@sjcrh/proteinpaint-client 2.25.0 → 2.26.0

package/dist/{2dmaf-99e42f50.js → 2dmaf-a12a3c3c.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-b45bc7b4.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,o as a,E as n,b8 as i,p as r,l,f as o,a as c,ay as p,aL as h,q as d,w as f,$ as u}from"./app-91ecaaa4.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 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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])+" 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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=$.append("g").attr("transform","translate("+(_+M+I)+","+(w+X)+")");const lt="#FFBEAD";rt.append("rect").attr("fill",lt).attr("fill-opacity",0).attr("x",0).attr("width",3).attr("height",R-X);c({axis:rt.call(g().scale(it).tickValues([0,x])),showline:true,fontsize:A*.8});rt.append("g").attr("transform","translate(-"+A/2+","+(R-X)/2+")").append("text").text("D total").attr("font-size",A*.8).attr("font-family",r).attr("fill","black").attr("text-anchor","middle").attr("dominant-baseline","middle").attr("transform","rotate(-90)");const ot=rt.selectAll().data(i).enter().append("g").attr("transform",(t=>{t.posstring="translate("+J(t.maf1)+","+it(t["TinD.D"])+")";return t.posstring}));ot.filter((t=>t.Dcnvloh)).append("circle").attr("cy",(t=>t.issnv?S(t["TinD.R"]):C/2)).attr("fill","#858585").attr("r",O);ot.filter((t=>t.Rcnvloh)).append("circle").attr("cx",(t=>t.issnv?-S(t["TinD.D"]):-C/2)).attr("fill","#858585").attr("r",O);nt=ot;for(const t in F){nt.filter(F[t]).append(t).attr("class",(t=>t.symbol?"twodmaf-"+t.symbol:null)).attr("r",(t=>t.symbol?null:S(t["TinD.R"]))).attr("d",(t=>!t.symbol?null:m.type(B[t.symbol]).size(W(t["TinD.R"]))())).attr("fill",(t=>t.style.fill)).attr("fill-opacity",(t=>t.style.fillopacity)).attr("stroke",(t=>t.style.stroke)).attr("stroke-opacity",(t=>t.style.strokeopacity)).attr("stroke-dasharray",(t=>t.chr=="chrX"?"5,5":"none")).on("mouseover",((t,e)=>j(t,e,a))).on("mouseout",((t,e)=>L(t,e,a))).on("click",((t,e)=>V(t,s.header,e)))}nt.append("line").attr("stroke",(t=>t.style.stroke)).attr("stroke-opacity",(t=>t.style.strokeopacity)).attr("x1",-3).attr("y1",-3).attr("x2",3).attr("y2",3);nt.append("line").attr("stroke",(t=>t.style.stroke)).attr("stroke-opacity",(t=>t.style.strokeopacity)).attr("x1",-3).attr("y1",3).attr("x2",3).attr("y2",-3);const ct=l().domain([0,x]).range([0,I-X]);const pt=$.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=$.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};

package/dist/Disco-10039f85.js

@@ -0,0 +1 @@
+import{_ as t}from"./tslib.es6-62bb2d8e.js";import{M as e,E as s,q as n,aJ as i,az as o}from"./app-91ecaaa4.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-a90add32.js";import{a as h,l as u}from"./line-264f8f9e.js";import{t as d}from"./math-2fb199c6.js";import"path";function p(t,e){return e<t?-1:e>t?1:e>=t?0:NaN}function g(t){return t}function m(){var t=g,e=p,s=null,n=a(0),i=a(d),o=a(0);function r(r){var a,l=(r=h(r)).length,c,u,p=0,g=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),b;for(a=0;a<l;++a){if((b=m[g[a]=a]=+t(r[a],a,r))>0){p+=b}}if(e!=null)g.sort((function(t,s){return e(m[t],m[s])}));else if(s!=null)g.sort((function(t,e){return s(r[t],r[e])}));for(a=0,u=p?(v-l*R)/p:0;a<l;++a,f=A){c=g[a],b=m[c],A=f+(b>0?b*u:0)+R,m[c]={data:r[c],index:a,value:b,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 b=1e-12;var M=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 E(t){return t.startAngle}function O(t){return t.endAngle}function w(){return 0}function S(t){var e=y,s=I,n=L,i=L,o=E,r=O,a=w,c=null;function h(){var h,u=e.apply(this,arguments),d=s.apply(this,arguments),p=a.apply(this,arguments)/2,g=M.call(arguments),m=+n.apply(this,(g[0]=u,g)),x=o.apply(this,g)-R,C=r.apply(this,g)-R,y=+i.apply(this,(g[0]=d,g)),I=o.apply(this,g)-R,L=r.apply(this,g)-R;if(!c)c=h=l();if(p>b){if(f(C-x)>p*2+b)C>x?(x+=p,C-=p):(x-=p,C+=p);else x=C=(x+C)/2;if(f(L-I)>p*2+b)L>I?(I+=p,L-=p):(I-=p,L+=p);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 E=+t.apply(this,arguments),O=y-E,w=(I+L)/2;c.quadraticCurveTo(0,0,O*v(I),O*A(I));c.lineTo(y*v(w),y*A(w));c.lineTo(O*v(L),O*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 T{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 D;(function(t){t["Intrachromosomal"]="#1B9E77";t["Interchromosomal"]="#6A3D9A"})(D||(D={}));class z{static getColor(t,e){if(t!=e){return D.Interchromosomal.valueOf()}else{return D.Intrachromosomal.valueOf()}}}class k{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=T.create();i.enter().append("path").attr("class","chord").attr("d",n).attr("fill",(t=>z.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 P{constructor(t){this.downloadClickListener=t}render(t){t.append("span").