@sjcrh/proteinpaint-client 2.19.2 → 2.23.1-0

package/README.md

@@ -1,6 +1,6 @@
 # Proteinpaint Client
 
-The frontend code for the ProteinPaint application
+The client code for the ProteinPaint application
 
 ## Installation
 

package/dist/{2dmaf-099e0c08.js → 2dmaf-48551990.js}

@@ -1 +1 @@
-import{M as t,bb as e,bc as s,n as a,D as n,b8 as i,o as r,l,f as o,a as c,ay as p,aL as h,p as d,v as f,_ as u}from"./app-efdeb195.js";import{d as m,c as y,b as g}from"./axis-6cb4f314.js";import{s as x,b,e as k,a as v,f as _,d as D,c as w,S as T}from"./symbol-fc7cbd41.js";import"path";import"./math-2fb199c6.js";import"./constant-426a1483.js";class N{constructor(t){this.opts=t;this.anchorType=t.anchorType;this.shareheight=t.shareheight;this.sharewidth=t.sharewidth;const e="x"in t?t.x:0;const s="y"in t?t.y:0;this.settings={visible:true,opacity:.3,x:e,y:s,xOffset:t.axiswidth+t.sp+t.sample2height,yOffset:t.shareheight,currX:t.axiswidth+t.sp+t.sample2height+e,currY:t.shareheight-s,strokeWidth:"strokeWidth"in t?t.strokeWidth:5,stroke:"stroke"in t?t.stroke:"red",xarmlen:"xarmlen"in t?t.xarmlen:25};this.addControls(this.anchorType?null:this.opts.headerdiv)}setWrapper(t){this.opts.wrapper=t}addControls(e=null){if(e){e.append("button").text("Anchors").on("click",(t=>{this.anchormenu.showunder(t.target);this.xInput.property("value",(this.settings.x/this.sharewidth).toFixed(2));this.yInput.property("value",(this.settings.y/this.sharewidth).toFixed(2))}))}this.anchormenu=new t({border:"solid 1px black"});this.anchormenu.d.style("text-align","center");this.addCoordInput();this.addColorInput();this.addOpacityInput();if(!this.anchorType)this.addSubmitBtns();else this.addDeleteBtn()}addColorInput(){const t=this.anchormenu.d.append("div");t.append("label").html("Color:&nbsp;");this.strokeInput=t.append("input");this.strokeInput.attr("this.anchorType","text").property("value",this.settings.stroke).style("width","50px")}addOpacityInput(){const t=this.anchormenu.d.append("div");t.append("label").html("Opacity:&nbsp;");this.opacityInput=t.append("input");this.opacityInput.attr("this.anchorType","number").attr("min",0).attr("max",1).attr("step",.01).property("value",this.settings.opacity).style("width","50px")}addSubmitBtns(){if(this.anchorType)return;const t=this.anchormenu.d.append("div");t.append("label").html("Add Anchor: ");t.append("button").html("R").on("click",(()=>{new R(this.getSettings("r"));this.anchormenu.hide()}));t.append("button").html("D").on("click",(()=>{new R(this.getSettings("d"));this.anchormenu.hide()}));t.append("button").html("X").on("click",(()=>{new R(this.getSettings("x"));this.anchormenu.hide()}));t.append("button").html("synced").on("click",(()=>{new R(this.getSettings("synced"));this.anchormenu.hide()}))}getSettings(t){return Object.assign({},this.opts,{anchorType:t,opacity:this.opacityInput.property("value"),x:this.xInput.property("value")*this.sharewidth,y:this.yInput.property("value")*this.shareheight,stroke:this.strokeInput.property("value")})}addCoordInput(){const t=this.anchormenu.d.append("div");t.append("label").html("X:&nbsp;");this.xInput=t.append("input");this.xInput.attr("this.anchorType","number").attr("min",0).attr("max",1).attr("step",.01).property("value",0).style("width","80px");const e=this.anchormenu.d.append("div");e.append("label").html("Y:&nbsp;");this.yInput=e.append("input");this.yInput.attr("this.anchorType","number").attr("min",0).attr("max",1).attr("step",.01).property("value",0).style("width","80px")}addDeleteBtn(){if(!this.anchorType)return;const t=this.anchormenu.d.append("div");t.append("button").html("Delete").on("click",(()=>{this.g_anchor.remove();this.anchormenu.hide()}))}}class R extends N{constructor(t){super(t);this.render();this.strokeInput.on("change",(()=>{this.settings.stroke=this.strokeInput.property("value");this.g_anchor.style("stroke",this.settings.stroke);this.anchormenu.hide()}));this.opacityInput.on("change",(()=>{this.settings.opacity=input.property("value");this.g_anchor.style("opacity",this.settings.opacity);this.anchormenu.hide()}));this.xInput.on("change",(()=>{this.settings.x=+this.xInput.property("value")*this.sharewidth;this.settings.currX=this.settings.x+this.settings.xOffset;if(this.d_anchor){this.d_anchor.transition().duration(1e3).attr("x1",this.settings.currX).attr("x2",this.settings.currX)}if(this.x_anchor){this.x_anchor.transition().duration(1e3).attr("transform","translate("+this.settings.currX+","+this.settings.currY+")")}this.anchormenu.hide()}));this.yInput.on("change",(()=>{this.settings.y=+this.yInput.property("value")*this.shareheight;this.settings.currY=-this.settings.y+this.settings.yOffset;if(this.r_anchor){this.r_anchor.transition().duration(1e3).attr("y1",this.settings.currY).attr("y2",this.settings.currY)}if(this.x_anchor){this.x_anchor.transition().duration(1e3).attr("transform","translate("+this.settings.currX+","+this.settings.currY+")")}this.anchormenu.hide()}))}render(){this.g_anchor=this.opts.wrapper.append("g").style("stroke",this.settings.stroke).style("opacity",this.settings.opacity).style("display",this.settings.visible?"":"none").style("stroke-width",this.settings.strokeWidth).on("click",this.anchorType=="synced"?null:t=>{this.anchormenu.showunder(t.target)});this.renderD();this.renderR();this.renderX()}renderD(){if(!["synced","d"].includes(this.anchorType))return;this.d_anchor=this.g_anchor.append("line");const t=this.opts;this.updateD(t.shareheight+t.sp2,t.shareheight+t.sample1height)}updateD(t,e){if(!["synced","d"].includes(this.anchorType))return;this.settings.D={y1:t,y2:e};this.d_anchor.attr("x1",this.settings.currX).attr("x2",this.settings.currX).attr("y1",t).attr("y2",e)}renderR(){if(!["synced","r"].includes(this.anchorType))return;this.r_anchor=this.g_anchor.append("line");const t=this.opts;this.updateR(t.axiswidth+t.sp,t.sample2height+t.sp)}updateR(t,e){if(!["synced","r"].includes(this.anchorType))return;this.settings.R={x1:t,x2:e};this.r_anchor.attr("x1",t).attr("x2",e).attr("y1",this.settings.currY).attr("y2",this.settings.currY)}renderX(){if(!["synced","x"].includes(this.anchorType))return;this.x_anchor=this.g_anchor.append("g").attr("transform","translate("+this.settings.currX+","+this.settings.currY+")");this.bindXDrag();this.x_anchor.append("circle").attr("cx",0).attr("cy",0).attr("r",this.settings.xarmlen).style("opacity",0);this.x_anchor.append("line").attr("x1",-this.settings.xarmlen).attr("x2",this.settings.xarmlen).attr("y1",0).attr("y2",0);this.x_anchor.append("line").attr("x1",0).attr("x2",0).attr("y1",this.settings.xarmlen).attr("y2",-this.settings.xarmlen)}bindXDrag(){if(!["synced"].includes(this.anchorType))return;this.x_anchor.on("mousedown",(t=>{const e=t.clientX;const s=t.clientY;let a=this.settings.currX,n=this.settings.currY;this.x_anchor.on("mousemove",(t=>{a=this.settings.currX-e+t.clientX;n=this.settings.currY-s+t.clientY;this.r_anchor.attr("y1",n).attr("y2",n);this.d_anchor.attr("x1",a).attr("x2",a);this.x_anchor.attr("transform","translate("+a+","+n+")")})).on("mouseup",(t=>{this.x_anchor.on("mousemove",null);a=this.settings.currX-e+t.clientX;n=this.settings.currY-s+t.clientY;if(a==this.settings.currX&&n==this.settings.currY){this.g_anchor.remove();return}this.settings.x=a<this.settings.xOffset?0:a-this.settings.xOffset;this.settings.y=n>this.settings.yOffset?0:-(n-this.settings.yOffset);this.settings.currX=this.settings.x+this.settings.xOffset;this.settings.currY=-this.settings.y+this.settings.yOffset;this.r_anchor.transition().duration(100).attr("y1",this.settings.currY).attr("y2",this.settings.currY);this.d_anchor.transition().duration(100).attr("x1",this.settings.currX).attr("x2",this.settings.currX);this.x_anchor.transition().duration(100).attr("transform","translate("+this.settings.currX+","+this.settings.currY+")")})).on("mouseleave",(()=>{this.x_anchor.on("mousemove",null)}))}))}}const I="#f9766c";const M="#609cff";const X="#01b937";const B={circle:x,cross:b,diamond:k,square:v,star:_,triangle:D,wye:w};const F={path:t=>t.symbol,circle:t=>!t.symbol};const Y={path:t=>t.symbol,ellipse:t=>!t.symbol};function A(t,a){let n,i,r,l,o,c;if(a!==undefined)[i,r,l,o,c]=e(a,t);else{[n,i,r,l,o,c]=s(100,100,t);n.header.text("2DMAF: mutant allele fraction plot between a pair of samples");n.body.style("margin","10px")}i.append("div").style("margin-top","20px").html("<ul>"+'<li><a href="https://docs.google.com/document/d/1anyEDMcW1lTSf8399Li2G9r57V-Fqp2591WvoODY7n4/edit#heading=h.mne2ecmp9m13" target=_blank>File format</a></li>'+'<li>To define samples differently than "Diagnosis/Relapse", <a href=https://plus.google.com/+XinZhou_s/posts/WqBVvmd3wYR target=_blank>see how</a>.</li>'+"</ul>");i.append("p").html("<a href=https://proteinpaint.stjude.org/ppdemo/hg19/2dmaf/2dmaf.txt target=_blank>Example file</a>");function p(t,e){o.style("color",e?"red":"black").html(t)}const h=()=>{l.selectAll("*").remove();const e=l.append("input").attr("type","file").on("change",(e=>{const s=e.target.files[0];if(!s){h();return}if(!s.size){p("Invalid file "+s.name);h();return}const a=new FileReader;a.onload=e=>{const a=r.options[r.selectedIndex].innerHTML;const n=C(e.target.result.trim().split(/\r?\n/),t[a],s.name,c);if(n){p(n,1);h();return}i.remove();l.remove();o.remove()};a.onerror=function(){p("Error reading file "+s.name,1);h();return};a.readAsText(s,"utf8")}));setTimeout((()=>e.node().focus()),1100)};h()}function z(t,e){if(!t.genome){a(e,".genome missing for 2dmaf");return}if(!t.input){a(e,".input missing for 2dmaf");return}const s=C(t.input.trim().split(/\r?\n/),t.genome,t.datasetname||"unnamed dataset",e);if(s){a(e,"2DMAF data error: "+s)}}function C(t,e,s,a){const[r,l,o]=O(t[0].trim());if(r){return r}const c={};const p={};const h={};const d={good:0,purity1set:false,purity2set:false,pairsetname:{}};const f=[];const u={};for(const t in n){u[n[t].label.toUpperCase()]=t}for(let e=1;e<t.length;e++){if(t[e]=="")continue;if(t[e][0]=="#"){if(t[e].startsWith("##samplename")){const s=t[e].trim().split(/[\s\t]+/);if(s.length==4){d.pairsetname[s[1]]={1:s[2],2:s[3]}}else{return"Line "+(e+1)+': invalid samplename line: must be "##samplename [patient] [sample1] [sample2]"'}}continue}const s=t[e].trim().split("\t");const a={};for(let t=0;t<l.length;t++){if(s[t]!=undefined&&s[t]!=""){a[l[t]]=s[t]}}if(!a.sample){return"Line "+(e+1)+": missing sample"}if(a.chr){if(a.chr.indexOf("chr")!=0){a.chr="chr"+a.chr}}if(a.chrstart){a.chrstart=Number.parseInt(a.chrstart);if(Number.isNaN(a.chrstart)){return"Line "+(e+1)+": invalid chromosome position"}}if(a.Dcnvloh){a.Dcnvlohraw=a.Dcnvloh;const t=a.Dcnvloh.toLowerCase();if(t=="yes"||t!="diploid"&&t!="haploid"){a.Dcnvloh=true}else{a.Dcnvloh=false}}if(a.Rcnvloh){a.Rcnvlohraw=a.Rcnvloh;const t=a.Rcnvloh.toLowerCase();if(t=="yes"||t!="diploid"&&t!="haploid"){a.Rcnvloh=true}else{a.Rcnvloh=false}}if(!a.call_d){f.push([e,"missing call_d",s]);continue}if(a.call_d!="somatic"&&a.call_d!="wildtype"){f.push([e,"call_d is neither somatic nor wildtype",s]);continue}if(!a.call_r){f.push([e,"missing call_r",s]);continue}if(a.call_r!="somatic"&&a.call_r!="wildtype"){f.push([e,"call_r is neither somatic nor wildtype",s]);continue}if(a.call_d=="somatic"){if(a.call_r=="somatic"){a.set_share=true}else{a.set_1=true}}else{if(a.call_r=="somatic"){a.set_2=true}}if(!a.type){f.push([e,"missing type",s]);continue}const i=a.type.toLowerCase();if(i=="snv"||i=="snp"||i=="mnv"||i=="complex"){a.issnv=true}else if(i=="indel"||i=="ins"||i=="del"){a.isindel=true}else{f.push([e,"type must be either SNV or INDEL",s]);continue}let r="MinD.D";let o=Number.parseInt(a[r]);if(Number.isNaN(o)||o<0){f.push([e,"invalid "+r+" value",s]);continue}a[r]=o;r="TinD.D";o=Number.parseInt(a[r]);if(Number.isNaN(o)||o<0){f.push([e,"invalid "+r+" value",s]);continue}a[r]=o;if(a["TinD.D"]<a["MinD.D"]){f.push([e,"TinD.D value lower than MinD.D",s]);continue}r="MinN.D";if(r in a){o=Number.parseInt(a[r]);if(Number.isNaN(o)||o<0){delete a[r]}else{a[r]=o}}r="TinN.D";if(r in a){o=Number.parseInt(a[r]);if(Number.isNaN(o)||o<0){delete a[r]}else{a[r]=o}}r="MinD.R";o=Number.parseInt(a[r]);if(Number.isNaN(o)||o<0){f.push([e,"invalid "+r+" value",s]);continue}a[r]=o;r="TinD.R";o=Number.parseInt(a[r]);if(Number.isNaN(o)||o<0){f.push([e,"invalid "+r+" value",s]);continue}a[r]=o;if(a["TinD.R"]<a["MinD.R"]){f.push([e,"TinD.R value lower than MinD.R",s]);continue}r="MinN.R";if(r in a){o=Number.parseInt(a[r]);if(Number.isNaN(o)||o<0){delete a[r]}else{a[r]=o}}r="TinN.R";if(r in a){o=Number.parseInt(a[r]);if(Number.isNaN(o)||o<0){delete a[r]}else{a[r]=o}}if(a.symbol){if(!B[a.symbol]){f.push([e,"Invalid symbol value='"+a.symbol+"'",s]);continue}}if(a.class){const t=a.class.toUpperCase();if(t in u){a.class=u[t]}else{f.push([e,"invalid mutation class "+a.class,s]);continue}}a.style={fill:a.issnv?"white":"black",fillhl:a.class?n[a.class].color:"#ccc",stroke:a.chr=="chrX"?"black":a.issnv?"black":"none",strokehl:a.class?n[a.class].color:"black",fillopacity:a.issnv?0:.2,strokeopacity:.2};if(a["TinD.D"]>0){a.maf1=a["MinD.D"]/a["TinD.D"]}if(a["TinD.R"]>0){a.maf2=a["MinD.R"]/a["TinD.R"]}p[a.sample]=1;if(a.gene){h[a.gene]=1}if(!(a.sample in c)){c[a.sample]={name:a.sample,shown:false,header:l,mlst:[]}}const m=c[a.sample];m.mlst.push(a);if(a.purity1){let t=Number.parseFloat(a.purity1);if(Number.isNaN(t)){f.push([e,"diagnosis tumor purity should be a number"]);t=0}else{if(t>1){t/=100}}if(t>0){if(m.purity1==undefined){m.purity1=t;d.purity1set=true}else if(m.purity1!=t){f.push([e,"diagnosis tumor purity value "+t+" is different from existing value "+m.purity1+" in "+a.sample,s])}}}if(a.purity2){let t=Number.parseFloat(a.purity2);if(Number.isNaN(t)){f.push([e,"relapse tumor purity should be a number"]);t=0}else{if(t>1){t/=100}}if(t>0){if(m.purity2==undefined){m.purity2=t;d.purity2set=true}else if(m.purity2!=t){f.push([e,"relapse tumor purity value "+t+" is different from existing value "+m.purity2+" in "+a.sample,s])}}}d.good++}if(f.length>0){i(l,f)}if(d.good==0){return"No valid data."}a.append("p").text("File: "+s);let m=0;for(const t in h)m++;const y=16;const g=a.append("table");const x=g.append("tr");const b=x.append("td").attr("valign","top");b.append("div").html('<div style="display:inline-block;width:'+y+"px;height:"+y+"px;background-color:"+I+'"></div> Diagnosis only '+'<div style="display:inline-block;width:'+y+"px;height:"+y+"px;background-color:"+X+'"></div> Shared '+'<div style="display:inline-block;width:'+y+"px;height:"+y+"px;background-color:"+M+'"></div> Relapse only');const k=b.append("div").style("margin-top","10px").style("height","200px").style("width","300px").style("padding","5px").style("overflow-y","scroll").style("resize","both").style("border","solid 1px #ccc");b.append("div").style("margin-top","10px").style("height","200px").style("width","300px").style("padding","5px").style("overflow-y","scroll").style("resize","both").style("border","solid 1px #ccc");const v=x.append("td").style("vertical-align","top");for(const t in c){const e=d.pairsetname[t];if(e){c[t].setname=e}else{c[t].setname={1:"Diagnosis",2:"Relapse"}}}const _={genome:e,pairs:c,color1:I,color2:M,colorshare:X,rowh:y,peoplewidth:150,genewidth:150,showholder:v,genelimit:Math.min(20,m),purity1set:d.purity1set,purity2set:d.purity2set};E(_,k)}function O(t){const e=t.toLowerCase().split("\t");const s=t.split("\t");if(s.length<=1){return["invalid file header"]}const a=(...t)=>{for(const s of t){const t=e.indexOf(s);if(t!