@sjcrh/proteinpaint-client 2.14.4 → 2.16.0

package/dist/{2dmaf-cffe38b5.js → 2dmaf-3337d1ac.js}

@@ -1 +1 @@
-import{M as t,ba as e,bb as s,n as a,D as n,b7 as i,o as r,l,f as o,a as c,ay as p,aK as h,p as d,v as f,_ as u}from"./app-4b5e0214.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://pecan.stjude.cloud/static/hg19/2dmaf.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(P.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=Z.append("g").attr("transform","translate("+(_+M+I)+","+(w+X)+")");const 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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=Z.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=Z.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. 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a=ft.append("g").on("click",(()=>{s.hidden=!s.hidden;P.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,ba as e,bb as s,n as a,D as n,b7 as i,o as r,l,f as o,a as c,ay as p,aK as h,p as d,v as f,_ as u}from"./app-482b690b.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://pecan.stjude.cloud/static/hg19/2dmaf.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(P.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=Z.append("g").attr("transform","translate("+(_+M+I)+","+(w+X)+")");const 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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=Z.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=Z.append("g").attr("transform","translate(0,"+(w+X)+")");let ut=A;ft.append("text").text(u).attr("font-size",A).attr("y",ut);const mt=S(20),yt=S(x);ut+=A+yt;let gt;ft.append("text").text("SNV coverage").attr("y",ut).attr("dominant-baseline","middle").each((function(){gt=this.getBBox().width}));gt+=mt+10;ft.append("circle").attr("cx",gt).attr("cy",ut).attr("r",mt).attr("stroke","black").attr("fill","none");ft.append("text").text(20).attr("x",gt).attr("y",ut).attr("text-anchor","middle").attr("dominant-baseline","middle");gt+=mt+yt+10;ft.append("circle").attr("cx",gt).attr("cy",ut).attr("r",yt).attr("stroke","black").attr("fill","none");ft.append("text").text(x).attr("x",gt).attr("y",ut).attr("text-anchor","middle").attr("dominant-baseline","middle");ut+=yt+10;ft.append("text").text("Indel").attr("y",ut).attr("dominant-baseline","middle").each((function(){gt=this.getBBox().width}));ft.append("circle").attr("cx",gt+10+C/2).attr("cy",ut).attr("r",C/2).attr("fill","black").attr("fill-opacity",.3);ut+=30;ft.append("text").text("chrX").attr("y",ut).attr("dominant-baseline","middle").each((function(){gt=this.getBBox().width}));gt+=mt+10;ft.append("circle").attr("cx",gt).attr("cy",ut).attr("r",10).attr("stroke","black").attr("stroke-dasharray","5,5").attr("fill","none");ut+=30;ft.append("text").text("D. CNV/LOH").attr("y",ut).attr("dominant-baseline","middle").each((function(){gt=this.getBBox().width}));gt+=mt+10;ft.append("circle").attr("cx",gt).attr("cy",ut).attr("r",10).attr("stroke","black").attr("fill","none");ft.append("circle").attr("cx",gt).attr("cy",ut+10).attr("r",O).attr("fill","black");ut+=30;ft.append("text").text("R. 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a=ft.append("g").on("click",(()=>{s.hidden=!s.hidden;P.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/{app-01a5bf4f.js → app-2772b7c6.js}

@@ -1 +1 @@
-import{az as e,p as t,aL as s,aD as i,ae as r,ab as a,aB as o,M as l,S as n,aA as c}from"./app-4b5e0214.js";import{g as d,i as p,b as h,d as m,s as u,n as f,v as y}from"./filter-9fae1052.js";import{termInfoInit as b}from"./termInfo-74f89c2c.js";import"path";import"./table-46e929d8.js";const v="25px";const g="root";const _=20;const x="400px";const T="termdiv",k="termchilddiv",C="termbtn",w="termlabel",I="termloading",S="termcheck";class A{constructor(e){this.type="tree";B(this);j(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=d(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[g];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]={[g]:{id:g,__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 D=e(A);function j(e){e.renderBranch=(t,s,i)=>{if(!t||!t.terms)return;if(t.terms.length>=_){if(s.classed("sjpp_hide_scrollbar"));else{s.style("max-height",x).style("padding","10px 10px 20px 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(p(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("."+I).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("."+T).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("."+k).filter((e=>e.id==i.id)),s.selectAll("."+C).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=p(s,e.state.usecase);i.style("display","");const o=e.state.expandedTermIds.includes(s.id);i.select("."+C).text(o?"-":"+");i.select("."+k).style("display",o?"block":"none");const l=e.state.selectedTerms.find((e=>e.name===s.name&&e.type===s.type));i.select("."+w).style("background-color",!a.has("plot")||r?"":l?"rgba(255, 194, 10,0.5)":"#cfe2f3");i.select("."+S).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=p(s,e.state.usecase);const a=t(this).attr("class",T).style("margin",s.isleaf?"":"2px").style("padding","0px 5px");if(r.has("branch")){a.append("div").attr("class","sja_menuoption "+C).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",w).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 "+w).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 "+w).