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){this.checkBoxClickListener=t}render(t,e,s){if(s){const s=t.append("span").append("input").attr("type","checkbox").attr("id","genes-checkbox").property("checked",e);t.append("label").attr("for","genes-checkbox").text("Prioritize Cancer Gene Census");s.on("change",(()=>{this.checkBoxClickListener(s.property("checked"))}))}}}class ${constructor(t,e,s,n){this.renders=t;this.legendRenderer=e;this.fusionRenderer=new k;this.downloadButtonRenderer=new P(s);this.prioritizeGenesCheckboxRenderer=new B(n)}render(t,e){const s=t.append("div");const n=s.append("div").style("display","inline-block").style("font-family","Arial");const i=n.append("div");this.downloadButtonRenderer.render(i);this.prioritizeGenesCheckboxRenderer.render(i,e.settings.label.prioritizeGeneLabelsByGeneSets,e.settings.label.showPrioritizeGeneLabelsByGeneSets);const o=n.append("svg").attr("width",e.width).attr("height",e.height+e.legendHeight);const r=o.append("g").attr("class","mainG").attr("transform",`translate(${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(r,n,i)}this.fusionRenderer.render(r,e.fusions);this.legendRenderer.render(r,e.legend,-1*(e.settings.rings.labelLinesInnerRadius+e.settings.rings.labelsToLinesDistance+50),e.width,e.height/2)}}class G{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-91ecaaa4.js").then((function(t){return t.bR}));yield i.default(t)}));this.prioritizeGenesCheckboxListener=t=>{e.app.dispatch({type:"plot_edit",id:e.opts.id,config:{settings:{label:{prioritizeGeneLabelsByGeneSets: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.prioritizedGenes=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.prioritizedGenes.some((e=>e==t.gene)),chrA:t.chrA,chrB:t.chrB,geneA:t.geneA,geneB:t.geneB,posA:t.posA,posB:t.posB,strandA:t.strandA,strandB:t.strandB}}}var H;(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"})(H||(H={}));class j{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==H.SNV;this.fusionFilter=t=>t.dt==H.FUSION||t.dt==H.SV;this.cnvFilter=t=>t.dt==H.CNV;this.lohFilter=t=>t.dt==H.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(mt.snvClassLayer[e.mClass]);this.snvRingFilter=e=>t.rings.snvRingFilters.includes(mt.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==H.SNV){if(s!=-1){this.addData(t,e)}}else if(t.dt==H.FUSION||t.dt==H.SV){if(n!=-1&&i!=-1){this.addData(t,e)}}else if([H.CNV,H.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,hasPrioritizedGenes: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 U{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 q{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 _{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 q(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 J{static provide(t){const e=Math.min(Math.max(t,0),1);const s=Math.round(e*255);return`rgb(${s}, ${s}, ${s})`}}class K{constructor(t,e){this.minValue=t;this.maxValue=e;this.colorStartValue=J.provide(t);this.colorEndValue=J.provide(e)}}var Q;(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"})(Q||(Q={}));class Y{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 Q.CHROMOSOME:return this.rings.chromosomesRing?this.rings.chromosomesRing.elements:[];case Q.LABEL:return this.rings.labelsRing.elementsToDisplay;case Q.NONEXONICSNV:return this.rings.nonExonicArcRing?this.rings.nonExonicArcRing.elements:[];case Q.SNV:return this.rings.snvArcRing?this.rings.snvArcRing.elements:[];case Q.CNV:return this.rings.cnvArcRing?this.rings.cnvArcRing.elements:[];case Q.LOH:return this.rings.lohArcRing?this.rings.lohArcRing.elements:[];default:throw new Error(`ringType ${t} not defined`)}}getCollisions(t){if(t==Q.LABEL){return this.rings.labelsRing.collisions}else{return undefined}}calculateLegendHeight(t){const e=this.settings.legend.rowHeight;return e*t.legendCount()}}class Z{constructor(t,e,s){this.innerRadius=t;this.outerRadius=t+e;this.width=e;this.elements=s}}class tt{constructor(){const t={};for(const e in s){t[s[e].label]=s[e];t[e]=s[e]}this.mlabel=t}static getInstance(){if(!tt.instance){tt.instance=new tt}return tt.instance}}class et{constructor(t,e,s){this.snvType=t;this.color=e;this.count=s}}class st{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=tt.getInstance().mlabel?tt.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=tt.getInstance().mlabel[t];return new et(s.label,s.color,e)}}class nt{constructor(t,e,s,n){this.text=t;this.cnvType=e;this.color=s;this.value=n}}var it;(function(t){t[t["Loss"]=0]="Loss";t[t["Gain"]=1]="Gain";t[t["Cap"]=2]="Cap"})(it||(it={}));class ot{static getColor(t,e){const s=e.cnv;const n=e.cnv.capping;const i=-1*e.cnv.capping;if(t<i){return s.cappedLossColor}else if(t>=i&&t<=0){return s.lossColor}else if(t>0&&t<=n){return s.ampColor}else{return s.cappedAmpColor}}}class rt{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 nt("Max",o>0?it.Gain:it.Loss,this.getColor(o),o);const c=new nt("Min",r>0?it.Gain:it.Loss,this.getColor(r),r);const h=new nt("Capping",it.Loss,this.getColor(r>0?r:o),this.settings.cnv.capping);this.cnvClassMap.set(it.Gain,l);this.cnvClassMap.set(it.Loss,c);this.cnvClassMap.set(it.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){return ot.getColor(t,this.settings)}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 at{constructor(t,e){this.points=new Array;this.points=t;this.color=e}}class lt{static createLabel(t,e,s,n,i,o,r,a,l,c,h=false,u,d,p){const g=(t+e)/2;const m=g-Math.PI/2;const f=`rotate(${g*180/Math.PI-90}) translate(${n})${g>Math.PI?"rotate(180)":""}`;const v=g>Math.PI?"end":"";const A=s;const x=n-u;const R=[];const b={x:A*Math.cos(m),y:A*Math.sin(m)};const M={x:x*Math.cos(m),y:x*Math.sin(m)};R.push(b);R.push(M);const C=new at(R,r);const y={startAngle:t,endAngle:e,innerRadius:s,outerRadius:n,angle:g,value:i,text:o,color:r,transform:f,textAnchor:v,ccAngle:m,line:C,isPrioritized:h,start:c,stop:c,chr:l,mutationsTooltip:d?[d]:undefined,fusionTooltip:p?