=-1)return t}return-1};let i=a("person","sample","samplename","patient");if(i==-1)return["sample missing from header"];s[i]="sample";i=a("type");if(i==-1)return["type missing from header"];s[i]="type";i=a("mind.d1_g1","mind.d","mind");if(i==-1)return["MinD.D missing from header"];s[i]="MinD.D";i=a("tind.d1_g1","tind.d","tind");if(i==-1)return["TinD.D missing from header"];s[i]="TinD.D";i=a("mind.r1_g1","mind.r","minr");if(i==-1)return["MinD.R missing from header"];s[i]="MinD.R";i=a("tind.r1_g1","tind.r","tinr");if(i==-1)return["TinD.R missing from header"];s[i]="TinD.R";i=a("call_d1_g1","call_d");if(i==-1)return["call_d missing from header"];s[i]="call_d";i=a("call_r1_g1","call_r");if(i==-1)return["call_r missing from header"];s[i]="call_r";i=a("genename","gene");if(i==-1)return["gene missing from header"];s[i]="gene";i=a("amino_acid_change","annovar_sj_aachange","aachange","protein_change");if(i==-1)return["amino_acid_change missing from header"];s[i]="mname";i=a("class","mclass","variant_class","variant_classification","annovar_sj_class");if(i==-1)return["variant_class missing from header"];s[i]="class";i=a("chromosome","chr");if(i==-1)return["chromosome missing from header"];s[i]="chr";i=a("start","start_position","wu_hg19_pos","chr_position");if(i==-1)return["start missing from header"];s[i]="chrstart";i=a("minn.d1_g1","minn.d");if(i!=-1)s[i]="MinN.D";i=a("tinn.d1_g1","tinn.d");if(i!=-1)s[i]="TinN.D";i=a("minn.r1_g1","minn.r");if(i!=-1)s[i]="MinN.R";i=a("tinn.r1_g1","tinn.r");if(i!=-1)s[i]="TinN.R";i=a("mrna_accession","refseq_mrna_id","annovar_sj_filter_isoform","refseq");if(i!=-1)s[i]="isoform";i=a("primary_purity","purity_d");if(i!=-1)s[i]="purity1";i=a("relapse_purity","purity_r");if(i!=-1)s[i]="purity2";i=a("tag_d_cnvloh","cnvloh_d");if(i!=-1)s[i]="Dcnvloh";i=a("tag_r_cnvloh","cnvloh_r");if(i!=-1)s[i]="Rcnvloh";const r=[];for(const t of s){switch(t){case"Dcnvloh":r.push({label:"D. CNV/LOH",get:t=>t.Dcnvlohraw});break;case"Rcnvloh":r.push({label:"R. CNV/LOH",get:t=>t.Rcnvlohraw});break;case"type":r.push({label:"Type",get:t=>t.type});break;case"chr":break;case"chrstart":r.push({label:"Genome Loc.",get:t=>t.chr+":"+(t.chrstart+1)});break;case"class":r.push({label:"Class",get:t=>{if(t.class==p){return t.originalclasslabel?t.originalclasslabel:n[t.class].label}return n[t.class].label}});break;case"mname":r.push({label:"Mutation",get:t=>{let e=t.mname;if(!e)e=t.cdna_change;return e}});break;case"MinD.D":r.push({ismaf:true,width:60,height:14,readcountcredible:30,get:t=>t.maf_diagnosis,label:"D. tumor MAF",fill:"#F7483B",fillbg:"#FCBAB6"});break;case"TinD.D":break;case"MinD.R":r.push({ismaf:true,width:60,height:14,readcountcredible:30,get:t=>t.maf_relapse,label:"R. tumor MAF",fill:"#146EFF",fillbg:"#B6D5FC"});break;case"TinD.R":break;case"MinN.D":r.push({ismaf:true,width:60,height:14,readcountcredible:30,get:t=>t.maf_diagnosis_normal,label:"D. normal MAF",fill:"#F7483B",fillbg:"#FCBAB6"});break;case"TinN.D":break;case"MinN.R":r.push({ismaf:true,width:60,height:14,readcountcredible:30,get:t=>t.maf_relapse_normal,label:"R. normal MAF",fill:"#146EFF",fillbg:"#B6D5FC"});break;case"TinN.R":break;case"call_d":r.push({label:"D. call",get:t=>t.call_d});break;case"call_r":r.push({label:"R. call",get:t=>t.call_r});break;case"purity1":r.push({label:"D. purity",get:t=>t.purity1});break;case"purity2":r.push({label:"R. purity",get:t=>t.purity2});break;default:r.push({label:t,get:e=>e[t]})}}return[null,s,r]}function S(e,s){const a=new t({border:"solid 1px black"});const i=[];const o=[];const p=[];const f=s.mlst;const u=f[0].sample;const m=T();let x=0;let b={};const k={};for(const t of f){if(t["TinD.D"]>0){x=Math.max(x,t["TinD.D"])}if(t["TinD.R"]>0){x=Math.max(x,t["TinD.R"])}if(t.set_share){p.push(t)}else if(t.set_1){i.push(t)}else if(t.set_2){o.push(t)}if(!(t.class in k)){k[t.class]=0}if(t.symbol){if(!b[t.symbol]){b[t.symbol]={numlines:0,label:t.symbollabel,hidden:false}}b[t.symbol].numlines++}k[t.class]++}const v=Math.min(window.innerWidth,window.innerHeight);const _=50,D=v*.5,w=v*.5,R=w/2,I=D/2,M=_/3,X=R/5,A=Math.min(20,12*v/500),z=v/40,C=z*.7,O=3;const S=l().domain([0,x]).range([z/2,z]);const W=t=>Math.PI*Math.pow(S(t),2);for(const t of f){t.radius=Math.max(t["TinD.D"]?S(t["TinD.D"]):0,t["TinD.R"]?S(t["TinD.R"]):0)}const E=e.append("table");const H=E.append("tr");const q=H.append("td").style("vertical-align","top");const G=H.append("td").style("vertical-align","top");G.append("div").style("margin","10px").text("Name: "+u);const U=q.append("div");U.append("button").text("Hide").on("click",(()=>{s.shown=false;if(s.handle){s.handle.attr("font-weight","normal")}E.remove()}));const P=new N({axiswidth:_,sp:M,sp2:X,sample1height:R,sample2height:I,shareheight:w,sharewidth:D,headerdiv:U});U.append("button").text("Screenshot").on("click",(()=>{h(Z.node(),"2dmaf_"+s.name)}));{const t=U.append("select").on("change",(t=>{const e=t.target.options[t.target.selectedIndex].value;if(e=="all"){at.transition().attr("transform",(t=>t.posstring+" scale(1)"));ot.transition().attr("transform",(t=>t.posstring+" scale(1)"));dt.transition().attr("transform",(t=>t.posstring+" scale(1)"));return}at.transition().attr("transform",(t=>t.posstring+" scale("+(t.class==e?1:0)+")"));ot.transition().attr("transform",(t=>t.posstring+" scale("+(t.class==e?1:0)+")"));dt.transition().attr("transform",(t=>t.posstring+" scale("+(t.class==e?1:0)+")"))}));t.append("option").text("Show all mutation classes").property("value","all");const e=[];for(const t in k){e.push([t,k[t]])}e.sort(((t,e)=>e[1]-t[1]));for(const s of e){t.append("option").text((s[0]in n?n[s[0]].label:s[0])+" ("+s[1]+")").property("value",s[0])}}const Z=q.append("svg").attr("width",_+M+I+D+M*2).attr("height",_+M+R+w+M*2);const J=Z.append("g").attr("transform","translate("+M+","+M+")");P.setWrapper(J.append("g"));const K=l().domain([0,1]).range([0,D]);const Q=J.append("g").attr("transform","translate("+(_+M+I)+","+(w+R+M)+")").call(y().scale(K).tickSize(5));c({axis:Q,showline:true,fontsize:A*.8});const $=i.length+p.length;Q.append("text").text(s.setname[1]+", n="+$+(s.purity1?", purity="+s.purity1:"")).attr("x",D/2).attr("y",_-4).attr("text-anchor","middle").attr("font-size",A);const tt=l().domain([0,1]).range([w,0]);const et=J.append("g").attr("transform","translate("+_+",0)").call(g().scale(tt).tickSize(5));c({axis:et,showline:true,fontsize:A*.8});const st=o.length+p.length;et.append("text").text(s.setname[2]+", n="+st+(s.purity2?", purity="+s.purity2:"")).attr("transform","translate("+(A-_-10)+","+w/2+") 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Y){nt.filter(Y[t]).append(t).attr("rx",(t=>t.symbol?null:S(t["TinD.D"]))).attr("ry",(t=>t.symbol?null:S(t["TinD.R"]))).attr("d",(t=>!t.symbol?null:m.type(B[t.symbol]).size(W(t["TinD.D"])+W(t["TinD.R"])/2)())).attr("fill",(t=>t.style.fill)).attr("fill-opacity",(t=>t.style.fillopacity)).attr("stroke",(t=>t.style.stroke)).attr("stroke-opacity",(t=>t.style.strokeopacity)).attr("stroke-dasharray",(t=>t.chr=="chrX"?"5,5":"none")).on("mouseover",((t,e)=>j(t,e,a))).on("mouseout",((t,e)=>L(t,e,a))).on("click",((t,e)=>V(t,s.header,e)))}nt.append("line").attr("stroke",(t=>t.style.stroke)).attr("stroke-opacity",(t=>t.style.strokeopacity)).attr("x1",-3).attr("y1",-3).attr("x2",3).attr("y2",3);nt.append("line").attr("stroke",(t=>t.style.stroke)).attr("stroke-opacity",(t=>t.style.strokeopacity)).attr("x1",-3).attr("y1",3).attr("x2",3).attr("y2",-3);const it=l().domain([0,x]).range([R-X,0]);const rt=J.append("g").attr("transform","translate("+(_+M+I)+","+(w+X)+")");const lt="#FFBEAD";rt.append("rect").attr("fill",lt).attr("fill-opacity",0).attr("x",0).attr("width",3).attr("height",R-X);c({axis:rt.call(g().scale(it).tickValues([0,x])),showline:true,fontsize:A*.8});rt.append("g").attr("transform","translate(-"+A/2+","+(R-X)/2+")").append("text").text("D total").attr("font-size",A*.8).attr("font-family",r).attr("fill","black").attr("text-anchor","middle").attr("dominant-baseline","middle").attr("transform","rotate(-90)");const ot=rt.selectAll().data(i).enter().append("g").attr("transform",(t=>{t.posstring="translate("+K(t.maf1)+","+it(t["TinD.D"])+")";return t.posstring}));ot.filter((t=>t.Dcnvloh)).append("circle").attr("cy",(t=>t.issnv?S(t["TinD.R"]):C/2)).attr("fill","#858585").attr("r",O);ot.filter((t=>t.Rcnvloh)).append("circle").attr("cx",(t=>t.issnv?-S(t["TinD.D"]):-C/2)).attr("fill","#858585").attr("r",O);nt=ot;for(const t in F){nt.filter(F[t]).append(t).attr("class",(t=>t.symbol?"twodmaf-"+t.symbol:null)).attr("r",(t=>t.symbol?null:S(t["TinD.R"]))).attr("d",(t=>!t.symbol?null:m.type(B[t.symbol]).size(W(t["TinD.R"]))())).attr("fill",(t=>t.style.fill)).attr("fill-opacity",(t=>t.style.fillopacity)).attr("stroke",(t=>t.style.stroke)).attr("stroke-opacity",(t=>t.style.strokeopacity)).attr("stroke-dasharray",(t=>t.chr=="chrX"?"5,5":"none")).on("mouseover",((t,e)=>j(t,e,a))).on("mouseout",((t,e)=>L(t,e,a))).on("click",((t,e)=>V(t,s.header,e)))}nt.append("line").attr("stroke",(t=>t.style.stroke)).attr("stroke-opacity",(t=>t.style.strokeopacity)).attr("x1",-3).attr("y1",-3).attr("x2",3).attr("y2",3);nt.append("line").attr("stroke",(t=>t.style.stroke)).attr("stroke-opacity",(t=>t.style.strokeopacity)).attr("x1",-3).attr("y1",3).attr("x2",3).attr("y2",-3);const ct=l().domain([0,x]).range([0,I-X]);const pt=J.append("g").attr("transform","translate("+(_+M)+",0)");pt.append("rect").attr("fill",lt).attr("fill-opacity",0).attr("y",w).attr("width",I-X).attr("height",3);const ht=pt.append("g").attr("transform","translate(0,"+w+")").call(y().scale(ct).tickValues([0,x]));c({axis:ht,showline:true,fontsize:A*.8});pt.append("text").text("R total").attr("font-size",A*.8).attr("font-family",r).attr("fill","black").attr("x",(I-X)/2).attr("y",w+A).attr("text-anchor","middle");const dt=pt.selectAll().data(o).enter().append("g").attr("transform",(t=>{t.posstring="translate("+ct(t["TinD.R"])+","+tt(t.maf2)+")";return t.posstring}));dt.filter((t=>t.Dcnvloh)).append("circle").attr("cy",(t=>t.issnv?S(t["TinD.R"]):C/2)).attr("fill","#858585").attr("r",O);dt.filter((t=>t.Rcnvloh)).append("circle").attr("cx",(t=>t.issnv?-S(t["TinD.D"]):-C/2)).attr("fill","#858585").attr("r",O);nt=dt;for(const t in F){nt.filter(F[t]).append(t).attr("class",(t=>t.symbol?"twodmaf-"+t.symbol:null)).attr("r",(t=>t.symbol?null:S(t["TinD.D"]))).attr("d",(t=>!t.symbol?null:m.type(B[t.symbol]).size(W(t["TinD.R"]))())).attr("fill",(t=>t.style.fill)).attr("fill-opacity",(t=>t.style.fillopacity)).attr("stroke",(t=>t.style.stroke)).attr("stroke-opacity",(t=>t.style.strokeopacity)).attr("stroke-dasharray",(t=>t.chr=="chrX"?"5,5":"none")).on("mouseover",((t,e)=>j(t,e,a))).on("mouseout",((t,e)=>L(t,e,a))).on("click",((t,e)=>V(t,s.header,e)))}nt.append("line").attr("stroke",(t=>t.style.stroke)).attr("stroke-opacity",(t=>t.style.strokeopacity)).attr("x1",-3).attr("y1",-3).attr("x2",3).attr("y2",3);nt.append("line").attr("stroke",(t=>t.style.stroke)).attr("stroke-opacity",(t=>t.style.strokeopacity)).attr("x1",-3).attr("y1",3).attr("x2",3).attr("y2",-3);const ft=J.append("g").attr("transform","translate(0,"+(w+X)+")");let ut=A;ft.append("text").text(u).attr("font-size",A).attr("y",ut);const mt=S(20),yt=S(x);ut+=A+yt;let gt;ft.append("text").text("SNV 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CNV/LOH").attr("y",ut).attr("dominant-baseline","middle").each((function(){gt=this.getBBox().width}));gt+=mt+10;ft.append("circle").attr("cx",gt).attr("cy",ut).attr("r",10).attr("stroke","black").attr("fill","none");ft.append("circle").attr("cx",gt).attr("cy",ut+10).attr("r",O).attr("fill","black");ut+=30;ft.append("text").text("R. CNV/LOH").attr("y",ut).attr("dominant-baseline","central").each((function(){gt=this.getBBox().width}));gt+=mt+10;ft.append("circle").attr("cx",gt).attr("cy",ut).attr("r",10).attr("stroke","black").attr("fill","none");ft.append("circle").attr("cx",gt-10).attr("cy",ut).attr("r",O).attr("fill","black");ut+=30;if(s.purity1!=undefined||s.purity2!=undefined){ft.append("text").text("Expected MAF").attr("y",ut).attr("dominant-baseline","middle").each((function(){gt=this.getBBox().width}));gt+=10;ft.append("rect").attr("fill",lt).attr("x",gt).attr("y",ut).attr("width",40).attr("height",3);ut+=30}const xt=Object.keys(b);if(xt.length){ft.append("text").text("Symbols").attr("y",ut).attr("dominant-baseline","middle").each((function(){gt=this.getBBox().width}));let t;for(const e in b){const s=b[e];const a=ft.append("g").on("click",(()=>{s.hidden=!s.hidden;Z.selectAll(".twodmaf-"+e).style("display",s.hidden?"none":"");n.style("text-decoration",s.hidden?"line-through":"")}));t=gt+20;a.append("path").attr("transform","translate("+t+","+ut+")").attr("d",m.type(B[e]).size(100)()).attr("stroke","black").attr("fill","none").each((function(){t+=this.getBBox().width}));const n=a.append("text").text(s.label?s.label+" ("+s.numlines+")":"").attr("y",ut+2).attr("x",t).attr("dominant-baseline","middle").style("text-decoration",s.hidden?"line-through":"");ut+=30}ut+=30}const bt={},kt={},vt={},_t={};for(const t of f){if(!t.gene)continue;if(!(t.gene in bt)){bt[t.gene]=[]}bt[t.gene].push(t);if(t.set_1){kt[t.gene]=1}else if(t.set_2){vt[t.gene]=1}else if(t.set_share){_t[t.gene]=1}}const Dt=[];for(const t in kt){Dt.push(t)}for(const t in vt){if(!(t in kt)){Dt.push(t)}}for(const t in _t){if(!(t in kt)&&!(t in vt)){Dt.push(t)}}const wt=G.append("div").style("height",w+R+"px").style("margin","10px").style("padding","10px").style("border","solid 1px #ccc").style("overflow-y","scroll").style("resize","both").append("table");{const t=wt.append("tr");t.append("td").text("Gene");t.append("td").text(s.setname[1]+" only");t.append("td").text(s.setname[2]+" only");t.append("td").text("Shared")}let Tt=true;for(const t of Dt){const e=wt.append("tr");if(Tt){e.style("background-color","#f3f3f3")}Tt=!Tt;e.append("td").text(t);let s=[];if(t in bt){s=bt[t]}const a=[],n=[],i=[];for(const t of s){if(t.set_share)i.push(t);else if(t.set_1)a.push(t);else if(t.set_2)n.push(t)}let r=e.append("td");if(a.length){for(const t of a){const e=r.append("div").attr("class","sja_clbtext").style("color",t.style.fillhl).text(t.mname||"").on("click",(e=>{Nt(e.target,t,ot)}));if(t.labelIsVisible){Nt(e.node(),t,ot)}}}r=e.append("td");if(n.length){for(const t of n){const e=r.append("div").attr("class","sja_clbtext").style("color",t.style.fillhl).text(t.mname||"").on("click",(e=>{Nt(e.target,t,dt)}));if(t.labelIsVisible){Nt(e.node(),t,ot)}}}r=e.append("td");if(i.length){for(const t of i){const e=r.append("div").attr("class","sja_clbtext").style("color",t.style.fillhl).text(t.mname||"").on("click",(e=>{Nt(e.target,t,at)}));if(t.labelIsVisible){Nt(e.node(),t,ot)}}}}function Nt(t,e,s){if(e.selected){t.style.border="";e.selected=false}else{t.style.border="solid 1px black";e.selected=true}const a=s.filter((t=>t.gene==e.gene&&t.class==e.class&&t.mname==e.mname));a.selectAll("rect").attr("fill-opacity",e.selected?.5:e.style.fillopacity).attr("fill",e.selected?e.style.fillhl:e.style.fill);a.selectAll("circle,ellipse,line").attr("stroke-opacity",e.selected?1:e.style.strokeopacity).attr("stroke",e.selected?e.style.strokehl:e.style.stroke).attr("stroke-width",e.selected?2:1);if(e.selected){let t=Math.max(20,e.radius),s=0;if((e.set_1||e.set_share)&&e.maf1>=.8){t=-e.radius;s=e.radius*2}const n=a.append("g").attr("class","sja_2dmaf_mlabel").attr("transform","translate("+t+","+s+")");let i;n.append("text").text(e.labelAs?e.labelAs:e.gene+" "+e.mname).attr("fill",e.style.fillhl).attr("dominant-baseline","middle").attr("text-anchor","start").attr("font-size",e.radius).each((function(){i=this.getBBox().width}));n.append("rect").attr("y",-e.radius/2).attr("width",i).attr("height",e.radius).attr("fill","black").attr("fill-opacity",0).on("mouseover",(t=>d(t.target).attr("fill-opacity",.2))).on("mouseout",(t=>d(t.target).attr("fill-opacity",0))).on("mousedown",(e=>{const