attr("id","sjpp_disco_plot_holder_div").style("display","inline-block");const n=this.app.getState();for(const t in this.features){this.features[t].update({state:this.state,appState:n})}const i=new It(this.viewModel.cappedCnvMaxAbsValue,t.label.fontSize);const a=new q(this.getRingRenderers(t,this.viewModel,this.discoInteractions.geneClickListener),i);a.render(s,this.viewModel)}}))}getState(t){return t.plots.find((t=>t.id===this.id))}getRingRenderers(t,e,s){const n=new Lt(t.padAngle,t.rings.chromosomeInnerRadius,t.rings.chromosomeInnerRadius+t.rings.chromosomeWidth);const i=new Dt(t.label.animationDuration,s);const a=new Pt(s);const o=new Ot(t.rings.snvRingWidth,s);const r=t.Disco.cnvRenderingType===ut.heatmap?new Vt(e.positivePercentile80,e.negativePercentile80):new Et;const l=new Nt;const c=new Map;c.set(at.CHROMOSOME,n);c.set(at.LABEL,i);c.set(at.NONEXONICSNV,a);c.set(at.SNV,o);c.set(at.CNV,r);c.set(at.LOH,l);return c}toggleVisibility(t){this.app.dispatch({type:"plot_edit",id:this.opts.id,config:{settings:{Disco:{isOpen:!t}}}})}}const zt=p(St);const Bt=zt;function Gt(e){return t(this,void 0,void 0,(function*(){return{chartType:"Disco",subfolder:"disco",extension:"ts",settings:Tt(e.overrides)}}))}export{Bt as componentInit,zt as discoInit,Gt as getPlotConfig};
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t==="function"?t:P(+t),c):n};c.targetRadius=function(t){return arguments.length?(i=typeof t==="function"?t:P(+t),c):i};c.startAngle=function(t){return arguments.length?(a=typeof t==="function"?t:P(+t),c):a};c.endAngle=function(t){return arguments.length?(o=typeof t==="function"?t:P(+t),c):o};c.padAngle=function(t){return arguments.length?(r=typeof t==="function"?t:P(+t),c):r};c.source=function(t){return arguments.length?(e=t,c):e};c.target=function(t){return arguments.length?(s=t,c):s};c.context=function(t){return arguments.length?(l=t==null?null:t,c):l};return c}function G(){return B()}function $(t,e){return e<t?-1:e>t?1:e>=t?0:NaN}function k(t){return t}function W(){var t=k,e=$,s=null,n=f(0),i=f(M),a=f(0);function o(o){var r,l=(o=A(o)).length,c,h,d=0,p=new Array(l),u=new Array(l),g=+n.apply(this,arguments),m=Math.min(M,Math.max(-M,i.apply(this,arguments)-g)),f,v=Math.min(Math.abs(m)/l,a.apply(this,arguments)),x=v*(m<0?-1:1),R;for(r=0;r<l;++r){if((R=u[p[r]=r]=+t(o[r],r,o))>0){d+=R}}if(e!=null)p.sort((function(t,s){return e(u[t],u[s])}));else if(s!=null)p.sort((function(t,e){return s(o[t],o[e])}));for(r=0,h=d?(m-l*x)/d:0;r<l;++r,g=f){c=p[r],R=u[c],f=g+(R>0?R*h:0)+x,u[c]={data:o[c],index:r,value:R,startAngle:g,endAngle:f,padAngle:v}}return u}o.value=function(e){return arguments.length?(t=typeof e==="function"?e:f(+e),o):t};o.sortValues=function(t){return arguments.length?(e=t,s=null,o):e};o.sort=function(t){return arguments.length?(s=t,e=null,o):s};o.startAngle=function(t){return arguments.length?(n=typeof t==="function"?t:f(+t),o):n};o.endAngle=function(t){return arguments.length?(i=typeof t==="function"?t:f(+t),o):i};o.padAngle=function(t){return arguments.length?(a=typeof t==="function"?t:f(+t),o):a};return o}class F{constructor(t,e,s){this.radius=t;this.width=e;this.color=s}render(t){const e=g();const s={startAngle:0,endAngle:Math.PI*2,innerRadius:this.radius,outerRadius:this.radius+this.width,color:this.color,text:"No label"};const n=[];n.push(s);const i=t.append("g");i.selectAll("path").data(n).enter().append("path").attr("d",(t=>e(t))).attr("fill",(t=>t.color))}}class j{static create(){const t=new e({padding:5});t.d.style("border","1px solid #FFF").style("position","absolute").style("z-index",1001);return t}}var _;(function(t){t["Intrachromosomal"]="#1B9E77";t["Interchromosomal"]="#6A3D9A"})(_||(_={}));class H{static getColor(t,e){if(t!=e){return _.Interchromosomal.valueOf()}else{return _.Intrachromosomal.valueOf()}}}class U{render(t,e){let n=0;if(e.length>0){n=e[0].target.radius;const s=new F(n,2,"#6464641A");s.render(t)}const i=G().radius(n);const a=t.selectAll(".chord").data(e);const o=j.create();a.enter().append("path").attr("class","chord").attr("d",i).attr("fill",(t=>H.getColor(t.source.positionInChromosome.chromosome,t.target.positionInChromosome.chromosome))).on("mouseover",((t,e)=>{const n=s({holder:o.d});this.createTooltip(n,e);o.show(t.x,t.y)})).on("mouseout",(()=>{o.clear();o.hide()}))}createTooltip(t,e){{const[e,s]=t.addRow();e.text("Data type");s.append("span").style("margin-left","5px").text("Fusion transcript")}{const s=e.source.positionInChromosome;const n=e.target.positionInChromosome;const[i,a]=t.addRow();i.text("Position");a.append("span").style("margin-left","5px").text(` ${e.source.gene?e.source.gene:""} ${s.chromosome}:${s.position} ${e.source.strand=="+"?"forward":"reverse"} > `+` ${e.target.gene?e.target.gene:""} ${n.chromosome}:${n.position} ${e.target.strand=="+"?"forward":"reverse"} `)}}}class q{constructor(t,e){this.renders=t;this.legendRenderer=e;this.fusionRenderer=new U}render(t,e){const s=t.append("div").style("display","inline-block").style("font-family","Arial");const n=s.append("svg").attr("id","sjpp_disco_plot").attr("data-testid","sjpp_disco_plot").attr("width",e.width).attr("height",e.height+e.legendHeight);const i=n.append("g").attr("class","mainG").attr("transform",`translate(${e.settings.rings.labelLinesInnerRadius+e.settings.rings.labelsToLinesDistance+100},${e.height/2})`);for(const[t,s]of this.renders){const n=e.getElements(t);const a=e.getCollisions(t);s.render(i,n,a)}this.fusionRenderer.render(i,e.fusions);this.legendRenderer.render(i,e.legend,-1*(e.settings.rings.labelLinesInnerRadius+e.settings.rings.labelsToLinesDistance+50),e.width,e.height/2)}}class X{constructor(e){this.discoApp=e;this.downloadClickListener=t=>{const e=this.discoApp.state.settings.downloadImgName||"disco.plot";const s=document.createElement("a");document.body.appendChild(s);s.addEventListener("click",(()=>{const n=new XMLSerializer;const i=new Blob([n.serializeToString(t)],{type:"image/svg+xml"});s.download=e+".svg";s.href=URL.createObjectURL(i);document.body.removeChild(s)}),false);s.click()};this.geneClickListener=(e,s)=>t(this,void 0,void 0,(function*(){const{filter:t,filter0:n}=this.discoApp.app.getState().termfilter;const i={holder:this.discoApp.app.opts.holder,genome:this.discoApp.app.opts.state.args.genome,nobox:true,query:e,tklst:[{type:"mds3",dslabel:this.discoApp.app.opts.state.dslabel,hlaachange:s.join(","),filter0:n,filterObj:t}]};const a=yield import("./app-3d14cbe4.js").then((function(t){return t.c3}));yield a.default(i)}))}}class K{constructor(t,e,s){this.chromosomes=[];this.chromosomesOrder=[];this.keysArray=[];this.totalSizeArray=[];this.chrSizesArray=[];const n=s||e;this.settings=t;this.chromosomesOrder=[];let i=0;this.totalPadAngle=Object.keys(n).length*this.settings.padAngle;this.totalChromosomesAngle=2*Math.PI-this.totalPadAngle;for(const t in n){const e=t.slice(0,3)==="chr"?t.slice(3):t;this.chromosomesOrder.push(t);this.keysArray.push(e);this.totalSizeArray.push(i);this.chrSizesArray.push(n[t]);i+=n[t]}this.totalSize=i;let a=0;for(let t=0;t<this.keysArray.length;t++){const e=this.totalChromosomesAngle*(this.chrSizesArray[t]/i);const s=t==0?this.settings.padAngle/2:a+this.settings.padAngle;const n=t==0?this.settings.padAngle/2+e:a+this.settings.padAngle+e;const o={start:this.totalSizeArray[t],size:this.chrSizesArray[t],factor:1,startAngle:s,endAngle:n,angle:(s+n)/2,innerRadius:this.settings.chromosomeInnerRadius,outerRadius:this.settings.chromosomeInnerRadius+this.settings.chromosomeWidth,color:"#AAA",text:this.keysArray[t]};this.chromosomes.push(o);if(o.endAngle!=null){a=o.endAngle}}}}class J{constructor(t,e){this.sampleName=t;this.prioritizedGenes=e}map(t){return{dt:t.dt,mname:t.mname,mClass:t.class,gene:t.gene,chr:t.chr,ref:t.ref,alt:t.alt,position:t.pos?t.pos:t.position,poschr:t.poschr,posbins:t.posbins,poslabel:t.poslabel,sampleName:this.sampleName,ssm_id:t.ssm_id,start:t.start,stop:t.stop,value:t.value,segmean:t.segmean,isPrioritized:this.prioritizedGenes.some((e=>e==t.gene)),chrA:t.chrA,chrB:t.chrB,geneA:t.geneA,geneB:t.geneB,posA:t.posA,posB:t.posB,strandA:t.strandA,strandB:t.strandB}}}class Q{map(t,e){return this.calculatePercentileForPositivesAndNegatives(t,e)}calculatePercentileForPositivesAndNegatives(t,e){const s=t.filter((t=>t>0));const n=t.filter((t=>t<0)).map((t=>-1*t));let i=NaN;let a=NaN;if(s.length>0){i=this.calculatePercentile(s,e)}if(n.length>0){a=-1*this.calculatePercentile(n,e)}return{positive:i,negative:a}}calculatePercentile(t,e){if(t.length===0){throw new Error("Array must contain at least one element.")