[p]: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 p=[];const g={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};p.push(g);p.push(m);p.push(f);p.push(v);const A=new at(p,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 b=t.mutationsTooltip?t.mutationsTooltip[0].color:t.fusionTooltip?t.fusionTooltip[0].color:undefined;const M={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:b,line:A,isPrioritized:t.isPrioritized,start:t.start,stop:t.stop,chr:t.chr,mutationsTooltip:t.mutationsTooltip,fusionTooltip:t.fusionTooltip};return M}}class ct{constructor(t,e,s){this.labelMap=new Map;this.settings=t;this.sampleName=e;this.reference=s}map(t,e=[]){const s=this.settings.rings.labelLinesInnerRadius;const n=s+this.settings.rings.labelsToLinesDistance;t.forEach((t=>{if(t.dt==H.SNV){const e=this.calculateStartAngle(t.chr,t.position);const i=this.calculateEndAngle(t.chr,t.position);const o=tt.getInstance().mlabel?tt.getInstance().mlabel[t.mClass]:undefined;this.addLabelOrMutation(t,t.gene,t.mname,e,i,s,n,o.color,o.label)}if(t.dt==H.FUSION){const e=z.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,t.posA,i,o,s,n,e)}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,t.posB,i,o,s,n,e)}}}));const i=Array.from(this.labelMap.values());i.forEach((t=>{e.forEach((e=>{if(t.stop>=e.start&&e.stop>=t.start&&t.chr==e.chr){const s={value:e.value,color:ot.getColor(e.value,this.settings),chr:e.chr,start:e.start,stop:e.stop};if(t.cnvTooltip){t.cnvTooltip.push(s)}else{t.cnvTooltip=[];t.cnvTooltip.push(s)}}}))}));return Array.from(this.labelMap.values())}addLabelOrMutation(t,e,s,n,i,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,lt.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.start=Math.min(c.start,t.position);c.stop=Math.max(c.stop,t.position);c.mutationsTooltip.push(h)}else{c.mutationsTooltip=[];c.start=Math.min(c.start,t.position);c.stop=Math.max(c.stop,t.position);c.mutationsTooltip.push(h)}}}addLabelOrFusion(t,e,s,n,i,o,r,a){const l=this.labelMap.get(e);const c={color:a,chrA:t.chrA,chrB:t.chrB,posA:t.posA,posB:t.posB,geneA:t.geneA,geneB:t.geneB,strandA:t.strandA,strandB:t.strandB};if(!l){this.labelMap.set(e,lt.createLabel(n,i,o,r,t.value,e,a,"Fusion transcript",t.chr,t.position,t.isPrioritized,this.settings.rings.labelsToLinesGap,undefined,c))}else{if(l.fusionTooltip){l.start=Math.min(l.start,s);l.stop=Math.max(l.stop,s);l.fusionTooltip.push(c)}else{l.fusionTooltip=[];l.start=Math.min(l.start,s);l.stop=Math.max(l.stop,s);l.fusionTooltip.push(c)}}}calculateStartAngle(t,e){const s=this.reference.chromosomesOrder.findIndex((e=>e==t));const n=this.reference.chromosomes[s];return n.startAngle+(n.endAngle-n.startAngle)*(Number(e)/n.size)}calculateEndAngle(t,e){const s=this.reference.chromosomesOrder.findIndex((e=>e==t));const n=this.reference.chromosomes[s];return n.startAngle+(n.endAngle-n.startAngle)*(Number(e)/n.size)}}class ht extends Z{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.filteredPrioritizedGenesList=[];this.settings=t;this.hasPrioritizedGenes=s;const n=2*Math.PI*(t.rings.labelLinesInnerRadius+t.rings.labelsToLinesDistance);this.overlapAngle=this.settings.label.overlapAngleFactor*this.settings.label.fontSize/n;this.calculateCollisions()}calculateCollisions(){this.collisions=[];let t=[];if(this.hasPrioritizedGenes){t=this.elements.filter((t=>t.isPrioritized));this.filteredPrioritizedGenesList=this.getLabelsWithoutPrioritizedGenes(t);const e=this.elements.filter((t=>!t.isPrioritized));const s=e.concat(this.filteredPrioritizedGenesList).sort(((t,e)=>t.startAngle<e.startAngle?-1:t.startAngle>e.startAngle?1:0));this.elementsToDisplay=this.getAllLabels(s)}else{this.elementsToDisplay=this.getLabelsWithoutPrioritizedGenes(this.elements)}}getLabelsWithoutPrioritizedGenes(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=lt.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=lt.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 ut{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=tt.getInstance().mlabel?tt.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 dt{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=J.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 pt{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 gt{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 ct(this.settings,this.sampleName,this.reference);const n=s.map(e.labelData,e.cnvData);const i=new ht(this.settings,n,e.hasPrioritizedGenes);const o=new Z(this.settings.rings.chromosomeInnerRadius,this.settings.rings.chromosomeWidth,this.reference.chromosomes);const r=new ut(e.nonExonicInnerRadius,this.settings.rings.nonExonicRingWidth,this.sampleName,this.reference);const a=r.map(e.nonExonicSnvData);if(a.length>0){this.nonExonicArcRing=new Z(e.nonExonicInnerRadius,this.settings.rings.nonExonicRingWidth,a)}this.snvArcsMapper=new st(e.snvInnerRadius,this.settings.rings.snvRingWidth,this.sampleName,this.reference);const l=this.snvArcsMapper.map(e.snvRingDataMap);if(l.length>0){this.snvArcRing=new Z(e.snvInnerRadius,this.settings.rings.snvRingWidth,l)}const c=new dt(e.lohInnerRadius,this.settings.rings.lohRingWidth,this.sampleName,this.reference);const h=c.map(e.lohData);if(h.length>0){this.lohArcRing=new Z(e.lohInnerRadius,this.settings.rings.lohRingWidth,h)}this.cnvArcsMapper=new rt(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 