a=t,i=s,r=e.clientX,l=e.clientY,o=d(document.body);o.on("mousemove",(e=>{e.preventDefault();t=a+e.clientX-r;s=i+e.clientY-l;n.attr("transform","translate("+t+","+s+")")}));o.on("mouseup",(()=>{o.on("mousemove",null).on("mouseup",null)}))}))}else{a.select(".sja_2dmaf_mlabel").remove()}}return E}function j(t,e,s){if(!e.selected){d(t.target).attr("fill",e.style.fillhl).attr("fill-opacity",.2)}s.clear();s.show(t.clientX,t.clientY);s.d.append("div").html((e.gene||"no gene")+' <span style="color:'+e.style.fillhl+'">'+(e.mname||"")+"</span>"+(e.class?' <span style="font-size:70%">'+n[e.class].label+"</span>":""))}function L(t,e,s){if(!e.selected){d(t.ele).attr("fill",e.style.fill).attr("fill-opacity",e.style.fillopacity).attr("stroke",e.style.stroke)}s.hide()}function V(t,e,s){const a=f({x:t.clientX+30,y:t.clientY-30});a.header.text((s.gene?s.gene:"No gene")+" "+(s.mname?s.mname:""));var n=[];for(let t=0;t<e.length;t++){n.push({k:e[t],v:s[e[t]]})}u(a.body,n)}function W(t,e){const s=t.pairs[e];if(s.shown){s.shown=false;s.holder.remove();if(s.handle){s.handle.attr("font-weight","normal")}}else{s.shown=true;if(s.holder){t.showholder.node().appendChild(s.holder.node())}else{s.holder=S(t.showholder,s)}if(s.handle){s.handle.attr("font-weight","bold")}}}function E(t,e){const s=[];for(const e in t.pairs){s.push([e,t.pairs[e].mlst.length])}e.selectAll("*").remove();const a=e.append("div").style("margin-bottom","5px");a.append("span").text(s.length+" individual"+(s.length>1?"s":""));const n=e.append("svg");const i=5,p=20,h=t.rowh;let d=0;for(const t of s){n.append("text").text(t[0]).attr("font-size",h).attr("font-family",r).each((function(){d=Math.max(d,this.getBBox().width)})).remove()}n.attr("width",d+i+t.peoplewidth+30).attr("height",p+i+h*s.length);s.sort(((t,e)=>e[1]-t[1]));let f=0;for(const e in t.pairs){f=Math.max(f,t.pairs[e].mlst.length)}const u=n.append("g").attr("transform","translate("+(d+i)+","+p+")").call(m().scale(l().domain([0,f]).range([0,t.peoplewidth])).tickFormat(o("d")).ticks(3));c({axis:u,showline:true,color:"black"});const y=t.peoplewidth/f;let g=p+i;for(const e of s){const s=e[0];t.pairs[s].handle=n.append("text").text(s).attr("class","sja_svgtext2").attr("font-size",h-2).attr("font-family",r).attr("x",d).attr("y",g+i+h/2).attr("text-anchor","end").on("click",(()=>{W(t,s)}));let a=0,l=0,o=0;for(const e of t.pairs[s].mlst){if(e.set_1)a++;else if(e.set_2)l++;else if(e.set_share)o++}const c=n.append("g").attr("transform","translate("+(d+i)+","+g+")");if(a>0){c.append("rect").attr("width",y*a).attr("height",h-1).attr("fill",t.color1)}if(o>0){c.append("rect").attr("x",y*a).attr("width",y*o).attr("height",h-1).attr("fill",t.colorshare)}if(l>0){c.append("rect").attr("x",y*(a+o)).attr("width",y*l).attr("height",h-1).attr("fill",t.color2)}g+=h}}export{z as d2mafparseinput,A as d2mafui};
+import{M as t,bb as e,bc as s,n as a,D as n,b8 as i,o as r,l,f as o,a as c,ay as p,aL as h,p as d,v as f,_ as u}from"./app-7e06239d.js";import{d as m,c as y,b as g}from"./axis-6cb4f314.js";import{s as x,b,e as k,a as v,f as _,d as D,c as w,S as T}from"./symbol-fc7cbd41.js";import"path";import"./math-2fb199c6.js";import"./constant-426a1483.js";class N{constructor(t){this.opts=t;this.anchorType=t.anchorType;this.shareheight=t.shareheight;this.sharewidth=t.sharewidth;const e="x"in t?t.x:0;const s="y"in t?t.y:0;this.settings={visible:true,opacity:.3,x:e,y:s,xOffset:t.axiswidth+t.sp+t.sample2height,yOffset:t.shareheight,currX:t.axiswidth+t.sp+t.sample2height+e,currY:t.shareheight-s,strokeWidth:"strokeWidth"in t?t.strokeWidth:5,stroke:"stroke"in t?t.stroke:"red",xarmlen:"xarmlen"in t?t.xarmlen:25};this.addControls(this.anchorType?null:this.opts.headerdiv)}setWrapper(t){this.opts.wrapper=t}addControls(e=null){if(e){e.append("button").text("Anchors").on("click",(t=>{this.anchormenu.showunder(t.target);this.xInput.property("value",(this.settings.x/this.sharewidth).toFixed(2));this.yInput.property("value",(this.settings.y/this.sharewidth).toFixed(2))}))}this.anchormenu=new t({border:"solid 1px black"});this.anchormenu.d.style("text-align","center");this.addCoordInput();this.addColorInput();this.addOpacityInput();if(!this.anchorType)this.addSubmitBtns();else this.addDeleteBtn()}addColorInput(){const t=this.anchormenu.d.append("div");t.append("label").html("Color:&nbsp;");this.strokeInput=t.append("input");this.strokeInput.attr("this.anchorType","text").property("value",this.settings.stroke).style("width","50px")}addOpacityInput(){const t=this.anchormenu.d.append("div");t.append("label").html("Opacity:&nbsp;");this.opacityInput=t.append("input");this.opacityInput.attr("this.anchorType","number").attr("min",0).attr("max",1).attr("step",.01).property("value",this.settings.opacity).style("width","50px")}addSubmitBtns(){if(this.anchorType)return;const t=this.anchormenu.d.append("div");t.append("label").html("Add Anchor: ");t.append("button").html("R").on("click",(()=>{new R(this.getSettings("r"));this.anchormenu.hide()}));t.append("button").html("D").on("click",(()=>{new R(this.getSettings("d"));this.anchormenu.hide()}));t.append("button").html("X").on("click",(()=>{new R(this.getSettings("x"));this.anchormenu.hide()}));t.append("button").html("synced").on("click",(()=>{new R(this.getSettings("synced"));this.anchormenu.hide()}))}getSettings(t){return Object.assign({},this.opts,{anchorType:t,opacity:this.opacityInput.property("value"),x:this.xInput.property("value")*this.sharewidth,y:this.yInput.property("value")*this.shareheight,stroke:this.strokeInput.property("value")})}addCoordInput(){const t=this.anchormenu.d.append("div");t.append("label").html("X:&nbsp;");this.xInput=t.append("input");this.xInput.attr("this.anchorType","number").attr("min",0).attr("max",1).attr("step",.01).property("value",0).style("width","80px");const e=this.anchormenu.d.append("div");e.append("label").html("Y:&nbsp;");this.yInput=e.append("input");this.yInput.attr("this.anchorType","number").attr("min",0).attr("max",1).attr("step",.01).property("value",0).style("width","80px")}addDeleteBtn(){if(!this.anchorType)return;const t=this.anchormenu.d.append("div");t.append("button").html("Delete").on("click",(()=>{this.g_anchor.remove();this.anchormenu.hide()}))}}class R extends N{constructor(t){super(t);this.render();this.strokeInput.on("change",(()=>{this.settings.stroke=this.strokeInput.property("value");this.g_anchor.style("stroke",this.settings.stroke);this.anchormenu.hide()}));this.opacityInput.on("change",(()=>{this.settings.opacity=input.property("value");this.g_anchor.style("opacity",this.settings.opacity);this.anchormenu.hide()}));this.xInput.on("change",(()=>{this.settings.x=+this.xInput.property("value")*this.sharewidth;this.settings.currX=this.settings.x+this.settings.xOffset;if(this.d_anchor){this.d_anchor.transition().duration(1e3).attr("x1",this.settings.currX).attr("x2",this.settings.currX)}if(this.x_anchor){this.x_anchor.transition().duration(1e3).attr("transform","translate("+this.settings.currX+","+this.settings.currY+")")}this.anchormenu.hide()}));this.yInput.on("change",(()=>{this.settings.y=+this.yInput.property("value")*this.shareheight;this.settings.currY=-this.settings.y+this.settings.yOffset;if(this.r_anchor){this.r_anchor.transition().duration(1e3).attr("y1",this.settings.currY).attr("y2",this.settings.currY)}if(this.x_anchor){this.x_anchor.transition().duration(1e3).attr("transform","translate("+this.settings.currX+","+this.settings.currY+")")}this.anchormenu.hide()}))}render(){this.g_anchor=this.opts.wrapper.append("g").style("stroke",this.settings.stroke).style("opacity",this.settings.opacity).style("display",this.settings.visible?"":"none").style("stroke-width",this.settings.strokeWidth).on("click",this.anchorType=="synced"?null:t=>{this.anchormenu.showunder(t.target)});this.renderD();this.renderR();this.renderX()}renderD(){if(!["synced","d"].includes(this.anchorType))return;this.d_anchor=this.g_anchor.append("line");const t=this.opts;this.updateD(t.shareheight+t.sp2,t.shareheight+t.sample1height)}updateD(t,e){if(!["synced","d"].includes(this.anchorType))return;this.settings.D={y1:t,y2:e};this.d_anchor.attr("x1",this.settings.currX).attr("x2",this.settings.currX).attr("y1",t).attr("y2",e)}renderR(){if(!["synced","r"].includes(this.anchorType))return;this.r_anchor=this.g_anchor.append("line");const t=this.opts;this.updateR(t.axiswidth+t.sp,t.sample2height+t.sp)}updateR(t,e){if(!["synced","r"].includes(this.anchorType))return;this.settings.R={x1:t,x2:e};this.r_anchor.attr("x1",t).attr("x2",e).attr("y1",this.settings.currY).attr("y2",this.settings.currY)}renderX(){if(!["synced","x"].includes(this.anchorType))return;this.x_anchor=this.g_anchor.append("g").attr("transform","translate("+this.settings.currX+","+this.settings.currY+")");this.bindXDrag();this.x_anchor.append("circle").attr("cx",0).attr("cy",0).attr("r",this.settings.xarmlen).style("opacity",0);this.x_anchor.append("line").attr("x1",-this.settings.xarmlen).attr("x2",this.settings.xarmlen).attr("y1",0).attr("y2",0);this.x_anchor.append("line").attr("x1",0).attr("x2",0).attr("y1",this.settings.xarmlen).attr("y2",-this.settings.xarmlen)}bindXDrag(){if(!["synced"].includes(this.anchorType))return;this.x_anchor.on("mousedown",(t=>{const e=t.clientX;const s=t.clientY;let a=this.settings.currX,n=this.settings.currY;this.x_anchor.on("mousemove",(t=>{a=this.settings.currX-e+t.clientX;n=this.settings.currY-s+t.clientY;this.r_anchor.attr("y1",n).attr("y2",n);this.d_anchor.attr("x1",a).attr("x2",a);this.x_anchor.attr("transform","translate("+a+","+n+")")})).on("mouseup",(t=>{this.x_anchor.on("mousemove",null);a=this.settings.currX-e+t.clientX;n=this.settings.currY-s+t.clientY;if(a==this.settings.currX&&n==this.settings.currY){this.g_anchor.remove();return}this.settings.x=a<this.settings.xOffset?0:a-this.settings.xOffset;this.settings.y=n>this.settings.yOffset?0:-(n-this.settings.yOffset);this.settings.currX=this.settings.x+this.settings.xOffset;this.settings.currY=-this.settings.y+this.settings.yOffset;this.r_anchor.transition().duration(100).attr("y1",this.settings.currY).attr("y2",this.settings.currY);this.d_anchor.transition().duration(100).attr("x1",this.settings.currX).attr("x2",this.settings.currX);this.x_anchor.transition().duration(100).attr("transform","translate("+this.settings.currX+","+this.settings.currY+")")})).on("mouseleave",(()=>{this.x_anchor.on("mousemove",null)}))}))}}const I="#f9766c";const M="#609cff";const X="#01b937";const B={circle:x,cross:b,diamond:k,square:v,star:_,triangle:D,wye:w};const F={path:t=>t.symbol,circle:t=>!t.symbol};const Y={path:t=>t.symbol,ellipse:t=>!t.symbol};function A(t,a){let n,i,r,l,o,c;if(a!==undefined)[i,r,l,o,c]=e(a,t);else{[n,i,r,l,o,c]=s(100,100,t);n.header.text("2DMAF: mutant allele fraction plot between a pair of samples");n.body.style("margin","10px")}i.append("div").style("margin-top","20px").html("<ul>"+'<li><a href="https://docs.google.com/document/d/1anyEDMcW1lTSf8399Li2G9r57V-Fqp2591WvoODY7n4/edit#heading=h.mne2ecmp9m13" target=_blank>File format</a></li>'+'<li>To define samples differently than "Diagnosis/Relapse", <a href=https://plus.google.com/+XinZhou_s/posts/WqBVvmd3wYR target=_blank>see how</a>.</li>'+"</ul>");i.append("p").html("<a href=https://proteinpaint.stjude.org/ppdemo/hg19/2dmaf/2dmaf.txt target=_blank>Example file</a>");function p(t,e){o.style("color",e?"red":"black").html(t)}const h=()=>{l.selectAll("*").remove();const e=l.append("input").attr("type","file").on("change",(e=>{const s=e.target.files[0];if(!s){h();return}if(!s.size){p("Invalid file "+s.name);h();return}const a=new FileReader;a.onload=e=>{const a=r.options[r.selectedIndex].innerHTML;const n=C(e.target.result.trim().split(/\r?\n/),t[a],s.name,c);if(n){p(n,1);h();return}i.remove();l.remove();o.remove()};a.onerror=function(){p("Error reading file "+s.name,1);h();return};a.readAsText(s,"utf8")}));setTimeout((()=>e.node().focus()),1100)};h()}function z(t,e){if(!t.genome){a(e,".genome missing for 2dmaf");return}if(!t.input){a(e,".input missing for 2dmaf");return}const s=C(t.input.trim().split(/\r?\n/),t.genome,t.datasetname||"unnamed dataset",e);if(s){a(e,"2DMAF data error: "+s)}}function C(t,e,s,a){const[r,l,o]=O(t[0].trim());if(r){return r}const c={};const p={};const h={};const d={good:0,purity1set:false,purity2set:false,pairsetname:{}};const f=[];const u={};for(const t in n){u[n[t].label.toUpperCase()]=t}for(let e=1;e<t.length;e++){if(t[e]=="")continue;if(t[e][0]=="#"){if(t[e].startsWith("##samplename")){const s=t[e].trim().split(/[\s\t]+/);if(s.length==4){d.pairsetname[s[1]]={1:s[2],2:s[3]}}else{return"Line "+(e+1)+': invalid samplename line: must be "##samplename [patient] [sample1] [sample2]"'}}continue}const s=t[e].trim().split("\t");const a={};for(let t=0;t<l.length;t++){if(s[t]!=undefined&&s[t]!=""){a[l[t]]=s[t]}}if(!a.sample){return"Line "+(e+1)+": missing sample"}if(a.chr){if(a.chr.indexOf("chr")!=0){a.chr="chr"+a.chr}}if(a.chrstart){a.chrstart=Number.parseInt(a.chrstart);if(Number.isNaN(a.chrstart)){return"Line "+(e+1)+": invalid chromosome position"}}if(a.Dcnvloh){a.Dcnvlohraw=a.Dcnvloh;const t=a.Dcnvloh.toLowerCase();if(t=="yes"||t!="diploid"&&t!="haploid"){a.Dcnvloh=true}else{a.Dcnvloh=false}}if(a.Rcnvloh){a.Rcnvlohraw=a.Rcnvloh;const t=a.Rcnvloh.toLowerCase();if(t=="yes"||t!="diploid"&&t!="haploid"){a.Rcnvloh=true}else{a.Rcnvloh=false}}if(!a.call_d){f.push([e,"missing call_d",s]);continue}if(a.call_d!="somatic"&&a.call_d!="wildtype"){f.push([e,"call_d is neither somatic nor wildtype",s]);continue}if(!a.call_r){f.push([e,"missing call_r",s]);continue}if(a.call_r!="somatic"&&a.call_r!="wildtype"){f.push([e,"call_r is neither somatic nor wildtype",s]);continue}if(a.call_d=="somatic"){if(a.call_r=="somatic"){a.set_share=true}else{a.set_1=true}}else{if(a.call_r=="somatic"){a.set_2=true}}if(!a.type){f.push([e,"missing type",s]);continue}const i=a.type.toLowerCase();if(i=="snv"||i=="snp"||i=="mnv"||i=="complex"){a.issnv=true}else if(i=="indel"||i=="ins"||i=="del"){a.isindel=true}else{f.push([e,"type must be either SNV or INDEL",s]);continue}let r="MinD.D";let o=Number.parseInt(a[r]);if(Number.isNaN(o)||o<0){f.push([e,"invalid "+r+" value",s]);continue}a[r]=o;r="TinD.D";o=Number.parseInt(a[r]);if(Number.isNaN(o)||o<0){f.push([e,"invalid "+r+" value",s]);continue}a[r]=o;if(a["TinD.D"]<a["MinD.D"]){f.push([e,"TinD.D value lower than MinD.D",s]);continue}r="MinN.D";if(r in a){o=Number.parseInt(a[r]);if(Number.isNaN(o)||o<0){delete a[r]}else{a[r]=o}}r="TinN.D";if(r in a){o=Number.parseInt(a[r]);if(Number.isNaN(o)||o<0){delete a[r]}else{a[r]=o}}r="MinD.R";o=Number.parseInt(a[r]);if(Number.isNaN(o)||o<0){f.push([e,"invalid "+r+" value",s]);continue}a[r]=o;r="TinD.R";o=Number.parseInt(a[r]);if(Number.isNaN(o)||o<0){f.push([e,"invalid "+r+" value",s]);continue}a[r]=o;if(a["TinD.R"]<a["MinD.R"]){f.push([e,"TinD.R value lower than MinD.R",s]);continue}r="MinN.R";if(r in a){o=Number.parseInt(a[r]);if(Number.isNaN(o)||o<0){delete a[r]}else{a[r]=o}}r="TinN.R";if(r in a){o=Number.parseInt(a[r]);if(Number.isNaN(o)||o<0){delete a[r]}else{a[r]=o}}if(a.symbol){if(!B[a.symbol]){f.push([e,"Invalid symbol value='"+a.symbol+"'",s]);continue}}if(a.class){const t=a.class.toUpperCase();if(t in u){a.class=u[t]}else{f.push([e,"invalid mutation class "+a.class,s]);continue}}a.style={fill:a.issnv?"white":"black",fillhl:a.class?n[a.class].color:"#ccc",stroke:a.chr=="chrX"?"black":a.issnv?"black":"none",strokehl:a.class?n[a.class].color:"black",fillopacity:a.issnv?0:.2,strokeopacity:.2};if(a["TinD.D"]>0){a.maf1=a["MinD.D"]/a["TinD.D"]}if(a["TinD.R"]>0){a.maf2=a["MinD.R"]/a["TinD.R"]}p[a.sample]=1;if(a.gene){h[a.gene]=1}if(!(a.sample in c)){c[a.sample]={name:a.sample,shown:false,header:l,mlst:[]}}const m=c[a.sample];m.mlst.push(a);if(a.purity1){let t=Number.parseFloat(a.purity1);if(Number.isNaN(t)){f.push([e,"diagnosis tumor purity should be a number"]);t=0}else{if(t>1){t/=100}}if(t>0){if(m.purity1==undefined){m.purity1=t;d.purity1set=true}else if(m.purity1!