}const s=t.sort(((t,e)=>t-e));const n=e/100*(s.length-1);const i=Math.floor(n);const a=Math.ceil(n);const o=n-i;if(i===a){return s[i]}return s[i]+o*(s[a]-s[i])}}class Y{constructor(t,e,s,l=[]){this.labelData=[];this.nonExonicSnvData=[];this.nonExonicInnerRadius=0;this.snvRingDataMap=new Map;this.snvInnerRadius=0;this.snvData=[];this.bpx=0;this.onePxArcAngle=0;this.filteredSnvData=[];this.lohData=[];this.lohInnerRadius=0;this.cnvData=[];this.cnvInnerRadius=0;this.fusionData=[];this.fusionRadius=0;this.hasPrioritizedGenes=false;this.cnvLossMaxValue=0;this.cnvGainMaxValue=0;this.percentilePositive=0;this.percentileNegative=0;this.cnvMaxPercentileAbs=0;this.lohMaxValue=undefined;this.lohMinValue=undefined;this.snvFilter=t=>t.dt==n;this.fusionFilter=t=>t.dt==i||t.dt==a;this.cnvFilter=t=>t.dt==o;this.lohFilter=t=>t.dt==r;this.compareData=(t,e)=>{const s=this.reference.chromosomesOrder.indexOf(t.chr)-this.reference.chromosomesOrder.indexOf(e.chr);if(s!=0){return s}const n=t.pos?t.pos:t.start;const i=e.pos?e.pos:e.start;return n-i};this.settings=t;this.reference=e;this.sample=s;this.lastInnerRadious=this.settings.rings.chromosomeInnerRadius;this.gainCapped=this.settings.Disco.cnvCapping;this.lossCapped=-1*this.settings.Disco.cnvCapping;this.nonExonicFilter=e=>{if(l.length>0&&this.settings.Disco.prioritizeGeneLabelsByGeneSets){return l.includes(e.gene)&&t.rings.nonExonicFilterValues.includes(yt.snvClassLayer[e.mClass])}else{return t.rings.nonExonicFilterValues.includes(yt.snvClassLayer[e.mClass])}};this.snvRingFilter=e=>{if(l.length>0&&this.settings.Disco.prioritizeGeneLabelsByGeneSets){return l.includes(e.gene)&&t.rings.snvRingFilters.includes(yt.snvClassLayer[e.mClass])}else{return t.rings.snvRingFilters.includes(yt.snvClassLayer[e.mClass])}};this.dataObjectMapper=new J(s,l)}map(t){const e=[];t.forEach((t=>{const s=this.reference.chromosomesOrder.indexOf(t.chr);const l=this.reference.chromosomesOrder.indexOf(t.chrA);const c=this.reference.chromosomesOrder.indexOf(t.chrB);if(t.dt==n){if(s!=-1&&this.snvData.length<this.settings.snv.maxMutationCount){this.addData(t,e)}}else if(t.dt==i||t.dt==a){if(l!=-1&&c!=-1){this.addData(t,e)}}else if([o,r].includes(Number(t.dt))){this.addData(t,e)}else{throw Error("Unknown mutation type!")}}));const s=e.sort(this.compareData);if(this.settings.rings.nonExonicRingEnabled){s.forEach((t=>{this.filterNonExonicSnvData(t)}))}if(this.nonExonicSnvData.length>0){this.nonExonicInnerRadius=this.lastInnerRadious-this.settings.rings.nonExonicRingWidth;this.lastInnerRadious=this.nonExonicInnerRadius}s.forEach((t=>{this.filterSnvs(t)}));s.forEach((t=>{this.filterLohs(t)}));if(this.lohData.length>0){this.lohInnerRadius=this.lastInnerRadious-this.settings.rings.lohRingWidth;this.lastInnerRadious=this.lohInnerRadius}s.forEach((t=>{this.filterCnvs(t)}));if(this.cnvData.length>0){this.cnvInnerRadius=this.lastInnerRadious-this.settings.rings.cnvRingWidth;this.lastInnerRadious=this.cnvInnerRadius;this.cappedCnvMaxAbsValue=Math.min(this.settings.Disco.cnvCapping,Math.max(Math.abs(Y.capMaxValue(this.cnvLossMaxValue,this.gainCapped,this.lossCapped)),Math.abs(Y.capMaxValue(this.cnvGainMaxValue,this.gainCapped,this.lossCapped))));const t=(new Q).map(this.cnvData.map((t=>t.value)),this.settings.Disco.cnvPercentile);this.percentilePositive=Y.capMaxValue(t.positive,this.gainCapped,this.lossCapped);this.percentileNegative=Y.capMaxValue(t.negative,this.gainCapped,this.lossCapped);this.cnvMaxPercentileAbs=Math.min(this.settings.Disco.cnvCapping,Math.max(this.percentilePositive,Math.abs(this.percentileNegative)))}s.forEach((t=>{this.filterFusion(t)}));if(this.fusionData.length>0){this.fusionRadius=this.lastInnerRadious}const l={labelData:this.labelData,nonExonicSnvData:this.nonExonicSnvData,nonExonicInnerRadius:this.nonExonicInnerRadius,snvRingDataMap:this.snvRingDataMap,snvInnerRadius:this.snvInnerRadius,snvData:this.snvData,bpx:this.bpx,onePxArcAngle:this.onePxArcAngle,filteredSnvData:this.filteredSnvData,lohData:this.lohData,lohInnerRadius:this.lohInnerRadius,cnvData:this.cnvData,cnvInnerRadius:this.cnvInnerRadius,fusionData:this.fusionData,fusionRadius:this.fusionRadius,hasPrioritizedGenes:this.hasPrioritizedGenes,cnvGainMaxValue:this.cnvGainMaxValue,cnvLossMaxValue:this.cnvLossMaxValue,cappedCnvMaxAbsValue:this.cappedCnvMaxAbsValue,percentilePositive:this.percentilePositive,percentileNegative:this.percentileNegative,cnvMaxPercentileAbs:this.cnvMaxPercentileAbs,lohMaxValue:this.lohMaxValue,lohMinValue:this.lohMinValue};return l}addData(t,e){const s=this.dataObjectMapper.map(t);if(s.isPrioritized){this.hasPrioritizedGenes=true}e.push(s)}filterNonExonicSnvData(t){if(this.snvFilter(t)){if(this.settings.rings.nonExonicRingEnabled&&this.nonExonicFilter(t)){this.nonExonicSnvData.push(t)}}}filterSnvs(t){if(this.snvFilter(t)){this.snvData.push(t);if(this.snvRingFilter(t)){if(this.snvInnerRadius==0){this.snvInnerRadius=this.lastInnerRadious-this.settings.rings.snvRingWidth;this.lastInnerRadious=this.snvInnerRadius;this.bpx=Math.floor(this.reference.totalSize/(this.reference.totalChromosomesAngle*this.snvInnerRadius));this.onePxArcAngle=1/this.snvInnerRadius}this.filteredSnvData.push(t);this.labelData.push(t);const e=this.calculateArcAngle(t);let s=this.snvRingDataMap.get(e);if(!s){s=new Array}s.push(t);this.snvRingDataMap.set(e,s)}}}filterFusion(t){if(this.fusionFilter(t)){t.isPrioritized=true;this.fusionData.push(t);this.labelData.push(t)}}filterLohs(t){if(this.lohFilter(t)){if(this.lohMaxValue==undefined||this.lohMaxValue<t.value){this.lohMaxValue=t.segmean}if(this.lohMinValue==undefined||this.lohMinValue>t.value){this.lohMinValue=t.segmean}this.lohData.push(t)}}filterCnvs(t){if(this.cnvFilter(t)){if(this.cnvGainMaxValue==undefined||this.cnvGainMaxValue<t.value){this.cnvGainMaxValue=t.value}if(this.cnvLossMaxValue==undefined||this.cnvLossMaxValue>t.value){this.cnvLossMaxValue=t.value}this.cnvData.push(t)}}calculateArcAngle(t){const e=this.reference.chromosomes[this.reference.chromosomesOrder.findIndex((e=>t.chr==e))];const s=Math.floor(t.position/this.bpx);return e.startAngle+s*this.onePxArcAngle}static capMaxValue(t,e,s){if(t&&Math.sign(t)==1){return t>e?e:t}if(Math.sign(t)==-1){return t<s?s:t}return 0}static capMinValue(t,e=1){if(Math.sign(t)==1){return t>e?t:e}if(Math.sign(t)==-1){return t<-1*e?t:-1*e}return 1}}class Z{constructor(t,e,s,n,i,a,o,r,l){this.snvTitle=t;this.cnvTitle=e;this.lohTitle=s;this.fusionTitle=n;this.snvClassMap=i;this.cnvClassMap=a;this.cnvRenderingType=o;this.lohLegend=l;this.fusionLegend=r}legendCount(){return(this.snvClassMap.size>0?1:0)+(this.cnvClassMap.size>0?1:0)+(this.lohLegend?1:0)+(this.fusionLegend?1:0)}}class tt{constructor(t,e,s,n,i){this.source=t;this.target=e;this.genes=s;this.count=n;this.endpts=i}}class et{constructor(t,e,s,n,i,a,o,r){this.startAngle=t;this.endAngle=e;this.radius=s;this.gene=n;this.value=i;this.genes=a;this.positionInChromosome=o;this.strand=r}}class st{constructor(t,e,s){this.radius=t;this.sampleName=e;this.reference=s}map(t){const e=[];t.forEach((t=>{const s=new Set;s.add(t.geneA);s.add(t.geneB);const n=new et(this.calculateStartAngle(t.chrA,t.posA),this.calculateEndAngle(t.chrA,t.posA),this.radius,t.geneA,t.value,s,{chromosome:t.chrA,position:t.posA},t.strandA);const i=new et(this.calculateStartAngle(t.chrB,t.posB),this.calculateEndAngle(t.chrB,t.posB),this.radius,t.geneB,t.value,s,{chromosome:t.chrB,position:t.posB},t.strandB);const a=new tt(n,i,"genes",-1,"Endpoints");e.push(a)}));return e}calculateStartAngle(t,e){const s=this.reference.chromosomesOrder.indexOf(t);const n=this.reference.chromosomes[s];return n.startAngle+(n.endAngle-n.startAngle)*(Number(e)/n.size)-.01}calculateEndAngle(t,e){const s=this.reference.chromosomesOrder.indexOf(t);const n=this.reference.chromosomes[s];return.01+n.startAngle+(n.endAngle-n.startAngle)*(Number(e)/n.size)}}class