Z(e.cnvInnerRadius,this.settings.rings.cnvRingWidth,u)}const d=new _(e.fusionRadius,this.sampleName,this.reference);const p=d.map(e.fusionData);let g;if(this.settings.legend.lohLegendEnabled&&e.lohMinValue&&e.lohMaxValue){g=new K(e.lohMinValue,e.lohMaxValue)}const m=new U(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,p.length>0,g);const f=new pt(i,o,this.nonExonicArcRing,this.snvArcRing,this.cnvArcRing,this.lohArcRing);return new Y(this.settings,f,m,p)}}class mt{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.genome;const o=i&&i.geneset[0]&&this.settings.label.prioritizeGeneLabelsByGeneSets?i.geneset[0].lst:[];const r=t.args.data;const a=new W(this.settings,s,e);const l=new j(this.settings,a,n,o);return new gt(this.settings,l,a,n).map(r)}}mt.dtNums=[2,5,4,10,1,"exonic","non-exonic"];mt.dtAlias={1:"snv",2:"sv",3:"geneexpression",4:"cnv",5:"sv",6:"snv",7:"snv",8:"snv",9:"snv",10:"loh"};mt.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 ft{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(it.Gain);const i=t.cnvClassMap.get(it.Loss);const o=t.cnvClassMap.get(it.Cap);if(n&&i&&o){let r=0;const a=[];if(n.value>0){a.push({termid:t.cnvTitle,key:it.Gain,text:`Max: ${n.value}`,color:n.color,order:r++,border:"1px solid #ccc"})}if(i.value<0){a.push({termid:t.cnvTitle,key:it.Loss,text:`Min: ${i.value}`,color:i.color,order:r++,border:"1px solid #ccc"})}a.push({termid:t.cnvTitle,key:it.Cap,text:`Capping: ${o.value}`,color:o.color,order:r++,border:"1px solid #ccc",onClickCallback:this.onClickCallback});e.push({name:t.cnvTitle,order:s,items:a})}}mapLoh(t,e,s){if(!t.lohLegend)return;const n=[];n.push({termid:t.lohTitle,key:"min",text:"min",color:t.lohLegend.colorStartValue,order:0,border:"1px solid #ccc"});n.push({termid:t.lohTitle,key:"max",text:"max",color:t.lohLegend.colorEndValue,order:1,border:"1px solid #ccc"});e.push({name:t.lohTitle,order:s,items:n})}mapFusion(t,e,s){const n=[];n.push({termid:t.fusionTitle,key:D.Interchromosomal,text:"Interchromosomal",color:D.Interchromosomal.valueOf(),order:0,border:"1px solid #ccc"});n.push({termid:t.fusionTitle,key:D.Intrachromosomal,text:"Intrachromosomal",color:D.Intrachromosomal.valueOf(),order:1,border:"1px solid #ccc"});e.push({name:t.fusionTitle,order:s,items:n})}}class vt{constructor(t,e,s){this.fontSize=e;this.legendJSONMapper=new ft(t,s)}render(t,e,s,n,i){const o=c({holder:t.append("g"),rectFillFxn:t=>t.color,iconStroke:"#aaa"});const r={xOffset:s};const a=this.legendJSONMapper.map(e);o(a,{settings:Object.assign({},{svgw:n,svgh:i,dimensions:r,fontsize:this.fontSize})})}}class At{constructor(t,e,s){this.padAngle=t;this.innerRadius=e;this.outerRadius=s}render(t,e){const s=m().padAngle(this.padAngle).value((t=>t.size)).sort(null);const n=s(e);const i=r().innerRadius(this.innerRadius).outerRadius(this.outerRadius);const o=t.append("g");o.selectAll("path").data(n).enter().append("path").attr("d",i).attr("fill","black");o.selectAll("text").data(n).enter().append("text").attr("transform",(t=>`translate(${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 xt{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=T.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 /> `}))}if(t.cnvTooltip){t.cnvTooltip.forEach((t=>{e+=`CNV: <span style="color: ${t.color}">${t.value}</span> ${t.chr}:${t.start}-${t.stop}`}))}return e}}function Rt(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,prioritizeGeneLabelsByGeneSets:false,showPrioritizeGeneLabelsByGeneSets:false},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 bt{constructor(t){this.geneClickListener=t}render(t,e){const s=r();const n=t.append("g");const i=T.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{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=T.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 Ct{render(t,e){const s=r();const n=t.append("g");const i=T.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 yt{constructor(t){this.menuPadding=t}render(t,e){const s=r();const n=t.append("g");const i=T.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 It{constructor(t){this.type="Disco";this.opts=t;this.discoInteractions=new G(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 mt(t);const s=e.map(this.app.getState());const n=this.opts.holder;n.selectAll("*").remove();const i=new vt(t.cnv.capping,t.label.fontSize,this.discoInteractions.cappingClickCallback);const o=new $(this.getRingRenderers(t,this.discoInteractions.geneClickListener),i,this.discoInteractions.downloadClickListener,this.discoInteractions.prioritizeGenesCheckboxListener);o.render(n,s)}))}getRingRenderers(t,e){const s=new At(t.padAngle,t.rings.chromosomeInnerRadius,t.rings.chromosomeInnerRadius+t.rings.chromosomeWidth);const n=new xt(t.label.animationDuration,e);const i=new bt(e);const o=new Mt(t.rings.snvRingWidth,e);const r=new yt(t.menu.padding);const a=new Ct;const l=new Map;l.set(Q.CHROMOSOME,s);l.set(Q.LABEL,n);l.set(Q.NONEXONICSNV,i);l.set(Q.SNV,o);l.set(Q.CNV,r);l.set(Q.LOH,a);return l}}const Lt=o(It);const Et=Lt;function Ot(e){return t(this,void 0,void 0,(function*(){return{chartType:"Disco",subfolder:"disco",extension:"ts",settings:Rt(e.overrides)}}))}export{Et as componentInit,Lt as discoInit,Ot as getPlotConfig};

package/dist/app-5b6cae4a.js

@@ -0,0 +1 @@