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){b({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",S).style("color","#008000").style("display",o?"inline-block":"none").html("&check;")}if(!s.isleaf){a.append("div").attr("class",k).style("padding-left",v)}}}function B(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("."+k).filter((e=>e.id===i.id)).style("display","block").append("div").text("Loading...").attr("class",I).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 V={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=V;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(g)}else{if(e.tree.expandedTermIds[0]!=g){e.tree.expandedTermIds.unshift(g)}}}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=m(this.state.termfilter.filter,s.$id);if(i==s){this.state.termfilter.filter=t}else{const e=i.lst.indexOf(s);i.lst[e]=t}}},submenu_set(e){const t=e.submenu&&e.submenu.term;if(!t){this.state.submenu={};this.state.tree.expandedTermIds=[g]}else{const s=[g];if(t.__ancestors){s.push(...t.__ancestors)}if(p(t).has("plot")){Object.assign(this.state.submenu,e.submenu)}else{s.push(t.id);delete this.state.submenu.term}this.state.tree.expandedTermIds=s}}};const N=i(O);class z{constructor(e){this.type="submenu";this.dom={holder:e.holder};R(this)}reactsTo(e){if(e.type.startsWith("submenu_"))return true;if(e.type=="app_refresh")return true}getState(e){return{type:e.submenu.type,term:e.submenu.term,termfilter:e.termfilter}}main(){if(!this.state.term){this.dom.holder.style("display","none");return}if(this.state.type=="tvs")this.showTvsMenu(this.state.term);else throw`unsupported submenu.type='${this.state.type}'`}}const E=e(z);function R(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:{}})));u({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 ${constructor(e){this.type="search";this.customEvents=["postSearch"];W(this);F(this);this.dom={holder:e.holder};this.isVisible="isVisible"in e?e.isVisible:true}async init(e){this.initUI(this.getState(e))}reactsTo(e){if(e.type=="app_refresh")return true;const t=e.type.split("_")[0];return["search","cohort","submenu"].includes(t)}getState(e){return{isVisible:!e.submenu.term&&this.isVisible,cohortStr:e.activeCohort==-1||!e.termdbConfig.selectCohort?"":e.termdbConfig.selectCohort.values[e.activeCohort].keys.slice().sort().join(","),allowedTermTypes:e.termdbConfig.allowedTermTypes||[],expandedTermIds:e.tree.expandedTermIds,selectedTerms:e.selectedTerms,usecase:e.tree.usecase,search:e.search}}async main(){this.dom.holder.style("display",this.state.isVisible?"block":"none");this.renderSelectedNonDictTerms()}async doSearch(e){if(!e){this.clear();this.bus.emit("postSearch",[]);return}const t=await this.app.vocabApi.findTerm(e,this.state.cohortStr,this.state.usecase);if(!t.lst||t.lst.length==0){this.noResult()}else{this.showTerms(t)}this.bus.emit("postSearch",t)}}const J=e($);function W(e){e.initUI=t=>{e.dom.holder.style("display",e.search&&e.search.isVisible==false?"none":"block");const s=t.allowedTermTypes.includes("geneVariant")?" terms or genes":"...";e.dom.input=e.dom.holder.style("text-align","left").append("input").attr("type","search").attr("class","tree_search").attr("placeholder","Search"+s).style("width","190px").style("margin","10px").style("display","block").on("input",r.debounce(e.onInput,300));e.dom.resultDiv=e.opts.resultsHolder?e.opts.resultsHolder:e.dom.holder.append("div");e.dom.resultDiv.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.noResult=()=>{e.clear();e.dom.resultDiv.append("div").text("No match").style("padding","3px 3px 3px 0px").style("opacity",.5)};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.append("table").selectAll().data(t.lst).enter().append("tr").each(e.showTerm)};e.showTerm=function(s){const i=t(this);const r=i.append("td").text(s.name);const a=p(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=[g];if(s.type=="geneVariant"&&e.opts.handleGeneVariant){e.opts.handleGeneVariant(s)}else if(f.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.selectAll("*").remove()};e.renderSelectedNonDictTerms=function(){const t=e.state.selectedTerms.filter((e=>f.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 F(e){e.onInput=async()=>{const t=e.dom.input.property("value");try{await e.doSearch(t)}catch(t){e.clear();a(e.dom.resultDiv,"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 l({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 n("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 y({app:this.api,state:t,fetchOpts:this.opts.fetchOpts})}e.appInit=H}catch(e){console.log(e);throw e}}async init(){try{this.store=await N({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:J({app:this.api,holder:this.dom.searchDiv,isVisible:e!=="hide_search"}),tree:D({app:this.api,holder:this.dom.treeDiv,expandAll:e=="hide_search"})};if(this.opts.tree&&this.opts.tree.click_term2select_tvs){t.submenu=E({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){a(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=p(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 H=o(M);export{H as appInit};