nt{static provide(t){const e=Math.min(Math.max(t,0),1);const s=Math.round(e*255);return`rgb(${s}, ${s}, ${s})`}}class it{constructor(t,e){this.minValue=t;this.maxValue=e;this.colorStartValue=nt.provide(t);this.colorEndValue=nt.provide(e)}}var at;(function(t){t[t["CHROMOSOME"]=0]="CHROMOSOME";t[t["LABEL"]=1]="LABEL";t[t["NONEXONICSNV"]=2]="NONEXONICSNV";t[t["SNV"]=3]="SNV";t[t["CNV"]=4]="CNV";t[t["LOH"]=5]="LOH";t[t["FUSION"]=6]="FUSION"})(at||(at={}));class ot{constructor(t,e,s,n,i,a,o){this.settings=t;this.rings=e;this.legend=s;this.fusions=n;this.genesetName=a;this.width=1.2*(this.settings.horizontalPadding+this.settings.rings.labelLinesInnerRadius+this.settings.rings.labelsToLinesDistance);this.height=2*(this.settings.rings.labelLinesInnerRadius+this.settings.rings.labelsToLinesDistance+this.settings.verticalPadding);this.legendHeight=this.calculateLegendHeight(s);this.snvDataLength=i.snvData.length;this.filteredSnvDataLength=i.filteredSnvData.length;this.snvDataLengthAll=o;this.cnvMaxValue=i.cnvGainMaxValue;this.cnvMinValue=i.cnvLossMaxValue;this.cappedCnvMaxAbsValue=i.cappedCnvMaxAbsValue;this.negativePercentile80=i.percentileNegative;this.positivePercentile80=i.percentilePositive}getElements(t){switch(t){case at.CHROMOSOME:return this.rings.chromosomesRing?this.rings.chromosomesRing.elements:[];case at.LABEL:return this.rings.labelsRing.elementsToDisplay;case at.NONEXONICSNV:return this.rings.nonExonicArcRing?this.rings.nonExonicArcRing.elements:[];case at.SNV:return this.rings.snvArcRing?this.rings.snvArcRing.elements:[];case at.CNV:return this.rings.cnvArcRing?this.rings.cnvArcRing.elements:[];case at.LOH:return this.rings.lohArcRing?this.rings.lohArcRing.elements:[];default:throw new Error(`ringType ${t} not defined`)}}getCollisions(t){if(t==at.LABEL){return this.rings.labelsRing.collisions}else{return undefined}}calculateLegendHeight(t){const e=this.settings.legend.rowHeight;return e*t.legendCount()}}class rt{constructor(t,e,s){this.innerRadius=t;this.outerRadius=t+e;this.width=e;this.elements=s}}class lt{constructor(){const t={};for(const e in l){t[l[e].label]=l[e];t[e]=l[e]}this.mlabel=t}static getInstance(){if(!lt.instance){lt.instance=new lt}return lt.instance}}class ct{constructor(t,e,s){this.snvType=t;this.color=e;this.count=s}}class ht{constructor(t,e,s,n){this.snvClassMap=new Map;this.svnInnerRadius=t;this.svnWidth=e;this.sampleName=s;this.reference=n;this.bpx=Math.floor(this.reference.totalSize/(this.reference.totalChromosomesAngle*t));this.onePxArcAngle=1/t}map(t){const e=[];for(const s of t.keys()){const n=t.get(s);if(n){const t=n.length;for(let i=0;i<n.length;i++){const a=n[i];const o=this.snvClassMap.get(a.mClass);if(o){this.snvClassMap.set(a.mClass,this.createSnvLegend(a.mClass,++o.count))}else{this.snvClassMap.set(a.mClass,this.createSnvLegend(a.mClass,1))}const r=s;const l=s+this.onePxArcAngle;const c=lt.getInstance().mlabel?lt.getInstance().mlabel[a.mClass]:undefined;const h={startAngle:r,endAngle:l,innerRadius:this.svnInnerRadius+i*this.svnWidth/t,outerRadius:this.svnInnerRadius+(i+1)*this.svnWidth/t,color:c.color,text:a.gene,dataClass:c.label,mname:a.mname,chr:a.chr,pos:a.position,sampleName:[a.sampleName]};e.push(h)}}}return e}createSnvLegend(t,e){const s=lt.getInstance().mlabel[t];return new ct(s.label,s.color,e)}}class dt{constructor(t,e,s,n){this.text=t;this.cnvType=e;this.color=s;this.value=n}}var pt;(function(t){t[t["Loss"]=0]="Loss";t[t["Gain"]=1]="Gain";t[t["Cap"]=2]="Cap"})(pt||(pt={}));var ut;(function(t){t["heatmap"]="heatmap";t["bar"]="bar"})(ut||(ut={}));class gt{static getColor(t,e,s=0){const n=e.cnv;const i=e.Disco.cnvRenderingType==ut.heatmap?e.Disco.cnvCapping:s;const a=e.Disco.cnvRenderingType==ut.heatmap?-1*e.Disco.cnvCapping:-1*s;if(t<a){return n.cappedLossColor}else if(t>=a&&t<=0){return n.lossColor}else if(t>0&&t<=i){return n.ampColor}else{return n.cappedAmpColor}}}class mt{constructor(t,e,s,n,i,a=0,o=0,r=0,l=0,c="",h){this.cnvClassMap=new Map;this.cnvInnerRadius=t;this.cnvWidth=e;this.settings=s;this.sampleName=n;this.reference=i;this.cnvMaxValue=a;this.cnvMinValue=o;this.cnvMaxAbsValue=r;this.cnvAbsPercentile=l;this.cnvUnit=c;this.cnvRenderingType=h;this.gainCapped=Math.min(l,this.settings.Disco.cnvCapping);this.lossCapped=-1*Math.min(l,this.settings.Disco.cnvCapping);this.lossOnly=a<=0;this.gainOnly=o>=0;this.onePxArcAngle=1/this.cnvInnerRadius;const d=new dt("Max",a>0?pt.Gain:pt.Loss,this.getColor(a),a);const p=new dt("Min",o>0?pt.Gain:pt.Loss,this.getColor(o),o);const u=new dt("Capping",pt.Loss,this.getColor(o>0?o:a),this.settings.Disco.cnvCapping);this.cnvClassMap.set(pt.Gain,d);this.cnvClassMap.set(pt.Loss,p);this.cnvClassMap.set(pt.Cap,u)}map(t){const e=[];t.forEach((t=>{let s=this.calculateStartAngle(t);let n=this.calculateEndAngle(t);if(n-s<this.onePxArcAngle){const t=this.onePxArcAngle-(n-s);s=s-t/2;n=s+t/2}const i=this.calculateInnerRadius(t);const a=this.calculateOuterRadius(t);const o=this.getColor(t.value);const r={startAngle:s,endAngle:n,innerRadius:i,outerRadius:a,color:o,text:t.gene,chr:t.chr,start:t.start,stop:t.stop,value:t.value,unit:this.cnvUnit,sampleName:[this.sampleName]};e.push(r)}));return e}calculateStartAngle(t){const e=this.reference.chromosomesOrder.indexOf(t.chr);const s=this.reference.chromosomes[e];return s.startAngle+(s.endAngle-s.startAngle)*(Number(t.start)/s.size)}calculateEndAngle(t){const e=this.reference.chromosomesOrder.indexOf(t.chr);const s=this.reference.chromosomes[e];return s.startAngle+(s.endAngle-s.startAngle)*(Number(t.stop)/s.size)}getColor(t){return gt.getColor(t,this.settings,this.cnvAbsPercentile)}calculateInnerRadius(t){if(this.cnvRenderingType==ut.heatmap){return this.cnvInnerRadius}if(this.gainOnly){return this.cnvInnerRadius}if(this.lossOnly){const e=this.cnvInnerRadius+this.cnvWidth;return e+Y.capMinValue(this.cnvWidth*Y.capMaxValue(t.value,this.gainCapped,this.lossCapped)/this.cnvAbsPercentile)}const e=this.cnvInnerRadius+this.cnvWidth/2;if(Math.sign(t.value)==1){return e}if(Math.sign(t.value)==-1){return e+Y.capMinValue(Y.capMaxValue(t.value,this.gainCapped,this.lossCapped)/this.cnvAbsPercentile*(this.cnvWidth/2))}return 1}calculateOuterRadius(t){const e=this.cnvInnerRadius+this.cnvWidth;if(this.cnvRenderingType==ut.heatmap){return e}if(this.gainOnly){return this.cnvInnerRadius+Y.capMinValue(this.cnvWidth*Y.capMaxValue(t.value,this.gainCapped,this.lossCapped)/this.cnvAbsPercentile)}if(this.lossOnly){return e}const s=this.cnvInnerRadius+this.cnvWidth/2;if(Math.sign(t.value)==1){return s+Y.capMinValue(Y.capMaxValue(t.value,this.gainCapped,this.lossCapped)/this.cnvMaxAbsValue*(this.cnvWidth/2))}if(Math.sign(t.value)==-1){return s}return 1}}class ft{constructor(t,e){this.points=new Array;this.points=t;this.color=e}}class vt{static createLabel(t,e,s,n,i,a,o,r,l,c,h=false,d,p,u){const g=(t+e)/2;const m=g-Math.PI/2;const f=`rotate(${g*180/Math.PI-90}) translate(${n})${g>Math.PI?"rotate(180)":""}`;const v=g>Math.PI?"end":"";const A=s;const x=n-d;const M=[];const R={x:A*Math.cos(m),y:A*Math.sin(m)};const b={x:x*Math.cos(m),y:x*Math.sin(m)};M.push(R);M.push(b);const C=new ft(M,o);const y={startAngle:t,endAngle:e,innerRadius:s,outerRadius:n,angle:g,value:i,text:a,color:o,transform:f,textAnchor:v,ccAngle:m,line:C,isPrioritized:h,start:c,stop:c,chr:l,mutationsTooltip:p?[p]:undefined,fusionTooltip:u?