=t){f.push([e,"diagnosis tumor purity value "+t+" is different from existing value "+m.purity1+" in "+a.sample,s])}}}if(a.purity2){let t=Number.parseFloat(a.purity2);if(Number.isNaN(t)){f.push([e,"relapse tumor purity should be a number"]);t=0}else{if(t>1){t/=100}}if(t>0){if(m.purity2==undefined){m.purity2=t;d.purity2set=true}else if(m.purity2!=t){f.push([e,"relapse tumor purity value "+t+" is different from existing value "+m.purity2+" in "+a.sample,s])}}}d.good++}if(f.length>0){i(l,f)}if(d.good==0){return"No valid data."}a.append("p").text("File: "+s);let m=0;for(const t in h)m++;const y=16;const g=a.append("table");const x=g.append("tr");const b=x.append("td").attr("valign","top");b.append("div").html('<div style="display:inline-block;width:'+y+"px;height:"+y+"px;background-color:"+I+'"></div> Diagnosis only '+'<div style="display:inline-block;width:'+y+"px;height:"+y+"px;background-color:"+X+'"></div> Shared '+'<div style="display:inline-block;width:'+y+"px;height:"+y+"px;background-color:"+M+'"></div> Relapse only');const k=b.append("div").style("margin-top","10px").style("height","200px").style("width","300px").style("padding","5px").style("overflow-y","scroll").style("resize","both").style("border","solid 1px #ccc");b.append("div").style("margin-top","10px").style("height","200px").style("width","300px").style("padding","5px").style("overflow-y","scroll").style("resize","both").style("border","solid 1px #ccc");const v=x.append("td").style("vertical-align","top");for(const t in c){const e=d.pairsetname[t];if(e){c[t].setname=e}else{c[t].setname={1:"Diagnosis",2:"Relapse"}}}const _={genome:e,pairs:c,color1:I,color2:M,colorshare:X,rowh:y,peoplewidth:150,genewidth:150,showholder:v,genelimit:Math.min(20,m),purity1set:d.purity1set,purity2set:d.purity2set};E(_,k)}function O(t){const e=t.toLowerCase().split("\t");const s=t.split("\t");if(s.length<=1){return["invalid file header"]}const a=(...t)=>{for(const s of t){const t=e.indexOf(s);if(t!=-1)return t}return-1};let i=a("person","sample","samplename","patient");if(i==-1)return["sample missing from header"];s[i]="sample";i=a("type");if(i==-1)return["type missing from header"];s[i]="type";i=a("mind.d1_g1","mind.d","mind");if(i==-1)return["MinD.D missing from header"];s[i]="MinD.D";i=a("tind.d1_g1","tind.d","tind");if(i==-1)return["TinD.D missing from header"];s[i]="TinD.D";i=a("mind.r1_g1","mind.r","minr");if(i==-1)return["MinD.R missing from header"];s[i]="MinD.R";i=a("tind.r1_g1","tind.r","tinr");if(i==-1)return["TinD.R missing from header"];s[i]="TinD.R";i=a("call_d1_g1","call_d");if(i==-1)return["call_d missing from header"];s[i]="call_d";i=a("call_r1_g1","call_r");if(i==-1)return["call_r missing from header"];s[i]="call_r";i=a("genename","gene");if(i==-1)return["gene missing from header"];s[i]="gene";i=a("amino_acid_change","annovar_sj_aachange","aachange","protein_change");if(i==-1)return["amino_acid_change missing from header"];s[i]="mname";i=a("class","mclass","variant_class","variant_classification","annovar_sj_class");if(i==-1)return["variant_class missing from header"];s[i]="class";i=a("chromosome","chr");if(i==-1)return["chromosome missing from header"];s[i]="chr";i=a("start","start_position","wu_hg19_pos","chr_position");if(i==-1)return["start missing from header"];s[i]="chrstart";i=a("minn.d1_g1","minn.d");if(i!=-1)s[i]="MinN.D";i=a("tinn.d1_g1","tinn.d");if(i!=-1)s[i]="TinN.D";i=a("minn.r1_g1","minn.r");if(i!=-1)s[i]="MinN.R";i=a("tinn.r1_g1","tinn.r");if(i!=-1)s[i]="TinN.R";i=a("mrna_accession","refseq_mrna_id","annovar_sj_filter_isoform","refseq");if(i!=-1)s[i]="isoform";i=a("primary_purity","purity_d");if(i!=-1)s[i]="purity1";i=a("relapse_purity","purity_r");if(i!=-1)s[i]="purity2";i=a("tag_d_cnvloh","cnvloh_d");if(i!=-1)s[i]="Dcnvloh";i=a("tag_r_cnvloh","cnvloh_r");if(i!=-1)s[i]="Rcnvloh";const r=[];for(const t of s){switch(t){case"Dcnvloh":r.push({label:"D. CNV/LOH",get:t=>t.Dcnvlohraw});break;case"Rcnvloh":r.push({label:"R. CNV/LOH",get:t=>t.Rcnvlohraw});break;case"type":r.push({label:"Type",get:t=>t.type});break;case"chr":break;case"chrstart":r.push({label:"Genome Loc.",get:t=>t.chr+":"+(t.chrstart+1)});break;case"class":r.push({label:"Class",get:t=>{if(t.class==p){return t.originalclasslabel?t.originalclasslabel:n[t.class].label}return n[t.class].label}});break;case"mname":r.push({label:"Mutation",get:t=>{let e=t.mname;if(!e)e=t.cdna_change;return e}});break;case"MinD.D":r.push({ismaf:true,width:60,height:14,readcountcredible:30,get:t=>t.maf_diagnosis,label:"D. tumor MAF",fill:"#F7483B",fillbg:"#FCBAB6"});break;case"TinD.D":break;case"MinD.R":r.push({ismaf:true,width:60,height:14,readcountcredible:30,get:t=>t.maf_relapse,label:"R. tumor MAF",fill:"#146EFF",fillbg:"#B6D5FC"});break;case"TinD.R":break;case"MinN.D":r.push({ismaf:true,width:60,height:14,readcountcredible:30,get:t=>t.maf_diagnosis_normal,label:"D. normal MAF",fill:"#F7483B",fillbg:"#FCBAB6"});break;case"TinN.D":break;case"MinN.R":r.push({ismaf:true,width:60,height:14,readcountcredible:30,get:t=>t.maf_relapse_normal,label:"R. normal MAF",fill:"#146EFF",fillbg:"#B6D5FC"});break;case"TinN.R":break;case"call_d":r.push({label:"D. call",get:t=>t.call_d});break;case"call_r":r.push({label:"R. call",get:t=>t.call_r});break;case"purity1":r.push({label:"D. purity",get:t=>t.purity1});break;case"purity2":r.push({label:"R. purity",get:t=>t.purity2});break;default:r.push({label:t,get:e=>e[t]})}}return[null,s,r]}function S(e,s){const a=new t({border:"solid 1px black"});const i=[];const o=[];const p=[];const f=s.mlst;const u=f[0].sample;const m=T();let x=0;let b={};const k={};for(const t of f){if(t["TinD.D"]>0){x=Math.max(x,t["TinD.D"])}if(t["TinD.R"]>0){x=Math.max(x,t["TinD.R"])}if(t.set_share){p.push(t)}else if(t.set_1){i.push(t)}else if(t.set_2){o.push(t)}if(!(t.class in k)){k[t.class]=0}if(t.symbol){if(!b[t.symbol]){b[t.symbol]={numlines:0,label:t.symbollabel,hidden:false}}b[t.symbol].numlines++}k[t.class]++}const v=Math.min(window.innerWidth,window.innerHeight);const _=50,D=v*.5,w=v*.5,R=w/2,I=D/2,M=_/3,X=R/5,A=Math.min(20,12*v/500),z=v/40,C=z*.7,O=3;const S=l().domain([0,x]).range([z/2,z]);const W=t=>Math.PI*Math.pow(S(t),2);for(const t of f){t.radius=Math.max(t["TinD.D"]?S(t["TinD.D"]):0,t["TinD.R"]?S(t["TinD.R"]):0)}const E=e.append("table");const H=E.append("tr");const q=H.append("td").style("vertical-align","top");const G=H.append("td").style("vertical-align","top");G.append("div").style("margin","10px").text("Name: "+u);const U=q.append("div");U.append("button").text("Hide").on("click",(()=>{s.shown=false;if(s.handle){s.handle.attr("font-weight","normal")}E.remove()}));const P=new N({axiswidth:_,sp:M,sp2:X,sample1height:R,sample2height:I,shareheight:w,sharewidth:D,headerdiv:U});U.append("button").text("Screenshot").on("click",(()=>{h(Z.node(),"2dmaf_"+s.name)}));{const t=U.append("select").on("change",(t=>{const e=t.target.options[t.target.selectedIndex].value;if(e=="all"){at.transition().attr("transform",(t=>t.posstring+" scale(1)"));ot.transition().attr("transform",(t=>t.posstring+" scale(1)"));dt.transition().attr("transform",(t=>t.posstring+" scale(1)"));return}at.transition().attr("transform",(t=>t.posstring+" scale("+(t.class==e?1:0)+")"));ot.transition().attr("transform",(t=>t.posstring+" scale("+(t.class==e?1:0)+")"));dt.transition().attr("transform",(t=>t.posstring+" scale("+(t.class==e?1:0)+")"))}));t.append("option").text("Show all mutation classes").property("value","all");const e=[];for(const t in k){e.push([t,k[t]])}e.sort(((t,e)=>e[1]-t[1]));for(const s of e){t.append("option").text((s[0]in n?n[s[0]].label:s[0])+" ("+s[1]+")").property("value",s[0])}}const Z=q.append("svg").attr("width",_+M+I+D+M*2).attr("height",_+M+R+w+M*2);const J=Z.append("g").attr("transform","translate("+M+","+M+")");P.setWrapper(J.append("g"));const K=l().domain([0,1]).range([0,D]);const Q=J.append("g").attr("transform","translate("+(_+M+I)+","+(w+R+M)+")").call(y().scale(K).tickSize(5));c({axis:Q,showline:true,fontsize:A*.8});const $=i.length+p.length;Q.append("text").text(s.setname[1]+", n="+$+(s.purity1?", purity="+s.purity1:"")).attr("x",D/2).attr("y",_-4).attr("text-anchor","middle").attr("font-size",A);const tt=l().domain([0,1]).range([w,0]);const et=J.append("g").attr("transform","translate("+_+",0)").call(g().scale(tt).tickSize(5));c({axis:et,showline:true,fontsize:A*.8});const st=o.length+p.length;et.append("text").text(s.setname[2]+", n="+st+(s.purity2?", purity="+s.purity2:"")).attr("transform","translate("+(A-_-10)+","+w/2+") rotate(-90)").attr("text-anchor","middle").attr("font-size",A);J.append("path").attr("d","M"+(_+M)+",0"+"h"+(I+D)+"v"+(w+R)+"h-"+D+"v-"+(R+w)+"M"+(_+M)+",0"+"v"+w+"h"+(I+D)+"M"+(_+M+I)+","+w+"l"+D+",-"+w).attr("fill","none").attr("stroke","black").attr("shape-rendering","crispEdges").attr("stroke-dasharray","5,5");const at=J.append("g").attr("transform","translate("+(_+M+I)+",0)").selectAll().data(p).enter().append("g").attr("transform",(t=>{t.posstring="translate("+K(t.maf1)+","+tt(t.maf2)+")";return t.posstring}));at.filter((t=>t.Dcnvloh)).append("circle").attr("cy",(t=>t.issnv?S(t["TinD.R"]):C/2)).attr("fill","#858585").attr("r",O);at.filter((t=>t.Rcnvloh)).append("circle").attr("cx",(t=>t.issnv?-S(t["TinD.D"]):-C/2)).attr("fill","#858585").attr("r",O);let nt=at;for(const t in Y){nt.filter(Y[t]).append(t).attr("rx",(t=>t.symbol?null:S(t["TinD.D"]))).attr("ry",(t=>t.symbol?null:S(t["TinD.R"]))).attr("d",(t=>!t.symbol?null:m.type(B[t.symbol]).size(W(t["TinD.D"])+W(t["TinD.R"])/2)())).attr("fill",(t=>t.style.fill)).attr("fill-opacity",(t=>t.style.fillopacity)).attr("stroke",(t=>t.style.stroke)).attr("stroke-opacity",(t=>t.style.strokeopacity)).attr("stroke-dasharray",(t=>t.chr=="chrX"?"5,5":"none")).on("mouseover",((t,e)=>j(t,e,a))).on("mouseout",((t,e)=>L(t,e,a))).on("click",((t,e)=>V(t,s.header,e)))}nt.append("line").attr("stroke",(t=>t.style.stroke)).attr("stroke-opacity",(t=>t.style.strokeopacity)).attr("x1",-3).attr("y1",-3).attr("x2",3).attr("y2",3);nt.append("line").attr("stroke",(t=>t.style.stroke)).attr("stroke-opacity",(t=>t.style.strokeopacity)).attr("x1",-3).attr("y1",3).attr("x2",3).attr("y2",-3);const it=l().domain([0,x]).range([R-X,0]);const rt=J.append("g").attr("transform","translate("+(_+M+I)+","+(w+X)+")");const lt="#FFBEAD";rt.append("rect").attr("fill",lt).attr("fill-opacity",0).attr("x",0).attr("width",3).attr("height",R-X);c({axis:rt.call(g().scale(it).tickValues([0,x])),showline:true,fontsize:A*.8});rt.append("g").attr("transform","translate(-"+A/2+","+(R-X)/2+")").append("text").text("D total").attr("font-size",A*.8).attr("font-family",r).attr("fill","black").attr("text-anchor","middle").attr("dominant-baseline","middle").attr("transform","rotate(-90)");const ot=rt.selectAll().data(i).enter().append("g").attr("transform",(t=>{t.posstring="translate("+K(t.maf1)+","+it(t["TinD.D"])+")";return t.posstring}));ot.filter((t=>t.Dcnvloh)).append("circle").attr("cy",(t=>t.issnv?S(t["TinD.R"]):C/2)).attr("fill","#858585").attr("r",O);ot.filter((t=>t.Rcnvloh)).append("circle").attr("cx",(t=>t.issnv?-S(t["TinD.D"]):-C/2)).attr("fill","#858585").attr("r",O);nt=ot;for(const t in F){nt.filter(F[t]).append(t).attr("class",(t=>t.symbol?"twodmaf-"+t.symbol:null)).attr("r",(t=>t.symbol?null:S(t["TinD.R"]))).attr("d",(t=>!t.symbol?null:m.type(B[t.symbol]).size(W(t["TinD.R"]))())).attr("fill",(t=>t.style.fill)).attr("fill-opacity",(t=>t.style.fillopacity)).attr("stroke",(t=>t.style.stroke)).attr("stroke-opacity",(t=>t.style.strokeopacity)).attr("stroke-dasharray",(t=>t.chr=="chrX"?"5,5":"none")).on("mouseover",((t,e)=>j(t,e,a))).on("mouseout",((t,e)=>L(t,e,a))).on("click",((t,e)=>V(t,s.header,e)))}nt.append("line").attr("stroke",(t=>t.style.stroke)).attr("stroke-opacity",(t=>t.style.strokeopacity)).attr("x1",-3).attr("y1",-3).attr("x2",3).attr("y2",3);nt.append("line").attr("stroke",(t=>t.style.stroke)).attr("stroke-opacity",(t=>t.style.strokeopacity)).attr("x1",-3).attr("y1",3).attr("x2",3).attr("y2",-3);const ct=l().domain([0,x]).range([0,I-X]);const pt=J.append("g").attr("transform","translate("+(_+M)+",0)");pt.append("rect").attr("fill",lt).attr("fill-opacity",0).attr("y",w).attr("width",I-X).attr("height",3);const ht=pt.append("g").attr("transform","translate(0,"+w+")").call(y().scale(ct).tickValues([0,x]));c({axis:ht,showline:true,fontsize:A*.8});pt.append("text").text("R total").attr("font-size",A*.8).attr("font-family",r).attr("fill","black").attr("x",(I-X)/2).attr("y",w+A).attr("text-anchor","middle");const dt=pt.selectAll().data(o).enter().append("g").attr("transform",(t=>{t.posstring="translate("+ct(t["TinD.R"])+","+tt(t.maf2)+")";return t.posstring}));dt.filter((t=>t.Dcnvloh)).append("circle").attr("cy",(t=>t.issnv?S(t["TinD.R"]):C/2)).attr("fill","#858585").attr("r",O);dt.filter((t=>t.Rcnvloh)).append("circle").attr("cx",(t=>t.issnv?-S(t["TinD.D"]):-C/2)).attr("fill","#858585").attr("r",O);nt=dt;for(const t in F){nt.filter(F[t]).append(t).attr("class",(t=>t.symbol?"twodmaf-"+t.symbol:null)).attr("r",(t=>t.symbol?null:S(t["TinD.D"]))).attr("d",(t=>!t.symbol?null:m.type(B[t.symbol]).size(W(t["TinD.R"]))())).attr("fill",(t=>t.style.fill)).attr("fill-opacity",(t=>t.style.fillopacity)).attr("stroke",(t=>t.style.stroke)).attr("stroke-opacity",(t=>t.style.strokeopacity)).attr("stroke-dasharray",(t=>t.chr=="chrX"?"5,5":"none")).on("mouseover",((t,e)=>j(t,e,a))).on("mouseout",((t,e)=>L(t,e,a))).on("click",((t,e)=>V(t,s.header,e)))}nt.append("line").attr("stroke",(t=>t.style.stroke)).attr("stroke-opacity",(t=>t.style.strokeopacity)).attr("x1",-3).attr("y1",-3).attr("x2",3).attr("y2",3);nt.append("line").attr("stroke",(t=>t.style.stroke)).attr("stroke-opacity",(t=>t.style.strokeopacity)).attr("x1",-3).attr("y1",3).attr("x2",3).attr("y2",-3);const ft=J.append("g").attr("transform","translate(0,"+(w+X)+")");let ut=A;ft.append("text").text(u).attr("font-size",A).attr("y",ut);const mt=S(20),yt=S(x);ut+=A+yt;let gt;ft.append("text").text("SNV coverage").attr("y",ut).attr("dominant-baseline","middle").each((function(){gt=this.getBBox().width}));gt+=mt+10;ft.append("circle").attr("cx",gt).attr("cy",ut).attr("r",mt).attr("stroke","black").attr("fill","none");ft.append("text").text(20).attr("x",gt).attr("y",ut).attr("text-anchor","middle").attr("dominant-baseline","middle");gt+=mt+yt+10;ft.append("circle").attr("cx",gt).attr("cy",ut).attr("r",yt).attr("stroke","black").attr("fill","none");ft.append("text").text(x).attr("x",gt).attr("y",ut).attr("text-anchor","middle").attr("dominant-baseline","middle");ut+=yt+10;ft.append("text").text("Indel").attr("y",ut).attr("dominant-baseline","middle").each((function(){gt=this.getBBox().width}));ft.append("circle").attr("cx",gt+10+C/2).attr("cy",ut).attr("r",C/2).attr("fill","black").attr("fill-opacity",.3);ut+=30;ft.append("text").text("chrX").attr("y",ut).attr("dominant-baseline","middle").each((function(){gt=this.getBBox().width}));gt+=mt+10;ft.append("circle").attr("cx",gt).attr("cy",ut).attr("r",10).attr("stroke","black").attr("stroke-dasharray","5,5").attr("fill","none");ut+=30;ft.append("text").text("D. CNV/LOH").attr("y",ut).attr("dominant-baseline","middle").each((function(){gt=this.getBBox().width}));gt+=mt+10;ft.append("circle").attr("cx",gt).attr("cy",ut).attr("r",10).attr("stroke","black").attr("fill","none");ft.append("circle").attr("cx",gt).attr("cy",ut+10).attr("r",O).attr("fill","black");ut+=30;ft.append("text").text("R. CNV/LOH").attr("y",ut).attr("dominant-baseline","central").each((function(){gt=this.getBBox().width}));gt+=mt+10;ft.append("circle").attr("cx",gt).attr("cy",ut).attr("r",10).attr("stroke","black").attr("fill","none");ft.append("circle").attr("cx",gt-10).attr("cy",ut).attr("r",O).attr("fill","black");ut+=30;if(s.purity1!