+import{az as e,p as t,aL as s,aD as i,ae as r,ab as a,aB as o,M as l,S as n,aA as d}from"./app-482b690b.js";import{b as c,i as p,g as h,a as m,s as u,n as f,v as y}from"./filter-1ccb2fdf.js";import{termInfoInit as b}from"./termInfo-46ab59d5.js";import"path";import"./table-5164f31e.js";const v="25px";const g="root";const _=20;const x="400px";const T="termdiv",k="termchilddiv",C="termbtn",w="termlabel",I="termloading",S="termcheck";class A{constructor(e){this.type="tree";B(this);j(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=c(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[g];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]={[g]:{id:g,__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 D=e(A);function j(e){e.renderBranch=(t,s,i)=>{if(!t||!t.terms)return;if(t.terms.length>=_){if(s.classed("sjpp_hide_scrollbar"));else{s.style("max-height",x).style("padding","10px 10px 20px 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(p(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("."+I).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("."+T).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("."+k).filter((e=>e.id==i.id)),s.selectAll("."+C).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=p(s,e.state.usecase);i.style("display","");const o=e.state.expandedTermIds.includes(s.id);i.select("."+C).text(o?"-":"+");i.select("."+k).style("display",o?"block":"none");const l=e.state.selectedTerms.find((e=>e.name===s.name&&e.type===s.type));i.select("."+w).style("background-color",!a.has("plot")||r?"":l?"rgba(255, 194, 10,0.5)":"#cfe2f3");i.select("."+S).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=p(s,e.state.usecase);const a=t(this).attr("class",T).style("margin",s.isleaf?"":"2px").style("padding","0px 5px");if(r.has("branch")){a.append("div").attr("class","sja_menuoption "+C).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",w).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 "+w).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 "+w).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){b({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",S).style("color","#008000").style("display",o?"inline-block":"none").html("&check;")}if(!s.isleaf){a.append("div").attr("class",k).style("padding-left",v)}}}function B(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("."+k).filter((e=>e.id===i.id)).style("display","block").append("div").text("Loading...").attr("class",I).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 V={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=V;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(g)}else{if(e.tree.expandedTermIds[0]!=g){e.tree.expandedTermIds.unshift(g)}}}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=m(this.state.termfilter.filter,s.$id);if(i==s){this.state.termfilter.filter=t}else{const e=i.lst.indexOf(s);i.lst[e]=t}}},submenu_set(e){const t=e.submenu&&e.submenu.term;if(!t){this.state.submenu={};this.state.tree.expandedTermIds=[g]}else{const s=[g];if(t.__ancestors){s.push(...t.__ancestors)}if(p(t).has("plot")){Object.assign(this.state.submenu,e.submenu)}else{s.push(t.id);delete this.state.submenu.term}this.state.tree.expandedTermIds=s}}};const N=i(O);class z{constructor(e){this.type="submenu";this.dom={holder:e.holder};R(this)}reactsTo(e){if(e.type.startsWith("submenu_"))return true;if(e.type=="app_refresh")return true}getState(e){return{type:e.submenu.type,term:e.submenu.term,termfilter:e.termfilter}}main(){if(!this.state.term){this.dom.holder.style("display","none");return}if(this.state.type=="tvs")this.showTvsMenu(this.state.term);else throw`unsupported submenu.type='${this.state.type}'`}}const E=e(z);function R(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:{}})));u({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 ${constructor(e){this.type="search";this.customEvents=["postSearch"];W(this);F(this);this.dom={holder:e.holder};this.isVisible="isVisible"in e?e.isVisible:true}async init(e){this.initUI(this.getState(e))}reactsTo(e){if(e.type=="app_refresh")return true;const t=e.type.split("_")[0];return["search","cohort","submenu"].includes(t)}getState(e){return{isVisible:!e.submenu.term&&this.isVisible,cohortStr:e.activeCohort==-1||!e.termdbConfig.selectCohort?"":e.termdbConfig.selectCohort.values[e.activeCohort].keys.slice().sort().join(","),allowedTermTypes:e.termdbConfig.allowedTermTypes||[],expandedTermIds:e.tree.expandedTermIds,selectedTerms:e.selectedTerms,usecase:e.tree.usecase,search:e.search}}async main(){this.dom.holder.style("display",this.state.isVisible?"block":"none");this.renderSelectedNonDictTerms()}async doSearch(e){if(!e){this.clear();this.bus.emit("postSearch",[]);return}const t=await this.app.vocabApi.findTerm(e,this.state.cohortStr,this.state.usecase);if(!t.lst||t.lst.length==0){this.noResult()}else{this.showTerms(t)}this.bus.emit("postSearch",t)}}const J=e($);function W(e){e.initUI=t=>{e.dom.holder.style("display",e.search&&e.search.isVisible==false?"none":"block");const s=t.allowedTermTypes.includes("geneVariant")&&p({type:"geneVariant"},t.usecase).has("plot");const i=s?" variables or genes":" variables";e.dom.input=e.dom.holder.style("text-align","left").append("input").attr("type","search").attr("class","tree_search").attr("placeholder","Search"+i).style("width","220px").style("margin","10px").style("display","block").on("input",r.debounce(e.onInput,300));e.dom.resultDiv=(e.opts.resultsHolder||e.dom.holder).append("div").style("display","none").style("grid-template-columns","auto auto");const a=e.dom.resultDiv.append("div");const o=e.dom.resultDiv.append("div");e.dom.resultDiv_genes=a.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=o.