[u]:undefined};return y}static createMovedLabel(t,e){const s=t.startAngle+e;const n=t.endAngle+e;const i=(s+n)/2;const a=i-Math.PI/2;const o=t.innerRadius;const r=t.outerRadius-2;const l=(r-o)/3;const c=Math.cos(t.ccAngle);const h=Math.sin(t.ccAngle);const d=Math.cos(t.ccAngle+e);const p=Math.sin(t.ccAngle+e);const u=[];const g={x:o*c,y:o*h};const m={x:(o+l)*c,y:(o+l)*h};const f={x:(o+2*l)*d,y:(o+2*l)*p};const v={x:(o+3*l)*d,y:(o+3*l)*p};u.push(g);u.push(m);u.push(f);u.push(v);const A=new ft(u,t.color);const x="rotate("+(i*180/Math.PI-90)+")"+"translate("+t.outerRadius+")"+(i>Math.PI?"rotate(180)":"");const M=i>Math.PI?"end":"";const R=t.mutationsTooltip?t.mutationsTooltip[0].color:t.fusionTooltip?t.fusionTooltip[0].color:undefined;const b={startAngle:s,endAngle:n,innerRadius:t.innerRadius,outerRadius:t.outerRadius,angle:i,value:t.value,text:t.text,transform:x,textAnchor:M,ccAngle:a,color:R,line:A,isPrioritized:t.isPrioritized,start:t.start,stop:t.stop,chr:t.chr,mutationsTooltip:t.mutationsTooltip,fusionTooltip:t.fusionTooltip};return b}}class At{constructor(t,e,s,n=0){this.labelMap=new Map;this.settings=t;this.sampleName=e;this.reference=s;this.cnvMaxPercentileAbs=n}map(t,e=[]){const s=this.settings.rings.labelLinesInnerRadius;const a=s+this.settings.rings.labelsToLinesDistance;t.forEach((t=>{if(t.dt==n){const e=this.calculateStartAngle(t.chr,t.position);const n=this.calculateEndAngle(t.chr,t.position);const i=lt.getInstance().mlabel?lt.getInstance().mlabel[t.mClass]:undefined;this.addLabelOrMutation(t,t.gene,t.mname,e,n,s,a,i.color,i.label)}if(t.dt==i){const e=H.getColor(t.chrA,t.chrB);if(t.geneA){const n=this.calculateStartAngle(t.chrA,t.posA);const i=this.calculateEndAngle(t.chrA,t.posA);this.addLabelOrFusion(t,t.geneA,t.posA,n,i,s,a,e)}if(t.geneB&&t.geneA!=t.geneB){const n=this.calculateStartAngle(t.chrB,t.posB);const i=this.calculateEndAngle(t.chrB,t.posB);this.addLabelOrFusion(t,t.geneB,t.posB,n,i,s,a,e)}}}));const o=Array.from(this.labelMap.values());o.forEach((t=>{e.forEach((e=>{if(t.stop>=e.start&&e.stop>=t.start&&t.chr==e.chr){const s={value:e.value,color:gt.getColor(e.value,this.settings,this.cnvMaxPercentileAbs),chr:e.chr,start:e.start,stop:e.stop};if(t.cnvTooltip){t.cnvTooltip.push(s)}else{t.cnvTooltip=[];t.cnvTooltip.push(s)}}}))}));return Array.from(this.labelMap.values())}addLabelOrMutation(t,e,s,n,i,a,o,r,l){const c=this.labelMap.get(e);const h={mname:s,color:r,dataClass:l,chr:t.chr,position:t.position};if(!c){this.labelMap.set(e,vt.createLabel(n,i,a,o,t.value,e,r,l,t.chr,t.position,t.isPrioritized,this.settings.rings.labelsToLinesGap,h))}else{if(c.mutationsTooltip){c.start=Math.min(c.start,t.position);c.stop=Math.max(c.stop,t.position);c.mutationsTooltip.push(h)}else{c.mutationsTooltip=[];c.start=Math.min(c.start,t.position);c.stop=Math.max(c.stop,t.position);c.mutationsTooltip.push(h)}}}addLabelOrFusion(t,e,s,n,i,a,o,r){const l=this.labelMap.get(e);const c={color:r,chrA:t.chrA,chrB:t.chrB,posA:t.posA,posB:t.posB,geneA:t.geneA,geneB:t.geneB,strandA:t.strandA,strandB:t.strandB};if(!l){this.labelMap.set(e,vt.createLabel(n,i,a,o,t.value,e,r,"Fusion transcript",t.chr,t.position,t.isPrioritized,this.settings.rings.labelsToLinesGap,undefined,c))}else{if(l.fusionTooltip){l.start=Math.min(l.start,s);l.stop=Math.max(l.stop,s);l.fusionTooltip.push(c)}else{l.fusionTooltip=[];l.start=Math.min(l.start,s);l.stop=Math.max(l.stop,s);l.fusionTooltip.push(c)}}}calculateStartAngle(t,e){const s=this.reference.chromosomesOrder.findIndex((e=>e==t));const n=this.reference.chromosomes[s];return n.startAngle+(n.endAngle-n.startAngle)*(Number(e)/n.size)}calculateEndAngle(t,e){const s=this.reference.chromosomesOrder.findIndex((e=>e==t));const n=this.reference.chromosomes[s];return n.startAngle+(n.endAngle-n.startAngle)*(Number(e)/n.size)}}class xt extends rt{constructor(t,e,s){super(t.rings.labelLinesInnerRadius,t.rings.labelsToLinesDistance,e.sort(((t,e)=>t.startAngle<e.startAngle?-1:t.startAngle>e.startAngle?1:0)));this.elementsToDisplay=[];this.settings=t;this.hasPrioritizedGenes=s;const n=2*Math.PI*(t.rings.labelLinesInnerRadius+t.rings.labelsToLinesDistance);this.overlapAngle=this.settings.label.overlapAngleFactor*this.settings.label.fontSize/n;this.calculateCollisions()}calculateCollisions(){this.collisions=[];let t=[];t=this.elements.filter((t=>t.isPrioritized));if(this.settings.label.prioritizeGeneLabelsByGeneSets){this.elementsToDisplay=this.getLabelsWithPrioritizedGenes(t)}else if(this.hasPrioritizedGenes){const t=this.elements.filter((t=>t.isPrioritized));const e=this.getLabelsWithPrioritizedGenes(t);const s=this.elements.filter((t=>!t.isPrioritized));const n=[...s,...e].sort(((t,e)=>t.startAngle-e.startAngle));this.elementsToDisplay=this.getAllLabels(n)}else{this.elementsToDisplay=this.getLabelsWithPrioritizedGenes(this.elements)}}getLabelsWithPrioritizedGenes(t){const e=[];let s={endAngle:0};t.forEach(((t,n)=>{if(n==0){e.push(t);s=t}else{const n=s.endAngle-t.startAngle+this.overlapAngle;if(n>0&&n<this.settings.label.maxDeltaAngle){const i=vt.createMovedLabel(t,n);e===null||e===void 0?void 0:e.push(i);s=i}if(n<=0){e.push(t);s=t}}}));return e}getAllLabels(t){var e;const s=[];let n={endAngle:0};const i=t.length;let a=-1;for(let o=0;o<t.length;o++){const r=t[o];if(r.isPrioritized){s.push(r);a=o;n=r;continue}if(o==0){if(i>1){if(this.isElementOverlappingNextCancerGene(t,a,r,0)){continue}s.push(r);n=r}continue}const l=n.endAngle-r.startAngle+this.overlapAngle;if(l>0&&l<this.settings.label.maxDeltaAngle){if(o==length-1){s.push(r);continue}if(this.isElementOverlappingNextCancerGene(t,a,r,l)){continue}const i=vt.createMovedLabel(r,l);(e=this.collisions)===null||e===void 0?void 0:e.push(i);s.push(r);n=i}if(l<=0){if(this.isElementOverlappingNextCancerGene(t,a,r,0)){continue}s.push(r);n=r}}return s}isElementOverlappingNextCancerGene(t,e,s,n){const i=this.getNextLabelWithCancerGene(t,e);if(i){const t=s.endAngle+n-i.startAngle+this.overlapAngle;if(t>0){return true}}return false}getNextLabelWithCancerGene(t,e){return t.find(((t,s)=>t.isPrioritized&&s>e))}}class Mt{constructor(t,e,s,n){this.nonExonicInnerRadius=t;this.nonExonicWidht=e;this.sampleName=s;this.reference=n;this.onePxArcAngle=1/t}map(t){const e=this.nonExonicInnerRadius;const s=e+this.nonExonicWidht;const n=[];t.forEach((t=>{const i=lt.getInstance().mlabel?lt.getInstance().mlabel[t.mClass]:undefined;const a=this.calculateStartAngle(t);const o=this.calculateEndAngle(t);const r={startAngle:a,endAngle:o,innerRadius:e,outerRadius:s,color:i.color,text:t.gene,dataClass:i.label,mname:t.mname,chr:t.chr,pos:t.position,sampleName:[t.sampleName]};n.push(r)}));return n}calculateStartAngle(t){const e=this.reference.chromosomesOrder.indexOf(t.chr);const s=this.reference.chromosomes[e];return s.startAngle+(s.endAngle-s.startAngle)*(Number(t.position)/s.size)-this.onePxArcAngle}calculateEndAngle(t){const e=this.reference.chromosomesOrder.indexOf(t.chr);const s=this.reference.chromosomes[e];return this.onePxArcAngle+s.startAngle+(s.endAngle-s.startAngle)*(Number(t.position)/s.size)}}class Rt{constructor(t,e,s,n){this.lohInnerRadius=t;this.lohWidth=e;this.sampleName=s;this.reference=n}map(t){const e=[];t.forEach((t=>{const s=this.calculateStartAngle(t);const n=this.calculateEndAngle(t);const i=this.lohInnerRadius;const a=i+this.lohWidth;const o=nt.provide(t.segmean);const r={startAngle:s,endAngle:n,innerRadius:i,outerRadius:a,color:o,text:t.gene,chr:t.chr,start:t.start,stop:t.stop,value:t.segmean};e.push(r)}));return e}calculateStartAngle(t){const e=this.reference.chromosomesOrder.indexOf(t.chr);const s=this.reference.chromosomes[e];return s.startAngle+(s.endAngle-s.startAngle)*(Number(t.start)/s.size)}calculateEndAngle(t){const e=this.reference.chromosomesOrder.indexOf(t.chr);const s=this.reference.chromosomes[e];return s.startAngle+(s.endAngle-s.startAngle)*(Number(t.stop)/s.size)}}class bt{constructor(t,e,s,n,i,a){this.labelsRing=t;this.chromosomesRing=e;this.nonExonicArcRing=s;this.snvArcRing=n;this.cnvArcRing=i;this.lohArcRing=a}}class Ct{constructor(t,e,s,n,i){this.nonExonicArcRing=undefined;this.settings=t;this.dataMapper=e;this.reference=s;this.sampleName=n;this.genesetName=i}map(t){const e=this.dataMapper.map(t);const s=new At(this.settings,this.sampleName,this.reference,e.cnvMaxPercentileAbs);const i=s.map(e.labelData,e.cnvData);const a=new xt(this.settings,i,e.hasPrioritizedGenes);const o=new rt(this.settings.rings.chromosomeInnerRadius,this.settings.rings.chromosomeWidth,this.reference.chromosomes);const r=new Mt(e.nonExonicInnerRadius,this.settings.rings.nonExonicRingWidth,this.sampleName,this.reference);const l=r.map(e.nonExonicSnvData);if(l.length>0){this.nonExonicArcRing=new rt(e.nonExonicInnerRadius,this.settings.rings.nonExonicRingWidth,l)}this.snvArcsMapper=new ht(e.snvInnerRadius,this.settings.rings.snvRingWidth,this.sampleName,this.reference);const c=this.snvArcsMapper.map(e.snvRingDataMap);if(c.length>0){this.snvArcRing=new rt(e.snvInnerRadius,this.settings.rings.snvRingWidth,c)}const h=new Rt(e.lohInnerRadius,this.settings.rings.lohRingWidth,this.sampleName,this.reference);const