+import{az as e,q as t,aM as s,aD as i,ae as r,k as a,ac as o,aB as l,M as n,T as d,aA as c}from"./app-91ecaaa4.js";import{b as p,i as m,g as h,a as u,s as f,n as y,v as b}from"./filter-b0fbf437.js";import{termInfoInit as v}from"./termInfo-db451d46.js";import"path";import"./table-0c558ce8.js";const g="25px";const _="root";const x=20;const T="400px";const k="termdiv",C="termchilddiv",w="termbtn",I="termlabel",S="termloading",A="termcheck";class D{constructor(e){this.type="tree";V(this);B(this);this.loadingTermSet=new Set;this.termsByCohort={};this.expandAll="expandAll"in e?e.expandAll:false}init(){this.dom={holder:this.opts.holder.append("div")}}reactsTo(e){if(e.type.startsWith("tree_"))return true;if(e.type.startsWith("filter_"))return true;if(e.type.startsWith("cohort_"))return true;if(e.type.startsWith("info_"))return true;if(e.type.startsWith("submenu_"))return true;if(e.type=="app_refresh")return true}getState(e){const t=p(e.termfilter.filter);const s={isVisible:!e.submenu.term,activeCohort:e.activeCohort,expandedTermIds:e.tree.expandedTermIds,selectedTerms:e.selectedTerms,termfilter:{filter:t},usecase:e.tree.usecase};if(e.termdbConfig.selectCohort){s.toSelectCohort=true;const t=e.termdbConfig.selectCohort.values[e.activeCohort];if(t){s.cohortValuelst=t.keys}}return s}async main(){if(!this.state.isVisible){this.dom.holder.style("display","none");return}if(this.state.toSelectCohort){if(!this.state.cohortValuelst){return}}this.termsById=this.getTermsById();const e=this.termsById[_];e.terms=await this.requestTermRecursive(e);this.dom.holder.style("display","block");this.renderBranch(e,this.dom.holder)}getTermsById(){if(!(this.state.activeCohort in this.termsByCohort)){this.termsByCohort[this.state.activeCohort]={[_]:{id:_,__tree_isroot:true}}}return this.termsByCohort[this.state.activeCohort]}async requestTermRecursive(e){const t=await this.app.vocabApi.getTermChildren(e,this.state.toSelectCohort?this.state.cohortValuelst:null);if(t.error)throw t.error;if(!t.lst||t.lst.length==0){return[]}const s=[];for(const e of t.lst){const t=Object.assign({},e);s.push(t);if(this.state.expandedTermIds.includes(t.id)){t.terms=await this.requestTermRecursive(t)}else{const e=this.termsById[t.id];if(e&&e.terms){t.terms=e.terms}}this.termsById[t.id]=t}return s}bindKey(e){return e.id}}const j=e(D);function B(e){e.renderBranch=(t,s,i)=>{if(!t||!t.terms)return;if(t.terms.length>=x){if(s.classed("sjpp_hide_scrollbar"));else{s.style("max-height",T).style("padding","10px").style("resize","vertical").classed("sjpp_hide_scrollbar",true)}}if(e.opts.disable_terms){t.terms.forEach((t=>{if(t.disabled)e.opts.disable_terms.push(t.id)}))}e.included_terms=[];if(e.state.usecase){for(const s of t.terms){if(m(s,e.state.usecase).size){e.included_terms.push(s)}}}else{e.included_terms.push(...t.terms)}if(!(t.id in e.termsById)||!e.included_terms.length){s.style("display","none");return}if(e.loadingTermSet.has(t.id)){e.loadingTermSet.delete(t.id);s.select("."+S).remove()}const r=e.state.expandedTermIds;if(!r.includes(t.id)){s.style("display","none");if(i)i.text("+");return}s.style("display","block");if(i)i.text("-");const a=s.selectAll("."+k).data(e.included_terms,e.bindKey);a.exit().each(e.hideTerm);a.each(e.updateTerm);a.enter().append("div").each(e.addTerm);for(const i of t.terms){if(r.includes(i.id)){e.renderBranch(i,s.selectAll("."+C).filter((e=>e.id==i.id)),s.selectAll("."+w).filter((e=>e.id==i.id)))}}};e.hideTerm=function(s){if(s.id in e.termsById&&e.state.expandedTermIds.includes(s.id))return;t(this).style("display","none")};e.updateTerm=function(s){const i=t(this);if(!(s.id in e.termsById)){i.style("display","none");return}const r=e.opts.disable_terms?.includes(s.id);const a=m(s,e.state.usecase);i.style("display","");const o=e.state.expandedTermIds.includes(s.id);i.select("."+w).text(o?"-":"+");i.select("."+C).style("display",o?"block":"none");const l=e.state.selectedTerms.find((e=>e.name===s.name&&e.type===s.type));i.select("."+I).style("background-color",!a.has("plot")||r?"":l?"rgba(255, 194, 10,0.5)":"#cfe2f3");i.select("."+A).style("display",a.has("plot")&&l&&!r?"inline-block":"none")};e.addTerm=async function(s){const i=e.opts.disable_terms?.includes(s.id);const r=m(s,e.state.usecase);const a=t(this).attr("class",k).style("margin",s.isleaf?"":"2px").style("padding","0px 5px");if(r.has("branch")){a.append("div").attr("class","sja_menuoption "+w).style("display","inline-block").style("padding","4px 9px").style("font-family","courier").text("+").on("click",(t=>{t.stopPropagation();e.toggleBranch(s)}));if(e.expandAll)e.toggleBranch(s)}const o=e.state.selectedTerms.find((e=>e.name===s.name&&e.type===s.type));const l=a.append("div").attr("class",I).style("display","inline-block").style("padding","5px").style("opacity",i?.4:null).text(s.name);let n;if(s.hashtmldetail){n=a.append("div").style("display","inline-block")}if(r.size>0){if(i){l.attr("class","sja_tree_click_term_disabled "+I).style("padding","5px 8px").style("margin","1px 0px").style("opacity",.4)}else if(r.has("plot")){l.attr("class","ts_pill sja_filter_tag_btn sja_tree_click_term "+I).style("color","black").style("padding","5px 8px").style("border-radius","6px").style("background-color",o?"rgba(255, 194, 10,0.5)":"#cfe2f3").style("margin","1px 0px").style("cursor","default").on("click",(()=>e.clickTerm(s)))}if(s.samplecount!