=undefined||s.purity2!=undefined){ft.append("text").text("Expected MAF").attr("y",ut).attr("dominant-baseline","middle").each((function(){gt=this.getBBox().width}));gt+=10;ft.append("rect").attr("fill",lt).attr("x",gt).attr("y",ut).attr("width",40).attr("height",3);ut+=30}const xt=Object.keys(b);if(xt.length){ft.append("text").text("Symbols").attr("y",ut).attr("dominant-baseline","middle").each((function(){gt=this.getBBox().width}));let t;for(const e in b){const s=b[e];const a=ft.append("g").on("click",(()=>{s.hidden=!s.hidden;Z.selectAll(".twodmaf-"+e).style("display",s.hidden?"none":"");n.style("text-decoration",s.hidden?"line-through":"")}));t=gt+20;a.append("path").attr("transform","translate("+t+","+ut+")").attr("d",m.type(B[e]).size(100)()).attr("stroke","black").attr("fill","none").each((function(){t+=this.getBBox().width}));const n=a.append("text").text(s.label?s.label+" ("+s.numlines+")":"").attr("y",ut+2).attr("x",t).attr("dominant-baseline","middle").style("text-decoration",s.hidden?"line-through":"");ut+=30}ut+=30}const bt={},kt={},vt={},_t={};for(const t of f){if(!t.gene)continue;if(!(t.gene in bt)){bt[t.gene]=[]}bt[t.gene].push(t);if(t.set_1){kt[t.gene]=1}else if(t.set_2){vt[t.gene]=1}else if(t.set_share){_t[t.gene]=1}}const Dt=[];for(const t in kt){Dt.push(t)}for(const t in vt){if(!(t in kt)){Dt.push(t)}}for(const t in _t){if(!(t in kt)&&!(t in vt)){Dt.push(t)}}const wt=G.append("div").style("height",w+R+"px").style("margin","10px").style("padding","10px").style("border","solid 1px #ccc").style("overflow-y","scroll").style("resize","both").append("table");{const t=wt.append("tr");t.append("td").text("Gene");t.append("td").text(s.setname[1]+" only");t.append("td").text(s.setname[2]+" only");t.append("td").text("Shared")}let Tt=true;for(const t of Dt){const e=wt.append("tr");if(Tt){e.style("background-color","#f3f3f3")}Tt=!Tt;e.append("td").text(t);let s=[];if(t in bt){s=bt[t]}const a=[],n=[],i=[];for(const t of s){if(t.set_share)i.push(t);else if(t.set_1)a.push(t);else if(t.set_2)n.push(t)}let r=e.append("td");if(a.length){for(const t of a){const e=r.append("div").attr("class","sja_clbtext").style("color",t.style.fillhl).text(t.mname||"").on("click",(e=>{Nt(e.target,t,ot)}));if(t.labelIsVisible){Nt(e.node(),t,ot)}}}r=e.append("td");if(n.length){for(const t of n){const e=r.append("div").attr("class","sja_clbtext").style("color",t.style.fillhl).text(t.mname||"").on("click",(e=>{Nt(e.target,t,dt)}));if(t.labelIsVisible){Nt(e.node(),t,ot)}}}r=e.append("td");if(i.length){for(const t of i){const e=r.append("div").attr("class","sja_clbtext").style("color",t.style.fillhl).text(t.mname||"").on("click",(e=>{Nt(e.target,t,at)}));if(t.labelIsVisible){Nt(e.node(),t,ot)}}}}function Nt(t,e,s){if(e.selected){t.style.border="";e.selected=false}else{t.style.border="solid 1px black";e.selected=true}const a=s.filter((t=>t.gene==e.gene&&t.class==e.class&&t.mname==e.mname));a.selectAll("rect").attr("fill-opacity",e.selected?.5:e.style.fillopacity).attr("fill",e.selected?e.style.fillhl:e.style.fill);a.selectAll("circle,ellipse,line").attr("stroke-opacity",e.selected?1:e.style.strokeopacity).attr("stroke",e.selected?e.style.strokehl:e.style.stroke).attr("stroke-width",e.selected?2:1);if(e.selected){let t=Math.max(20,e.radius),s=0;if((e.set_1||e.set_share)&&e.maf1>=.8){t=-e.radius;s=e.radius*2}const n=a.append("g").attr("class","sja_2dmaf_mlabel").attr("transform","translate("+t+","+s+")");let i;n.append("text").text(e.labelAs?e.labelAs:e.gene+" "+e.mname).attr("fill",e.style.fillhl).attr("dominant-baseline","middle").attr("text-anchor","start").attr("font-size",e.radius).each((function(){i=this.getBBox().width}));n.append("rect").attr("y",-e.radius/2).attr("width",i).attr("height",e.radius).attr("fill","black").attr("fill-opacity",0).on("mouseover",(t=>d(t.target).attr("fill-opacity",.2))).on("mouseout",(t=>d(t.target).attr("fill-opacity",0))).on("mousedown",(e=>{const a=t,i=s,r=e.clientX,l=e.clientY,o=d(document.body);o.on("mousemove",(e=>{e.preventDefault();t=a+e.clientX-r;s=i+e.clientY-l;n.attr("transform","translate("+t+","+s+")")}));o.on("mouseup",(()=>{o.on("mousemove",null).on("mouseup",null)}))}))}else{a.select(".sja_2dmaf_mlabel").remove()}}return E}function j(t,e,s){if(!e.selected){d(t.target).attr("fill",e.style.fillhl).attr("fill-opacity",.2)}s.clear();s.show(t.clientX,t.clientY);s.d.append("div").html((e.gene||"no gene")+' <span style="color:'+e.style.fillhl+'">'+(e.mname||"")+"</span>"+(e.class?' <span style="font-size:70%">'+n[e.class].label+"</span>":""))}function L(t,e,s){if(!e.selected){d(t.ele).attr("fill",e.style.fill).attr("fill-opacity",e.style.fillopacity).attr("stroke",e.style.stroke)}s.hide()}function V(t,e,s){const a=f({x:t.clientX+30,y:t.clientY-30});a.header.text((s.gene?s.gene:"No gene")+" "+(s.mname?s.mname:""));var n=[];for(let t=0;t<e.length;t++){n.push({k:e[t],v:s[e[t]]})}u(a.body,n)}function W(t,e){const s=t.pairs[e];if(s.shown){s.shown=false;s.holder.remove();if(s.handle){s.handle.attr("font-weight","normal")}}else{s.shown=true;if(s.holder){t.showholder.node().appendChild(s.holder.node())}else{s.holder=S(t.showholder,s)}if(s.handle){s.handle.attr("font-weight","bold")}}}function E(t,e){const s=[];for(const e in t.pairs){s.push([e,t.pairs[e].mlst.length])}e.selectAll("*").remove();const a=e.append("div").style("margin-bottom","5px");a.append("span").text(s.length+" individual"+(s.length>1?"s":""));const n=e.append("svg");const i=5,p=20,h=t.rowh;let d=0;for(const t of s){n.append("text").text(t[0]).attr("font-size",h).attr("font-family",r).each((function(){d=Math.max(d,this.getBBox().width)})).remove()}n.attr("width",d+i+t.peoplewidth+30).attr("height",p+i+h*s.length);s.sort(((t,e)=>e[1]-t[1]));let f=0;for(const e in t.pairs){f=Math.max(f,t.pairs[e].mlst.length)}const u=n.append("g").attr("transform","translate("+(d+i)+","+p+")").call(m().scale(l().domain([0,f]).range([0,t.peoplewidth])).tickFormat(o("d")).ticks(3));c({axis:u,showline:true,color:"black"});const y=t.peoplewidth/f;let g=p+i;for(const e of s){const s=e[0];t.pairs[s].handle=n.append("text").text(s).attr("class","sja_svgtext2").attr("font-size",h-2).attr("font-family",r).attr("x",d).attr("y",g+i+h/2).attr("text-anchor","end").on("click",(()=>{W(t,s)}));let a=0,l=0,o=0;for(const e of t.pairs[s].mlst){if(e.set_1)a++;else if(e.set_2)l++;else if(e.set_share)o++}const c=n.append("g").attr("transform","translate("+(d+i)+","+g+")");if(a>0){c.append("rect").attr("width",y*a).attr("height",h-1).attr("fill",t.color1)}if(o>0){c.append("rect").attr("x",y*a).attr("width",y*o).attr("height",h-1).attr("fill",t.colorshare)}if(l>0){c.append("rect").attr("x",y*(a+o)).attr("width",y*l).attr("height",h-1).attr("fill",t.color2)}g+=h}}export{z as d2mafparseinput,A as d2mafui};

package/dist/Disco-eafea947.js

@@ -0,0 +1 @@
+import{_ as t}from"./tslib.es6-62bb2d8e.js";import{M as e,D as s,p as n,aJ as i,az as o}from"./app-7e06239d.js";import"./transform-f2cc07e6.js";import{d as r}from"./arc-3d6751aa.js";import{c as a,p as l}from"./constant-426a1483.js";import{s as c}from"./svg.legend-b357ac94.js";import{a as h,d as u}from"./line-d0284126.js";import{t as d}from"./math-2fb199c6.js";import"path";function g(t,e){return e<t?-1:e>t?1:e>=t?0:NaN}function p(t){return t}function m(){var t=p,e=g,s=null,n=a(0),i=a(d),o=a(0);function r(r){var a,l=(r=h(r)).length,c,u,g=0,p=new Array(l),m=new Array(l),f=+n.apply(this,arguments),v=Math.min(d,Math.max(-d,i.apply(this,arguments)-f)),A,x=Math.min(Math.abs(v)/l,o.apply(this,arguments)),R=x*(v<0?-1:1),M;for(a=0;a<l;++a){if((M=m[p[a]=a]=+t(r[a],a,r))>0){g+=M}}if(e!=null)p.sort((function(t,s){return e(m[t],m[s])}));else if(s!=null)p.sort((function(t,e){return s(r[t],r[e])}));for(a=0,u=g?(v-l*R)/g:0;a<l;++a,f=A){c=p[a],M=m[c],A=f+(M>0?M*u:0)+R,m[c]={data:r[c],index:a,value:M,startAngle:f,endAngle:A,padAngle:x}}return m}r.value=function(e){return arguments.length?(t=typeof e==="function"?e:a(+e),r):t};r.sortValues=function(t){return arguments.length?(e=t,s=null,r):e};r.sort=function(t){return arguments.length?(s=t,e=null,r):s};r.startAngle=function(t){return arguments.length?(n=typeof t==="function"?t:a(+t),r):n};r.endAngle=function(t){return arguments.length?(i=typeof t==="function"?t:a(+t),r):i};r.padAngle=function(t){return arguments.length?(o=typeof t==="function"?t:a(+t),r):o};return r}var f=Math.abs;var v=Math.cos;var A=Math.sin;var x=Math.PI;var R=x/2;var M=1e-12;var b=Array.prototype.slice;function C(t){return function(){return t}}function y(t){return t.source}function I(t){return t.target}function L(t){return t.radius}function O(t){return t.startAngle}function E(t){return t.endAngle}function w(){return 0}function S(t){var e=y,s=I,n=L,i=L,o=O,r=E,a=w,c=null;function h(){var h,u=e.apply(this,arguments),d=s.apply(this,arguments),g=a.apply(this,arguments)/2,p=b.call(arguments),m=+n.apply(this,(p[0]=u,p)),x=o.apply(this,p)-R,C=r.apply(this,p)-R,y=+i.apply(this,(p[0]=d,p)),I=o.apply(this,p)-R,L=r.apply(this,p)-R;if(!c)c=h=l();if(g>M){if(f(C-x)>g*2+M)C>x?(x+=g,C-=g):(x-=g,C+=g);else x=C=(x+C)/2;if(f(L-I)>g*2+M)L>I?(I+=g,L-=g):(I-=g,L+=g);else I=L=(I+L)/2}c.moveTo(m*v(x),m*A(x));c.arc(0,0,m,x,C);if(x!==I||C!==L){if(t){var O=+t.apply(this,arguments),E=y-O,w=(I+L)/2;c.quadraticCurveTo(0,0,E*v(I),E*A(I));c.lineTo(y*v(w),y*A(w));c.lineTo(E*v(L),E*A(L))}else{c.quadraticCurveTo(0,0,y*v(I),y*A(I));c.arc(0,0,y,I,L)}}c.quadraticCurveTo(0,0,m*v(x),m*A(x));c.closePath();if(h)return c=null,h+""||null}if(t)h.headRadius=function(e){return arguments.length?(t=typeof e==="function"?e:C(+e),h):t};h.radius=function(t){return arguments.length?(n=i=typeof t==="function"?t:C(+t),h):n};h.sourceRadius=function(t){return arguments.length?(n=typeof t==="function"?t:C(+t),h):n};h.targetRadius=function(t){return arguments.length?(i=typeof t==="function"?t:C(+t),h):i};h.startAngle=function(t){return arguments.length?(o=typeof t==="function"?t:C(+t),h):o};h.endAngle=function(t){return arguments.length?(r=typeof t==="function"?t:C(+t),h):r};h.padAngle=function(t){return arguments.length?(a=typeof t==="function"?t:C(+t),h):a};h.source=function(t){return arguments.length?(e=t,h):e};h.target=function(t){return arguments.length?(s=t,h):s};h.context=function(t){return arguments.length?(c=t==null?null:t,h):c};return h}function N(){return S()}class V{constructor(t,e,s){this.radius=t;this.width=e;this.color=s}render(t){const e=r();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 D{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 T;(function(t){t["Intrachromosomal"]="#1B9E77";t["Interchromosomal"]="#6A3D9A"})(T||(T={}));class ${static getColor(t,e){if(t!=e){return T.Interchromosomal.valueOf()}else{return T.Intrachromosomal.valueOf()}}}class z{render(t,e){let s=0;if(e.length>0){s=e[0].target.radius;const n=new V(s,2,"#6464641A");n.render(t)}const n=N().radius(s);const i=t.selectAll(".chord").data(e);const o=D.create();i.enter().append("path").attr("class","chord").attr("d",n).attr("fill",(t=>$.getColor(t.source.positionInChromosome.chromosome,t.target.positionInChromosome.chromosome))).on("mouseover",((t,e)=>{o.d.style("padding","2px").html(this.getTooltip(e));o.show(t.x,t.y)})).on("mouseout",(()=>{o.hide()}))}getTooltip(t){let e="";if(t.source.gene){e+=t.source.gene}const s=t.source.positionInChromosome;e+=` ${s.chromosome}:${s.position}<br />`;if(t.target.gene){e+=t.target.gene}const n=t.target.positionInChromosome;e+=` ${n.chromosome}:${n.position}`;return e}}class k{constructor(t){this.downloadClickListener=t}render(t){t.append("div").append("button").style("margin","2px 0 2px 30px").text("Download").on("click",(()=>{const e=t.selectAll("svg").node();this.downloadClickListener(e)}))}}class B{constructor(t,e,s){this.renders=t;this.legendRenderer=e;this.fusionRenderer=new z;this.downloadButtonRenderer=new k(s)}render(t,e){const s=t.append("div");const n=s.append("div").style("display","inline-block").style("font-family","Arial");this.downloadButtonRenderer.render(n);const i=n.append("svg").attr("width",e.width).attr("height",e.height+e.legendHeight);const o=i.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 i=e.getCollisions(t);s.render(o,n,i)}this.fusionRenderer.render(o,e.fusions);this.legendRenderer.render(o,e.legend,-1*(e.settings.rings.labelLinesInnerRadius+e.settings.rings.labelsToLinesDistance+50),e.width,e.height/2)}}class P{constructor(e){this.cappingClickCallback=(t,s)=>{const n=e.app.tip;n.clear();const i=e.app.tip.d;const o=i.append("span").html("Capping:").append("input").attr("type","number").on("change",(()=>{e.app.dispatch({type:"plot_edit",id:e.opts.id,config:{settings:{cnv:{capping:Number(o.property("value"))}}}});n.hide()}));const r=s.node().getBoundingClientRect();const a=r.left-20;const l=r.top-40;n.show(a,l)};this.downloadClickListener=t=>{const e=document.createElement("a");document.body.appendChild(e);e.addEventListener("click",(function(){const s=new XMLSerializer;const n=new Blob([s.serializeToString(t)],{type:"image/svg+xml"});e.download="disco"+".svg";e.href=URL.createObjectURL(n);document.body.removeChild(e)}),false);e.click()};this.geneClickListener=(s,n)=>t(this,void 0,void 0,(function*(){const t={holder:e.app.opts.holder,genome:e.app.opts.state.args.genome,nobox:true,query:s,tklst:[{type:"mds3",dslabel:e.app.opts.state.dslabel,hlaachange:n.join(",")}]};const i=yield import("./app-7e06239d.js").then((function(t){return t.bR}));yield i.default(t)}))}}class W{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 o=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:o+this.settings.padAngle;const n=t==0?this.settings.padAngle/2+e:o+this.settings.padAngle+e;const r={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(r);if(r.endAngle!=null){o=r.endAngle}}}}class F{constructor(t,e){this.sampleName=t;this.cancerGenes=e}map(t){return{dt:t.dt,mname:t.mname,mClass:t.class,gene:t.gene,chr:t.chr,pos:t.pos,ref:t.ref,alt:t.alt,position:t.position,sample:this.sampleName,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.cancerGenes.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}}}var G;(function(t){t[t["SNV"]=1]="SNV";t[t["FUSION"]=2]="FUSION";t[t["CNV"]=4]="CNV";t[t["SV"]=5]="SV";t[t["LOH"]=10]="LOH"})(G||(G={}));class H{constructor(t,e,s,n=[]){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.cnvMaxValue=undefined;this.cnvMinValue=undefined;this.lohMaxValue=undefined;this.lohMinValue=undefined;this.snvFilter=t=>t.dt==G.SNV;this.fusionFilter=t=>t.dt==G.FUSION||t.dt==G.SV;this.cnvFilter=t=>t.dt==G.CNV;this.lohFilter=t=>t.dt==G.LOH;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.nonExonicFilter=e=>t.rings.nonExonicFilterValues.includes(gt.snvClassLayer[e.mClass]);this.snvRingFilter=e=>t.rings.snvRingFilters.includes(gt.snvClassLayer[e.mClass]);this.dataObjectMapper=new F(s,n)}map(t){const e=[];t.forEach((t=>{const s=this.reference.chromosomesOrder.indexOf(t.chr);const n=this.reference.chromosomesOrder.indexOf(t.chrA);const i=this.reference.chromosomesOrder.indexOf(t.chrB);if(t.dt==G.SNV){if(s!=-1){this.addData(t,e)}}else if(t.dt==G.FUSION||t.dt==G.SV){if(n!=-1&&i!=-1){this.addData(t,e)}}else if([G.CNV,G.LOH].