d=h.map(e.lohData);if(d.length>0){this.lohArcRing=new rt(e.lohInnerRadius,this.settings.rings.lohRingWidth,d)}this.cnvArcsMapper=new mt(e.cnvInnerRadius,this.settings.rings.cnvRingWidth,this.settings,this.sampleName,this.reference,e.percentilePositive,e.percentileNegative,e.cappedCnvMaxAbsValue,e.cnvMaxPercentileAbs,this.settings.cnv.unit,this.settings.Disco.cnvRenderingType);const p=this.cnvArcsMapper.map(e.cnvData);if(p.length>0){this.cnvArcRing=new rt(e.cnvInnerRadius,this.settings.rings.cnvRingWidth,p)}const u=new st(e.fusionRadius,this.sampleName,this.reference);const g=u.map(e.fusionData);let m;if(this.settings.legend.lohLegendEnabled&&e.lohMinValue&&e.lohMaxValue){m=new it(e.lohMinValue,e.lohMaxValue)}const f=new Z(this.settings.legend.snvTitle,this.settings.legend.cnvTitle,this.settings.legend.lohTitle,this.settings.legend.fusionTitle,this.snvArcsMapper?this.snvArcsMapper.snvClassMap:new Map,this.cnvArcsMapper?this.cnvArcsMapper.cnvClassMap:new Map,this.settings.Disco.cnvRenderingType,g.length>0,m);const v=new bt(a,o,this.nonExonicArcRing,this.snvArcRing,this.cnvArcRing,this.lohArcRing);return new ot(this.settings,v,f,g,e,this.genesetName,t.filter((t=>t.dt==n)).length)}}class yt{constructor(t){this.settings=t}map(t){var e,s;const n=t.args.chromosomes;const i=t.args.genome.majorchr;const a=t.args.sampleName;const o=t.args.genome;const r=((e=o===null||o===void 0?void 0:o.geneset)===null||e===void 0?void 0:e[0])?o.geneset[0].lst:[];const l=((s=o===null||o===void 0?void 0:o.geneset)===null||s===void 0?void 0:s[0])?o.geneset[0].name:"";const c=t.args.data;const h=new K(this.settings,i,n);const d=new Y(this.settings,h,a,r);return new Ct(this.settings,d,h,a,l).map(c)}}yt.snvClassLayer={M:"exonic",E:"exonic",F:"exonic",N:"exonic",S:"exonic",D:"exonic",I:"exonic",P:"exonic",L:"exonic",Utr3:"exonic",Utr5:"exonic",ProteinAltering:"exonic",mnv:"non-exonic",ITD:"non-exonic",insertion:"non-exonic",deletion:"non-exonic",Intron:"non-exonic",X:"non-exonic",noncoding:"non-exonic"};class wt{constructor(t){this.cappedCnvMaxAbsValue=t}map(t){const e=[];let s=0;if(t.snvClassMap){this.mapSnv(t,e,s++)}if(t.cnvRenderingType==ut.heatmap){this.mapCnvHeatmap(t,e,s++)}else if(t.cnvRenderingType==ut.bar){if(t.cnvClassMap){this.mapCnvBar(t,e,s++)}}if(t.lohLegend){this.mapLoh(t,e,s++)}if(t.fusionLegend){this.mapFusion(t,e,s++)}return e}mapSnv(t,e,s){const n=[];let i=0;for(const[e,s]of t.snvClassMap){n.push({termid:t.snvTitle,key:e,text:`${s.snvType} (${s.count})`,color:s.color,order:i++,border:"1px solid #ccc"})}e.push({name:t.snvTitle,order:s,items:n})}mapCnvBar(t,e,s){if(!t.cnvClassMap)return;const n=t.cnvClassMap.get(pt.Gain);const i=t.cnvClassMap.get(pt.Loss);const a=t.cnvClassMap.get(pt.Cap);if(n&&i&&a){let o=0;const r=[];if(n.value>0){r.push({termid:t.cnvTitle,key:pt.Gain,text:`Max: ${n.value}`,color:n.color,order:o++,border:"1px solid #ccc"})}if(i.value<0){r.push({termid:t.cnvTitle,key:pt.Loss,text:`Min: ${i.value}`,color:i.color,order:o++,border:"1px solid #ccc"})}r.push({termid:t.cnvTitle,key:pt.Cap,text:`Capping: ${a.value}`,color:a.color,order:o++,border:"1px solid #ccc"});e.push({name:t.cnvTitle,order:s,items:r})}}mapCnvHeatmap(t,e,s){if(!t.cnvClassMap)return;const n=t.cnvClassMap.get(pt.Gain);const i=t.cnvClassMap.get(pt.Loss);const a=t.cnvClassMap.get(pt.Cap);if(n&&i&&a){let o=0;const r=[];if(n.value>0){r.push({termid:t.cnvTitle,key:pt.Gain,text:"Copy number gain",width:100,domain:[0,1],minLabel:0,maxLabel:n.value,order:o++,isLegendItem:true,dt:4,scale:c([0,1],["white",n.color])})}if(i.value<0){r.push({termid:t.cnvTitle,key:pt.Loss,text:"Copy number loss",width:100,domain:[0,1],minLabel:0,maxLabel:i.value,order:o++,isLegendItem:true,dt:4,scale:c([0,1],["white",i.color])})}r.push({termid:t.cnvTitle,key:pt.Cap,text:`Capping: ${a.value}`,color:a.color,order:o++,border:"1px solid #ccc"});e.push({name:t.cnvTitle,order:s,items:r})}}mapLoh(t,e,s){if(!t.lohLegend)return;const n=[];n.push({termid:t.lohTitle,key:"min",text:"min",color:t.lohLegend.colorStartValue,order:0,border:"1px solid #ccc"});n.push({termid:t.lohTitle,key:"max",text:"max",color:t.lohLegend.colorEndValue,order:1,border:"1px solid #ccc"});e.push({name:t.lohTitle,order:s,items:n})}mapFusion(t,e,s){const n=[];n.push({termid:t.fusionTitle,key:_.Interchromosomal,text:"Interchromosomal",color:_.Interchromosomal.valueOf(),order:0,border:"1px solid #ccc"});n.push({termid:t.fusionTitle,key:_.Intrachromosomal,text:"Intrachromosomal",color:_.Intrachromosomal.valueOf(),order:1,border:"1px solid #ccc"});e.push({name:t.fusionTitle,order:s,items:n})}}class It{constructor(t=0,e){this.fontSize=e;this.legendJSONMapper=new wt(t)}render(t,e,s,n,i){const a=v({holder:t.append("g").attr("data-testid","sjpp_disco_plot_legend"),rectFillFxn:t=>t.color,iconStroke:"#aaa"});const o={xOffset:s};const r=this.legendJSONMapper.map(e);a(r,{settings:Object.assign({},{svgw:n,svgh:i,dimensions:o,fontsize:this.fontSize})})}}class Lt{constructor(t,e,s){this.padAngle=t;this.innerRadius=e;this.outerRadius=s}render(t,e){const s=W().padAngle(this.padAngle).value((t=>t.size)).sort(null);const n=s(e);const i=g().innerRadius(this.innerRadius).outerRadius(this.outerRadius);const a=t.append("g").attr("data-testid","sjpp_chromosomes_arc_group");a.selectAll("path").data(n).enter().append("path").attr("d",i).attr("fill","black");a.selectAll("text").data(n).enter().append("text").attr("transform",(t=>`translate(${i.centroid(t)}) rotate(${t.data.angle*180/Math.PI-90})${t.data.angle>Math.PI?"rotate(180)":""}`)).attr("dy","0.35em").attr("text-anchor","middle").text((t=>t.data.text)).style("fill","white")}}class Dt{constructor(t,e){this.animationDuration=t;this.geneClickListener=e}render(t,e,n){const i=t.append("g");const a=x().x((t=>t.x)).y((t=>t.y));const o=j.create();i.selectAll(".group").data(e).enter().append("g").attr("class","group").each(((t,e,n)=>{const i=h(n[e]);i.append("text").attr("class","chord-text").attr("dy",".35em").attr("transform",t.transform).style("text-anchor",t.textAnchor).style("font-size","12px").style("fill",t.color).style("cursor","pointer").text(t.text).on("click",(()=>{if(t.mutationsTooltip){this.geneClickListener(t.text,t.mutationsTooltip.map((t=>t.mname)))}})).on("mouseover",(e=>{const n=s({holder:o.d});this.createTooltip(n,t);o.show(e.x,e.y)})).on("mouseout",(()=>{o.clear();o.hide()}));i.append("path").attr("class","chord-tick").datum(t.line.points).style("stroke",t.color).style("fill","none").attr("d",a)}));i.selectAll(".group").each(((t,e,s)=>{const i=n?n.find((e=>e.text===t.text)):undefined;if(i){const t=h(s[e]);t.selectAll(".chord-text").datum(i).transition().duration(this.animationDuration).attr("transform",i.transform).style("text-anchor",i.textAnchor);t.selectAll(".chord-tick").datum(i.line.points).transition().duration(this.animationDuration).style("fill","none").attr("d",a)}}))}createTooltip(t,e){if(e.mutationsTooltip){const[s,n]=t.addRow();s.text("Gene");n.append("span").style("margin-left","5px").text(e.text);e.mutationsTooltip.forEach((e=>{{const[s,n]=t.addRow();s.text("Consequence");n.append("span").text(e.mname);n.append("span").style("margin-left","5px").style("color",e.color).text(e.dataClass)}{const[s,n]=t.addRow();s.text("Mutation");n.append("span").text(`${e.chr}:${e.position}`)}}))}if(e.fusionTooltip){const[s,n]=t.addRow();s.text("Data type");n.append("span").text("Fusion transcript");e.fusionTooltip.forEach((e=>{const[s,n]=t.addRow();s.text("Break points");n.append("span").text(` ${e.geneA?e.geneA:""} ${e.chrA}:${e.posA} \n\t\t\t\t\t\t${e.strandA=="+"?"forward":"reverse"} > `+`${e.geneB?e.geneB:""} ${e.chrB}:${e.posB} ${e.strandB=="+"?"forward":"reverse"} `)}))}if(e.cnvTooltip){e.cnvTooltip.forEach((e=>{const[s,n]=t.addRow();s.text("CNV");n.append("span").style("color",e.color).text(e.value).append("span").style("margin-left","5px").text(`${e.chr}:${e.start}-${e.stop}`)}))}}}function Tt(t={}){const