==undefined){a.append("div").style("font-size",".8em").style("display","inline-block").style("margin-left","5px").style("color",s.samplecount?"#777":"#ddd").text("n="+s.samplecount)}}if(s.hashtmldetail){v({vocabApi:e.app.vocabApi,icon_holder:n,content_holder:a.append("div"),id:s.id,state:{term:s}})}if(e.opts.submit_lst){a.append("div").attr("class",A).style("color","#008000").style("display",o?"inline-block":"none").html("&check;")}if(!s.isleaf){a.append("div").attr("class",C).style("padding-left",g)}}}function V(e){e.toggleBranch=function(s){if(s.isleaf)return;const i=e.termsById[s.id];if(!i)throw"invalid term id";if(!i.terms){if(e.loadingTermSet.has(i.id))return;e.loadingTermSet.add(i.id);t(this.parentNode).selectAll("."+C).filter((e=>e.id===i.id)).style("display","block").append("div").text("Loading...").attr("class",S).style("opacity",.5).style("padding","5px")}const r=e.state.expandedTermIds.includes(s.id);const a=r?"tree_collapse":"tree_expand";e.app.dispatch({type:a,termId:s.id})};e.clickTerm=async t=>{if(e.opts.click_term2select_tvs){e.app.dispatch({type:"submenu_set",submenu:{term:t,type:"tvs"}});return}if(e.opts.click_term_wrapper){e.opts.click_term_wrapper(t);return}if(e.opts.submit_lst){const s=e.state.selectedTerms.findIndex((e=>e.name===t.name));if(s==-1){e.app.dispatch({type:"app_refresh",state:{selectedTerms:[...e.state.selectedTerms,t]}})}else{const t=e.state.selectedTerms.slice(0);t.splice(s,1);e.app.dispatch({type:"app_refresh",state:{selectedTerms:t}})}return}throw"missing term click callback"}}const N={header_mode:"search_only",activeCohort:0,tree:{usecase:{},expandedTermIds:[]},submenu:{},search:{isVisible:true},selectedTerms:[],termfilter:{filter:{type:"tvslst",in:true,join:"",lst:[]}}};class O{constructor(e){this.type="store";this.defaultState=N;s(this,e);this.prevGeneratedId=0}validateOpts(e){if(!e.state)throw".state{} missing";const t=e.state;if(t.vocab){if(t.vocab.dslabel){if(!t.vocab.genome)throw".state[.vocab].genome missing"}else if(t.vocab.genome){if(!t.vocab.dslabel)throw".state[.vocab].dslabel missing"}else{if(!Array.isArray(t.vocab.terms))throw"vocab.terms must be an array of objects"}}}validateState(){const e=this.state;if(e.tree.expandedTermIds.length==0){e.tree.expandedTermIds.push(_)}else{if(e.tree.expandedTermIds[0]!=_){e.tree.expandedTermIds.unshift(_)}}}async init(){this.state.termdbConfig=await this.app.vocabApi.getTermdbConfig();let e=h(this.state.termfilter.filter,"filterUiRoot");if(!e){this.state.termfilter.filter.tag="filterUiRoot";e=this.state.termfilter.filter}if(this.state.termdbConfig.selectCohort){let t=h(this.state.termfilter.filter,"cohortFilter");if(!t){t={tag:"cohortFilter",type:"tvs",tvs:{term:JSON.parse(JSON.stringify(this.state.termdbConfig.selectCohort.term)),values:this.state.activeCohort==-1?[]:this.state.termdbConfig.selectCohort.values[this.state.activeCohort].keys.map((e=>({key:e,label:e})))}};this.state.termfilter.filter={type:"tvslst",in:true,join:"and",lst:[t,e]}}else{const e=(e,t)=>e<t?-1:1;t.tvs.values.sort(((e,t)=>e.key<t.key?-1:1));const s=JSON.stringify(t.tvs.values.map((e=>e.key)).sort(e));const i=this.state.termdbConfig.selectCohort.values.findIndex((t=>s==JSON.stringify(t.keys.sort(e))));if(this.state.activeCohort!==-1&&this.state.activeCohort!==0&&i!==this.state.activeCohort){console.log("Warning: cohortFilter will override the state.activeCohort due to mismatch")}this.state.activeCohort=i}}else{this.state.activeCohort=-1;if(this.state.header_mode==="with_cohortHtmlSelect"){console.warn(`no termdbConfig.selectCohort to use for state.header_mode = 'with_cohortHtmlSelect'`);this.state.header_mode="search_only"}}}fromJson(e){const t=JSON.parse(e);return t}setId(e){e.$id=this.prevGeneratedId++;if(e.$lst){for(const t of e.$lst){this.setId(t)}}}}O.prototype.actions={app_refresh(e={}){this.state=this.copyMerge(this.toJson(this.state),e.state?e.state:{},this.replaceKeyVals)},cohort_set(e){this.state.activeCohort=e.activeCohort;const t=this.state.termdbConfig.selectCohort.values[e.activeCohort];const s=h(this.state.termfilter.filter,"cohortFilter");if(!s)throw`No item tagged with 'cohortFilter'`;s.tvs.values=t.keys.map((e=>({key:e,label:e})))},tree_expand(e){if(this.state.tree.expandedTermIds.includes(e.termId))return;this.state.tree.expandedTermIds.push(e.termId)},tree_collapse(e){const t=this.state.tree.expandedTermIds.indexOf(e.termId);if(t==-1)return;this.state.tree.expandedTermIds.splice(t,1)},filter_replace(e){const t=e.filter?e.filter:{type:"tvslst",join:"",in:1,lst:[]};if(!e.filter.tag){this.state.termfilter.filter=t}else{const s=h(this.state.termfilter.filter,e.filter.tag);if(!s)throw`cannot replace missing filter with tag '${e.filter.tag}'`;const i=u(this.state.termfilter.filter,s.$id);if(i==s){this.state.termfilter.filter=t}else{const e=i.lst.indexOf(s);i.lst[e]=t}}},submenu_set(e){const t=e.submenu&&e.submenu.term;if(!t){this.state.submenu={};this.state.tree.expandedTermIds=[_]}else{const s=[_];if(t.__ancestors){s.push(...t.