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.noResult=()=>{e.clear();e.dom.resultDiv.style("display","inline-grid");e.dom.resultDiv_terms.append("div").text("No match").style("padding","3px 3px 3px 0px").style("opacity",.5)};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=p(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=[g];if(s.type=="geneVariant"&&e.opts.handleGeneVariant){e.opts.handleGeneVariant(s)}else if(f.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=>f.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 F(e){e.onInput=async()=>{const t=e.dom.input.property("value");try{await e.doSearch(t)}catch(t){e.clear();e.dom.resultDiv.style("display","inline-grid");a(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 l({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 n("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 y({app:this.api,state:t,fetchOpts:this.opts.fetchOpts})}e.appInit=U}catch(e){console.log(e);throw e}}async init(){try{this.store=await N({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:J({app:this.api,holder:this.dom.searchDiv,isVisible:e!=="hide_search"}),tree:D({app:this.api,holder:this.dom.treeDiv,expandAll:e=="hide_search"})};if(this.opts.tree&&this.opts.tree.click_term2select_tvs){t.submenu=E({app:this.api,holder:this.dom.holder.append("div").style("display","none")})}this.components=await d(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){a(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=p(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 U=o(M);export{U as appInit};

package/dist/app-3fa81075.js

@@ -0,0 +1 @@
+import{az as t,M as e,ae as s,p as o,ab as i,aA as r,S as a,aB as n,a0 as l}from"./app-482b690b.js";import{r as p,s as c}from"./recover-dfa531ec.js";import{g as d,f as h,v as m}from"./filter-1ccb2fdf.js";import{c as u,g as f}from"./sampleScatter.interactivity-6f5f1c97.js";import{r as b}from"./table-5164f31e.js";import{summaryInit as y}from"./summary-3a6cdf42.js";import"path";import"./samplelst-51b9b98c.js";import"./termsetting-ebf19198.js";import"./app-2772b7c6.js";import"./termInfo-46ab59d5.js";import"./violin-126a3e77.js";import"./controls-48e2636c.js";import"./controls.btns-f3b13ad7.js";import"./controls.config-f7078e66.js";import"./controls.overlay-7c4f8fb1.js";import"./controls.term1-f9cf1245.js";import"./controls.divide-cf4d189e.js";import"./violin.renderer-2a9a71dc.js";import"./brush-4b8de14c.js";import"./pointer-c7475677.js";import"./nodrag-ed453278.js";import"./transform-f2cc07e6.js";import"./axis-6cb4f314.js";import"./area-db27c86c.js";import"./line-d0284126.js";import"./constant-426a1483.js";import"./log-790cfc41.js";import"./html.legend-cb566ed8.js";import"./violin.interactivity-9d1edfdb.js";import"./barchart-49f1cafc.js";import"./bars.settings-f7884503.js";import"./bars.renderer-f340711b.js";import"./svg.legend-e8afe260.js";import"./barchart.events-a4483ff2.js";import"./sampleScatter-2ffb7d55.js";import"./sampleScatter.renderer-73f34c44.js";import"./zoom-e9ac04aa.js";import"./lasso-a1000d68.js";import"./drag-263332ba.js";import"./symbol-fc7cbd41.js";import"./math-2fb199c6.js";class v{constructor(t){this.type="search";j(this);x(this)}async init(t){this.dom={holder:this.opts.holder,holderNode:this.opts.holder.node(),tip:new e({padding:"5px"})};this.initUI()}reactsTo(t){return t.type.startsWith("search")||t.type.startsWith("cohort")}getState(t){return{cohortStr:t.activeCohort==-1||!t.termdbConfig.selectCohort?"":t.termdbConfig.selectCohort.values[t.activeCohort].keys.slice().sort().join(","),search:t.search}}async main(){this.dom.holder.style("display",this.state.search.isVisible?"inline-block":"none")}async doSearch(t){if(!t){this.clear({hide:true});this.bus.emit("postSearch",[]);return}const e=await this.app.vocabApi.findTerm(t,this.state.cohortStr,this.opts.usecase);if(!e.lst||e.lst.length==0){this.noResult()}else{this.showTerms(e)}this.bus.emit("postSearch",e)}}const g=t(v);function j(t){t.initUI=()=>{t.dom.holder.style("display",t.search&&t.search.isVisible==false?"none":"inline-block");t.dom.input=t.dom.holder.style("text-align","center").append("input").attr("type","search").attr("class","tree_search").attr("placeholder","Search").style("width","180px").style("display","block").on("input",s.debounce(t.onInput,300));t.dom.resultDiv=t.dom.tip.d.style("border-left",t.opts.resultsHolder?"":"solid 1px rgb(133,182,225)").style("padding-left","5px")};t.noResult=()=>{t.clear();t.dom.resultDiv.append("div").text("No match").style("padding","3px 3px 3px 0px").style("opacity",.5)};t.showTerms=e=>{if(t.opts.disable_terms)e.lst.forEach((e=>{if(e.disabled)t.opts.disable_terms.push(e.id)}));t.clear({hide:!e.lst.length});if(e.lst.length){t.dom.resultDiv.append("table").selectAll().data(e.lst).enter().append("tr").each(t.showTerm)}};t.showTerm=function(e){const s=o(this);const i=s.append("td").text(e.name);if(e.type){i.style("cursor","pointer").attr("class","sja_menuoption").on("click",(()=>{t.app.dispatch({type:"plot_create",config:{chartType:e.type=="survival"?"survival":"summary",term:{id:e.id,term:e}}});t.clear({hide:true})}))}else{i.style("padding","5px 10px").style("opacity",.5)}s.append("td").text((e.