e={downloadImgName:"disco.plot",Disco:{cnvCapping:5,isOpen:false,prioritizeGeneLabelsByGeneSets:false,showPrioritizeGeneLabelsByGeneSets:false,cnvRenderingType:ut.heatmap,cnvPercentile:80},rings:{nonExonicRingWidth:20,snvRingWidth:20,lohRingWidth:20,cnvRingWidth:30,snvRingFilters:["exonic"],chromosomeInnerRadius:190,chromosomeWidth:20,labelLinesInnerRadius:210,labelsToLinesDistance:30,labelsToLinesGap:2,nonExonicRingEnabled:true,nonExonicFilterValues:["non-exonic"]},verticalPadding:70,horizontalPadding:500,layerScaler:1,padAngle:.002,label:{fontSize:12,maxDeltaAngle:.05,animationDuration:1e3,overlapAngleFactor:5},cnv:{capping:5,ampColor:"#D6683C",lossColor:"#67a9cf",cappedAmpColor:"#8B0000",cappedLossColor:"#00008B",unit:"Unit"},snv:{maxMutationCount:1e4},legend:{snvTitle:"SNV",cnvTitle:"CNV",lohTitle:"LOH",fusionTitle:"SV",lohLegendEnabled:true,fontSize:12,rowHeight:48},menu:{padding:5}};return d(e,t)}class Pt{constructor(t){this.geneClickListener=t}render(t,e){const i=g();const a=t.append("g");const o=j.create();a.selectAll("path").data(e).enter().append("path").attr("d",(t=>i(t))).attr("fill",(t=>t.color)).on("mouseover",((t,e)=>{const i=s({holder:o.d});const a=structuredClone(e);a.dt=n;a.class=e.dataClass;a.gene=a.text;{const[t,e]=i.addRow();t.text("Consequence");e.append("span").text(a.mname);e.append("span").style("margin-left","5px").style("color",a.color).style("font-size",".8em").text(a.dataClass)}{const[t,e]=i.addRow();t.text(a.ref&&a.alt?"Mutation":"Position");e.append("span").text(`${a.chr}:${a.pos+1} ${a.ref&&a.alt?a.ref+">"+a.alt:""}`)}if(a.gene){const[t,e]=i.addRow();t.text("Gene");e.text(a.gene)}if(a.occurrence>1){const[t,e]=i.addRow();t.text("Occurrence");e.text(a.occurrence)}o.show(t.x,t.y)})).on("mouseout",(()=>{o.clear();o.hide()})).on("click",((t,e)=>{this.geneClickListener(e.text,[e.mname])}))}}class Ot{constructor(t,e){this.svnWidth=t;this.geneClickListener=e}render(t,e){if(e.length>0){const s=e[0].innerRadius;const n=new F(s,this.svnWidth,"#6464641A");n.render(t)}const i=g();const a=t.append("g");const o=j.create();a.selectAll("path").data(e).enter().append("path").attr("d",(t=>i(t))).attr("fill",(t=>t.color)).on("mouseover",((t,e)=>{const i=s({holder:o.d});const a=structuredClone(e);a.dt=n;a.class=e.dataClass;a.gene=a.text;{const[t,e]=i.addRow();t.text("Consequence");e.append("span").text(a.mname);e.append("span").style("margin-left","5px").style("color",a.color).style("font-size",".8em").text(a.dataClass)}{const[t,e]=i.addRow();t.text(a.ref&&a.alt?"Mutation":"Position");e.append("span").text(`${a.chr}:${a.pos+1} ${a.ref&&a.alt?a.ref+">"+a.alt:""}`)}if(a.gene){const[t,e]=i.addRow();t.text("Gene");e.text(a.gene)}if(a.occurrence>1){const[t,e]=i.addRow();t.text("Occurrence");e.text(a.occurrence)}o.show(t.x,t.y)})).on("mouseout",(()=>{o.clear();o.hide()})).on("click",((t,e)=>{this.geneClickListener(e.text,[e.mname])}))}}class Nt{render(t,e){const n=g();const i=t.append("g");const a=j.create();i.selectAll("path").data(e).enter().append("path").attr("d",(t=>n(t))).attr("fill",(t=>t.color)).on("mouseover",((t,e)=>{const n=s({holder:a.d});const i=structuredClone(e);i.dt=r;i.gene=i.text;{const[t,e]=n.addRow();t.text("Data type");e.append("span").style("margin-left","5px").text("Loss of Heterozygosity")}const[o,l]=n.addRow();o.text("Position");l.append("span").text(`${e.chr}:${e.start}-${e.stop}`);a.show(t.x,t.y)})).on("mouseout",(()=>{a.clear();a.hide()}))}}class Et{render(t,e){const n=g();const i=t.append("g");const a=j.create();i.selectAll("path").data(e).enter().append("path").attr("d",(t=>n(t))).attr("fill",(t=>t.color)).on("mouseover",((t,e)=>{const n=structuredClone(e);n.dt=o;n.samples=[{sample_id:e.sampleName}];n.gene=n.text;const i=s({holder:a.d});{const[t,e]=i.addRow();t.text("Copy number change");e.html(`<span style="background:${n.color}">&nbsp;&nbsp;</span> ${n.value}`)}{const[t,e]=i.addRow();t.text("Position");e.text(n.chr+":"+n.start+"-"+n.stop)}{const[t,e]=i.addRow();t.text("Unit");e.text(n.value)}a.show(t.x,t.y)})).on("mouseout",(()=>{a.clear();a.hide()}))}}class Vt{constructor(t=0,e=0){this.positivePercentile80=t;this.negativePercentile80=e}render(t,e){const n=g();const i=t.append("g");const a=j.create();i.selectAll("path").data(e).enter().append("path").attr("d",(t=>n(t))).attr("fill",(t=>c([this.negativePercentile80,0,this.positivePercentile80],[t.color,"white",t.color]).clamp(true)(t.value))).on("mouseover",((t,e)=>{const n=s({holder:a.d});const i=structuredClone(e);i.dt=o;i.samples=[{sample_id:e.sampleName}];i.gene=i.text;{const[t,e]=n.addRow();t.text("Copy number change");e.html(`<span style="background:${i.color}">&nbsp;&nbsp;</span> ${i.value}`)}{const[t,e]=n.addRow();t.text("Position");e.text(i.chr+":"+i.start+"-"+i.stop)}{const[t,e]=n.addRow();t.text("Unit");e.text(i.value)}a.show(t.x,t.y)})).on("mouseout",(()=>{a.clear();a.hide()}))}}class St{constructor(t){this.recreateViewModel=false;this.type="Disco";this.opts=t;this.isOpen=false;this.discoInteractions=new X(this)}init(){return t(this,void 0,void 0,(function*(){const t=this.app.getState();const e=t.plots.find((t=>t.id===this.id)).settings;this.stateViewModelMapper=new yt(e);this.viewModel=this.stateViewModelMapper.map(t);const s=this.opts.holder;const n=s.append("div").style("display","inline-block").style("vertical-align","top");const i=n.append("div");const a=n.append("div");const o=this.getConfigInputsOptions(this.viewModel);this.features=yield u({topbar:R({app:this.app,id:this.id,downloadHandler:()=>this.discoInteractions.downloadClickListener(s.select('svg[id="sjpp_disco_plot"]').node()),callback:()=>this.toggleVisibility(this.isOpen),isOpen:()=>this.isOpen,holder:i}),config:b({app:this.app,id:this.id,holder:a,isOpen:()=>this.isOpen,inputs:o})})}))}getConfigInputsOptions(t){const e=[];if(t.settings.Disco.showPrioritizeGeneLabelsByGeneSets){const s=[{boxLabel:t.genesetName,label:`Filter mutations`,type:"checkbox",chartType:"Disco",settingsKey:"prioritizeGeneLabelsByGeneSets",title:`Only show mutations for ${t.genesetName} genes`}];e.push(...s)}const s=[{label:"CNV capping",type:"number",chartType:"Disco",settingsKey:"cnvCapping",title:"Cnv capping",min:0},{boxLabel:"",label:"CNV rendering type",type:"radio",chartType:"Disco",settingsKey:"cnvRenderingType",title:"CNV rendering type",options:[{label:"Heatmap",value:ut.heatmap},{label:"Bar",value:ut.bar}]},{label:"CNV percentile",type:"number",chartType:"Disco",settingsKey:"cnvPercentile",title:"Cnv percentile",min:1,max:100}];e.push(...s);return e}main(){return t(this,void 0,void 0,(function*(){const t=this.state.settings;this.isOpen=t.Disco.isOpen;if(this.recreateViewModel){this.stateViewModelMapper=new yt(t);this.viewModel=this.stateViewModelMapper.map(this.app.getState())}this.recreateViewModel=true;if(this.viewModel){const e=this.opts.holder;e.select('div[id="sjpp_disco_plot_holder_div"]').remove();const s=e.append("div").attr("id","sjpp_disco_plot_holder_div").style("display","inline-block");const n=this.app.getState();for(const t in this.features){this.features[t].update({state:this.state,appState:n})}const i=new It(this.viewModel.cappedCnvMaxAbsValue,t.label.fontSize);const a=new q(this.getRingRenderers(t,this.viewModel,this.discoInteractions.geneClickListener),i);a.render(s,this.viewModel)}}))}getState(t){return t.plots.find((t=>t.id===this.id))}getRingRenderers(t,e,s){const n=new Lt(t.padAngle,t.rings.chromosomeInnerRadius,t.rings.chromosomeInnerRadius+t.rings.chromosomeWidth);const i=new Dt(t.label.animationDuration,s);const a=new Pt(s);const o=new Ot(t.rings.snvRingWidth,s);const r=t.Disco.cnvRenderingType===ut.heatmap?new Vt(e.positivePercentile80,e.negativePercentile80):new Et;const l=new Nt;const c=new Map;c.set(at.CHROMOSOME,n);c.set(at.LABEL,i);c.set(at.NONEXONICSNV,a);c.set(at.SNV,o);c.set(at.CNV,r);c.set(at.LOH,l);return c}toggleVisibility(t){this.app.dispatch({type:"plot_edit",id:this.opts.id,config:{settings:{Disco:{isOpen:!t}}}})}}const zt=p(St);const Bt=zt;function Gt(e){return t(this,void 0,void 0,(function*(){return{chartType:"Disco",subfolder:"disco",extension:"ts",settings:Tt(e.overrides)}}))}export{Bt as componentInit,zt as discoInit,Gt as getPlotConfig};

package/dist/{Disco.UI-a5296c36.js → Disco.UI-b071cf7a.js}

@@ -1 +1 @@