__ancestors)}if(m(t).has("plot")){Object.assign(this.state.submenu,e.submenu)}else{s.push(t.id);delete this.state.submenu.term}this.state.tree.expandedTermIds=s}}};const E=i(O);class z{constructor(e){this.type="submenu";this.dom={holder:e.holder};P(this)}reactsTo(e){if(e.type.startsWith("submenu_"))return true;if(e.type=="app_refresh")return true}getState(e){return{type:e.submenu.type,term:e.submenu.term,termfilter:e.termfilter}}main(){if(!this.state.term){this.dom.holder.style("display","none");return}if(this.state.type=="tvs")this.showTvsMenu(this.state.term);else throw`unsupported submenu.type='${this.state.type}'`}}const R=e(z);function P(e){e.showTvsMenu=function(t){e.dom.holder.selectAll("*").remove();e.dom.holder.style("display","block").append("div").style("margin","20px").append("span").html("&laquo; Back to variable selection").attr("class","sja_clbtext").on("click",(()=>e.app.dispatch({type:"submenu_set",submenu:{}})));f({term:t,filter:e.state.termfilter.filter,holder:e.dom.holder.append("div"),vocabApi:e.app.vocabApi,debug:e.app.debug,getCategoriesArguments:e.app.opts.getCategoriesArguments,callback:e.app.opts.tree.click_term2select_tvs})}}class ${constructor(e){this.type="search";this.customEvents=["postSearch"];G(this);J(this);this.dom={holder:e.holder};this.isVisible="isVisible"in e?e.isVisible:true}async init(e){this.initUI(this.getState(e))}reactsTo(e){if(e.type=="app_refresh")return true;const t=e.type.split("_")[0];return["search","cohort","submenu"].includes(t)}getState(e){return{isVisible:!e.submenu.term&&this.isVisible,cohortStr:e.activeCohort==-1||!e.termdbConfig.selectCohort?"":e.termdbConfig.selectCohort.values[e.activeCohort].keys.slice().sort().join(","),allowedTermTypes:e.termdbConfig.allowedTermTypes||[],expandedTermIds:e.tree.expandedTermIds,selectedTerms:e.selectedTerms,usecase:e.tree.usecase,search:e.search,isGeneSetTermdb:e.termdbConfig.isGeneSetTermdb}}async main(){this.dom.holder.style("display",this.state.isVisible?"block":"none");this.renderSelectedNonDictTerms()}async doSearch(e,t){if(!e){this.clear();this.bus.emit("postSearch",[]);return}const s=await this.app.vocabApi.findTerm(e,this.state.cohortStr,this.state.usecase,t);if(!s.lst||s.lst.length==0){this.noResult()}else{this.showTerms(s)}this.bus.emit("postSearch",s)}}const q=e($);function G(e){e.initUI=t=>{e.dom.holder.style("display",e.search&&e.search.isVisible==false?"none":"block");e.dom.input=e.dom.holder.style("text-align","left").append("input").attr("type","search").attr("class","tree_search").attr("placeholder","Search"+e.getPrompt(t)).style("width","220px").style("margin","10px").style("display","block").on("input",r.debounce(e.onInput,300)).on("keyup",e.onKeyup);e.dom.input.node().focus();e.dom.resultDiv=(e.opts.resultsHolder||e.dom.holder).append("div").style("display","none").style("grid-template-columns","auto auto");const s=e.dom.resultDiv.append("div");const i=e.dom.resultDiv.append("div");e.dom.resultDiv_genes=s.append("div").style("border-left","solid 1px rgb(133,182,225)").style("margin","0px 0px 10px 10px").style("padding-left","5px");e.dom.resultDiv_terms=i.append("div").style("border-left",e.opts.resultsHolder?"":"solid 1px rgb(133,182,225)").style("margin","0px 0px 10px 10px").style("padding-left","5px");e.dom.nonDictDiv=e.dom.holder.append("div").style("margin","0px 0px 10px 10px").style("display","none");e.dom.nonDictDiv.append("div").style("font-weight",600).html("Selected genes");e.dom.selectedNonDictDiv=e.dom.nonDictDiv.append("div")};e.getPrompt=e=>{const t=e.allowedTermTypes.includes("geneVariant")&&m({type:"geneVariant"},e.usecase).has("plot");if(t)return" variables or genes";if(e.isGeneSetTermdb)return" gene sets";return" variables"};e.noResult=()=>{e.clear();e.dom.resultDiv.style("display","inline-grid");e.dom.resultDiv_terms.append("div").style("padding","3px 3px 3px 0px").style("opacity",.5).text("No match"+(e.app.vocabApi.termdbConfig?.queries?.snvindel?.allowSNPs?". Press ENTER to search SNP":""))};e.showTerms=t=>{if(e.opts.disable_terms){t.lst.forEach((t=>{if(t.disabled)e.opts.disable_terms.push(t.id)}))}e.clear();e.dom.resultDiv.style("display","inline-grid");const s=[],i=[];for(const e of t.lst){if(e.type=="geneVariant"){s.push(e)}else{i.push(e)}}if(s.length){e.dom.resultDiv_genes.append("table").selectAll().data(s).enter().append("tr").each(e.showTerm)}if(i.length){e.dom.resultDiv_terms.append("table").selectAll().data(i).enter().append("tr").each(e.showTerm)}};e.showTerm=function(s){const i=t(this);const r=i.append("td").text(s.name);const a=m(s,e.state.usecase);if((e.opts.click_term||e.app.opts?.tree?.click_term_wrapper)&&a.has("plot")){if("id"in s&&e.opts.disable_terms?.includes(s.id)){r.attr("class","sja_tree_click_term_disabled").style("display","block").style("padding","5px 8px").style("margin","1px 0px").style("opacity",.4)}else{r.attr("class","ts_pill sja_filter_tag_btn sja_tree_click_term").style("display","block").style("color","black").style("padding","5px 8px").style("border-radius","6px").style("background-color",s.type=="geneVariant"?"rgba(251,171,96,0.5)":"#cfe2f3").style("margin","1px 0px").style("cursor","default").on("click",(()=>{if(e.opts.click_term){e.opts.click_term(s)}else{e.app.opts.tree.click_term_wrapper(s)}e.clear();e.dom.input.property("value","")}))}if(s.samplecount!==undefined){i.append("td").append("div").style("font-size",".8em").style("display","inline-block").style("margin-left","5px").style("color",s.samplecount?"#777":"#ddd").text("n="+s.samplecount)}}else{r.attr("class","sja_menuoption").on("click",(()=>{e.clear();e.dom.input.property("value","");const t=[_];if(s.type=="geneVariant"&&e.opts.handleGeneVariant){e.opts.handleGeneVariant(s)}else if(y.has(s.type)){e.app.dispatch({type:"app_refresh",state:{selectedTerms:[...e.state.selectedTerms,s]}})}else{if(s.