__ancestorNames||[]).join(" > ")).style("opacity",.5).style("font-size",".7em")};t.clear=(e={})=>{t.dom.tip.clear();if(e.hide)t.dom.tip.hide();else t.dom.tip.showunder(t.dom.holderNode)}}function x(t){t.onInput=async()=>{const e=t.dom.input.property("value");try{await t.doSearch(e)}catch(e){t.clear();i(t.dom.resultDiv,"Error: "+(e.message||e));if(e.stack)console.log(e.stack)}}}let w=0;const C="_MASS_AUTOID_"+Math.random().toString().slice(-6);let k=(+new Date).toString().slice(-8);const D=new e({padding:"0px",offsetX:0,offsetY:0});D.d.style("z-index",5555);const S={top:"COHORT",mid:"NONE",btm:"",subheader:"cohort"};const _={top:"CHARTS",mid:"NONE",btm:"",subheader:"charts"};const T={top:"GROUPS",mid:"NONE",btm:"",subheader:"groups"};const N={top:"FILTER",mid:"NONE",btm:"",subheader:"filter"};function O(){return C+"_"+k++}class A{constructor(t){this.type="nav";this.instanceNum=w++;this.activeTab=0;this.activeCohort=0;this.searching=false;this.samplecounts={};this.massSessionDuration=t.massSessionDuration;this.sessionDaysLeft=t.app.opts.sessionDaysLeft||null;this.sessionId=t.app.opts.sessionId||null;L(this);E(this)}async init(t){try{this.cohortFilter=d(t.termfilter.filter,"cohortFilter");this.initUI(t);this.initCohort(t);this.components=await r({search:g({app:this.app,holder:this.dom.searchDiv,usecase:{target:"barchart",detail:"term"}}),filter:h({app:this.app,vocabApi:this.app.vocabApi,holder:this.dom.subheader.filter.append("div"),hideLabel:this.opts.header_mode==="with_tabs",emptyLabel:"+Add new filter",callback:t=>{this.app.dispatch({type:"filter_replace",filter:t})}}),charts:u({app:this.app,holder:this.dom.subheader.charts,vocab:this.opts.vocab}),groups:f({app:this.app,holder:this.dom.subheader.groups,vocab:this.opts.vocab}),recover:p({app:this.app,holder:this.dom.recoverDiv,getState:t=>t,reactsTo:t=>t.type!="plot_edit",maxHistoryLen:5})});this.mayShowMessage_sessionDaysLeft()}catch(t){throw t}}reactsTo(t){if(t.type.includes("cache_termq"))return true;if(t.type.startsWith("filter"))return true;if(t.type.startsWith("cohort"))return true;if(t.type.startsWith("tab"))return true;if(t.type=="plot_create")return true;if(t.type=="plot_delete")return true;if(t.type=="app_refresh")return true;if(t.type.endsWith("_customTerm"))return true}getState(t){return{searching:this.searching,nav:t.nav,activeCohort:t.activeCohort,termdbConfig:t.termdbConfig,filter:t.termfilter.filter,plots:t.plots,groups:t.groups}}async main(){this.dom.tabDiv.style("display",this.state.nav.header_mode==="with_tabs"?"inline-block":"none");this.dom.tip.hide();this.activeTab=this.state.nav.activeTab;this.prevCohort=this.activeCohort;this.activeCohort=+this.state.activeCohort;this.filterUiRoot=d(this.state.filter,"filterUiRoot");this.cohortFilter=d(this.state.filter,"cohortFilter");if(this.cohortNames){this.activeCohortName=this.cohortNames[this.activeCohort];if(this.activeCohort!==-1)this.activeCohortLabel=this.state.termdbConfig.selectCohort.values[this.activeCohort].shortLabel}this.filterJSON=JSON.stringify(this.state.filter);this.cohortsData=await this.app.vocabApi.getCohortsData();if(this.state.nav.header_mode==="with_tabs"){if(!(this.activeCohortName in this.samplecounts)){this.samplecounts[this.activeCohortName]=await this.app.vocabApi.getCohortSampleCount(this.activeCohortName)}if(!(this.filterJSON in this.samplecounts)){if(!this.filterUiRoot||!this.filterUiRoot.lst.length){this.samplecounts[this.filterJSON]=this.samplecounts[this.activeCohortName]}else{const t=await this.app.vocabApi.getFilteredSampleCount(this.filterJSON);this.samplecounts[this.filterJSON]=t}}}this.updateUI()}}const I=t(A);function E(t){t.initUI=s=>{const o=t.opts.holder.append("div").style("white-space","nowrap");const i=o.append("div").style("display","none").style("vertical-align","bottom");const r=o.append("div").style("vertical-align","top").style("margin","10px").style("display","inline-block");t.dom={holder:t.opts.holder,header:o,tabDiv:i,controlsDiv:r,searchDiv:r.append("div").style("margin","10px"),sessionDiv:r.append("div").style("display","inline-block"),recoverDiv:r.append("div").style("display","inline-block"),helpDiv:r.append("div").style("display","none"),sessionElapsedMessageDiv:r.append("div").style("display","none"),subheaderDiv:t.opts.holder.append("div").style("display","block").style("padding-top","5px").style("border-bottom","1px solid #000"),messageDiv:t.opts.holder.append("div").style("margin","30px").style("display","none"),tip:new e({padding:"5px"})};if(t.opts.header_mode==="with_cohortHtmlSelect"){t.dom.cohortStandaloneDiv=o.append("div").style("display","inline-block").style("margin","10px").style("vertical-align","top");t.dom.cohortStandaloneDiv.append("label").html("Cohort: ");t.dom.cohortSelect=t.dom.cohortStandaloneDiv.append("select").on("change",(function(){t.app.dispatch({type:"cohort_set",activeCohort:+this.value})}));t.dom.cohortSelect.selectAll("option").data(s.termdbConfig.selectCohort.values).enter().append("option").attr("value",((t,e)=>e)).property("selected",((t,e)=>e===s.activeCohort)).html((t=>t.shortLabel))}t.dom.subheader=Object.freeze({search:t.dom.subheaderDiv.append("div").style("display","none"),groups:t.dom.subheaderDiv.append("div").style("display","none"),charts:t.dom.subheaderDiv.append("div").style("display","none"),cohort:t.dom.subheaderDiv.append("div").style("display","none"),filter:t.dom.subheaderDiv.append("div").style("display","none"),cart:t.dom.subheaderDiv.append("div").style("display","none").html("<br/>Cart feature under construction - work in progress<br/>&nbsp;<br/>")});t.tabs=[_,T,N];if(s.termdbConfig.selectCohort)t.tabs.unshift(S);const a=t.dom.tabDiv.append("table").style("border-collapse","collapse");a.selectAll("tr").data(["top","mid","btm"]).enter().append("tr").style("font-size",((t,e)=>e==1?"20px":"12px")).selectAll("td").data(((e,s)=>t.tabs.map(((t,o)=>({rowNum:s,key:e,colNum:o,label:t[e],subheader:t.subheader}))))).enter().append("td").style("display","none").style("width","100px").style("padding",(t=>t.rowNum===0?"12px 12px 3px 12px":"3px 12px")).style("text-align","center").style("border-left","1px solid #ccc").style("border-right","1px solid #ccc").style("color","#aaa").style("cursor","pointer").html((t=>t.label)).on("click",t.setTab);t.dom.trs=a.selectAll("tr");t.dom.tds=a.selectAll("td");t.subheaderKeys=t.tabs.map((t=>t.subheader));t.dom.saveBtn=t.dom.sessionDiv.append("button").style("margin","10px").text("New Session").on("click",t.getSessionUrl);if(t.sessionDaysLeft!