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}s.forEach((t=>{this.filterFusion(t)}));if(this.fusionData.length>0){this.fusionRadius=this.lastInnerRadious}const n={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,hasCancerGenes:this.hasPrioritizedGenes,cnvMaxValue:this.cnvMaxValue,cnvMinValue:this.cnvMinValue,lohMaxValue:this.lohMaxValue,lohMinValue:this.lohMinValue};return n}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.cnvMaxValue==undefined||this.cnvMaxValue<t.value){this.cnvMaxValue=t.value}if(this.cnvMinValue==undefined||this.cnvMinValue>t.value){this.cnvMinValue=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.pos/this.bpx);return e.startAngle+s*this.onePxArcAngle}}class j{constructor(t,e,s,n,i,o,r,a){this.snvTitle=t;this.cnvTitle=e;this.lohTitle=s;this.fusionTitle=n;this.snvClassMap=i;this.cnvClassMap=o;this.lohLegend=a;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 U{constructor(t,e,s,n,i){this.source=t;this.target=e;this.genes=s;this.count=n;this.endpts=i}}class X{constructor(t,e,s,n,i,o,r){this.startAngle=t;this.endAngle=e;this.radius=s;this.gene=n;this.value=i;this.genes=o;this.positionInChromosome=r}}class q{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 X(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});const i=new X(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});const o=new U(n,i,"genes",-1,"Endpoints");e.push(o)}));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 _{static provide(t){const e=Math.min(Math.max(t,0),1);const s=Math.round(e*255);return`rgb(${s}, ${s}, ${s})`}}class J{constructor(t,e){this.minValue=t;this.maxValue=e;this.colorStartValue=_.provide(t);this.colorEndValue=_.provide(e)}}var K;(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"})(K||(K={}));class Q{constructor(t,e,s,n){this.settings=t;this.rings=e;this.legend=s;this.fusions=n;this.width=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)}getElements(t){switch(t){case K.CHROMOSOME:return this.rings.chromosomesRing?this.rings.chromosomesRing.elements:[];case K.LABEL:return this.rings.labelsRing.elementsToDisplay;case K.NONEXONICSNV:return this.rings.nonExonicArcRing?this.rings.nonExonicArcRing.elements:[];case K.SNV:return this.rings.snvArcRing?this.rings.snvArcRing.elements:[];case K.CNV:return this.rings.cnvArcRing?this.rings.cnvArcRing.elements:[];case K.LOH:return this.rings.lohArcRing?this.rings.lohArcRing.elements:[];default:throw new Error(`ringType ${t} not defined`)}}getCollisions(t){if(t==K.LABEL){return this.rings.labelsRing.collisions}else{return undefined}}calculateLegendHeight(t){const e=this.settings.legend.rowHeight;return e*t.legendCount()}}class Y{constructor(t,e,s){this.innerRadius=t;this.outerRadius=t+e;this.width=e;this.elements=s}}class Z{constructor(){const t={};for(const e in s){t[s[e].label]=s[e];t[e]=s[e]}this.mlabel=t}static getInstance(){if(!Z.instance){Z.instance=new Z}return Z.instance}}class tt{constructor(t,e,s){this.snvType=t;this.color=e;this.count=s}}class et{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 o=n[i];const r=this.snvClassMap.get(o.mClass);if(r){this.snvClassMap.set(o.mClass,this.createSnvLegend(o.mClass,++r.count))}else{this.snvClassMap.set(o.mClass,this.createSnvLegend(o.mClass,1))}const a=s;const l=s+this.onePxArcAngle;const c=Z.getInstance().mlabel?Z.getInstance().mlabel[o.mClass]:undefined;const h={startAngle:a,endAngle:l,innerRadius:this.svnInnerRadius+i*this.svnWidth/t,outerRadius:this.svnInnerRadius+(i+1)*this.svnWidth/t,color:c.color,text:o.gene,dataClass:c.label,mname:o.mname,chr:o.chr,pos:o.pos};e.push(h)}}}return e}createSnvLegend(t,e){const s=Z.getInstance().mlabel[t];return new tt(s.label,s.color,e)}}class st{constructor(t,e,s,n){this.text=t;this.cnvType=e;this.color=s;this.value=n}}var nt;(function(t){t[t["Loss"]=0]="Loss";t[t["Gain"]=1]="Gain";t[t["Cap"]=2]="Cap"})(nt||(nt={}));class it{constructor(t,e,s,n,i,o=0,r=0,a=""){this.cnvClassMap=new Map;this.cnvInnerRadius=t;this.cnvWidth=e;this.settings=s;this.sampleName=n;this.reference=i;this.cnvMaxValue=o;this.cnvMinValue=r;this.cnvUnit=a;this.gainCapped=this.settings.cnv.capping;this.lossCapped=-1*this.settings.cnv.capping;this.lossOnly=o<=0;this.gainOnly=r>=0;this.onePxArcAngle=1/this.cnvInnerRadius;const l=new st("Max",o>0?nt.Gain:nt.Loss,this.getColor(o),o);const c=new st("Min",r>0?nt.Gain:nt.Loss,this.getColor(r),r);const h=new st("Capping",nt.Loss,this.getColor(r>0?r:o),this.settings.cnv.capping);this.cnvClassMap.set(nt.Gain,l);this.cnvClassMap.set(nt.Loss,c);this.cnvClassMap.set(nt.Cap,h);this.maxAbsValue=Math.max(Math.abs(this.capMaxValue(r)),Math.abs(this.capMaxValue(o)))}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 o=this.calculateOuterRadius(t);const r=this.getColor(t.value);const a={startAngle:s,endAngle:n,innerRadius:i,outerRadius:o,color:r,text:t.gene,chr:t.chr,start:t.start,stop:t.stop,value:t.value,unit:this.cnvUnit};e.push(a)}));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){const e=this.settings.cnv;if(t<this.lossCapped){return e.cappedLossColor}else if(t>=this.lossCapped&&t<=0){return e.lossColor}else if(t>0&&t<=this.gainCapped){return e.ampColor}else if(t>this.gainCapped){return e.cappedAmpColor}}calculateInnerRadius(t){if(this.gainOnly){return this.cnvInnerRadius}if(this.lossOnly){const e=this.cnvInnerRadius+this.cnvWidth;return e-this.capMinValue(this.cnvWidth*this.capMaxValue(t.value)/this.maxAbsValue)}const e=this.cnvInnerRadius+this.cnvWidth/2;if(Math.sign(t.value)==1){return e}if(Math.sign(t.value)==-1){return e+this.capMinValue(this.capMaxValue(t.value)/this.maxAbsValue*(this.cnvWidth/2))}return 1}calculateOuterRadius(t){const e=this.cnvInnerRadius+this.cnvWidth;if(this.gainOnly){return this.cnvInnerRadius+this.capMinValue(this.cnvWidth*this.capMaxValue(t.value)/this.maxAbsValue)}if(this.lossOnly){return e}const s=this.cnvInnerRadius+this.cnvWidth/2;if(Math.sign(t.value)==1){return s+this.capMinValue(this.capMaxValue(t.value)/this.maxAbsValue*(this.cnvWidth/2))}if(Math.sign(t.value)==-1){return s}return 1}capMaxValue(t){if(Math.sign(t)==1){return t>this.gainCapped?this.gainCapped:t}if(Math.sign(t)==-1){return t<this.lossCapped?this.lossCapped:t}return 0}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 ot{constructor(t,e){this.points=new Array;this.points=t;this.color=e}}class rt{static createLabel(t,e,s,n,i,o,r,a,l,c,h=false,u,d,g){const p=(t+e)/2;const m=p-Math.PI/2;const f=`rotate(${p*180/Math.PI-90}) translate(${n})${p>Math.PI?"rotate(180)":""}`;const v=p>Math.PI?"end":"";const A=s;const x=n-u;const R=[];const M={x:A*Math.cos(m),y:A*Math.sin(m)};const b={x:x*Math.cos(m),y:x*Math.sin(m)};R.push(M);R.push(b);const C=new ot(R,r);const y={startAngle:t,endAngle:e,innerRadius:s,outerRadius:n,angle:p,value:i,text:o,color:r,transform:f,textAnchor:v,ccAngle:m,line:C,isPrioritized:h,mutationsTooltip:d?[d]:undefined,fusionTooltip:g?[g]:undefined};return y}static createMovedLabel(t,e){const s=t.startAngle+e;const n=t.endAngle+e;const i=(s+n)/2;const o=i-Math.PI/2;const r=t.innerRadius;const a=t.outerRadius-2;const l=(a-r)/3;const c=Math.cos(t.ccAngle);const h=Math.sin(t.ccAngle);const u=Math.cos(t.ccAngle+e);const d=Math.sin(t.ccAngle+e);const g=[];const p={x:r*c,y:r*h};const m={x:(r+l)*c,y:(r+l)*h};const f={x:(r+2*l)*u,y:(r+2*l)*d};const v={x:(r+3*l)*u,y:(r+3*l)*d};g.push(p);g.push(m);g.push(f);g.push(v);const A=new ot(g,t.color);const x="rotate("+(i*180/Math.PI-90)+")"+"translate("+t.outerRadius+")"+(i>Math.PI?"rotate(180)":"");const R=i>Math.PI?"end":"";const M=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:R,ccAngle:o,color:M,line:A,isPrioritized:t.isPrioritized,mutationsTooltip:t.mutationsTooltip,fusionTooltip:t.fusionTooltip};return b}}class at{constructor(t,e,s){this.labelMap=new Map;this.settings=t;this.sampleName=e;this.reference=s}map(t){const e=this.settings.rings.labelLinesInnerRadius;const s=e+this.settings.rings.labelsToLinesDistance;t.forEach((t=>{if(t.dt==G.SNV){const n=this.calculateStartAngle(t.chr,t.position);const i=this.calculateEndAngle(t.chr,t.position);const o=Z.getInstance().mlabel?Z.getInstance().mlabel[t.mClass]:undefined;this.addLabelOrMutation(t,t.gene,t.mname,n,i,e,s,o.color,o.label)}if(t.dt==G.FUSION){const n=$.getColor(t.chrA,t.chrB);if(t.geneA){const i=this.calculateStartAngle(t.chrA,t.posA);const o=this.calculateEndAngle(t.chrA,t.posA);this.addLabelOrFusion(t,t.geneA,i,o,e,s,n)}if(t.geneB&&t.geneA!=t.geneB){const i=this.calculateStartAngle(t.chrB,t.posB);const o=this.calculateEndAngle(t.chrB,t.posB);this.addLabelOrFusion(t,t.geneB,i,o,e,s,n)}}}));return Array.from(this.labelMap.values())}addLabelOrMutation(t,e,s,n,i,o,r,a,l){const c=this.labelMap.get(e);const h={mname:s,color:a,dataClass:l,chr:t.chr,position:t.position};if(!c){this.labelMap.set(e,rt.createLabel(n,i,o,r,t.value,e,a,l,t.chr,t.position,t.isPrioritized,this.settings.rings.labelsToLinesGap,h))}else{if(c.mutationsTooltip){c.mutationsTooltip.push(h)}else{c.mutationsTooltip=[];c.mutationsTooltip.push(h)}}}addLabelOrFusion(t,e,s,n,i,o,r){const a=this.labelMap.get(e);const l={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(!a){this.labelMap.set(e,rt.createLabel(s,n,i,o,t.value,e,r,"Fusion transcript",t.chr,t.position,t.isPrioritized,this.settings.rings.labelsToLinesGap,undefined,l))}else{if(a.fusionTooltip){a.fusionTooltip.push(l)}else{a.fusionTooltip=[];a.fusionTooltip.push(l)}}}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 lt extends Y{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.filteredHasCancerGenesList=[];this.settings=t;this.hasCancerGenes=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=[];if(this.hasCancerGenes){t=this.elements.filter((t=>t.isPrioritized));this.filteredHasCancerGenesList=this.getLabelsWithoutCancerGenes(t);const e=this.elements.filter((t=>!t.isPrioritized));const s=e.concat(this.filteredHasCancerGenesList).sort(((t,e)=>t.startAngle<e.startAngle?-1:t.startAngle>e.startAngle?1:0));this.elementsToDisplay=this.getAllLabels(s)}else{this.elementsToDisplay=this.getLabelsWithoutCancerGenes(this.elements)}}getLabelsWithoutCancerGenes(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=rt.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 o=-1;for(let r=0;r<t.length;r++){const a=t[r];if(a.isPrioritized){s.push(a);o=r;n=a;continue}if(r==0){if(i>1){if(this.isElementOverlappingNextCancerGene(t,o,a,0)){continue}s.push(a);n=a}continue}const l=n.endAngle-a.startAngle+this.overlapAngle;if(l>0&&l<this.settings.label.maxDeltaAngle){if(r==length-1){s.push(a);continue}if(this.isElementOverlappingNextCancerGene(t,o,a,l)){continue}const i=rt.createMovedLabel(a,l);(e=this.collisions)===null||e===void 0?void 0:e.push(i);s.push(a);n=i}if(l<=0){if(this.isElementOverlappingNextCancerGene(t,o,a,0)){continue}s.push(a);n=a}}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 ct{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=Z.getInstance().mlabel?Z.getInstance().mlabel[t.mClass]:undefined;const o=this.calculateStartAngle(t);const r=this.calculateEndAngle(t);const a={startAngle:o,endAngle:r,innerRadius:e,outerRadius:s,color:i.color,text:t.gene,dataClass:i.label,mname:t.mname,chr:t.chr,pos:t.pos};n.push(a)}));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 ht{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 o=i+this.lohWidth;const r=_.provide(t.segmean);const a={startAngle:s,endAngle:n,innerRadius:i,outerRadius:o,color:r,text:t.gene,chr:t.chr,start:t.start,stop:t.stop,value:t.segmean};e.push(a)}));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 ut{constructor(t,e,s,n,i,o){this.labelsRing=t;this.chromosomesRing=e;this.nonExonicArcRing=s;this.snvArcRing=n;this.cnvArcRing=i;this.lohArcRing=o}}class dt{constructor(t,e,s,n){this.nonExonicArcRing=undefined;this.settings=t;this.dataMapper=e;this.reference=s;this.sampleName=n}map(t){const e=this.dataMapper.map(t);const s=new at(this.settings,this.sampleName,this.reference);const n=s.map(e.labelData);const i=new lt(this.settings,n,e.hasCancerGenes);const o=new Y(this.settings.rings.chromosomeInnerRadius,this.settings.rings.chromosomeWidth,this.reference.chromosomes);const r=new ct(e.nonExonicInnerRadius,this.settings.rings.nonExonicRingWidth,this.sampleName,this.reference);const a=r.map(e.nonExonicSnvData);if(a.length>0){this.nonExonicArcRing=new Y(e.nonExonicInnerRadius,this.settings.rings.nonExonicRingWidth,a)}this.snvArcsMapper=new et(e.snvInnerRadius,this.settings.rings.snvRingWidth,this.sampleName,this.reference);const l=this.snvArcsMapper.map(e.snvRingDataMap);if(l.length>0){this.snvArcRing=new Y(e.snvInnerRadius,this.settings.rings.snvRingWidth,l)}const c=new ht(e.lohInnerRadius,this.settings.rings.lohRingWidth,this.sampleName,this.reference);const h=c.map(e.lohData);if(h.length>0){this.lohArcRing=new Y(e.lohInnerRadius,this.settings.rings.lohRingWidth,h)}this.cnvArcsMapper=new it(e.cnvInnerRadius,this.settings.rings.cnvRingWidth,this.settings,this.sampleName,this.reference,e.cnvMaxValue,e.cnvMinValue,this.settings.cnv.unit);const u=this.cnvArcsMapper.map(e.cnvData);if(u.length>0){this.cnvArcRing=new Y(e.cnvInnerRadius,this.settings.rings.cnvRingWidth,u)}const d=new q(e.fusionRadius,this.sampleName,this.reference);const g=d.map(e.fusionData);let p;if(this.settings.legend.lohLegendEnabled&&e.lohMinValue&&e.lohMaxValue){p=new J(e.lohMinValue,e.lohMaxValue)}const m=new j(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,g.length>0,p);const f=new ut(i,o,this.nonExonicArcRing,this.snvArcRing,this.cnvArcRing,this.lohArcRing);return new Q(this.settings,f,m,g)}}class gt{constructor(t){this.settings=t}map(t){const e=t.args.chromosomes;const s=t.args.genome.majorchr;const n=t.args.sampleName;const i=t.args.cancerGenes?t.args.cancerGenes:[];const o=t.args.data;const r=new W(this.settings,s,e);const a=new H(this.settings,r,n,i);return new dt(this.settings,a,r,n).map(o)}}gt.dtNums=[2,5,4,10,1,"exonic","non-exonic"];gt.dtAlias={1:"snv",2:"sv",3:"geneexpression",4:"cnv",5:"sv",6:"snv",7:"snv",8:"snv",9:"snv",10:"loh"};gt.snvClassLayer={M:"exonic",E:"exonic",F:"exonic",N:"exonic",S:"exonic",D:"exonic",I:"exonic",P:"exonic",L:"exonic",Utr3:"exonic",Utr5:"exonic",mnv:"non-exonic",ITD:"non-exonic",insertion:"non-exonic",deletion:"non-exonic",Intron:"non-exonic",X:"non-exonic",noncoding:"non-exonic"};class pt{constructor(t,e){this.cvnCapping=t;this.onClickCallback=e}map(t){const e=[];let s=0;if(t.snvClassMap){this.mapSnv(t,e,s++)}if(t.cnvClassMap){this.mapCnv(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})}mapCnv(t,e,s){if(!t.cnvClassMap)return;const n=t.cnvClassMap.get(nt.Gain);const i=t.cnvClassMap.get(nt.Loss);const o=t.cnvClassMap.get(nt.Cap);if(n&&i&&o){let r=0;const a=[];if(n.value>0){a.push({termid:t.cnvTitle,key:nt.Gain,text:`Max: ${n.value}`,color:n.color,order:r++,border:"1px solid #ccc"})}if(i.value<0){a.push({termid:t.cnvTitle,key:nt.Loss,text:`Min: ${i.value}`,color:i.color,order:r++,border:"1px solid #ccc"})}a.push({termid:t.cnvTitle,key:nt.Cap,text:`Capping: ${o.value}`,color:o.color,order:r++,border:"1px solid #ccc",onClickCallback:this.onClickCallback});e.push({name:t.cnvTitle,order:s,items:a})}}mapLoh(t,e,s){if(!t.lohLegend)return;const n=[];n.push({termid:t.lohTitle,key:"min",text:"min",color:t.lohLegend.colorStartValue,order:0,border:"1px solid #ccc"});n.push({termid:t.lohTitle,key:"max",text:"max",color:t.lohLegend.colorEndValue,order:1,border:"1px solid #ccc"});e.push({name:t.lohTitle,order:s,items:n})}mapFusion(t,e,s){const n=[];n.push({termid:t.fusionTitle,key:T.Interchromosomal,text:"Interchromosomal",color:T.Interchromosomal.valueOf(),order:0,border:"1px solid #ccc"});n.push({termid:t.fusionTitle,key:T.Intrachromosomal,text:"Intrachromosomal",color:T.Intrachromosomal.valueOf(),order:1,border:"1px solid #ccc"});e.push({name:t.fusionTitle,order:s,items:n})}}class mt{constructor(t,e,s){this.fontSize=e;this.legendJSONMapper=new pt(t,s)}render(t,e,s,n,i){const o=c({holder:t.append("g"),rectFillFxn:t=>t.color,iconStroke:"#aaa"});const r={xOffset:s};const a=this.legendJSONMapper.map(e);o(a,{settings:Object.assign({},{svgw:n,svgh:i,dimensions:r,fontsize:this.fontSize})})}}class ft{constructor(t,e,s){this.padAngle=t;this.innerRadius=e;this.outerRadius=s}render(t,e){const