__ancestors){t.push(...s.__ancestors)}if(!e.app.vocabApi.graphable(s))t.push(s.id);e.app.dispatch({type:"app_refresh",state:{tree:{expandedTermIds:t}}})}}))}i.append("td").text(s.type=="geneVariant"?"gene variant":(s.__ancestorNames||[]).join(" > ")).style("opacity",.5).style("font-size",".7em")};e.clear=()=>{e.dom.resultDiv_genes.selectAll("*").remove();e.dom.resultDiv_terms.selectAll("*").remove();e.dom.resultDiv.style("display","none")};e.renderSelectedNonDictTerms=function(){const t=e.state.selectedTerms.filter((e=>y.has(e.type)));e.dom.nonDictDiv.style("display",t.length?"":"none");const s=e.dom.selectedNonDictDiv.selectAll("div").data(t,(e=>e.name));s.exit().remove();s.enter().append("div").style("display","inline-block").style("margin","1px").style("padding","5px 8px").style("background-color","rgba(255, 194, 10,0.5)").style("border-radius","6px").html((e=>e.name))}}function J(e){e.onKeyup=t=>{if(!a(t))return;if(!e.app.vocabApi.termdbConfig?.queries?.snvindel?.allowSNPs)return;e.onInput(t,"snp")};e.onInput=async(t,s)=>{const i=e.dom.input.property("value");try{await e.doSearch(i,s)}catch(t){e.clear();e.dom.resultDiv.style("display","inline-grid");o(e.dom.resultDiv_terms,"Error: "+(t.message||t));if(t.stack)console.log(t.stack)}}}class M{constructor(e){this.type="app";if(!e.holder)t("body").append("div");const s=e.holder.append("div").style("display",e.tree?.submit_lst?"":"none").style("text-align","center").style("margin","10px 5px");const i=s.append("button").property("disabled",true).text(this.noSelectionPrompt).on("click",(()=>this.opts.tree?.submit_lst(this.state.selectedTerms)));const r=e.holder.append("div");this.dom={holder:e.holder,treeDiv:e.holder.append("div"),customTermDiv:e.holder.append("div").style("margin","10px"),submitDiv:s,submitBtn:i,topbar:r,searchDiv:r.append("div").style("display","inline-block"),filterDiv:r.append("div").style("display","none"),errdiv:e.holder.append("div"),tip:new n({padding:"5px"})}}validateOpts(e){if(e.vocabApi);else if(e.state&&e.state.vocab){if(typeof e.state.vocab!="object")throw"opts.state.vocab{} is not an object"}else if(e.state&&e.state.genome){const t=e.state;if(!t.vocab)t.vocab={};t.vocab.genome=t.genome;delete t.genome;if(t.dslabel){t.vocab.dslabel=t.dslabel;delete t.dslabel}}else{throw"neither state.vocab{} or opts.vocabApi provided"}if(e.tree){if(e.tree.disable_terms&&!e.tree.click_term&&!e.tree.click_term2select_tvs&&(!e.barchart||!e.barchart.bar_click_override)){throw`opts.tree.disable_terms is used only when opts.tree.click_term, opts.tree.click_term2select_tvs, or opts.barchart.bar_click_override is set`}if(!e.search)e.search={};if(e.tree.click_term2select_tvs){e.search.click_term=e=>this.api.dispatch({type:"submenu_set",submenu:{term:e,type:"tvs"}})}if(e.tree.click_term){e.tree.click_term_wrapper=async t=>{if(this.state.termdbConfig.termMatch2geneSet){const e=await d("termdb",{body:{genome:this.state.vocab.genome,dslabel:this.state.vocab.dslabel,genesetByTermId:t.id}});t._geneset=e}e.tree.click_term(t)}}if(e.tree.disable_terms)e.search.disable_terms=e.tree.disable_terms}return e}async preApiFreeze(e){try{if(this.opts.vocabApi){e.vocabApi=this.opts.vocabApi}else{const t={vocab:this.opts.state.vocab||{genome:this.opts.state.genome,dslabel:this.opts.state.dslabel}};e.vocabApi=await b({app:this.api,state:t,fetchOpts:this.opts.fetchOpts})}e.appInit=W}catch(e){console.log(e);throw e}}async init(){try{this.store=await E({app:this.api,state:this.opts.state});this.state=await this.store.copyState();await this.setComponents();await this.api.dispatch()}catch(e){this.printError(e)}}async setComponents(){try{const e=this.state.nav?.header_mode;const t={search:q({app:this.api,holder:this.dom.searchDiv,isVisible:e!=="hide_search"}),tree:j({app:this.api,holder:this.dom.treeDiv,expandAll:e=="hide_search"})};if(this.opts.tree&&this.opts.tree.click_term2select_tvs){t.submenu=R({app:this.api,holder:this.dom.holder.append("div").style("display","none")})}this.components=await c(t)}catch(e){throw e}}async main(){this.api.vocabApi.main();const e=this.state.selectedTerms.length;this.dom.submitBtn.property("disabled",!e).text(!e?"Search or click term(s)":`Submit ${e} term${e>1?"s":""}`);await this.mayShowCustomTerms()}printError(e){o(this.dom.errdiv,"Error: "+(e.message||e));if(e.stack)console.log(e.stack)}async mayShowCustomTerms(){const e=await this.api.vocabApi.getCustomTerms();if(!Array.isArray(e)||e.length==0)return this.dom.customTermDiv.style("display","none");const t=[];for(const s of e){const e=m(s.term,this.state.tree.usecase);if(e.has("plot"))t.push(s)}if(t.length==0)return this.dom.customTermDiv.style("display","none");this.dom.customTermDiv.selectAll("*").remove();this.dom.customTermDiv.append("div").text("CUSTOM VARIABLES").style("font-size",".7em");for(const e of t){this.dom.customTermDiv.append("div").style("margin-bottom","3px").append("div").text(e.term.name).attr("class","sja_filter_tag_btn").style("padding","3px 6px").style("border-radius","6px").on("click",(()=>{if(!this.opts.tree)return;if(this.opts.tree.click_term){this.opts.tree.click_term(e);return}if(this.opts.tree.click_term2select_tvs){this.api.dispatch({type:"submenu_set",submenu:{term:e.term,type:"tvs"}});return}}))}}}const W=l(M);export{W as appInit};