=null){t.dom.fileBtn=t.dom.sessionDiv.append("button").style("margin","10px").text("Export Session").on("click",(e=>{t.getSessionFile(e)}))}const n=s.termdbConfig.helpPages;if(n){t.dom.helpBtn=t.dom.helpDiv.style("display","inline-block").append("button").style("margin","10px").html("Help &#9660;").on("click",(t=>{const e=t.target.getBoundingClientRect();const s=D.clear().show(e.left-0,e.top+e.height+5).d.append("div");for(const t of n){s.append("div").style("margin","15px").append("a").attr("href",t.url).attr("target","_blank").text(t.label)}}))}};t.mayShowMessage_sessionDaysLeft=()=>{if(!Number.isFinite(t.sessionDaysLeft)){return}t.dom.sessionElapsedMessageDiv.style("display","block");t.dom.remainingDaysMessage=t.dom.sessionElapsedMessageDiv.append("div").style("display","block").style("opacity","0.65").html(`<u>${t.sessionDaysLeft} days</u> left till this session is removed. Click the New Session button to create a new one.`)};t.updateUI=async(e=false)=>{if(!t.dom.subheaderDiv)return;if(t.activeTab&&t.state.termdbConfig.selectCohort&&t.activeCohort==-1){t.dom.subheaderDiv.style("display","none");t.dom.messageDiv.selectAll("text").remove();t.dom.messageDiv.style("display","").text('No cohort selected. Please select a cohort in the "COHORT" tab.')}else{let s="block";if(e){s=t.dom.subheaderDiv.style("display")=="none"?"block":"none"}if(t.dom.subheaderDiv)t.dom.subheaderDiv.style("display",s);if(t.dom.messageDiv)t.dom.messageDiv.style("display","none")}const s=t.state.termdbConfig.selectCohort;t.dom.searchDiv.style("display",s&&t.activeCohort==-1?"none":"inline-block");t.dom.holder.style("margin-bottom",t.state.nav.header_mode==="with_tabs"?"20px":"");t.dom.header.style("border-bottom",t.state.nav.header_mode==="with_tabs"?"1px solid #000":"");t.dom.tds.style("display","").style("color",(e=>e.colNum==t.activeTab?"#000":"#aaa")).style("background-color",(e=>e.colNum==t.activeTab?"#ececec":"transparent")).html((function(e,s){if(e.key=="top")return this.innerHTML;if(e.subheader=="groups"){if(e.key=="mid")return t.state.groups.length||"NONE";return""}if(e.subheader==="charts"){const s=t.state.plots.length;if(e.key=="mid")return!s?"NONE":s;else return""}else if(e.subheader==="cohort"){if(t.activeCohortName&&t.activeCohortName in t.samplecounts){return e.key=="top"?this.innerHTML:e.key=="mid"?t.activeCohortLabel:"n="+t.samplecounts[t.activeCohortName]}else{return e.key=="mid"?"NONE":this.innerHTML}}else if(e.subheader==="filter"){const s=t.filterUiRoot?t.filterUiRoot:{lst:[]};if(s.lst.length===0){return e.key==="mid"?"NONE":t.samplecounts["undefined"]?`n=${t.samplecounts["undefined"]}`:""}else{const o=t.samplecounts[t.filterJSON]!=undefined?"n="+t.samplecounts[t.filterJSON]:"";return e.key==="mid"?s.lst.length:o}}else{return e.key==="mid"?this.innerHTML:"&nbsp;"}}));for(const e in t.dom.subheader){t.dom.subheader[e].style("display",t.tabs[t.activeTab].subheader===e?"block":"none")}t.renderCohortsTable();if(t.opts.header_mode==="with_cohort_select"){t.dom.cohortSelect.selectAll("option").property("value",appState.activeCohort)}};t.renderCohortsTable=()=>{if(!t.dom.cohortTable)return;t.dom.cohortTable.selectAll("*").remove();const e=[{label:"Feature"}];const s=[];const o=t.cohortsData;if("error"in o)throw o.error;for(const t of o.features)s.push([{value:t.name}]);for(const t of o.cohorts){e.push({label:t.cohort?`${t.name} (${t.cohort})`:t.name});for(const[e,i]of o.features.entries()){const r=o.cfeatures.find((e=>e.idfeature===i.idfeature&&e.cohort===t.cohort));if(r)s[e].push({value:r.value})}}b({rows:s,columns:e,div:t.dom.cohortTable,showLines:false,maxHeight:"60vh"});t.dom.cohortTable.select("table").style("border-collapse","collapse");t.dom.cohortTable.selectAll(`tbody > tr > td`).style("background-color","transparent");const i=t.state.termdbConfig.selectCohort;const r=i.values[t.activeCohort].keys;let a=`tbody > tr > td:nth-child(${t.activeCohort+2})`;const n=r.length>1;if(n){a="";for(const t of r){const e=o.cohorts.map((t=>t.cohort)).indexOf(t);if(a!