s=m().padAngle(this.padAngle).value((t=>t.size)).sort(null);const n=s(e);const i=r().innerRadius(this.innerRadius).outerRadius(this.outerRadius);const o=t.append("g");o.selectAll("path").data(n).enter().append("path").attr("d",i).attr("fill","black");o.selectAll("text").data(n).enter().append("text").attr("transform",(t=>`translate(${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 vt{constructor(t,e){this.animationDuration=t;this.geneClickListener=e}render(t,e,s){const i=t.append("g");const o=u().x((t=>t.x)).y((t=>t.y));const r=D.create();i.selectAll(".group").data(e).enter().append("g").attr("class","group").each(((t,e,s)=>{const i=n(s[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=>{r.d.style("padding","2px").html(this.createTooltipHtml(t));r.show(e.x,e.y)})).on("mouseout",(()=>{r.hide()}));i.append("path").attr("class","chord-tick").datum(t.line.points).style("stroke",t.color).style("fill","none").attr("d",o)}));i.selectAll(".group").each(((t,e,i)=>{const r=s?s.find((e=>e.text===t.text)):undefined;if(r){const t=n(i[e]);t.selectAll(".chord-text").datum(r).transition().duration(this.animationDuration).attr("transform",r.transform).style("text-anchor",r.textAnchor);t.selectAll(".chord-tick").datum(r.line.points).transition().duration(this.animationDuration).style("fill","none").attr("d",o)}}))}createTooltipHtml(t){let e="";if(t.mutationsTooltip){e+=`Gene: ${t.text} <br />`;t.mutationsTooltip.forEach((t=>{e+=`Consequence: ${t.mname} <span style="color: ${t.color}" >${t.dataClass}</span> <br />Mutation: ${t.chr}:${t.position} <br />`}))}if(t.fusionTooltip){e+=`Data type: Fusion transcript <br />`;t.fusionTooltip.forEach((t=>{e+=`Break points: ${t.geneA?t.geneA:""} ${t.chrA}:${t.posA} ${t.strandA=="+"?"forward":"reverse"} > `+`${t.geneB?t.geneB:""} ${t.chrB}:${t.posB} ${t.strandB=="+"?"forward":"reverse"} <br /> `}))}return e}}function At(t={}){const e={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"},legend:{snvTitle:"SNV",cnvTitle:"CNV",lohTitle:"LOH",fusionTitle:"SV",lohLegendEnabled:true,fontSize:12,rowHeight:40},menu:{padding:5}};return i(e,t)}class xt{constructor(t){this.geneClickListener=t}render(t,e){const s=r();const n=t.append("g");const i=D.create();n.selectAll("path").data(e).enter().append("path").attr("d",(t=>s(t))).attr("fill",(t=>t.color)).on("mouseover",((t,e)=>{i.d.style("padding","2px").html(`Gene: ${e.text} <br />${e.mname} <br /> <span style="color:${e.color}">${e.dataClass}</span> <br /> ${e.chr}:${e.pos}`);i.show(t.x,t.y)})).on("mouseout",(()=>{i.hide()})).on("click",((t,e)=>{this.geneClickListener(e.text,[e.mname])}))}}class Rt{constructor(t,e){this.svnWidth=t;this.geneClickListener=e}render(t,e){if(e.length>0){const s=e[0].innerRadius;const n=new V(s,this.svnWidth,"#6464641A");n.render(t)}const s=r();const n=t.append("g");const i=D.create();n.selectAll("path").data(e).enter().append("path").attr("d",(t=>s(t))).attr("fill",(t=>t.color)).on("mouseover",((t,e)=>{i.d.style("padding","2px").html(`Gene: ${e.text} <br />${e.mname} <br /> <span style="color:${e.color}">${e.dataClass}</span> <br /> ${e.chr}:${e.pos}`);i.show(t.x,t.y)})).on("mouseout",(()=>{i.hide()})).on("click",((t,e)=>{this.geneClickListener(e.text,[e.mname])}))}}class Mt{render(t,e){const s=r();const n=t.append("g");const i=D.create();n.selectAll("path").data(e).enter().append("path").attr("d",(t=>s(t))).attr("fill",(t=>t.color)).on("mouseover",((t,e)=>{i.d.style("padding","2px").html(`Loss of Heterozygosity  <br /> ${e.chr}:${e.start}-${e.stop}`);i.show(t.x,t.y)})).on("mouseout",(()=>{i.hide()}))}}class bt{constructor(t){this.menuPadding=t}render(t,e){const s=r();const n=t.append("g");const i=D.create();n.selectAll("path").data(e).enter().append("path").attr("d",(t=>s(t))).attr("fill",(t=>t.color)).on("mouseover",((t,e)=>{i.d.style("padding","2px").html(`Copy Number Variation <br /> ${e.chr}:${e.start}-${e.stop} <br /> ${e.unit}: ${e.value}  `);i.show(t.x,t.y)})).on("mouseout",(()=>{i.hide()}))}}class Ct{constructor(t){this.type="Disco";this.opts=t;this.discoInteractions=new P(this)}getState(t){return t.plots.find((t=>t.id===this.id))}main(){return t(this,void 0,void 0,(function*(){const t=this.state.settings;const e=new gt(t);const s=e.map(this.app.getState());const n=this.opts.holder;n.selectAll("*").remove();const i=new mt(t.cnv.capping,t.label.fontSize,this.discoInteractions.cappingClickCallback);const o=new B(this.getRingRenderers(t,this.discoInteractions.geneClickListener),i,this.discoInteractions.downloadClickListener);o.render(n,s)}))}getRingRenderers(t,e){const s=new ft(t.padAngle,t.rings.chromosomeInnerRadius,t.rings.chromosomeInnerRadius+t.rings.chromosomeWidth);const n=new vt(t.label.animationDuration,e);const i=new xt(e);const o=new Rt(t.rings.snvRingWidth,e);const r=new bt(t.menu.padding);const a=new Mt;const l=new Map;l.set(K.CHROMOSOME,s);l.set(K.LABEL,n);l.set(K.NONEXONICSNV,i);l.set(K.SNV,o);l.set(K.CNV,r);l.set(K.LOH,a);return l}}const yt=o(Ct);const It=yt;function Lt(e){return t(this,void 0,void 0,(function*(){return{chartType:"Disco",subfolder:"disco",extension:"ts",settings:At(e.overrides)}}))}export{It as componentInit,yt as discoInit,Lt as getPlotConfig};

package/dist/app-39afa63e.js

@@ -0,0 +1 @@
+import{az as t,M as e,ae as s,p as o,ab as r,aA as i,S as a,aB as n,a0 as l}from"./app-7e06239d.js";import{r as p,s as c}from"./recover-5edcc95f.js";import{g as d,f as h,v as m}from"./filter-f82a212e.js";import{c as u,g as b}from"./sampleScatter.interactivity-73ce689e.js";import{r as f}from"./table-d10a8225.js";import{summaryInit as y}from"./summary-ee8066f8.js";import"path";import"./samplelst-b1997fcc.js";import"./termsetting-5c900816.js";import"./tslib.es6-62bb2d8e.js";import"./app-c4a00870.js";import"./termInfo-6f2feed4.js";import"./violin-b294e506.js";import"./controls-556bec93.js";import"./controls.btns-4f9afa37.js";import"./controls.config-f6f4a58f.js";import"./controls.overlay-9ca3a4b6.js";import"./controls.term1-ff6da5c4.js";import"./controls.divide-05b85fef.js";import"./violin.renderer-c20536f5.js";import"./brush-d962535a.js";import"./pointer-c7475677.js";import"./nodrag-abb5b30b.js";import"./transform-f2cc07e6.js";import"./axis-6cb4f314.js";import"./area-db27c86c.js";import"./line-d0284126.js";import"./constant-426a1483.js";import"./log-1aa7ed02.js";import"./html.legend-3ec0d58f.js";import"./violin.interactivity-74137c2a.js";import"./barchart-f6e1c085.js";import"./bars.settings-f7884503.js";import"./bars.renderer-505ed2aa.js";import"./svg.legend-b357ac94.js";import"./barchart.events-539feb49.js";import"./sampleScatter-15790ae9.js";import"./sampleScatter.renderer-78402039.js";import"./zoom-ae7c1262.js";import"./lasso-6c6e5e67.js";import"./drag-2cf3ac67.js";import"./svg.download-f180ddb6.js";import"./symbol-fc7cbd41.js";import"./math-2fb199c6.js";class v{constructor(t){this.type="search";j(this);x(this)}async init(t){this.dom={holder:this.opts.holder,holderNode:this.opts.holder.node(),tip:new e({padding:"5px"})};this.initUI()}reactsTo(t){return t.type.startsWith("search")||t.type.startsWith("cohort")}getState(t){return{cohortStr:t.activeCohort==-1||!t.termdbConfig.selectCohort?"":t.termdbConfig.selectCohort.values[t.activeCohort].keys.slice().sort().join(","),search:t.search}}async main(){this.dom.holder.style("display",this.state.search.isVisible?"inline-block":"none")}async doSearch(t){if(!t){this.clear({hide:true});this.bus.emit("postSearch",[]);return}const e=await this.app.vocabApi.findTerm(t,this.state.cohortStr,this.opts.usecase);if(!e.lst||e.lst.length==0){this.noResult()}else{this.showTerms(e)}this.bus.emit("postSearch",e)}}const g=t(v);function j(t){t.initUI=()=>{t.dom.holder.style("display",t.search&&t.search.isVisible==false?"none":"inline-block");t.dom.input=t.dom.holder.style("text-align","center").append("input").attr("type","search").attr("class","tree_search").attr("placeholder","Search").style("width","180px").style("display","block").on("input",s.debounce(t.onInput,300));t.dom.resultDiv=t.dom.tip.d.style("border-left",t.opts.resultsHolder?"":"solid 1px rgb(133,182,225)").style("padding-left","5px")};t.noResult=()=>{t.clear();t.dom.resultDiv.append("div").text("No match").style("padding","3px 3px 3px 0px").style("opacity",.5)};t.showTerms=e=>{if(t.opts.disable_terms)e.lst.forEach((e=>{if(e.disabled)t.opts.disable_terms.push(e.id)}));t.clear({hide:!e.lst.length});if(e.lst.length){t.dom.resultDiv.append("table").selectAll().data(e.lst).enter().append("tr").each(t.showTerm)}};t.showTerm=function(e){const s=o(this);const r=s.append("td").text(e.name);if(e.type){r.style("cursor","pointer").attr("class","sja_menuoption").on("click",(()=>{t.app.dispatch({type:"plot_create",config:{chartType:e.type=="survival"?"survival":"summary",term:{id:e.id,term:e}}});t.clear({hide:true})}))}else{r.style("padding","5px 10px").style("opacity",.5)}s.append("td").text((e.__ancestorNames||[]).join(" > ")).style("opacity",.5).style("font-size",".7em")};t.clear=(e={})=>{t.dom.tip.clear();if(e.hide)t.dom.tip.hide();else t.dom.tip.showunder(t.dom.holderNode)}}function x(t){t.onInput=async()=>{const e=t.dom.input.property("value");try{await t.doSearch(e)}catch(e){t.clear();r(t.dom.resultDiv,"Error: "+(e.message||e));if(e.stack)console.log(e.stack)}}}let w=0;const C="_MASS_AUTOID_"+Math.random().toString().slice(-6);let D=(+new Date).toString().slice(-8);const k=new e({padding:"0px",offsetX:0,offsetY:0});k.d.style("z-index",5555);const S={top:"COHORT",mid:"NONE",btm:"",subheader:"cohort"};const _={top:"CHARTS",mid:"NONE",btm:"",subheader:"charts"};const T={top:"GROUPS",mid:"NONE",btm:"",subheader:"groups"};const N={top:"FILTER",mid:"NONE",btm:"",subheader:"filter"};function O(){return C+"_"+D++}class A{constructor(t){this.type="nav";this.instanceNum=w++;this.activeTab=0;this.activeCohort=0;this.searching=false;this.samplecounts={};this.massSessionDuration=t.massSessionDuration;this.sessionDaysLeft=t.app.opts.sessionDaysLeft||null;this.sessionId=t.app.opts.sessionId||null;L(this);E(this)}async init(t){try{this.cohortFilter=d(t.termfilter.filter,"cohortFilter");this.initUI(t);this.initCohort(t);this.components=await i({search:g({app:this.app,holder:this.dom.searchDiv,usecase:{target:"barchart",detail:"term"}}),filter:h({app:this.app,vocabApi:this.app.vocabApi,holder:this.dom.subheader.filter.append("div"),hideLabel:this.opts.header_mode==="with_tabs",emptyLabel:"+Add new filter",callback:t=>{this.app.dispatch({type:"filter_replace",filter:t})}}),charts:u({app:this.app,holder:this.dom.subheader.charts,vocab:this.opts.vocab}),groups:b({app:this.app,holder:this.dom.subheader.groups,vocab:this.opts.vocab}),recover:p({app:this.app,holder:this.dom.recoverDiv,getState:t=>t,reactsTo:t=>t.type!="plot_edit",maxHistoryLen:5})});this.mayShowMessage_sessionDaysLeft()}catch(t){throw t}}reactsTo(t){if(t.type.includes("cache_termq"))return true;if(t.type.startsWith("filter"))return true;if(t.type.startsWith("cohort"))return true;if(t.type.startsWith("tab"))return true;if(t.type=="plot_create")return true;if(t.type=="plot_delete")return true;if(t.type=="app_refresh")return true;if(t.type.endsWith("_customTerm"))return true;if(t.type.endsWith("_group"))return true}getState(t){return{searching:this.searching,nav:t.nav,activeCohort:t.activeCohort,termdbConfig:t.termdbConfig,filter:t.termfilter.filter,plots:t.plots,groups:t.groups}}async main(){this.dom.tabDiv.style("display",this.state.nav.header_mode==="with_tabs"?"inline-block":"none");this.dom.tip.hide();this.activeTab=this.state.nav.activeTab;this.prevCohort=this.activeCohort;this.activeCohort=+this.state.activeCohort;this.filterUiRoot=d(this.state.filter,"filterUiRoot");this.cohortFilter=d(this.state.filter,"cohortFilter");if(this.cohortNames){this.activeCohortName=this.cohortNames[this.activeCohort];if(this.activeCohort!==-1)this.activeCohortLabel=this.state.termdbConfig.selectCohort.values[this.activeCohort].shortLabel}this.filterJSON=JSON.stringify(this.state.filter);this.cohortsData=await this.app.vocabApi.getCohortsData();if(this.state.nav.header_mode==="with_tabs"){if(!(this.activeCohortName in this.samplecounts)){this.samplecounts[this.activeCohortName]=await this.app.vocabApi.getCohortSampleCount(this.activeCohortName)}if(!(this.filterJSON in this.samplecounts)){if(!this.filterUiRoot||!this.filterUiRoot.lst.length){this.samplecounts[this.filterJSON]=this.samplecounts[this.activeCohortName]}else{const t=await this.app.vocabApi.getFilteredSampleCount(this.filterJSON);this.samplecounts[this.filterJSON]=t}}}this.updateUI()}}const I=t(A);function E(t){t.initUI=s=>{const o=t.opts.holder.append("div").style("white-space","nowrap");const r=o.append("div").style("display","none").style("vertical-align","bottom");const i=o.append("div").style("vertical-align","top").style("margin","10px").style("display","inline-block");t.opts.holder.attr("class","sjpp-nav");t.dom={holder:t.opts.holder,header:o,tabDiv:r,controlsDiv:i,searchDiv:i.append("div").style("margin","10px"),sessionDiv:i.append("div").style("display","inline-block"),recoverDiv:i.append("div").style("display","inline-block"),helpDiv:i.append("div").style("display","none"),sessionElapsedMessageDiv:i.append("div").style("display","none"),subheaderDiv:t.opts.holder.append("div").style("display","block").style("padding-top","5px").style("border-bottom","1px solid #000"),messageDiv:t.opts.holder.append("div").style("margin","30px").style("display","none"),tip:new e({padding:"5px"})};if(t.opts.header_mode==="with_cohortHtmlSelect"){t.dom.cohortStandaloneDiv=o.append("div").style("display","inline-block").style("margin","10px").style("vertical-align","top");t.dom.cohortStandaloneDiv.append("label").html("Cohort: ");t.dom.cohortSelect=t.dom.cohortStandaloneDiv.append("select").on("change",(function(){t.app.dispatch({type:"cohort_set",activeCohort:+this.value})}));t.dom.cohortSelect.selectAll("option").data(s.termdbConfig.selectCohort.values).enter().append("option").attr("value",((t,e)=>e)).property("selected",((t,e)=>e===s.activeCohort)).html((t=>t.shortLabel))}t.dom.subheader=Object.freeze({search:t.dom.subheaderDiv.append("div").style("display","none"),groups:t.dom.subheaderDiv.append("div").style("display","none"),charts:t.dom.subheaderDiv.append("div").style("display","none"),cohort:t.dom.subheaderDiv.append("div").style("display","none"),filter:t.dom.subheaderDiv.append("div").style("display","none"),cart:t.dom.subheaderDiv.append("div").style("display","none").html("<br/>Cart feature under construction - work in progress<br/>&nbsp;<br/>")});t.tabs=[_,T,N];if(s.termdbConfig.selectCohort)t.tabs.unshift(S);const a=t.dom.tabDiv.append("table").style("border-collapse","collapse");a.selectAll("tr").data(["top","mid","btm"]).enter().append("tr").style("font-size",((t,e)=>e==1?"20px":"12px")).selectAll("td").data(((e,s)=>t.tabs.map(((t,o)=>({rowNum:s,key:e,colNum:o,label:t[e],subheader:t.subheader}))))).enter().append("td").style("display","none").style("width","100px").style("padding",(t=>t.rowNum===0?"12px 12px 3px 12px":"3px 12px")).style("text-align","center").style("border-left","1px solid #ccc").style("border-right","1px solid #ccc").style("color","#aaa").style("cursor","pointer").html((t=>t.label)).on("click",t.setTab);t.dom.trs=a.selectAll("tr");t.dom.tds=a.selectAll("td");t.subheaderKeys=t.tabs.map((t=>t.subheader));t.dom.saveBtn=t.dom.sessionDiv.append("button").style("margin","10px").text("New Session").on("click",t.getSessionUrl);if(t.sessionDaysLeft!