-import{_ as t}from"./tslib.es6-c3c2d88f.js";import{m as e,a as l,b as n,c as i,f as a,e as o}from"./uiUtils-ea7dfea2.js";import{T as s}from"./toggleButtons-c4d6f260.js";import{y as p,aT as d}from"./app-6fb77603.js";import{launch as c}from"./launch.adhoc-e124c993.js";import"./plot.app-2a805759.js";import"./recover-299ffdb3.js";import"./termsetting-492eefa7.js";import"path";import"./FilterRxComp-02e68f1b.js";import"./table-0daf2b89.js";import"./partjson.esm-b3f1fc21.js";import"./termdb.bins-39d11f24.js";import"./FilterStateless-16a33070.js";import"./app-d215327f.js";import"./termInfo-491b10af.js";import"./genesearch-ffd88bf2.js";import"./checkbox-96437f4d.js";import"./rehydrateFilter-12d118cb.js";function r(t,n,i){const a=t.append("div").style("margin","20px 20px 20px 40px").style("font-family","'Lucida Sans', 'Lucida Sans Regular', 'Lucida Grande', 'Lucida Sans Unicode', Geneva, Verdana, sans-serif").style("place-items","center left").style("overflow","hidden").classed("sjpp-app-ui",true).classed("sjpp-disco-ui",true);const o={data:[]};e(a,"Select Genome").style("font-size","1.15em").style("padding","10px 0px").style("color","#003366");m(a,n,o);e(a,"Provide Data").style("font-size","1.15em").style("padding","10px 0px 5px 0px").style("color","#003366");a.append("div").style("opacity",.75).style("padding","10px 10px 15px 20px").style("width","65vw").style("line-height","1.5em").html('<p>The plot accepts multiple data types. Input fields for each data type are available in the tabs below. Upload a file or paste data in at least one data type tab and click "Create Disco Plot". <a href="https://proteinpaint.stjude.org/ppdemo/hg38/disco/discoDemoData.tar.gz" target="Demo data">Download example files</a></p>');const s=a.append("div").style("margin-left","2vw");f(s,o);const p=a.append("div").style("display","flex").style("align-items","center").style("padding","15px 0px");h(p,o,n,a,t);l(p,o,".disco_input");if(i)window["doms"]=o;return o}function m(t,e,l){const i=t.append("div").style("margin-left","40px");const a=n(i,e).style("border","1px solid rgb(138, 177, 212)");l.genome=a.node()}function f(e,l){const n=[{label:"SNV Indel",active:true,callback:(e,n)=>t(this,void 0,void 0,(function*(){n.key="snv";const t=`<ol>\n\t\t\t\t\t<li>chr</li>\n\t\t\t\t\t<li>position</li>\n\t\t\t\t\t<li>gene</li>\n\t\t\t\t\t<li>aachange</li>\n\t\t\t\t\t<li>class</li></ol>\n\t\t\t\t\t<p>Example:</p>\n<pre style="margin-left: 10px;">\nchr1\t226252135\tH3F3A\tK28M\tM\nchr2\t98765432\tTestGene\tTestMutation\tF\n</pre>`;y(n,l,t)}))},{label:"SV",active:false,callback:(e,n)=>t(this,void 0,void 0,(function*(){n.key="sv";const t=`<ol>\n\t\t\t\t\t<li>chrA</li>\n\t\t\t\t\t<li>posA</li>\n\t\t\t\t\t<li>geneA (optional)</li>\n\t\t\t\t\t<li>chrB</li>\n\t\t\t\t\t<li>posB</li>\n\t\t\t\t\t<li>geneB (optional)</li>\n\t\t\t\t</ol>\n\t\t\t\t<p>Example (with genes):</p>\n<pre style="margin-left: 10px;">\nchr6\t3067605\tMDC1\tchr12\t61521661\tKMT2D\n</pre>\n\t\t\t\t<p>Example (without genes):</p>\n<pre style="margin-left: 10px;">\nchr6\t3067605\tchr12\t61521661\n</pre>`;y(n,l,t)}))},{label:"CNV",active:false,callback:(e,n)=>t(this,void 0,void 0,(function*(){n.key="cnv";const t=`<ol>\n\t\t\t\t<li>chr</li>\n\t\t\t\t<li>start</li>\n\t\t\t\t<li>stop</li>\n\t\t\t\t<li>value</li>\n\t\t\t\t</ol>\n\t\t\t\t<p>Example:</p>\n<pre style="margin-left: 10px;">\nchr1\t1\t100000000\t0.5\nchr1\t100000000\t200000000\t-0.5\n</pre>`;y(n,l,t)}))}];new s({holder:e,tabs:n,tabsPosition:"vertical",linePosition:"right"}).main()}function y(t,e,l){t.contentHolder.style("border","none").style("display","block").style("padding-left","30px");x(t,e);t.contentHolder.append("div").style("padding","15px 0px 0px 10px").style("opacity",.75).text(`Provide ${t.label} data in tab delimited format with the following columns:`).append("span").html(l);delete t.callback}function x(e,l){const n=95;const i=[{label:"Select File",active:true,width:n,callback:(n,i)=>t(this,void 0,void 0,(function*(){const t=e.key;i.contentHolder.style("border","none").style("display","block");d(i.contentHolder);i.contentHolder.append("div").style("padding","0px 0px 5px 15px").style("opacity",.65).text(`Select a local file`);u(i,l,t);delete i.callback}))},{label:"Paste Data",active:false,width:n,callback:(n,i)=>t(this,void 0,void 0,(function*(){const t=e.key;i.contentHolder.style("border","none").style("display","block");d(i.contentHolder);b(i,l,t);delete i.callback}))}];new s({holder:e.contentHolder,tabs:i}).main()}function u(t,e,l){const n=t.contentHolder.append("div").style("display","inline-block");const i=a(n).classed("disco_input",true);i.on("change",(t=>{const n=t.target.files[0];const i=new FileReader;i.onload=t=>{e.data[l+"Text"]=t.target.result};i.readAsText(n,"utf8")}))}function b(e,l,n){const i=e.contentHolder.append("div").style("display","block");const a=o({div:i,cols:50}).style("border","1px solid rgb(138, 177, 212)").style("margin","0px 0px 0px 20px").classed("disco_input",true).on("keyup",(()=>t(this,void 0,void 0,(function*(){l.data[n+"Text"]=a.property("value").trim()}))))}function h(t,e,l,n,a){const o=i({div:t,text:"Create Disco Plot"});const s=t.append("div");o.style("margin-right","10px").style("font-size","16px").classed("sjpp-ui-submitBtn",true).attr("type","submit").on("click",(()=>{if(!e.data||e.data==undefined){const t=s.append("div").style("display","inline-block").style("max-width","20vw");p(t,"Please provide data");setTimeout((()=>t.remove()),2e3)}else{const t=l[e.genome.options[e.genome.selectedIndex].text];n.remove();c(e.data,t,a);v(a,l)}}))}function v(t,e){t.append("button").html("&#171; Back").on("click",(()=>{t.selectAll("*").remove();r(t,e,false)}))}export{r as init_discoplotUI};
+import{_ as t}from"./tslib.es6-c3c2d88f.js";import{m as e,a as l,b as n,c as i,f as a,e as o}from"./uiUtils-57f4b1ba.js";import{T as s}from"./toggleButtons-2144daab.js";import{y as p,aT as c}from"./app-3d14cbe4.js";import{launch as d}from"./launch.adhoc-cb00917b.js";import"./plot.app-4dc30ebc.js";import"./recover-4888c2a9.js";import"./termsetting-7467350f.js";import"path";import"./FilterRxComp-e8de560c.js";import"./table-be2a9975.js";import"./partjson.esm-b3f1fc21.js";import"./termdb.bins-a60aaa77.js";import"./FilterStateless-75514d37.js";import"./app-bd9f016b.js";import"./termInfo-e16f90f2.js";import"./genesearch-0587c713.js";import"./checkbox-96437f4d.js";import"./rehydrateFilter-12d118cb.js";function r(t,n,i){const a=t.append("div").style("margin","20px 20px 20px 40px").style("font-family","'Lucida Sans', 'Lucida Sans Regular', 'Lucida Grande', 'Lucida Sans Unicode', Geneva, Verdana, sans-serif").style("place-items","center left").style("overflow","hidden").classed("sjpp-app-ui",true).classed("sjpp-disco-ui",true);const o={data:[]};e(a,"Select Genome").style("font-size","1.15em").style("padding","10px 0px").style("color","#003366");m(a,n,o);e(a,"Provide Data").style("font-size","1.15em").style("padding","10px 0px 5px 0px").style("color","#003366");a.append("div").style("opacity",.75).style("padding","10px 10px 15px 20px").style("width","65vw").style("line-height","1.5em").html('<p>The plot accepts multiple data types. Input fields for each data type are available in the tabs below. Upload a file or paste data in at least one data type tab and click "Create Disco Plot". <a href="https://proteinpaint.stjude.org/ppdemo/hg38/disco/discoDemoData.tar.gz" target="Demo data">Download example files</a></p>');const s=a.append("div").style("margin-left","2vw");y(s,o);const p=a.append("div").style("display","flex").style("align-items","center").style("padding","15px 0px");h(p,o,n,a,t);l(p,o,".disco_input");if(i)window["doms"]=o;return o}function m(t,e,l){const i=t.append("div").style("margin-left","40px");const a=n(i,e).style("border","1px solid rgb(138, 177, 212)");l.genome=a.node()}function y(e,l){const n=[{label:"SNV Indel",active:true,callback:(e,n)=>t(this,void 0,void 0,(function*(){n.key="snv";const t=`<ol>\n\t\t\t\t\t<li>chr</li>\n\t\t\t\t\t<li>position</li>\n\t\t\t\t\t<li>gene</li>\n\t\t\t\t\t<li>aachange</li>\n\t\t\t\t\t<li>class</li></ol>\n\t\t\t\t\t<p>Example:</p>\n<pre style="margin-left: 10px;">\nchr1\t226252135\tH3F3A\tK28M\tM\nchr2\t98765432\tTestGene\tTestMutation\tF\n</pre>`;f(n,l,t)}))},{label:"SV",active:false,callback:(e,n)=>t(this,void 0,void 0,(function*(){n.key="sv";const t=`<ol>\n\t\t\t\t\t<li>chrA</li>\n\t\t\t\t\t<li>posA</li>\n\t\t\t\t\t<li>geneA (optional)</li>\n\t\t\t\t\t<li>chrB</li>\n\t\t\t\t\t<li>posB</li>\n\t\t\t\t\t<li>geneB (optional)</li>\n\t\t\t\t</ol>\n\t\t\t\t<p>Example (with genes):</p>\n<pre style="margin-left: 10px;">\nchr6\t3067605\tMDC1\tchr12\t61521661\tKMT2D\n</pre>\n\t\t\t\t<p>Example (without genes):</p>\n<pre style="margin-left: 10px;">\nchr6\t3067605\tchr12\t61521661\n</pre>`;f(n,l,t)}))},{label:"CNV",active:false,callback:(e,n)=>t(this,void 0,void 0,(function*(){n.key="cnv";const t=`<ol>\n\t\t\t\t<li>chr</li>\n\t\t\t\t<li>start</li>\n\t\t\t\t<li>stop</li>\n\t\t\t\t<li>value</li>\n\t\t\t\t</ol>\n\t\t\t\t<p>Example:</p>\n<pre style="margin-left: 10px;">\nchr1\t1\t100000000\t0.5\nchr1\t100000000\t200000000\t-0.5\n</pre>`;f(n,l,t)}))}];new s({holder:e,tabs:n,tabsPosition:"vertical",linePosition:"right"}).main()}function f(t,e,l){t.contentHolder.style("border","none").style("display","block").style("padding-left","30px");b(t,e);t.contentHolder.append("div").style("padding","15px 0px 0px 10px").style("opacity",.75).text(`Provide ${t.label} data in tab delimited format with the following columns:`).append("span").html(l);delete t.callback}function b(e,l){const n=95;const i=[{label:"Select File",active:true,width:n,callback:(n,i)=>t(this,void 0,void 0,(function*(){const t=e.key;i.contentHolder.style("border","none").style("display","block");c(i.contentHolder);i.contentHolder.append("div").style("padding","0px 0px 5px 15px").style("opacity",.65).text(`Select a local file`);x(i,l,t);delete i.callback}))},{label:"Paste Data",active:false,width:n,callback:(n,i)=>t(this,void 0,void 0,(function*(){const t=e.key;i.contentHolder.style("border","none").style("display","block");c(i.contentHolder);u(i,l,t);delete i.callback}))}];new s({holder:e.contentHolder,tabs:i}).main()}function x(t,e,l){const n=t.contentHolder.append("div").style("display","inline-block");const i=a(n).classed("disco_input",true);i.on("change",(t=>{const n=t.target.files[0];const i=new FileReader;i.onload=t=>{e.data[l+"Text"]=t.target.result};i.readAsText(n,"utf8")}))}function u(e,l,n){const i=e.contentHolder.append("div").style("display","block");const a=o({div:i,cols:50}).style("border","1px solid rgb(138, 177, 212)").style("margin","0px 0px 0px 20px").classed("disco_input",true).on("keyup",(()=>t(this,void 0,void 0,(function*(){l.data[n+"Text"]=a.property("value").trim()}))))}function h(t,e,l,n,a){const o=i({div:t,text:"Create Disco Plot"});const s=t.append("div");o.style("margin-right","10px").style("font-size","16px").classed("sjpp-ui-submitBtn",true).attr("type","submit").on("click",(()=>{if(!e.data||e.data==undefined){const t=s.append("div").style("display","inline-block").style("max-width","20vw");p(t,"Please provide data");setTimeout((()=>t.remove()),2e3)}else{const t=l[e.genome.options[e.genome.selectedIndex].text];n.remove();d(e.data,t,a);v(a,l)}}))}function v(t,e){t.append("button").html("&#171; Back").on("click",(()=>{t.selectAll("*").remove();r(t,e,false)}))}export{r as init_discoplotUI};

package/dist/{DragControls-ca3fa0cf.js → DragControls-7961799c.js}

@@ -1 +1 @@
-import{P as e,R as t,V as n,a as r,M as o,E as i}from"./sampleScatter.rendererThree-ef289434.js";import"./app-6fb77603.js";const s=new e;const a=new t;const c=new n;const l=new r;const p=new r;const u=new r;const d=new o;class f extends i{constructor(e,t,n){super();n.style.touchAction="none";let r=null,o=null;const i=[];const f=this;function m(){n.addEventListener("pointermove",E);n.addEventListener("pointerdown",g);n.addEventListener("pointerup",j);n.addEventListener("pointerleave",j)}function v(){n.removeEventListener("pointermove",E);n.removeEventListener("pointerdown",g);n.removeEventListener("pointerup",j);n.removeEventListener("pointerleave",j);n.style.cursor=""}function h(){v()}function y(){return e}function b(){return a}function E(m){if(f.enabled===false)return;x(m);a.setFromCamera(c,t);if(r){if(a.ray.intersectPlane(s,p)){r.position.copy(p.sub(l).applyMatrix4(d))}f.dispatchEvent({type:"drag",object:r});return}if(m.pointerType==="mouse"||m.pointerType==="pen"){i.length=0;a.setFromCamera(c,t);a.intersectObjects(e,true,i);if(i.length>0){const e=i[0].object;s.setFromNormalAndCoplanarPoint(t.getWorldDirection(s.normal),u.setFromMatrixPosition(e.matrixWorld));if(o!==e&&o!==null){f.dispatchEvent({type:"hoveroff",object:o});n.style.cursor="auto";o=null}if(o!==e){f.dispatchEvent({type:"hoveron",object:e});n.style.cursor="pointer";o=e}}else{if(o!==null){f.dispatchEvent({type:"hoveroff",object:o});n.style.cursor="auto";o=null}}}}function g(o){if(f.enabled===false)return;x(o);i.length=0;a.setFromCamera(c,t);a.intersectObjects(e,true,i);if(i.length>0){r=f.transformGroup===true?e[0]:i[0].object;s.setFromNormalAndCoplanarPoint(t.getWorldDirection(s.normal),u.setFromMatrixPosition(r.matrixWorld));if(a.ray.intersectPlane(s,p)){d.copy(r.parent.matrixWorld).invert();l.copy(p).sub(u.setFromMatrixPosition(r.matrixWorld))}n.style.cursor="move";f.dispatchEvent({type:"dragstart",object:r})}}function j(){if(f.enabled===false)return;if(r){f.dispatchEvent({type:"dragend",object:r});r=null}n.style.cursor=o?"pointer":"auto"}function x(e){const t=n.getBoundingClientRect();c.x=(e.clientX-t.left)/t.width*2-1;c.y=-(e.clientY-t.top)/t.height*2+1}m();this.enabled=true;this.transformGroup=false;this.activate=m;this.deactivate=v;this.dispose=h;this.getObjects=y;this.getRaycaster=b}}export{f as DragControls};
+import{P as e,R as t,V as n,a as r,M as o,E as i}from"./sampleScatter.rendererThree-aa51e3c8.js";import"./app-3d14cbe4.js";const s=new e;const a=new t;const c=new n;const l=new r;const p=new r;const u=new r;const d=new o;class f extends i{constructor(e,t,n){super();n.style.touchAction="none";let r=null,o=null;const i=[];const f=this;function m(){n.addEventListener("pointermove",E);n.addEventListener("pointerdown",g);n.addEventListener("pointerup",j);n.addEventListener("pointerleave",j)}function v(){n.removeEventListener("pointermove",E);n.removeEventListener("pointerdown",g);n.removeEventListener("pointerup",j);n.removeEventListener("pointerleave",j);n.style.cursor=""}function h(){v()}function y(){return e}function b(){return a}function E(m){if(f.enabled===false)return;x(m);a.setFromCamera(c,t);if(r){if(a.ray.intersectPlane(s,p)){r.position.copy(p.sub(l).applyMatrix4(d))}f.dispatchEvent({type:"drag",object:r});return}if(m.pointerType==="mouse"||m.pointerType==="pen"){i.length=0;a.setFromCamera(c,t);a.intersectObjects(e,true,i);if(i.length>0){const e=i[0].object;s.setFromNormalAndCoplanarPoint(t.getWorldDirection(s.normal),u.setFromMatrixPosition(e.matrixWorld));if(o!==e&&o!==null){f.dispatchEvent({type:"hoveroff",object:o});n.style.cursor="auto";o=null}if(o!==e){f.dispatchEvent({type:"hoveron",object:e});n.style.cursor="pointer";o=e}}else{if(o!==null){f.dispatchEvent({type:"hoveroff",object:o});n.style.cursor="auto";o=null}}}}function g(o){if(f.enabled===false)return;x(o);i.length=0;a.setFromCamera(c,t);a.intersectObjects(e,true,i);if(i.length>0){r=f.transformGroup===true?e[0]:i[0].object;s.setFromNormalAndCoplanarPoint(t.getWorldDirection(s.normal),u.setFromMatrixPosition(r.matrixWorld));if(a.ray.intersectPlane(s,p)){d.copy(r.parent.matrixWorld).invert();l.copy(p).sub(u.setFromMatrixPosition(r.matrixWorld))}n.style.cursor="move";f.dispatchEvent({type:"dragstart",object:r})}}function j(){if(f.enabled===false)return;if(r){f.dispatchEvent({type:"dragend",object:r});r=null}n.style.cursor=o?"pointer":"auto"}function x(e){const t=n.getBoundingClientRect();c.x=(e.clientX-t.left)/t.width*2-1;c.y=-(e.clientY-t.top)/t.height*2+1}m();this.enabled=true;this.transformGroup=false;this.activate=m;this.deactivate=v;this.dispose=h;this.getObjects=y;this.getRaycaster=b}}export{f as DragControls};

package/dist/{DziViewer-28915c11.js → DziViewer-aa5b5706.js}

@@ -1,4 +1,4 @@
-import{_ as e}from"./tslib.es6-c3c2d88f.js";import{h as t}from"./app-6fb77603.js";import{c as i,a as n}from"./_commonjsHelpers-318dc0aa.js";var r=i((function(e){
+import{_ as e}from"./tslib.es6-c3c2d88f.js";import{h as t}from"./app-3d14cbe4.js";import{c as i,a as n}from"./_commonjsHelpers-318dc0aa.js";var r=i((function(e){
 //! openseadragon 4.1.1
 //! Built on 2024-04-01
 //! Git commit: v4.1.1-0-f90d9814