=="")a+=",";a+=`tbody > tr > td:nth-child(${e+2})`}}const l=t.dom.cohortTable.selectAll(a);l.style("background-color","yellow");t.dom.cohortInputs.property("checked",((e,s)=>s===t.activeCohort))};t.initCohort=async e=>{const s=e.termdbConfig.selectCohort;if(!s)return;t.dom.tds.filter((t=>t.colNum===0)).style("display","");t.cohortNames=s.values.map((t=>t.keys.slice().sort().join(",")));if(s.title){t.dom.cohortTitle=t.dom.subheader.cohort.append("h2").style("margin-left","10px").text(s.title)}if(s.description){t.dom.cohortDescription=t.dom.subheader.cohort.append("div").style("margin-left","10px").html(s.description)}if(s.prompt){t.dom.cohortPrompt=t.dom.subheader.cohort.append("div").style("margin-left","10px").style("padding-top","30px").style("padding-bottom","10px").style("font-weight","bold").text(s.prompt)}t.dom.cohortOpts=t.dom.subheader.cohort.append("div").style("margin-bottom","30px").style("margin-left","10px");t.dom.cohortOpts.append("table").selectAll("tr").data(s.values).enter().append("tr").each((function(e,s){const i=o(this);const r=i.append("td");const a="sja-termdb-cohort-"+t.instanceNum;const n=a+"-"+s;r.append("input").attr("type","radio").attr("name",a).attr("id",n).attr("value",s).property("checked",s===t.activeCohort).style("margin-right","5px").style("margin-left","0px").on("click",(()=>{t.app.dispatch({type:"cohort_set",activeCohort:s})}));r.append("label").attr("for",n).attr("colspan",2).style("cursor","pointer").html((t=>t.label));i.selectAll("td").style("max-width","600px").style("padding-bottom","10px").style("padding-right","20px").style("vertical-align","top")}));t.dom.cohortInputs=t.dom.cohortOpts.selectAll("input");t.dom.cohortTable=t.dom.subheader.cohort.append("div");if(s.asterisk){t.dom.cohortAsterisk=t.dom.subheader.cohort.append("div").style("margin-left","10px").style("padding-top","20px").style("padding-bottom","20px").style("font-size","small").text(s.asterisk)}}}function L(t){t.setTab=async(e,s)=>{if(s.colNum===t.activeTab&&!t.searching){t.prevCohort=t.activeCohort;await t.updateUI(true);if(t.bus)t.bus.emit("postRender");return}t.activeTab=s.colNum;t.searching=false;t.app.dispatch({type:"tab_set",activeTab:t.activeTab});if(t.activeTab==1&&t.activeCohort!=-1&&!t.state.plots.length){t.app.dispatch({type:"plot_create",id:O(),config:{chartType:"dictionary"}})}};t.getSessionUrl=async()=>{t.dom.saveBtn.property("disabled",true);const e=await a("/massSession",{method:"POST",body:JSON.stringify(t.app.getState())});const s=sessionStorage.getItem("hostURL")||`${window.location.protocol}//${window.location.host}`;const o=`${s}/?mass-session-id=${e.id}&noheader=1`;t.dom.tip.clear().showunder(t.dom.saveBtn.node());t.dom.tip.d.append("div").style("margin","10px").html(`<a href='${o}' target=_blank>${e.id}</a><br><div style="font-size:.8em;opacity:.6"><span>Click the link to recover this session. Bookmark or share this link.</span><br><span>This session will be saved for ${t.massSessionDuration} days.</span></div>`);setTimeout((()=>{t.dom.saveBtn.property("disabled",false)}),1e3)};t.getSessionFile=async e=>{const s=await a(`/massSession?id=${t.sessionId}`);const o=document.createElement("a");const i="data:application/json;charset=utf-8,"+encodeURIComponent(JSON.stringify(s.state));o.setAttribute("href",i);o.download=`${t.sessionId}.json`;o.click();o.remove()}}function U(t){switch(t){case"../plots/barchart.data.js":return import("./filter-1ccb2fdf.js").then((function(t){return t.p}));case"../plots/barchart.events.js":return import("./barchart.events-a4483ff2.js");case"../plots/barchart.js":return import("./barchart-49f1cafc.js");case"../plots/bars.renderer.js":return import("./bars.renderer-f340711b.js");case"../plots/bars.settings.js":return import("./bars.settings-f7884503.js");case"../plots/boxplot.js":return import("./boxplot-59248be2.js");case"../plots/controls.btns.js":return import("./controls.btns-f3b13ad7.js");case"../plots/controls.config.js":return import("./controls.config-f7078e66.js");case"../plots/controls.divide.js":return import("./controls.divide-cf4d189e.js");case"../plots/controls.js":return import("./controls-48e2636c.js");case"../plots/controls.overlay.js":return import("./controls.overlay-7c4f8fb1.js");case"../plots/controls.term1.js":return import("./controls.term1-f9cf1245.js");case"../plots/cuminc.js":return import("./cuminc-a6fac3f8.js");case"../plots/dataDownload.js":return import("./dataDownload-5d810204.js");case"../plots/dictionary.js":return import("./dictionary-80477bad.js");case"../plots/geneExpression.js":return import("./geneExpression-99a9f04b.js");case"../plots/genomeBrowser.controls.js":return import("./genomeBrowser.controls-e2898a27.js");case"../plots/genomeBrowser.js":return import("./genomeBrowser-4350e043.js");case"../plots/matrix.cells.js":return import("./matrix.cells-0f33d758.js");case"../plots/matrix.cluster.js":return import("./matrix.cluster-d80f11c8.js");case"../plots/matrix.config.js":return import("./matrix.config-7ce54e91.js");case"../plots/matrix.controls.js":return import("./matrix.controls-59b34304.js");case"../plots/matrix.dom.js":return import("./matrix.dom-85fda536.js");case"../plots/matrix.interactivity.js":return import("./matrix.interactivity-4ef817fc.js");case"../plots/matrix.js":return import("./matrix-0c17eaa9.js");case"../plots/matrix.renderers.js":return import("./matrix.renderers-f5467d3d.js");case"../plots/matrix.sort.js":return import("./matrix.sort-bd339df2.js");case"../plots/plot.app.js":return import("./plot.app-3f69805c.js");case"../plots/regression.inputs.js":return import("./regression.inputs-dc4eaef6.js").then((function(t){return t.b}));case"../plots/regression.inputs.term.js":return import("./regression.inputs-dc4eaef6.js").then((function(t){return t.a}));case"../plots/regression.inputs.values.table.js":return import("./regression.inputs.values.table-fb834ded.js");case"../plots/regression.js":return import("./regression.inputs-dc4eaef6.js").then((function(t){return t.r}));case"../plots/regression.results.js":return