=null){t.dom.fileBtn=t.dom.sessionDiv.append("button").style("margin","10px").text("Export Session").on("click",(e=>{t.getSessionFile(e)}))}const n=s.termdbConfig.helpPages;if(n){t.dom.helpBtn=t.dom.helpDiv.style("display","inline-block").append("button").style("margin","10px").html("Help &#9660;").on("click",(t=>{const e=t.target.getBoundingClientRect();const s=k.clear().show(e.left-0,e.top+e.height+5).d.append("div");for(const t of n){s.append("div").style("margin","15px").append("a").attr("href",t.url).attr("target","_blank").text(t.label)}}))}};t.mayShowMessage_sessionDaysLeft=()=>{if(!Number.isFinite(t.sessionDaysLeft)){return}t.dom.sessionElapsedMessageDiv.style("display","block");t.dom.remainingDaysMessage=t.dom.sessionElapsedMessageDiv.append("div").style("display","block").style("opacity","0.65").html(`<u>${t.sessionDaysLeft} days</u> left till this session is removed. Click the New Session button to create a new one.`)};t.updateUI=async(e=false)=>{if(!t.dom.subheaderDiv)return;if(t.activeTab&&t.state.termdbConfig.selectCohort&&t.activeCohort==-1){t.dom.subheaderDiv.style("display","none");t.dom.messageDiv.selectAll("text").remove();t.dom.messageDiv.style("display","").text('No cohort selected. Please select a cohort in the "COHORT" tab.')}else{let s="block";if(e){s=t.dom.subheaderDiv.style("display")=="none"?"block":"none"}if(t.dom.subheaderDiv)t.dom.subheaderDiv.style("display",s);if(t.dom.messageDiv)t.dom.messageDiv.style("display","none")}const s=t.state.termdbConfig.selectCohort;t.dom.searchDiv.style("display",s&&t.activeCohort==-1?"none":"inline-block");t.dom.header.style("border-bottom",t.state.nav.header_mode==="with_tabs"?"1px solid #000":"");t.dom.tds.style("display","").style("color",(e=>e.colNum==t.activeTab?"#000":"#aaa")).style("background-color",(e=>e.colNum==t.activeTab?"#ececec":"transparent")).html((function(e,s){if(e.key=="top")return this.innerHTML;if(e.subheader=="groups"){if(e.key=="mid")return t.state.groups.length||"NONE";return""}if(e.subheader==="charts"){const s=t.state.plots.length;if(e.key=="mid")return!s?"NONE":s;else return""}else if(e.subheader==="cohort"){if(t.activeCohortName&&t.activeCohortName in t.samplecounts){return e.key=="top"?this.innerHTML:e.key=="mid"?t.activeCohortLabel:"n="+t.samplecounts[t.activeCohortName]}else{return e.key=="mid"?"NONE":this.innerHTML}}else if(e.subheader==="filter"){const s=t.filterUiRoot?t.filterUiRoot:{lst:[]};if(s.lst.length===0){return e.key==="mid"?"NONE":t.samplecounts["undefined"]?`n=${t.samplecounts["undefined"]}`:""}else{const o=t.samplecounts[t.filterJSON]!=undefined?"n="+t.samplecounts[t.filterJSON]:"";return e.key==="mid"?s.lst.length:o}}else{return e.key==="mid"?this.innerHTML:"&nbsp;"}}));for(const e in t.dom.subheader){t.dom.subheader[e].style("display",t.tabs[t.activeTab].subheader===e?"block":"none")}t.renderCohortsTable();if(t.opts.header_mode==="with_cohort_select"){t.dom.cohortSelect.selectAll("option").property("value",appState.activeCohort)}};t.renderCohortsTable=()=>{if(!t.dom.cohortTable)return;t.dom.cohortTable.selectAll("*").remove();const e=[{label:"Feature"}];const s=[];const o=t.cohortsData;if("error"in o)throw o.error;for(const t of o.features)s.push([{value:t.name}]);for(const t of o.cohorts){e.push({label:t.cohort?`${t.name} (${t.cohort})`:t.name});for(const[e,r]of o.features.entries()){const i=o.cfeatures.find((e=>e.idfeature===r.idfeature&&e.cohort===t.cohort));if(i)s[e].push({value:i.value})}}f({rows:s,columns:e,div:t.dom.cohortTable,showLines:false,maxHeight:"60vh"});t.dom.cohortTable.select("table").style("border-collapse","collapse");t.dom.cohortTable.selectAll(`tbody > tr > td`).style("background-color","transparent");const r=t.state.termdbConfig.selectCohort;const i=r.values[t.activeCohort].keys;let a=`tbody > tr > td:nth-child(${t.activeCohort+2})`;const n=i.length>1;if(n){a="";for(const t of i){const e=o.cohorts.map((t=>t.cohort)).indexOf(t);if(a!=="")a+=",";a+=`tbody > tr > td:nth-child(${e+2})`}}const l=t.dom.cohortTable.selectAll(a);l.style("background-color","yellow");t.dom.cohortInputs.property("checked",((e,s)=>s===t.activeCohort))};t.initCohort=async e=>{const s=e.termdbConfig.selectCohort;if(!s)return;t.dom.tds.filter((t=>t.colNum===0)).style("display","");t.cohortNames=s.values.map((t=>t.keys.slice().sort().join(",")));if(s.title){t.dom.cohortTitle=t.dom.subheader.cohort.append("h2").style("margin-left","10px").text(s.title)}if(s.description){t.dom.cohortDescription=t.dom.subheader.cohort.append("div").style("margin-left","10px").html(s.description)}if(s.prompt){t.dom.cohortPrompt=t.dom.subheader.cohort.append("div").style("margin-left","10px").style("padding-top","30px").style("padding-bottom","10px").style("font-weight","bold").text(s.prompt)}t.dom.cohortOpts=t.dom.subheader.cohort.append("div").style("margin-bottom","30px").style("margin-left","10px");t.dom.cohortOpts.append("table").selectAll("tr").data(s.values).enter().append("tr").each((function(e,s){const r=o(this);const i=r.append("td");const a="sja-termdb-cohort-"+t.instanceNum;const n=a+"-"+s;i.append("input").attr("type","radio").attr("name",a).attr("id",n).attr("value",s).property("checked",s===t.activeCohort).style("margin-right","5px").style("margin-left","0px").on("click",(()=>{t.app.dispatch({type:"cohort_set",activeCohort:s})}));i.append("label").attr("for",n).attr("colspan",2).style("cursor","pointer").html((t=>t.label));r.selectAll("td").style("max-width","600px").style("padding-bottom","10px").style("padding-right","20px").style("vertical-align","top")}));t.dom.cohortInputs=t.dom.cohortOpts.selectAll("input");t.dom.cohortTable=t.dom.subheader.cohort.append("div");if(s.asterisk){t.dom.cohortAsterisk=t.dom.subheader.cohort.append("div").style("margin-left","10px").style("padding-top","20px").style("padding-bottom","20px").style("font-size","small").text(s.asterisk)}}}function L(t){t.setTab=async(e,s)=>{if(s.colNum===t.activeTab&&!t.searching){t.prevCohort=t.activeCohort;await t.updateUI(true);if(t.bus)t.bus.emit("postRender");return}t.activeTab=s.colNum;t.searching=false;t.app.dispatch({type:"tab_set",activeTab:t.activeTab});if(t.activeTab==1&&t.activeCohort!=-1&&!t.state.plots.length){t.app.dispatch({type:"plot_create",id:O(),config:{chartType:"dictionary"}})}};t.getSessionUrl=async()=>{t.dom.saveBtn.property("disabled",true);const e=await a("/massSession",{method:"POST",body:JSON.stringify(t.app.getState())});const s=sessionStorage.getItem("hostURL")||`${window.location.protocol}//${window.location.host}`;const o=`${s}/?mass-session-id=${e.id}&noheader=1`;t.dom.tip.clear().showunder(t.dom.saveBtn.node());t.dom.tip.d.append("div").style("margin","10px").html(`<a href='${o}' target=_blank>${e.id}</a><br><div style="font-size:.8em;opacity:.6"><span>Click the link to recover this session. Bookmark or share this link.</span><br><span>This session will be saved for ${t.massSessionDuration} days.</span></div>`);setTimeout((()=>{t.dom.saveBtn.property("disabled",false)}),1e3)};t.getSessionFile=async e=>{const s=await a(`/massSession?id=${t.sessionId}`);const o=document.createElement("a");const r="data:application/json;charset=utf-8,"+encodeURIComponent(JSON.stringify(s.state));o.setAttribute("href",r);o.download=`${t.sessionId}.json`;o.click();o.remove()}}function U(t){switch(t){case"../plots/Disco.js":return import("./Disco-eafea947.js");case"../plots/barchart.data.js":return import("./filter-f82a212e.js").then((function(t){return t.p}));case"../plots/barchart.events.js":return import("./barchart.events-539feb49.js");case"../plots/barchart.js":return import("./barchart-f6e1c085.js");case"../plots/bars.renderer.js":return import("./bars.renderer-505ed2aa.js");case"../plots/bars.settings.js":return import("./bars.settings-f7884503.js");case"../plots/boxplot.js":return import("./boxplot-672e1c69.js");case"../plots/controls.btns.js":return import("./controls.btns-4f9afa37.js");case"../plots/controls.config.js":return import("./controls.config-f6f4a58f.js");case"../plots/controls.divide.js":return import("./controls.divide-05b85fef.js");case"../plots/controls.js":return import("./controls-556bec93.js");case"../plots/controls.overlay.js":return import("./controls.overlay-9ca3a4b6.js");case"../plots/controls.term1.js":return import("./controls.term1-ff6da5c4.js");case"../plots/cuminc.js":return import("./cuminc-15fde0ae.js");case"../plots/dataDownload.js":return import("./dataDownload-18ba0a91.js");case"../plots/dictionary.js":return import("./dictionary-8f8fe915.js");case"../plots/geneExpression.js":return import("./geneExpression-a4c1df76.js");case"../plots/genomeBrowser.controls.js":return import("./genomeBrowser.controls-8d1754d2.js");case"../plots/genomeBrowser.js":return import("./genomeBrowser-9379fe74.js");case"../plots/matrix.cells.js":return import("./matrix.cells-ddb1510a.js");case"../plots/matrix.cluster.js":return import("./matrix.cluster-8dcbc3c4.js");case"../plots/matrix.config.js":return import("./matrix.config-92a38afb.js");case"../plots/matrix.controls.js":return import("./matrix.controls-b81ef6d4.js");case"../plots/matrix.dom.js":return import("./matrix.dom-75af76b9.js");case"../plots/matrix.interactivity.js":return import("./matrix.interactivity-82849be3.js");case"../plots/matrix.js":return import("./matrix-cb36d8ac.js");case"../plots/matrix.renderers.js":return import("./matrix.renderers-1cac71f8.js");case"../plots/matrix.sort.js":return import("./matrix.sort-e7aedd12.js");case"../plots/plot.app.js":return import("./plot.app-2f12106e.js");case"../plots/plot.disco.js":return import("./plot.disco-e2e4de80.js");case"../plots/plot.ssgq.js":return import("./plot.ssgq-24a08ec8.js");case"../plots/profileBarchart.js":return import("./profileBarchart-daa35b18.js");case"../plots/profilePolar.js":return import("./profilePolar-9d1cbb30.js");case"../plots/regression.inputs.js":return import("./regression.inputs-ede8c6d9.js").then((function(t){return t.b}));case"../plots/regression.inputs.term.js":return import("./regression.inputs-ede8c6d9.js").then((function(t){return t.a}));case"../plots/regression.inputs.values.table.js":return import("./regression.inputs.values.table-8742935c.js");case"../plots/regression.js":return import("./regression.inputs-ede8c6d9.js").then((function(t){return t.r}));case"../plots/regression.results.js":return import("./regression.results-ffa76c09.js");case"../plots/sampleScatter.interactivity.js":return import("./sampleScatter.interactivity-73ce689e.js").then((function(t){return t.d}));case"../plots/sampleScatter.js":return import("./sampleScatter-15790ae9.js");case"../plots/sampleScatter.renderer.js":return import("./sampleScatter.renderer-78402039.js");case"../plots/scatter.js":return import("./scatter-e14842dd.js");case"../plots/stattable.js":return import("./stattable-091e724d.js");case"../plots/summary.js":return import("./summary-ee8066f8.js");case"../plots/survival.js":return import("./survival-0b2a1b58.js");case"../plots/table.js":return import("./table-11c862d1.js");case"../plots/variantBrowser.js":return import("./variantBrowser-87fec91b.js");case"../plots/violin.interactivity.js":return import("./violin.interactivity-74137c2a.js");case"../plots/violin.js":return import("./violin-b294e506.js");case"../plots/violin.renderer.js":return import("./violin.renderer-c20536f5.js");default:return new Promise((function(e,s){(typeof queueMicrotask==="function"?queueMicrotask:setTimeout)(s.bind(null,new Error("Unknown variable dynamic import: "+t)))}))}}class R{constructor(t){this.type="plot";$(this);this.initUi(t)}reactsTo(t){if(t.type.includes("cache_termq"))return true;if(t.type.endsWith("_group"))return true;if(t.type.startsWith("plot_"))return t.id===this.id;if(t.type.startsWith("filter"))return true;if(t.type.startsWith("cohort"))return true;if(t.type=="app_refresh")return true;if(t.type.endsWith("customTerm"))return true}getState(t){const e=t.plots.find((t=>t.id===this.id));if(!e){throw`No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`}return{config:e,groups:t.groups,_scope_:t._scope_}}async main(){this.dom.errdiv.style("display","none");if(!this.components)await this.setComponents(this.opts)}async setComponents(t){this.components={recover:await p({app:this.app,holder:this.dom.localRecoverDiv,getState:t=>this.getState(t),reactsTo:t=>t.id==this.id&&(t.type=="plot_edit"||t.type=="plot_nestedEdits")&&t._track_!="none",plot_id:this.id,maxHistoryLen:10})};const e=await U(`../plots/${t.chartType}.js`);this.components.chart=await e.componentInit({app:this.app,holder:this.dom.viz,header:this.dom.paneTitleDiv,id:this.id,plotDiv:o(this.dom.holder.app_div.node().parentNode)})}destroy(){this.dom.holder.app_div.selectAll("*").remove();this.dom.holder.app_div.remove();for(const t in this.dom){delete this.dom[t]}}}const B=t(R);function $(t){t.initUi=function(s){const o=s.holder;o.header.style("padding",0);try{t.dom={tip:new e({padding:"0px"}),holder:o,paneTitleDiv:o.header.append("div").style("display","inline-block").style("color","#999").style("padding-left","7px").style("vertical-align","sub"),localRecoverDiv:o.header.append("div").style("display","inline-block"),body:o.body.style("white-space","nowrap").style("overflow-x","auto"),errdiv:o.body.append("div").style("display","none").style("padding","5px").style("background-color","rgba(255,100,100,0.2)"),viz:o.body.append("div")}}catch(e){t.dom.errdiv.style("display","none").text(e)}}}class M{constructor(t){if(t.addLoginCallback){t.addLoginCallback((()=>this.api.dispatch({type:"app_refresh"})))}this.type="app";this.dom={holder:t.holder,topbar:t.holder.append("div"),errdiv:t.holder.append("div"),plotDiv:t.holder.append("div")};this.plotIdToSandboxId={}}validateOpts(t={}){if(!t.holder)throw`missing opts.holder in the MassApp constructor argument`;if(!t.callbacks)t.callbacks={};if(!t.state.vocab)t.state.vocab={};if(typeof t.state.vocab!="object")throw"opts.state.vocab{} is not an object";if(t.state.genome){t.state.vocab.genome=t.state.genome;delete t.state.genome}if(t.state.dslabel){t.state.vocab.dslabel=t.state.dslabel;delete t.state.dslabel}return t}async preApiFreeze(t){try{t.tip=new e({padding:"5px"});t.printError=t=>this.printError(t);const s=this.opts.state.vocab;t.vocabApi=await m({app:t,state:{vocab:this.opts.state.vocab},fetchOpts:this.opts.fetchOpts,getDatasetAccessToken:this.opts.getDatasetAccessToken});t.hasWebGL=function(){try{var t=document.createElement("canvas");return!!(window.WebGLRenderingContext&&(t.getContext("webgl")||t.getContext("experimental-webgl")))}catch(t){return false}};this.opts.state.vocab=t.vocabApi.vocab}catch(t){throw t}}async init(){try{const t="debounceInterval"in this.opts?this.opts.debounceInterval:0;this.store=await c({app:this.api,state:this.opts.state,debounceInterval:t});this.state=await this.store.copyState();this.components={};if(this.state.nav.header_mode!="hidden"){this.components.nav=await I({app:this.api,holder:this.dom.topbar,header_mode:this.state&&this.state.nav&&this.state.nav.header_mode,vocab:this.state.vocab,massSessionDuration:this.state.termdbConfig.massSessionDuration})}this.components.plots={};await this.api.dispatch()}catch(t){this.printError(t);throw t}}async main(){await this.api.vocabApi.main();const t={};let e;for(const s of this.state.plots){if(!(s.id in this.components.plots)){e=l(this.dom.plotDiv,{close:()=>{this.api.dispatch({type:"plot_delete",id:s.id})},plotId:s.id,beforePlotId:s.insertBefore||null,style:{width:"98.5%"}});if(s.chartType=="summary")t[s.id]=y(Object.assign({app:this.api,holder:e},s));else t[s.id]=B(Object.assign({app:this.api,holder:e},s))}}const s=Object.keys(t).length;if(s){await Promise.all(Object.values(t));for(const e in t){this.components.plots[e]=await t[e]}}for(const t in this.components.plots){if(!this.state.plots.find((e=>e.id===t))){this.components.plots[t].destroy();delete this.components.plots[t]}}}printError(t){r(this.dom.errdiv||this.opts.holder,"Error: "+(t.message||t));if(t.stack)console.log(t.stack)}}const W=n(M);export{W as appInit};