import("./regression.results-a5e6db19.js");case"../plots/sampleScatter.interactivity.js":return import("./sampleScatter.interactivity-6f5f1c97.js").then((function(t){return t.b}));case"../plots/sampleScatter.js":return import("./sampleScatter-2ffb7d55.js");case"../plots/sampleScatter.renderer.js":return import("./sampleScatter.renderer-73f34c44.js");case"../plots/scatter.js":return import("./scatter-c93fe9bf.js");case"../plots/stattable.js":return import("./stattable-2635a1f2.js");case"../plots/summary.js":return import("./summary-3a6cdf42.js");case"../plots/survival.js":return import("./survival-e21d1c08.js");case"../plots/table.js":return import("./table-14674994.js");case"../plots/variantBrowser.js":return import("./variantBrowser-95376df8.js");case"../plots/violin.interactivity.js":return import("./violin.interactivity-9d1edfdb.js");case"../plots/violin.js":return import("./violin-126a3e77.js");case"../plots/violin.renderer.js":return import("./violin.renderer-2a9a71dc.js");default:return new Promise((function(e,s){(typeof queueMicrotask==="function"?queueMicrotask:setTimeout)(s.bind(null,new Error("Unknown variable dynamic import: "+t)))}))}}class R{constructor(t){this.type="plot";B(this);this.initUi(t)}reactsTo(t){if(t.type.includes("cache_termq"))return true;if(t.type.startsWith("plot_")){return t.id===this.id}if(t.type.startsWith("filter"))return true;if(t.type.startsWith("cohort"))return true;if(t.type=="app_refresh")return true;if(t.type.endsWith("customTerm"))return true}getState(t){const e=t.plots.find((t=>t.id===this.id));if(!e){throw`No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`}return{config:e,_scope_:t._scope_}}async main(){this.dom.errdiv.style("display","none");if(!this.components)await this.setComponents(this.opts)}async setComponents(t){this.components={recover:await p({app:this.app,holder:this.dom.localRecoverDiv,getState:t=>this.getState(t),reactsTo:t=>t.id==this.id&&(t.type=="plot_edit"||t.type=="plot_nestedEdits")&&t._track_!="none",plot_id:this.id,maxHistoryLen:10})};const e=await U(`../plots/${t.chartType}.js`);this.components.chart=await e.componentInit({app:this.app,holder:this.dom.viz,header:this.dom.paneTitleDiv,id:this.id})}destroy(){this.dom.holder.app_div.selectAll("*").remove();this.dom.holder.app_div.remove();for(const t in this.dom){delete this.dom[t]}}}const $=t(R);function B(t){t.initUi=function(s){const o=s.holder;o.header.style("padding",0);try{t.dom={tip:new e({padding:"0px"}),holder:o,paneTitleDiv:o.header.append("div").style("display","inline-block").style("color","#999").style("padding-left","7px").style("vertical-align","sub"),localRecoverDiv:o.header.append("div").style("display","inline-block"),body:o.body.style("white-space","nowrap").style("overflow-x","auto"),errdiv:o.body.append("div").style("display","none").style("padding","5px").style("background-color","rgba(255,100,100,0.2)"),viz:o.body.append("div")}}catch(e){t.dom.errdiv.style("display","none").text(e)}}}class M{constructor(t){if(t.addLoginCallback){t.addLoginCallback((()=>this.api.dispatch({type:"app_refresh"})))}this.type="app";this.dom={holder:t.holder,topbar:t.holder.append("div"),errdiv:t.holder.append("div"),plotDiv:t.holder.append("div")};this.plotIdToSandboxId={}}validateOpts(t={}){if(!t.holder)throw`missing opts.holder in the MassApp constructor argument`;if(!t.callbacks)t.callbacks={};if(!t.state.vocab)t.state.vocab={};if(typeof t.state.vocab!="object")throw"opts.state.vocab{} is not an object";if(t.state.genome){t.state.vocab.genome=t.state.genome;delete t.state.genome}if(t.state.dslabel){t.state.vocab.dslabel=t.state.dslabel;delete t.state.dslabel}return t}async preApiFreeze(t){try{t.tip=new e({padding:"5px"});t.printError=t=>this.printError(t);const s=this.opts.state.vocab;t.vocabApi=await m({app:t,state:{vocab:this.opts.state.vocab},fetchOpts:this.opts.fetchOpts,getDatasetAccessToken:this.opts.getDatasetAccessToken});this.opts.state.vocab=t.vocabApi.vocab}catch(t){throw t}}async init(){try{const t="debounceInterval"in this.opts?this.opts.debounceInterval:0;this.store=await c({app:this.api,state:this.opts.state,debounceInterval:t});this.state=await this.store.copyState();this.components={};if(this.state.nav.header_mode!="hidden"){this.components.nav=await I({app:this.api,holder:this.dom.topbar,header_mode:this.state&&this.state.nav&&this.state.nav.header_mode,vocab:this.state.vocab,massSessionDuration:this.state.termdbConfig.massSessionDuration})}this.components.plots={};await this.api.dispatch()}catch(t){this.printError(t);throw t}}async main(){await this.api.vocabApi.main();const t={};let e;for(const s of this.state.plots){if(!(s.id in this.components.plots)){e=l(this.dom.plotDiv,{close:()=>{this.api.dispatch({type:"plot_delete",id:s.id})},plotId:s.id,beforePlotId:s.insertBefore||null,style:{width:"98.5%"}});if(s.chartType=="summary")t[s.id]=y(Object.assign({app:this.api,holder:e},s));else t[s.id]=$(Object.assign({app:this.api,holder:e},s))}}const s=Object.keys(t).length;if(s){await Promise.all(Object.values(t));for(const e in t){this.components.plots[e]=await t[e]}}for(const t in this.components.plots){if(!this.state.plots.find((e=>e.id===t))){this.components.plots[t].destroy();delete this.components.plots[t]}}}printError(t){i(this.dom.errdiv||this.opts.holder,"Error: "+(t.message||t));if(t.stack)console.log(t.stack)}}const H=n(M);export{H as appInit};